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Zhu S, Zou M, Li C, Tang Y, Luo H, Dong X. MC1R regulates T regulatory cell differentiation through metabolic reprogramming to promote colon cancer. Int Immunopharmacol 2024; 138:112546. [PMID: 38917522 DOI: 10.1016/j.intimp.2024.112546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
BACKGROUND Until 2021, colon cancer was a leading cancer globally. Early detection improves outcomes; however, advanced cases still having poor prognosis. Therefore, an understanding of associated molecular mechanisms is crucial for developing new preventive and therapeutic strategies for colon cancer. METHODS The TCGA database was analyzed to assess melanocortin 1receptor (MC1R) expression in colon cancer and its link with patient prognosis. Further, models and diverse experimental techniques were employed to investigate the impact of MC1R on colon cancer progression and its underlying mechanism was elucidated. RESULTS In a follow-up study of clinical patients, the important role of MC1R was identified in the development of colon cancer. First, MC1R was expressed more highly in colon tumor tissues than in adjacent tissues. In addition, MC1R was associated with colon cancer prognosis, and higher expression of MC1R tended to predict a worse prognosis. This conclusion was verified in MC1R-/- mice, which showed a greater resistance to tumor growth than wild-type mice, as expected. Further investigation revealed a significant change in the portion of Tregs in MC1R-/- mice, while the portion of CD4 + and CD8 + T cells remained unchanged. The in vitro experiments revealed a weaker ability of the MC1R-/- T cells to differentiate into Tregs. Previous studies report that the functional integrity of Tregs is interwoven with cellular metabolism. Therefore, MC1R was deduced to regulate the differentiation of Tregs by reprogramming the metabolism. As expected, MC1R-/- T cells exhibited weaker mitochondrial function and a lower aerobic oxidation capacity. Concurrently, the MC1R-/- T cells had stronger limiting effects on colon cancer cells. According to these results, the MC1R inhibitor was hypothesized as a potential therapeutic agent to suppress colon cancer. The results showed that upon MC1R suppression, the tumors in the mice developed more slowly, and the mice survived longer, potentially providing a novel strategy to treat clinical colon cancer. CONCLUSION By regulating Tregs differentiation, MC1R overexpression in colon cancer correlates with poor prognosis, while MC1R inhibition shows potential as a therapeutic approach to slow tumor growth and enhance survival.
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Affiliation(s)
- Shaoliang Zhu
- Department of Hepatobiliary, Pancreas and Spleen Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China
| | - Mengjie Zou
- Department of Nephrology, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China
| | - Chunxing Li
- Department of Operating Room, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China
| | - Yuntian Tang
- Department of Hepatobiliary, Pancreas and Spleen Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China.
| | - Honglin Luo
- Institute of Oncology, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China.
| | - Xiaofeng Dong
- Department of Hepatobiliary, Pancreas and Spleen Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, 530021, Guangxi, China.
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Rusbjerg-Weberskov CE, Hollensen AK, Damgaard CK, Løvendorf MB, Skov L, Enghild JJ, Nielsen NS. Mapping the Periostin splice isoforms in atopic dermatitis and an in vitro asthma model - A multi-platform analysis using mass spectrometry and RT-qPCR. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141031. [PMID: 38977230 DOI: 10.1016/j.bbapap.2024.141031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Periostin is a matricellular protein known to be alternatively spliced to produce ten isoforms with a molecular weight of 78-91 kDa. Within the extracellular matrix, periostin attaches to cell surfaces to induce signaling via integrin-binding and actively participates in fibrillogenesis, orchestrating the arrangement of collagen in the extracellular environment. In atopic diseases such as atopic dermatitis (AD) and asthma, periostin is known to participate in driving the disease-causing type 2 inflammation. The periostin isoforms expressed in these diseases and the implication of the alternative splicing events are unknown. Here, we present two universal assays to map the expression of periostin isoforms at the mRNA (RT-qPCR) and protein (PRM-based mass spectrometry) levels. We use these assays to study the splicing profile of periostin in AD lesions as well as in in vitro models of AD and asthma. In these conditions, periostin displayed overexpression with isoforms 3 and 5 standing out as highly overexpressed. Notably, isoforms 9 and 10 exhibited a divergent pattern relative to the remaining isoforms. Isoforms 9 and 10 are often overlooked in periostin research and this paper presents the first evidence of their expression at the protein level. This underlines the necessity to include isoforms 9 and 10 in future research addressing periostin splice isoforms. The assays presented in this paper hold the potential to improve our insight into the splicing profile of periostin in tissues and diseases of interest. The application of these assays to AD lesions and in vitro models demonstrated their potential for identifying isoforms of particular significance, warranting a further in-depth investigation.
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Affiliation(s)
| | - Anne Kruse Hollensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, C, Denmark
| | | | - Marianne Bengtson Løvendorf
- Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte, Hellerup, Denmark; LEO Foundation Skin Immunology Research Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lone Skov
- Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte, Hellerup, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, C, Denmark.
| | - Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, C, Denmark
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Seidemann L, Lippold CP, Rohm CM, Eckel JC, Schicht G, Matz-Soja M, Berg T, Seehofer D, Damm G. Sex hormones differently regulate lipid metabolism genes in primary human hepatocytes. BMC Endocr Disord 2024; 24:135. [PMID: 39090659 PMCID: PMC11292922 DOI: 10.1186/s12902-024-01663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) is higher in men than in women. Hormonal and genetic causes may account for the sex differences in MASLD. Current human in vitro liver models do not sufficiently take the influence of biological sex and sex hormones into consideration. METHODS Primary human hepatocytes (PHHs) were isolated from liver specimen of female and male donors and cultured with sex hormones (17β-estradiol, testosterone and progesterone) for up to 72 h. mRNA expression levels of 8 hepatic lipid metabolism genes were analyzed by RT-qPCR. Sex hormones and their metabolites were determined in cell culture supernatants by LC-MS analyses. RESULTS A sex-specific expression was observed for LDLR (low density lipoprotein receptor) with higher mRNA levels in male than female PHHs. All three sex hormones were metabolized by PHHs and the effects of hormones on gene expression levels varied depending on hepatocyte sex. Only in female PHHs, 17β-estradiol treatment affected expression levels of PPARA (peroxisome proliferator-activated receptor alpha), LIPC (hepatic lipase) and APOL2 (apolipoprotein L2). Further changes in mRNA levels of female PHHs were observed for ABCA1 (ATP-binding cassette, sub-family A, member 1) after testosterone and for ABCA1, APOA5 (apolipoprotein A-V) and PPARA after progesterone treatment. Only the male PHHs showed changing mRNA levels for LDLR after 17β-estradiol and for APOA5 after testosterone treatment. CONCLUSIONS Male and female PHHs showed differences in their expression levels of hepatic lipid metabolism genes and their responsiveness towards sex hormones. Thus, cellular sex should be considered, especially when investigating the pathophysiological mechanisms of MASLD.
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Affiliation(s)
- Lena Seidemann
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany
- Saxonian Incubator for Clinical Translation (SIKT), Leipzig University, 04103, Leipzig, Germany
| | - Clara Paula Lippold
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany
- Saxonian Incubator for Clinical Translation (SIKT), Leipzig University, 04103, Leipzig, Germany
| | - Carolin Marie Rohm
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany
- Saxonian Incubator for Clinical Translation (SIKT), Leipzig University, 04103, Leipzig, Germany
| | - Julian Connor Eckel
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany
- Saxonian Incubator for Clinical Translation (SIKT), Leipzig University, 04103, Leipzig, Germany
| | - Gerda Schicht
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany
- Saxonian Incubator for Clinical Translation (SIKT), Leipzig University, 04103, Leipzig, Germany
| | - Madlen Matz-Soja
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, 04103, Leipzig, Germany
| | - Thomas Berg
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, 04103, Leipzig, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, Clinic for Visceral, Transplant, Thoracic and Vascular Surgery, Leipzig University Medical Center, 04103, Leipzig, Germany.
- Saxonian Incubator for Clinical Translation (SIKT), Leipzig University, 04103, Leipzig, Germany.
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Virtanen MI, Iversen MH, Patel DM, Brinchmann MF. Daily crowding stress has limited, yet detectable effects on skin and head kidney gene expression in surgically tagged Atlantic salmon (Salmo salar). FISH & SHELLFISH IMMUNOLOGY 2024:109794. [PMID: 39089638 DOI: 10.1016/j.fsi.2024.109794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
To ensure welfare-friendly and effective internal tagging, the tagging process should not cause a long-term burden on individuals given that tagged fish serve as representatives for the entire population in telemetry applications. To some extent, stress is inevitable within regular aquaculture practices, and thus, the consequences of long-term stress should be described in terms of their effects on internal tagging. In fish, stressors activate the Hypothalamus-Pituitary-Interrenal (HPI) and Brain-Sympathetic-Chromaffin Cell (BSC) axes, leading to neuroimmunoendocrine communication and paracrine interactions among stress hormones. The interrelation between wound healing and stress is complex, owing to their shared components, pathways, and energy demands. This study assessed 14 genes (mmp9, mmp13, il-2, il-4, il-8a, il-10, il-12, il-17d, il-1b, tnfa, ifng, leg-3, igm, and crh) in the skin (1.5 cm from the wound) and head kidney over eight weeks. These genes, associated with cell signaling in immunity, wound healing, and stress, have previously been identified as influenced and regulated by these processes. Half of a group of Atlantic salmon (n=90) with surgically implanted dummy smart-tags were exposed to daily crowding stress. The goal was to investigate how this gene panel responds to a wound alone and then to the combined effects of wounding and daily crowding stress. Our observations indicate that chronic stress impacts inflammation and impedes wound healing, as seen through the expression of matrix metalloproteinases genes in the skin but not in the head kidney. This difference is likely due to the ongoing internal wound repair, in contrast to the externally healed wound incision. Cytokine expression, when significant in the skin, was mainly downregulated in both treatments compared to control values, particularly in the study's first half. Conversely, the head kidney showed initial cytokine downregulation followed by upregulation. Across all weeks observed and combining both tissues, the significantly expressed gene differences were 12% between the Wound and Stress+ groups, 28% between Wound and Control, and 25% between Stress+ and Control. Despite significant fluctuations in cytokines, sustained variations across multiple weeks are only evident in a few select genes. Furthermore, Stress+ individuals demonstrated the most cytokine correlations within the head kidney, which may suggest that chronic stress affects cytokine expression. This investigation unveils that the presence of stress and prolonged activation of the HPI axis in an eight weeklong study has limited yet detectable effects on the selected gene expression within immunity, wound healing, and stress, with notable tissue-specific differences.
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Wahbeh MH, Boyd RJ, Yovo C, Rike B, McCallion AS, Avramopoulos D. A functional schizophrenia-associated genetic variant near the TSNARE1 and ADGRB1 genes. HGG ADVANCES 2024; 5:100303. [PMID: 38702885 PMCID: PMC11130735 DOI: 10.1016/j.xhgg.2024.100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/01/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Recent collaborative genome-wide association studies (GWAS) have identified >200 independent loci contributing to risk for schizophrenia (SCZ). The genes closest to these loci have diverse functions, supporting the potential involvement of multiple relevant biological processes, yet there is no direct evidence that individual variants are functional or directly linked to specific genes. Nevertheless, overlap with certain epigenetic marks suggest that most GWAS-implicated variants are regulatory. Based on the strength of association with SCZ and the presence of regulatory epigenetic marks, we chose one such variant near TSNARE1 and ADGRB1, rs4129585, to test for functional potential and assay differences that may drive the pathogenicity of the risk allele. We observed that the variant-containing sequence drives reporter expression in relevant neuronal populations in zebrafish. Next, we introduced each allele into human induced pluripotent cells and differentiated four isogenic clones homozygous for the risk allele and five clones homozygous for the non-risk allele into neural progenitor cells. Employing RNA sequencing, we found that the two alleles yield significant transcriptional differences in the expression of 109 genes at a false discovery rate (FDR) of <0.05 and 259 genes at a FDR of <0.1. We demonstrate that these genes are highly interconnected in pathways enriched for synaptic proteins, axon guidance, and regulation of synapse assembly. Exploration of genes near rs4129585 suggests that this variant does not regulate TSNARE1 transcripts, as previously thought, but may regulate the neighboring ADGRB1, a regulator of synaptogenesis. Our results suggest that rs4129585 is a functional common variant that functions in specific pathways likely involved in SCZ risk.
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Affiliation(s)
- Marah H Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel J Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bailey Rike
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Watanabe H, Kobikov Y, Nosova O, Sarkisyan D, Galatenko V, Carvalho L, Maia GH, Lukoyanov N, Lavrov I, Ossipov MH, Hallberg M, Schouenborg J, Zhang M, Bakalkin G. The Left-Right Side-Specific Neuroendocrine Signaling from Injured Brain: An Organizational Principle. FUNCTION 2024; 5:zqae013. [PMID: 38985004 PMCID: PMC11237900 DOI: 10.1093/function/zqae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 07/11/2024] Open
Abstract
A neurological dogma is that the contralateral effects of brain injury are set through crossed descending neural tracts. We have recently identified a novel topographic neuroendocrine system (T-NES) that operates via a humoral pathway and mediates the left-right side-specific effects of unilateral brain lesions. In rats with completely transected thoracic spinal cords, unilateral injury to the sensorimotor cortex produced contralateral hindlimb flexion, a proxy for neurological deficit. Here, we investigated in acute experiments whether T-NES consists of left and right counterparts and whether they differ in neural and molecular mechanisms. We demonstrated that left- and right-sided hormonal signaling is differentially blocked by the δ-, κ- and µ-opioid antagonists. Left and right neurohormonal signaling differed in targeting the afferent spinal mechanisms. Bilateral deafferentation of the lumbar spinal cord abolished the hormone-mediated effects of the left-brain injury but not the right-sided lesion. The sympathetic nervous system was ruled out as a brain-to-spinal cord-signaling pathway since hindlimb responses were induced in rats with cervical spinal cord transections that were rostral to the preganglionic sympathetic neurons. Analysis of gene-gene co-expression patterns identified the left- and right-side-specific gene co-expression networks that were coordinated via the humoral pathway across the hypothalamus and lumbar spinal cord. The coordination was ipsilateral and disrupted by brain injury. These findings suggest that T-NES is bipartite and that its left and right counterparts contribute to contralateral neurological deficits through distinct neural mechanisms, and may enable ipsilateral regulation of molecular and neural processes across distant neural areas along the neuraxis.
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Affiliation(s)
- Hiroyuki Watanabe
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
- Department of Molecular Medicine, University of Southern Denmark, Odense, DK-5230, Denmark
| | - Yaromir Kobikov
- Volunteer Associate at Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Olga Nosova
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Daniil Sarkisyan
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, SE-751 08, Sweden
| | | | - Liliana Carvalho
- Departamento de Biomedicina da Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Gisela H Maia
- Centro de Investigação em Saúde Translacional e Biotecnologia Médica (TBIO)/Rede de Investigação em Saúde (RISE-Health), Escola Superior de Saúde, Instituto Politécnico do Porto, Porto 4200-072, Portugal
- Medibrain, Vila do Conde 4480-807, Portugal
- Brain Research Institute, Porto 4450-208, Portugal
| | - Nikolay Lukoyanov
- Departamento de Biomedicina da Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
- Brain Research Institute, Porto 4450-208, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal
| | - Igor Lavrov
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael H Ossipov
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, AZ 85724-5050, USA
| | - Mathias Hallberg
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Jens Schouenborg
- Neuronano Research Center, Department of Experimental Medical Science, Lund University, Lund 223 63, Sweden
| | - Mengliang Zhang
- Department of Molecular Medicine, University of Southern Denmark, Odense, DK-5230, Denmark
- Neuronano Research Center, Department of Experimental Medical Science, Lund University, Lund 223 63, Sweden
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
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Rahimov F, Nieminen P, Kumari P, Juuri E, Nikopensius T, Paraiso K, German J, Karvanen A, Kals M, Elnahas AG, Karjalainen J, Kurki M, Palotie A, Heliövaara A, Esko T, Jukarainen S, Palta P, Ganna A, Patni AP, Mar D, Bomsztyk K, Mathieu J, Ruohola-Baker H, Visel A, Fakhouri WD, Schutte BC, Cornell RA, Rice DP. High incidence and geographic distribution of cleft palate cases in Finland are associated with a regulatory variant in IRF6. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.09.24310146. [PMID: 39040165 PMCID: PMC11261923 DOI: 10.1101/2024.07.09.24310146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip with or without cleft palate (CL/P). This trend contrasts to that in other European countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial clefts, which include CL/P and CP, in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is highly enriched in Finns and Estonians, as being strongly associated with CP ( P = 5.25 × 10 -34 , OR = 8.65, 95% CI 6.11-12.25), but not with CL/P ( P = 7.2 × 10 -5 ), with genome-wide significance. The risk allele frequency of rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in independent cohorts of CP cases from Finland ( P = 8.82 × 10 -28 ) and Estonia ( P = 1.25 × 10 -5 ). The risk allele of rs570516915 disrupts a conserved binding site for the transcription factor IRF6 within a previously characterized enhancer upstream of the IRF6 gene. Through reporter assay experiments we found that the risk allele of rs570516915 diminishes the enhancer activity. Oral epithelial cells derived from CRISPR-Cas9 edited induced pluripotent stem cells demonstrate that the CP-associated allele of rs570516915 concomitantly decreases the binding of IRF6 and the expression level of IRF6 , suggesting impaired IRF6 autoregulation as a molecular mechanism underlying the risk for CP.
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Murad M, Chen Y, Iaria J, Fonseca Teixeira A, Zhu HJ. A Novel Method for the Early Detection of Single Circulating, Metastatic and Self-Seeding Cancer Cells in Orthotopic Breast Cancer Mouse Models. Cells 2024; 13:1166. [PMID: 39056749 PMCID: PMC11275056 DOI: 10.3390/cells13141166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/21/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Metastasis is the main cause of cancer-related deaths, but efficient targeted therapies against metastasis are still missing. Major gaps exist in our understanding of the metastatic cascade, as existing methods cannot combine sensitivity, robustness, and practicality to dissect cancer progression. Addressing this issue requires improved strategies to distinguish early metastatic colonization from metastatic outgrowth. METHODS Luciferase-labelled MDA-MB-231, MCF7, and 4T1 breast cancer cells were spiked into samples from tumour-naïve mice to establish the limit of detection for disseminated tumour cells. Luciferase-labelled breast cancer cells (±unlabelled cancer-associated fibroblasts; CAFs) were orthotopically implanted in immunocompromised mice. An ex vivo luciferase assay was used to quantify tumour cell dissemination. RESULTS In vitro luciferase assay confirmed a linear and positive correlation between cancer cell numbers and the bioluminescence detected at single cell level in blood, brain, lung, liver, and mammary fat pad samples. Remarkably, single luciferase-labelled cancer cells were detectable in all of these sites, as the bioluminescence quantified in the analysed samples was substantially higher than background levels. Ex vivo, circulating tumour cells, metastasis, and tumour self-seeding were detected in all samples from animals implanted with highly metastatic luciferase-labelled MDA-MB-231 cells. In turn, detection of poorly metastatic luciferase-labelled MCF7 cells was scarce but significantly enhanced upon co-implantation with CAFs as early as 20 days after the experiment was initiated. CONCLUSIONS These results demonstrate the feasibility of using an ultrasensitive luciferase-based method to dissect the mechanisms of early metastatic colonization to improving the development of antimetastatic therapies.
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Affiliation(s)
- Muhammad Murad
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, 5th Floor Clinical Sciences Building, Parkville, VIC 3050, Australia; (M.M.); (Y.C.); (J.I.); (A.F.T.)
| | - Yanjiang Chen
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, 5th Floor Clinical Sciences Building, Parkville, VIC 3050, Australia; (M.M.); (Y.C.); (J.I.); (A.F.T.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211806, China
| | - Josephine Iaria
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, 5th Floor Clinical Sciences Building, Parkville, VIC 3050, Australia; (M.M.); (Y.C.); (J.I.); (A.F.T.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211806, China
| | - Adilson Fonseca Teixeira
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, 5th Floor Clinical Sciences Building, Parkville, VIC 3050, Australia; (M.M.); (Y.C.); (J.I.); (A.F.T.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211806, China
| | - Hong-Jian Zhu
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, 5th Floor Clinical Sciences Building, Parkville, VIC 3050, Australia; (M.M.); (Y.C.); (J.I.); (A.F.T.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211806, China
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Xiao R, Hu S, Du X, Wang Y, Fang K, Zhu Y, Lou N, Yuan C, Yang J. Revolutionizing Senescence Detection: Advancements from Traditional Methods to Cutting-Edge Techniques. Aging Dis 2024:AD.202.0565. [PMID: 39012669 DOI: 10.14336/ad.202.0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
The accumulation of senescent cells is an important factor in the complex progression of aging, with significant implications for the development of numerous diseases. Thus, understanding the fundamental mechanisms of senescence is paramount for advancing preventive and therapeutic approaches to age-related conditions. Important to this pursuit is the precise identification and examination of senescent cells, contingent upon the recognition of specific biomarkers. Historically, detection methods relied on assessing molecular protein and mRNA levels and various staining techniques. While these conventional approaches have contributed substantially to the field, they possess limitations in capturing the dynamic evolution of cellular aging in real time. The emergence of novel technologies has led to a paradigm shift in senescence research. Gene-edited mouse models and the application of advanced probes have revolutionized our ability to detect senescent cells. These cutting-edge methodologies provide a more detailed and accurate means of dynamically monitoring, characterizing and potentially eliminating senescent cells, thus enhancing our understanding of the complex mechanisms of aging. This review comprehensively explores both traditional and innovative senescent cell detection methods, elucidating their advantages, limitations and implications for future investigations and could serve as a comprehensive guide and catalyst for further advancements in the understanding of aging and associated pathologies.
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10
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Maniego J, Harding C, Habershon-Butcher J, Hincks P, Ryder E. Administration and detection of a multi-target rAAV gene doping vector in horses using multiple matrices and molecular techniques. Gene Ther 2024:10.1038/s41434-024-00462-0. [PMID: 38972888 DOI: 10.1038/s41434-024-00462-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Gene doping, which includes the non-therapeutic use of genes or genetic elements that have the capacity to enhance athletic performance, is prohibited in horseracing and equestrian sports. To provide a comprehensive assessment of matrix and detection techniques, a custom adeno-associated virus serotype 8 vector was designed to include PCR binding sites for multiple target genes and assay types. The vector was injected via an intramuscular route into two Thoroughbred horses and matrices collected at defined timepoints. DNA was analysed using 3 detection methods: qPCR, digital PCR, and NGS. Overall, there was a strong correlation across the different detection methods employed, although digital PCR was less sensitive at lower concentrations. High concentrations of vector were detected at early timepoints in plasma and whole blood, which rapidly dropped after 0.5 d to trace levels by 4 d and 9 d post-administration respectively, following a similar pattern to previous studies. Vector was detected in dried blood spots at lower levels than whole blood, but with a similar detection time. Detection in hair root bulbs in one horse was observed at over a month post-administration, which opens new avenues for future gene doping testing in humans and animals.
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Affiliation(s)
- Jillian Maniego
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, CB7 5WW, UK
| | - Caitlin Harding
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, CB7 5WW, UK
| | | | - Pamela Hincks
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, CB7 5WW, UK
| | - Edward Ryder
- Sport and Specialised Analytical Services, LGC, Newmarket Road, Fordham, Cambridgeshire, CB7 5WW, UK.
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11
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Spielbauer J, Glotfelty EJ, Sarlus H, Harris RA, Diaz Heijtz R, Karlsson TE. Bacterial peptidoglycan signalling in microglia: Activation by MDP via the NF-κB/MAPK pathway. Brain Behav Immun 2024; 121:43-55. [PMID: 38971207 DOI: 10.1016/j.bbi.2024.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024] Open
Abstract
Bacterial peptidoglycan (PGN) fragments are commonly studied in the context of bacterial infections. However, PGN fragments recently gained recognition as signalling molecules from the commensal gut microbiota in the healthy host. Here we focus on the minimal bioactive PGN motif muramyl dipeptide (MDP), found in both Gram-positive and Gram-negative commensal bacteria, which signals through the Nod2 receptor. MDP from the gut microbiota translocates to the brain and is associated with changes in neurodevelopment and behaviour, yet there is limited knowledge about the underlying mechanisms. In this study we demonstrate that physiologically relevant doses of MDP induce rapid changes in microglial gene expression and lead to cytokine and chemokine secretion. In immortalised microglial (IMG) cells, C-C Motif Chemokine Ligand 5 (CCL5/RANTES) expression is acutely sensitive to the lowest physiologically prevalent dose (0.1 µg/ml) of MDP. As CCL5 plays an important role in memory formation and synaptic plasticity, microglial CCL5 might be the missing link in elucidating MDP-induced alterations in synaptic gene expression. We observed that a higher physiological dose of MDP elevates the expression of cytokines TNF-α and IL-1β, indicating a transition toward a pro-inflammatory phenotype in IMG cells, which was validated in primary microglial cultures. Furthermore, MDP induces the translocation of NF-κB subunit p65 into the nucleus, which is blocked by MAPK p38 inhibitor SB202190, suggesting that an interplay of both the NF-κB and MAPK pathways is responsible for the MDP-specific microglial phenotype. These findings underscore the significance of different MDP levels in shaping microglial function in the CNS and indicate MDP as a potential mediator for early inflammatory processes in the brain. It also positions microglia as an important target in the gut microbiota-brain-axis pathway through PGN signalling.
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Affiliation(s)
- Julia Spielbauer
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Elliot J Glotfelty
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Heela Sarlus
- Department of Clinical Neuroscience, Karolinska Institutet, Centre for Molecular Medicine, Karolinska Hospital at Solna, 171 77 Stockholm, Sweden
| | - Robert A Harris
- Department of Clinical Neuroscience, Karolinska Institutet, Centre for Molecular Medicine, Karolinska Hospital at Solna, 171 77 Stockholm, Sweden
| | | | - Tobias E Karlsson
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
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12
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Wang H, Cheng Z, Luo R, Yang Q, Zeng Y, Yang Y, Chen Y, Li W, Liu X. RPA-CRISPR-Cas13a-assisted detection method of transmissible gastroenteritis virus. Front Vet Sci 2024; 11:1428591. [PMID: 39015106 PMCID: PMC11249537 DOI: 10.3389/fvets.2024.1428591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
Background and aim Transmissible gastroenteritis virus (TGEV) is a highly contagious gastrointestinal virus that causes diarrhea, vomiting, anorexia, dehydration, and weight loss in piglets. In clinical practice, it often occurs in mixed infections with other pathogens, and is therefore difficult to diagnose and prevent. It mainly harms piglets of about 2 weeks old, causing huge losses on farms. The clinical confirmation of TGEV usually requires a laboratory diagnosis, but traditional PCR and immunofluorescence assays have some limitations. Moreover, most farms in China are ill-equipped to accurately diagnose the disease. Therefore, a new detection method with high sensitivity and specificity and less dependence on instrumentation is required. Methods We used recombinase polymerase amplification (RPA), combined with the nuclease characteristics of the activated Cas13a protein to establish a visual CRISPR-Cas13a-assisted detection method for TGEV by adding a reporter RNA with fluorescent and quenching moieties to the system. Result We selected the optimal RPA primer and best CRISPR RNA (crRNA). The reaction system was optimized and its repeatability, specificity, and sensitivity verified. The TGEV detection system did not cross-react with other common diarrhea viruses, and its detection limit was 101 copies, which is similar with the sensitivity of qPCR. We successfully established an RPA-CRISPR-Cas13a-assisted detection method, and used this detection system to analyze 123 pig blood samples. qPCR was used as the gold standard method. The sensitivity, specificity, positive coincidence rate, and negative coincidence rate of the new method were 100, 98.93, 96.66, and 100%, respectively.
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Affiliation(s)
- Haoyu Wang
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Zhimeng Cheng
- Division of Biliary Tract Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ran Luo
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Qiyue Yang
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Yongping Zeng
- Southwest University, College of Veterinary Medicine, Chongqing, China
| | - Yijun Yang
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yuankun Chen
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Wenting Li
- Department of Infectious and Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiao Liu
- Southwest University, College of Veterinary Medicine, Chongqing, China
- State Key Laboratory of Silkworm Genome Biology, Chongqing, China
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13
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Moir RD, Merheb E, Chitu V, Richard Stanley E, Willis IM. Molecular basis of neurodegeneration in a mouse model of Polr3-related disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571310. [PMID: 38168294 PMCID: PMC10760057 DOI: 10.1101/2023.12.12.571310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pathogenic variants in subunits of RNA polymerase (Pol) III cause a spectrum of Polr3-related neurodegenerative diseases including 4H leukodystrophy. Disease onset occurs from infancy to early adulthood and is associated with a variable range and severity of neurological and non-neurological features. The molecular basis of Polr3-related disease pathogenesis is unknown. We developed a postnatal whole-body mouse model expressing pathogenic Polr3a mutations to examine the molecular mechanisms by which reduced Pol III transcription results primarily in central nervous system phenotypes. Polr3a mutant mice exhibit behavioral deficits, cerebral pathology and exocrine pancreatic atrophy. Transcriptome and immunohistochemistry analyses of cerebra during disease progression show a reduction in most Pol III transcripts, induction of innate immune and integrated stress responses and cell type-specific gene expression changes reflecting neuron and oligodendrocyte loss and microglial activation. Earlier in the disease when integrated stress and innate immune responses are minimally induced, mature tRNA sequencing revealed a global reduction in tRNA levels and an altered tRNA profile but no changes in other Pol III transcripts. Thus, changes in the size and/or composition of the tRNA pool have a causal role in disease initiation. Our findings reveal different tissue- and brain region-specific sensitivities to a defect in Pol III transcription.
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Affiliation(s)
- Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - Emilio Merheb
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - Violeta Chitu
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - E. Richard Stanley
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx NY 10461, USA
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14
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024; 20:767-798. [PMID: 38755290 PMCID: PMC11219738 DOI: 10.1038/s44320-024-00039-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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15
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Cunha-Oliveira T, Ioannidis JPA, Oliveira PJ. Best practices for data management and sharing in experimental biomedical research. Physiol Rev 2024; 104:1387-1408. [PMID: 38451234 DOI: 10.1152/physrev.00043.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building on results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers' careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers.
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Affiliation(s)
- Teresa Cunha-Oliveira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - John P A Ioannidis
- Meta-Research Innovation Center at Stanford (METRICS), Stanford, California, United States
- Department of Statistics, Stanford University, Stanford, California, United States
| | - Paulo J Oliveira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
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16
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Wetthasinghe L, Ng HF, Ngeow YF, Chew KS, Lee WS. Navigating the intricacies of RT-qPCR data analysis in gene expression studies. Funct Integr Genomics 2024; 24:115. [PMID: 38910215 DOI: 10.1007/s10142-024-01393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Affiliation(s)
- Linah Wetthasinghe
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
| | - Hien Fuh Ng
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia.
| | - Yun Fong Ngeow
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Kuala Lumpur, 50603, Malaysia
| | - Way Seah Lee
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
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17
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Fonseca Júnior AA, Laguardia-Nascimento M, Barbosa AAS, da Silva Gonçalves VL, Camargos MF. Interfering factors in the diagnosis of Senecavirus A. Mol Biol Rep 2024; 51:777. [PMID: 38904698 DOI: 10.1007/s11033-024-09692-2] [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: 02/20/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Senecavirus A (SV-A) is an RNA virus that belongs to the genus Senecavirus within the family Picornaviridae. This study aimed to analyze factors that can influence the molecular diagnosis of Senecavirus A, such as oligonucleotides, RNA extraction methods, and RT-qPCR kits. METHODS Samples from suspected cases of vesicular disease in Brazilian pigs were analyzed for foot-and-mouth disease, swine vesicular disease, and vesicular stomatitis. All tested negative for these diseases but positive for SV-A. RT-qPCR tests were used, comparing different reagent kits and RNA extraction methods. Sensitivity and repeatability were evaluated, demonstrating efficacy in detecting SV-A in clinical samples. RESULTS In RNA extraction, significant reduction in Cq values was observed with initial dilutions, particularly with larger supernatant volumes. Trizol and Maxwell showed greater sensitivity in automated equipment protocols, though results varied in tissue tests. RT-qPCR kit comparison revealed differences in amplification using viral RNA but minimal differences with plasmid DNA. Sensitivity among methods was comparable, with slight variations in non-amplified samples. Repeatability tests showed consistent results among RT-qPCRs, demonstrating similarity between methods despite minor discrepancies in Cq values. CONCLUSIONS Trizol, silica columns, and semi-automated extraction were compared, as well as different RT-qPCR kits. The study found significant variations that could impact the final diagnosis.
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18
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Dolgova AS, Kanaeva OI, Antonov SA, Shabalina AV, Klyuchnikova EO, Sbarzaglia VA, Gladkikh AS, Ivanova OE, Kozlovskaya LI, Dedkov VG. Qualitative real-time RT-PCR assay for nOPV2 poliovirus detection. J Virol Methods 2024; 329:114984. [PMID: 38885908 DOI: 10.1016/j.jviromet.2024.114984] [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: 03/27/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
Based on the success of the Sabin2-based vaccine, a next-generation nOPV2 poliovirus vaccine has been developed. For epidemic monitoring and conducting epidemiological investigations, it is necessary to have a diagnostic assay with the ability to differentiate this variant from others. Here we describe such a real-time RT-PCR assay. The region with the cre insertion in the 5'-UTR was chosen as the target, and the limit of detection was 103 copies/mL (2.5×103 copies/mL using Probit analysis) determined using armored RNA particles. Sensitivity and specificity were 86.28 - 100 % and 76.84 - 100 %, respectively (with 95 % CI). Thus, this method can be effectively used when it is necessary to make a differential diagnosis of poliovirus strains.
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Affiliation(s)
- A S Dolgova
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia.
| | - O I Kanaeva
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - S A Antonov
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - A V Shabalina
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - E O Klyuchnikova
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - V A Sbarzaglia
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - A S Gladkikh
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia
| | - O E Ivanova
- Federal State Autonomous Scientific Institution "Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences" (Institute of Poliomyelitis), Moscow, Russia; Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - L I Kozlovskaya
- Federal State Autonomous Scientific Institution "Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences" (Institute of Poliomyelitis), Moscow, Russia; Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - V G Dedkov
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Saint Petersburg, Russia; Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
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19
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Liu J, Jin P, Li M, Yi X, Tian Y, Zhang Z, Liu J, Shi L. The energy metabolism of the freshwater leech Whitmania pigra in response to fasting. Comp Biochem Physiol B Biochem Mol Biol 2024; 274:110999. [PMID: 38852903 DOI: 10.1016/j.cbpb.2024.110999] [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: 11/21/2023] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024]
Abstract
Non-blood-feeding leeches, Whitmania pigra, have evolved unique digestive structures and physiological mechanisms to cope with fasting. However, the metabolic changes and molecular mechanisms induced by fasting remain unclear. Therefore, this study recorded the weights of leeches during the fasting process. The weight changes were divided into two stages: a rapid decline period (1-9 weeks) and a fluctuating decline period (9-24 weeks). Leeches fasted for 4 (H4), 11 (H11), and 24 (H24) weeks were selected for transcriptome sequencing. Compared to the control group (H0), 436, 1157, and 337 differentially expressed genes (DEGs) were identified, which were mainly related to glycolysis/gluconeogenesis, amino acid metabolism, and the lipid metabolism pathway. The 6-phosphofructokinase (Pfk), pyruvate kinase (PK), and phosphoenolpyruvate carboxykinase (Pck) transcription levels revealed glycolysis/gluconeogenesis activation during the early stage of fasting and peaked at 11 weeks. Decreased expression of the rate-limiting enzyme acetyl-CoA carboxylase (ACC) in fatty acid synthesis during fasting may impede fatty acid synthesis. These results indicated that the nutrient storage and energy-supplying pathways in W. pigra were modified to improve fasting resistance. The findings of this study provided guidance for exploring the mechanism underlying fasting metabolism and laid a foundation for artificial breeding to improve the resistance of leeches.
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Affiliation(s)
- Jiali Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Panpan Jin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Mingyue Li
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xiaozhe Yi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yu Tian
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, 067000, China
| | - Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, 067000, China
| | - Jinxin Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Linchun Shi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
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20
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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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21
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Chen K, He Y, Wang W, Yuan X, Carbone DP, Yang F. Development of new techniques and clinical applications of liquid biopsy in lung cancer management. Sci Bull (Beijing) 2024; 69:1556-1568. [PMID: 38641511 DOI: 10.1016/j.scib.2024.03.062] [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: 09/25/2023] [Revised: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 04/21/2024]
Abstract
Lung cancer is an exceedingly malignant tumor reported as having the highest morbidity and mortality of any cancer worldwide, thus posing a great threat to global health. Despite the growing demand for precision medicine, current methods for early clinical detection, treatment and prognosis monitoring in lung cancer are hampered by certain bottlenecks. Studies have found that during the formation and development of a tumor, molecular substances carrying tumor-related genetic information can be released into body fluids. Liquid biopsy (LB), a method for detecting these tumor-related markers in body fluids, maybe a way to make progress in these bottlenecks. In recent years, LB technology has undergone rapid advancements. Therefore, this review will provide information on technical updates to LB and its potential clinical applications, evaluate its effectiveness for specific applications, discuss the existing limitations of LB, and present a look forward to possible future clinical applications. Specifically, this paper will introduce technical updates from the prospectives of engineering breakthroughs in the detection of membrane-based LB biomarkers and other improvements in sequencing technology. Additionally, it will summarize the latest applications of liquid biopsy for the early detection, diagnosis, treatment, and prognosis of lung cancer. We will present the interconnectedness of clinical and laboratory issues and the interplay of technology and application in LB today.
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Affiliation(s)
- Kezhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Yue He
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing 100191, China
| | - David P Carbone
- Thoracic Oncology Center, Ohio State University, Columbus 43026, USA.
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China.
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22
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Colombino E, Gariglio M, Biasato I, Ferrocino I, Pozzo S, Fragola E, Battisti E, Zanet S, Ferroglio E, Capucchio MT, Schiavone A. Insect live larvae as a new nutritional model in duck: effects on gut health. Anim Microbiome 2024; 6:31. [PMID: 38812012 PMCID: PMC11137933 DOI: 10.1186/s42523-024-00316-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND This study aimed to evaluate the effects of Hermetia illucens (Black soldier fly-BSF) and Tenebrio molitor (Yellow mealworm-YMW) live larvae as a new nutritional model on duck's gut health, considering gut histomorphometry, mucin composition, cytokines transcription levels, and microbiota. A total of 126, 3-days-old, females Muscovy ducks were randomly allotted to three dietary treatments (6 replicates/treatment, 7 birds/pen): (i) C: basal diet; (ii) BSF: C + BSF live larvae; (iii) YMW: C + YMW live larvae. BSF and YMW live larvae were administered on top of the basal diet, based on the 5% of the expected daily feed intake. The live weight, average daily gain, average daily feed intake and feed conversion ratio were evaluated for the whole experimental period. On day 52, 12 ducks/treatment (2 birds/replicate) were slaughtered and samples of duodenum, jejunum, ileum, spleen, liver, thymus and bursa of Fabricius were collected for histomorphometry. Mucin composition was evaluated in the small intestine through histochemical staining while jejunal MUC-2 and cytokines transcription levels were evaluated by rt-qPCR. Cecal microbiota was also analyzed by means of 16 S rRNA gene sequencing. RESULTS Birds' growth performance and histomorphometry were not influenced by diet, with a proximo-distal decreasing gradient from duodenum to ileum (p < 0.001), respecting the physiological gut development. Mucin staining intensity and MUC-2 gene expression did not vary among dietary treatments, even though mucin intensity increased from duodenum to ileum, according to normal gut mucus physiology (p < 0.001). Regarding local immune response, IL-6 was higher in YMW group when compared to the other groups (p = 0.009). Insect live larvae did not affect cecal microbiota diversity, but BSF and YMW groups showed a higher presence of Helicobacter, Elusimicrobium, and Succinatimonas and a lower abundance of Coriobacteriaceae and Phascolarctobacterium compared to C birds (p < 0.05). CONCLUSIONS The use of BSF and YMW live larvae as new nutritional model did not impair gut development and mucin composition of Muscovy ducks, but slightly improved the intestinal immune status and the microbiota composition by enhancing regulatory cytokine IL-6 and by increasing minor Operational Taxonomic Units (OTUs) involved in short-chain fatty acids production.
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Affiliation(s)
- Elena Colombino
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Marta Gariglio
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy.
| | - Ilaria Biasato
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Sara Pozzo
- National Research Council, Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Milano, 20133, MI, Italy
| | - Emma Fragola
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Elena Battisti
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Stefania Zanet
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Ezio Ferroglio
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Maria Teresa Capucchio
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
- National Research Council, Institute of Science of Food Production, Grugliasco, 10095, TO, Italy
| | - Achille Schiavone
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
- National Research Council, Institute of Science of Food Production, Grugliasco, 10095, TO, Italy
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23
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Vargas-Barona A, Bernáldez-Sarabia J, Castro-Ceseña AB. Lipid-polymer hybrid nanoparticles loaded with N-acetylcysteine for the modulation of neuroinflammatory biomarkers in human iPSC-derived PSEN2 (N141I) astrocytes as a model of Alzheimer's disease. J Mater Chem B 2024; 12:5085-5097. [PMID: 38713059 DOI: 10.1039/d4tb00521j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by cognitive impairment associated with the accumulation of beta-amyloid protein (Aβ). Aβ activates glial cells in the brain, increasing the secretion of proinflammatory cytokines, which leads to neuroinflammation and neuronal death. Currently, there are no effective treatments that cure or stop its progression; therefore, AD is considered a global health priority. The main limitations are the low drug bioavailability and impermeability of the blood-brain barrier (BBB). Fortunately, nanomedicine has emerged as a promising field for the development of new nanosystems for the controlled and targeted delivery of drugs to the brain. Therefore, in this work, lipid-polymer hybrid nanoparticles (LPHNPs) conjugated with transferrin (Tf) to facilitate crossing the BBB and loaded with N-acetylcysteine (NAC) for its anti-inflammatory effect were synthesized, and their physicochemical characterization was carried out. Subsequently, an in vitro model involving human astrocytes derived from induced pluripotent stem cells (iPSC) from an AD-diagnosed patient was developed, which was brought to a reactive state by stimulation with lipopolysaccharides (LPSs). The cell culture was treated with either Tf-conjugated LPHNPs loaded with NAC (NAC-Tf-LPHNPs) at 0.25 mg mL-1, or free NAC at 5 mM. The results showed that NAC-Tf-LPHNPs favorably modulated the expression of proinflammatory genes such as interleukin-1β (IL-1β), amyloid precursor protein (APP) and glial fibrillary acidic protein (GFAP). In addition, they reduced the secretion of the proinflammatory cytokines interleukin 6 (IL-6), IL-1β and interferon-gamma (INF-γ). Results for both cases were compared to the group of cells that did not receive any treatment. In contrast, free NAC only had this effect on the expression of IL-1β and the secretion of the cytokines IL-6 and INF-γ. These results indicate the potential of NAC-Tf-LPHNPs for AD treatment.
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Affiliation(s)
- Alondra Vargas-Barona
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada- Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
| | - Johanna Bernáldez-Sarabia
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada- Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
| | - Ana B Castro-Ceseña
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada- Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
- CONAHCYT-Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico
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24
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Zhao X, He Y, Shao S, Ci Q, Chen L, Lu X, Liu Q, Chen J. CRISPR/Cas14 and G-Quadruplex DNAzyme-Driven Biosensor for Paper-Based Colorimetric Detection of African Swine Fever Virus. ACS Sens 2024; 9:2413-2420. [PMID: 38635911 PMCID: PMC11216275 DOI: 10.1021/acssensors.4c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The highly contagious nature and 100% fatality rate contribute to the ongoing and expanding impact of the African swine fever virus (ASFV), causing significant economic losses worldwide. Herein, we developed a cascaded colorimetric detection using the combination of a CRISPR/Cas14a system, G-quadruplex DNAzyme, and microfluidic paper-based analytical device. This CRISPR/Cas14a-G4 biosensor could detect ASFV as low as 5 copies/μL and differentiate the wild-type and mutated ASFV DNA with 2-nt difference. Moreover, this approach was employed to detect ASFV in porcine plasma. A broad linear detection range was observed, and the limit of detection in spiked porcine plasma was calculated to be as low as 42-85 copies/μL. Our results indicate that the developed paper platform exhibits the advantages of high sensitivity, excellent specificity, and low cost, making it promising for clinical applications in the field of DNA disease detection and suitable for popularization in low-resourced areas.
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Affiliation(s)
- Xue Zhao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shengjie Shao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Qiaoqiao Ci
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lin Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
| | - Xiaonan Lu
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Qian Liu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Bioengineering, University of California, Riverside, California 92521, United States
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25
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Pan Y, Zhao Y, Zeng HR, Wu JQ, Song YY, Rao YH, Li GQ, Jin L. Reference Genes for Expression Analyses by qRT-PCR in Enterobacter cancerogenus. Microorganisms 2024; 12:1024. [PMID: 38792853 PMCID: PMC11123693 DOI: 10.3390/microorganisms12051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
The Enterobacter cancerogenus strain EcHa1 was isolated from the dead larvae of Helicoverpa armigera, and has the potential for biocontrol of some Lepidoptera insects. In order to screen insecticidal-related genes by qRT-PCR, stable endogenous reference genes used for normalizing qRT-PCR data were selected and evaluated from 13 housekeeping genes (HKGs). The expression levels of the HKGs were determined using qRT-PCR under different experimental conditions, including two culture temperatures and three bacterial OD values. Five stability analysis methods (Ct, BestKeeper, NormFinder, geNorm, and RefFinder) were used to comprehensively rank the candidate genes. The results showed that the optimal reference genes varied under different experimental conditions. The combination of gyrA and gyrB was recommended as the best reference gene combination at 28 °C, while gyrA and rpoB was the best combination at 37 °C. When the OD values were 0.5, 1.0 and 2.0, the recommended reference gene combinations were ftsZ and gyrA, rpoB and gyrB, and gyrA and pyk, respectively. The most suitable reference genes were gyrA and gyrB under all experimental conditions. Using gyrA and gyrB as the reference genes for qRT-PCR, EcHa1 was found to invade all tissues of the H. armigera larvae, and expressed a candidate pathogenic factor Hcp at high levels in gut, Malpighian tubules, and epidermis tissues. This study not only establishes an accurate and reliable normalization for qRT-PCR in entomopathogenic bacteria but also lays a solid foundation for further study of functional genes in E. cancerogenus.
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Affiliation(s)
| | | | | | | | | | | | | | - Lin Jin
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.P.); (Y.Z.); (H.-R.Z.); (J.-Q.W.); (Y.-Y.S.); (Y.-H.R.); (G.-Q.L.)
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26
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Schwanke D, Schüle S, Stewart S, Fatanmi OO, Wise SY, Hackenbroch C, Wiegel T, Singh VK, Port M, Abend M, Ostheim P. Validating a Four-gene Set for H-ARS Severity Prediction in Peripheral Blood Samples of Irradiated Rhesus Macaques. Radiat Res 2024; 201:504-513. [PMID: 38471521 DOI: 10.1667/rade-23-00162.1] [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: 08/11/2023] [Accepted: 10/26/2023] [Indexed: 03/14/2024]
Abstract
Increased radiological and nuclear threats require preparedness. Our earlier work identified a set of four genes (DDB2, FDXR, POU2AF1 and WNT3), which predicts severity of the hematological acute radiation syndrome (H-ARS) within the first three days postirradiation In this study of 41 Rhesus macaques (Macaca mulatta, 27 males, 14 females) irradiated with 5.8-7.2 Gy (LD29-50/60), including some treated with gamma-tocotrienol (GT3, a radiation countermeasure) we independently validated these genes as predictors in both sexes and examined them after three days. At the Armed Forces Radiobiology Research Institute/Uniformed Services University of the Health Sciences, peripheral whole blood (1 ml) of Rhesus macaques was collected into PAXgene® Blood RNA tubes pre-irradiation after 1, 2, 3, 35 and 60 days postirradiation, stored at -80°C for internal experimental analyses. Leftover tubes from these already ongoing studies were kindly provided to Bundeswehr Institute of Radiobiology. RNA was isolated (QIAsymphony), converted into cDNA, and for further gene expression (GE) studies quantitative RT-PCR was performed. Differential gene expression (DGE) was measured relative to the pre-irradiation Rhesus macaques samples. Within the first three days postirradiation, we found similar results to human data: 1. FDXR and DDB2 were up-regulated, FDXR up to 3.5-fold, and DDB2 up to 13.5-fold in the median; 2. POU2AF1 appeared down regulated around tenfold in nearly all Rhesus macaques; 3. Contrary to human data, DDB2 was more up-regulated than FDXR, and the difference of the fold change (FC) ranged between 2.4 and 10, while the median fold changes of WNT3, except days 1 and 35, were close to 1. Nevertheless, 46% of the Rhesus macaques showed down-regulated WNT3 on day one postirradiation, which decreased to 12.2% on day 3 postirradiation. Considering the extended phase, there was a trend towards decreased fold changes at day 35, with median-fold changes ranging from 0.7 for DDB2 to 0.1 for POU2AF1, and on day 60 postirradiation, DGE in surviving animals was close to pre-exposure values for all four genes. In conclusion, the diagnostic significance for radiation-induced H-ARS severity prediction of FDXR, DDB2, and POU2AF1 was confirmed in this Rhesus macaques model. However, DDB2 showed higher GE values than FDXR. As shown in previous studies, the diagnostic significance of WNT3 could not be reproduced in Rhesus macaques; this could be due to the choice of animal model and methodological challenges.
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Affiliation(s)
- D Schwanke
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - S Schüle
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - S Stewart
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - O O Fatanmi
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, and
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - S Y Wise
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, and
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - C Hackenbroch
- Department of Radiology, Bundeswehrkrankenhaus Ulm, Ulm Germany
| | - T Wiegel
- Department of Radiation Oncology, University Hospital, Ulm, Germany
| | - V K Singh
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, and
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - M Port
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - M Abend
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - P Ostheim
- Bundeswehr Institute of Radiobiology, Munich, Germany
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27
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Wang D, Trimbos KB, Gomes SIF, Jacquemyn H, Merckx VSFT. Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR. THE NEW PHYTOLOGIST 2024; 242:1825-1834. [PMID: 37929750 DOI: 10.1111/nph.19385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.
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Affiliation(s)
- Deyi Wang
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, 2333 CC, Leiden University, Leiden, the Netherlands
| | - Sofia I F Gomes
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, 3001, Leuven, Belgium
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
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28
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Schwanke D, Fatanmi OO, Wise SY, Ostheim P, Schüle S, Kaletka G, Stewart S, Wiegel T, Singh VK, Port M, Abend M. Validating Radiosensitivity with Pre-Exposure Differential Gene Expression in Peripheral Blood Predicting Survival and Non-Survival in a Second Irradiated Rhesus Macaque Cohort. Radiat Res 2024; 201:384-395. [PMID: 38282135 DOI: 10.1667/rade-23-00099.1] [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: 06/02/2023] [Accepted: 09/27/2023] [Indexed: 01/30/2024]
Abstract
Radiosensitivity differs in humans and possibly in closely related nonhuman primates. The reasons for variation in radiosensitivity are not well known. In an earlier study, we examined gene expression (GE) pre-radiation in peripheral blood among male (n = 62) and female (n = 60) rhesus macaques (n = 122), which did or did not survive (up to 60 days) after whole-body exposure of 7.0 Gy (LD66/60). Eight genes (CHD5, CHI3L1, DYSF, EPX, IGF2BP1, LCN2, MBOAT4, SLC22A4) revealed significant associations with survival. Access to a second rhesus macaque cohort (males = 40, females = 23, total n = 63) irradiated with 5.8-7.2 Gy (LD29-50/60) and some treated with gamma-tocotrienol (GT3, a radiation countermeasure) allowed us to validate these gene expression changes independently. Total RNA was isolated from whole blood samples and examined by quantitative RT-PCR on a 96-well format. cycle threshold (Ct)-values normalized to 18S rRNA were analyzed for their association with survival. Regardless of the species-specific TaqMan assay, similar results were obtained. Two genes (CHD5 and CHI3L1) out of eight revealed a significant association with survival in the second cohort, while only CHD5 (involved in DNA damage response and proliferation control) showed mean gene expression changes in the same direction for both cohorts. No expected association of CHD5 GE with dose, treatment, or sex could be established. Instead, we observed significant associations for those comparisons comprising pre-exposure samples with CHD5 Ct values ≤ 11 (total n = 17). CHD5 Ct values ≤ 11 in these comparisons were mainly associated with increased frequencies (61-100%) of non-survivors, a trend which depending on the sample numbers, reached significance (P = 0.03) in males and, accordingly, in females. This was also reflected by a logistic regression model including all available samples from both cohorts comprising CHD5 measurements (n = 104, odds ratio 1.38, 95% CI 1.07-1.79, P = 0.01). However, this association was driven by males (odds ratio 1.62, 95% CI 1.10-2.38, P = 0.01) and CHD5 Ct values ≤ 11 since removing low CHD5 Ct values from this model, converted to insignificance (P = 0.19). A second male subcohort comprising high CHD5 Ct values ≥ 14.4 in both cohorts (n = 5) appeared associated with survival. Removing these high CHD5 Ct values converted the model borderline significant (P = 0.051). Based on the probability function of the receiver operating characteristics (ROC) curves, 8 (12.3%) and 5 (7.7%) from 65 pre-exposure RNA measurements in males, death and survival could be predicted with a negative and positive predictive value ranging between 85-100%. An associated odds ratio reflected a 62% elevated risk for dying or surviving per unit change (Ct-value) in gene expression, considering the before-mentioned CHD5 thresholds in RNA copy numbers. In conclusion, we identified two subsets of male animals characterized by increased (Ct values ≤ 11) and decreased (Ct values ≥ 14.4) CHD5 GE copy numbers before radiation exposure, which independently of the cohort, radiation exposure or treatment appeared to predict the death or survival in males.
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Affiliation(s)
- D Schwanke
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - O O Fatanmi
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, and
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - S Y Wise
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, and
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - P Ostheim
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - S Schüle
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - G Kaletka
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - S Stewart
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - T Wiegel
- Department of Radiation Oncology, University Hospital, Ulm, Germany
| | - V K Singh
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, and
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - M Port
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - M Abend
- Bundeswehr Institute of Radiobiology, Munich, Germany
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29
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Regon P, Saha B, Jyoti SY, Gupta D, Kundu B, Tanti B, Panda SK. Transcriptional networks revealed late embryogenesis abundant genes regulating drought mitigation in aromatic Keteki Joha rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14348. [PMID: 38769068 DOI: 10.1111/ppl.14348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Climate change has become increasingly intertwined with the occurrence and severity of droughts. As global temperatures rise due to greenhouse gas emissions, weather patterns are altered, leading to shifts in precipitation levels and distribution. These exacerbate the risk of drought in many regions, with potentially devastating consequences. A comprehensive transcriptome analysis was performed on Keteki Joha, an aromatic rice from North East India, with the aim of elucidating molecular responses to drought. Numerous genes linked to drought were activated, with both ABA-dependent and ABA-independent pathways playing crucial roles. Upregulated genes were enriched with gene ontology terms with response to abscisic acid and abscisic acid-activated signalling pathway, suggesting the existence of an ABA-dependent pathway for drought mitigation. The upregulated genes were also enriched with responses to stress, water, heat, jasmonic acid, and hydrogen peroxide, indicating the presence of an ABA-independent pathway alongside the ABA-dependent mechanism. Weighted Correlation Network Analysis (WGCNA) identified 267 genes that specifically govern drought mitigation in Keteki Joha. The late embryogenesis abundant (LEA) gene family emerges as the most overrepresented in both RNA sequencing data and WGCNA analysis, suggesting their dominant role in mitigating drought. Notably, 31 LEA genes were induced in seedlings and 32 in mature stages under drought stress. The LEA3-1, LEA14/WSI18, RAB16A, RAB16B, DHN1, DHN6, LEA1, LEA3, LEA17, and LEA33 exhibited and established co-expression with numerous other drought stress-related genes, indicating their inseparable role in alleviating drought. Consequently, LEA genes have been proposed to be primary and crucial responders to drought in Keteki Joha.
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Affiliation(s)
- Preetom Regon
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Bedabrata Saha
- Plant Pathology and Weed Research Department, Newe Ya'ar Research Centre, Agricultural Research Organization, Israel
| | - Sabnoor Yeasrin Jyoti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Divya Gupta
- Plant Functional Genomics and Molecular Biology Laboratory, Department of Biochemistry, Central University of Rajasthan, Ajmer, Bandarsindri, Rajasthan, India
| | - Bikash Kundu
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Bhaben Tanti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Sanjib Kumar Panda
- Plant Functional Genomics and Molecular Biology Laboratory, Department of Biochemistry, Central University of Rajasthan, Ajmer, Bandarsindri, Rajasthan, India
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30
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Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan KK, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia. J Mol Diagn 2024; 26:349-363. [PMID: 38395408 PMCID: PMC11090205 DOI: 10.1016/j.jmoldx.2024.01.013] [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: 09/07/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires approximately 15 hours to detect the presence of a pathogen. We, therefore, assessed the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 17 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 88% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1-mL sample input and sample-to-answer time of 6 hours. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection.
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Affiliation(s)
- April Aralar
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Nanda Ramchandar
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California; Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Shelley M Lawrence
- Division of Neonatology, Department of Pediatrics, The University of Utah, Salt Lake City, Utah
| | | | | | | | - David T Pride
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Peiting Kuo
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Khrissa Lecrone
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Megan Chiu
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Karen K Mestan
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Eniko Sajti
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Michelle Vanderpool
- Department of Pathology and Laboratory Medicine, Rady Children's Hospital-San Diego, San Diego, California
| | - Sarah Lazar
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Melanie Crabtree
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Yordanos Tesfai
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, California.
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31
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Shen Y, Yang CT, Li W, Zhou X. Single-virus-sensitive barcode qPCR mediated by the aggregation of gold nanoparticle probes. Analyst 2024; 149:2556-2560. [PMID: 38587837 DOI: 10.1039/d4an00121d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Herein, we developed a gold nanoparticle (GNP)-mediated barcode qPCR strategy with a sensitivity for a single virus particle per reaction for the detection of influenza virus H3N2. The analysis of the results for pure virus and real virus samples show that GNP-mediated barcode qPCR is ∼16 times more sensitive than conventional qPCR, demonstrating the potential to reduce false negatives and improve early diagnosis of viral infections.
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Affiliation(s)
- Yuanzhao Shen
- College of Veterinary Medicine, Institute of Comparative Medicine, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| | - Chih-Tsung Yang
- Future Industries Institute, University of South Australia, Mawson Lakes Blvd, Mawson Lakes, South Australia 5095, Australia
| | - Weiwei Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai 201102, China.
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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32
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Bhadra M, Sachan M, Nara S. Current strategies for early epithelial ovarian cancer detection using miRNA as a potential tool. Front Mol Biosci 2024; 11:1361601. [PMID: 38690293 PMCID: PMC11058280 DOI: 10.3389/fmolb.2024.1361601] [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: 12/26/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Ovarian cancer is one of the most aggressive and significant malignant tumor forms in the female reproductive system. It is the leading cause of death among gynecological cancers owing to its metastasis. Since its preliminary disease symptoms are lacking, it is imperative to develop early diagnostic biomarkers to aid in treatment optimization and personalization. In this vein, microRNAs, which are short sequence non-coding molecules, displayed great potential as highly specific and sensitive biomarker. miRNAs have been extensively advocated and proven to serve an instrumental part in the clinical management of cancer, especially ovarian cancer, by promoting the cancer cell progression, invasion, delayed apoptosis, epithelial-mesenchymal transition, metastasis of cancer cells, chemosensitivity and resistance and disease therapy. Here, we cover our present comprehension of the most up-to-date microRNA-based approaches to detect ovarian cancer, as well as current diagnostic and treatment strategies, the role of microRNAs as oncogenes or tumor suppressor genes, and their significance in ovarian cancer progression, prognosis, and therapy.
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33
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Grosjean N, Blaudez D, Chalot M, Flayac J, Gross EM, Le Jean M. Rare earth elements perturb root architecture and ion homeostasis in Arabidopsis thaliana. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133701. [PMID: 38364576 DOI: 10.1016/j.jhazmat.2024.133701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
Rare earth elements (REEs) are crucial elements for current high-technology and renewable energy advances. In addition to their increasing usage and their low recyclability leading to their release into the environment, REEs are also used as crop fertilizers. However, little is known regarding the cellular and molecular effects of REEs in plants, which is crucial for better risk assessment, crop safety and phytoremediation. Here, we analysed the ionome and transcriptomic response of Arabidopsis thaliana exposed to a light (lanthanum, La) and a heavy (ytterbium, Yb) REE. At the transcriptome level, we observed the contribution of ROS and auxin redistribution to the modified root architecture following REE exposure. We found indications for the perturbation of Fe homeostasis by REEs in both roots and leaves of Arabidopsis suggesting competition between REEs and Fe. Furthermore, we propose putative ways of entry of REEs inside cells through transporters of microelements. Finally, similar to REE accumulating species, organic acid homeostasis (e.g. malate and citrate) appears critical as a tolerance mechanism in response to REEs. By combining ionomics and transcriptomics, we elucidated essential patterns of REE uptake and toxicity response of Arabidopsis and provide new hypotheses for a better evaluation of the impact of REEs on plant homeostasis.
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Affiliation(s)
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France
| | - Michel Chalot
- Université de Franche-Comté, CNRS, Chrono-Environnement, F-25000 Montbéliard, France; Université de Lorraine, F-54000 Nancy, France
| | - Justine Flayac
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France
| | | | - Marie Le Jean
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France.
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34
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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35
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Mao Z, Qian Y, Liu Z, Shi Y, Fan L, Zhang Q. LINC00158 modulates the function of BEAS-2B cells via targeting BCL11B and ameliorates OVA-LPS-induced severe asthma in mice models. Int Immunopharmacol 2024; 130:111739. [PMID: 38442574 DOI: 10.1016/j.intimp.2024.111739] [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: 12/04/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Persistent type (T) 2 airway inflammation plays an important role in the development of severe asthma. However, the molecular mechanisms leading to T2 severe asthma have yet to be fully clarified. Human normal lung epithelial cells (BEAS-2B cells) were transfected with LINC00158/BCL11B plasmid/small interfering RNA (siRNA). Levels of epithelial-mesenchymal transition (EMT)-related markers were measured using real-time qPCR (RT-qPCR) and western blot. A dual luciferase reporter assay was used to validate the targeting relationship between LINC00158 and BCL11B. The effects of LINC00158-lentivirus vector-mediated overexpression and dexamethasone on ovalbumin (OVA)/lipopolysaccharide (LPS)-induced severe asthma were investigated in mice in vivo. Our study showed that overexpression of LINC00158/BCL11B inhibited the levels of EMT-related proteins, apoptosis, and promoted the proliferation of BEAS-2B cells. BCL11B was a direct target of LINC00158. And LINC00158 targeted BCL11B to regulate EMT, apoptosis, and cell proliferation of BEAS-2B cells. Compared with severe asthma mice, LINC00158 overexpression alleviated OVA/LPS-induced airway hyperresponsiveness and airway inflammation, including reductions in T helper 2 cells factors in lung tissue and BALF, serum total- and OVA-specific IgE, inflammatory cell infiltration, and goblet cells hyperplasia. In addition, LINC00158 overexpression alleviated airway remodeling, including reduced plasma TGF-β1 and collagen fiber deposition, as well as suppression of EMT. Additionally, overexpression of LINC00158 enhanced the therapeutic effect of dexamethasone in severe asthmatic mice models. LINC00158 regulates BEAS-2B cell biological function by targeting BCL11B. LINC00158 ameliorates T2 severe asthma in vivo and provides new insights into the clinical treatment of severe asthma.
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Affiliation(s)
- Zhengdao Mao
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Yan Qian
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Zhiguang Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Yujia Shi
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Liang Fan
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Qian Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213003, China; Changzhou Medical Center, Nanjing Medical University, Changzhou 213003, China.
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36
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Yang L, Hu X, Ren M, Ma F, Fu J, Cui H. Stem-cell-expressed DEVIL-like small peptides maintain root growth under abiotic stress via abscisic acid signaling. PLANT PHYSIOLOGY 2024; 194:2372-2386. [PMID: 38096479 DOI: 10.1093/plphys/kiad659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 04/02/2024]
Abstract
Stem cells are essential to plant growth and development. Through data mining, we identified five DEVIL-like (DVL) small peptide genes that are preferentially expressed in the quiescent center of Arabidopsis (Arabidopsis thaliana) root but whose functions are unknown. When overexpressed, these genes caused a dramatic decrease in root length and pleiotropic phenotypes in the shoot. No root-growth defect was observed in the single-gene mutants, but the quintuple mutant exhibited slightly longer roots than the wild type (WT). Through transcriptome analysis with DVL20-overexpressing plants, we found that many genes involved in abscisic acid (ABA) signaling were regulated by these peptides. Consistent with this finding, we demonstrated that, relative to the WT, DVL20-overexpressing plants were more tolerant whereas the quintuple mutant was more sensitive to ABA. Using RT-qPCR, we showed that ABA signaling-associated genes were affected in an opposite manner when the plants were grown in normal or ABA-containing medium. Strikingly, ectopic expression of ABA signaling genes such as PYRABACTIN RESISTANCE 1-LIKE (PYL) 4, 5, or 6 or suppression of HIGHLY ABA-INDUCED 2 (HAI2) and MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 18 (MAPKKK18) not only largely rescued the root growth defects in DVL20-overexpressing plants in normal growth condition but also conferred tolerance to ABA. Based on these results, we propose that DVL1, 2, 5, 8 and 20 function redundantly in root stem-cell maintenance under abiotic stress, and this role is achieved via ABA signaling.
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Affiliation(s)
- Liyun Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaochen Hu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengfei Ren
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Ma
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Fu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Cui
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Thorn HI, Guruceaga X, Martin-Vicente A, Nywening AV, Xie J, Ge W, Fortwendel JR. MOB-mediated regulation of septation initiation network (SIN) signaling is required for echinocandin-induced hyperseptation in Aspergillus fumigatus. mSphere 2024; 9:e0069523. [PMID: 38349166 DOI: 10.1128/msphere.00695-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/17/2024] [Indexed: 03/27/2024] Open
Abstract
Aspergillus fumigatus is a major invasive mold pathogen and the most frequent etiologic agent of invasive aspergillosis. The currently available treatments for invasive aspergillosis are limited in both number and efficacy. Our recent work has uncovered that the β-glucan synthase inhibitors, the echinocandins, are fungicidal against strains of A. fumigatus with defects in septation initiation network (SIN) kinase activity. These drugs are known to be fungistatic against strains with normal septation. Surprisingly, SIN kinase mutant strains also failed to invade lung tissue and were significantly less virulent in immunosuppressed mouse models. Inhibiting septation in filamentous fungi is therefore an exciting therapeutic prospect to both reduce virulence and improve current antifungal therapy. However, the SIN remains understudied in pathogenic fungi. To address this knowledge gap, we characterized the putative regulatory components of the A. fumigatus SIN. These included the GTPase, SpgA, it's two-component GTPase-activating protein, ByrA/BubA, and the kinase activators, SepM and MobA. Deletion of spgA, byrA, or bubA resulted in no overt septation or echinocandin susceptibility phenotypes. In contrast, our data show that deletion of sepM or mobA largely phenocopies disruption of their SIN kinase binding partners, sepL and sidB, respectively. Reduced septum formation, echinocandin hypersusceptibility, and reduced virulence were generated by loss of either gene. These findings provide strong supporting evidence that septa are essential not only for withstanding the cell wall disrupting effects of echinocandins but are also critical for the establishment of invasive disease. Therefore, pharmacological SIN inhibition may be an exciting strategy for future antifungal drug development.IMPORTANCESepta are important structural determinants of echinocandin susceptibility and tissue invasive growth for the ubiquitous fungal pathogen Aspergillus fumigatus. Components of the septation machinery therefore represent promising novel antifungal targets to improve echinocandin activity and reduce virulence. However, little is known about septation regulation in A. fumigatus. Here, we characterize the predicted regulatory components of the A. fumigatus septation initiation network. We show that the kinase activators SepM and MobA are vital for proper septation and echinocandin resistance, with MobA playing an essential role. Null mutants of mobA displayed significantly reduced virulence in a mouse model, underscoring the importance of this pathway for A. fumigatus pathogenesis.
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Affiliation(s)
- Harrison I Thorn
- Graduate Program in Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xabier Guruceaga
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Adela Martin-Vicente
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Ashley V Nywening
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Integrated Program in Biomedical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jinhong Xie
- Graduate Program in Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Wenbo Ge
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jarrod R Fortwendel
- Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Microbiology, Immunology, and Biochemistry, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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38
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Zhang Y, Lin X, Xia T, Chen H, Huang F, Wei C, Qiu G. Effects of intensive chlorine disinfection on nitrogen and phosphorus removal in WWTPs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170273. [PMID: 38280590 DOI: 10.1016/j.scitotenv.2024.170273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/25/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
The increased use of disinfection since the pandemic has led to increased effective chlorine concentration in municipal wastewater. Whereas, the specific impacts of active chlorine on nitrogen and phosphorus removal, the mediating communities, and the related metabolic activities in wastewater treatment plants (WWTPs) lack systematic investigation. We systematically analyzed the influences of chlorine disinfection on nitrogen and phosphorus removal activities using activated sludge from five full-scale WWTPs. Results showed that at an active chlorine concentration of 1.0 mg/g-SS, the nitrogen and phosphorus removal systems were not significantly affected. Major effects were observed at 5.0 mg/g-SS, where the nitrogen and phosphorus removal efficiency decreased by 38.9 % and 44.1 %, respectively. At an active chlorine concentration of 10.0 mg/g-SS, the nitrification, denitrification, phosphorus release and uptake activities decreased by 15.1 %, 69.5-95.9 %, 49.6 % and 100 %, respectively. The proportion of dead cells increased by 6.1 folds. Reverse transcriptional quantitative polymerase chain reaction (RT-qPCR) analysis showed remarkable inhibitions on transcriptions of the nitrite oxidoreductase gene (nxrB), the nitrite reductase genes (nirS and nirK), and the nitrite reductase genes (narG). The nitrogen and phosphorus removal activities completely disappeared with an active chlorine concentration of 25.0 mg/g-SS. Results also showed distinct sensitivities of different functional bacteria in the activated sludge. Even different species within the same functional group differ in their susceptibility. This study provides a reference for the understanding of the threshold active chlorine concentration values which may potentially affect biological nitrogen and phosphorus removal in full-scale WWTPs, which are expected to be beneficial for decision-making in WWTPs to counteract the potential impacts of increased active chlorine concentrations in the influent wastewater.
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Affiliation(s)
- Yixing Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xueran Lin
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Tang Xia
- Guangzhou Sewage Purification Co., Ltd, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Fu Huang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China.
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Zhou Y, Wu W, Sun Y, Shen Y, Mao L, Dai Y, Yang B, Liu Z. Integrated transcriptome and metabolome analysis reveals anthocyanin biosynthesis mechanisms in pepper (Capsicum annuum L.) leaves under continuous blue light irradiation. BMC PLANT BIOLOGY 2024; 24:210. [PMID: 38519909 PMCID: PMC10960449 DOI: 10.1186/s12870-024-04888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Different metabolic compounds give pepper leaves and fruits their diverse colors. Anthocyanin accumulation is the main cause of the purple color of pepper leaves. The light environment is a critical factor affecting anthocyanin biosynthesis. It is essential that we understand how to use light to regulate anthocyanin biosynthesis in plants. RESULT Pepper leaves were significantly blue-purple only in continuous blue light or white light (with a blue light component) irradiation treatments, and the anthocyanin content of pepper leaves increased significantly after continuous blue light irradiation. This green-to-purple phenotype change in pepper leaves was due to the expression of different genes. We found that the anthocyanin synthesis precursor-related genes PAL and 4CL, as well as the structural genes F3H, DFR, ANS, BZ1, and F3'5'H in the anthocyanin synthesis pathway, had high expression under continuous blue light irradiation. Similarly, the expression of transcription factors MYB1R1-like, MYB48, MYB4-like isoform X1, bHLH143-like, and bHLH92-like isoform X3, and circadian rhythm-related genes LHY and COP1, were significantly increased after continuous blue light irradiation. A correlation network analysis revealed that these transcription factors and circadian rhythm-related genes were positively correlated with structural genes in the anthocyanin synthesis pathway. Metabolomic analysis showed that delphinidin-3-O-glucoside and delphinidin-3-O-rutinoside were significantly higher under continuous blue light irradiation relative to other light treatments. We selected 12 genes involved in anthocyanin synthesis in pepper leaves for qRT-PCR analysis, and the accuracy of the RNA-seq results was confirmed. CONCLUSIONS In this study, we found that blue light and 24-hour irradiation together induced the expression of key genes and the accumulation of metabolites in the anthocyanin synthesis pathway, thus promoting anthocyanin biosynthesis in pepper leaves. These results provide a basis for future study of the mechanisms of light quality and photoperiod in anthocyanin synthesis and metabolism, and our study may serve as a valuable reference for screening light ratios that regulate anthocyanin biosynthesis in plants.
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Affiliation(s)
- Yao Zhou
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Weisheng Wu
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Ying Sun
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yiyu Shen
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Lianzhen Mao
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yunhua Dai
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Bozhi Yang
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Zhoubin Liu
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Li X, Dang Z, Tang W, Zhang H, Shao J, Jiang R, Zhang X, Huang F. Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a. BIOSENSORS 2024; 14:145. [PMID: 38534252 DOI: 10.3390/bios14030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.
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Affiliation(s)
- Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People's Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jianwei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Rui Jiang
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
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Tiwari V, Bussi Y, Kamara I, Faigenboim A, Irihimovitch V, Charuvi D. Priming avocado with sodium hydrosulfide prior to frost conditions induces the expression of genes involved in protection and stress responses. PHYSIOLOGIA PLANTARUM 2024; 176:e14291. [PMID: 38628053 DOI: 10.1111/ppl.14291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/10/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024]
Abstract
Priming plants with chemical agents has been extensively investigated as a means for improving their tolerance to many biotic and abiotic stresses. Earlier, we showed that priming young avocado (Persea americana Mill cv. 'Hass') trees with sodium hydrosulfide (NaHS), a donor of hydrogen sulfide, improves the response of photosynthesis to simulated frost (cold followed by high light) conditions. In the current study, we performed a transcriptome analysis to gain insight into the molecular response of avocado 'Hass' leaves to frost, with or without NaHS priming. The analysis revealed 2144 (down-regulated) and 2064 (up-regulated) differentially expressed genes (DEGs) common to both non-primed and primed trees. Non-primed trees had 697 (down) and 559 (up) unique DEGs, while primed trees exhibited 1395 (down) and 1385 (up) unique DEGs. We focus on changes in the expression patterns of genes encoding proteins involved in photosynthesis, carbon cycle, protective functions, biosynthesis of isoprenoids and abscisic acid (ABA), as well as ABA-regulated genes. Notably, the differential expression results depict the enhanced response of primed trees to the frost and highlight gene expression changes unique to primed trees. Amongst these are up-regulated genes encoding pathogenesis-related proteins, heat shock proteins, enzymes for ABA metabolism, and ABA-induced transcription factors. Extending the priming experiments to field conditions, which showed a benefit to the physiology of trees following chilling, suggests that it can be a possible means to improve trees' response to cold stress under natural winter conditions.
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Affiliation(s)
- Vivekanand Tiwari
- Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Institute, Rishon LeZion, Israel
| | - Yuval Bussi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Itzhak Kamara
- Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Institute, Rishon LeZion, Israel
| | - Adi Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Institute, Rishon LeZion, Israel
| | - Vered Irihimovitch
- Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Institute, Rishon LeZion, Israel
| | - Dana Charuvi
- Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Institute, Rishon LeZion, Israel
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Sands M, Zhang X, Gal A, Laws M, Spinella M, Erdogan ZM, Irudayaraj J. Comparative hepatotoxicity of novel lithium bis(trifluoromethanesulfonyl)imide (LiTFSI, ie. HQ-115) and legacy Perfluorooctanoic acid (PFOA) in male mice: Insights into epigenetic mechanisms and pathway-specific responses. ENVIRONMENT INTERNATIONAL 2024; 185:108556. [PMID: 38461777 DOI: 10.1016/j.envint.2024.108556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/02/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024]
Abstract
Lithium Bis(trifluoromethanesulfonyl)imide (LiTFSI ie. HQ-115), a polymer electrolyte used in energy applications, has been detected in the environment, yet its health risks and environmental epigenetic effects remain unknown. This study aims to unravel the potential health risks associated with LiTFSI, investigate the role of DNA methylation-induced toxic mechanisms in its effects, and compare its hepatotoxic impact with the well-studied Perfluorooctanoic Acid (PFOA). Using a murine model, six-week-old male CD1 mice were exposed to 10 and 20 mg/kg/day of each chemical for 14 days as 14-day exposure and 1 and 5 mg/kg/day for 30 days as 30-day exposure. Results indicate that PFOA exposure induced significant hepatotoxicity, characterized by liver enlargement, and elevated serum biomarkers. In contrast, LiTFSI exposure showed lower hepatotoxicity, accompanied by mild liver injuries. Despite higher bioaccumulation of PFOA in serum, LiTFSI exhibited a similar range of liver concentrations compared to PFOA. Reduced Representative Bisulfite Sequencing (RRBS) analysis revealed distinct DNA methylation patterns between 14-day and 30-day exposure for the two compounds. Both LiTFSI and PFOA implicated liver inflammatory pathways and lipid metabolism. Transcriptional results showed that differentially methylated regions in both exposures are enriched with cancer/disease-related motifs. Furthermore, Peroxisome proliferator-activated receptor alpha (PPARα), a regulator of lipid metabolism, was upregulated in both exposures, with downstream genes indicating potential oxidative damages. Overall, LiTFSI exhibits distinct hepatotoxicity profiles, emphasizing the need for comprehensive assessment of emerging PFAS compounds.
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Affiliation(s)
- Mia Sands
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xing Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Arnon Gal
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Mary Laws
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Michael Spinella
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zeynep-Madak Erdogan
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph Irudayaraj
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Tavares LS, Oliveira-Silva RL, Moura MT, da Silva JB, Benko-Iseppon AM, Lima-Filho JV. Reference genes for gene expression profiling in mouse models of Listeria monocytogenes infection. Biotechniques 2024; 76:104-113. [PMID: 38112054 DOI: 10.2144/btn-2023-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
RT-qPCR dissects transcription-based processes but requires reference genes (RGs) for data normalization. This study prospected RGs for mouse macrophages (pMØ) and spleen infected with Listeria monocytogenes. The pMØ were infected in vitro with L. monocytogenes or vehicle for 4 h. Mice were injected with L. monocytogenes (or vehicle) and euthanized 24 h post-injection. The RGs came from a multispecies primer set, from the literature or designed here. The RG ranking relied on GeNorm, NormFinder, BestKeeper, Delta-CT and RefFinder. B2m-H3f3a-Ppia were the most stable RGs for pMØ, albeit RG indexes fine-tuned estimations of cytokine relative expression. Actβ-Ubc-Ppia were the best RGs for spleen but modestly impacted the cytokine relative expression. Hence, mouse models of L. monocytogenes require context-specific RGs for RT-qPCR, thus reinforcing its paramount contribution to accurate gene expression profiling.
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Affiliation(s)
| | | | - Marcelo Tigre Moura
- Departamento de Biologia Celular e Molecular, Centro de Biotecnologia, Campus I, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | | | | | - José Vitor Lima-Filho
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Recife, PE, Brasil
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Vittori C, Faia C, Wyczechowska D, Trauth A, Plaisance-Bonstaff K, Meyaski-Schluter M, Reiss K, Peruzzi F. IKAROS expression drives the aberrant metabolic phenotype of macrophages in chronic HIV infection. Clin Immunol 2024; 260:109915. [PMID: 38286172 PMCID: PMC10922842 DOI: 10.1016/j.clim.2024.109915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/02/2024] [Accepted: 01/23/2024] [Indexed: 01/31/2024]
Abstract
The increased risk for acquiring secondary illnesses in people living with HIV (PLWH) has been associated with immune dysfunction. We have previously found that circulating monocytes from PLWH display a trained phenotype. Here, we evaluated the metabolic profile of these cells and found increased mitochondrial respiration and glycolysis of monocyte-derived macrophages (MDMs) from PLWH. We additionally found that cART shifted the energy metabolism of MDMs from controls toward increased utilization of mitochondrial respiration. Importantly, both downregulation of IKAROS expression and inhibition of the mTOR pathway reversed the metabolic profile of MDMs from PLWH and cART-treated control-MDMs. Altogether, this study reveals a very specific metabolic adaptation of MDMs from PLWH, which involves an IKAROS/mTOR-dependent increase of mitochondrial respiration and glycolysis. We propose that this metabolic adaptation decreases the ability of these cells to respond to environmental cues by "locking" PLWH monocytes in a pro-inflammatory and activated phenotype.
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Affiliation(s)
- Cecilia Vittori
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA
| | - Celeste Faia
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA
| | - Dorota Wyczechowska
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA
| | - Amber Trauth
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA
| | - Karlie Plaisance-Bonstaff
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA
| | - Mary Meyaski-Schluter
- Clinical and Translational Research Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Krzysztof Reiss
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA
| | - Francesca Peruzzi
- Louisiana State University Health Sciences Center and Louisiana Cancer Research Center, New Orleans, LA 70112, USA; Louisiana State University Health Sciences Center, Department of Medicine, Louisiana Cancer Research Center; New Orleans, LA 70112, USA.
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Bergez-Hernández F, Luque-Ortega F, García-Magallanes N, Alvarez-Arrazola M, Arámbula-Meraz E. Deletion in a regulatory region is associated with underexpression of miR-148b‑3p in patients with prostate cancer. Biomed Rep 2024; 20:52. [PMID: 38357236 PMCID: PMC10865175 DOI: 10.3892/br.2024.1740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Prostate cancer (PCa) is the leading cause of cancer-related death in men. This pathology is complex and heterogeneous; therefore, elucidating the molecular mechanisms that lead to its origin and progression is imperative. MicroRNAs (miRNAs or miRs) are part of the epigenetic machinery that regulates the expression of human genes, therefore, mutations in the genes that encode them can lead to a dysregulation in their expression, which directly impacts their target genes, which could be oncogenes or tumor suppressor genes. In PCa several dysregulated expression levels of miRNAs are associated with perturbed cellular processes. A differential expression of miRNAs such as miR-145-5p and miR-148-3p has been observed in PCa, possibly due to mutations in regions near the miRNAs. However, the molecular mechanisms that lead to the dysregulation of these miRNAs still need to be clarified. Therefore, the present study aimed to analyze the expression of miRNAs and their relationship with mutations in patients with and without PCa. In total, 71 patients were analyzed: 41 of whom had PCa (CAP group) and 30 with benign pathology (BPD group). Underexpression was observed in miR-145-5p and miR-148b-3p in PCa patients (P=0.03 and P=0.001, respectively). In miR-145-5p, no mutations related to its expression were identified. For miR-148b-3p, a set of mutations were identified in the chr12:54337042/54337043 region, which were grouped into the mutation named DelsAAG. Although this mutation's abnormal allele is related to PCa (P=0.017), a statistically significant difference was observed in the expression of miR-148b-3p between carriers and non-carriers of the mutated allele, identifying a mechanism likely to be involved in the miR-148b-3p dysregulation.
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Affiliation(s)
- Fernando Bergez-Hernández
- Postgraduate in Biomedical Sciences, Faculty of Chemical-Biological Sciences, Autonomous University of Sinaloa, Culiacán, 80010 Sinaloa, México
| | - Fred Luque-Ortega
- Basic Sciences Laboratory, Faculty of Dentistry, Autonomous University of Sinaloa, Culiacán, 80100 Sinaloa, México
| | - Noemí García-Magallanes
- Laboratory of Biomedicine and Molecular Biology, Biotechnology Engineering, Polytechnic University of Sinaloa, Mazatlán, 82199 Sinaloa, México
| | | | - Eliakym Arámbula-Meraz
- Postgraduate in Biomedical Sciences, Faculty of Chemical-Biological Sciences, Autonomous University of Sinaloa, Culiacán, 80010 Sinaloa, México
- Laboratory of Genetics and Molecular Biology, Faculty of Chemical-Biological Sciences, Autonomous University of Sinaloa, Culiacán, 80010 Sinaloa, México
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Neidhardt L, Cloots E, Friemel N, Weiss CAM, Harding HP, McLaughlin SH, Janssens S, Ron D. The IRE1β-mediated unfolded protein response is repressed by the chaperone AGR2 in mucin producing cells. EMBO J 2024; 43:719-753. [PMID: 38177498 PMCID: PMC10907699 DOI: 10.1038/s44318-023-00014-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Effector mechanisms of the unfolded protein response (UPR) in the endoplasmic reticulum (ER) are well-characterised, but how ER proteostasis is sensed is less well understood. Here, we exploited the beta isoform of the UPR transducer IRE1, that is specific to mucin-producing cells in order to gauge the relative regulatory roles of activating ligands and repressing chaperones of the specialised ER of goblet cells. Replacement of the stress-sensing luminal domain of endogenous IRE1α in CHO cells (normally expressing neither mucin nor IRE1β) with the luminal domain of IRE1β deregulated basal IRE1 activity. The mucin-specific chaperone AGR2 repressed IRE1 activity in cells expressing the domain-swapped IRE1β/α chimera, but had no effect on IRE1α. Introduction of the goblet cell-specific client MUC2 reversed AGR2-mediated repression of the IRE1β/α chimera. In vitro, AGR2 actively de-stabilised the IRE1β luminal domain dimer and formed a reversible complex with the inactive monomer. These features of the IRE1β-AGR2 couple suggest that active repression of IRE1β by a specialised mucin chaperone subordinates IRE1 activity to a proteostatic challenge unique to goblet cells, a challenge that is otherwise poorly recognised by the pervasive UPR transducers.
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Affiliation(s)
- Lisa Neidhardt
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Eva Cloots
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Natalie Friemel
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Caroline A M Weiss
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Heather P Harding
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sophie Janssens
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
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Fujita Y, Taniguchi A, Yamamoto H, Obinata H, Kogo H, Iizuka-Kogo A, Ikezawa M, Tajika Y, Yokoo S, Matsuzaki T. Aquaporin-5 Protein Is Selectively Reduced in Rat Parotid Glands under Conditions of Fasting or a Liquid Diet. Acta Histochem Cytochem 2024; 57:25-33. [PMID: 38463206 PMCID: PMC10918431 DOI: 10.1267/ahc.24-00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 03/12/2024] Open
Abstract
Aquaporin-5 (AQP5) water channel, transmembrane protein 16A (TMEM16A) Ca2+-activated Cl- channel, and Na+-K+-2Cl- cotransporter (NKCC1) are membrane proteins on salivary gland acinar cells that function in watery saliva secretion. We examined their expression changes in rat parotid glands under reduced mastication. Rats were either fed regular chow as a control group, fasted for 48 hr or fed a liquid diet for 48 hr or 1 week to reduce mastication. The parotid glands were then resected to analyze the protein and mRNA levels by immunofluorescence, immunoblotting, and reverse-transcription quantitative PCR (RT-qPCR). AQP5 protein was significantly decreased in both liquid diet groups and the fasting group but its mRNA levels showed no apparent changes compared with the control group. The protein and mRNA levels of TMEM16A and NKCC1 showed no significant changes between any of the groups other than an increase in NKCC1 mRNA in the 1-week liquid diet group. These results suggest that reduced mastication may increase the AQP5 protein degradation, but not that of other membrane proteins necessary for saliva secretion.
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Affiliation(s)
- Yoshie Fujita
- Department of Oral and Maxillofacial Surgery, and Plastic Surgery, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Akie Taniguchi
- Department of Oral and Maxillofacial Surgery, and Plastic Surgery, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Hanako Yamamoto
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Hideru Obinata
- Laboratory for Analytical Instruments, Education and Research Support Center, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Hiroshi Kogo
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Akiko Iizuka-Kogo
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Maiko Ikezawa
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Yukiko Tajika
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Satoshi Yokoo
- Department of Oral and Maxillofacial Surgery, and Plastic Surgery, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
| | - Toshiyuki Matsuzaki
- Department of Anatomy and Cell Biology, Gunma University Graduate School of Medicine, 3–39–22, Showa-machi, Maebashi Gunma 371–8511, Japan
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Sunny SS, Lachova J, Kasparek P, Palkova M, Spoutil F, Prochazka J, Sedlacek R, Liskova P, Kozmik Z. Ovol2 promoter mutations in mice and human illuminate species-specific phenotypic divergence. Hum Mol Genet 2024; 33:491-500. [PMID: 37971355 DOI: 10.1093/hmg/ddad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/06/2022] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Pathogenic variants in the highly conserved OVOL2 promoter region cause posterior polymorphous corneal dystrophy (PPCD) 1 by inducing an ectopic expression of the endothelial OVOL2 mRNA. Here we produced an allelic series of Ovol2 promoter mutations in the mouse model including the heterozygous c.-307T>C variant (RefSeq NM_021220.4) causing PPCD1 in humans. Despite the high evolutionary conservation of the Ovol2 promoter, only some alterations of its sequence had phenotypic consequences in mice. Four independent sequence variants in the distal part of the Ovol2 promoter had no significant effect on endothelial Ovol2 mRNA level or caused any ocular phenotype. In contrast, the mutation c.-307T>C resulted in increased Ovol2 expression in the corneal endothelium. However, only a small fraction of adult mice c.-307T>C heterozygotes developed ocular phenotypes such as irido-corneal adhesions, and corneal opacity. Interestingly, phenotypic penetrance was increased at embryonic stages. Notably, c.-307T>C mutation is located next to the Ovol1/Ovol2 transcription factor binding site. Mice carrying an allele with a deletion encompassing the Ovol2 binding site c.-307_-320del showed significant Ovol2 gene upregulation in the cornea endothelium and exhibited phenotypes similar to the c.-307T>C mutation. In conclusion, although the mutations c.-307T>C and -307_-320del lead to a comparably strong increase in endothelial Ovol2 expression as seen in PPCD1 patients, endothelial dystrophy was not observed in the mouse model, implicating species-specific differences in endothelial cell biology. Nonetheless, the emergence of dominant ocular phenotypes associated with Ovol2 promoter variants in mice implies a potential role of this gene in eye development and disease.
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Affiliation(s)
- Sweetu Susan Sunny
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Prague, Czech Republic
| | - Jitka Lachova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Prague, Czech Republic
| | - Petr Kasparek
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, 513 Parnassus Avenue, CA 94158, San Francisco, United States
| | - Marcela Palkova
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Frantisek Spoutil
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 121 08, Prague 2, Prague Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, U Nemocnice 2, 128 08, Prague 2, Prague, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Prague, Czech Republic
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García-Topete DA, Álvarez-Lee LA, Carballo-López GI, Uriostegui-Campos MA, Guzmán-Uribe C, Castro-Ceseña AB. Antifibrotic activity of carbon quantum dots in a human in vitro model of non-alcoholic steatohepatitis using hepatic stellate cells. Biomater Sci 2024; 12:1307-1319. [PMID: 38263852 DOI: 10.1039/d3bm01710a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Around 33% of the global population suffers from non-alcoholic fatty liver disease (NAFLD). From these patients, 30% of them progress into non-alcoholic steatohepatitis (NASH), the critical point where lack of treatment leads to cirrhosis and hepatic failure. Moreover, to date, there are no approved therapeutic options available for NASH. It is known that hepatic stellate cell (HSC) activation contributes the most to hepatic disfunction, leading to reactive oxygen species (ROS) accumulation and chronic inflammation, and that the use of nanomaterials to deliver antioxidants may have potential to reduce the activity of activated HSCs. Therefore, we implemented a human in vitro co-culture model in which we take into consideration two factors related to NASH and fibrosis: human hepatic stellate cells from a NASH diagnosed donor (HHSC-N) and peripheral blood mononuclear cells (PBMCs), particularly lymphocytes. The co-cultures were treated with: (1) carbon quantum dots (CD) or (2) lactoferrin conjugated CD (CD-LF) for 24 h or 72 h. CD and CD-LF treatments significantly downregulated profibrotic genes' expression levels of ACTA2, COL1A1, and TIMP1 in co-cultured HHSC-N at 72 h. Also, we assayed the inflammatory response by quantifying the concentrations of cytokines IL-22, IL-10, IFN-γ and IL-4 present in the co-culture's conditioned media whose concentrations may suggest a resolution-associated response in progress. Our findings may serve as a starting point for the development of a NASH treatment using bio-nanotechnology.
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Affiliation(s)
- David A García-Topete
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
| | - Laura A Álvarez-Lee
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
- CONAHCYT-Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico
| | - Gabriela I Carballo-López
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
| | - Marco A Uriostegui-Campos
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
| | - Carlos Guzmán-Uribe
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
- Centro de Nanociencias y Nanotecnología, UNAM. Km 107, Carretera Tijuana-Ensenada, C.P. 22800, Ensenada, Baja California, Mexico
| | - Ana B Castro-Ceseña
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico.
- CONAHCYT-Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, C.P. 22860, Ensenada, Baja California, Mexico
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Huang Z, Yu X, Liu Q, Maki T, Alam K, Wang Y, Xue F, Tang S, Du P, Dong Q, Wang D, Huang J. Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168818. [PMID: 38036132 DOI: 10.1016/j.scitotenv.2023.168818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.
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Affiliation(s)
- Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China; Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
| | - Xinrong Yu
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qiantao Liu
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Teruya Maki
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan
| | - Khan Alam
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan
| | - Yongkai Wang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fanli Xue
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shihan Tang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Pengyue Du
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qing Dong
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Danfeng Wang
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
| | - Jianping Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China; Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China.
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