Gene Expression Studies Research Articles

Virus susceptibility of a new cell line derived from the muscle of koi (Cyprinus carpio koi).

In this study, a continuous cell line (KM cells) derived from koi (Cyprinus carpio koi) muscle was established and characterized. The KM cells were subcultured for more than 70 passages and showed high viability after long-term cryopreservation. The KM cell line was optimally cultured in medium 199 containing 10% foetal bovine serum at 25°C. A chromosome analysis indicated that the cell line remained diploid, with a mean chromosome count of 100. DNA sequencing and comparative analysis of the 16S rRNA and cytochrome oxidase I gene sequences showed that the KM cell line originated from koi. In transfection experiments using the plasmid pEGFP, KM cells demonstrated a high level of transfection efficiency, suggesting their potential for use in foreign gene expression studies. Inoculation with spring viraemia of carp virus (SVCV) resulted in a substantial cytopathic effect, and the level of production of SVCV in KM cells was higher than that in the epithelioma papulosum cyprinid (EPC) cell line that is normally used to produce the virus. However, no cytopathic effect was observed when these cells were inoculated with koi herpesvirus, carp oedema virus, or grass carp reovirus. These observations suggest that the newly established KM cell line will be a valuable tool for investigating the pathogenesis of infection with spring viraemia of carp virus.

Gene Expression Study in Gilthead Seabream (Sparus aurata): Effects of Dietary Supplementation with Olive Oil Polyphenols on Immunity, Metabolic, and Oxidative Stress Pathways

In an era with an ever-growing population, sustainability and green transition are the main milestones to be considered within the current European Green Deal program, and the recovery of by-products for the integration of feed with bioactive molecules, that are sustainable and with high nutritional value, is an ambitious mission to be explored also in aquaculture. Olive oil extraction produces a range of solid and liquid by-products, in varying proportions depending on the utilized production techniques, all of which are considered as possible pollutants. However, these products are also rich of polyphenols, bioactive molecules with several and well-known beneficial properties (antimicrobic, anti-inflammatory, antioxidant, and immune-modulating). On this basis, this work aimed at evaluating the effects of dietary supplementation with polyphenols derived from olive mill wastewater on growth performance and on gene expression modulation, by means of RT-qPCR assays, in farmed Sparus aurata. Particularly, some target genes of metabolic, immunity, and oxidative stress pathways have been investigated in breeding gilthead seabream. Differential gene expression analysis was carried out, and differences between the control group (n = 9) and the treated one (n = 9) were computed with Student’s t test. The results have highlighted that supplemented feed enhanced fish growth, with a significant feed conversion ratio between the two groups. Furthermore, the polyphenol diet had a beneficial impact on gene expression fold with a level of significance for fatty acid binding protein 2, superoxide dismutase 1, and interleukin-12 genes at hepatic or intestinal district. These significant and promising preliminary findings promote, in the future, other investigations on polyphenolic by-products and on their putative or possible re-utilization in fish feeding.

Determination of qPCR reference genes suitable for normalizing gene expression in a novel model of Duchenne muscular dystrophy, the D2-mdx mouse.

Duchenne muscular dystrophy (DMD) is a X-linked neuromuscular disorder arising from mutations in the dystrophin gene, leading to a progressive muscle wasting and disability. Currently there is no universal therapy, and there is thus a strong interest in preclinical studies for finding novel treatments. The most widely used and characterized mouse model for DMD is the C57BL/10ScSn-Dmdmdx/J (BL10-mdx), but this model exhibits mild pathology and does not replicate key features of human disease. The D2.B10-Dmdmdx/J (D2-mdx) mouse is a more recent model which seems to better mimics the complex human DMD phenotype. However, the D2-mdx mouse remains less extensively characterised than its BL10-mdx counterpart. Quantitative PCR analysis of gene expression is an important tool to monitor disease progression and evaluate therapeutic efficacy, but measurements must be normalised to stably expressed reference genes, which should ideally be determined and validated empirically. We examined gene expression in the gastrocnemius (GC), diaphragm (DIA) and heart in the D2-mdx mouse, the BL10-mdx mouse, and appropriate strain-matched wild-type controls (D2-wt and BL10-wt), from 4 to 52 weeks of age, using a large panel of candidate references (ACTB, AP3D1, CSNK2A2, GAPDH, HPRT1, PAK1IP1, RPL13A, SDHA, and in the heart, also HTATSF1 and HMBS). Data was analyzed using GeNorm, Bestkeeper, deltaCt and Normfinder algorithms to identify stable references under multiple possible scenarios. We show that CSNK2A2, AP3D1 and ACTB represent strong universal reference genes in both GC and DIA, regardless of age, muscle type, strain and genotype, while HTATSF1 and SDHA are optimal for the heart. GAPDH, HPRT1 and RPL13A were conversely revealed to be poor references, showing tissue-, age- or disease-specific changes in expression. Our results illustrate the importance of determining appropriate reference genes for specific comparative scenarios, but also reconfirm that universal panels can nevertheless be identified for normalising gene expression studies in even complex pathological states.

Abstract 4134456: Hybrid Cardiac Targeting Peptide Ameliorates HFpEF Phenotype in Mice

Introduction: Heart failure with preserved ejection fraction (HFpEF) is a form of heart failure which is rapidly rising in incidence in the US today. Despite this, no therapies with mortality benefit exist for this syndrome. Previous work with our novel hybrid cardiac targeting peptide (hCTP), a cardiomyocyte-specific cell penetrating peptide, has shown multiple beneficial biological effects (improved calcium handling, anti-inflammatory properties) beyond its transduction abilities. Therefore, we hypothesized that treatment with hCTP in a mouse model of HFpEF would ameliorate the pathophysiology of this disease. Methods: To establish a HFpEF model, 6-week-old, C57BL/6NJ mice were placed on a high-fat diet (HFD), 60% kCal from lard, and water with 0.5 g/L of an iNOS inhibitor (N-Nitro-L-arginine methylester) to induce hypertension. After 5 weeks of the diet, HFD mice and their littermate controls underwent baseline exercise testing and echocardiograms. Exercise capacity was measured after 2 days of exercise training with 2 days of rest in between; mice were placed on a treadmill at a 10-degree angle and made to run at increasingly fast speeds (5-30 m/min) until exhaustion. Echocardiograms were performed under 1.5% inhalational isoflurane. After baseline testing, the mice were treated with vehicle, or either 2.5 or 5 mg/Kg hCTP, either 3 or 5 days a week (five groups, n = 3 per group). After four weeks of treatment, the mice were again subjected to the same battery of tests and euthanized. Data was compared using two way ANOVA with Sidak’s test to compare measurements pre- and post-treatment. Results: Treatment with hCTP at either concentration for five days/week led to an increase in running distance from 39.8 m to 116.3 m (p = 0.03, n = 6), compared to changes in control distance from 208.4 m to 157.8 m (p = 0.399). Running distance did not correlate with weight (R 2 < .001). Treatment with 5 mg/Kg hCTP for 5 days/week led to a normalization of the E/e’ ratio, from 43.3 to 26.9 (p = 0.004, n = 3) compared to a change in the control of 34.7 to 26.1 (p = 0.312). Ejection fractions remained consistent (>55%) across all groups. Conclusions: Our data suggests that hCTP appears to be a promising treatment in ameliorating some of the physiological effects in a murine model of HFpEF. Gene and protein expression studies in heart tissue are underway. Further work is warranted with a larger sample size.

Nanopore-Based Sequencing of the Full-Length Transcriptome of Male and Female Cleavage-Stage Embryos of the Chinese Mitten Crab (Eriocheir sinensis)

The cleavage stage plays a crucial role in embryo development, characterized by a swift surge in cell proliferation alongside the accurate genetic material transmission to offspring. To delve into the characteristics of sex development during the cleavage stage of embryos, we generated the full-length transcriptome of Eriocheir sinensis male and female cleavage-stage embryos using Oxford Nanopore Technologies (ONT). Notably, this investigation represents the first sequencing effort distinguishing between genders in E. sinensis embryos. In the transcriptome structure analysis, male and female cleavage-stage embryos, while not clustered, exhibited a comparable frequency of alternative splicing (AS) occurrences. We also successfully identified 2875 transcription factors (TFs). The quantitative analysis showed the top 150 genes, in which the highly expressed genes in male embryos predominantly related to protein synthesis and metabolism. Further investigation unveiled 500 differentially expressed genes (DEGs), of which 7 male-biased ribosomal protein genes (RPGs) were particularly noteworthy and further confirmed. These analyses suggest that there may be a more active protein synthesis process in male E. sinensis cleavage-stage embryos. Furthermore, among the 2875 identified TFs, we predicted that 18 TFs could regulate the differentially expressed RPGs, with most TFs belonging to the zf-C2H2 and Homeobox families, which are crucial for embryonic development. During the cleavage stage of E. sinensis, the differential RPGs between genders were intricately linked to energy metabolism. We proposed that these RPGs exert regulatory effects on gene expression in E. sinensis, thereby regulating the difference of development between male and females. Our research sheds light on the developmental mechanisms of E. sinensis during the embryo stage and establishes a groundwork for a deeper understanding of sex development in E. sinensis. The results also provide comprehensive full-length transcriptome data for future gene expression and genetic studies in E. sinensis.

Neutrophil and mononuclear leukocyte pathways and upstream regulators revealed by serum proteomics of adult and juvenile dermatomyositis.

Serum protein abundance was assessed in adult and juvenile dermatomyositis (DM and JDM) patients to determine differentially regulated proteins, altered pathways, and candidate disease activity biomarkers. Serum protein expression from 17 active adult DM and JDM patients each was compared to matched, healthy control subjects by a multiplex immunoassay. Pathway analysis and protein clustering of the differentially regulated proteins were examined to assess underlying mechanisms. Candidate disease activity biomarkers were identified by correlating protein expression with disease activity measures. Seventy-eight of 172 proteins were differentially expressed in the sera of DM and JDM patients compared to healthy controls. Forty-eight proteins were differentially expressed in DM, 32 proteins in JDM, and 14 proteins in both DM and JDM. Twelve additional differentially expressed proteins were identified after combining the DM and JDM cohorts. C-X-C motif chemokine ligand 10 (CXCL10) was the most strongly upregulated protein in both DM and JDM sera. Other highly upregulated proteins in DM included S100 calcium binding protein A12 (S100A12), CXCL9, and nicotinamide phosphoribosyltransferase (NAMPT), while highly upregulated proteins in JDM included matrix metallopeptidase 3 (MMP3), growth differentiation factor 15 (GDF15), and von Willebrand factor (vWF). Pathway analysis indicated that phosphoinositide 3-kinase (PI3K), p38 mitogen-activated protein kinase (MAPK), and toll-like receptor 7 (TLR7) signaling were activated in DM and JDM. Additional pathways specific to DM or JDM were identified. A protein cluster associated with neutrophils and mononuclear leukocytes and a cluster of interferon-associated proteins were observed in both DM and JDM. Twenty-two proteins in DM and 24 proteins in JDM sera correlated with global, muscle, and/or skin disease activity. Seven proteins correlated with disease activity measures in both DM and JDM sera. IL-1 receptor like 1 (IL1RL1) emerged as a candidate global disease activity biomarker in DM and JDM. Coordinate analysis of protein expression in DM and JDM patient sera by a multiplex immunoassay validated previous gene expression studies and identified novel dysregulated proteins, altered signaling pathways, and candidate disease activity biomarkers. These findings may further inform the assessment of DM and JDM patients and aid in the identification of potential therapeutic targets.

Multi-Omics Approach Reveals Genes and Pathways Affected in Miller-Dieker Syndrome.

Miller-Dieker syndrome (MDS) is a rare neurogenetic disorder resulting from a heterozygous deletion of 26 genes in the MDS locus on human chromosome 17. MDS patients often die in utero and only 10% of those who are born reach 10years of age. Current treatments mostly prevent complications and control seizures. A detailed understanding of the pathogenesis of MDS through gene expression studies would be useful in developing precise medical approaches toward MDS. To better understand MDS at the molecular level, we performed RNA sequencing on RNA and mass spectrometry on total protein isolated from BJ (non-MDS) cells and GM06097 (MDS) cells, which were derived from a healthy individual and an MDS patient, respectively. Differentially expressed genes (DEGs) at the RNA and protein levels involved genes associated with phenotypic features reported in MDS patients (CACNG4, ADD2, SPTAN1, SHANK2), signaling pathways (GABBR2, CAMK2B, TRAM-1), and nervous system development (CAMK2B, BEX1, ARSA). Functional assays validated enhanced calcium signaling, downregulated protein translation, and cell migration defects in MDS. Interestingly, overexpression of methyltransferase-like protein 16 (METTL16), a protein encoded in the MDS locus, restored defects in protein translation, phosphorstates of mTOR (mammalian target of rapamycin) pathway regulators, and cell migration in MDS cells. Although DNA- and RNA-modifying enzymes were among the DEGs and the intracellular SAM/SAH ratio was eightfold lower in MDS cells, global nucleoside modifications remained unchanged. Thus, this study identified specific genes and pathways responsible for the gene expression changes, which could lead to better therapeutics for MDS patients.

Evaluation and Validation of Reliable Reference Genes for Quantitative Real-Time PCR Analysis of the Gene Expression in Macadamia integrifolia

Macadamia is an economically significant crop, with its kernel oil being abundant in monounsaturated fatty acids (MUFA). Analyzing the expression of genes related to MUFA biosynthesis is essential for understanding the complex regulatory networks in Macadamia. However, there are few reports on the identification of suitable reference genes for use as internal controls in this species. Consequently, selecting a reliable reference gene for gene expression studies under various conditions is critical. In this study, we evaluated the expression stability of 11 traditional housekeeping genes: α-tubulin (TUBa), β-tubulin (TUBb), malate dehydrogenase (MDH), 18S ribosomal RNA (18S), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-elongation factor 1 (EF1a), β-elongation factor 1 (EF1b), ubiquitin (UBQ), ubiquitin-conjugating enzyme (UBC), cyclophilin (CYP), and actin (ACT) under abiotic stresses, hormonal treatments and in variety of plant tissues using the online tool RefFinder, which integrates four commonly used software programs: ΔCt, geNorm (version 3.4), NormFinder (version 0953), and BestKeeper (version 1.0). A comprehensive expression stability ranking was established by integrating results from these four methods based on the geometric mean. The findings indicated that ACT was the most stable gene across all samples, including those subjected to cold stress, NaCl stress, PEG stress, ABA treatment, MeJA treatment, and both stem and leaf tissues. EF1b was identified as the most stable gene in GA treatment and heat stress samples, while UBC and CYP were ranked highest in ethrel treatment and root tissue samples, respectively. Finally, the reliability of these findings was further validated using the target gene SAD through qRT-PCR. In summary, this study evaluated and validated appropriate reference genes for qRT-PCR, which will facilitate future investigations into the molecular mechanisms in Macadamia.

β-1,3-glucan from Euglena gracilis: a promising epidrug targeting epigenetic regulators PRMTs and SIRTs for therapeutic applications in ovarian cancer

Natural products serve as a valuable resource in drug discovery and the identification of bioactive molecules in the field of epimedicine, which targets epigenetic regulator enzymes through epidrugs. In this study, β-1,3-glucan (BG), a natural storage polysaccharide in Euglena gracilis, a well-known immunostimulatory agent, is propounded as a promising epidrug. To elucidate the therapeutic efficacy of BG against ovarian cancer, the molecular interactions between BG and epigenetic regulators, Protein Arginine Methyltransferases (PRMTs) and Sirtuins (SIRTs) were investigated using computational methods followed by in vitro gene expression studies in SKOV-3 ovarian cancer cell line. The binding energies of PRMT5 and SIRT5 against BG were observed as −65.5 and −68.2 kcal/mol, respectively. The in vitro cytotoxic effects of BG against human ovarian cancer cell line, SKOV-3 showed an IC50 of 150 µg/mL at 48 h. Significant epigenetic modifications were observed to be influenced by BG which increased the gene expression of PRMT5, SIRT5 and Nrf2 to 0.3, 0.5, and 0.7 fold-change respectively, while the Nrf1/2 plasmid showed reduced reporter activity by 29%. Collectively, both in silico and in vitro studies provided valuable insights into the epigenetic regulation of PRMT5 and SIRT5 by BG via Nrf1/2. Nonetheless, further preclinical and clinical investigations are essential to validate the therapeutic properties of BG as an epidrug against ovarian cancer.

Trans, Trans-Farnesol Enhances the Anti-Bacterial and Anti-Biofilm Effect of Arachidonic Acid on the Cariogenic Bacteria Streptococcus mutans and Streptococcus sobrinus.

Streptococcus mutans and Streptococcus sobrinus are Gram-positive bacteria involved in the development of dental caries, as they are able to form biofilms on tooth enamel, ferment sugars into acids, and survive under acidic conditions. This ultimately leads to a local lowering of the pH value on the tooth surface, which causes enamel cavities. One measure to reduce caries is to limit the growth of cariogenic bacteria by using two anti-bacterial agents with different mechanisms of action. The hypothesis of this study was that the anti-bacterial activity of ω-6 polyunsaturated arachidonic acid (AA) against S. mutans and S. sobrinus can be enhanced by the sesquiterpene alcohol trans, trans-farnesol (t,t-farnesol). The anti-bacterial activity of single and combined treatment was determined by the checkerboard assay. Bacterial viability was assessed by live/dead SYTO 9/propidium iodide (PI) staining on flow cytometry. Anti-biofilm activity was determined by MTT metabolic assay, crystal violet staining of biofilm biomass, SYTO 9/PI staining by spinning disk confocal microscopy (SDCM) and high-resolution scanning electron microscopy (HR-SEM). t,t-Farnesol lowered the minimum inhibitory concentration (MIC) and the minimum biofilm inhibitory concentration (MBIC) of AA at sub-MICs. AA reduced the metabolic activity of preformed mature biofilms, while t,t-farnesol had no significant effect. The enhanced anti-bacterial effect of the combined t,t-farnesol/AA treatment was further evidenced by increased PI uptake, indicating membrane perforation. The enhanced anti-biofilm effect was further verified by SDCM and HR-SEM. Gene expression studies showed reduced expression of some biofilm-related genes. Altogether, our study suggests a potential use of the two naturally occurring compounds arachidonic acid and t,t-farnesol for preventing biofilm formation by the cariogenic bacteria S. mutans and S. sobrinus. These findings have implications for caries prevention.

Validation of reference genes for cardiac RT-qPCR studies spanning the fetal to adult period

Many genes used as internal controls for mRNA expression studies are unstable (change) over development. This study determined an approach to validate reference genes for mRNA studies spanning the fetal period to adulthood in sheep hearts.•We determined the mRNA expression of 12 candidate reference genes (ACTB, GAPDH, H3-3A, HYAL2, PPIA, RNA18S1, RPL32, RPL37A, RPL41, RPLP0, RPS15, and YWHAZ) via RT-qPCR. Per RefFinder, which incorporates computational algorithms by BestKeeper, comparative delta Ct, GeNorm, and NormFinder, RPL32, RPL37A, HYAL2, ACTB and GAPDH were the most stable reference genes, although none were unchanged across all ages.•Systematical calculation of the geometric means of 3 reference genes revealed the combination of HYAL2, RPL32, and RPL37A was unchanged across the 5 fetal, neonatal, and adult ages.•We determined the most stable combination of reference genes for cardiac gene expression studies in sheep from fetus to newborn to adult; these steps are applicable to determine internal controls for mRNA studies in other organs, other species, and periods in which reference gene instability is high.

Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics.

Spatial transcriptomics technologies aim to advance gene expression studies by profiling the entire transcriptome with intact spatial information from a single histological slide. However, the application of spatial transcriptomics is limited by low resolution, limited transcript coverage, complex procedures, poor scalability and high costs of initial setup and/or individual experiments. Seq-Scope repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, overcoming these limitations. It offers submicrometer resolution, high capture efficiency, rapid turnaround time and precise annotation of histopathology at a much lower cost than commercial alternatives. This protocol details the implementation of Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell, allowing the profiling of multiple tissue sections in an area of 7 mm × 7 mm or larger. We describe the preparation of a fresh-frozen tissue section for both histological imaging and sequencing library preparation and provide a streamlined computational pipeline with comprehensive instructions to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single-cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Aside from array production and sequencing, which can be done in batches, tissue processing, library preparation and running the computational pipeline can be completed within 3 days by researchers with experience in molecular biology, histology and basic Unix skills. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology.

Association of antipsychotic drugs on type 2 diabetes mellitus risk in patients with schizophrenia: a population-based cohort and in vitro glucose homeostasis-related gene expression study

BackgroundType 2 diabetes mellitus (T2DM) and its related complications are associated with schizophrenia. However, the relationship between antipsychotic medications (APs) and T2DM risk remains unclear. In this population-based, retrospective cohort study across the country, we investigated schizophrenia and the effect of APs on the risk of T2DM, and glucose homeostasis-related gene expression.MethodsWe used information from the Longitudinal Health Insurance Database of Taiwan for individuals newly diagnosed with schizophrenia (N = 4,606) and a disease-free control cohort (N = 4,606). The differences in rates of development of T2DM between the two cohorts were assessed using a Cox proportional hazards regression model. The effects of APs on the expression of glucose homeostasis-related genes in liver and muscle cell lines were assessed using quantitative real-time PCR.ResultsAfter controlling potential associated confounding factors, the risk of T2DM was higher in the case group than that in the control group [adjusted hazard ratio (aHR), 1.80, p < 0.001]. Moreover, the likelihood of T2DM incidence in patients with schizophrenia without AP treatment (aHR, 2.83) was significantly higher than that in non-schizophrenia controls and those treated with APs (aHR ≤ 0.60). In an in vitro model, most APs did not affect the expression of hepatic gluconeogenesis genes but upregulated those beneficial for glucose homeostasis in muscle cells.ConclusionThis study demonstrates the impact of schizophrenia and APs and the risk of developing T2DM in Asian populations. Unmeasured confounding risk factors for T2DM may not have been included in the study. These findings may help psychiatric practitioners identify patients at risk of developing T2DM.

The Effect of Variegated Grasshopper Meal (Zonocerous variegatus) on Growth, Nutrient Utilization and Gene Expression Study in Juvenile Clarias gariepinus (Burchell, 1822)

Over the years there has been research on how to improve fish yield. This study investigated the effects of variegated grasshopper meal (Zonocerous variegatus) on growth performance, nutrient utilization, and gene expressions in juvenile Clarias gariepinus (African catfish). The variegated grasshopper meal diets (VGDMs) were incorporated with the other feed ingredients at 25% (VGDM1), 50% (VGDM2), 75% (VGDM2), and 100% (VGDM3) diets while the remaining group served as control. Growth performance, nutrient utilization, and gene expression study were evaluated. The mRNA expression of Growth hormone (GH), Heat Shock Protein (HSP70), Melatonin (MEL 1C), tumour necrosis factor-alpha (TNF-α), and interleukin 1 beta (IL-1β) were investigated in the liver and muscle of C. gariepinus fed with varying doses of grasshopper meals (VGDMs) using reverse transcriptase–polymerase chain reaction. There were significant (p&gt;0.05) variations in all parameters in all the treatments. There was a significant upregulation (p&lt;0.05) in the gene expression of GH, HSP70, MEL 1C, and TNF-α in VGDM1 compared to control in both tissue groups. In addition, there was significant downregulation (p&lt;0.05) in interleukin 1 (IL-1β) gene expression in liver VGDM2. This study suggests that dietary variations involving VGMD have the potential to boost growth and improve the immune responses of this fish species.

Intraspecific diversity is critical to population-level risk assessments

Environmental risk assessment (ERA) is critical for protecting life by predicting population responses to contaminants. However, routine toxicity testing often examines only one genotype from surrogate species, potentially leading to inaccurate risk assessments, as natural populations typically consist of genetically diverse individuals. To evaluate the importance of intraspecific variation in translating toxicity testing to natural populations, we quantified the magnitude of phenotypic variation between 20 Daphnia magna clones exposed to two levels of microcystins, a cosmopolitan cyanobacterial toxin. We observed significant genetic variation in survival, growth, and reproduction, which increased under microcystins exposure. Simulations of survival showed that using a single genotype for toxicity tolerance estimates on average failed to produce accurate predictions within the 95% confidence interval over half of the time. Whole genome sequencing of the 20 clones tested for correlations between toxicological responses and genomic divergence, including candidate loci from prior gene expression studies. We found no overall correlations, indicating that clonal variation, rather than variation at candidate genes, predicts population-level responses to toxins. These results highlight the importance of incorporating broad intraspecific genetic variation, without focusing specifically on variation in candidate genes, into ERAs to more reliably predict how local populations will respond to contaminants.

Efficacy of two different microbial consortia on salinity tolerance in chickpea: an in-planta evaluation on biochemical, histochemical, and genomic aspects.

This study aimed to identify and characterize actinobacteria and rhizobia with plant growth-promoting (PGP) traits from chickpea plants. Out of 275 isolated bacteria, 25 actinobacteria and 5 chickpea rhizobia showed 1-aminocyclopropane-1-carboxylate deaminase (ACCd) activity. Selected chickpea rhizobia were tested for their nodulating capacity under sterile and non-sterile soil conditions. Further screening on salinity and PGP traits identified three promising isolates: Nocardiopsis alba KG13, Sinorhizobium meliloti KGCR17, and Bacillus safensis KGCR11. These three isolates were analyzed for their compatibility and made into a consortium (Consortium 1). This along with another consortium made from our salinity-tolerant lab strains Chryseobacterium indologenes ICKM4 and Stenotrophomonas maltophilia ICKM15 (Consortium 2) was compared in planta studies. Trials revealed that Consortium 2 showed significant (p < 0.05) tolerance and on above-ground, below-ground traits and yield components than Consortium 1. Moreover, both consortia induced nodulation in saline-stressed plants, alleviated electrolyte leakage (2.3 vs. 0.4 in ICCV 2; 1.8 vs. 0.6 in JG 11), and increased chlorophyll content. Histochemical staining indicated reduced oxidative stress and lipid peroxidation in consortium-treated plants under salinity stress. Further, gene expression studies revealed mixed patterns, with up-regulation of antioxidant and transporter genes observed in consortium-treated plants, particularly in Consortium 2. Overall, Consortium 2 showed better gene expression levels for antioxidant and transporter genes, indicating its superior efficacy in mitigating salinity stress in chickpea plants. This study provides valuable insights into the potential use of these microbial isolates in improving chickpea productivity by enhancing salinity tolerance.

Comparative evaluation of DNA synthesis for qPCR analysis from oral squamous cell carcinoma tissues - A rapid and robust isolation technique for gene expression studies

BackgroundDNA isolation from biological materials is the initial step in several bioanalytical processes, including the polymerase chain reaction (PCR). This procedure works best with pure DNA devoid of potential amplification reaction inhibitors. Since the quantity and quality of biological samples are limited, it is essential to extract as much DNA as possible from the original sample. The solid-phase extraction technique is frequently used to purify DNA. In this process, the DNA is adsorbed onto a solid support, any contaminants from the reaction are eliminated by washing, and the purified DNA is then eluted from the support. The quality and concentration of DNA have a direct effect on the gene analysis procedure. Therefore, before interpreting the results of PCR-based diagnostic assays, it is imperative to confirm the DNA preparation and integrity, particularly if no pathogenic DNA is identified. MethodsA comparative study was carried out using two standardized protocols for DNA synthesis in comparison with a test protocol incorporating carrier RNA and proteinase K from a viral detection kit. The quality and quantity of the synthesized DNA are assessed by qPCR analysis for gene amplification of metastasis suppressor genes NDRG1, RhoGDI, and KISS 1. Results and conclusionThe test protocol showed higher yields of DNA in comparison to the standard protocol. The concentration of DNA obtained was validated by the concentration of gene expressed from q PCR analysis. The gene expression was significantly higher when the test protocol method was followed for DNA synthesis. Thus the study validates the potential of nucleic acid carrier RNA molecules to improve DNA extraction processes used in tissue samples for gene analysis procedures.

Gravitropic Gene Expression Divergence Associated With Adaptation to Contrasting Environments in an Australian Wildflower.

Plants adapt to their local environment through complex interactions between genes, gene networks and hormones. Although the impact of gene expression on trait regulation and evolution has been recognised for many decades, its role in the evolution of adaptation is still a subject of intense exploration. We used a Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which we derived from crossing multiple parents from two distinct coastal ecotypes of an Australia wildflower, Senecio lautus. We focused on studying the contrasting gravitropic behaviours of these ecotypes, which have evolved independently multiple times and show strong responses to natural selection in field experiments, emphasising the role of natural selection in their evolution. Here, we investigated how gene expression differences have contributed to the adaptive evolution of gravitropism. We studied gene expression in 60 pools at five time points (30, 60, 120, 240 and 480 min) after rotating half of the pools 90°. We found 428 genes with differential expression in response to the 90° rotation treatment. Of these, 81 genes (~19%) have predicted functions related to the plant hormones auxin and ethylene, which are crucial for the gravitropic response. By combining insights from Arabidopsis mutant studies and analysing our gene networks, we propose a preliminary model to explain the differences in gravitropism between ecotypes. This model suggests that the differences arise from changes in the transport and availability of the two hormones auxin and ethylene. Our findings indicate that the genetic basis of adaptation involves interconnected signalling pathways that work together to give rise to new ecotypes.

Preparation of bimetallic calcium chromatite nanocomposite using Stevia rebaudiana leaf extract for inducing apoptosis in human cancer cell lines

Abstract Despite the widespread industrial use of chromium-based compounds, there are concerns regarding their toxicity in biomedical applications. Herein, bimetallic calcium chromatite nanocomposite (CC) was prepared through green synthesis using Stevia rebaudiana leaf extract. A porous nanorod of CC was obtained through calcinations at 800oC. The formation of CC was confirmed by SEM (scanning electron microscopy), EDAX (Energy-dispersive X-ray spectroscopy), HRTEM (High-resolution transmission electron microscopy), TGA (Thermal gravimetric analysis), and BET (Brunauer-Emmett-Teller). The cytotoxicity of the CC was evaluated by the MTT method against cancer lines (HeLa, U87, A549) and primary cell line (HUVEC). The IC50 value of CC against cancer cell lines was lower than the primary cell lines. The calculated specificity index was greater than one, indicating that this CC might target cancer cells without the use of a targeting moiety. Gene expression studies revealed that CC upregulated the proapoptotic gene, BAX and downregulated the anti-apoptotic gene, Bcl-2, to induce apoptosis. The KDR and VEGF genes responsible for angiogenesis were down-regulated, indicating that CC decreases angiogenesis to promote apoptosis. The findings suggest CC prepared using phytoextract could be considered an adjuvant cancer therapy treatment.

Three-dimensional view of microglia-amyloid plaque interactions.

Recent gene expression studies have revealed about 10 different states of microglia, some of which are characteristic for Alzheimer-like amyloid plaque pathology. However, it is not presently known how these translate into morphological features that would reflect microglia interaction with amyloid plaques. With optimized conditions for confocal microscopy in amyloid plaque forming APP/PS1 transgenic mice we reveal new details of how microglia processes interact with amyloid plaques. The microglia contacts differed drastically between purely diffuse plaque and those with a fibrillar core. We identified microglia that extend their enlarged processes through the diffuse shell of the amyloid plaques and cover the fibrillar plaque core with snowplow-like expanded end-feet. These end-feet were filled with the lysosomal marker CD68, while both non-fibrillar and fibrillar amyloid was found in perinuclear vesicles of some "snowplower" microglia. In the organized dense-core plaques, we consistently saw a layer of Apolipoprotein E (ApoE) between the fibrillar core and the microglial end-feet. ApoE covered also loose fibrillar amyloid and diffuse amyloid plaques that were about 10 μm or larger in diameter. These findings are compatible with both amyloid plaque phagocytosis and compaction by microglia. Further, they support a chemotactic role of ApoE for microglia contacts with amyloid plaques.