Changes In Gene Expression Levels Research Articles

Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens.

In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.

Altered gene expression in human brain microvascular endothelial cells in response to the infection of influenza H1N1 virus

Influenza viruses not only cause respiratory illness, but also have been reported to elicit neurological manifestations following acute viral infection. The central nervous system (CNS) has a specific defense mechanism against pathogens structured by cerebral microvasculature lined with brain endothelial cells to form the blood–brain barrier (BBB). To investigate the response of human brain microvascular endothelial cells (hBMECs) to the Influenza A virus (IAV), we inoculated the cells with the A/WSN/33 (H1N1) virus. We then conducted an RNAseq experiment to determine the changes in gene expression levels and the activated disease pathways following infection. The analysis revealed an effective activation of the innate immune defense by inducing the pattern recognition receptors (PRRs). Along with the production of proinflammatory cytokines, we detected an upregulation of interferons and interferon-stimulated genes, such as IFN-β/λ, ISG15, CXCL11, CXCL3 and IL-6, etc. Moreover, infected hBMECs exhibited a disruption in the cytoskeletal structure both on the transcriptomic and cytological levels. The RNAseq analysis showed different pathways and candidate genes associated with the neuroactive ligand-receptor interaction, neuroinflammation, and neurodegenerative diseases, together with a predicted activation of the neuroglia. Likewise, some genes linked with the mitochondrial structure and function displayed a significantly altered expression. En masse, this data supports that hBMECs could be infected by the IAV, which induces the innate and inflammatory immune response. The results suggest that the influenza virus infection could potentially induce a subsequent aggravation of neurological disorders.

Sealing Behavior of a New Material Combination in Two-Part Dental Implant Systems: An In Vitro Examination.

To test a newly introduced implant-abutment material combination against bacterial endotoxin leakage in a human whole blood assay. Two dental implant systems with internal connections and the following material combinations at the implant-abutment interface (IAI) were used (implant material/abutment material): yttrium-stabilized tetragonal zirconium dioxide (Y-TZP)/polyetherketoneketone (PEKK), and titanium (Ti/Ti). Test implants were inoculated with lipopolysaccharide (LPS) and sealed and submerged in human whole blood. Untreated implants served as the control groups. Changes in gene expression levels of inflammatory markers indicating LPS leakage were assessed after 1, 8, and 24 hours using quantitative real-time polymerase chain reaction. In the Y-TZP/PEKK test group, a significant influence of the implant system (P < .001) on increases in gene expression indicating leakage were detected after 8 hours for TLR-4 and after 24 hours for interleukin 1-β and nuclear factor kappa-light-chain-enhancer of activated B-cells (NF-κB), indicating microleakage of LPS at the IAI. In the Ti/Ti test group, differences in gene expression were found only for NF-κB after 8 hours. The internal hexalobe IAI of two-piece dental implants fabricated from Y-TZP and PEKK do not prevent LPS molecular microleakage.

Monitoring and recovery of hyperglycaemia-induced endothelial dysfunction with rheopheresis in diabetic lower extremity ulceration with hyperviscosity.

Rheopheresis is an extracorporeal haematotherapy that improves haemorheological status by filtering proteins that enhance blood viscosity. It also has anti-inflammatory effects by removing inflammatory cytokines. Our study aims to examine the effects of rheopheresis on the endothelial status in diabetic lower extremity ulceration. In vitro experiments were performed in a HUVEC model to mimic hyperglycaemic stress. We determined the changes in gene expression levels of IL-6, IL-8, TNF-alpha, endothelin convertase enzyme, ET-1, and NO synthase, as well as the ROS and intracellular GSH levels upon hyperglycaemia. In in vivo studies, two rheopheresis procedures were performed on seven patients with diabetic lower extremity ulceration with hyperviscosity, and we measured the changes in plasma concentrations of ET-1, TXB2, SOD enzyme activity, and extracellular components of the glutathione pool depending on treatments. Our results showed that hyperglycaemia increases endothelial expression of inflammatory cytokines, ET-1, and endothelin convertase enzyme, while NO synthase was decreased. As a result of rheopheresis, we observed decreased ET-1 and TXB2 concentrations in the plasma and beneficial changes in the parameters of the glutathione pool. To summarize our results, hyperglycaemia-induced oxidative stress and endothelial inflammation can be moderated by rheopheresis in diabetic lower extremity ulceration with hyperviscosity.

Three Heat Shock Protein Genes and Antioxidant Enzymes Protect Pardosa pseudoannulata (Araneae: Lycosidae) from High Temperature Stress.

Pardosa pseudoannulata (P. pseudoannulata) is an essential natural predatory enemy in rice ecosystems. The fluctuating climate may cause them to experience heat stress, whereas heat shock proteins (HSPs) and antioxidant enzymes help resist heat damage. Herein, we cloned and characterized the full-length genes PpHSP27, PpHSP60, and PpHSC70 from P. pseudoannulata. Changes in gene expression levels and superoxide dismutase (SOD), catalase (CAT), and glutathione transferase (GST) activities in adult male and female P. pseudoannulata were measured at different stress exposure times and temperatures. We found that the abovementioned HSP genes belong to the sHSP, HSP60, and HSP70 families. The expression of the three HSP genes and the activities of SOD, CAT, and GST were significantly upregulated with the increasing stress temperature and time. The knockdown of the three HSP genes via RNA interference significantly decreased the survival rate of male and female P. pseudoannulata during high temperature stress. Thus, PpHSP27, PpHSP60, and PpHSC70 play an important role in the heat tolerance of P. pseudoannulata, and SOD, CAT, and GST enable recovery heat stress-induced oxidative damage. Their changes and regulation during high temperature stress can improve spiders' adaptability in the field and enhance the biological control of environmental pests.

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants.

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.

Mechanisms of estrogen deficiency-induced osteoporosis based on transcriptome and DNA methylation.

Osteoporosis is a disease that impacts the elderly. Low estrogen is related to changes in DNA methylation and consequent alterations in gene expression, leading to a new direction in research related to the pathophysiology of osteoporosis. We constructed an Ovariectomized (OVX) mouse model in our study, and the mouse models had osteoporosis based on the phenotype and methylation levels in the mouse's bone. Furthermore, the methylation level of the OVX mice was significantly changed compared to that of SHAM mice. Therefore, we performed genome-level analysis on the mouse model using transcriptome and Whole Genome Bisulfite Sequencing (WGBS) by combining the data of two omics and discovered that the changes in gene expression level caused by osteoporosis primarily focused on the decrease of bone and muscle development and the activation of the immune system. According to intersection analysis of methylation and transcriptome data, the differentially expressed genes and pathways are consistent with the differentially expressed methylation locations and regions. Further, the differentially expressed methylation sites were mainly concentrated in promoters, exons, and other critical functional regions of essential differentially expressed genes. This is also the primary cause of gene differential expression variations, indicating that estrogen deficiency might regulate gene expression by altering methylation modification, leading to osteoporosis. We demonstrated the clinical value of methylation modification research, and these findings would improve the current understanding of underlying molecular mechanisms of osteoporosis incidence and development and provide new ideas for early detection and treatment of osteoporosis.

A 9‑gene expression signature to predict stage development in resectable stomach adenocarcinoma

BackgroundStomach adenocarcinoma (STAD) is a highly heterogeneous disease and is among the leading causes of cancer-related death worldwide. At present, TNM stage remains the most effective prognostic factor for STAD. Exploring the changes in gene expression levels associated with TNM stage development may help oncologists to better understand the commonalities in the progression of STAD and may provide a new way of identifying early-stage STAD so that optimal treatment approaches can be provided.MethodsThe RNA profile retrieving strategy was utilized and RNA expression profiling was performed using two large STAD microarray databases (GSE62254, n = 300; GSE15459, n = 192) from the Gene Expression Omnibus (GEO) and the RNA-seq database within the Cancer Genome Atlas (TCGA, n = 375). All sample expression information was obtained from STAD tissues after radical resection. After excluding data with insufficient staging information and lymph node number, samples were grouped into earlier-stage and later-stage. Samples in GSE62254 were randomly divided into a training group (n = 172) and a validation group (n = 86). Differentially expressed genes (DEGs) were selected based on the expression of mRNAs in the training group and the TCGA group (n = 156), and hub genes were further screened by least absolute shrinkage and selection operator (LASSO) logistic regression. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the hub genes in distinguishing STAD stage in the validation group and the GSE15459 dataset. Univariate and multivariate Cox regressions were performed sequentially.Results22 DEGs were commonly upregulated (n = 19) or downregulated (n = 3) in the training and TCGA datasets. Nine genes, including MYOCD, GHRL, SCRG1, TYRP1, LYPD6B, THBS4, TNFRSF17, SERPINB2, and NEBL were identified as hub genes by LASSO-logistic regression. The model achieved discrimination in the validation group (AUC = 0.704), training-validation group (AUC = 0.743), and GSE15459 dataset (AUC = 0.658), respectively. Gene Set Enrichment Analysis (GSEA) was used to identify the potential stage-development pathways, including the PI3K-Akt and Calcium signaling pathways. Univariate Cox regression indicated that the nine-gene score was a significant risk factor for overall survival (HR = 1.28, 95% CI 1.08–1.50, P = 0.003). In the multivariate Cox regression, only SCRG1 was an independent prognostic predictor of overall survival after backward stepwise elimination (HR = 1.21, 95% CI 1.11–1.32, P < 0.001).ConclusionThrough a series of bioinformatics and validation processes, a nine-gene signature that can distinguish STAD stage was identified. This gene signature has potential clinical application and may provide a novel approach to understanding the progression of STAD.

Transcriptome analysis of malate-induced Schizochytrium sp. FJU-512 reveals a novel pathway for biosynthesis of docosahexaenoic acid with enhanced expression of genes responsible for acetyl-CoA and NADPH accumulation.

Schizochytrium is one of the few oleaginous microalgae that produce docosahexaenoic acid (DHA)-rich lipids. In this study, global changes in gene expression levels of Schizochytrium sp. FJU-512 cultured with malate in a 15 l-bioreactor was analyzed using comparative transcriptomics. The changes were found mainly in the genes involved in oxidative phosphorylation, β-oxidation, and pentose phosphate pathways. Consequently, the global changes in genes associated with the pathways could lead to an increase in the influx throughputs of pyruvate, branched-chain amino acids, fatty acids, and vitamin B6. Our transcriptome analysis indicated pyruvate dehydrogenase E2 component and acetolactate synthase I/II/III large subunit as major contributors to acetyl-CoA biosynthesis, whereas glucose-6-phosphate dehydrogenase was indicated as the major contributor to the biosynthesis of NADPH. An increase in DHA titer of up to 22% was achieved with the addition of malate to the fed-batch culture of Schizochytrium sp. FJU-512. This study provides an alternate method to enhance DHA production in Schizochytrium sp. FJU-512 through malate induced upregulation of genes responsible for acetyl-CoA and NADPH biosynthesis.

Feline Oncogenomics: What Do We Know about the Genetics of Cancer in Domestic Cats?

Simple SummaryCancer is a significant cause of suffering and death in domestic cats. In humans, an understanding of the genetics of different types of cancers has become clinically important for all aspects of patient care and forms the basis for most emerging diagnostics and therapies. The field of ‘oncogenomics’ characterises the alterations of cancer-associated genes that are found in tumours. Such a thorough understanding of the oncogenome of human tumours has only been possible due to a high-quality reference genome and an understanding of the genetic variation that can exist between people. Although a high-quality reference genome for cats has only recently been generated, investigations into understanding the genetics of feline cancers have been underway for many years, using a range of different technologies. This review summarises what is currently known of the genetics of both common and rare types of cancer in domestic cats. Drawing attention to our current understanding of the feline oncogenome will hopefully bring this topic into focus and serve as a springboard for more much-needed research into the genetics of cancer in domestic cats.Cancer is a significant cause of morbidity and mortality in domestic cats. In humans, an understanding of the oncogenome of different cancer types has proven critical and is deeply interwoven into all aspects of patient care, including diagnostics, prognostics and treatments through the application of targeted therapies. Investigations into understanding the genetics of feline cancers started with cytogenetics and was then expanded to studies at a gene-specific level, looking for mutations and expression level changes of genes that are commonly mutated in human cancers. Methylation studies have also been performed and together with a recently generated high-quality reference genome for cats, next-generation sequencing studies are starting to deliver results. This review summarises what is currently known of the genetics of both common and rare cancer types in cats, including lymphomas, mammary tumours, squamous cell carcinomas, soft tissue tumours, mast cell tumours, haemangiosarcomas, pulmonary carcinomas, pancreatic carcinomas and osteosarcomas. Shining a spotlight on our current understanding of the feline oncogenome will hopefully serve as a springboard for more much-needed research into the genetics of cancer in domestic cats.

MPN-225 Next Generation Sequencing (NGS) in the Diagnosis, Prognosis and Features of the Disease in Ph-Negative Myeloproliferative Neoplasms.

Over the past decade NGS has expanded our understanding of the genomic landscape of hematological malignancies. New biomarkers discovered during NGS are now widely used in clinical practice to improve diagnosis, stratify patients into prognostic groups, and select targeted therapy for Ph-MPN patients. To assess possibilities of NGS in diagnosis and determination of prognostic features of disease course in Ph-MPN patients. The study included 36 patients from clinics in Moscow and St. Petersburg (17 men and 19 women), the median age was 55 (IQR 27-79) with diagnosed PV, ET, PMF, MDS, AML. A panel of 116 genes with an average reading depth of 200x or 1000x on MiSeq (Illumina) was used. NGS panel had a detection limit of 3% variant allele frequency. The clinical significance of mutations was determined using COSMIC and ClinVar. Genetic abnormalities were detected in all patients. On average, 10 mutations per one patient were revealed, including 4 somatic mutations in 92% (33/36) patients. In 70% (25/36), from 1 to 3 mutations with known clinical significance were found. In all patients without driver and somatic mutations (ASXL1, EZH2, etc.) and chromosomal aberrations, somatic mutations (both clinically significant and unknown clinical significance) were detected, that served as clonality confirmation. All patients were divided into two groups: 1) driver mutations, normal karyotype (16/36) (favorable prognosis) and 2) triple-negative mutational status (20/36) with additional patients having mutations in epigenetic regulators genes (4/36) (unfavorable prognosis). In the first group, NGS revealed additional mutations in 8/16 (50%) patients (ASXL1, EZH2, IDH1) and in 3/16 (19%) were noted mutations in TET2 gene. In an unfavorable group, additional mutations were also found in genes of epigenetic regulation (ASXL1, IDH1, SRSF2) and in signal transduction genes (RAS genes, PTPN11) and TET2. NGS data can confirm disease clonal nature, assess disease prognosis, and select target therapy for patients with Ph-negative myeloproliferative neoplasms. To get new information it is possible to expand the panel of sequenced genes, as well as study other genetic mechanisms underlying disease pathogenesis (e.g., changes in gene expression level, microRNAs, or transcription factors).

Immune-Related Gene Profile in HIV-Infected Patients with Discordant Immune Response.

In spite of many reports on persistent low CD4 T cell counts and change in immune-related gene expression level in patients with HIV infection, there is still uncertainty about significant association between gene expression level and HIV infection in patients with and without DIR. The aim of this study was to compare the expression level of CD4, CCL5, IFN-γ, STAT1, APOBEC3G, CD45, and ICAM-1 genes in HIV-1-positive patients with and without DIR. In this study, 30 HIV-1-positive patients (15 patients with and 15 patients without DIR [control group]) were included. PBMCs of the patients were collected through density radient centrifugation with Ficoll-Hypaque. RNeasy Plus Mini kit was used to extract RNA. Relative expression levels of CD4, CCL5, IFN-γ, STAT1, APOBEC3G, CD45, and ICAM-1 genes were evaluated by real-time PCR. The data were analyzed using one-way ANOVA. CD4 T cell counts were significantly lower in DIR patients than the control group (p < 0.01). While there was no significant difference in the relative expression levels of CD4, CCL5, IFN-γ, STAT1, CD45, and ICAM-1 between patients with DIR and control group, APOBEC3G expression level was significantly higher in the patients with DIR as compare to the control group (p < 0.01). Our findings suggest a significantly higher APOBEC3G expression level in patients with DIR, suggesting the potential role of APOBEC3G in patients with immunological discordance besides its suppressing role in HIV-1 infection. Confirmation of this hypothesis requires further research.

Abscisic acid induces the expression of AsKIN during the recovery period of garlic cryopreservation.

Abscisic acid induced the expression of AsKIN during the recovery period of garlic cryopreservation. AsKIN was identified as a gene involved in cold and osmotic stress resistance. Cryopreservation has been proven to be effective in removing viruses from garlic. However, oxidative damage in cryopreservation has a significant impact on the survival after preservation. Abscisic acid (ABA) has been shown to reduce oxidative stress and promote the survival after cryopreservation. However, it is not clear which genes play important roles in this process. In this study, we added ABA to the dehydration step and analyzed the transcriptomic divergences between the ABA-treated group and the control group in three cryogenic steps (dehydration, unloading and recovery). By short time-series expression miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), the recovery step was identified as the period of significant changes in gene expression levels in cryopreservation. The addition of ABA promoted the upregulated expression of microtubule-related genes in the recovery step. We further identified AsKIN as a hub gene in the recovery step and verified its function. The results showed that overexpression of AsKIN enhanced the tolerance of Arabidopsis to oxidative stress in cryopreservation, influenced the expression of genes in response to cold and osmotic stress and promoted plant growth after stress. The AsKIN gene is likely to be involved in the plant response to cold stress and osmotic stress. These results reveal the molecular mechanisms of ABA in cryopreservation and elucidate the potential biological functions of the kinesin-14 subfamily.

Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

BackgroundHot pepper (Capsicum annuum L.) is one of the world’s oldest domesticated crops. It has poor waterlogging tolerance, and flooding frequently results in plant death and yield reduction. Therefore, understanding the molecular mechanisms associated with pepper waterlogging tolerance is essential to grow new varieties with stronger tolerance.ResultsIn this study, we discovered that after 5 days of flooding, the growth rate of waterlogging-tolerant pepper cultivars did not reduce to a large extent. Physiological data revealed that chlorophyll concentration was not significantly affected by flooding; however, stomatal conductance was altered considerably 0–5 days after flooding, and the net photosynthesis rate changed substantially 5–10 days after flooding. In addition, the root activity of waterlogging-tolerant varieties was substantially higher after flooding for 10 days than that of the control. This implies that the effect of flooding is associated with changes in the root environment, which ultimately affects photosynthesis. We evaluated changes in gene expression levels between two pepper types at the same time point and the same pepper variety at different time points after flooding stress treatment and performed a screening for multiple potential genes. These differentially expressed genes (DEGs) were further analyzed for functional enrichment, and the results revealed that antioxidase genes, cell wall synthesis pathway genes, and calcium ion regulation pathway genes might be associated with waterlogging tolerance. Other genes identified in peppers with waterlogging tolerance included those associated with lignin synthesis regulation, reactive oxygen species (ROS) regulation pathways, and others associated with stress resistance. Considerable changes in the expression levels of these genes were recorded 5 days after waterlogging, which was consistent with a considerable increase in oxidase content that was also noted on the fifth day after flooding. The quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) findings revealed that among the 20 selected DEGs, including genes such as mitogen-activated protein kinase 3 (MPK3) and calcium-binding protein 4 (CML4), approximately 80% of the gene expression patterns were consistent with our RNA-seq dataset.ConclusionsThe findings of this study suggest that ROS modulation, increased antioxidase activity, lignin formation, and the expression of stress resistance genes help peppers with waterlogging tolerance resist flooding stress in the early stages. These findings provide a basis for further investigation of the molecular mechanisms responsible for waterlogging tolerance in pepper and may be a critical reference for the breeding of hot pepper.

Gene expression of carbonic anhydrase 9 (CA9) in de novo acute leukemia as a predictive marker for prognosis

Carbonic anhydrase 9 (CA9) is a marker for decreased O2 concentration and acidosis, associated with poor prognosis in cancerous patients. The current study suggested that the changes in CA9 gene expression level might be used as a predictive marker to assess early prognosis at the time of detection of de novo leukemia, and then monitor tumor progress during treatment. This study highlights the level of CA9 gene expression in leukemic patients. A total of 44 cases (acute myeloid leukaemia (AML) group: 23 cases; acute lymphoid leukaemia (ALL) group: 13 cases; control group: 8 healthy volunteers) were selected for this study. The CA9 gene expression was assessed by a real-time PCR with the SYBR green assay. A high level of CA9 gene expression was noticed in AML patients compared to the control group, while the results were not significant in ALL patients. After treatment follow-up, significant differences were observed in CA9 gene expression between a complete response and no response in AML patients. As a result, the CA9 tumor gene could act as a potential early marker for acute leukemia prognosis. A low level of CA9 expression was associated with better clinical outcomes, while a high level was related to a negative prognosis in patients with AML.

CCL2 Gene Expression and Protein Level Changes Observed in Response to Wingate Anaerobic Test in High-Trained Athletes and Non-Trained Controls.

Intensive, acute exercise may bring a large systemic inflammatory response marked by substantial increases in inflammatory cytokines and chemokines. One such chemokines–CCL2–is a key factor involved in inflammatory reaction to exercise. The direct aim of the study was to describe the changes in the CCL2 expression levels after anaerobic exercise in well-trained athletes adapted to long-term training and in non-trained participants. The expression of CCL2 mRNA was evaluated in peripheral blood MNCs and CCL2 protein level was observed in blood plasma. The changes were assessed as the response to an acute, intensive bout of exercise (Wingate Anaerobic Test) in two groups of participants: well-trained soccer players and non-trained individuals. An increase of CCL2 expression inn both mRNA and protein levels was observed. The response was greater in non-trained individuals and elevated levels of CCL2 transcripts persisted for more than 24 h after exercise. Well-trained individuals responded more modestly and the effect was attenuated relatively quickly. This shows muscular adaptation to a continuous training regime in well-trained individuals and better control of immune reactions to muscular injury. In non-training individuals, the induction of the inflammatory response was greater, suggesting presence of more serious myotrauma.

Polyvinyl alcohol/gelatin hydrogels regulate cell adhesion and chromatin accessibility

Cell adhesion has a critical influence on various processes such as cancer metastasis and wound healing. Many substrates have been used for studying cell adhesion and its related biological processes, it is still highly desirable to have a simply prepared and low-cost substrate suitable for regulating cell adhesion. In this study, we produced a series of polyvinyl alcohol/gelatin hydrogels with different gelatin concentrations via dry-annealing method. Our data showed that the protein adsorbing capability was enhanced and cell adhesion area and the ratio of non-spherical cells were increased with the increment of gelatin concentration. We also observed that varying cell adhesion conditions induced by polyvinyl alcohol /gelatin hydrogels resulted in expression level changes of genes involved in mechanotransduction from extracellular matrices (ECM) to the nucleus. In particular, we detected a widespread increase in chromatin accessibility under poor cell adhesion condition. This work provides a useful hydrogel system for regulating cell adhesion and opens up new possibilities for the design of biomaterials for cell adhesion study.

Xenobiotic responses of Drosophila melanogaster to insecticides with different modes of action and entry.

Depending on their chemical structure, insecticides enter the insect body either through the cuticle or by ingestion (mode of entry[MoE]), and, naturally, harm or even kill insects through different mechanisms (modes of action). In parallel, they trigger a systemic detoxification response, especially by activation of detoxification gene expression. We monitored the acute genetic alterations of known xenobiotic response target genes against five different insecticides with two most common MoEs (contact toxicity and stomach toxicity), found that: 1. only a few genes were detected responding to acute exposure to insecticides (LD90 ); 2. The expression of cyp12d1 was upregulated in all experiments, except for dichlorodiphenyltrichloroethaneexposure, suggesting that cyp12d1 is a general first response gene of the xenobiotic response; 3. The contact and stomach entries did not show any notable difference, both MoEs induced the response of JNK signaling pathway, possibly serving as the driver of the response of cyp12d1 and a few other genes. In conclusion, the changes in gene expression levels were relatively modest and no significant differences were found between the two MoEs, so the insecticide entry route does not seem to have an impact on the detoxification response. However, the two MoEs of the same insecticide showed different efficiencies in our test. Thus, the study of these two MoEs will help to develop more efficient release and management methods for the use of such insecticides.

Morpho-physiological, biochemical and molecular characterization of coastal rice landraces to identify novel genetic sources of salinity tolerance

Soil salinity is a leading cause for yield losses in rice, affecting nearly 6% of global rice cultivable area. India is host to a rich diversity of coastal rice landraces that are naturally tolerant to salinity and an untapped source to identify novel determinants of salinity tolerance. In the present study, we have assessed the relative salinity tolerance of 43 previously genotyped rice landraces at seedling stage, using thirteen morpho-physiological and biochemical parameters using a hydroponics system. Among 43 rice varieties, 25 were tolerant, 15 were moderately tolerant, 1 was moderately susceptible and 2 sensitive checks were found to be highly susceptible based on standard salinity scoring methods. In addition to previously known saline tolerant genotypes (Pokkali, FL478 and Nona Bokra), the present study has novel genotypes such as Katrangi, Orkyma, Aduisen 1, Orumundakan 1, Hoogla, and Talmugur 2 as potential sources of salinity tolerance through measurement of morpho-physiological and biochemical parameters including Na+, K+ estimations and Na+/K+ ratios. Further, Pallipuram Pokkali may be an important source of the tissue tolerance trait under salinity. Four marker trait associations (RM455-root Na+; RM161-shoot and root Na+/K+ ratios; RM237-salinity tolerance index) accounted for phenotypic variations in the range of 20.97–39.82%. A significant increase in root endodermal and exodermal suberization was observed in selected rice landraces under salinity. For the first time, variation in the number of suberized sclerenchymatous layers as well as passage cells is reported, in addition to expression level changes in suberin biosynthetic genes (CYP86A2, CYP81B1, CYP86A8 and PERL).

Transcriptome Analysis Reveals Potential Mechanisms of L-Serine Production by Escherichia coli Fermentation in Different Carbon-Nitrogen Ratio Medium.

L-serine is an industrially valuable amino acid that is widely used in the food, cosmetics and pharmaceutical industries. In this study, transcriptome sequencing technology was applied to analyze the changes in gene expression levels during the synthesis of L-serine in Escherichia coli fermentation. The optimal carbon–nitrogen ratio for L-serine synthesis in E. coli was determined by setting five carbon–nitrogen ratios for shake flask fermentation. Transcriptome sequencing was performed on E. coli fermented in five carbon–nitrogen ratio medium in which a total of 791 differentially expressed genes (DEGs) were identified in the CZ4_vs_CZ1 group, including 212 upregulated genes and 579 downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of these DEGs showed that the effect of an altered carbon–nitrogen ratio on the fermentability of E. coli was mainly focused on metabolic pathways such as GABAergic synapse and the two-component system (TCS) in which the genes playing key roles were mainly gadB, gadA, glsA, glnA, narH and narJ. In summary, these potential key metabolic pathways and key genes were proposed to provide valuable information for improving glucose conversion during E. coli fermentation.