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Sandhu AK, Fischer BR, Subramanian S, Hoppe AD, Brözel VS. Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596975. [PMID: 38853965 PMCID: PMC11160724 DOI: 10.1101/2024.06.01.596975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed in Bradyrhizobium diazoefficiens USDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of other Bradyrhizobium strains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments. Bradyrhizobium's utilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.
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Affiliation(s)
- Armaan Kaur Sandhu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006
| | - Brady R. Fischer
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD 57006
| | - Senthil Subramanian
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006
| | - Adam D. Hoppe
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD 57006
| | - Volker S. Brözel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006
- Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Shin JC, Jeong JY, Son SG, Choi SH, Nam HC, Yoon TH, Kim HJ, Choi DG, Lee H, Lee U, Yang SM, Kang I, Jung DY, Lee HW, Lee MK, Lee TJ, Kim G, Park HO, Lee SW. Developing centrifugal force real-time digital PCR for detecting extremely low DNA concentration. Sci Rep 2024; 14:11522. [PMID: 38769102 DOI: 10.1038/s41598-024-62199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Digital PCR (dPCR) is a technique for absolute quantification of nucleic acid molecules. To develop a dPCR technique that enables more accurate nucleic acid detection and quantification, we established a novel dPCR apparatus known as centrifugal force real-time dPCR (crdPCR). This system is efficient than other systems with only 2.14% liquid loss by dispensing samples using centrifugal force. Moreover, we applied a technique for analyzing the real-time graph of the each micro-wells and distinguishing true/false positives using artificial intelligence to mitigate the rain, a persistent issue with dPCR. The limits of detection and quantification were 1.38 and 4.19 copies/μL, respectively, showing a two-fold higher sensitivity than that of other comparable devices. With the integration of this new technology, crdPCR will significantly contribute to research on next-generation PCR targeting absolute micro-analysis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ukyeol Lee
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | - Il Kang
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | | | - Moon-Keun Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Tae Jae Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Geehong Kim
- Nano-Convergence Systems Research Division, Korea Institute of Machinery & Materials, Daejeon, Republic of Korea
| | - Han-Oh Park
- Bioneer Corporation, Daejeon, Republic of Korea
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Lai Q, Dannenfelser R, Roussarie JP, Yao V. Disentangling associations between complex traits and cell types with seismic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592534. [PMID: 38765980 PMCID: PMC11100625 DOI: 10.1101/2024.05.04.592534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Integrating single-cell RNA sequencing (scRNA-seq) with Genome-Wide Association Studies (GWAS) can help reveal GWAS-associated cell types, furthering our understanding of the cell-type-specific biological processes underlying complex traits and disease. However, current methods have technical limitations that hinder them from making systematic, scalable, interpretable disease-cell-type associations. In order to rapidly and accurately pinpoint associations, we develop a novel framework, seismic, which characterizes cell types using a new specificity score. We compare seismic with alternative methods across over 1,000 cell type characterizations at different granularities and 28 traits, demonstrating that seismic both corroborates findings and identifies trait-relevant cell groups which are not apparent through other methodologies. Furthermore, as part of the seismic framework, the specific genes driving cell type-trait associations can easily be accessed and analyzed, enabling further biological insights. The advantages of seismic are particularly salient in neurodegenerative diseases such as Parkinson's and Alzheimer's, where disease pathology has not only cell-specific manifestations, but also brain region-specific differences. Interestingly, a case study of Alzheimer's disease reveals the importance of considering GWAS endpoints, as studies relying on clinical diagnoses consistently identify microglial associations, while GWAS with a tau biomarker endpoint reveals neuronal associations. In general, seismic is a computationally efficient, powerful, and interpretable approach for identifying associations between complex traits and cell type-specific expression.
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Affiliation(s)
- Qiliang Lai
- Department of Computer Science, Rice University
| | | | | | - Vicky Yao
- Department of Computer Science, Rice University
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Brown CA, Wren JD. AutoGDC: A Python Package for DNA Methylation and Transcription Meta-Analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.14.589445. [PMID: 38659836 PMCID: PMC11042378 DOI: 10.1101/2024.04.14.589445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Motivation 0.1The Genomic Data Commons is a powerful resource which facilitates the exploration of molecular alterations across various diseases. However, utilizing this resource for meta-analysis requires many different tools to query, download, organize, and analyze the data. In order to facilitate a more rapid, simple means of analyzing DNA methylation and RNA sequencing datasets from the GDC we developed autogdc, a python package that integrates data curation and preprocessing with meta-analysis functionality into one simplified bioinformatic pipeline. Availability and Implementation 0.2The autogdc python package is available under the GPLv3 license at along with several examples of typical use-case scenarios in the form of a jupyter notebook. The data is all originally provided by the GDC, and is therefore available under the NIH Genomic Data Sharing (GDS) and NCI GDS policies.
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Affiliation(s)
- Chase Alan Brown
- University of Oklahoma Health Science Center, Oklahoma Medical Research Foundation
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5
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Salcedo-Tacuma D, Asad N, Howells G, Anderson R, Smith DM. Proteasome hyperactivation rewires the proteome enhancing stress resistance, proteostasis, lipid metabolism and ERAD in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588128. [PMID: 38617285 PMCID: PMC11014606 DOI: 10.1101/2024.04.04.588128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Proteasome dysfunction is implicated in the pathogenesis of neurodegenerative diseases and age-related proteinopathies. Using a C. elegans model, we demonstrate that 20S proteasome hyperactivation, facilitated by 20S gate-opening, accelerates the targeting of intrinsically disordered proteins. This leads to increased protein synthesis, extensive rewiring of the proteome and transcriptome, enhanced oxidative stress defense, accelerated lipid metabolism, and peroxisome proliferation. It also promotes ER-associated degradation (ERAD) of aggregation-prone proteins, such as alpha-1 antitrypsin (ATZ) and various lipoproteins. Notably, our results reveal that 20S proteasome hyperactivation suggests a novel role in ERAD with broad implications for proteostasis-related disorders, simultaneously affecting lipid homeostasis and peroxisome proliferation. Furthermore, the enhanced cellular capacity to mitigate proteostasis challenges, alongside unanticipated acceleration of lipid metabolism is expected to contribute to the longevity phenotype of this mutant. Remarkably, the mechanism of longevity induced by 20S gate opening appears unique, independent of known longevity and stress-resistance pathways. These results support the therapeutic potential of 20S proteasome activation in mitigating proteostasis-related disorders broadly and provide new insights into the complex interplay between proteasome activity, cellular health, and aging.
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Affiliation(s)
- David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr., Morgantown, WV USA
| | - Nadeeem. Asad
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr., Morgantown, WV USA
| | - Giovanni Howells
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr., Morgantown, WV USA
| | - Raymond Anderson
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr., Morgantown, WV USA
| | - David M. Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr., Morgantown, WV USA
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia, USA
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Çelik S. Gene expression analysis of potato drought-responsive genes under drought stress in potato ( Solanum tuberosum L.) cultivars. PeerJ 2024; 12:e17116. [PMID: 38525286 PMCID: PMC10960530 DOI: 10.7717/peerj.17116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
The potato (Solanum tuberosum L.), an important field crop consumed extensively worldwide, is adversely affected by abiotic stress factors especially drought. Therefore, it is vital to understand the genetic mechanism under drought stress to decrease loose of yield and quality . This trial aimed to screen drought-responsive gene expressions of potato and determine the drought-tolerant potato cultivar. The trial pattern is a completely randomized block design (CRBD) with four replications under greenhouse conditions. Four cultivars (Brooke, Orwell, Vr808, Shc909) were irrigated with four different water regimes (control and three stress conditions), and the gene expression levels of 10 potato genes were investigated. The stress treatments as follows: Control = 100% field capacity; slight drought = 75% field capacity; moderate drought = 50% field capacity, and severe drought 25% field capacity. To understand the gene expression under drought stress in potato genotypes, RT-qPCR analysis was performed and results showed that the genes most associated with drought tolerance were the StRD22 gene, MYB domain transcription factor, StERD7, Sucrose Synthase (SuSy), ABC Transporter, and StDHN1. The StHSP100 gene had the lowest genetic expression in all cultivars. Among the cultivars, the Orwell exhibited the highest expression of the StRD22 gene under drought stress. Overall, the cultivar with the highest gene expression was the Vr808, closely followed by the Brooke cultivar. As a result, it was determined that potato cultivars Orwell, Vr808, and Brooke could be used as parents in breeding programs to develop drought tolerant potato cultivars.
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Affiliation(s)
- Sadettin Çelik
- Genç Vocational School, Forestry Department, Bingol University, Bingol, Turkey
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Alasiri G, Alrfaei B, Alaseem AM, AlKhamees OA, Aldali JA, Aljehani AM, Alfahed A, Aziz MA, Almuhaini G, Alshehri MM. The role of TAOK3 in cancer progression and development as a prognostic marker: A pan-cancer analysis study. Saudi Pharm J 2024; 32:101942. [PMID: 38318319 PMCID: PMC10840358 DOI: 10.1016/j.jsps.2023.101942] [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] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
The protein kinase TAOK3, belongs to the MAP kinase family, is one of three closely related members, namely TAOK1, TAOK2, and TAOK3. We performed a pan-cancer investigation of TAOK3 across different cancer types, including uterine carcinosarcoma, adenocarcinoma of the stomach and pancreas, and endometrial carcinoma of the uterus, to better understand TAOK3's role in cancer. In at least 16 types of cancer, our findings indicate that TAOK3 expression levels differ considerably between normal and tumor tissues. In addition, our study is the first to identify the oncogenic role of TAOK3 locus S331 and S471 in renal clear cell carcinoma, Glioblastoma Multiforme, hepatocellular carcinoma, Lung adenocarcinoma, and Pancreatic adenocarcinoma, indicating their involvement in cancer progression. In addition, our data analysis indicates that copy number variation is the most prevalent form of mutation in the TAOK3 gene, and that there is a negative correlation between TAOK3 mRNA and DNA promoter methylation. Moreover, our analysis suggests that TAOK3 may serve as a prognostic marker for several kinds of cancer, including Colon adenocarcinoma, renal clear cell carcinoma, Lower Grade Glioma, Lung adenocarcinoma, Mesothelioma, and hepatocellular carcinoma. In addition, our research on signature cancer genes has uncovered a positive association between TAOK3 and SMAD2, SMAD4, and RNF168 in most of the malignancies we have examined. TAOK3 is also correlated with the frequency of mutations and microsatellite instability in four types of cancer. Numerous immune-related genes are closely associated with TAOK3 levels in numerous malignancies. TAOK3 expression is positively correlated with immune infiltrates, which include activated CD4 T cells, CD8 T cells, and type 2T helper cells. Our pan-cancer analysis of TAOK3 provides vital insight into its potential role across a variety of cancer types.
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Affiliation(s)
- Glowi Alasiri
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 5701, Saudi Arabia
| | - Bahauddeen Alrfaei
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNGHA), Saudi Arabia
- King Abullah International Medical Research Center, MNGHA, Saudi Arabia
| | - Ali M. Alaseem
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 5701, Saudi Arabia
| | - Osama A. AlKhamees
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 5701, Saudi Arabia
| | - Jehad A. Aldali
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 5701, Saudi Arabia
| | - Ala M. Aljehani
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 5701, Saudi Arabia
| | - Abdulaziz Alfahed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Mohammad Azhar Aziz
- Interdisciplinary Nanotechnology Center, Aligarh Muslim University, Aligarh 202002, India
| | - Ghadir Almuhaini
- King Saud bin Abdulaziz University for Health Sciences, Saudi Arabia
| | - Mana M. Alshehri
- King Abullah International Medical Research Center, MNGHA, Saudi Arabia
- Connell and O'Reilly Families-Cell Manipulation Core Facility, Dana-Farber Cancer Institute, Harvard University, Boston, MA 02115, USA
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Porco D, Purnomo CA, Glesener L, Proess R, Lippert S, Jans K, Colling G, Schneider S, Stassen R, Frantz AC. eDNA-based monitoring of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans with ddPCR in Luxembourg ponds: taking signals below the Limit of Detection (LOD) into account. BMC Ecol Evol 2024; 24:4. [PMID: 38178008 PMCID: PMC10768104 DOI: 10.1186/s12862-023-02189-9] [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: 08/07/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two pathogenic fungi that are a significant threat to amphibian communities worldwide. European populations are strongly impacted and the monitoring of the presence and spread of these pathogens is crucial for efficient decision-making in conservation management. RESULTS Here we proposed an environmental DNA (eDNA) monitoring of these two pathogenic agents through droplet digital PCR (ddPCR) based on water samples from 24 ponds in Luxembourg. In addition, amphibians were swabbed in eight of the targeted ponds in order to compare the two approaches at site-level detection. This study allowed the development of a new method taking below-Limit of Detection (LOD) results into account thanks to the statistical comparison of the frequencies of false positives in no template controls (NTC) and below-LOD results in technical replicates. In the eDNA-based approach, the use of this method led to an increase in Bd and Bsal detection of 28 and 50% respectively. In swabbing, this resulted in 8% more positive results for Bd. In some samples, the use of technical replicates allowed to recover above-LOD signals and increase Bd detection by 35 and 33% respectively for eDNA and swabbing, and Bsal detection by 25% for eDNA. CONCLUSIONS These results confirmed the usefulness of technical replicates to overcome high levels of stochasticity in very low concentration samples even for a highly sensitive technique such as ddPCR. In addition, it showed that below-LOD signals could be consistently recovered and the corresponding amplification events assigned either to positive or negative detection via the method developed here. This methodology might be particularly worth pursuing in pathogenic agents' detection as false negatives could have important adverse consequences. In total, 15 ponds were found positive for Bd and four for Bsal. This study reports the first record of Bsal in Luxembourg.
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Affiliation(s)
- David Porco
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg.
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg.
| | - Chanistya Ayu Purnomo
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Liza Glesener
- Naturschutzsyndikat SICONA, 12, rue de Capellen, L-8393 Olm, Luxembourg, Luxembourg
| | - Roland Proess
- Umweltplanungsbüro Ecotop, 45, Schlassuecht, L-7435 Hollenfels, Luxembourg, Luxembourg
| | - Stéphanie Lippert
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Kevin Jans
- Natur&ëmwelt Fondation Hëllef fir d'Natur, 5, Route de Luxembourg, L-1899, Kockelscheuer, Luxembourg
| | - Guy Colling
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg
| | - Simone Schneider
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Naturschutzsyndikat SICONA, 12, rue de Capellen, L-8393 Olm, Luxembourg, Luxembourg
| | - Raf Stassen
- Biota.lu, 9a, Rue Principale, L-6990, Hostert, Luxembourg
| | - Alain C Frantz
- Musée national d'histoire naturelle du Luxembourg, 25, rue Münster, Luxembourg, L-2160, Luxembourg
- Fondation Faune Flore, 24, rue Münster, Luxembourg, L-2160, Luxembourg
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Speare L, Zhao L, Pavelsky MN, Jackson A, Smith S, Tyagi B, Sharpe GC, Woo M, Satkowiak L, Bolton T, Gifford SM, Septer AN. Flagella are required to coordinately activate competition and host colonization factors in response to a mechanical signal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573711. [PMID: 38260499 PMCID: PMC10802311 DOI: 10.1101/2023.12.31.573711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Bacteria employ antagonistic strategies to eliminate competitors of an ecological niche. Contact-dependent mechanisms, such as the type VI secretion system (T6SS), are prevalent in host-associated bacteria, yet we know relatively little about how T6SS+ strains make contact with competitors in highly viscous environments, such as host mucus. To better understand how cells respond to and contact one another in such environments, we performed a genome-wide transposon mutant screen of the T6SS-wielding beneficial bacterial symbiont, Vibrio fischeri, and identified two sets of genes that are conditionally required for killing. LPS/capsule and flagellar-associated genes do not affect T6SS directly and are therefore not required for interbacterial killing when cell contact is forced yet are necessary for killing in high-viscosity liquid (hydrogel) where cell-cell contact must be biologically mediated. Quantitative transcriptomics revealed that V. fischeri significantly increases expression of both T6SS genes and cell surface modification factors upon transition from low- to high-viscosity media. Consistent with coincubation and fluorescence microscopy data, flagella are not required for T6SS expression in hydrogel. However, flagella play a key role in responding to the physical environment by promoting expression of the surface modification genes identified in our screen, as well as additional functional pathways important for host colonization including uptake of host-relevant iron and carbon sources, and nitric oxide detoxification enzymes. Our findings suggest that flagella may act as a mechanosensor for V. fischeri to coordinately activate competitive strategies and host colonization factors, underscoring the significance of the physical environment in directing complex bacterial behaviors.
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Affiliation(s)
- Lauren Speare
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
- Department of Microbiology, Oregon State University, Corvallis, OR
| | - Liang Zhao
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Morgan N. Pavelsky
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Aundre Jackson
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Stephanie Smith
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Bhavyaa Tyagi
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Garrett C. Sharpe
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Madison Woo
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Lizzie Satkowiak
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Trinity Bolton
- Department of Chemistry, Morgan State University, Baltimore, MD
| | - Scott M. Gifford
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
| | - Alecia N. Septer
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC
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Chappell TC, Maiello KG, Tierney AJ, Yanagi K, Lee JA, Lee K, Mace CR, Bennett CS, Nair NU. Rapid spectrophotometric detection for optimized production of landomycins and characterization of their therapeutic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566088. [PMID: 37986805 PMCID: PMC10659386 DOI: 10.1101/2023.11.07.566088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Microbial derived natural products remain a major source of structurally diverse bioactive compounds and chemical scaffolds that have potential as new therapeutics to target drug resistant pathogens and cancers. In particular, genome mining has revealed the vast number of cryptic or low yield biosynthetic gene clusters in the genus Streptomyces . Here, we describe our efforts to improve yields of landomycins - angucycline family polyketides under investigation as cancer therapeutics - by a genetically modified Streptomyces cyanogenus 136. After simplifying the extraction process from S. cyanogenus cultures, we identified a wavelength at which the major landomycin products absorb in culture extracts, which we used to systematically explore culture medium compositions to improve total landomycin titers. Through correlational analysis, we simplified the culture optimization process by identifying an alternative wavelength at which culture supernatants absorb yet is representative of total landomycin titers. Using the subsequently improved sample throughput, we explored landomycin production during the culturing process to further increase landomycin yield and reduce culture time. Testing the antimicrobial activity of the isolated landomycins, we report broad inhibition of Gram-positive bacteria, inhibition of fungi by landomycinone, and broad landomycin resistance by Gram-negative bacteria that is likely mediated by exclusion of landomycins by the bacterial membrane. Finally, the anticancer activity of the isolated landomycins against A549 lung carcinoma cells agrees with previous reports on other cell lines that glycan chain length correlates with activity. Given the prevalence of natural products produced by Streptomyces , as well as the light-absorbing moieties common to bioactive natural products and their metabolic precursors, our method is relevant to improving the yields of other natural products of interest.
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Bodelón A, Fablet M, Siqueira de Oliveira D, Vieira C, García Guerreiro MP. Impact of Heat Stress on Transposable Element Expression and Derived Small RNAs in Drosophila subobscura. Genome Biol Evol 2023; 15:evad189. [PMID: 37847062 PMCID: PMC10627563 DOI: 10.1093/gbe/evad189] [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: 03/03/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023] Open
Abstract
Global warming is forcing insect populations to move and adapt, triggering adaptive genetic responses. Thermal stress is known to alter gene expression, repressing the transcription of active genes, and inducing others, such as those encoding heat shock proteins. It has also been related to the activation of some specific transposable element (TE) families. However, the actual magnitude of this stress on the whole genome and the factors involved in these genomic changes are still unclear. We studied mRNAs and small RNAs in gonads of two Drosophila subobscura populations, considered a good model to study adaptation to temperature changes. In control conditions, we found that a few genes and TE families were differentially expressed between populations, pointing out their putative involvement in the adaptation of populations to their different environments. Under heat stress, sex-specific changes in gene expression together with a trend toward overexpression, mainly of heat shock response-related genes, were observed. We did not observe large changes of TE expression nor small RNA production due to stress. Only population and sex-specific expression changes of some TE families (mainly retrotransposons), or the amounts of siRNAs and piRNAs, derived from specific TE families were observed, as well as the piRNA production from some piRNA clusters. Changes in small RNA amounts and TE expression could not be clearly correlated, indicating that other factors as chromatin modulation could also be involved. This work provides the first whole transcriptomic study including genes, TEs, and small RNAs after a heat stress in D. subobscura.
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Affiliation(s)
- Alejandra Bodelón
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
- Institut universitaire de France, Paris, France
| | - Daniel Siqueira de Oliveira
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São Paulo, Brazil
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Maria Pilar García Guerreiro
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Barcelona, Spain
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12
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Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.21.563358. [PMID: 37905150 PMCID: PMC10614956 DOI: 10.1101/2023.10.21.563358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The genomes of Leishmania and trypanosomes are organized into polycistronic transcription units flanked by a modified DNA base J involved in promoting RNA polymerase II (Pol II) termination. We recently characterized a Leishmania complex containing a J-binding protein, PP1 protein phosphatase 1, and PP1 regulatory protein (PNUTS) that controls transcription termination potentially via dephosphorylation of Pol II by PP1. While T. brucei contains eight PP1 isoforms, none purified with the PNUTS complex, suggesting a unique PP1-independent mechanism of termination. We now demonstrate that the PP1-binding motif of TbPNUTS is required for function in termination in vivo and that TbPP1-1 modulates Pol II termination in T. brucei involving dephosphorylation of the C-terminal domain of the large subunit of Pol II. PP1-1 knock-down results in increased cellular levels of phosphorylated large subunit of Pol II accompanied by readthrough transcription and pervasive transcription of the entire genome by Pol II, including Pol I transcribed loci that are typically silent, such as telomeric VSG expression sites involved in antigenic variation and production of TERRA RNA. These results provide important insights into the mechanism underlying Pol II transcription termination in primitive eukaryotes that rely on polycistronic transcription and maintain allelic exclusion of VSG genes.
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Meng G, Pan Y, Tang W, Zhang L, Cui Y, Schumacher FR, Wang M, Wang R, He S, Krischer J, Li Q, Feng H. imply: improving cell-type deconvolution accuracy using personalized reference profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559579. [PMID: 37808714 PMCID: PMC10557724 DOI: 10.1101/2023.09.27.559579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Real-world clinical samples are often admixtures of signal mosaics from multiple pure cell types. Using computational tools, bulk transcriptomics can be deconvoluted to solve for the abundance of constituent cell types. However, existing deconvolution methods are conditioned on the assumption that the whole study population is served by a single reference panel, which ignores person-to-person heterogeneity. Here we present imply, a novel algorithm to deconvolute cell type proportions using personalized reference panels. imply can borrow information across repeatedly measured samples for each subject, and obtain precise cell type proportion estimations. Simulation studies demonstrate reduced bias in cell type abundance estimation compared with existing methods. Real data analyses on large longitudinal consortia show more realistic deconvolution results that align with biological facts. Our results suggest that disparities in cell type proportions are associated with several disease phenotypes in type 1 diabetes and Parkinson's disease. Our proposed tool imply is available through the R/Bioconductor package ISLET at https://bioconductor.org/packages/ISLET/.
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Affiliation(s)
- Guanqun Meng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, OH, USA
| | - Yue Pan
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, 38105, TN, USA
| | - Wen Tang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, OH, USA
| | - Lijun Zhang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, OH, USA
| | - Ying Cui
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, CA, USA
| | - Fredrick R. Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, OH, USA
| | - Ming Wang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, OH, USA
| | - Rui Wang
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Cleveland, 44106, OH, USA
| | - Sijia He
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Jeffrey Krischer
- Health Informatics Institute, University of South Florida, Tampa, 38105, FL, USA
| | - Qian Li
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, 38105, TN, USA
| | - Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, 44106, OH, USA
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Zhang Y, Sabatini R. Leishmania PNUTS discriminates between PP1 catalytic subunits through a RVxF-ΦΦ-F motif and polymorphisms in the PP1 C-tail and catalytic domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558696. [PMID: 37790576 PMCID: PMC10542515 DOI: 10.1101/2023.09.20.558696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
PP1 phosphatases lack substrate specificity and associate with specific regulatory subunits to achieve selectivity. Among the eight PP1 isotypes in Leishmania, PP1-8e associates with the regulatory protein PNUTS along with the structural factors JBP3 and Wdr82 in the PJW/PP1 complex that modulates RNA polymerase II (Pol II) phosphorylation and transcription termination. Little is known regarding interactions involved in PJW/PP1 complex formation, including how PP1-8e is the selective isotype associated with PNUTS. Here, we show that PNUTS uses an established RVxF-ΦΦ-F motif to bind the PP1 catalytic domain with similar interfacial interactions as mammalian PP1- PNUTS and non-canonical motifs. These atypical interactions involve residues within the PP1-8e catalytic domain and N- and C-terminus for isoform specific regulator binding. This work advances our understanding of PP1 isoform selectivity and reveals key roles of PP1 residues in regulator binding. We also explore the role of PNUTS as a scaffold protein for the complex by identifying the C-terminal region involved in binding JBP3 and Wdr82, and impact of PNUTS on the stability of complex components and function in Pol II transcription in vivo . Taken together, these studies provide a potential mechanism where multiple motifs within PNUTS are used combinatorially to tune binding affinity to PP1, and the C-termini for independent binding of JBP3 and Wdr82, in the Leishmania PJW/PP1 complex. Overall, our data provide insights in the formation of the PJW/PP1 complex involved in regulating Pol II transcription in divergent protozoans where little is understood.
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Tsyganov MM, Ibragimova MK. MALAT1 Long Non-coding RNA and Its Role in Breast Carcinogenesis. Acta Naturae 2023; 15:32-41. [PMID: 37538803 PMCID: PMC10395780 DOI: 10.32607/actanaturae.11905] [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: 12/26/2022] [Accepted: 03/02/2023] [Indexed: 08/05/2023] Open
Abstract
Our genome consists not only of protein-coding DNA, but also of the non-coding part that plays a very important role in the regulation of all cellular processes. A part of the non-coding genome comes with non-coding RNAs (ncRNAs), and disruption of the functional activity of these RNAs may be associated with oncogenesis in various cancer types. There exist two types of ncRNAs: small and long non-coding RNAs, which are classified according to their transcript length. Long non-coding metastasis-associated lung adenocarcinoma transcript 1, MALAT1 RNA (NEAT2), is a long non-coding RNA of particular interest. The aforementioned transcript takes part in the regulation of numerous cellular processes and pathogenesis of different malignant tumors, including breast tumors. This review focuses on experimental and clinical studies into the role of MALAT1 in carcinogenesis and the progression of breast cancer.
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Affiliation(s)
- M. M. Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050 Russian Federation
- Siberian State Medical University, Tomsk, 634050 Russian Federation
| | - M. K. Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050 Russian Federation
- Siberian State Medical University, Tomsk, 634050 Russian Federation
- National Research Tomsk State University, Tomsk, 634050 Russian Federation
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Das P, Mazumder DH. An extensive survey on the use of supervised machine learning techniques in the past two decades for prediction of drug side effects. Artif Intell Rev 2023; 56:1-28. [PMID: 36819660 PMCID: PMC9930028 DOI: 10.1007/s10462-023-10413-7] [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] [Accepted: 02/01/2023] [Indexed: 02/19/2023]
Abstract
Approved drugs for sale must be effective and safe, implying that the drug's advantages outweigh its known harmful side effects. Side effects (SE) of drugs are one of the common reasons for drug failure that may halt the whole drug discovery pipeline. The side effects might vary from minor concerns like a runny nose to potentially life-threatening issues like liver damage, heart attack, and death. Therefore, predicting the side effects of the drug is vital in drug development, discovery, and design. Supervised machine learning-based side effects prediction task has recently received much attention since it reduces time, chemical waste, design complexity, risk of failure, and cost. The advancement of supervised learning approaches for predicting side effects have emerged as essential computational tools. Supervised machine learning technique provides early information on drug side effects to develop an effective drug based on drug properties. Still, there are several challenges to predicting drug side effects. Thus, a near-exhaustive survey is carried out in this paper on the use of supervised machine learning approaches employed in drug side effects prediction tasks in the past two decades. In addition, this paper also summarized the drug descriptor required for the side effects prediction task, commonly utilized drug properties sources, computational models, and their performances. Finally, the research gap, open problems, and challenges for the further supervised learning-based side effects prediction task have been discussed.
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Affiliation(s)
- Pranab Das
- Department of Computer Science and Engineering, National Institute of Technology Nagaland, Chumukedima, Dimapur, Nagaland 797103 India
| | - Dilwar Hussain Mazumder
- Department of Computer Science and Engineering, National Institute of Technology Nagaland, Chumukedima, Dimapur, Nagaland 797103 India
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Raffo-Romero A, Aboulouard S, Bouchaert E, Rybicka A, Tierny D, Hajjaji N, Fournier I, Salzet M, Duhamel M. Establishment and characterization of canine mammary tumoroids for translational research. BMC Biol 2023; 21:23. [PMID: 36737789 PMCID: PMC9898911 DOI: 10.1186/s12915-023-01516-2] [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: 02/22/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cancer heterogeneity is a main obstacle for the development of effective therapies, as its replication in in vitro preclinical models is challenging. Around 96% of developed drugs are estimated to fail from discovery to the clinical trial phase probably because of the unsuitability and unreliability of current preclinical models (Front Pharmacol 9:6, 2018; Nat Rev Cancer 8: 147-56, 2008) in replicating the overall biology of tumors, for instance the tumor microenvironment. Breast cancer is the most frequent cancer among women causing the greatest number of cancer-related deaths. Breast cancer can typically be modeled in vitro through the use of tumoroids; however, current approaches using mouse tumoroids fail to reproduce crucial aspect of human breast cancer, while access to human cells is limited and the focus of ethical concerns. New models of breast cancer, such as companion dogs, have emerged given the resemblance of developed spontaneous mammary tumors to human breast cancer in many clinical and molecular aspects; however, they have so far failed to replicate the tumor microenvironment. The present work aimed at developing a robust canine mammary tumor model in the form of tumoroids which recapitulate the tumor diversity and heterogeneity. RESULTS We conducted a complete characterization of canine mammary tumoroids through histologic, molecular, and proteomic analysis, demonstrating their strong similarity to the primary tumor. We demonstrated that these tumoroids can be used as a drug screening model. In fact, we showed that paclitaxel, a human chemotherapeutic, could kill canine tumoroids with the same efficacy as human tumoroids with 0.1 to 1 μM of drug needed to kill 50% of the cells. Due to easy tissue availability, canine tumoroids can be produced at larger scale and cryopreserved to constitute a biobank. We have demonstrated that cryopreserved tumoroids keep the same histologic and molecular features (ER, PR, and HER2 expression) as fresh tumoroids. Furthermore, two cryopreservation techniques were compared from a proteomic point of view which showed that tumoroids made from frozen material allowed to maintain the same molecular diversity as from freshly dissociated tumor. CONCLUSIONS These findings revealed that canine mammary tumoroids can be easily generated and may provide an adequate and more reliable preclinical model to investigate tumorigenesis mechanisms and develop new treatments for both veterinary and human medicine.
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Affiliation(s)
- Antonella Raffo-Romero
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France
| | - Soulaimane Aboulouard
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France
| | - Emmanuel Bouchaert
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Agata Rybicka
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Dominique Tierny
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Nawale Hajjaji
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.452351.40000 0001 0131 6312Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Isabelle Fournier
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France. .,Institut Universitaire de France, Paris, France.
| | - Marie Duhamel
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France.
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18
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Zhao N, Yuan R, Usman B, Qin J, Yang J, Peng L, Mackon E, Liu F, Qin B, Li R. Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice ( Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1. Biomolecules 2022; 12:biom12121850. [PMID: 36551278 PMCID: PMC9775987 DOI: 10.3390/biom12121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.
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Affiliation(s)
- Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruizhi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Babar Usman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jiaming Qin
- Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Liyun Peng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
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Wang H, Yang S, Liu J, Fu Z, Liu Y, Zhou L, Guo H, Lan K, Chen Y. Human adenoviruses: A suspect behind the outbreak of acute hepatitis in children amid the COVID-19 pandemic. CELL INSIGHT 2022; 1:100043. [PMID: 37192861 PMCID: PMC10120317 DOI: 10.1016/j.cellin.2022.100043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 05/18/2023]
Abstract
As of 10 May 2022, at least 450 cases of pediatric patients with acute hepatitis of unknown cause have been reported worldwide. Human adenoviruses (HAdVs) have been detected in at least 74 cases, including the F type HAdV41 in 18 cases, which indicates that adenoviruses may be associated with this mysterious childhood hepatitis, although other infectious agents or environmental factors cannot be excluded. In this review, we provide a brief introduction of the basic features of HAdVs and describe diseases caused by different HAdVs in humans, aiming to help understand the biology and potential risk of HAdVs and cope with the outbreak of acute child hepatitis.
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Affiliation(s)
- Hongyun Wang
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shimin Yang
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiejie Liu
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhiying Fu
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yingle Liu
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA
| | - Ke Lan
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center, Institute for Vaccine Research, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, China
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De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing. Genetica 2021; 150:59-66. [PMID: 34825293 DOI: 10.1007/s10709-021-00141-7] [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: 06/17/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species.
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21
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Differential miRNA Expression in Osteoporotic Elderly Patients with Hip Fractures Compared to Young Patients. Indian J Orthop 2021; 56:399-411. [PMID: 35251503 PMCID: PMC8854460 DOI: 10.1007/s43465-021-00561-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/30/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND The expression pattern of micro-RNAs (miRNA) has been implicated in the pathomechanism of various bone disorders, and has a role in differentiation of osteoblasts and osteoclasts. The purpose of the study was to investigate the differential miRNA profiles of osteoporotic hip fractures compared to young patients with hip fractures. METHODS Blood samples from ten osteoporosis patients and ten young, healthy patients, presenting with acute hip fractures were collected and subjected to an initial miRNA profiling to detect those miRNAs with significant variations between the two groups based on polymerase chain reactions performed in duplicate. A real-time quantitative polymerase chain reaction-based analysis was then performed for validation of specific miRNAs that were significantly different between the two groups. RESULTS A total of 182 miRNAs were analyzed. Thirty-nine of them showed significant differences between the two groups in the initial miRNA profiling. The validation results suggested that five miRNAs related to bone metabolism had significantly different expression among the osteoporotic hip fracture group compared to the young, healthy group: miR-23b-3p and miR-140-3p were up-regulated; miR-21-5p, miR-122-5p and miR-125b-5p were down-regulated. CONCLUSIONS Differential expression of selected miRNAs in patients with osteoporotic hip fracture suggests a possible role of miRNAs as potential biomarkers in prevention or timely prediction of osteoporotic fractures in the elderly. Further research is required to elucidate the mechanism of their involvement in osteoporosis. LEVEL OF EVIDENCE Not applicable.
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22
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Evaluation of novel genomic markers for pedigree construction in an isolated population of Weddell Seals (Leptonychotes weddellii) at White Island, Antarctica. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01237-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Erasmus LM, van Marle-Köster E. Moving towards sustainable breeding objectives and cow welfare in dairy production: a South African perspective. Trop Anim Health Prod 2021; 53:470. [PMID: 34549341 DOI: 10.1007/s11250-021-02914-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/10/2021] [Indexed: 01/11/2023]
Abstract
Genetic advancements have resulted in improved dairy production over many decades, due to the focus of breeding objectives on production as the driving force for genetic progress and overall farm profitability. Major advancements were made in the easy-to-measure traits with moderate to high heritability, which resulted in unintended consequences on herd fertility, health, and welfare of cows. In addition, climate change and animal welfare concerns demanded balanced breeding objectives and selection approaches for sustainable production-including health and longevity. The inclusion of genomic information into genetic evaluations has been proved to benefit traits associated with welfare and sustainable production. Cow welfare traits remain complex and suitable phenotypes are not always easy to measure or readily available for genetic evaluations. The challenge for improvement of cow welfare often lies within implementation of sensitive and measurable parameters. The aim of this review was to explore the reconsideration of breeding objectives in the dairy industry towards sustainable dairy production and cow welfare with reference to selection of dairy animals in South Africa.
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Affiliation(s)
- Lize-Mari Erasmus
- Department of Animal Science, University of Pretoria, Pretoria, South Africa.
| | - E van Marle-Köster
- Department of Animal Science, University of Pretoria, Pretoria, South Africa.
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24
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Jaemthaworn T, Kalapanulak S, Saithong T. Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava. Sci Rep 2021; 11:7872. [PMID: 33846415 PMCID: PMC8041763 DOI: 10.1038/s41598-021-86806-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/19/2021] [Indexed: 02/01/2023] Open
Abstract
Robustness, a naïve property of biological systems, enables organisms to maintain functions during perturbation and is crucial for improving the resilience of crops to prevailing stress conditions and diseases, guaranteeing food security. Most studies of robustness in crops have focused on genetic superiority based upon individual genes, overlooking the collaborative actions of multiple responsive genes and the regulatory network topology. This research aims to uncover patterns of gene cooperation leading to organismal robustness by studying the topology of gene co-expression networks (GCNs) of both CBSV virus resistant and susceptible cassava cultivars. The resulting GCNs show higher topological clustering of cooperative genes in the resistant cultivar, suggesting that the network architecture is central to attaining robustness. Despite a reduction in the number of hub genes in the resistant cultivar following the perturbation, essential biological functions contained in the network were maintained through neighboring genes that withstood the shock. The susceptible cultivar seemingly coped by inducing more gene actions in the network but could not maintain the functions required for plant growth. These findings underscore the importance of regulatory network architecture in ensuring phenotypic robustness and deepen our understanding of transcriptional regulation.
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Affiliation(s)
- Thanakorn Jaemthaworn
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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Gheytanchi E, Saeednejad Zanjani L, Ghods R, Abolhasani M, Shahin M, Vafaei S, Naseri M, Fattahi F, Madjd Z. High expression of tumor susceptibility gene 101 (TSG101) is associated with more aggressive behavior in colorectal carcinoma. J Cancer Res Clin Oncol 2021; 147:1631-1646. [PMID: 33616717 DOI: 10.1007/s00432-021-03561-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Identification of genetic determinants such as exosomal content that drives progression and metastasis of colorectal cancer (CRC) has received considerable attention. The present study aims to identify a suitable biomarker in CRC tissues and exosomes based on bioinformatics data to evaluate its expression patterns in CRC tissues as well as its clinicopathological significance. MATERIALS AND METHODS Protein-protein interaction (PPI) network and enrichment analysis were applied to identify up-regulated genes that contributed in CRC exosomes to select the marker. The expression patterns and clinical significance of selected exosomal marker were evaluated in tissue microarrays (TMAs) of 445 CRC tumors and 39 adjacent normal tissues using immunohistochemistry method. RESULTS Based on bioinformatics data, TSG101 gene was prominent amongst the tumor tissues and exosomes. Expression of TSG101 was significantly up-regulated in tumor cells compared to adjacent normal tissues (p-value = 0.04). Moreover, higher expressions of TSG101 (cytoplasmic and nuclear) were significantly associated with tumor differentiation (p-value = 0.042) and distant metastasis (p-value = 0.027). A significant association was found in the cytoplasmic expression of TSG101 between well and moderate tumor differentiation (p-value = 0.005) as well as moderate and poor differentiation (p-value = 0.050). CONCLUSION These findings indicate that the exploration of crosstalk between exosome content and CRC may be valuable for the development of novel exosomal biomarkers. Increased expression of TSG101, as a promising exosome marker, is more associated with more aggressive tumor behaviors, metastasis, and progression of CRC, which paves the way for therapeutic strategies and CRC management. However, further investigations are warranted to clarify the molecular mechanisms of TSG101 in CRC.
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Affiliation(s)
- Elmira Gheytanchi
- Oncopathology Research Center, Department of Molecular Medicine, Iran University of Medical Sciences (IUMS), Hemmat Street (Highway), Tehran, 14496-14530, Iran
| | - Leili Saeednejad Zanjani
- Oncopathology Research Center, Department of Molecular Medicine, Iran University of Medical Sciences (IUMS), Hemmat Street (Highway), Tehran, 14496-14530, Iran
| | - Roya Ghods
- Oncopathology Research Center, Department of Molecular Medicine, Iran University of Medical Sciences (IUMS), Hemmat Street (Highway), Tehran, 14496-14530, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Maryam Abolhasani
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Shahin
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Vafaei
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Naseri
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fahimeh Fattahi
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Madjd
- Oncopathology Research Center, Department of Molecular Medicine, Iran University of Medical Sciences (IUMS), Hemmat Street (Highway), Tehran, 14496-14530, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Galvão-Lima LJ, Morais AHF, Valentim RAM, Barreto EJSS. miRNAs as biomarkers for early cancer detection and their application in the development of new diagnostic tools. Biomed Eng Online 2021; 20:21. [PMID: 33593374 PMCID: PMC7885381 DOI: 10.1186/s12938-021-00857-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Over the last decades, microRNAs (miRNAs) have emerged as important molecules associated with the regulation of gene expression in humans and other organisms, expanding the strategies available to diagnose and handle several diseases. This paper presents a systematic review of literature of miRNAs related to cancer development and explores the main techniques used to quantify these molecules and their limitations as screening strategy. The bibliographic research was conducted using the online databases, PubMed, Google Scholar, Web of Science, and Science Direct searching the terms “microRNA detection”, “miRNA detection”, “miRNA and prostate cancer”, “miRNA and cervical cancer”, “miRNA and cervix cancer”, “miRNA and breast cancer”, and “miRNA and early cancer diagnosis”. Along the systematic review over 26,000 published papers were reported, and 252 papers were returned after applying the inclusion and exclusion criteria, which were considered during this review. The aim of this study is to identify potential miRNAs related to cancer development that may be useful for early cancer diagnosis, notably in the breast, prostate, and cervical cancers. In addition, we suggest a preliminary top 20 miRNA panel according to their relevance during the respective cancer development. Considering the progressive number of new cancer cases every year worldwide, the development of new diagnostic tools is critical to refine the accuracy of screening tests, improving the life expectancy and allowing a better prognosis for the affected patients.
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Affiliation(s)
- Leonardo J Galvão-Lima
- Advanced Nucleus of Technological Innovation (NAVI), Federal Institute of Rio Grande do Norte (IFRN), Avenue Senador Salgado Filho 1559, Natal, RN, 59015-000, Brazil.
| | - Antonio H F Morais
- Advanced Nucleus of Technological Innovation (NAVI), Federal Institute of Rio Grande do Norte (IFRN), Avenue Senador Salgado Filho 1559, Natal, RN, 59015-000, Brazil
| | - Ricardo A M Valentim
- Laboratory of Technological Innovation in Health (LAIS), Hospital Universitário Onofre Lopes (HUOL), Federal University of Rio Grande do Norte (UFRN), Campus Lagoa Nova, Natal, RN, Brazil
| | - Elio J S S Barreto
- Division of Oncology and Hematology, Hospital Universitário Onofre Lopes (HUOL), Federal University of Rio Grande do Norte (UFRN), Campus Lagoa Nova, Natal, RN, Brazil
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Bhandari N, Khare S, Walambe R, Kotecha K. Comparison of machine learning and deep learning techniques in promoter prediction across diverse species. PeerJ Comput Sci 2021; 7:e365. [PMID: 33817015 PMCID: PMC7959599 DOI: 10.7717/peerj-cs.365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are reported for the prediction of promoters. However, since all promoter sequences do not show explicit features, the prediction performance of these techniques is poor. Therefore, many machine learning and deep learning models have been proposed for promoter prediction. In this work, we studied methods for vector encoding and promoter classification using genome sequences of three distinct higher eukaryotes viz. yeast (Saccharomyces cerevisiae), A. thaliana (plant) and human (Homo sapiens). We compared one-hot vector encoding method with frequency-based tokenization (FBT) for data pre-processing on 1-D Convolutional Neural Network (CNN) model. We found that FBT gives a shorter input dimension reducing the training time without affecting the sensitivity and specificity of classification. We employed the deep learning techniques, mainly CNN and recurrent neural network with Long Short Term Memory (LSTM) and random forest (RF) classifier for promoter classification at k-mer sizes of 2, 4 and 8. We found CNN to be superior in classification of promoters from non-promoter sequences (binary classification) as well as species-specific classification of promoter sequences (multiclass classification). In summary, the contribution of this work lies in the use of synthetic shuffled negative dataset and frequency-based tokenization for pre-processing. This study provides a comprehensive and generic framework for classification tasks in genomic applications and can be extended to various classification problems.
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Affiliation(s)
- Nikita Bhandari
- Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India
| | - Satyajeet Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, MH, India
| | - Rahee Walambe
- Symbiosis Centre for Applied Artificial Intelligence, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Electronics and Telecommunication Dept, Symbiosis Institute of Technology, Pune, Maharashtra, India
| | - Ketan Kotecha
- Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India
- Symbiosis Centre for Applied Artificial Intelligence, Symbiosis International (Deemed University), Pune, Maharashtra, India
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28
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Heterochiasmy and Sexual Dimorphism: The Case of the Barn Swallow ( Hirundo rustica, Hirundinidae, Aves). Genes (Basel) 2020; 11:genes11101119. [PMID: 32987748 PMCID: PMC7650650 DOI: 10.3390/genes11101119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/23/2022] Open
Abstract
Heterochiasmy, a sex-based difference in recombination rate, has been detected in many species of animals and plants. Several hypotheses about evolutionary causes of heterochiasmy were proposed. However, there is a shortage of empirical data. In this paper, we compared recombination related traits in females and males of the barn swallow Hirundo rustica (Linnaeus, 1758), the species under strong sexual selection, with those in the pale martin Riparia diluta (Sharpe and Wyatt, 1893), a related and ecologically similar species with the same karyotype (2N = 78), but without obvious sexual dimorphism. Recombination traits were examined in pachytene chromosome spreads prepared from spermatocytes and oocytes. Synaptonemal complexes and mature recombination nodules were visualized with antibodies to SYCP3 and MLH1 proteins, correspondingly. Recombination rate was significantly higher (p = 0.0001) in barn swallow females (55.6 ± 6.3 recombination nodules per autosomal genome), caused by the higher number of nodules at the macrochromosomes, than in males (49.0 ± 4.5). They also showed more even distribution of recombination nodules along the macrochromosomes. At the same time, in the pale martin, sexual differences in recombination rate and distributions were rather small. We speculate that an elevated recombination rate in the female barn swallows might have evolved as a compensatory reaction to runaway sexual selection in males.
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29
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Zhongying Q, Huihui C, Hao Y, Yuan H, Huimeng L, Xia L, Xingchun G. Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae). Zookeys 2020; 969:23-42. [PMID: 33013166 PMCID: PMC7515930 DOI: 10.3897/zookeys.969.49278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/14/2020] [Indexed: 11/12/2022] Open
Abstract
In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.
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Affiliation(s)
- Qiu Zhongying
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
| | - Chang Huihui
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
| | - Yuan Hao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Normal University Xi'an China
| | - Huang Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Normal University Xi'an China
| | - Lu Huimeng
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China Northwestern Polytechnical University Xi'an China
| | - Li Xia
- Huizhou No.8 High School, Hui'zhou 516001, China Huizhou No.8 High School Hui'zhou China
| | - Gou Xingchun
- Shaanxi Key Laboratory of Brain Disorders &School of Basic Medical Sciences, Xi'an Medical University, Xi'an,710021, China Xi'an Medical University Xi'an China
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30
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Abbas SZ, Qadir MI, Muhammad SA. Systems-level differential gene expression analysis reveals new genetic variants of oral cancer. Sci Rep 2020; 10:14667. [PMID: 32887903 PMCID: PMC7473858 DOI: 10.1038/s41598-020-71346-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 07/20/2020] [Indexed: 01/28/2023] Open
Abstract
Oral cancer (OC) ranked as eleventh malignancy worldwide, with the increasing incidence among young patients. Limited understanding of complications in cancer progression, its development system, and their interactions are major restrictions towards the progress of optimal and effective treatment strategies. The system-level approach has been designed to explore genetic complexity of the disease and to identify novel oral cancer related genes to detect genomic alterations at molecular level, through cDNA differential analysis. We analyzed 21 oral cancer-related cDNA datasets and listed 30 differentially expressed genes (DEGs). Among 30, we found 6 significant DEGs including CYP1A1, CYP1B1, ADCY2, C7, SERPINB5, and ANAPC13 and studied their functional role in OC. Our genomic and interactive analysis showed significant enrichment of xenobiotics metabolism, p53 signaling pathway and microRNA pathways, towards OC progression and development. We used human proteomic data for post-translational modifications to interpret disease mutations and inter-individual genetic variations. The mutational analysis revealed the sequence predicted disordered region of 14%, 12.5%, 10.5% for ADCY2, CYP1B1, and C7 respectively. The MiRNA target prediction showed functional molecular annotation including specific miRNA-targets hsa-miR-4282, hsa-miR-2052, hsa-miR-216a-3p, for CYP1B1, C7, and ADCY2 respectively associated with oral cancer. We constructed the system level network and found important gene signatures. The drug-gene interaction of OC source genes with seven FDA approved OC drugs help to design or identify new drug target or establishing novel biomedical linkages regarding disease pathophysiology. This investigation demonstrates the importance of system genetics for identifying 6 OC genes (CYP1A1, CYP1B1, ADCY2, C7, SERPINB5, and ANAPC13) as potential drugs targets. Our integrative network-based system-level approach would help to find the genetic variants of OC that can accelerate drug discovery outcomes to develop a better understanding regarding treatment strategies for many cancer types.
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Affiliation(s)
- Syeda Zahra Abbas
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Imran Qadir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.
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31
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O'Rourke JA, McCabe CE, Graham MA. Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Funct Integr Genomics 2020; 20:321-341. [PMID: 31655948 PMCID: PMC7152590 DOI: 10.1007/s10142-019-00709-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/11/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Abstract
Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the USA and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. In this study, we directly compared whole-genome expression responses of leaves and roots to iron (Fe) and phosphate (Pi) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 h. While soybean responds largely to -Fe deficiency, it responds strongly to Pi resupply. Though the timing of the responses was different, both nutrient stress signals used the same molecular pathways. Our study is the first to demonstrate the speed and diversity of the soybean stress response to multiple nutrient deficiencies. We also designed the study to examine gene expression changes in response to multiple stress events. We identified 865 and 3375 genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress event. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.
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Affiliation(s)
- Jamie A O'Rourke
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA.
- Department of Agronomy, Iowa State University, 1567 Agronomy Hall, Ames, IA, 50011, USA.
| | - Chantal E McCabe
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
| | - Michelle A Graham
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, 1567 Agronomy Hall, Ames, IA, 50011, USA
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González-Becerra K, Ramos-Lopez O, Barrón-Cabrera E, Riezu-Boj JI, Milagro FI, Martínez-López E, Martínez JA. Fatty acids, epigenetic mechanisms and chronic diseases: a systematic review. Lipids Health Dis 2019; 18:178. [PMID: 31615571 PMCID: PMC6792183 DOI: 10.1186/s12944-019-1120-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022] Open
Abstract
Background Chronic illnesses like obesity, type 2 diabetes (T2D) and cardiovascular diseases, are worldwide major causes of morbidity and mortality. These pathological conditions involve interactions between environmental, genetic, and epigenetic factors. Recent advances in nutriepigenomics are contributing to clarify the role of some nutritional factors, including dietary fatty acids in gene expression regulation. This systematic review assesses currently available information concerning the role of the different fatty acids on epigenetic mechanisms that affect the development of chronic diseases or induce protective effects on metabolic alterations. Methods A targeted search was conducted in the PubMed/Medline databases using the keywords “fatty acids and epigenetic”. The data were analyzed according to the PRISMA-P guidelines. Results Consumption fatty acids like n-3 PUFA: EPA and DHA, and MUFA: oleic and palmitoleic acid was associated with an improvement of metabolic alterations. On the other hand, fatty acids that have been associated with the presence or development of obesity, T2D, pro-inflammatory profile, atherosclerosis and IR were n-6 PUFA, saturated fatty acids (stearic and palmitic), and trans fatty acids (elaidic), have been also linked with epigenetic changes. Conclusions Fatty acids can regulate gene expression by modifying epigenetic mechanisms and consequently result in positive or negative impacts on metabolic outcomes.
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Affiliation(s)
- K González-Becerra
- Institute of Traslational Nutrigenetics and Nutrigenomics, Health Sciences University Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - O Ramos-Lopez
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain.,Faculty of Medicine and Psychology, Autonomous University of Baja California, Tijuana, B.C., Mexico
| | - E Barrón-Cabrera
- Institute of Traslational Nutrigenetics and Nutrigenomics, Health Sciences University Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - J I Riezu-Boj
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - F I Milagro
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, Madrid, Spain
| | - E Martínez-López
- Institute of Traslational Nutrigenetics and Nutrigenomics, Health Sciences University Center, University of Guadalajara, Guadalajara, Jalisco, Mexico. .,Department of Molecular Biology in Medicine, Health Sciences University Center, University of Guadalajara, Sierra Mojada 950, 44340, Guadalajara, Jalisco, Mexico.
| | - J A Martínez
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, Madrid, Spain.,Madrid Institute of Advanced Studies (IMDEA Food), Madrid, Spain
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Bezerra-Neto JP, de Araújo FC, Ferreira-Neto JRC, da Silva MD, Pandolfi V, Aburjaile FF, Sakamoto T, de Oliveira Silva RL, Kido EA, Barbosa Amorim LL, Ortega JM, Benko-Iseppon AM. Plant Aquaporins: Diversity, Evolution and Biotechnological Applications. Curr Protein Pept Sci 2019; 20:368-395. [PMID: 30387391 DOI: 10.2174/1389203720666181102095910] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]
Abstract
The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.
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Affiliation(s)
- João P Bezerra-Neto
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - José R C Ferreira-Neto
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Manassés D da Silva
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Valesca Pandolfi
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Flavia F Aburjaile
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Tetsu Sakamoto
- Universidade Federal de Minas Gerais, Department of Biochemistry and Immunology, Belo Horizonte, Brazil
| | - Roberta L de Oliveira Silva
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Ederson A Kido
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
| | - Lidiane L Barbosa Amorim
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia do Piauí, Campus Oeiras, Avenida Projetada, s/n, 64.500-000, Oeiras, Piauí, Brazil
| | - José M Ortega
- Universidade Federal de Minas Gerais, Department of Biochemistry and Immunology, Belo Horizonte, Brazil
| | - Ana M Benko-Iseppon
- Universidade Federal de Pernambuco, Genetics Department, Center of Biosciences, Av. Prof. Moraes Rego, 1235, 50.670-423, Recife, Pernambuco, Brazil
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Lin SL, Su YT, Feng SW, Chang WJ, Fan KH, Huang HM. Enhancement of natural killer cell cytotoxicity by using static magnetic field to increase their viability. Electromagn Biol Med 2019; 38:131-142. [DOI: 10.1080/15368378.2019.1591439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Shu-Li Lin
- Dental Department, Cathay General Hospital, Taipei, Taiwan
| | - Yi-Tsai Su
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Wei Feng
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Jen Chang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kan-Hsin Fan
- Dental Department, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Haw-Ming Huang
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
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35
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Semenov GA, Basheva EA, Borodin PM, Torgasheva AA. High rate of meiotic recombination and its implications for intricate speciation patterns in the white wagtail (Motacilla alba). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Georgy A Semenov
- Ecology and Evolutionary Biology, University of Colorado, Ramaley Hall, Boulder, CO, USA
- Institute of Systematics and Ecology of Animals, Frunze, Novosibirsk, Russian Federation
- Ecology and Evolutionary Biology, University of Colorado, Ramaley Hall, Boulder, CO, USA
| | - Ekaterina A Basheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
- Novosibirsk State Research University, Department of Cytology and Genetics, Pirogova st., Novosibirsk, Russian Federation
| | - Anna A Torgasheva
- Institute of Systematics and Ecology of Animals, Frunze, Novosibirsk, Russian Federation
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
- Novosibirsk State Research University, Department of Cytology and Genetics, Pirogova st., Novosibirsk, Russian Federation
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Paula DP, Togawa RC, do Carmo Costa MM, Grynberg P, Martins NF, Andow DA. Systemic and sex-biased regulation of OBP expression under semiochemical stimuli. Sci Rep 2018; 8:6035. [PMID: 29662070 PMCID: PMC5902564 DOI: 10.1038/s41598-018-24297-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/27/2018] [Indexed: 11/12/2022] Open
Abstract
Constitutive expression of Odorant-Binding Proteins (OBPs) in antennae and other body parts has been examined mainly to infer their involvement in insect olfaction, while their regulation in response to semiochemical stimuli has remained poorly known. Previous studies of semiochemical response were basically done using electrophysiology, which integrates the response of the set of OBPs present in an antenna or sensillum, without revealing the regulation of OBPs or which ones might be involved. In this study we used boll weevil as a model and mined its OBPs by RNA-Seq to study their simultaneous antennal expression by qPCR under controlled semiochemical stimuli with aggregation pheromone and plant volatiles. In the absence of a semiochemical stimulus, 23 of 24 OBPs were constitutively expressed in the antenna in both sexes. Semiochemicals changed systemically the expression of OBPs in both sexes. There were different patterns of up- and down-regulation in female antennae for each semiochemical stimulus, consistent with female chemical ecology. On the other hand, the only response in males was down-regulation of some OBPs. We suggest that these systemic changes in OBP expression might be related to enhancing detection of the semiochemical stimuli and/or priming the olfactory system to detect other environmental chemicals.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF, 70770-917, Brazil.
| | - Roberto Coiti Togawa
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF, 70770-917, Brazil
| | - Marcos Mota do Carmo Costa
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF, 70770-917, Brazil
| | - Priscila Grynberg
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF, 70770-917, Brazil
| | - Natália Florêncio Martins
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF, 70770-917, Brazil
| | - David Alan Andow
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN, 55108, USA
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37
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Zhang S. Comparisons of gene coexpression network modules in breast cancer and ovarian cancer. BMC SYSTEMS BIOLOGY 2018; 12:8. [PMID: 29671401 PMCID: PMC5907153 DOI: 10.1186/s12918-018-0530-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Breast cancer and ovarian cancer are hormone driven and are known to have some predisposition genes in common such as the two well known cancer genes BRCA1 and BRCA2. The objective of this study is to compare the coexpression network modules of both cancers, so as to infer the potential cancer-related modules. Methods We applied the eigen-decomposition to the matrix that integrates the gene coexpression networks of both breast cancer and ovarian cancer. With hierarchical clustering of the related eigenvectors, we obtained the network modules of both cancers simultaneously. Enrichment analysis on Gene Ontology (GO), KEGG pathway, Disease Ontology (DO), and Gene Set Enrichment Analysis (GSEA) in the identified modules was performed. Results We identified 43 modules that are enriched by at least one of the four types of enrichments. 31, 25, and 18 modules are enriched by GO terms, KEGG pathways, and DO terms, respectively. The structure of 29 modules in both cancers is significantly different with p-values less than 0.05, of which 25 modules have larger densities in ovarian cancer. One module was found to be significantly enriched by the terms related to breast cancer from GO, KEGG and DO enrichment. One module was found to be significantly enriched by ovarian cancer related terms. Conclusion Breast cancer and ovarian cancer share some common properties on the module level. Integration of both cancers helps identifying the potential cancer associated modules. Electronic supplementary material The online version of this article (10.1186/s12918-018-0530-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuqin Zhang
- Center for Computational Systems Biology, Shanghai Key Laboratory for Contemporary Applied Mathematics, School of Mathematical Sciences, Fudan University, No.220 Handan Road, Shanghai, 200433, China.
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Cao Q, Gu J, Wang D, Liang F, Zhang H, Li X, Yin S. Physiological mechanism of osmoregulatory adaptation in anguillid eels. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:423-433. [PMID: 29344774 PMCID: PMC5862950 DOI: 10.1007/s10695-018-0464-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/03/2018] [Indexed: 06/07/2023]
Abstract
In recent years, the production of eel larvae has dramatic declines due to reductions in spawning stocks, overfishing, growth habitat destruction and access reductions, and pollution. Therefore, it is particularly important and urgent for artificial production of glass eels. However, the technique of artificial hatching and rearing larvae is still immature, which has long been regarded as an extremely difficult task. One of the huge gaps is artificial condition which is far from the natural condition to develop their capability of osmoregulation. Thus, understanding their osmoregulatory mechanisms will help to improve the breed and adapt to the changes in the environment. In this paper, we give a general review for a study progress of osmoregulatory mechanisms in eels from five aspects including tissues and organs, ion transporters, hormones, proteins, and high throughput sequencing methods.
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Affiliation(s)
- Quanquan Cao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Jie Gu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Dan Wang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Fenfei Liang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Hongye Zhang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Xinru Li
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu Province, 210023, China.
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Lopez W, Page AM, Carlson DJ, Ericson BL, Cserhati MF, Guda C, Carlson KA. Analysis of immune-related genes during Nora virus infection of Drosophila melanogaster using next generation sequencing. AIMS Microbiol 2018; 4:123-139. [PMID: 29707694 PMCID: PMC5915338 DOI: 10.3934/microbiol.2018.1.123] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Drosophila melanogaster depends upon the innate immune system to regulate and combat viral infection. This is a complex, yet widely conserved process that involves a number of immune pathways and gene interactions. In addition, expression of genes involved in immunity are differentially regulated as the organism ages. This is particularly true for viruses that demonstrate chronic infection, as is seen with Nora virus. Nora virus is a persistent non-pathogenic virus that replicates in a horizontal manner in D. melanogaster. The genes involved in the regulation of the immune response to Nora virus infection are largely unknown. In addition, the temporal response of immune response genes as a result of infection has not been examined. In this study, D. melanogaster either infected with Nora virus or left uninfected were aged for 2, 10, 20 and 30 days. The RNA from these samples was analyzed by next generation sequencing (NGS) and the resulting immune-related genes evaluated by utilizing both the PANTHER and DAVID databases, as well as comparison to lists of immune related genes and FlyBase. The data demonstrate that Nora virus infected D. melanogaster exhibit an increase in immune related gene expression over time. In addition, at day 30, the data demonstrate that a persistent immune response may occur leading to an upregulation of specific immune response genes. These results demonstrate the utility of NGS in determining the potential immune system genes involved in Nora virus replication, chronic infection and involvement of antiviral pathways.
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Affiliation(s)
- Wilfredo Lopez
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Alexis M Page
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Darby J Carlson
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Brad L Ericson
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Matyas F Cserhati
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kimberly A Carlson
- Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA
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Chen J, Ni P, Li X, Han J, Jakovlić I, Zhang C, Zhao S. Population size may shape the accumulation of functional mutations following domestication. BMC Evol Biol 2018; 18:4. [PMID: 29351740 PMCID: PMC5775542 DOI: 10.1186/s12862-018-1120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. RESULTS Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e . CONCLUSIONS Our results confirm the classical population genetics theory prediction and highlight the important role of species' N e in shaping the patterns of accumulation of functional mutations, especially radical mutations, in domesticated animals. The results aid our understanding of the mechanisms underlying the accumulation of functional mutations after domestication, which is critical for understanding the phenotypic diversification associated with this process.
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Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xinyun Li
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, 00100 Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, 430075 People’s Republic of China
| | - Chengjun Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 People’s Republic of China
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. THE PHARMACOGENOMICS JOURNAL 2018; 19:136-146. [PMID: 29352165 PMCID: PMC6462828 DOI: 10.1038/s41397-017-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 11/06/2017] [Indexed: 12/30/2022]
Abstract
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
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del Priore L, Pigozzi MI. Broad-scale recombination pattern in the primitive bird Rhea americana (Ratites, Palaeognathae). PLoS One 2017; 12:e0187549. [PMID: 29095930 PMCID: PMC5667853 DOI: 10.1371/journal.pone.0187549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/20/2017] [Indexed: 12/02/2022] Open
Abstract
Birds have genomic and chromosomal features that make them an attractive group to analyze the evolution of recombination rate and the distribution of crossing over. Yet, analyses are biased towards certain species, especially domestic poultry and passerines. Here we analyze for the first time the recombination rate and crossover distribution in the primitive ratite bird, Rhea americana (Rheiformes, Palaeognathae). Using a cytogenetic approach for in situ mapping of crossovers we found that the total genetic map is 3050 cM with a global recombination rate of 2.1 cM/Mb for female rheas. In the five largest macrobivalents there were 3 or more crossovers in most bivalents. Recombination rates for macrobivalents ranges between 1.8-2.1 cM/Mb and the physical length of their synaptonemal complexes is highly predictive of their genetic lengths. The crossover rate at the pseudoautosomal region is 2.1 cM/Mb, similar to those of autosomal pairs 5 and 6 and only slightly higher compared to other macroautosomes. It is suggested that the presence of multiple crossovers on the largest macrobivalents is a feature common to many avian groups, irrespective of their position throughout phylogeny. These data provide new insights to analyze the heterogeneous recombination landscape of birds.
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Affiliation(s)
- Lucía del Priore
- INBIOMED Instituto de Investigaciones Biomédicas UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Inés Pigozzi
- INBIOMED Instituto de Investigaciones Biomédicas UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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Chen T, Li M, He Q, Zou L, Li Y, Chang C, Zhao D, Zhu Y. LiverWiki: a wiki-based database for human liver. BMC Bioinformatics 2017; 18:452. [PMID: 29029599 PMCID: PMC5640914 DOI: 10.1186/s12859-017-1852-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort. RESULTS We present LiverWiki, a first wiki-based database that integrates liver-related genes, homolog genes, gene expressions in microarray datasets and RNA-Seq datasets, proteins, protein interactions, post-translational modifications, associated pathways, diseases, metabolites identified in the metabolomics datasets, and literatures into an easily accessible and searchable resource for community-driven sharing. LiverWiki houses information in a total of 141,897 content pages, including 19,787 liver-related gene pages, 17,077 homolog gene pages, 50,251 liver-related protein pages, 36,122 gene expression pages, 2067 metabolites identified in the metabolomics datasets, 16,366 disease-related molecules, and 227 liver disease pages. Other than assisting users in searching, browsing, reviewing, refining the contents on LiverWiki, the most important contribution of LiverWiki is to allow the community to create and update biological data of liver in visible and editable tables. This integrates newly produced data with existing knowledge. Implemented in mediawiki, LiverWiki provides powerful extensions to support community contributions. CONCLUSIONS The main goal of LiverWiki is to provide the research community with comprehensive liver-related data, as well as to allow the research community to share their liver-related data flexibly and efficiently. It also enables rapid sharing new discoveries by allowing the discoveries to be integrated and shared immediately, rather than relying on expert curators. The database is available online at http://liverwiki.hupo.org.cn /.
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Affiliation(s)
- Tao Chen
- Beijing Institute of Life Omics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, 33 Life Science Park Rd, Changping District, Beijing, 102206, China
| | - Mansheng Li
- Beijing Institute of Life Omics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, 33 Life Science Park Rd, Changping District, Beijing, 102206, China
| | - Qiang He
- School of Software and Electrical Engineering, Swinburne University of Technology, Melbourne, Victoria, 3122, Australia
| | - Lei Zou
- Institute of Computer Science and Technology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, 100871, China
| | - Youhuan Li
- Institute of Computer Science and Technology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, 100871, China
| | - Cheng Chang
- Beijing Institute of Life Omics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, 33 Life Science Park Rd, Changping District, Beijing, 102206, China
| | - Dongyan Zhao
- Institute of Computer Science and Technology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, 100871, China
| | - Yunping Zhu
- Beijing Institute of Life Omics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine, 33 Life Science Park Rd, Changping District, Beijing, 102206, China.
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Development of EST-SSR markers through de novo RNA sequencing and application for biomass productivity in kenaf (Hibiscus cannabinus L.). Genes Genomics 2017. [DOI: 10.1007/s13258-017-0582-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Yao J, Yang H, Dai R. Characterization of the complete mitochondrial genome of Acanthoscelides obtectus (Coleoptera: Chrysomelidae: Bruchinae) with phylogenetic analysis. Genetica 2017; 145:397-408. [PMID: 28730527 DOI: 10.1007/s10709-017-9975-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/04/2017] [Indexed: 11/26/2022]
Abstract
Acanthoscelides obtectus is a common species of the subfamily Bruchinae and a worldwide-distributed seed-feeding beetle. The complete mitochondrial genome of A. obtectus is 16,130 bp in length with an A + T content of 76.4%. It contains a positive AT skew and a negative GC skew. The mitogenome of A. obtectus contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a non-coding region (D-loop). All PCGs start with an ATN codon, and seven (ND3, ATP6, COIII, ND3, ND4L, ND6, and Cytb) of them terminate with TAA, while the remaining five (COI, COII, ND1, ND4, and ND5) terminate with a single T, ATP8 terminates with TGA. Except tRNA Ser , the secondary structures of 21 tRNAs that can be folded into a typical clover-leaf structure were identified. The secondary structures of lrRNA and srRNA were also predicted in this study. There are six domains with 48 helices in lrRNA and three domains with 32 helices in srRNA. The control region of A. obtectus is 1354 bp in size with the highest A + T content (83.5%) in a mitochondrial gene. Thirteen PCGs in 19 species have been used to infer their phylogenetic relationships. Our results show that A. obtectus belongs to the family Chrysomelidae (subfamily-Bruchinae). This is the first study on phylogenetic analyses involving the mitochondrial genes of A. obtectus and could provide basic data for future studies of mitochondrial genome diversities and the evolution of related insect lineages.
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Affiliation(s)
- Jie Yao
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Hong Yang
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Renhuai Dai
- The Provincial Key Laboratory for Agricultural Pest Management Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, 550025, Guizhou, People's Republic of China.
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Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber. Sci Rep 2017; 7:4778. [PMID: 28684750 PMCID: PMC5500473 DOI: 10.1038/s41598-017-05312-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/26/2017] [Indexed: 02/02/2023] Open
Abstract
Animal gut harbors diverse microbes that play crucial roles in the nutrition uptake, metabolism, and the regulation of host immune responses. The intestinal microbiota homeostasis is critical for health but poorly understood. Probiotics Paracoccus marcusii DB11 and Bacillus cereus G19, and antibiotics florfenicol did not significantly impact species richness and the diversity of intestinal microbiota of sea cucumber, in comparison with those in the control group by high-throughput sequencing. Molecular ecological network analysis indicated that P. marcusii DB11 supplementation may lead to sub-module integration and the formation of a large, new sub-module, and enhance species-species interactions and connecter and module hub numbers. B. cereus G19 supplementation decreased sub-module numbers, and increased the number of species-species interactions and module hubs. Sea cucumber treated with florfenicol were shown to have only one connecter and the lowest number of operational taxonomic units (OTUs) and species-species interactions within the ecological network. These results suggested that P. marcusii DB11 or B. cereus G19 may promote intestinal microbiota homeostasis by improving modularity, enhancing species-species interactions and increasing the number of connecters and/or module hubs within the network. In contrast, the use of florfenicol can lead to homeostatic collapse through the deterioration of the ecological network.
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ElSayed AI, Lehrer A, Ebrahim M, Mohamed AH, Komor E. Assessment of sucrose transporters, metabolites and sucrose phosphate synthase in different sugarcane tissues. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:703-712. [PMID: 28878508 PMCID: PMC5567715 DOI: 10.1007/s12298-017-0454-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/28/2017] [Accepted: 05/25/2017] [Indexed: 05/29/2023]
Abstract
The expression of sucrose-phosphate synthase II (SPSII) and sucrose transporters ShSUT1A and ShSUT4 were determined by RT-PCR and qRT-PCR in the sink and source leaves and in rind and pith of mature internodes of four high-yielding Hawaiian sugarcane cultivars. Expression of SPSII, ShSUT1A, and ShSUT4 was lower in pith than in rind, except in one cultivar, but else quite similar in the cultivars. The strong expression of transporter ShSUT4 in the rind of the internodes may hint to a special role of ShSUT4 in the rind. ShSUT4-expression in the sink and source leaves was similar in all four cultivars, whereas large differences were found for the expression of ShSUT1A and SPSII between the source and sink leaves and between the cultivars. The levels of sucrose precursors were doubled in source leaves compared to sink leaves, whereas they were higher in immature internode compared to mature internode. The role of sucrose transporters and SPSII in leaves and internodes is discussed, but the large differences, which were observed in the transcript levels of SPSII and sucrose transporters between some cultivars, although all the cultivars were similarly high-yielding cultivars, show that SPSII and SUT transcript levels cannot be used as indicators of high-yield cultivars.
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Affiliation(s)
- Abdelaleim Ismail ElSayed
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44519 Egypt
- Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Axel Lehrer
- Hawaii Agriculture Research Center, Kunia, HI USA
| | - Mohsen Ebrahim
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Azza H. Mohamed
- Biochemistry Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Ewald Komor
- Plant Physiology, University of Bayreuth, 95440 Bayreuth, Germany
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Selenina A, Tsimokha A, Tomilin A. Proteasomes in Protein Homeostasis of Pluripotent Stem Cells. Acta Naturae 2017; 9:39-47. [PMID: 29104774 PMCID: PMC5662272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Indexed: 11/05/2022] Open
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) are subjects of high interest not only in basic research, but also in various applied fields, particularly, in regenerative medicine. Despite the tremendous interest to these cells, the molecular mechanisms that control protein homeostasis in these cells remain largely unknown. The ubiquitin-proteasome system (UPS) acts via post-translational protein modifications and protein degradation and, therefore, is involved in the control of virtually all cellular processes: cell cycle, self-renewal, signal transduction, transcription, translation, oxidative stress, immune response, apoptosis, etc. Therefore, studying the biological role and action mechanisms of the UPS in pluripotent cells will help to better understand the biology of cells, as well as to develop novel approaches for regenerative medicine.
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Affiliation(s)
- A.V. Selenina
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, Saint-Petersburg, 194064 , Russia
- St-Petersburg State University, University Emb. 7/9, St-Petersburg, 199034, Russia
| | - A.S. Tsimokha
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, Saint-Petersburg, 194064 , Russia
| | - A.N. Tomilin
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, Saint-Petersburg, 194064 , Russia
- St-Petersburg State University, University Emb. 7/9, St-Petersburg, 199034, Russia
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Heiss E, Handschuh S, Aerts P, Van Wassenbergh S. A tongue for all seasons: extreme phenotypic flexibility in salamandrid newts. Sci Rep 2017; 7:1006. [PMID: 28432290 PMCID: PMC5430857 DOI: 10.1038/s41598-017-00674-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/08/2017] [Indexed: 01/23/2023] Open
Abstract
Many organisms faced with seasonally fluctuating abiotic and biotic conditions respond by altering their phenotype to account for the demands of environmental changes. Here we discovered that newts, which switch seasonally between an aquatic and terrestrial lifestyle, grow a complex adhesive system on their tongue pad consisting of slender lingual papillae and mucus-producing cells to increase the efficiency of prey capture as they move from water onto land. The adhesive system is reduced again as newts switch back to their aquatic stage, where they use suction to capture prey. As suction performance is also enhanced seasonally by reshaping of the mouth due to the growth of labial lobes, our results show that newts are exceptional in exhibiting phenotypic flexibility in two alternating components (i.e. tongue pad and labial lobes) within a single functional system, and suggest that this form of phenotypic flexibility demands complex genetic regulation.
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Affiliation(s)
- Egon Heiss
- Institute of Systematic Zoology and Evolutionary Biology, Friedrich-Schiller-University Jena, Erbertstr. 1, 07743, Jena, Germany.
| | - Stephan Handschuh
- VetCore Facility for Research, Imaging Unit, University for Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Peter Aerts
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.,Department of Movement and Sports Sciences, Ghent University, Watersportlaan 2, B-9000, Ghent, Belgium
| | - Sam Van Wassenbergh
- Department of Biology, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.,Departement d'Ecologie et de Gestion de la Biodiversité, Muséum National d' Histoire Naturelle, 57 rue Cuvier, Case postale 55, 75231, Paris Cedex 5, France
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50
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Mocali S, Chiellini C, Fabiani A, Decuzzi S, de Pascale D, Parrilli E, Tutino ML, Perrin E, Bosi E, Fondi M, Lo Giudice A, Fani R. Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach. Sci Rep 2017; 7:839. [PMID: 28404986 PMCID: PMC5429795 DOI: 10.1038/s41598-017-00876-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Cold environments dominate Earth's biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp. TB41 (PspTB41). Although the genome size of PspTB41 is considerably larger than PhTAC125, the higher number of genes did not reflect any higher metabolic versatility at 4 °C as compared to PhTAC125. Remarkably, protein S-thiolation regulated by glutathione and glutathionylspermidine appeared to be a new possible mechanism for cold adaptation in PhTAC125. More in general, this study represents an example of how 'multi-omic' information might potentially contribute in filling the gap between genotypic and phenotypic features related to cold-adaptation mechanisms in bacteria.
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Affiliation(s)
- Stefano Mocali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.
| | - Carolina Chiellini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Arturo Fabiani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy
| | - Silvia Decuzzi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Elena Perrin
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Emanuele Bosi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Marco Fondi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Angelina Lo Giudice
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122, Messina, Italy.,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontrès 31, 98166, Messina, Italy
| | - Renato Fani
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
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