Transcript Abundance Of Genes Research Articles

Expression profiling of Nuclear Factor-Y (NF-Y) transcription factors during dehydration and salt stress in finger millet reveals potential candidate genes for multiple stress tolerance.

Expression profiling of NF-Y transcription factors during dehydration and salt stress in finger millet genotypes contrastingly differing in tolerance levels identifies candidate genes for further characterization and functional studies. The Nuclear Factor-Y (NF-Y) transcription factors are known for imparting abiotic stress tolerance in different plant species. However, there is no information on the role of this transcription factor family in naturally drought-tolerant crop finger millet (Eleusine coracana L.). Therefore, interpretation of expression profiles against drought and salinity stress may provide valuable insights into specific and/or overlapping expression patterns of Eleusine coracana Nuclear Factor-Y (EcNF-Y) genes. Given this, we identified 59 NF-Y (18 NF-YA, 23 NF-YB, and 18 NF-YC) encoding genes and designated them EcNF-Y genes. Expression profiling of these genes was performed in two finger millet genotypes, PES400 (dehydration and salt stress tolerant) and VR708 (dehydration and salt stress sensitive), subjected to PEG-induced dehydration and salt (NaCl) stresses at different time intervals (0, 6, and 12h). The qRT-PCR expression analysis reveals that the six EcNF-Y genes namely EcNF-YA1, EcNF-YA5, EcNF-YA16, EcNF-YB6, EcNF-YB10, and EcNF-YC2 might be associated with tolerance to both dehydration and salinity stress in early stress condition (6h), suggesting the involvement of these genes in multiple stress responses in tolerant genotype. In contrast, the transcript abundance of finger millet EcNF-YA5 genes was also observed in the sensitive genotype VR708 under late stress conditions (12h) of both dehydration and salinity stress. Therefore, the EcNF-YA5 gene might be important for adaptation to salinity and dehydration stress in sensitive finger millet genotypes. Therefore, this gene could be considered as a susceptibility determinant, which can be edited to impart tolerance. The phylogenetic analyses revealed that finger millet NF-Y genes share strong evolutionary and functional relationship to NF-Ys governing response to abiotic stresses in rice, sorghum, maize, and wheat. This is the first report of expression profiling of EcNF-Ys genes identified from the finger millet genome and reveals potential candidate for enhancing dehydration and salt tolerance.

Expression of honey bee (Apis mellifera) sterol homeostasis genes in food jelly producing glands of workers.

Adult workers of Western honey bees (Apis mellifera L.) acquire sterols from their pollen diet. These food sterols are transported by the hemolymph to peripheral tissues such as the mandibular and the hypopharyngeal glands in the worker bees' heads that secrete food jelly which is fed to developing larvae. As sterols are obligatory components of biological membranes and essential precursors for molting hormone synthesis in insects, they are indispensable to normal larval development. Thus, the study of sterol delivery to larvae is important for a full understanding of honey bee larval nutrition and development. Whereas hypopharyngeal glands only require sterols for their membrane integrity, mandibular glands add sterols, primarily 24-methylenecholesterol, to its secretion. For this, sterols must be transported through the glandular epithelial cells. We have analyzed for the first time in A. mellifera the expression of genes which are involved in intracellular movement of sterols. Mandibular and hypopharyngeal glands were dissected from newly emerged bees, 6-day-old nurse bees that feed larvae and 26-day-old forager bees. The expression of seven genes involved in intracellular sterol metabolism was measured with quantitative real-time PCR. Relative transcript abundance of sterol metabolism genes was significantly influenced by the age of workers and specific genes but not by gland type. Newly emerged bees had significantly more transcripts for six out of seven genes than older bees indicating that the bulk of the proteins needed for sterol metabolism are produced directly after emergence.

Fasting as a precursor to high-fat diet enhances mitochondrial resilience in Drosophila melanogaster.

Changes in diet type and nutrient availability can impose significant environmental stress on organisms, potentially compromising physiological functions and reproductive success. In nature, dramatic fluctuations in dietary resources are often observed and adjustments to restore cellular homeostasis are crucial to survive this type of stress. In this study, we exposed male Drosophila melanogaster to two modulated dietary treatments: one without a fasting period before exposure to a high-fat diet and the other with a 24-h fasting period. We then investigated mitochondrial metabolism and molecular responses to these treatments. Exposure to a high-fat diet without a preceding fasting period resulted in disrupted mitochondrial respiration, notably at the level of complex I. On the other hand, a short fasting period before the high-fat diet maintained mitochondrial respiration. Generally, transcript abundance of genes associated with mitophagy, heat-shock proteins, mitochondrial biogenesis, and nutrient sensing pathways increased either slightly or significantly following a fasting period and remained stable when flies were subsequently put on a high-fat diet, whereas a drastic decrease of almost all transcript abundances was observed for all these pathways when flies were exposed directly to a high-fat diet. Moreover, mitochondrial enzymatic activities showed less variation after the fasting period than the treatment without a fasting period. Overall, our study sheds light on the mechanistic protective effects of fasting prior to a high-fat diet and highlights the metabolic flexibility of Drosophila mitochondria in response to abrupt dietary changes and have implication for adaptation of species to their changing environment.

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.

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.

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.

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.

Perception of strigolactones and the coordinated phytohormonal regulation on rice (Oryza sativa) tillering is affected by endogenous ascorbic acid.

Phytohormones play a key role in regulating tiller number. Ascorbic acid (Asc)-phytohormone interaction plays a pivotal role in the regulation of senescence. We analysed the relationship between Asc and the enzyme concentrations and gene transcript abundances related to the signal perception of strigolactones (SLs), the contents of four phytohormones (abscisic acid, ABA; jasmonic acid, JA; indole acetic acid, IAA; cytokinin, CTK), the enzyme concentrations and gene transcript abundances related to the synthesis or transportation of these four phytohormones. Our results showed that Asc deficiency leads to the upregulation of enzyme concentrations, gene transcript abundances related to the SL signal perception, ABA synthesis and IAA transport. The altered level of Asc also leads to a change in the contents of ABA, JA, IAA and CTK. These findings support the conclusion that Asc or Asc/DHA play an important role in the signal perception and transduction of SLs, and Asc may affect the coordinated regulation of SL, IAA and CTK on rice (Oryza sativa ) tillering.

The fasciclin-like arabinogalactan protein FLA11 of Ostrya rehderiana impacts wood formation and salt stress in Populus

Wood is an abundant source of biomass and an important biomaterial for renewable resources and industrial products worldwide. Fasciclin-like arabinogalactan proteins (FLAs) are essential for plant growth, development, and responses to various abiotic stresses and are also closely associated with wood formation. However, the biological roles of FLAs in trees remain largely unclear. Here, we identified the FLA family in the ironwood tree (Ostrya rehderiana) and elucidated its possible function in poplar. Our results showed that OreFLAs underwent significant gene expansion due to multiple duplication events, leading to apparent functional redundancy. Among these genes, OreFLA11 was highly expressed in the xylem and roots. Overexpression of OreFLA11 in Populus alba var. pyramidalis altered xylem structure and cell wall composition, such as thickening the xylem and secondary cell wall (SCW), decreasing lignin contents and increasing cellulose contents, resulting in increased stem tensile strength but decreased salt tolerance, suggesting that OreFLA11 plays a negative role in the salt stress response. The mutant Palfla11 generated using CRIPSR-Cas9 methods showed the opposite phenotype compared to that of OreFLA11-OE poplars, indicating that the orthologues function similarly in wood formation. Furthermore, the transcriptome analysis showed that genes such as PME, BGAL and BGLU, related to cell wall biosynthesis, were up-regulated while the genes associated with salt stress resistance (CYSB, TSPO, RCI2B and CIPK6) were down-regulated in OreFLA11-OE poplars. These results indicated that OreFLA11 promotes wood formation and modulates stem mechanical properties but decreases tolerance to salt stress by decreasing the transcript abundance of salt-responsive genes in trees.

Selenium suppressed the LPS-induced oxidative stress of bovine endometrial stromal cells through Nrf2 pathway with high cortisol background.

Stress and infection seriously threaten the reproductive performance and health of dairy cows. Various perinatal stresses increase plasma cortisol concentrations in cows, and chronically high cortisol levels may increase the incidence and severity of the uterine diseases. Selenium (Se) enhances antioxidant capacity of cows. The aim of this study was to explore how Se affects the oxidative stress of primary bovine endometrial stromal cells (BESC) with high cortisol background. The levels of reactive oxygen species (ROS) and other biomarkers of oxidative stress were measured using flow cytometry and assay kits. The changes in nuclear NF-E2-related factor 2 (Nrf2) pathway were detected by Western blot, qPCR, and immunofluorescence. The result showed that lipopolysaccharide (LPS) increased (P < 0.01) ROS and malondialdehyde (MDA) content and reduced (P < 0.01) superoxide dismutase (SOD) concentration, provoking BESC oxidative stress. The elevated levels of cortisol resulted in the accumulation (P < 0.05) of ROS and MDA and inhibition (P < 0.05) of SOD in unstimulated BESC but demonstrated an antioxidative effect in LPS-stimulated cells. Pretreatment with Se reduced (P < 0.01) the levels of ROS and MDA, while increasing (P < 0.05) the antioxidant capacities and the relative abundance of gene transcripts and proteins related to the Nrf2 pathway in BESC. This antioxidant effect was more pronounced in the presence of high cortisol level. In conclusion, cortisol alone induced the oxidative damage but provided an antioxidant protection in the presence of LPS. Se alleviated the LPS-induced cellular oxidative stress, which is probably achieved through activating Nrf2 pathway. At high cortisol levels, Se supplement has a more significant protective effect on BESC oxidative stress. This study provided evidence for the protective role of Se in bovine endometrial oxidative damage of stressed animals and suggested the potential regulatory mechanism in vitro.

Comparative transcript abundance of gibberellin oxidases genes in two barley (Hordeum vulgare) genotypes with contrasting lodging resistance under different regimes of water deficit.

Barley (Hordeum vulgare ) is the world's fourth most important cereal crop, and is particularly well adapted to harsh environments. However, lodging is a major productivity constraint causing 13-65% yield losses. Gibberellic acid (GA) homeostatic genes such as HvGA20ox, HvGA3ox and HvGA2ox are responsible for changes in plant phenotype for height and internodal length that contribute towards lodging resistance. This study explored the expression of different HvGAox transcripts in two contrasting barley genotypes (5-GSBON-18, lodging resistant; and 5-GSBON-70, lodging sensitive), which were sown both under controlled (hydroponic, completely randomised factorial design) and field conditions (split-plot, completely randomised block design) with two irrigation treatments (normal with three irrigation events; and water deficit with one irrigation event). In the hydroponic experiment, expression analysis was performed on seedlings at 0, ¾, 1½, 3 and 6h after application of treatment. In the field experiment, leaf, shoot nodes and internodes were sampled. Downregulation of HvGA20ox.1 transcript and 2-fold upregulation of HvGA2ox.2 transcript were observed in 5-GSBON-18 under water deficit conditions. This genotype also showed a significant reduction in plant height (18-20%), lodging (<10%), and increased grain yield (15-18%) under stress. Utilisation of these transcripts in barley breeding has the potential to reduce plant height, lodging and increased grain yield.

Severe body condition loss lowers hepatic output of IGF1 with adverse effects on the dominant follicle in dairy cows

The severe loss of body condition score (BCS) during the early lactation period has been associated with infertility in cows. However, the mechanisms are not fully understood. The aim of this study was to examine the effect of BCS loss on liver health, and ovarian functions in cows during early lactation. Retrospectively multiparous cows from two farms were categorized based on units of BCS (1–5 scale) loss as Moderate (MOD, <0.75 units; n = 11) or Severe (SEV, ≥0.75 units; n = 9) loss groups. From Weeks −3 to 7, relative to calving, MOD and SEV cows lost on average 0.4 and 1.0-unit BCS, respectively. All data except hepatic transcriptomes were analyzed with PROC MIXED procedure of SAS. The plasma concentration of non-esterified fatty acids at Week 0 and 1, ß-hydroxy butyrate at Week 1, and γ-glutamyl transferase at Weeks 1 and 7 relative to calving were higher in SEV cows. Hepatic transcriptome analysis showed that 1 186 genes were differentially expressed in SEV (n = 3) compared to MOD (n = 3) cows at Week 7 after calving. Pathway analysis revealed that significant DEGs in SEV cows enriched in lipid metabolisms including, lipid metabolic process, ether lipid metabolism, fatty acid beta-oxidation, fatty acid biosynthetic process, fatty acid metabolic process, fat digestion and absorption, linoleic acid metabolism, alpha-linolenic acid metabolism. The impaired liver function in SEV cows was associated with 1.5-fold reduction of hepatic IGF1 gene expression and lower serum IGF1 concentrations. At the ovarian level, SEV cows had lower IGF1 concentration in the follicular fluid of the dominant follicle of the synchronized follicular wave compared to that of MOD cows at 7 weeks after calving. Further, the follicular fluid concentration of estradiol-17β was lower in SEV cows along with lower transcript abundance of genes from granulosa cells associated with dominant follicle competence, including CYP19A1, NR5A2, IGF1, and LHCGR. These data show that SEV loss of BCS during early lactation leading up to the planned start of breeding is associated with liver dysfunction, including lower IGF1 secretion, and impaired function of the dominant follicle in the ovary.

Embryonic Exposure to the Benzotriazole Ultraviolet Stabilizer 2-(2H-benzotriazol-2-yl)-4-methylphenol Decreases Fertility of Adult Zebrafish (Danio rerio).

Benzotriazole ultraviolet stabilizers (BUVSs) are emerging contaminants of concern. They are added to a variety of products, including building materials, personal care products, paints, and plastics, to prevent degradation caused by ultraviolet (UV) light. Despite widespread occurrence in aquatic environments, little is known regarding the effects of BUVSs on aquatic organisms. The aim of the present study was to characterize the effects of exposure to 2-(2H-benzotriazol-2-yl)-4-methylphenol (UV-P) on the reproductive success of zebrafish (Danio rerio) following embryonic exposure. Embryos were exposed, by use of microinjection, to UV-P at <1.5 (control), 2.77, and 24.25 ng/g egg, and reared until sexual maturity, when reproductive performance was assessed, following which molecular and biochemical endpoints were analyzed. Exposure to UV-P did not have a significant effect on fecundity. However, there was a significant effect on fertilization success. Using UV-P-exposed males and females, fertility was decreased by 8.75% in the low treatment group and by 15.02% in the high treatment group relative to control. In a reproduction assay with UV-P-exposed males and control females, fertility was decreased by 11.47% in the high treatment group relative to the control. Embryonic exposure to UV-P might have perturbed male sex steroid synthesis as indicated by small changes in blood plasma concentrations of 17β-estradiol and 11-ketotestosterone, and small statistically nonsignificant decreases in mRNA abundances of cyp19a1a, cyp11c1, and hsd17b3. In addition, decreased transcript abundances of genes involved in spermatogenesis, such as nanos2 and dazl, were observed. Decreases in later stages of sperm development were observed, suggesting that embryonic exposure to UV-P impaired spematogenesis, resulting in decreased sperm quantity. The present study is the first to demonstrate latent effects of BUVSs, specifically on fish reproduction. Environ Toxicol Chem 2024;43:385-397. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

IRON MAN interacts with Cu-DEFICIENCY INDUCED TRANSCRIPTION FACTOR 1 to maintain copper homeostasis.

Copper (Cu) is essential for plant growth and development. IRON MAN (IMA) is a family of small peptides that can bind both iron (Fe) and Cu ions. It was reported that IMAs mediate Fe homeostasis in Arabidopsis thaliana. However, it remains unclear whether IMAs are involved in Cu homeostasis. The transcript abundance of IMA genes decreased in response to Cu deficiency. The combined disruption of all IMA genes caused enhanced tolerance to Cu deficiency and resulted in an increase in the transcript abundance of Cu uptake genes, whereas the overexpression of IMA1 or IMA3 led to the opposite results. Protein interaction assays indicated that IMAs interact with Cu-DEFICIENCY INDUCED TRANSCRIPTION FACTOR1 (CITF1), which is a positive regulator of the Cu uptake genes. Further studies showed that IMAs not only interfere with the DNA binding of CITF1 but also repress the transcriptional activation activity of CITF1, hence resulting in downregulation of the Cu uptake genes. Genetic analyses indicated that IMAs modulate Cu homeostasis in a CITF1-dependent manner. Our findings indicate that IMAs inhibit the functions of CITF1 in regulating Cu deficiency responses, thereby providing a conceptual framework for comprehending the regulation of Cu homeostasis.

Food deprivation reduces sensitivity of liver Igf1 synthesis pathways to growth hormone in juvenile gopher rockfish (Sebastes carnatus)

Growth hormone (Gh) regulates growth in part by stimulating the liver to synthesize and release insulin-like growth factor-1 (Igf1), which then promotes somatic growth. However, for fish experiencing food limitation, elevated blood Gh can occur even with low circulating Igf1 and slow growth, suggesting that nutritional stress can alter the sensitivity of liver Igf1 synthesis pathways to Gh. Here, we examined how recent feeding experience affected Gh regulation of liver Igf1 synthesis pathways in juvenile gopher rockfish (Sebastes carnatus) to illuminate mechanisms underlying the nutritional modulation of Igf1 production. Juvenile gopher rockfish were maintained under conditions of feeding or complete food deprivation (fasting) for 14 d and then treated with recombinant sea bream (Sparus aurata) Gh or saline control. Gh upregulated hepatic igf1 mRNA levels in fed fish but not in fasted fish. The liver of fasted rockfish also showed a lower relative abundance of gene transcripts encoding teleost Gh receptors 1 (ghr1) and 2 (ghr2), as well as reduced protein levels of phosphorylated janus tyrosine kinase 2 (pJak2) and signal transducer and activator of transcription 5 (pStat5), which function to induce igf1 gene transcription following Gh binding to Gh receptors. Relative hepatic mRNA levels for suppressors of cytokine signaling (Socs) genes socs2, socs3a, and socs3b were also lower in fasted rockfish. Socs2 can suppress Gh activation of Jak2/Stat5, and fasting-related variation in socs expression may reflect modulated inhibitory control of igf1 gene transcription. Fasted rockfish also had elevated liver mRNA abundances for lipolytic hormone-sensitive lipase 1 (hsl1) and Igf binding proteins igfbp1a, -1b and –3a, reduced liver mRNAs encoding igfbp2b and an Igfbp acid labile subunit-like (igfals) gene, and higher transcript abundances for Igf1 receptors igf1ra and igf1rb in skeletal muscle. Together, these findings suggest that food deprivation impacts liver Igf1 responsiveness to Gh via multiple mechanisms that include a downregulation of hepatic Gh receptors, modulation of the intracellular Jak2/Stat5 transduction pathway, and possible shifts in Socs-inhibitory control of igf1 gene transcription, while also demonstrating that these changes occur in concert with shifts in liver Igfbp expression and muscle Gh/Igf1 signaling pathway components.

ROS scavenging enzyme-encoding genes play important roles in the desert moss Syntrichia caninervis response to extreme cold and desiccation stresses

Abiotic stress is one of the major environmental constraints limiting plant growth. Syntrichia caninervis is one of the unique plant models that can cope with harsh environments. Reactive oxygen species (ROS) are a vital signaling molecule for protecting plants from oxidative stress, but research on ROS in S. caninervis is limited. Here, we identified 112 ROS genes in S. caninervis, including 40 GSTs, 51 PODs, 9 SODs, 6 CATs, 3 GPXs and 3 APXs families. GO and KEGG analyses showed that ROS genes are involved in responses to various stimuli and phenylpropanoid biosynthesis. ROS genes contain many stress-responsive and hormonal cis-elements in their promoter regions. More ROS genes were induced by cold stress than desiccation stress, and both conditions changed the transcript abundances of several ROS genes. CAT and POD, H2O2, MDA, and GSH were also induced under biotic stress, specifically CAT activity. The results indicated that the ScCAT genes and their activities could be strongly associated with the regulation of ROS production. This is the first systematic identification of ROS genes in S. caninervis and our findings contribute to further research into the roles of ScROS adjustment under abiotic stress while also providing excellent genetic resources for plant breeding.

Ablation of OCT4 function in cattle embryos by double electroporation of CRISPR-Cas for DNA and RNA targeting (CRISPR-DART)

Abstract CRISPR-Cas ribonucleoproteins are important tools for gene editing in pre-implantation embryos. However, the inefficient production of biallelic deletions in cattle zygotes has hindered mechanistic studies of gene function. In addition, the presence of maternal RNAs that support embryo development until embryonic genome activation may cause confounding phenotypes. Here, we aimed to improve the efficiency of biallelic deletions and deplete specific maternal RNAs in cattle zygotes using CRISPR-Cas editing technology. Two electroporation sessions with Cas9D10A ribonucleoproteins targeting exon 1 and the promoter of OCT4 produced biallelic deletions in 91% of the embryos tested. In most cases, the deletions were longer than 1000 nucleotides long. Electroporation of Cas13a ribonucleoproteins prevents the production of the corresponding proteins. We electroporated Cas9D10A ribonucleoproteins targeting exon 1, including the promoter region, of OCT4 in two sessions with inclusion of Cas13a ribonucleoproteins targeting OCT4 mRNAs in the second session to ablate OCT4 function in cattle embryos. A lack of OCT4 resulted in embryos arresting development prior to blastocyst formation at a greater proportion (13%) than controls (31.6%, P&amp;lt;0.001). The few embryos that developed past the morula stage did not form a normal inner cell mass. Transcriptome analysis of single blastocysts, confirmed to lack exon 1 and promoter region of OCT4, revealed a significant (FDR&amp;lt;0.1) reduction in transcript abundance of many genes functionally connected to stemness, including markers of pluripotency (CADHD1, DPPA4, GNL3, RRM2). The results confirm that OCT4 is key regulator of genes that modulate pluripotency and is required to form a functional blastocyst in cattle.

The overlooked role of denitrifying bacteria in mediating vanadate reduction

Microbial vanadate [V(V)] reduction is the key process of vanadium geochemical cycling, while the identified functional microbes are rather limited. Considering the structural similarity of metavanadate and nitrate, widespread denitrifying bacteria are expected to be able to mediate V(V) reduction, but this process has not been fully understood. This study confirmed the effectiveness of two denitrifying bacteria, i.e., Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002, in reducing V(V). During 120-h incubation, the V(V) removal efficiency was 89.0 ± 1.83% and 96.0 ± 1.43% by strain BoFeN1 and strain 2002, respectively. V(V) was reduced to tetravalent vanadium [V(IV)] both intracellularly and extracellularly. Use of inhibitors and metabolomic analysis revealed enzyme catalysis and electron transfer pathways for V(V) reduction. Enzyme catalysis was identified by analyses of gene abundance, transcript abundance, and enzymatic activity. Electron transfer was verified through quantifying electron transporters, monitoring electron transport system activity, and performing cyclic voltammetry analysis. For strain BoFeN1, nitrite and nitrous oxide reductases played vital roles in V(V) reduction, together with cytochrome c (Cyt c) and nicotinamide adenine dinucleotide (NADH) mediated electron transfer. Differentially expressed riboflavin produced by strain BoFeN1 also promoted electron transfer. Strain 2002 mainly utilized periplasmic nitrate reductase to reduce V(V). Aquifer sediment bioaugmented with these strains enhanced V(V) reduction by 10.5%−51.1%. They well colonized and collaborated with indigenous microorganisms to reduce V(V) to V(IV). This study advances understanding of environmental biogeochemistry of vanadium and provides molecular insights into V(V) bio-reduction as a sustainable bioremediation strategy.

Transcriptomic analysis implicates ABA signaling and carbon supply in the differential outgrowth of petunia axillary buds

BackgroundShoot branching of flowering plants exhibits phenotypic plasticity and variability. This plasticity is determined by the activity of axillary meristems, which in turn is influenced by endogenous and exogenous cues such as nutrients and light. In many species, not all buds on the main shoot develop into branches despite favorable growing conditions. In petunia, basal axillary buds (buds 1–3) typically do not grow out to form branches, while more apical axillary buds (buds 6 and 7) are competent to grow.ResultsThe genetic regulation of buds was explored using transcriptome analyses of petunia axillary buds at different positions on the main stem. To suppress or promote bud outgrowth, we grew the plants in media with differing phosphate (P) levels. Using RNA-seq, we found many (> 5000) differentially expressed genes between bud 6 or 7, and bud 2. In addition, more genes were differentially expressed when we transferred the plants from low P to high P medium, compared with shifting from high P to low P medium. Buds 6 and 7 had increased transcript abundance of cytokinin and auxin-related genes, whereas the basal non-growing buds (bud 2 and to a lesser extent bud 3) had higher expression of strigolactone, abscisic acid, and dormancy-related genes, suggesting the outgrowth of these basal buds was actively suppressed. Consistent with this, the expression of ABA associated genes decreased significantly in apical buds after stimulating growth by switching the medium from low P to high P. Furthermore, comparisons between our data and transcriptome data from other species suggest that the suppression of outgrowth of bud 2 was correlated with a limited supply of carbon to these axillary buds. Candidate genes that might repress bud outgrowth were identified by co-expression analysis.ConclusionsPlants need to balance growth of axillary buds into branches to fit with available resources while allowing some buds to remain dormant to grow after the loss of plant parts or in response to a change in environmental conditions. Here we demonstrate that different buds on the same plant with different developmental potentials have quite different transcriptome profiles.