201
|
Li S, Mao X, Diao X, Yang K, Shan K, Li C. Effects of sodium tripolyphosphate on the quality and digestion properties of PSE pork. Food Chem 2024; 460:140558. [PMID: 39067389 DOI: 10.1016/j.foodchem.2024.140558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
This study aimed to examine the impact of sodium tripolyphosphate (STPP) on the quality and digestive characteristics of PSE pork. The results showed a notable decrease in cooking loss of PSE pork from 29.11% to 25.67% with increasing STPP concentration (P < 0.05). Additionally, the gastric digestibility of PSE pork decreased significantly from 52.01% to 45.81% (P < 0.05). The particle size of digesta decreased significantly after gastrointestinal digestion (P < 0.05). These changes were primarily due to the enhanced cross-linking of proteins through ionic interactions, hydrogen bonds and hydrophobic interactions, and resulted in the embedding of hydrophobic groups and endogenous fluorophores. Furthermore, denser network was formed. These findings give a new insight into considering the impact of STPP on meat nutrition when used to enhance texture and water holding capacity.
Collapse
Affiliation(s)
- Shanshan Li
- State Key Laboratory of Meat Quality Control and Cultured Meat, MOST; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xinrui Mao
- State Key Laboratory of Meat Quality Control and Cultured Meat, MOST; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xinyue Diao
- State Key Laboratory of Meat Quality Control and Cultured Meat, MOST; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Kun Yang
- State Key Laboratory of Meat Quality Control and Cultured Meat, MOST; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Kai Shan
- State Key Laboratory of Meat Quality Control and Cultured Meat, MOST; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chunbao Li
- State Key Laboratory of Meat Quality Control and Cultured Meat, MOST; Key Laboratory of Meat Processing, MOA; Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China.
| |
Collapse
|
202
|
Zhao K, Wang X, Yue X, Lv J, Xu X, Lu H, Zuo J, Xu X, Chen B, Yuan S, Wang Q. A comprehensive physiological and -Omic analysis of trypsin-mediated protection of green pepper fruits from chilling injury. Food Chem 2024; 460:140547. [PMID: 39068792 DOI: 10.1016/j.foodchem.2024.140547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/11/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
Chilling injury (CI) in green pepper fruits during low-temperature storage causes a significant decline in quality. The present study utilized physiological, transcriptomic, and metabolomic analyses to idneitfy the mechanisms by which trypsin mitigates CI in green peppers stored at 4 °C for 8 days, followed by 3 days of shelf life. Results indicated that the trypsin treatment significantly reduced electrolyte leakage and the CI index in peppers, effectively extending their shelf life and preserving postharvest quality. After 4 days of storage, comparative -omic analyses identified 2514 differentially expressed genes (DEGs) and 397 differentially abundant metabolites (DAMs) between trypsin-treated and control peppers. The trypsin treatment induced changes in sugar metabolism, modulating the expression of HK, SUS, INV, and GLGC, which affected the abundance of metabolites such as CDP-glucose and α-D-p-glucose. Trypsin also enhanced carotenoid metabolism, altering the abundance of rhodopinal glucoside, 1'-hydroxyl-γ-carotene glucoside, and farnesyl 1-PP, and influencing the expression of PDS, CRTH, CRTB, and LUT5. Notably, the trypsin treatment activated the mitogen-activated protein kinase (MAPK) pathway that plays an integral role in the signal transduction of abiotic stress. Differential expression of FLS2, ELF18, PTO, PR1, PTI5, WPKY, MEKK1, and MPK6 genes in the MAPK pathway was observed, which was correlated with CI mitigation in green peppers during cold storage. In conclusion, trypsin is an effective treatment for reducing CI in green peppers during cold storage. The present study provides valuable insights into its physiological and molecular impact on green pepper fruit.
Collapse
Affiliation(s)
- Keyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuanqi Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China; School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Xiaozhen Yue
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jieyu Lv
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China; School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Xiaodi Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongshan Lu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiangbin Xu
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Bin Chen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Institute of Agri-food Processing and Nutrition, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
203
|
Nippert KE, Rowland CP, Vazey EM, Moorman DE. Alcohol, flexible behavior, and the prefrontal cortex: Functional changes underlying impaired cognitive flexibility. Neuropharmacology 2024; 260:110114. [PMID: 39134298 DOI: 10.1016/j.neuropharm.2024.110114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024]
Abstract
Cognitive flexibility enables individuals to alter their behavior in response to changing environmental demands, facilitating optimal behavior in a dynamic world. The inability to do this, called behavioral inflexibility, is a pervasive behavioral phenotype in alcohol use disorder (AUD), driven by disruptions in cognitive flexibility. Research has repeatedly shown that behavioral inflexibility not only results from alcohol exposure across species but can itself be predictive of future drinking. Like many high-level executive functions, flexible behavior requires healthy functioning of the prefrontal cortex (PFC). The scope of this review addresses two primary themes: first, we outline tasks that have been used to investigate flexibility in the context of AUD or AUD models. We characterize these based on the task features and underlying cognitive processes that differentiate them from one another. We highlight the neural basis of flexibility measures, focusing on the PFC, and how acute or chronic alcohol in humans and non-human animal models impacts flexibility. Second, we consolidate findings on the molecular, physiological and functional changes in the PFC elicited by alcohol, that may contribute to cognitive flexibility deficits seen in AUD. Collectively, this approach identifies several key avenues for future research that will facilitate effective treatments to promote flexible behavior in the context of AUD, to reduce the risk of alcohol related harm, and to improve outcomes following AUD. This article is part of the Special Issue on "PFC circuit function in psychiatric disease and relevant models".
Collapse
Affiliation(s)
- Kathryn E Nippert
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Courtney P Rowland
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Elena M Vazey
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA; Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
| | - David E Moorman
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, MA, 01003, USA; Department of Psychological and Brain Sciences, University of Massachusetts, Amherst, MA, 01003, USA.
| |
Collapse
|
204
|
Sacramento CM, Saito MT, Casati MZ, Sallum EA, Casarin RCV, Silvério KG. CCKR signaling map, G-Protein bindings, hormonal regulation, and neural mechanisms may influence the osteogenic/cementogenic differentiation potential of hPDLSCs. Arch Oral Biol 2024; 168:106069. [PMID: 39208712 DOI: 10.1016/j.archoralbio.2024.106069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE Periodontal regeneration poses challenges due to the periodontium's complexity, relying on mesenchymal cells from the periodontal ligament (hPDLSCs) to regenerate hard tissues like bone and cementum. While some hPDLSCs have high regeneration potential (HOP-hPDLSCs), most are low potential (LOP-hPDLSCs). This study analyzed hPDLSCs from a single donor to minimize inter-individual variability and focus on key differences in differentiation potentials. DESIGN This study used RNA-seq, genomic databases, and bioinformatics tools to explore signaling pathways (SPs), biological processes (BPs), and molecular functions (MFs) guiding HOP cells to mineralized matrix production. It also investigated limitations of LOP cells and strategies for enhancing their osteo/cementogenesis. RESULTS In basal conditions, HOP exhibited a multifunctional gene network with higher expression of genes related to osteo/cementogenesis, cell differentiation, immune modulation, stress response, and hormonal regulation. In contrast, LOP focused on steroid hormone biosynthesis and nucleic acid maintenance. During osteo/cementogenic induction, HOP showed strong modulation of genes related to angiogenesis, cell division, mesenchymal differentiation, and extracellular matrix production. LOP demonstrated neural synaptic-related processes and preserved cellular cytoskeleton integrity. CCKR map signaling and G-protein receptor bindings gained significance during osteo/cementogenesis in HOP-hPDLSCs. Both HOP and LOP shared common BPs related to gastrointestinal and reproductive system development. CONCLUSION The osteo/cementogenic differentiation of HOP cells may be regulated by CCKR signaling, G-protein bindings, and specific hormonal regulation. LOP cells seem committed to neural mechanisms. This study sheds light on hPDLSCs' complex characteristics, offering a deeper understanding of their differentiation potential for future periodontal regeneration research and therapies.
Collapse
Affiliation(s)
- Catharina Marques Sacramento
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil
| | - Miki Taketomi Saito
- Faculdade de Odontologia, Universidade Federal do Pará - UFPA, Departamento de Saúde Coletiva, Belém 66075-110, Brazil.
| | - Márcio Zaffalon Casati
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Enilson Antonio Sallum
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Renato Correa Viana Casarin
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Karina Gonzales Silvério
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| |
Collapse
|
205
|
Oliveira LS, Goel S, Amreen K, Lucena-Silva N, Oliveira MDL, Andrade CAS. Microfluid biosensor for detection of hpv in patient scraping samples: Determining E6 and E7 oncogenes. Bioelectrochemistry 2024; 160:108795. [PMID: 39146929 DOI: 10.1016/j.bioelechem.2024.108795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
E6 and E7 oncogenes are pivotal in the carcinogenic transformation in HPV infections and efficient diagnostic methods can ensure the detection and differentiation of HPV genotype. This study describes the development and validation of an electrochemical, label-free genosensor coupled with a microfluidic system for detecting the E6 and E7 oncogenes in cervical scraping samples. The nanostructuring employed was based on a cysteine and graphene quantum dots layer that provides functional groups, surface area, and interesting electrochemical properties. Biorecognition tests with cervical scraping samples showed differentiation in the voltammetric response. Low-risk HPV exhibited a lower biorecognition response, reflected in ΔI% values of 82.33 % ± 0.29 for HPV06 and 80.65 % ± 0.68 for HPV11 at a dilution of 1:100. Meanwhile, high-risk, HPV16 and HPV18, demonstrated ΔI% values of 96.65 % ± 1.27 and 93 % ± 0.026, respectively, at the same dilution. Therefore, the biorecognition intensity followed the order: HPV16 >HPV18 >HPV06 >HPV11. The limit of detection and the limit of quantification of E6E7 microfluidic LOC-Genosensor was 26 fM, and 79.6 fM. Consequently, the E6E7 biosensor is a valuable alternative for clinical HPV diagnosis, capable of detecting the potential for oncogenic progression even in the early stages of infection.
Collapse
Affiliation(s)
- Léony S Oliveira
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil; Laboratório de Biodispositivos Nanoestruturados, Departamento de Bioquímica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Sanket Goel
- MEMS, Microfluidics and Nanoelectronics Laboratory, Department of Electrical and Electronics Engineering, Birla Institute of Technology and Science, Hyderabad, 500078, India
| | - Khairunnisa Amreen
- MEMS, Microfluidics and Nanoelectronics Laboratory, Department of Electrical and Electronics Engineering, Birla Institute of Technology and Science, Hyderabad, 500078, India
| | - Norma Lucena-Silva
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (Fiocruz), 50670-420 Recife, PE, Brazil; Laboratório de Biologia Molecular, Departamento de Oncologia Pediátrica, Instituto de Medicina Integral Professor Fernando Figueira (IMIP), 50070-550 Recife, PE, Brazil
| | - Maria D L Oliveira
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil; Laboratório de Biodispositivos Nanoestruturados, Departamento de Bioquímica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Cesar A S Andrade
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil; Laboratório de Biodispositivos Nanoestruturados, Departamento de Bioquímica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil.
| |
Collapse
|
206
|
Daneshnia F, Floyd DJ, Ryan AP, Ghahfarokhy PM, Ebadati A, Jusuf S, Munoz J, Jeffries NE, Elizabeth Yvanovich E, Apostolopoulou A, Perry AM, Lass-Flörl C, Birinci A, Hilmioğlu-Polat S, Ilkit M, Butler G, Nobile CJ, Arastehfar A, Mansour MK. Evaluation of outbreak persistence caused by multidrug-resistant and echinocandin-resistant Candida parapsilosis using multidimensional experimental and epidemiological approaches. Emerg Microbes Infect 2024; 13:2322655. [PMID: 38380673 PMCID: PMC10916928 DOI: 10.1080/22221751.2024.2322655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Candida parapsilosis is known to cause severe and persistent outbreaks in clinical settings. Patients infected with multidrug-resistant C. parapsilosis (MDR Cp) isolates were identified in a large Turkish hospital from 2017-2020. We subsequently identified three additional patients infected with MDR Cp isolates in 2022 from the same hospital and two echinocandin-resistant (ECR) isolates from a single patient in another hospital. The increasing number of MDR and ECR isolates contradicts the general principle that the severe fitness cost associated with these phenotypes could prevent their dominance in clinical settings. Here, we employed a multidimensional approach to systematically assess the fitness costs of MDR and ECR C. parapsilosis isolates. Whole-genome sequencing revealed a novel MDR genotype infecting two patients in 2022. Despite severe in vitro defects, the levels and tolerances of the biofilms of our ECR and MDR isolates were generally comparable to those of susceptible wild-type isolates. Surprisingly, the MDR and ECR isolates showed major alterations in their cell wall components, and some of the MDR isolates consistently displayed increased tolerance to the fungicidal activities of primary human neutrophils and were more immunoevasive during exposure to primary human macrophages. Our systemic infection mouse model showed that MDR and ECR C. parapsilosis isolates had comparable fungal burden in most organs relative to susceptible isolates. Overall, we observed a notable increase in the genotypic diversity and frequency of MDR isolates and identified MDR and ECR isolates potentially capable of causing persistent outbreaks in the future.
Collapse
Affiliation(s)
- Farnaz Daneshnia
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel J. Floyd
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam P. Ryan
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Pegah Mosharaf Ghahfarokhy
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Arefeh Ebadati
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Sebastian Jusuf
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Julieta Munoz
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | | | | | - Anna Apostolopoulou
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin M. Perry
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
| | - Cornelia Lass-Flörl
- Medical University Innsbruck, Institute of Hygiene and Medical Microbiology, Innsbruck, Austria
| | - Asuman Birinci
- Department of Medical Microbiology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Türkiye
| | | | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California – Merced, Merced, CA, USA
- Health Sciences Research Institute, University of California – Merced, Merced, CA, USA
| | - Amir Arastehfar
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael K. Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
207
|
Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
Collapse
Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| |
Collapse
|
208
|
Li C, Azad MAK, Zhu Q, Cheng Y, Gui J, Song B, Zhou Z, Kong X. Differences in intestinal and renal Ca and P uptake in three different breeds of growing-finishing pigs. Vet Q 2024; 44:1-16. [PMID: 38965863 PMCID: PMC11229737 DOI: 10.1080/01652176.2024.2371609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/17/2024] [Indexed: 07/06/2024] Open
Abstract
This study investigated the differences in bone growth and turnover and calcium (Ca) and phosphorus (P) uptake among three different breeds of growing-finishing pigs. Ninety healthy Duroc, Xiangcun black (XCB), and Taoyuan black (TYB) pigs (30 pigs per breed) at 35 day-old (D) with the average body weight (BW) of their respective breed were assigned and raised to 185 D. The results showed that Duroc pigs had higher bone weight and length than the XCB and TYB pigs at 80, 125, and 185 D and the bone index at 185 D (p < 0.05). Duroc pigs had higher bone mineral densities (femur and tibia) compared with the other two breeds at 80 D and 125 D, whereas TYB pigs had higher mineral content and bone breaking load (rib) compared with the other two breeds at 185 D (p < 0.05). The bone morphogenetic protein-2 and osteocalcin concentrations were higher, and TRACP5b concentration was lower in serum of TYB pigs at 125 D (p < 0.05). Meanwhile, 1,25-dihydroxyvitamin D3, parathyroid hormone, thyroxine, and fibroblast growth factor 23 concentrations were higher in serum of TYB pigs at 185 D (p < 0.05). The TYB pigs had higher apparent total tract digestibility of P at 80 D and 185 D and bone Ca and P contents at 185 D in comparison to the Duroc pigs (p < 0.05). Furthermore, gene expressions related to renal uptake of Ca and P differed among the three breeds of pigs. Collectively, Duroc pigs have higher bone growth, whereas TYB pigs have a higher potential for mineral deposition caused by more active Ca uptake.
Collapse
Affiliation(s)
- Chenjian Li
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, Jiangsu, China
| | - Md. Abul Kalam Azad
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Zhu
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yating Cheng
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Jue Gui
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bo Song
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenlei Zhou
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, Jiangsu, China
| | - Xiangfeng Kong
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, Jiangsu, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
209
|
Götz T, Cong X, Rauber S, Angeli M, Lang E, Ramming A, Schmidkonz C. A novel Slide-seq based image processing software to identify gene expression at the single cell level. J Pathol Inform 2024; 15:100384. [PMID: 39027045 PMCID: PMC11254742 DOI: 10.1016/j.jpi.2024.100384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024] Open
Abstract
Analysis of gene expression at the single-cell level could help predict the effectiveness of therapies in the field of chronic inflammatory diseases such as arthritis. Here, we demonstrate an adopted approach for processing images from the Slide-seq method. Using a puck, which consists of about 50,000 DNA barcode beads, an RNA sequence of a cell is to be read. The pucks are repeatedly brought into contact with liquids and then recorded with a conventional epifluorescence microscope. The image analysis initially consists of stitching the partial images of a sequence recording, registering images from different sequences, and finally reading out the bases. The new method enables the use of an inexpensive epifluorescence microscope instead of a confocal microscope.
Collapse
Affiliation(s)
- Th.I. Götz
- Department of Internal Medicine, University Hospital Erlangen, Erlangen, Germany
- Department of Industrial Engineering and Health, Technical University of Applied Sciences Amberg-Weiden, Weiden, Germany
| | - X. Cong
- Department of Internal Medicine, University Hospital Erlangen, Erlangen, Germany
| | - S. Rauber
- Department of Internal Medicine, University Hospital Erlangen, Erlangen, Germany
| | - M. Angeli
- Department of Internal Medicine, University Hospital Erlangen, Erlangen, Germany
| | - E.W. Lang
- CIML Group, Biophysics, University of Regensburg, 93040 Regensburg, Germany
| | - A. Ramming
- Department of Internal Medicine, University Hospital Erlangen, Erlangen, Germany
| | - C. Schmidkonz
- Department of Nuclear Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
- Department of Industrial Engineering and Health, Technical University of Applied Sciences Amberg-Weiden, Weiden, Germany
| |
Collapse
|
210
|
Wang X, Gao X, Fan X, Huai Z, Zhang G, Yao M, Wang T, Huang X, Lai L. WUREN: Whole-modal union representation for epitope prediction. Comput Struct Biotechnol J 2024; 23:2122-2131. [PMID: 38817963 PMCID: PMC11137340 DOI: 10.1016/j.csbj.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
B-cell epitope identification plays a vital role in the development of vaccines, therapies, and diagnostic tools. Currently, molecular docking tools in B-cell epitope prediction are heavily influenced by empirical parameters and require significant computational resources, rendering a great challenge to meet large-scale prediction demands. When predicting epitopes from antigen-antibody complex, current artificial intelligence algorithms cannot accurately implement the prediction due to insufficient protein feature representations, indicating novel algorithm is desperately needed for efficient protein information extraction. In this paper, we introduce a multimodal model called WUREN (Whole-modal Union Representation for Epitope predictioN), which effectively combines sequence, graph, and structural features. It achieved AUC-PR scores of 0.213 and 0.193 on the solved structures and AlphaFold-generated structures, respectively, for the independent test proteins selected from DiscoTope3 benchmark. Our findings indicate that WUREN is an efficient feature extraction model for protein complexes, with the generalizable application potential in the development of protein-based drugs. Moreover, the streamlined framework of WUREN could be readily extended to model similar biomolecules, such as nucleic acids, carbohydrates, and lipids.
Collapse
Affiliation(s)
| | | | - Xuezhe Fan
- XtalPi Innovation Center, Beijing, China
| | - Zhe Huai
- XtalPi Innovation Center, Beijing, China
| | | | | | | | | | - Lipeng Lai
- XtalPi Innovation Center, Beijing, China
| |
Collapse
|
211
|
Aalders J, Léger L, Hassannia B, Goossens V, Vanden Berghe T, van Hengel J. Improving cardiac differentiation of human pluripotent stem cells by targeting ferroptosis. Regen Ther 2024; 27:21-31. [PMID: 38496011 PMCID: PMC10940893 DOI: 10.1016/j.reth.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/25/2024] [Indexed: 03/19/2024] Open
Abstract
Generation of cardiomyocytes from human pluripotent stem cells (hPSCs) is of high interest for disease modelling and regenerative medicine. hPSCs can provide an unlimited source of patient-specific cardiomyocytes that are otherwise difficult to obtain from individuals. Moreover, the low proliferation rate of adult cardiomyocytes and low viability ex vivo limits the quantity of study material. Most protocols for the differentiation of cardiomyocytes from hPSCs are based on the temporal modulation of the Wnt pathway. However, during the initial stage of GSK-3 inhibition, a substantial number of cells are lost due to detachment. In this study, we aimed to increase the efficiency of generating cardiomyocytes from hPSCs. We identified cell death as a detrimental factor during this initial stage of in vitro cardiomyocyte differentiation. Through pharmacological targeting of different types of cell death, we discovered that ferroptosis was the main cell death type during the first 48 h of the in vitro differentiation procedure. Inhibiting ferroptosis using ferrostatin-1 during cardiomyocyte differentiation resulted in increased robustness and cell yield.
Collapse
Affiliation(s)
- Jeffrey Aalders
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Entrance 37a, 2nd floor, 9000, Ghent, Belgium
| | - Laurens Léger
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Entrance 37a, 2nd floor, 9000, Ghent, Belgium
| | - Behrouz Hassannia
- Cell Death Signalling Lab, Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Tom Vanden Berghe
- Cell Death Signalling Lab, Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9000 Ghent, Belgium
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium
| | - Jolanda van Hengel
- Medical Cell Biology Research Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, Entrance 37a, 2nd floor, 9000, Ghent, Belgium
| |
Collapse
|
212
|
Carpenter KA, Altman RB. Databases of ligand-binding pockets and protein-ligand interactions. Comput Struct Biotechnol J 2024; 23:1320-1338. [PMID: 38585646 PMCID: PMC10997877 DOI: 10.1016/j.csbj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
Collapse
Affiliation(s)
- Kristy A. Carpenter
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
213
|
Cruz TM, Lima AS, Zhou F, Zhang L, Azevedo L, Marques MB, Granato D. Bioaccessibility of bioactive compounds from Pereskia aculeata and their cellular antioxidant effect. Food Chem 2024; 460:140484. [PMID: 39047477 DOI: 10.1016/j.foodchem.2024.140484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/14/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024]
Abstract
Ora-pro-nobis (Pereskia aculeata) is a Cactaceae plant with edible leaves and fruits whose extracts are consumed to promote health, albeit bioactive compounds' bioaccessibility was still not assessed. To address this, ora-pro-nobis fruits (FE) and leaf extracts (LE) were subjected to in vitro digestion to better understand how this process impacts the bioactivities of the extracts. The study investigated the composition of the extracts, their cytotoxicity, and their chemical, plasmatic, and cellular antioxidant capacity. The results revealed that total polyphenolics were about 70% bioaccessible in LE and FE, with phenylalanine being the most bioaccessible essential amino acid in leaves (42.7%) and fruits (83.6%). The samples' antioxidant activity (CUPRAC) was reduced by 25%. LE demonstrated antioxidant activity against human plasma oxidation and haemolysis (21.8%), but digestion mitigated these activities. FE diminished haemolysis (47.0%) and presented cytotoxicity (IC50 = 1086 μg/mL) to HUVEC cells, but these properties were lost following digestion. Ultimately, digestion partially degraded the samples' bioactive compounds, diminishing their cellular protection against oxidative stress.
Collapse
Affiliation(s)
- Thiago M Cruz
- Graduation Program in Chemistry, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, PR, Brazil.; Bioactivity & Applications Laboratory, Department of Biological Sciences, Faculty of Science and Engineering, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland
| | - Amanda S Lima
- Bioactivity & Applications Laboratory, Department of Biological Sciences, Faculty of Science and Engineering, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland.; In vitro and in vivo Nutritional and Toxicological Analysis Lab, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 714, 37130-000 Alfenas, MG, Brazil
| | - Feng Zhou
- Anhui Agricultural University, State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Liang Zhang
- Anhui Agricultural University, State Key Laboratory of Tea Plant Biology and Utilization, Hefei 230036, China
| | - Luciana Azevedo
- Bioactivity & Applications Laboratory, Department of Biological Sciences, Faculty of Science and Engineering, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland.; In vitro and in vivo Nutritional and Toxicological Analysis Lab, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 714, 37130-000 Alfenas, MG, Brazil
| | - Mariza B Marques
- Graduation Program in Chemistry, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, PR, Brazil
| | - Daniel Granato
- Bioactivity & Applications Laboratory, Department of Biological Sciences, Faculty of Science and Engineering, School of Natural Sciences, University of Limerick, V94 T9PX Limerick, Ireland.; Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland.
| |
Collapse
|
214
|
Lucas-González R, Carrillo C, Purriños L, Pateiro M, Bermúdez R, Lorenzo JM. Effect of different pre-treatment on acrylamide content, nutrition value, starch digestibility and anthocyanin bioaccessibility of purple sweet potato (Ipomoea batata) deep-fried chips. Food Chem 2024; 460:140535. [PMID: 39068802 DOI: 10.1016/j.foodchem.2024.140535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
Veggie chips have gained popularity in the European market. These are considered healthier than potato chips by consumers. However, few works evaluate their nutritional and digestibility. The current work aimed to evaluate the effect of four pre-frying treatments (soaking, blanching, pulsed electric field (PEF) and PEF + blanching combination (PEFB)) on the chemical composition, anthocyanins, acrylamide, and digestive behavior (starch hydrolysis and anthocyanins bioaccessibility) of purple sweet potato deep-fried chips. In total 15 independent batches were made, three for each studied treatment (also a control without pretreatment was developed). The studied pretreatments impacted on fat and starch content, especially blanching and PEFB, which caused an increase in fat absorption and break starch, generating maltodextrins. Nineteen anthocyanins were detected, mainly cyanidin and peonidin derivatives, but a drastic loss was observed in blanched, PEF-treated and PEF-B-Treated chips. Acrylamide values ranged from 504.11 to 6350.0- μg/kg, with the highest values reported by untreated chips and the lowest by PEF-B-treated chips (p < 0.05). The anthocyanin's bioaccessibility ranged between 66.57 and 92.88%, with soaked chips that showed the highest values.
Collapse
Affiliation(s)
- Raquel Lucas-González
- Institute for Agri-Food and Agri-Environmental Research and Innovation, Miguel Hernández University (CIAGRO-UMH), Ctra. Beniel km 3.2, 03312 Orihuela, Alicante, Spain
| | - Celia Carrillo
- Área de Nutrición y Bromatología, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Laura Purriños
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia n° 4, Parque Tecnológico de Galicia, Ourense, San Cibrao das Viñas 32900, Spain
| | - Mirian Pateiro
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia n° 4, Parque Tecnológico de Galicia, Ourense, San Cibrao das Viñas 32900, Spain
| | - Roberto Bermúdez
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia n° 4, Parque Tecnológico de Galicia, Ourense, San Cibrao das Viñas 32900, Spain
| | - José Manuel Lorenzo
- Centro Tecnológico de la Carne de Galicia, Avda. Galicia n° 4, Parque Tecnológico de Galicia, Ourense, San Cibrao das Viñas 32900, Spain; Área de Tecnoloxía dos Alimentos, Facultade de Ciencias, Universidade de Vigo, 32004 Ourense, Spain.
| |
Collapse
|
215
|
Wang R, Wang Y, Han J, Wu S, Dong P, Raghavan V, Wang J. Employing conductive porous hydrogen-bonded organic framework for ultrasensitive detection of peanut allergen Ara h1. Food Chem 2024; 460:140777. [PMID: 39128370 DOI: 10.1016/j.foodchem.2024.140777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/13/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Peanut allergy has garnered worldwide attention due to its high incidence rate and severe symptoms, stimulating the demand for the ultrasensitive detection method of peanut allergen. Herein, we successfully developed a novel electrochemical aptasensor for ultrasensitive detection Ara h1, a major allergenic protein present in peanuts. A conductive nickel atoms Anchored Hydrogen-Bonded Organic Frameworks (PFC-73-Ni) were utilized as excellent electrocatalysts toward hydroquinone (HQ) oxidation to generate a readable current signal. The developed electrochemical aptasensor offers wide linear range (1-120 nM) and low detection limit (0.26 nM) for Ara h1. This method demonstrated a recovery rate ranging from 95.00% to 107.42% in standard addition detection of non-peanut food samples. Additionally, the developed electrochemical method was validated with actual samples and demonstrated good consistency with the results obtained from a commercial ELISA kit. This indicates that the established Ara h1 detection method is a promising tool for peanut allergy prevention.
Collapse
Affiliation(s)
- Rui Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Youfa Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Jie Han
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Shuang Wu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Pengfei Dong
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Vijaya Raghavan
- Department of Bioresource Engineering, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Rd, Sainte-Anne-de-Bellevue, H9X3V9, QC, Canada
| | - Jin Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China.
| |
Collapse
|
216
|
Bojja SL, Anand S, Minz RW, Medhi B. Metformin alleviates reactive gliosis and neurodegeneration, improving cognitive deficit in a rat model of temporal lobe epilepsy. Brain Res 2024; 1844:149138. [PMID: 39134259 DOI: 10.1016/j.brainres.2024.149138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/17/2024]
Abstract
Cognitive impairment is a prevalent co-morbidity associated with epilepsy. Emerging studies indicate that neuroinflammation could be a possible link between epilepsy and its comorbidities, including cognitive impairment. In this context, the roles of glial activation, proinflammatory mediators, and neuronal death have been well studied and correlated with epilepsy-associated cognitive impairment in animal studies. While recent reports have demonstrated the anti-epileptogenic and anti-convulsant actions of metformin, its effect on epilepsy associated cognitive deficit remains unknown. Therefore, the current study investigated the effect of metformin treatment on neuroinflammation, neurodegeneration, and cognitive deficits after inducing status epilepticus (SE) with lithium-pilocarpine in rats. Metformin treatment improved the hippocampal-dependent spatial and recognition memory in Morris water maze and Novel object recognition tasks, respectively. Further, metformin treatment attenuated microglial and astroglial activation, accompanied by reduced IL-1β, COX-2 and NF-ĸβ gene expression. Additionally, metformin conferred neuroprotection by inhibiting the neuronal death as assessed by Nissl staining and transmission electron microscopy. These findings suggest that metformin holds promise as a therapeutic intervention for cognitive impairment associated with epilepsy, possibly through its modulation of glial activation and neuronal survival. Further research is needed to elucidate the precise mechanisms and to assess the long-term effect of metformin in epilepsy-associated cognitive impairment.
Collapse
Affiliation(s)
- Sree Lalitha Bojja
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Shashi Anand
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ranjana W Minz
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India.
| |
Collapse
|
217
|
Ashokkumar M, Palanisamy K, Ganesh Kumar A, Muthusamy C, Senthil Kumar KJ. Green synthesis of silver and copper nanoparticles and their composites using Ocimum sanctum leaf extract displayed enhanced antibacterial, antioxidant and anticancer potentials. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:438-448. [PMID: 39239690 DOI: 10.1080/21691401.2024.2399938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 09/07/2024]
Abstract
Green-synthesized silver and copper nanoparticles (NPs), along with their composites, exhibit various biological activities. Ocimum sanctum (Holy basil), traditionally used as medicine in South Asia, treats respiratory disorders, digestive issues, skin diseases and inflammatory conditions. Modern scientific studies support these bioactivities; however, no studies have investigated their bioactivity in combination with NPs. In this study, silver and copper NPs were synthesized using AgNO3 and CuSO4·5H2O solutions, respectively, with Ocimum sanctum leaf extract, and their antibacterial, antioxidant and anticancer properties were examined. Spectroscopic analyses, including Fourier transform infra-red (FTIR), transmission electron microscopy (TEM) and X-ray diffraction (XRD), elucidated the physicochemical characteristics of the green-synthesized nanoparticles (Os-AgNPs and Os-CuNPs), revealing sizes of 11.7 and 13.1 nm, respectively. The Os-AgNPs:Os-CuNPs nano-composite with a 1:2 ratio exhibited a zone of inhibition ranging from 8 to 12 mm against tested bacterial pathogens. Additionally, the NPs and their composites demonstrated potent antioxidant activity, with notable 2-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity observed in composites with ratios of 2:1 and 1:2. Furthermore, they displayed potential anticancer activity against human leukaemia (Jurkat) cancer cells. Although no distinct difference in anticancer property was observed among the NPs and their composites, our study highlights their well-defined nanostructure and significant biological activity, suggesting their potential as therapeutic agents in the pharmaceutical industry.
Collapse
Affiliation(s)
- M Ashokkumar
- Department of Physics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Thandalam, India
| | - K Palanisamy
- Department of Chemistry, Srinivasan College of Arts and Science(Affiliated to Bharathidasan University, Tiruchirappalli), Perambalur, India
| | - A Ganesh Kumar
- Department of Microbiology, Centre for Research and Development, Hindustan College of Arts & Science, Kelambakkam, India
| | - C Muthusamy
- Department of Biotechnology, Srinivasan College of Arts and Science (Affiliated to Bharathidasan University, Tiruchirappalli), Perambalur, India
| | - K J Senthil Kumar
- Center for General Education, National Chung Hsing University, Taichung, Taiwan
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
218
|
Izadifar Z, Charrez B, Almeida M, Robben S, Pilobello K, van der Graaf-Mas J, Marquez SL, Ferrante TC, Shcherbina K, Gould R, LoGrande NT, Sesay AM, Ingber DE. Organ chips with integrated multifunctional sensors enable continuous metabolic monitoring at controlled oxygen levels. Biosens Bioelectron 2024; 265:116683. [PMID: 39213819 PMCID: PMC11391946 DOI: 10.1016/j.bios.2024.116683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Despite remarkable advances in Organ-on-a-chip (Organ Chip) microfluidic culture technology, recreating tissue-relevant physiological conditions, such as the region-specific oxygen concentrations, remains a formidable technical challenge, and analysis of tissue functions is commonly carried out using one analytical technique at a time. Here, we describe two-channel Organ Chip microfluidic devices fabricated from polydimethylsiloxane and gas impermeable polycarbonate materials that are integrated with multiple sensors, mounted on a printed circuit board and operated using a commercially available Organ Chip culture instrument. The novelty of this system is that it enables the recreation of physiologically relevant tissue-tissue interfaces and oxygen tension as well as non-invasive continuous measurement of transepithelial electrical resistance, oxygen concentration and pH, combined with simultaneous analysis of cellular metabolic activity (ATP/ADP ratio), cell morphology, and tissue phenotype. We demonstrate the reliable and reproducible functionality of this system in living human Gut and Liver Chip cultures. Changes in tissue barrier function and oxygen tension along with their functional and metabolic responses to chemical stimuli (e.g., calcium chelation, oligomycin) were continuously and noninvasively monitored on-chip for up to 23 days. A physiologically relevant microaerobic microenvironment that supports co-culture of human intestinal cells with living Lactococcus lactis bacteria also was demonstrated in the Gut Chip. The integration of multi-functional sensors into Organ Chips provides a robust and scalable platform for the simultaneous, continuous, and non-invasive monitoring of multiple physiological functions that can significantly enhance the comprehensive and reliable evaluation of engineered tissues in Organ Chip models in basic research, preclinical modeling, and drug development.
Collapse
Affiliation(s)
- Zohreh Izadifar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Berenice Charrez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Micaela Almeida
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Stijn Robben
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA; Department of Microelectronics, Technical University Delft, Delft, 2628 CD, Netherlands
| | - Kanoelani Pilobello
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Janet van der Graaf-Mas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Susan L Marquez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Thomas C Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Kostyantyn Shcherbina
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Russell Gould
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Nina T LoGrande
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Adama M Sesay
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA; Vascular Biology Program and Department of Surgery, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA; Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
219
|
Pollak J, Mayonu M, Jiang L, Wang B. The development of machine learning approaches in two-dimensional NMR data interpretation for metabolomics applications. Anal Biochem 2024; 695:115654. [PMID: 39187053 DOI: 10.1016/j.ab.2024.115654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]
Abstract
Metabolomics has been widely applied in human diseases and environmental science to study the systematic changes of metabolites over diverse types of stimuli. NMR-based metabolomics has been widely used, but the peak overlap problems in the one-dimensional (1D) NMR spectrum could limit the accuracy of quantitative analysis for metabolomics applications. Two-dimensional (2D) NMR has been applied to solve the 1D NMR overlap problem, but the data processing is still challenging. In this study, we built an automatic approach to process the 2D NMR data for quantitative applications using machine learning approaches. Partial least square discriminant analysis (PLS-DA), artificial neural network classification (ANN-DA), gradient boosted trees classification (XGBoost-DA), and artificial deep learning neural network classification (ANNDL-DA) were applied in combination with an automatic peak selection approach. Standard mixtures, sea anemone extracts, and mouse fecal samples were tested to demonstrate the approach. Our results showed that ANN-DA and ANNDL-DA have high accuracy in selecting 2D NMR peaks (around 90 %), which have a high potential application in 2D NMR-based metabolomics quantitively study, while PLS-DA and XGBoost-DA showed limitations in either data variation or overfitting. Our study built an automatic approach to applying 2D NMR data to routine quantitative analysis in metabolomics.
Collapse
Affiliation(s)
- Julie Pollak
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 West University Boulevard, Melbourne, FL, 32901-6975, USA
| | - Moses Mayonu
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 West University Boulevard, Melbourne, FL, 32901-6975, USA
| | - Lin Jiang
- Natural Sciences Division, New College of Florida, 5800 Bay Shore Road, Sarasota, FL, 34243, USA; Department of Chemistry and Biochemistry, Stetson University, 421 N. Woodland Blvd., DeLand, Florida, 32723, USA
| | - Bo Wang
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 West University Boulevard, Melbourne, FL, 32901-6975, USA.
| |
Collapse
|
220
|
Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR. An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients. Dev Biol 2024; 516:59-70. [PMID: 39098630 DOI: 10.1016/j.ydbio.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/06/2024]
Abstract
Dicer substrate interfering RNAs (DsiRNAs) destroy targeted transcripts using the RNA-Induced Silencing Complex (RISC) through a process called RNA interference (RNAi). This process is ubiquitous among eukaryotes. Here we report the utility of DsiRNA in embryos of the sea urchin Lytechinus variegatus (Lv). Specific knockdowns phenocopy known morpholino and inhibitor knockdowns, and DsiRNA offers a useful alternative to morpholinos. Methods are described for the design of specific DsiRNAs that lead to destruction of targeted mRNA. DsiRNAs directed against pks1, an enzyme necessary for pigment production, show how successful DsiRNA perturbations are monitored by RNA in situ analysis and by qPCR to determine relative destruction of targeted mRNA. DsiRNA-based knockdowns phenocopy morpholino- and drug-based inhibition of nodal and lefty. Other knockdowns demonstrate that the RISC operates early in development as well as on genes that are first transcribed hours after gastrulation is completed. Thus, DsiRNAs effectively mediate destruction of targeted mRNA in the sea urchin embryo. The approach offers significant advantages over other widely used methods in the urchin in terms of cost, and ease of procurement, and offers sizeable experimental advantages in terms of ease of handling, injection, and knockdown validation.
Collapse
Affiliation(s)
- Keen Wilson
- University of Cincinnati, Blue Ash College, Biology Dept. 9555 Plainfield Rd., Blue Ash, Ohio; Department of Biology, Duke University, Durham, NC, USA
| | - Carl Manner
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | | | - David R McClay
- Department of Biology, Duke University, Durham, NC, USA.
| |
Collapse
|
221
|
Beteinakis S, Papachristodoulou A, Stathopoulos P, Mikros E, Halabalaki M. A multilevel LC-HRMS and NMR correlation workflow towards foodomics advancement: Application in table olives. Talanta 2024; 280:126641. [PMID: 39142126 DOI: 10.1016/j.talanta.2024.126641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/09/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024]
Abstract
Foodomics employs advanced analytical techniques to provide answers regarding food composition, authenticity control, marker identification and issues related to food quality and safety. Nuclear magnetic resonance (NMR) spectroscopy and chromatography hyphenated to mass spectrometry (MS) are the main analytical platforms used in this field. Nevertheless, they are rarely employed in an integrated manner, and even then, the contribution of each technique remains vague. Table olives (Olea europaea L.) are a food commodity of high economic and nutritional value with an increasing production tendency over the last two decades, which, however, suffers from extensive fraud incidents and quality determination uncertainties. Thus, the current attempt aims towards two axes with the first being the multilevel integration of LC-HRMS and NMR data of the same samples and table olives being the selected matrix. In more detail, UPLC-HRMS/MS-based analysis was compared at different stages within an untargeted metabolomics workflow with an NMR-based study and the complementarity of the two platforms was evaluated. Furthermore, statistical heterospectroscopy (SHY), rarely employed in foodomics, combining the spectroscopic with spectrometric datasets and aiming to increase the confidence level of annotated biomarkers was applied. Amongst these lines, the second parallel axis of this study was the detailed characterization of table olives' metabolome in search for quality markers considering the impact of geographical (from Northern to Southern Greece) and botanical origin (Kalamon, Konservolia, Chalkidikis cultivars), as well as processing parameters (Spanish, Greek). To that end, using deep dereplication tools including statistical methods, with SHY employed for the first time in table olives, different biomarkers, belonging to the classes of phenyl alcohols, phenylpropanoids, flavonoids, secoiridoids and triterpenoids were identified as responsible for the observed classifications. The current binary pipeline, focusing on biomarkers' identification confidence, could be suggested as a meaningful workflow not only in olive-based products, but also in food quality control and foodomics in general.
Collapse
Affiliation(s)
- Stavros Beteinakis
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Anastasia Papachristodoulou
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Panagiotis Stathopoulos
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece
| | - Maria Halabalaki
- Division of Pharmacognosy and Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771, Athens, Greece.
| |
Collapse
|
222
|
Sharma S, Chaurasia S, Dinday S, Srivastava G, Singh A, Chanotiya CS, Ghosh S. High-level biosynthesis of enantiopure germacrene D in yeast. Appl Microbiol Biotechnol 2024; 108:50. [PMID: 38183482 PMCID: PMC10789846 DOI: 10.1007/s00253-023-12885-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 01/08/2024]
Abstract
Germacrene D, a sesquiterpenoid compound found mainly in plant essential oils at a low level as (+) and/or (-) enantiomeric forms, is an ingredient for the fragrance industry, but a process for the sustainable supply of enantiopure germacrene D is not yet established. Here, we demonstrate metabolic engineering in yeast (Saccharomyces cerevisiae) achieving biosynthesis of enantiopure germacrene D at a high titer. To boost farnesyl pyrophosphate (FPP) flux for high-level germacrene D biosynthesis, a background yeast chassis (CENses5C) was developed by genomic integration of the expression cassettes for eight ergosterol pathway enzymes that sequentially converted acetyl-CoA to FPP and by replacing squalene synthase promoter with a copper-repressible promoter, which restricted FPP flux to the competing pathway. Galactose-induced expression of codon-optimized plant germacrene D synthases led to 13-30 fold higher titers of (+) or (-)-germacrene D in CENses5C than the parent strain CEN.PK2.1C. Furthermore, genomic integration of germacrene D synthases in GAL80, LPP1 and rDNA loci generated CENses8(+D) and CENses8(-D) strains, which produced 41.36 µg/ml and 728.87 µg/ml of (+) and (-)-germacrene D, respectively, without galactose supplementation. Moreover, coupling of mitochondrial citrate pool to the cytosolic acetyl-CoA, by expressing a codon-optimized ATP-citrate lyase of oleaginous yeast, resulted in 137.71 µg/ml and 815.81 µg/ml of (+) or (-)-germacrene D in CENses8(+D)* and CENses8(-D)* strains, which were 67-120 fold higher titers than in CEN.PK2.1C. In fed-batch fermentation, CENses8(+D)* and CENses8(-D)* produced 290.28 µg/ml and 2519.46 µg/ml (+) and (-)-germacrene D, respectively, the highest titers in shake-flask fermentation achieved so far. KEY POINTS: • Engineered S. cerevisiae produced enantiopure (+) and (-)-germacrene D at high titers • Engineered strain produced up to 120-fold higher germacrene D than the parental strain • Highest titers of enantiopure (+) and (-)-germacrene D achieved so far in shake-flask.
Collapse
Affiliation(s)
- Shubha Sharma
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Seema Chaurasia
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sandeep Dinday
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Gaurav Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Anamika Singh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Phytochemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sumit Ghosh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
223
|
Rodríguez JM, Jorge I, Martinez-Val A, Barrero-Rodríguez R, Magni R, Núñez E, Laguillo A, Devesa CA, López JA, Camafeita E, Vázquez J. iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data. Comput Struct Biotechnol J 2024; 23:452-459. [PMID: 38235360 PMCID: PMC10792623 DOI: 10.1016/j.csbj.2023.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
Many bioinformatics tools are available for the quantitative analysis of proteomics experiments. Most of these tools use a dedicated statistical model to derive absolute quantitative protein values from mass spectrometry (MS) data. Here, we present iSanXoT, a standalone application that processes relative abundances between MS signals and then integrates them sequentially to upper levels using the previously published Generic Integration Algorithm (GIA). iSanXoT offers unique capabilities that complement conventional quantitative software applications, including statistical weighting and independent modeling of error distributions in each integration, aggregation of technical or biological replicates, quantification of posttranslational modifications, and analysis of coordinated protein behavior. iSanXoT is a standalone, user-friendly application that accepts output from popular proteomics pipelines and enables unrestricted creation of quantification workflows and fully customizable reports that can be reused across projects or shared among users. Numerous publications attest the successful application of diverse integrative workflows constructed using the GIA for the analysis of high-throughput quantitative proteomics experiments. iSanXoT has been tested with the main operating systems. Download links for the corresponding distributions are available at https://github.com/CNIC-Proteomics/iSanXoT/releases.
Collapse
Affiliation(s)
- Jose Manuel Rodríguez
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Inmaculada Jorge
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ana Martinez-Val
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Rafael Barrero-Rodríguez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Ricardo Magni
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Estefanía Núñez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Andrea Laguillo
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Cristina A. Devesa
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Juan A. López
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Emilio Camafeita
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| |
Collapse
|
224
|
Zhao J, Wang Y, Feng C, Yin M, Gao Y, Wei L, Song C, Ai B, Wang Q, Zhang J, Zhu J, Li C. SCInter: A comprehensive single-cell transcriptome integration database for human and mouse. Comput Struct Biotechnol J 2024; 23:77-86. [PMID: 38125297 PMCID: PMC10731004 DOI: 10.1016/j.csbj.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq), which profiles gene expression at the cellular level, has effectively explored cell heterogeneity and reconstructed developmental trajectories. With the increasing research on diseases and biological processes, scRNA-seq datasets are accumulating rapidly, highlighting the urgent need for collecting and processing these data to support comprehensive and effective annotation and analysis. Here, we have developed a comprehensive Single-Cell transcriptome integration database for human and mouse (SCInter, https://bio.liclab.net/SCInter/index.php), which aims to provide a manually curated database that supports the provision of gene expression profiles across various cell types at the sample level. The current version of SCInter includes 115 integrated datasets and 1016 samples, covering nearly 150 tissues/cell lines. It contains 8016,646 cell markers in 457 identified cell types. SCInter enabled comprehensive analysis of cataloged single-cell data encompassing quality control (QC), clustering, cell markers, multi-method cell type automatic annotation, predicting cell differentiation trajectories and so on. At the same time, SCInter provided a user-friendly interface to query, browse, analyze and visualize each integrated dataset and single cell sample, along with comprehensive QC reports and processing results. It will facilitate the identification of cell type in different cell subpopulations and explore developmental trajectories, enhancing the study of cell heterogeneity in the fields of immunology and oncology.
Collapse
Affiliation(s)
- Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Yuezhu Wang
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Chenchen Feng
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Mingxue Yin
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yu Gao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Chao Song
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Chunquan Li
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Key Laboratory of Multi-omics And Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan, 421001, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| |
Collapse
|
225
|
Montanari Borges B, Gama de Santana M, Willian Preite N, de Lima Kaminski V, Trentin G, Almeida F, Vieira Loures F. Extracellular vesicles from virulent P. brasiliensis induce TLR4 and dectin-1 expression in innate cells and promote enhanced Th1/Th17 response. Virulence 2024; 15:2329573. [PMID: 38511558 PMCID: PMC10962619 DOI: 10.1080/21505594.2024.2329573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
Extracellular vesicles (EVs) are membrane-enclosed nanoparticles that transport several biomolecules and are involved in important mechanisms and functions related to the pathophysiology of fungal diseases. EVs from Paracoccidioides brasiliensis, the main causative agent of Paracoccidioidomycosis (PCM), modulate the immune response of macrophages. In this study, we assessed the EVs proteome from a virulent P. brasiliensis isolated from granulomatous lesions and compared their immunomodulatory ability with EVs isolated from the fungus before the animal passage (control EVs) when challenging macrophages and dendritic cells (DCs). Proteome showed that virulent EVs have a higher abundance of virulence factors such as GP43, protein 14-3-3, GAPDH, as well as virulence factors never described in PCM, such as aspartyl aminopeptidase and a SidJ analogue compared with control EVs. Virulent extracellular vesicles induced higher expression of TLR4 and Dectin-1 than control EVs in macrophages and dendritic cells (DCs). In opposition, a lower TLR2 expression was induced by virulent EVs. Additionally, virulent EVs induced lower expression of CD80, CD86 and TNF-α, but promoted a higher expression of IL-6 and IL-10, suggesting that EVs isolated from virulent P. brasiliensis-yeast promote a milder DCs and macrophage maturation. Herein, we showed that EVs from virulent fungi stimulated a higher frequency of Th1/Tc1, Th17, and Treg cells, which gives new insights into fungal extracellular vesicles. Taken together, our results suggest that P. brasiliensis utilizes its EVs as virulence bags that manipulate the immune system in its favour, creating a milder immune response and helping with fungal evasion from the immune system.
Collapse
Affiliation(s)
- Bruno Montanari Borges
- Institute of Science and Technology (ICT), Federal University of São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| | - Monique Gama de Santana
- Institute of Science and Technology (ICT), Federal University of São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| | - Nycolas Willian Preite
- Institute of Science and Technology (ICT), Federal University of São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| | - Valéria de Lima Kaminski
- Institute of Science and Technology (ICT), Federal University of São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| | - Gabriel Trentin
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Flávio Vieira Loures
- Institute of Science and Technology (ICT), Federal University of São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| |
Collapse
|
226
|
Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
Collapse
Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| |
Collapse
|
227
|
Tian Y, Wu X, Luo S, Xiong D, Liu R, Hu L, Yuan Y, Shi G, Yao J, Huang Z, Fu F, Yang X, Tang Z, Zhang J, Hu K. A multi-omic single-cell landscape of cellular diversification in the developing human cerebral cortex. Comput Struct Biotechnol J 2024; 23:2173-2189. [PMID: 38827229 PMCID: PMC11141146 DOI: 10.1016/j.csbj.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/04/2024] Open
Abstract
The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell. We computationally reconstructed the differentiation trajectories of excitatory projection neurons of cortical origin and inferred the regulatory logic governing lineage bifurcation decisions for neuronal diversification. We demonstrated that neuronal diversity arises from progenitor cell lineage specificity and postmitotic differentiation at distinct stages. Our data paves the way for understanding the primarily coordinated regulatory logic for neuronal diversification in the neocortex.
Collapse
Affiliation(s)
- Yuhan Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Xia Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Songhao Luo
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Xiong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Rong Liu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Lanqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuchen Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Guowei Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiwei Huang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Fang Fu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Xin Yang
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 511436, China
| | - Zhonghui Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiajun Zhang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Kunhua Hu
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Public Platform Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| |
Collapse
|
228
|
Yu Y, Liu T, Wang Y, Liu L, He X, Li J, Martin FM, Peng W, Tan H. Comparative analyses of Pleurotus pulmonarius mitochondrial genomes reveal two major lineages of mini oyster mushroom cultivars. Comput Struct Biotechnol J 2024; 23:905-917. [PMID: 38370975 PMCID: PMC10869244 DOI: 10.1016/j.csbj.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Pleurotus pulmonarius, commonly known as the mini oyster mushroom, is highly esteemed for its crisp texture and umami flavor. Limited genetic diversity among P. pulmonarius cultivars raises concerns regarding its sustainable industrial production. To delve into the maternal genetic diversity of the principal P. pulmonarius cultivars, 36 cultivars and five wild isolates were subjected to de novo sequencing and assembly to generate high-quality mitogenome sequences. The P. pulmonarius mitogenomes had lengths ranging from 69,096 to 72,905 base pairs. The mitogenome sizes of P. pulmonarius and those of other mushroom species in the Pleurotus genus showed a significant positive correlation with the counts of LAGLIDAG and GIY-YIG homing endonucleases encoded by intronic open reading frames. A comparison of gene arrangements revealed an inversion of a fragment containing atp9-nad3-nad2 between P. pulmonarius and P. ostreatus. The mitogenomes of P. pulmonarius were clustered into three distinct clades, two of which were crowded with commercial cultivars. Clade I, all of which possess an inserted dpo gene, shared a maternal origin linked to an ancestral cultivar from Taiwan. Primers were designed to target the dpo gene, potentially safeguarding intellectual property rights. The wild isolates in Clade III exhibited more divergent mitogenomes, rendering them valuable for breeding.
Collapse
Affiliation(s)
- Yang Yu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Tianhai Liu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- Sichuan Agricultural University, Chengdu 610000, China
| | - Yong Wang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Lixu Liu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Xiaolan He
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Jianwei Li
- Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est, Nancy, Champenoux 54280, France
| | - Weihong Peng
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
| | - Hao Tan
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610000, China
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| |
Collapse
|
229
|
Kobetitsch S, Gierlikowska B, Kunert O, Mazen AM, Raab P, Kretschmer N, Donolo C, Pirker T, Bauer R, Kiss AK, Pferschy-Wenzig EM. Salvadora persica leaves: phytochemical profile and in vitro-inhibitory activity on inflammatory mediators implicated in periodontal disease. PHARMACEUTICAL BIOLOGY 2024; 62:563-576. [PMID: 39021070 PMCID: PMC11259067 DOI: 10.1080/13880209.2024.2374801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/22/2024] [Indexed: 07/20/2024]
Abstract
CONTEXT Virtually all parts of Salvadora persica L. (Salvadoraceae) are used in traditional medicine. The twigs and leaves are used for oral health, but leaves are far less investigated. OBJECTIVE This study assesses the oral health-promoting potential of S. persica leaves with emphasis on anti-inflammatory and antiproliferative effects and provides an in depth-characterization of their metabolite profile. MATERIALS AND METHODS Hot-water and methanolic S. persica leaf extracts (1, 10, and 100 µg/mL) and their major constituents (5, 10, and 50 µM), were subjected to cellular assays on IL-8 and TNFα release in LPS-stimulated human neutrophils, NO-release in LPS/IFNγ stimulated mouse macrophages, and proliferation of HNO97 human tongue carcinoma cells. Metabolite profiling was performed by UHPLC-HRMS analysis. Major constituents were isolated and structurally elucidated. RESULTS AND DISCUSSION Both extracts showed pronounced anti-inflammatory activity in LPS-stimulated neutrophils. Major identified compound classes were flavonoid glycosides, the glucosinolate glucotropaeolin, phenyl- and benzylglycoside sulfates, and megastigmane glycosylsulfates, the latter ones identified for the first time in S. persica. Glucotropaeolin strongly inhibited the release of IL-8 and TNF-α (13.3 ± 2.0 and 22.7 ± 2.6% of the release of stimulated control cells at 50 µM), while some flavonoids and 3-(3'-O-sulfo-β-d-glucopyranosyloxy)-7,8-dihydro-β-ionone, a newly isolated megastigmane glycosylsulfate, were moderately active. Benzylisothiocyanate, which is likely formed from glucotropaeolin during traditional application of S. persica, showed considerable antiproliferative activity (IC50 in HNO97 cells: 10.19 ± 0.72 µM) besides strongly inhibiting IL-8 and TNFα release. CONCLUSIONS Glucotropaeolin and benzylisothiocyanate are likely implicated in the oral health-promoting effects of S. persica leaves. The chemistry and pharmacology of the newly identified megastigmane glycosylsulfates should be further evaluated.
Collapse
Affiliation(s)
- Sabine Kobetitsch
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Graz, Austria
| | - Barbara Gierlikowska
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Olaf Kunert
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Ahmed M.A. Mazen
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, Egypt
| | - Pia Raab
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Graz, Austria
| | - Nadine Kretschmer
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Graz, Austria
| | - Carina Donolo
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Graz, Austria
| | - Teresa Pirker
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Graz, Austria
| | - Rudolf Bauer
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Graz, Austria
| | - Anna K. Kiss
- Chair and Department of Pharmaceutical Biology, Medical University of Warsaw, Warsaw, Poland
| | | |
Collapse
|
230
|
Meng F, Zhou N, Hu G, Liu R, Zhang Y, Jing M, Hou Q. A comprehensive overview of recent advances in generative models for antibodies. Comput Struct Biotechnol J 2024; 23:2648-2660. [PMID: 39027650 PMCID: PMC11254834 DOI: 10.1016/j.csbj.2024.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Therapeutic antibodies are an important class of biopharmaceuticals. With the rapid development of deep learning methods and the increasing amount of antibody data, antibody generative models have made great progress recently. They aim to solve the antibody space searching problems and are widely incorporated into the antibody development process. Therefore, a comprehensive introduction to the development methods in this field is imperative. Here, we collected 34 representative antibody generative models published recently and all generative models can be divided into three categories: sequence-generating models, structure-generating models, and hybrid models, based on their principles and algorithms. We further studied their performance and contributions to antibody sequence prediction, structure optimization, and affinity enhancement. Our manuscript will provide a comprehensive overview of the status of antibody generative models and also offer guidance for selecting different approaches.
Collapse
Affiliation(s)
- Fanxu Meng
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Na Zhou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250100, China
- National Institute of Health Data Science of China, Shandong University, Jinan 250100, China
| | - Guangchun Hu
- School of Information Science and Engineering, University of Jinan, Jinan 250022, China
| | - Ruotong Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250100, China
- National Institute of Health Data Science of China, Shandong University, Jinan 250100, China
| | - Yuanyuan Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Ming Jing
- Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
- Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan 250000, China
| | - Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250100, China
- National Institute of Health Data Science of China, Shandong University, Jinan 250100, China
| |
Collapse
|
231
|
Ali AH, Öztürk Hİ, Eylem CC, Nemutlu E, Tarique M, Subhash A, Liu SQ, Kamal-Eldin A, Ayyash M. Biological activities, Peptidomics and in silico analysis of low-fat Cheddar cheese after in vitro digestion: Impact of blending camel and bovine Milk. Food Chem 2024; 460:140760. [PMID: 39137574 DOI: 10.1016/j.foodchem.2024.140760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Cheesemaking with camel milk (CM) presents unique challenges and additional health benefits. This study involved preparing low-fat Cheddar cheese (LFCC) by blending bovine milk (BM) with varying levels of CM. Control cheese was made exclusively with BM. After 180 days of ripening, LFCC samples underwent in vitro digestion to determine antioxidant capacities, α-amylase and α-glucosidase inhibition, and angiotensin-converting enzyme inhibition. The peptide profile of LFCC treatments was analyzed using liquid chromatography-quadrupole-time of flight-mass spectrometry. Antioxidant and biological activities were influenced by BM-CM blends and digestion. At days 120 and 180, the number of αs1-casein-derived peptides increased in all samples except for LFCC made with 15% CM. Generally, 88 peptides exhibited ACE inhibition activity after 120 days of ripening, increasing to 114 by day 180. These findings suggest that ripening time positively affects the health-promoting aspects of functional cheese products.
Collapse
Affiliation(s)
- Abdelmoneim H Ali
- Department of Food Science, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; Department of Chemical and Petroleum Engineering, College of Engineering and Physical Sciences, Khalifa University of Sciences and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Hale İnci Öztürk
- Department of Food Engineering, Faculty of Engineering and Architecture, Konya Food and Agriculture University, Konya 42080, Turkey; Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul 34210, Turkiye
| | - Cemil Can Eylem
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara 06100, Turkey
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara 06100, Turkey
| | - Mohammad Tarique
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates
| | - Athira Subhash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates
| | - Shao-Quan Liu
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Science Drive 2, 117542, Singapore
| | - Afaf Kamal-Eldin
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates
| | - Mutamed Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, P.O. Box 15551, United Arab Emirates.
| |
Collapse
|
232
|
Camacho-Jiménez L, Peregrino-Uriarte AB, Leyva-Carrillo L, Gómez-Jiménez S, Yepiz-Plascencia G. Peroxiredoxin 6 (Prx6) of Penaeus vannamei and effect of phenanthrene on Prx6 and glutathione peroxidase 4 expression, glutathione-dependent peroxidase activity and lipid peroxidation. Comp Biochem Physiol C Toxicol Pharmacol 2024; 286:110014. [PMID: 39218132 DOI: 10.1016/j.cbpc.2024.110014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/16/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene (PHE), are common pollutants found in coastal areas where shrimp farming is developed. Even though PAHs can have adverse effects on physiology, shrimp can detoxify and metabolize toxic compounds and neutralize the reactive oxygen species (ROS) produced during this process. This requires the activation of multiple antioxidant enzymes, including peroxiredoxin 6 (Prx6). Prx6 uses glutathione (GSH) to reduce phospholipid hydroperoxides, a function shared with GSH peroxidase 4 (GPx4). Prx6 has been scarcely studied in crustaceans exposed to pollutants. Herein, we report a novel Prx6 from the shrimp Penaeus vannamei that is abundantly expressed in gills and hepatopancreas. To elucidate the involvement of Prx6 in response to PAHs, we analyzed its expression in the hepatopancreas of shrimp sub-lethally exposed to PHE (3.3 μg/L) and acetone (control) for 24, 48, 72, and 96 h, along with GPx4 expression, GSH-dependent peroxidase activity, and lipid peroxidation (indicated by TBARS). We found that GPx4 expression is not affected by PHE, but Prx6 expression and peroxidase activity decreased during the trial. This might contribute to the rise of TBARS found at 48 h of exposure. However, maintaining GPx4 expression could aid to minimize lipid damage during longer periods of exposure to PHE.
Collapse
Affiliation(s)
- Laura Camacho-Jiménez
- Group of Comparative Biochemistry and Physiology, Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora C.P. 83304, Mexico
| | - Alma B Peregrino-Uriarte
- Group of Comparative Biochemistry and Physiology, Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora C.P. 83304, Mexico
| | - Lilia Leyva-Carrillo
- Group of Comparative Biochemistry and Physiology, Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora C.P. 83304, Mexico
| | - Silvia Gómez-Jiménez
- Group of Comparative Biochemistry and Physiology, Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora C.P. 83304, Mexico
| | - Gloria Yepiz-Plascencia
- Group of Comparative Biochemistry and Physiology, Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora C.P. 83304, Mexico.
| |
Collapse
|
233
|
Caira S, Troise AD, Picariello G, De Pascale S, Pinto G, Pesce M, Marino F, Sarnelli G, Scaloni A, Addeo F. Beyond the gut: Investigating the mechanism of formation of β-casomorphins in human blood. Food Chem 2024; 460:140477. [PMID: 39047470 DOI: 10.1016/j.foodchem.2024.140477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/03/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
To evaluate the potential differences in the propensity of β-casein A1 (β-CNA1) and A2 (β-CNA2) from bovine milk to release health-relevant β-casomorphins (BCMs), food-derived peptides were monitored over time in the blood of eight human volunteers who consumed milk containing both protein variants. Liquid chromatography coupled with high resolution tandem mass spectrometry revealed interindividual variability of milk peptidomic profiles in human blood. BCMs were not detected, whereas BCM precursors originating from both β-CNA1 and β-CNA2 were ascertained, with β-CNA2-derived peptides showing a slightly greater susceptibility to proteolysis. Ten synthetic peptides mimicking circulating BCM precursors from β-CNA1 and β-CNA2, which were incubated ex vivo with the blood of two volunteers, showed comparable potential to generate BCMs. The formation of BCMs seemed to depend mainly on the size of the BCM precursors and less on the presence of His67 or Pro67. These findings challenge the belief that BCMs are released exclusively from β-CNA1 and support the nutritional safety of conventional milk, informing health policies regarding milk consumption.
Collapse
Affiliation(s)
- Simonetta Caira
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, National Research Council, 80055 Portici, Italy.
| | - Antonio Dario Troise
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, National Research Council, 80055 Portici, Italy
| | - Gianluca Picariello
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy
| | - Sabrina De Pascale
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, National Research Council, 80055 Portici, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples "Federico II", 80126 Naples, Italy
| | - Marcella Pesce
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesca Marino
- Department of Clinical Medicine and Surgery, Endocrinology Unit, University of Naples "Federico II", 80131 Naples, Italy
| | - Giovanni Sarnelli
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131 Naples, Italy
| | - Andrea Scaloni
- Proteomics, Metabolomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, National Research Council, 80055 Portici, Italy.
| | - Francesco Addeo
- Department of Agriculture, University of Naples "Federico II", 80055 Portici, Italy
| |
Collapse
|
234
|
Li Z, Leeming MG, Hastie M, Frank D, Ha M, Warner RD. Targeted-metabolomic and untargeted-proteomic approaches reveal the effects of muscle fibre type and postmortem ageing on taste-active compounds in beef. Food Chem 2024; 460:140506. [PMID: 39053267 DOI: 10.1016/j.foodchem.2024.140506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/29/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
The taste of beef is caused by taste-active compounds detected in the mouth during mastication. We hypothesised that the concentration of taste-active compounds in beef is influenced by muscle-fibre-type and postmortem ageing. To test this, and unravel the underlying mechanisms, we investigated the taste-active compounds, and proteomic profiles, in beef masseter [oxidative muscle, all type I fibres) and cutaneous trunci (glycolytic muscle, mostly type II fibres) before and after 14-days postmortem ageing. Our results showed that nucleotides were initially higher and degraded slower in cutaneous trunci (P < 0.05 for both), which could be explained by the profile of nucleotide metabolism enzymes. In contrast, free amino acids were initially higher and increased more in masseter compared to cutaneous trunci (P < 0.05 for all), which might be explained by the profile and activity of proteases in these two muscles. Our results indicate the taste of beef is affected by the muscle-fibre-type and postmortem ageing.
Collapse
Affiliation(s)
- Zhenzhao Li
- Faculty of Science, The University of Melbourne, Australia
| | | | | | | | - Minh Ha
- Faculty of Science, The University of Melbourne, Australia
| | - Robyn D Warner
- Faculty of Science, The University of Melbourne, Australia.
| |
Collapse
|
235
|
Pan Y, Ming K, Guo D, Liu X, Deng C, Chi Q, Liu X, Wang C, Xu K. Non-targeted metabolomics and explainable artificial intelligence: Effects of processing and color on coniferyl aldehyde levels in Eucommiae cortex. Food Chem 2024; 460:140564. [PMID: 39089015 DOI: 10.1016/j.foodchem.2024.140564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/15/2024] [Accepted: 07/20/2024] [Indexed: 08/03/2024]
Abstract
Eucommia ulmoides, a plant native to China, is valued for its medicinal properties and has applications in food, health products, and traditional Chinese medicine. Processed Eucommiae Cortex (EC) has historically been a highly valued medicine. Ancient doctors had ample experience processing EC, especially with ginger juice, as documented in traditional Chinese medical texts. The combination of EC and ginger juice helps release and transform the active ingredients, strengthening the medicine's effectiveness and improving its taste and shelf life. However, the lack of quality control standards for Ginger-Eucommiae Cortex (G-EC), processed from EC and ginger, presents challenges for its industrial and clinical use. This study optimized G-EC processing using the CRITIC and Box-Behnken methods. Metabolomics showed 517 chemical changes between raw and processed G-EC, particularly an increase in coniferyl aldehyde (CFA). Explainable artificial intelligence techniques revealed the feasibility of using color to CFA content, providing insights into quality indicators.
Collapse
Affiliation(s)
- Yijing Pan
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China
| | - Kehong Ming
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China
| | - Dongmei Guo
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China
| | - Xinyue Liu
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China
| | - Chenxi Deng
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China
| | - Qingjia Chi
- Hubei Key Laboratory of Theory and Application of Advanced Materials Mechanics, Department of Mechanics and Engineering Structure, Wuhan University of Technology, China.
| | - Xianqiong Liu
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China.
| | - Chunli Wang
- Hubei Shizhen Laboratory, Wuhan 430065, China; School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Kang Xu
- Hubei Provincial Engineering Technology Research Center for Chinese Medicine Processing, School of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Wuhan 430065, China; Center of Traditional Chinese Medicine Modernization for Liver Diseases, Hubei University of Chinese Medicine, Wuhan 430065, China.
| |
Collapse
|
236
|
Meng K, Meng F, Wu Y, Lin L. Multi-omics analysis identified extracellular vesicles as biomarkers for cardiovascular diseases. Talanta 2024; 280:126710. [PMID: 39213888 DOI: 10.1016/j.talanta.2024.126710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Cell-derived extracellular vesicles (EVs) have emerged as a promising non-invasive liquid biopsy technique due to their accessibility and their ability to encapsulate and transport diverse biomolecules. EVs have garnered substantial research interest, notably in cardiovascular diseases (CVDs), where their roles in pathophysiology and as diagnostic and prognostic biomarkers are increasingly recognized. This review provides a comprehensive overview of EVs, starting with their origins, followed by the techniques used for their isolation and characterization. We explore the diverse cargo of EVs, including nucleic acids, proteins, lipids, and metabolites, highlighting their roles in intercellular communication and as potential biomarkers. We then delve into the application of genomics, transcriptomics, proteomics, and metabolomics in the analysis of EVs, particularly within the context of CVDs. Finally, we discuss how integrated multi-omics approaches are unveiling novel biomarkers, offering fresh insights into the diagnosis and prognosis of CVDs. This review underscores the growing importance of EVs in clinical diagnostics and the potential of multi-omics to propel future advancements in CVD biomarker discovery.
Collapse
Affiliation(s)
- Ke Meng
- Medical College, Guangxi University, Nanning, Guangxi, China
| | - Fanqi Meng
- Xiamen Cardiovascular Hospital, Xiamen University, Xiamen, 361004, Fujian, China
| | - Yuan Wu
- Department of Cardiac Surgery, Yuebei People's Hospital, Shaoguan, Guangdong, China.
| | - Ling Lin
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
237
|
Pan W, Chen L, Zhu S, Li D, Shen Z, Wu ZS. Persistent autonomous molecular motion of DNA walker along a single-molecule nano-track for intracellular MicroRNA imaging. Talanta 2024; 280:126735. [PMID: 39173244 DOI: 10.1016/j.talanta.2024.126735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
While the intracellular imaging of miRNA biomarkers is of significant importance for the diagnosis and treatment of human cancers, DNA assembled nanoprobe has recently attracted considerable attention for imaging intracellular biomolecules. However, the complex construction process, intrinsic vulnerability to nuclease degradation and the limited signal transduction efficiency hamper its widespread application. In this contribution, based on persistent autonomous molecular motion of DNAzyme walker along a nano-substrate track, a DNA nanosphere probe (PNLD) is developed for the sensitive intracellular miR-21 imaging. Specifically, DNA nanosphere (called PN, single-molecule nano-track) is assembled from only one palindromic substrate, into which the locking strand-silenced DNAzymes (LD) are installed in a controlled manner. PNLD (made of PN and LD) can protect all DNA components against nuclease attack and maintain its structural integrity in serum solution over 24 h. Upon the activation by target miRNA, DNAzyme walker can move on the substrate scattered within PNLD (or on the surface) and between different PNLD objects and cleave many DNA substrates, generating an amplified signal. As a result, miR-21 can be detected down to 6.83 pM without the detectable interference from co-existing nontarget miRNAs. Moreover, PNLD system can accurately screen the different expression levels of miR-21 within the same type of cells and different types of cells, which is consistent with gold standard polymerase chain reaction (PCR) assay. Via changing the target recognition sequence, the PNLD system can be suitable for the intracellular imaging of miR-155, exhibiting the desirable universality. In addition, the DNAzyme walker-based PNLD system can be used to distinguish cancer cells from healthy cells, implying the potential application in cancer diagnosis and prognosis.
Collapse
Affiliation(s)
- Wenhao Pan
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Linhuan Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Shidan Zhu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Dongyu Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| |
Collapse
|
238
|
Li S, Luo S, Yin X, Zhao X, Wang X, Gao S, Xu S, Lu J, Zhou J. Screening of ent-copalyl diphosphate synthase and metabolic engineering to achieve de novo biosynthesis of ent-copalol in Saccharomyces cerevisiae. Synth Syst Biotechnol 2024; 9:784-792. [PMID: 39021361 PMCID: PMC11253141 DOI: 10.1016/j.synbio.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
The diterpene ent-copalol is an important precursor to the synthesis of andrographolide and is found only in green chiretta (Andrographis paniculata). De novo biosynthesis of ent-copalol has not been reported, because the catalytic activity of ent-copalyl diphosphate synthase (CPS) is very low in microorganisms. In order to achieve the biosynthesis of ent-copalol, Saccharomyces cerevisiae was selected as the chassis strain, because its endogenous mevalonate pathway and dephosphorylases could provide natural promotion for the synthesis of ent-copalol. The strain capable of synthesizing diterpene geranylgeranyl pyrophosphate was constructed by strengthening the mevalonate pathway genes and weakening the competing pathway. Five full-length ApCPSs were screened by transcriptome sequencing of A. paniculata and ApCPS2 had the best activity and produced ent-CPP exclusively. The peak area of ent-copalol was increased after the ApCPS2 saturation mutation and its configuration was determined by NMR and ESI-MS detection. By appropriately optimizing acetyl-CoA supply and fusion-expressing key enzymes, 35.6 mg/L ent-copalol was generated. In this study, de novo biosynthesis and identification of ent-copalol were achieved and the highest titer ever reported. It provides a platform strain for the further pathway analysis of andrographolide and derivatives and provides a reference for the synthesis of other pharmaceutical intermediates.
Collapse
Affiliation(s)
- Shan Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Shuangshuang Luo
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xinran Yin
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xingying Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xuyang Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Sha Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jian Lu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Rd, Wuxi, Jiangsu, 214122, China
| |
Collapse
|
239
|
McDonnell L, Evans S, Lu Z, Suchoronczak M, Leighton J, Ordeniza E, Ritchie B, Valado N, Walsh N, Antoney J, Wang C, Luna-Flores CH, Scott C, Speight R, Vickers CE, Peng B. Cyanamide-inducible expression of homing nuclease I- SceI for selectable marker removal and promoter characterisation in Saccharomyces cerevisiae. Synth Syst Biotechnol 2024; 9:820-827. [PMID: 39072146 PMCID: PMC11277796 DOI: 10.1016/j.synbio.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
In synthetic biology, microbial chassis including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale. Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements, such as the galactose-inducible (GAL) promoter in S. cerevisiae. Here, we prototyped the cyanamide-induced I- SceI expression, which triggered double-strand DNA breaks (DSBs) for selectable marker removal. We further combined cyanamide-induced I- SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter substitution, which simplified the molecular cloning procedure for promoter characterisation. We then characterised three tetracycline-inducible promoters showing differential strength, a non-leaky β-estradiol-inducible promoter, cyanamide-inducible DDI2 promoter, bidirectional MAL32/MAL31 promoters, and five pairs of bidirectional GAL1/GAL10 promoters. Overall, alternative regulatory controls for genome engineering tools can be developed to facilitate genomic engineering for synthetic biology and metabolic engineering applications.
Collapse
Affiliation(s)
- Liam McDonnell
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Samuel Evans
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Zeyu Lu
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mitch Suchoronczak
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Jonah Leighton
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Eugene Ordeniza
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Blake Ritchie
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Nik Valado
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Niamh Walsh
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - James Antoney
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Chengqiang Wang
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong Province, 271018, People's Republic of China
| | - Carlos Horacio Luna-Flores
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, 2601, Australia
| | - Robert Speight
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia
| | - Claudia E. Vickers
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
| | - Bingyin Peng
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
240
|
Li F, Wang W, Cheng H, Li M. Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp ( Opsariichthys bidens). Comput Struct Biotechnol J 2024; 23:2465-2477. [PMID: 38882676 PMCID: PMC11179538 DOI: 10.1016/j.csbj.2024.05.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.
Collapse
Affiliation(s)
- Fengbo Li
- Zhejiang Institute of Freshwater Fisheries, 999 Hangchangqiao South Road, Huzhou 313001, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Beijing 100101, China
| | - Haihua Cheng
- Zhejiang Institute of Freshwater Fisheries, 999 Hangchangqiao South Road, Huzhou 313001, China
| | - Ming Li
- Jinhua Fisheries Technology Extension Center, 828 Shuanglong South Street, Jinhua 321013, China
| |
Collapse
|
241
|
Sharma M, Alessandro P, Cheriyamundath S, Lopus M. Therapeutic and diagnostic applications of carbon nanotubes in cancer: recent advances and challenges. J Drug Target 2024; 32:287-299. [PMID: 38252035 DOI: 10.1080/1061186x.2024.2309575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Carbon nanotubes (CNTs) are allotropes of carbon, composed of carbon atoms forming a tube-like structure. Their high surface area, chemical stability, and rich electronic polyaromatic structure facilitate their drug-carrying capacity. Therefore, CNTs have been intensively explored for several biomedical applications, including as a potential treatment option for cancer. By incorporating smart fabrication strategies, CNTs can be designed to specifically target cancer cells. This targeted drug delivery approach not only maximizes the therapeutic utility of CNTs but also minimizes any potential side effects of free drug molecules. CNTs can also be utilised for photothermal therapy (PTT) which uses photosensitizers to generate reactive oxygen species (ROS) to kill cancer cells, and in immunotherapeutic applications. Regarding the latter, for example, CNT-based formulations can preferentially target intra-tumoural regulatory T-cells. CNTs also act as efficient antigen presenters. With their capabilities for photoacoustic, fluorescent and Raman imaging, CNTs are excellent diagnostic tools as well. Further, metallic nanoparticles, such as gold or silver nanoparticles, are combined with CNTs to create nanobiosensors to measure biological reactions. This review focuses on current knowledge about the theranostic potential of CNT, challenges associated with their large-scale production, their possible side effects and important parameters to consider when exploring their clinical usage.
Collapse
Affiliation(s)
- Muskan Sharma
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, India
| | - Parodi Alessandro
- Department of Translational Medicine, Sirius University of Science and Technology, Sirius, Russia
| | - Sanith Cheriyamundath
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, India
| | - Manu Lopus
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, India
| |
Collapse
|
242
|
Rigo YR, Benvenutti R, Portela LV, Strogulski NR. Neurogenic potential of NG2 in neurotrauma: a systematic review. Neural Regen Res 2024; 19:2673-2683. [PMID: 38595286 PMCID: PMC11168526 DOI: 10.4103/nrr.nrr-d-23-01031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/20/2023] [Accepted: 02/07/2024] [Indexed: 04/11/2024] Open
Abstract
Regenerative approaches towards neuronal loss following traumatic brain or spinal cord injury have long been considered a dogma in neuroscience and remain a cutting-edge area of research. This is reflected in a large disparity between the number of studies investigating primary and secondary injury as therapeutic targets in spinal cord and traumatic brain injuries. Significant advances in biotechnology may have the potential to reshape the current state-of-the-art and bring focus to primary injury neurotrauma research. Recent studies using neural-glial factor/antigen 2 (NG2) cells indicate that they may differentiate into neurons even in the developed brain. As these cells show great potential to play a regenerative role, studies have been conducted to test various manipulations in neurotrauma models aimed at eliciting a neurogenic response from them. In the present study, we systematically reviewed the experimental protocols and findings described in the scientific literature, which were peer-reviewed original research articles (1) describing preclinical experimental studies, (2) investigating NG2 cells, (3) associated with neurogenesis and neurotrauma, and (4) in vitro and/or in vivo, available in PubMed/MEDLINE, Web of Science or SCOPUS, from 1998 to 2022. Here, we have reviewed a total of 1504 papers, and summarized findings that ultimately suggest that NG2 cells possess an inducible neurogenic potential in animal models and in vitro. We also discriminate findings of NG2 neurogenesis promoted by different pharmacological and genetic approaches over functional and biochemical outcomes of traumatic brain injury and spinal cord injury models, and provide mounting evidence for the potential benefits of manipulated NG2 cell ex vivo transplantation in primary injury treatment. These findings indicate the feasibility of NG2 cell neurogenesis strategies and add new players in the development of therapeutic alternatives for neurotrauma.
Collapse
Affiliation(s)
- Yuri R. Rigo
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Radharani Benvenutti
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Luis V. Portela
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Nathan R. Strogulski
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, University of Dublin, Dublin, Ireland
| |
Collapse
|
243
|
Telek A, Molnár Z, Takács K, Varga B, Grolmusz V, Tasnádi G, Vértessy BG. Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining. Appl Microbiol Biotechnol 2024; 108:101. [PMID: 38229296 DOI: 10.1007/s00253-023-12871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.
Collapse
Grants
- K119493 National Research, Development and Innovation Office
- K135231 National Research, Development and Innovation Office
- VEKOP-2.3.2-16-2017-00013 National Research, Development and Innovation Office
- NKP-2018-1.2.1-NKP-2018-00005 National Research, Development and Innovation Office
- TKP2021-EGA-02 National Research, Development and Innovation Office
- ÚNKP-22-4-II-BME-158 National Research, Development and Innovation Office
- RRF-2.3.1-21-2022-000 15 National Research, Development and Innovation Office
- C1580174 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- ELTE TKP 2021-NKTA-62 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
- 2022-1.2.2-TÉT-IPARI-UZ-2022-00003 Nemzeti Kutatási, Fejlesztési és Innovaciós Alap
Collapse
Affiliation(s)
- András Telek
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary
| | - Zsófia Molnár
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös University, Budapest, Hungary
| | - Gábor Tasnádi
- Servier Research Institute of Medicinal Chemistry, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Budapest, Hungary.
| |
Collapse
|
244
|
Tamayo E, Nada B, Hafermann I, Benz JP. Correlating sugar transporter expression and activities to identify transporters for an orphan sugar substrate. Appl Microbiol Biotechnol 2024; 108:83. [PMID: 38189952 PMCID: PMC10774165 DOI: 10.1007/s00253-023-12907-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 01/09/2024]
Abstract
Filamentous fungi like Neurospora crassa are able to take up and metabolize important sugars present, for example, in agricultural and human food wastes. However, only a fraction of all putative sugar transporters in filamentous fungi has been characterized to date, and for many sugar substrates, the corresponding transporters are unknown. In N. crassa, only 14 out of the 42 putative major facilitator superfamily (MFS)-type sugar transporters have been characterized so far. To uncover this hidden potential for biotechnology, it is therefore necessary to find new strategies. By correlation of the uptake profile of sugars of interest after different induction conditions with the expression profiles of all 44 genes encoding predicted sugar transporters in N. crassa, together with an exhaustive phylogenetic analysis using sequences of characterized fungal sugar transporters, we aimed to identify transporter candidates for the tested sugars. Following this approach, we found a high correlation of uptake rates and expression strengths for many sugars with dedicated transporters, like galacturonic acid and arabinose, while the correlation is loose for sugars that are transported by several transporters due to functional redundancy. Nevertheless, this combinatorial approach allowed us to elucidate the uptake system for the disaccharide lactose, a by-product of the dairy industry, which consists of the two main cellodextrin transporters CDT-1 and CDT-2 with a minor contribution of the related transporter NCU00809. Moreover, a non-MFS transporter involved in glycerol transport was also identified. Deorphanization of sugar transporters or identification of transporters for orphan sugar substrates by correlation of uptake kinetics with transporter expression and phylogenetic information can thus provide a way to optimize the reuse of food industry by-products and agricultural wastes by filamentous fungi in order to create economic value and reduce their environmental impact. KEY POINTS: • The Neurospora crassa genome contains 30 uncharacterized putative sugar transporter genes. • Correlation of transporter expression and sugar uptake profiles can help to identify transporters for orphan sugar substrates. • CDT-1, CDT-2, and NCU00809 are key players in the transport of the dairy by-product lactose in N. crassa.
Collapse
Affiliation(s)
- Elisabeth Tamayo
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Basant Nada
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Isabell Hafermann
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - J Philipp Benz
- Fungal Biotechnology in Wood Science, Holzforschung München, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| |
Collapse
|
245
|
Liu F, Wang ZK, Li MY, Zhang XL, Cai FC, Wang XD, Gao XF, Li W. Characterization of biliary and duodenal microbiota in patients with primary and recurrent choledocholithiasis. Health Inf Sci Syst 2024; 12:29. [PMID: 38584761 PMCID: PMC10994894 DOI: 10.1007/s13755-023-00267-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/27/2023] [Indexed: 04/09/2024] Open
Abstract
Purpose To explore the biliary and duodenal microbiota features associated with the formation and recurrence of choledocholithiasis (CDL). Methods We prospectively recruited patients with primary (P-CDL, n = 29) and recurrent CDL (R-CDL, n = 27) for endoscopic retrograde cholangiopancreatography (ERCP). Duodenal mucosa (DM), bile and bile duct stones (BDS) samples were collected in P- and R-CDL patients. DM samples were also collected in 8 healthy controls (HC). The microbiota profile analysis was performed with 16S rRNA gene sequencing. Results Short-course antibiotic application before ERCP showed no significant effects in alpha and beta diversities of the biliary and duodenal microbiota in CDL. Alpha diversity showed no difference between DM and bile samples in CDL. The duodenal microbial richness and diversity was lower in both P- and R-CDL than HC. The biliary microbiota composition showed a high similarity between P- and R-CDL. Fusobacterium and Enterococcus were higher abundant in DM, bile, and BDS samples of R-CDL than P-CDL, as well as Escherichia and Klebsiella in bile samples of R-CDL. The enriched duodenal and biliary bacteria in CDL were closely associated with cholecystectomy, inflammation and liver dysfunction. The bile-associated microbiota of R-CDL expressed enhanced capacity of D-glucuronide and D-glucuronate degradation, implicating an elevated level of β-glucuronidase probably produced by enriched Escherichia and Klebsiella in bile. Conclusions The duodenal microbiota was in an imbalance in CDL. The duodenal microbiota was probably the main source of the biliary microbiota and was closely related to CDL formation and recurrence. Enterococcus, Fusobacterium, Escherichia and Klebsiella might contribute to CDL recurrence. Clinical trials The study was registered at the Chinese Clinical Trial Registry (https://www.chictr.org.cn/index.html, ChiCTR2000033940). Supplementary Information The online version contains supplementary material available at 10.1007/s13755-023-00267-2.
Collapse
Affiliation(s)
- Fang Liu
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Zi-Kai Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Ming-Yang Li
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Xiu-li Zhang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Feng-Chun Cai
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Xiang-Dong Wang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Xue-Feng Gao
- Integrative Microecology Clinical Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, The Clinical Innovation & Research Center, Shenzhen Hospital, Southern Medical University, Shenzhen, 518000 Guangdong China
| | - Wen Li
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
- Minimally Invasive Digestive Disease Center, Beijing and Shenzhen United Family Hospital, Beijing, China
| |
Collapse
|
246
|
Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
Collapse
Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
247
|
Briceño-Islas G, Mojica L, Urías-Silvas JE. Functional chia (Salvia hispanica L.) co-product protein hydrolysate: An analysis of biochemical, antidiabetic, antioxidant potential and physicochemical properties. Food Chem 2024; 460:140406. [PMID: 39047480 DOI: 10.1016/j.foodchem.2024.140406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/22/2024] [Accepted: 07/07/2024] [Indexed: 07/27/2024]
Abstract
Protein hydrolysates with antioxidant potential have been reported to act as adjuvants in preventing and treating type-2 diabetes (T2D). This work investigated the biochemical, antidiabetic, antioxidant potential, and physicochemical properties of chia meal protein hydrolysate (CMPH). Bands smaller than 14 kDa were observed in the electrophoretic profile. The predominant amino acids were hydrophobic and aromatic. CMPH had the potential to inhibit α-amylase (IC50: 1.76 ± 0.13 mg/mL), α-glucosidase (IC50: 0.42 ± 0.13 mg/mL), and DPP-IV (IC50: 0.46 ± 0.14 mg/mL). Antioxidant activity for ABTS (IC50: 0.236 mg/mL), DPPH (8.83 ± 0.52%), and ORAC (IC25: 0.115 mg/mL). Against chia meal protein isolate (CMPI), CMPH has a broad solubility (pH 2-12.46). Particle size (624.5 ± 247.3 nm), low PDI (0.22 ± 0.06), ζ-potential (-31.1 ± 2.5 mV), and surface hydrophobicity (11,183.33 ± 2024.11) and the intrinsic fluorescence peak of CMPH was lower than that of CMPI. CMPH represents an alternative to add value to the agri-food co-product of the chia seed oil industry, generating food ingredients with outstanding antidiabetic and antioxidant potential.
Collapse
Affiliation(s)
- Gislane Briceño-Islas
- Food Technology, Center for Research and Assistance in Technology and Design of the State of Jalisco, A.C. (CIATEJ), Camino Arenero 1227, El Bajío Arenal, 45019 Zapopan, Jalisco, Mexico
| | - Luis Mojica
- Food Technology, Center for Research and Assistance in Technology and Design of the State of Jalisco, A.C. (CIATEJ), Camino Arenero 1227, El Bajío Arenal, 45019 Zapopan, Jalisco, Mexico
| | - Judith E Urías-Silvas
- Food Technology, Center for Research and Assistance in Technology and Design of the State of Jalisco, A.C. (CIATEJ), Camino Arenero 1227, El Bajío Arenal, 45019 Zapopan, Jalisco, Mexico.
| |
Collapse
|
248
|
Nguyen MD, Osborne MT, Prevot GT, Churcher ZR, Johnson PE, Simine L, Dauphin-Ducharme P. Truncations and in silico docking to enhance the analytical response of aptamer-based biosensors. Biosens Bioelectron 2024; 265:116680. [PMID: 39213817 DOI: 10.1016/j.bios.2024.116680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Aptamers are short oligonucleotides capable of binding specifically to various targets (i.e., small molecules, proteins, and whole cells) which have been introduced in biosensors such as in the electrochemical aptamer-based (E-AB) sensing platform. E-AB sensors are comprised of a redox-reporter-modified aptamer attached to an electrode that undergoes, upon target addition, a binding-induced change in electron transfer rates. To date, E-AB sensors have faced a limitation in the translatability of aptamers into the sensing platform presumably because sequences obtained from Systematic Evolution of Ligands by Exponential Enrichment (SELEX) are typically long (>80 nucleotides) and that obtaining structural information remains time and resource consuming. In response, we explore the utility of aptamer base truncations and in silico docking to improve their translatability into E-AB sensors. Here, we first apply this to the glucose aptamer, which we characterize in solution using NMR methods to guide design and translate truncated variants in E-AB biosensors. We further investigated the applicability of the truncation and computational approaches to four other aptamer systems (vancomycin, cocaine, methotrexate and theophylline) from which we derived functional E-AB sensors. We foresee that our strategy will increase the success rate of translating aptamers into sensing platforms to afford low-cost measurements of molecules directly in undiluted complex matrices.
Collapse
Affiliation(s)
- Minh-Dat Nguyen
- Département de chimie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Meghan T Osborne
- Department of Chemistry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Guy Terence Prevot
- Département de chimie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Zachary R Churcher
- Department of Chemistry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Lena Simine
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
| | | |
Collapse
|
249
|
Poplin T, Ironside M, Kuplicki R, Aupperle RL, Guinjoan SM, Khalsa SS, Stewart JL, Victor TA, Paulus MP, Kirlic N. The unique face of comorbid anxiety and depression: Increased frontal, insula and cingulate cortex response during Pavlovian fear-conditioning. J Affect Disord 2024; 366:98-105. [PMID: 39187192 DOI: 10.1016/j.jad.2024.08.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 08/03/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
BACKGROUND Dysregulation of fear processing through altered sensitivity to threat is thought to contribute to the development of anxiety disorders and major depressive disorder (MDD). However, fewer studies have examined fear processing in MDD than in anxiety disorders. The current study used propensity matching to examine the hypothesis that comorbid MDD and anxiety (AnxMDD) shows greater neural correlates of fear processing than MDD, suggesting that the co-occurrence of AnxMDD is exemplified by exaggerated defense related processes. METHODS 195 individuals with MDD (N = 65) or AnxMDD (N = 130) were recruited from the community and completed multi-level assessments, including a Pavlovian fear learning task during functional imaging. Visual images paired with threat (conditioned stimuli: CS+) were compared to stimuli not paired with threat (CS-). RESULTS MDD and AnxMDD showed significantly different patterns of activation for CS+ vs CS- in the dorsal anterior insula/inferior frontal gyrus (partial eta squared; ηp2 = 0.02), dorsolateral prefrontal cortex (ηp2 = 0.01) and dorsal anterior/mid cingulate cortex (ηp2 = 0.01). These differences were driven by greater activation to the CS+ in AnxMDD versus MDD. LIMITATIONS Limitations include the cross-sectional design, a scream US rather than shock and half the number of MDD as AnxMDD participants. CONCLUSIONS AnxMDD showed a pattern of increased activation in regions identified with fear processing. Effects were consistently driven by threat, further suggesting fear signaling as the emergent target process. Differences emerged in regions associated with salience processing, attentional orienting/conflict, self-relevant processing and executive functioning in comorbid anxiety and depression, thereby highlighting potential treatment targets for this prevalent and treatment resistant group.
Collapse
Affiliation(s)
- Tate Poplin
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA
| | - Maria Ironside
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA; University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA.
| | - Rayus Kuplicki
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA
| | - Robin L Aupperle
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA; University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Salvador M Guinjoan
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA; University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Sahib S Khalsa
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer L Stewart
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA; University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Teresa A Victor
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA
| | - Martin P Paulus
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA; University of Tulsa, 800 South Tucker Drive, Tulsa, OK 74104, USA
| | - Namik Kirlic
- Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA
| |
Collapse
|
250
|
Pang F, Long Q, Liang S. Designing a multi-epitope subunit vaccine against Orf virus using molecular docking and molecular dynamics. Virulence 2024; 15:2398171. [PMID: 39258802 DOI: 10.1080/21505594.2024.2398171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/04/2024] [Accepted: 05/19/2024] [Indexed: 09/12/2024] Open
Abstract
Orf virus (ORFV) is an acute contact, epitheliotropic, zoonotic, and double-stranded DNA virus that causes significant economic losses in the livestock industry. The objective of this study is to design an immunoinformatics-based multi-epitope subunit vaccine against ORFV. Various immunodominant cytotoxic T lymphocytes (CTL), helper T lymphocytes (HTL), and B-cell epitopes from the B2L, F1L, and 080 protein of ORFV were selected and linked by short connectors to construct a multi-epitope subunit vaccine. Immunogenicity was enhanced by adding an adjuvant β-defensin to the N-terminal of the vaccine using the EAAAK linker. The vaccine exhibited a significant degree of antigenicity and solubility, without allergenicity or toxicity. The 3D formation of the vaccine was subsequently anticipated, improved, and verified. The optimized model exhibited a lower Z-score of -4.33, indicating higher quality. Molecular docking results demonstrated that the vaccine strongly binds to TLR2 and TLR4. Molecular dynamics results indicated that the docked vaccine-TLR complexes were stable. Immune simulation analyses further confirmed that the vaccine can induce a marked increase in IgG and IgM antibody titers, and elevated levels of IFN-γ and IL-2. Finally, the optimized DNA sequence of the vaccine was cloned into the vector pET28a (+) for high expression in the E.coli expression system. Overall, the designed multi-epitope subunit vaccine is highly stable and can induce robust humoral and cellular immunity, making it a promising vaccine candidate against ORFV.
Collapse
MESH Headings
- Vaccines, Subunit/immunology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/chemistry
- Molecular Docking Simulation
- Animals
- Orf virus/immunology
- Orf virus/genetics
- Viral Vaccines/immunology
- Viral Vaccines/chemistry
- Viral Vaccines/genetics
- Molecular Dynamics Simulation
- Mice
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Toll-Like Receptor 4/immunology
- Toll-Like Receptor 4/chemistry
- Ecthyma, Contagious/prevention & control
- Ecthyma, Contagious/immunology
- Ecthyma, Contagious/virology
- Mice, Inbred BALB C
- Female
- T-Lymphocytes, Cytotoxic/immunology
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
Collapse
Affiliation(s)
- Feng Pang
- Department of Veterinary Medicine, College of Animal Science, Guizhou University, Guiyang, China
| | - Qinqin Long
- Department of Veterinary Medicine, College of Animal Science, Guizhou University, Guiyang, China
| | - Shaobo Liang
- Department of Veterinary Medicine, College of Animal Science, Guizhou University, Guiyang, China
| |
Collapse
|