Transcript Abundance Research Articles

Comprehensive Analyses of Four PhNF-YC Genes from Petunia hybrida and Impacts on Flowering Time.

Nuclear Factor Y (NF-Y) is a class of heterotrimeric transcription factors composed of three subunits: NF-A, NF-YB, and NF-YC. NF-YC family members play crucial roles in various developmental processes, particularly in the regulation of flowering time. However, their functions in petunia remain poorly understood. In this study, we isolated four PhNF-YC genes from petunia and confirmed their subcellular localization in both the nucleus and cytoplasm. We analyzed the transcript abundance of all four PhNF-YC genes and found that PhNF-YC2 and PhNF-YC4 were highly expressed in apical buds and leaves, with their transcript levels decreasing before flower bud differentiation. Silencing PhNF-YC2 using VIGS resulted in a delayed flowering time and reduced chlorophyll content, while PhNF-YC4-silenced plants only exhibited a delayed flowering time. Furthermore, we detected the transcript abundance of flowering-related genes involved in different signaling pathways and found that PhCO, PhGI, PhFBP21, PhGA20ox4, and PhSPL9b were regulated by both PhNF-YC2 and PhNF-YC4. Additionally, the transcript abundance of PhSPL2, PhSPL3, and PhSPL4 increased only in PhNF-YC2-silenced plants. Overall, these results provide evidence that PhNF-YC2 and PhNF-YC4 negatively regulate flowering time in petunia by modulating a series of flowering-related genes.

Interindividual behavioural variation in response to elevated CO2 predicts mRNA transcript abundance of genes related to acid-base regulation in medaka (Oryzias latipes)

Rising carbon dioxide (CO2) in aquatic ecosystems due to climate change is a challenge for aquatic ectotherms. We examined whether interindividual variation in behavioural responses to CO2 could predict how a teleost fish would respond to elevated CO2 for multiple phenotypic and molecular traits. To this end, we first quantified behavioural responses of individuals exposed to acute elevated CO2, and used these to assign individuals as either high or low responders relative to the population mean. Subsequently, we exposed both high and low responders to elevated CO2 for 6 weeks and quantified the effect on body condition, behaviour, and mRNA transcript responses of gill and liver genes associated with relevant physiological processes. Generally, we found few relationships between the phenotypic groups and body condition and behaviour following the CO2 exposure period; however, stark differences between the phenotypic groups with respect to gene transcripts from each tissue related to various processes were found, mostly independent of CO2 exposure. The most pronounced changes were in the gill transcripts related to acid-base regulation, suggesting that the observed behavioural variation used to assign fish to phenotypic groups may have an underlying molecular origin. Should the link between behaviour and gene transcripts be shown to have a fitness advantage and be maintained across generations, interindividual variation in behavioural responses to acute CO2 exposure may be a viable and non-invasive tool to predict future population responses to elevated aquatic CO2.

129 Selenium-form affects de novo cholesterol synthesis and catabolism of cholesterol and progesterone in the liver of beef heifers

Abstract A deficiency of selenium (Se) in soils and hence forages poses a challenge to producers in the southeast United States, necessitating supplementation of this trace mineral to the diet of pasture fed cattle. Se occurs in either inorganic (ISe) or organic (OSe) forms; ISe is conventionally available in commercial supplements, while OSe is available in grazed forages. We have investigated supplementation with either ISe or a 1:1 mixture of ISe:OSe (MIX) and demonstrated that MIX increases the relative abundance of mRNA encoding the low-density lipoprotein receptor (LDLR) and enzymes involved in de novo cholesterol synthesis in the corpus luteum, concurrent with a MIX-induced increase in systemic progesterone (P4) during the early luteal phase. We also observed a MIX-induced decrease in circulating cholesterol and low-density/very low-density lipoproteins during early gestation, and a MIX-induced increase in conceptus length at maternal recognition of pregnancy (MRP). The objective herein was to investigate the effect of form of Se (ISe versus MIX) on de novo cholesterol synthesis and cholesterol/steroid catabolism in the liver at MRP. We hypothesized form of Se would affect the abundance of transcripts that regulate synthesis, catabolism, and local concentrations of cholesterol and P4. Angus-cross heifers were supplemented with ISe or MIX for at least 90 d before insemination at observed estrus. On d 17 of pregnancy, heifers (n = 6/TRT) were killed and their reproductive tracts and conceptuses recovered. Hepatic samples were collected for qPCR analysis of mRNA transcripts encoding proteins involved in de novo cholesterol synthesis, regulation of cholesterol availability and steroid catabolism. Additionally, on d 7 and d 17 of pregnancy, we quantified systemic concentrations of high-density lipoproteins (HDL), indicative of cholesterol recycling to the liver. We quantified the relative abundance of 22 mRNAs and observed that heifers supplemented with MIX-form Se had an increase in the relative abundance of mRNA encoding the very low-density lipoprotein receptor (VLDLR, P = 0.01). Unexpectedly, we failed to detect an effect of TRT on the abundance of mRNA encoding the high-density lipoprotein receptor (SCARB1, P > 0.05) which was consistent with our inability to detect an effect on the serum concentration of total or free HDL (P > 0.05) during early pregnancy and at MRP. Of the 11 mRNA transcripts encoding enzymes involved in catabolism of cholesterol and progesterone, including steroid alpha reductases (SRD5A1 and SRD5A3) and cytochrome P450 enzymes (CYP4A2, CYP4A11, CYP11A1, and CYP17A1), we were unable to detect a difference in the relative abundance of any transcript. Overall, it appears that the form of Se is altering circulating concentrations of cholesterol and further affecting whole animal physiology and fertility; however, the mechanism involved remains to be fully elucidated and warrants further investigation.

Auxin and carbohydrate control flower bud development in Anthurium andraeanum during early stage of sexual reproduction

BackgroundFlower buds of Anthurium andraeanum frequently cease to grow and abort during the early flowering stage, resulting in prolonged planting times and increased commercialization costs. Nevertheless, limited knowledge exists of the mechanism of flower development after initiation in A. andraeanum.ResultsIn this study, the measurement of carbohydrate flow and intensity between leaves and flowers during different growth stages showed that tender leaves are strong sinks and their concomitant flowers are weak ones. This suggested that the tender leaves compete with their concomitant flower buds for carbohydrates during the early growth stages, potentially causing the abortion of the flower buds. The analysis of transcriptomic differentially expressed genes suggested that genes related to sucrose metabolism and auxin response play an important role during flower bud development. Particularly, co-expression network analysis found that AaSPL12 is a hub gene engaged in flower development by collaborating carbohydrate and auxin signals. Yeast Two Hybrid assays revealed that AaSPL12 can interact with AaARP, a protein that serves as an indicator of dormancy. Additionally, the application of exogenous IAA and sucrose can suppress the expression of AaARP, augment the transcriptional abundance of AaSPL12, and consequently expedite flower development in Anthurium andraeanum.ConclusionsCollectively, our findings indicated that the combination of auxin and sugar signals could potentially suppress the repression of AaARP protein to AaSPL12, thus advancing the development of flower buds in Anthurium andraeanum.

Eukaryotic plankton size structure and species composition in the wetland lakes

Eukaryotic plankton play an important role in the wetland lake ecosystems. However, the size structure and species composition of eukaryotic plankton in shallow wetland lake ecosystems remains largely unexplored. To address this gap, our study employed high-throughput sequencing and quantitative PCR techniques to investigate the size structure (pico-0.7–5 μm and nano-5–20 μm) and species composition of eukaryotic plankton in two shallow wetland lakes in China during August 2016. Our findings reveal that the diversity index values of the pico-size fraction were significantly higher than those of the nano-size fraction. Additionally, there was a significant difference in community structure between these two size fractions. Furthermore, different dominant taxa were associated with each particle size, with certain lineages being enriched exclusively in one of the size fractions. In particular, biomarkers differed between the pico- and nano- fractions. The abundance of the 18S rDNA gene did not differ significantly between the two fractions. However, there was a significant difference in the abundance of gene transcripts. Moreover, the pico- fraction exhibited a significantly higher rRNA: rDNA ratio compared to the nano- fraction. It is important to note that certain taxa had lower absolute abundance in specific samples, despite their higher relative abundance.

In vitro toxicity of Lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) on Human Renal and Hepatoma Cells

We evaluate the cytotoxicity, intracellular redox conditions, apoptosis, and methylation of DNMTs/TETs upon exposure to LiTFSI, a novel Per and Polyfluoroalkyl Substances (PFAS) commonly found in lithium-ion batteries, on human renal carcinoma cells (A498) and hepatoma cells (HepG2). The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay showed both Perfluorooctane sulfonate (PFOS) and Lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) had a dose-dependent effect on A498 and HepG2, with LiTFSI being less toxic. Intracellular redox conditions were assessed with a microplate reader and confocal, which showed a significant decrease in Reactive Oxygen Species (ROS) levels and an increase in Superoxide dismutase (SOD) content in both cells. Exposure to LiTFSI enhanced cell apoptosis, with HepG2 being more susceptible than A498. Quantitative analysis of mRNA expression levels of 19 genes associated with kidney injury, methylation, lipid metabolism and transportation was performed. LiTFSI exposure impacted kidney function by downregulating smooth muscle alpha-actin (Acta2) and upregulating transforming growth factor beta 1 (Tgfb1), B-cell lymphoma 2-like 1) Bcl2l1, hepatitis A virus cellular receptor 1 (Harvcr1), nuclear factor erythroid 2-like 2 (Nfe2l2), and hairy and enhancer of split 1 (Hes1) expression. LiTFSI exposure also affected the abundance of transcripts associated with DNA methylation by the expression of ten-eleven translocation (TET) and DNA methyltransferase (DNMT) genes. Furthermore, LiTFSI exposure induced an increase in lipid anabolism and alterations in lipid catabolism in HepG2. Our results provide new insight on the potential role of a new contaminant, LiTFSI in the regulation of oxidative stress, apoptosis and methylation in human renal carcinoma and hepatoma cells.

Characterization of a CrPME indicates its possible role in determining vindoline accumulation in Catharanthus roseus leaves.

The leaf-specific Catharanthus roseus alkaloid, vindoline, is the major bottleneck precursor in the production of scarce and costly anticancer bisindoles (vincristine and vinblastine). The final steps of its biosynthesis and storage occur in the laticifers. Earlier, we have shown that vindoline content is directly related to laticifer number. Pectin remodeling enzymes, like pectin methylesterase (PME), are known to be involved in laticifer development. A search in the croFGD yielded a leaf-abundant CrPME isoform that co-expressed with a few vindoline biosynthetic genes. Full-length cloning, tissue-specific expression profiling, and in silico analysis of CrPME were carried out. It was found to possess all the specific characteristics of a typical plant PME. Transient silencing (through VIGS) and overexpression of CrPME in C. roseus indicated a direct relationship between its expression and vindoline content. Comparative analysis of transcript abundance and enzyme activity in three familial C. roseus genotypes differing significantly in their vindoline content and laticifer count (CIM-Sushil > Dhawal > Nirmal) also corroborated the positive relationship of CrPME expression with vindoline content. This study highlights the possible role of CrPME, a cell wall remodeling enzyme, in modulating laticifer-associated secondary metabolism.

LncRNA NEAT1 promotes angiogenesis of retinoblastoma cells through regulation of the miR-106a/HIF-1α axis

ObjectiveTo explore the role and mechanisms of lncRNA nuclear enriched abundant transcript 1 (NEAT1) in angiogenesis of retinoblastoma (RB) cells. MethodsThis study investigated the roles of NEAT1 in RB progression. The RNA expression levels of NEAT1, miR-106a, and hypoxia-inducible factor-1alpha (HIF-1α) examined by quantitative reverse transcription polymerase chain reaction (RT-qPCR) were compared between RB cells and normal retinal pigment epithelial (RPE) cells. The binding sites between NEAT1 and miR-106a, and between miR-106a and HIF-1α were predicted by the TargetScan database and verified using the dual-luciferase reporter assay. By transfection of overexpression plasmid or shRNA of NEAT1, and/or treatment of miR-106a inhibitor or mimics, proliferation, invasion, and angiogenesis of RB cells (measured by the MTT assay, the Transwell assay, and the tube formation assay, respectively) were compared between groups. Group comparisons were analyzed using one-way analysis of variance (ANOVA), and Tukey's post-hoc test was employed for further statistical assessment. P-value less than 0.05 was considered statistically significant. ResultsThe RNA expression levels of NEAT1 and HIF-1α were upregulated in RB cells, whereas the expression level of miR-106a was downregulated compared with RPE cells. NEAT1 overexpression or miR-106a knockdown advanced proliferation, invasion, and tube formation of RB cells. As a target of NEAT1, miR-106a could sponge HIF-1α to downregulate HIF-1α expression level. Functional analyses indicated that miR-106a knockdown reversed the inhibitory effects of NEAT1 silencing on the proliferation, invasion, and tube formation of RB cells. Furthermore, miR-106a overexpression suppressed RB cell angiogenesis by downregulating HIF-1α expression level. ConclusionNEAT1 promoted proliferation, invasion, and angiogenesis of RB cells through upregulation of HIF-1α expression level by sponging miR-106a, demonstrating that NEAT1 may be a novel target for RB treatment.

DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory.

The conformational state of DNA fine-tunes the transcriptional rate and abundance of RNA. Here, we report that G-quadruplex DNA (G4-DNA) accumulates in neurons, in an experience-dependent manner, and that this is required for the transient silencing and activation of genes that are critically involved in learning and memory in male C57/BL6 mice. In addition, site-specific resolution of G4-DNA by dCas9-mediated deposition of the helicase DHX36 impairs fear extinction memory. Dynamic DNA structure states therefore represent a key molecular mechanism underlying memory consolidation.One-Sentence Summary: G4-DNA is a molecular switch that enables the temporal regulation of the gene expression underlying the formation of fear extinction memory.

Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants.

Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation-tolerant moss, provides valuable insights into survival of water-limited conditions. We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana. The genome was assembled into 12 chromosomes encompassing 21 169 protein-coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation-associated gene families, and highlighted genome-level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)-responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA-insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA-dependent stress response in Arabidopsis. The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.

Effects of serta and sertb knockout on aggression in zebrafish (Danio rerio).

Zebrafish (Danio rerio) are unusual in having two paralogues of the serotonin re-uptake transporter (Sert), slc6a4a (serta) and slc6a4b (sertb), the transporter that serves in serotonin re-uptake from a synapse into the pre-synaptic cell or in serotonin uptake from the extracellular milieu into cells in the peripheral tissues. To address a knowledge gap concerning the specific roles of these paralogues, we used CRISPR/Cas9 technology to generate zebrafish knockout lines predicted to lack functional expression of Serta or Sertb. The consequences of loss-of-function of Serta or Sertb were assessed at the gene expression level, focusing on the serotonergic signalling pathway, and at the behaviour level, focusing on aggression. Whereas serta mRNA was expressed in all tissues examined, with high expression in the heart, gill and brain, only the brain displayed substantial sertb mRNA expression. In both serta-/- and sertb-/- fish, changes in transcript abundances of multiple components of the serotonin signalling pathway were detected, including proteins involved in serotonin synthesis (tph1a, tph1b, tph2, ddc), packaging (vmat2) and degradation (mao), and serotonin receptors (htr1aa, htr1ab). Using a mirror aggression test, serta-/- male but not female fish exhibited greater aggression than wildtype fish. However, both male and female sertb-/- fish displayed less aggression than their wildtype counterparts. These differences in behaviour between serta-/- and sertb-/- individuals hold promise for increasing our understanding of the neurophysiological basis of aggression in zebrafish.

Blood and cerebellar abundance of ATXN3 splice variants in spinocerebellar ataxia type 3/Machado-Joseph disease

Spinocerebellar ataxia type 3 (SCA3)/Machado-Joseph disease (MJD) is a heritable proteinopathy disorder, whose causative gene, ATXN3, undergoes alternative splicing. Ataxin-3 protein isoforms differ in their toxicity, suggesting that certain ATXN3 splice variants may be crucial in driving the selective toxicity in SCA3. Using RNA-seq datasets we identified and determined the abundance of annotated ATXN3 transcripts in blood (n = 60) and cerebellum (n = 12) of SCA3 subjects and controls. The reference transcript (ATXN3–251), translating into an ataxin-3 isoform harbouring three ubiquitin-interacting motifs (UIMs), showed the highest abundance in blood, while the most abundant transcript in the cerebellum (ATXN3–208) was of unclear function. Noteworthy, two of the four transcripts that encode full-length ataxin-3 isoforms but differ in the C-terminus were strongly related with tissue expression specificity: ATXN3–251 (3UIM) was expressed in blood 50-fold more than in the cerebellum, whereas ATXN3–214 (2UIM) was expressed in the cerebellum 20-fold more than in the blood. These findings shed light on ATXN3 alternative splicing, aiding in the comprehension of SCA3 pathogenesis and providing guidance in the design of future ATXN3 mRNA-lowering therapies.

Expression patterns of m6A RNA methylation regulators under apoptotic conditions in various human cancer cell lines.

Cancer is a complex disease that involves both genetic and epigenetic factors. While emerging evidence clearly suggests that changes in epitranscriptomics play a crucial role in cancer pathogenesis, a comprehensive understanding of the writers, erasers, and readers of epitranscriptomic processes, particularly under apoptotic conditions remains lacking. The aim of this study was to uncover the changes in the expression of m6A RNA modifiers under apoptotic conditions across various cancer cell lines. Initially, we quantified the abundance of m6A RNA modifiers in cervical (HeLa and ME180), breast (MCF7 and MDA-MB-231), lung (A549 and H1299), and colon (Caco-2 and HCT116) cancer cell lines using qPCR. Subsequently, we induced apoptosis using cisplatin and tumor necrosis factor-alpha (TNF-α) to activate intrinsic and extrinsic pathways, respectively, and assessed apoptosis rates via flow cytometry. Further, we examined the transcript abundance of m6A RNA modifiers under apoptotic conditions in cervical, breast, and lung cancer cell lines using qPCR. Overall, treatment with cisplatin increased the abundance of m6A modifiers, whereas TNF-α treatment decreased their expression in cervical, breast, and lung cancer cell lines. Specifically, cisplatin-induced apoptosis, but not TNF-α-mediated apoptosis, resulted in decreased abundance of METTL14 and FTO transcripts. Additionally, cisplatin treatment drastically reduced the abundance of IGF2BP2 and IGF2BP3 readers. These results suggest that the differential response of cancer cells to apoptotic inducers may be partially attributed to the expression of m6A RNA modifiers.

Epigenetic-related transcriptional reprogramming elucidated by identification and validation of a novel reference gene combination for RT-qPCR studies in porcine oocytes of contrasting quality

BackgroundReliable RT-qPCR results are dependent on appropriate normalisation. Oocyte maturation studies can be challenging in this respect, as the stage of development can distinctively affect reference gene transcript abundance. The aim of this study was to validate the use of reference genes in oocyte in vitro maturation RT-qPCR studies, and thereafter, examine the abundance of transcripts supporting histone modification during oocyte and early embryo development in oocytes of contrasting quality.Methods and resultsTotal RNA from oocytes from prepubertal gilts and sows was extracted either directly succeeding follicle aspiration or after 44 h in vitro maturation, followed by RT-qPCR. The stability of YWHAG, HPRT1, ACTB, GAPDH, HMBS and PFKP, was analysed by NormFinder and further cross-validated by assessing results generated following application of different combinations of potential reference genes for normalisation of the RT-qPCR data. Combining ACTB and PFKP generated high stability according to NormFinder and concordant results. Applying this normalisation, gilt derived oocytes displayed significantly higher abundance than oocytes from sows of almost all the epigenetic-related transcripts studied (HDAC2, SIRT1, SALL4, KDM1A, KDM1B, KDM5A), both before and after maturation.ConclusionsThis study identified the combined use of ACTB and PFKP as the optimal normalisation for porcine oocyte RT-qPCR data. In oocytes collected from prepubertal gilts, transcription did not appear to be silenced at the time of aspiration, and accumulation of transcripts supporting histone modification facilitating proper fertilization and further embryo development seemed delayed. The results imply the epigenetic-related transcripts may have potential as markers of oocyte quality.

The Crucial Role of SlGSNOR in Regulating Postharvest Tomato Fruit Ripening.

S-nitrosoglutathione reductase (GSNOR) is a well-known regulator in controlling protein S-nitrosylation modification and nitric oxide (NO) homeostasis. Here, a GSNOR inhibitor N6022 and SlGSNOR silencing were applied to investigate the roles of SlGSNOR in tomato fruit postharvest ripening. We found that the application of N6022 and S-nitrosoglutathione (GSNO, a NO donor), and SlGSNOR silencing delayed the transition of fruit skin color by improving total chlorophyll level by 88.57%, 44.78%, and 91.03%, respectively. Meanwhile, total carotenoid and lycopene contents were reduced by these treatments. Concurrently, the activity of chlorophyll biosynthesis enzymes and the expression of related genes were upregulated, and the transcript abundances of total carotenoid bioproduction genes were downregulated, by N6022 and GSNO treatments and SlGSNOR silencing. In addition, fruit softening was postponed by N6022, GSNO, and SlGSNOR silencing, through delaying the decrease of firmness and declining cell wall composition; structure-related enzyme activity; and gene expression levels. Furthermore, N6022, GSNO, and SlGSNOR silencing enhanced the accumulation of titratable acid; ascorbic acid; total phenol; and total flavonoid, but repressed the content of soluble sugar and soluble protein accompanied with the expression pattern changes of nutrition-related genes. In addition, the endogenous NO contents were elevated by 197.55%; 404.59%; and 713.46%, and the endogenous SNOs contents were enhanced by 74.65%; 93.49%; and 94.85%; by N6022 and GSNO treatments and SlGSNOR silencing, respectively. Altogether, these results indicate that SlGSNOR positively promotes tomato postharvest fruit ripening, which may be largely on account of its negative roles in the endogenous NO level.

Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil

BackgroundThe final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).ResultsThe analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.ConclusionsThe predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils.7k5euw-hvBknz_jds4sXXfVideo

Detrimental impacts of concomitant application of cadmium and pesticides are ameliorated by 24-epibrassinolide through alteration in oxidative status and CYP genes expression in Zea mays L.

The ameliorative impact of 24-epibrassinolide (EBL) was assessed under toxicity of cadmium (Cd) and three different pesticides including diazinon (DZ), imidacloprid (IMI), and chlorpyrifos (CPS) in maize plants. Maize seeds were pre-treated with 0.01 μM of EBL and grown in soil contaminated with 100 μM Cd for one month. Then, at five fully expanded leaf stage, plants received DZ, IMI, and CPS pesticides separately by foliar spray and were harvested five days later. The EBL seed primed plants, grown in soil contaminated with Cd and exposed to pesticides, exhibited higher deleterious photosynthesis (Pn) and stomatal conductivity (Gs) compared to un-EBL-treated plants. A considerable decrease was observed in the pesticide's residue and Cd, MDA and H2O2 contents of EBL + Cd + Pesticide treated plants compared to the Cd + Pesticide groups plants. Higher phenol, flavonoid and protein contents, as well as increment in SOD, CAT, POD, APX, PAL, GST, and GR enzymes activity were detected in EBL + Cd + Pesticide groups compared to the plants imposed with Cd + Pesticides. The expression analyses of four CYP family members including CYP71C1, CYP71C3v2, CYP72A5, and CYP81A9 revealed downregulation under Cd and Cd + pesticides treatments, while EBL seed priming highly induced transcript abundance of CYP71C1 (EBL + Cd + IMI); CYP71C3v2 (EBL + Cd + DZ & EBL + Cd + IMI) and CYP81A9 (EBL + Cd + DZ & EBL + Cd + CPS), specifically. The higher mRNA accumulation of CYP72A5 gene was exhibited under all three different EBL + Cd + pesticides treatments. The 24-epibrassinolide alleviates the adverse impacts of Cd and pesticides via the activation of enzymatic and non-enzymatic components to eliminate ROS through the up-regulation of CYP genes. This facilitates conjugation of glutathione to pesticides residue, leading to their rapid transportation into the vacuole or out of the membrane.

Genomic characterization, phylogenetic and expression analysis of foraging gene in Apis mellifera

The genomic characterization of the foraging gene and its expression analysis are required to better understand the behavior of honey bees (Apis mellifera). The present study performed a genome-wide characterization of the foraging gene, analyzing its physicochemical properties, phylogenetic features, and expression. An in silico analysis was carried out to characterize the foraging gene and the motifs and conserved domains of the encoded protein to predict its physicochemical properties. Moreover, a phylogenetic analysis of the foraging gene was performed in different species using MEGAX. The relative expression of the foraging gene was determined using qRT-PCR in two groups of forager bee samples (incoming and outgoing bees) during two seasons (five times per day). In addition, the queen effect was evaluated in another experiment. The results revealed that foraging gene expression and bee traffic were influenced by the interaction of season and daytime. The daily foraging traffic and transcription level of the foraging gene were the same in both seasons. The traffic of bees and the transcription abundance of the foraging gene were the highest in the middle and at the end of the day in the first and second seasons, respectively. Furthermore, the mRNA expression of the foraging gene was relatively higher in incoming bees than in outgoing bees. The queen also had a significant effect on the outgoing bees. We conclude that gene–environment interactions affect the foraging behavior of bees through the modulation of the foraging gene transcription.

Pseudomonas aeruginosa transcriptome analysis of metal restriction in ex vivo cystic fibrosis sputum.

Chronic Pseudomonas aeruginosa lung infections are a feature of cystic fibrosis (CF) that many patients experience even with the advent of highly effective modulator therapies. Identifying factors that impact P. aeruginosa in the CF lung could yield novel strategies to eradicate infection or otherwise improve outcomes. To complement published P. aeruginosa studies using laboratory models or RNA isolated from sputum, we analyzed transcripts of strain PAO1 after incubation in sputum from different CF donors prior to RNA extraction. We compared PAO1 gene expression in this "spike-in" sputum model to that for P. aeruginosa grown in synthetic cystic fibrosis sputum medium to determine key genes, which are among the most differentially expressed or most highly expressed. Using the key genes, gene sets with correlated expression were determined using the gene expression analysis tool eADAGE. Gene sets were used to analyze the activity of specific pathways in P. aeruginosa grown in sputum from different individuals. Gene sets that we found to be more active in sputum showed similar activation in published data that included P. aeruginosa RNA isolated from sputum relative to corresponding in vitro reference cultures. In the ex vivo samples, P. aeruginosa had increased levels of genes related to zinc and iron acquisition which were suppressed by metal amendment of sputum. We also found a significant correlation between expression of the H1-type VI secretion system and CFTR corrector use by the sputum donor. An ex vivo sputum model or synthetic sputum medium formulation that imposes metal restriction may enhance future CF-related studies.IMPORTANCEIdentifying the gene expression programs used by Pseudomonas aeruginosa to colonize the lungs of people with cystic fibrosis (CF) will illuminate new therapeutic strategies. To capture these transcriptional programs, we cultured the common P. aeruginosa laboratory strain PAO1 in expectorated sputum from CF patient donors. Through bioinformatic analysis, we defined sets of genes that are more transcriptionally active in real CF sputum compared to a synthetic cystic fibrosis sputum medium. Many of the most differentially active gene sets contained genes related to metal acquisition, suggesting that these gene sets play an active role in scavenging for metals in the CF lung environment which may be inadequately represented in some models. Future studies of P. aeruginosa transcript abundance in CF may benefit from the use of an expectorated sputum model or media supplemented with factors that induce metal restriction.

DNA methylation: an emerging paradigm of gene regulation under drought stress in plants.

Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.