Transcript Abundance Of Genes Research Articles

Detecting the genetic basis of local adaptation in loblolly pine (Pinus taeda L.) using whole exome-wide genotyping and an integrative landscape genomics analysis approach.

In the Southern United States, the widely distributed loblolly pine contributes greatly to lumber and pulp production, as well as providing many important ecosystem services. Climate change may affect the productivity and range of loblolly pine. Nevertheless, we have insufficient knowledge of the adaptive potential and the genetics underlying the adaptability of loblolly pine. To address this, we tested the association of 2.8 million whole exome‐based single nucleotide polymorphisms (SNPs) with climate and geographic variables, including temperature, precipitation, latitude, longitude, and elevation data. Using an integrative landscape genomics approach by combining multiple environmental association and outlier detection analyses, we identified 611 SNPs associated with 56 climate and geographic variables. Longitude, maximum temperature of the warm months and monthly precipitation associated with most SNPs, indicating their importance and complexity in shaping the genetic variation in loblolly pine. Functions of candidate genes related to terpenoid synthesis, pathogen defense, transcription factors, and abiotic stress response. We provided evidence that environment‐associated SNPs also composed the genetic structure of adaptive phenotypic traits including height, diameter, metabolite levels, and gene transcript abundance. Our study promotes understanding of the genetic basis of local adaptation in loblolly pine and provides promising tools for selecting genotypes adapted to local environments in a changing climate.

Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 × 10−1–1.20 × 10−4 copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that >22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGs.

Biochar-Mediated Anaerobic Oxidation of Methane.

Biochar was recently identified as an effective soil amendment for CH4 capture. Corresponding mechanisms are currently recognized to be from physical properties of biochar, providing a favorable growth environment for aerobic methanotrophs which perform aerobic methane (CH4) oxidation. However, our study shows that the chemical reactivity of biochar can also stimulate anaerobic oxidation of CH4 (AOM) by anaerobic methanotrophic archaea (ANME) of ANME-2d, which proposes another plausible mechanism for CH4 mitigation by biochar amendment in anaerobic environments. It was found that, by adding biochar as the sole electron acceptor in an anaerobic environment, CH4 was biologically oxidized, with CO2 production of 106.3 ± 5.1 μmol g-1 biochar. In contrast, limited CO2 production was observed with chemically reduced biochar amendment. This biological nature of the process was confirmed by mcr gene transcript abundance as well as sustained dominance of ANME-2d in the microbial community during microbial incubations with active biochar amendment. Combined FTIR and XPS analyses demonstrated that the redox activity of biochar is related to its oxygen-based functional groups. On the basis of microbial community evolution as well as intermediate production during incubation, different pathways in terms of direct or indirect interactions between ANME-2d and biochar were proposed for biochar-mediated AOM.

Transcriptomic profiling reveals MEP pathway contributing to ginsenoside biosynthesis in Panax ginseng

BackgroundPanax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from terpene precursors, IPP and DMAPP, through the cytoplasmic mevalonate (MVA) pathway. Another plastic 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was proved also contributing to ginsenoside generation in the roots of P. ginseng by using specific chemical inhibitors recently. But their gene expression characteristics are still under reveal in P. ginseng. With the development of the high-throughput next generation sequencing (NGS) technologies, we have opportunities to discover more about the complex ginsenoside biosynthesis pathways in P. ginseng.ResultsWe carried out deep RNA sequencing and comprehensive analyses on the ginseng root samples of 1–5 years old and five different tissues of 5 years old ginseng plants. The de novo assembly totally generated 48,165 unigenes, including 380 genes related to ginsenoside biosynthesis and all the genes encoding the enzymes of the MEP pathway and the MVA pathway. We further illustrated the gene expression profiles related to ginsenoside biosynthesis among 1–5 year-old roots and different tissues of 5 year-old ginseng plants. Particularly for the first time, we revealed that the gene transcript abundances of the MEP pathway were similar to those of the MVA pathway in ginseng roots but higher in ginseng leaves. The IspD was predicated to be the rate-limiting enzyme in the MEP pathway through both co-expression network and gene expression profile analyses.ConclusionsAt the transcriptional level, the MEP pathway has similar contribution to ginsenoside biosynthesis in ginseng roots, but much higher in ginseng leaves, compared with the MVA pathway. The IspD might be the key enzyme for ginsenoside generation through the MEP pathway. These results provide new information for further synthetic biology study on ginsenoside metabolic regulation.

Acute toxicity of triflumizole to freshwater green algae Chlorella vulgaris

Triflumizole is one of imidazole fungicides that works by inhibiting ergosterol biosynthesis, and is widely used for the control of powdery mildew and scabs on various fruits and crops. Triflumizole residue has been frequently detected in soil and aquatic ecosystems. While many studies have focused on its toxic effect on terrestrial and aquatic animals, little attention has been paid to aquatic algae, the primary producers of aquatic environments. Therefore, we evaluated the acute (96 h) toxicity effects of triflumizole on the freshwater algae Chlorella vulgaris, by examining growth, cell morphology, photosynthesis, and oxidative stress. The results showed that the 96 h median inhibition concentration (96 h-EC50) was 0.82 mg/L (95% confidential interval 0.70–0.98 mg/L).The growth of algal cells was conspicuously inhibited by triflumizole exposure, and the cell surfaces appeared to be shrunkThe chlorophyll content (including Chl-a, Chl-b and T-Chl) dramatically decreased at triflumizole concentrations of 0.2 and 1.0 mg/L. In addition, the transcript abundance of photosynthesis-related genes (psaB, psbC and rbcL) showed obvious decreases in above treatments after 96 h of exposure to triflumizole. Moreover, the algal growth inhibition was accompanied by an increase in intracellular reactive oxygen species and malondialdehyde content, as well as increased activity of antioxidant enzymes such as superoxide dismutase and peroxidase, indicating oxidative stress and lipid peroxidation. Our findings reveal that triflumizole has potential toxicity to the primary producers (freshwater algae) in aquatic ecosystems.

Overexpression of tomato SlbHLH22 transcription factor gene enhances fruit sensitivity to exogenous phytohormones and shortens fruit shelf-life

The basic helix-loop-helix (bHLH) proteins comprise the second largest superfamily of transcription factor that mediate various biochemical, physiological, and developmental processes in plants. The biological roles of these TFs are unknown, particularly in tomato. In this study, we isolated the tomato SlbHLH22 expressing significantly in fruits at early and later stages of development. The SlbHLH22 was overexpressed under control of CaMV 35S promoter. The transgenic tomato fruits exhibited sensitivity to exogenous phytohormone, such as ABA and IAA and ripened fast than WT fruits. However, the fruits remain insensitive to GA. It was observed that the transcript abundance of ABA and IAA related genes were also significantly upregulated in fruits overexpressing SlbHLH22. Compared to WT, the activities of peroxidase, superoxide dismutase, and catalase was lower in the transgenic fruits, while the MDA concentration was higher than in WT fruits. Similarly, the induced expressions of cell wall metabolism related genes (SlEXP1, SlLoxA, SlMAN, SlPE, and SlXTH5) were also observed in transgenic fruits. These results demonstrate that tomato SlbHLH22 expressions were regulated by phytohormones and identification of SlbHLH22 roles in post-harvest helps limit losses during handling, storage, and transportation.

Boron Alleviates Drought Stress by Enhancing Gene Expression and Antioxidant Enzyme Activity

Drought is one of the major abiotic stress factors for plants, especially in arid and semiarid areas, where plants are facing with boron (B) contamination problem as well. In these soils, plants deal up with two destructive phenomena: excessive B and water scarcity. The current study aims to understand the adaptation strategy of tomato plant against excess B and drought stresses. For this purpose, hydroponically grown tomato seedlings were subjected with excess B (+B), drought (+PEG), and excess B with drought (B+PEG) stresses. Antioxidant enzyme activities (superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR)); chlorophyll, soluble protein, and MDA contents; and the root histograms were analyzed. In addition, expression of stress-related genes (GR1, MT2, and Hsp90) was determined by qRT-PCR method. Compared to the non-treated (control) or B+ and PEG+ treated plants, the transcript abundance of the stress-related genes was significantly increased in plants grown under B+PEG condition. The highest relative increase was observed on GR1 gene (~ 7–8-fold), indicating the activation of oxidative stress enzymes. At the same time, chlorophyll content analysis showed a significant increase; MDA level showed a reduction under B+PEG condition. SOD activity was limited, while APX and GR enzymes were found to be increased upon B+PEG application. Activation of stress-related genes and antioxidant enzymes under B+PEG condition could help to protect plants against excess B and drought stresses. Inclusion of B can enhance the drought adaptation of plants by stimulating the early stress response mechanisms.

Interactions of long-term food ration variation and short-term fasting on insulin-like growth factor-1 (IGF-1) pathways in copper rockfish (Sebastes caurinus)

Variation in food intake affects somatic growth by altering the expression of hormones in the somatotropic endocrine axis including insulin-like growth factor-1 (IGF-1). Here, we examined IGF-1 pathway responses to long- and short-term variation in food availability in copper rockfish (Sebastes caurinus), a nearshore Pacific rockfish important for commercial and recreational fisheries. Juvenile copper rockfish were raised under differing ration amounts (3% or 9% mass feed·g−1 fish wet mass·day−1) for 140 d to simulate ‘long-term’ feeding variation, after which some fish from both rations were fasted for 12 d to generate ‘short-term’ conditions of food deprivation. Rockfish on the 9% ration treatment grew more quickly than those on the 3% ration and were larger in mass, length, and body condition (k) after 152 d. Fish on the 9% ration had higher blood glucose than those on the 3% ration, with fasting decreasing blood glucose in both ration treatments, indicating that both long-term and short-term feed treatments altered energy status. Plasma IGF-1 was higher in rockfish from the 9% ration than those in the 3% ration and was also higher in fed fish than fasted fish. Additionally, plasma IGF-1 related positively to individual variation in specific growth rate (SGR). The positive association between IGF-1 and SGR showed discordance in fish that had experienced different levels of food and growth over the long-term but not short-term, suggesting that long-term nutritional experience can influence the relationship between IGF-1 and growth in this species. Rockfish on the 3% ration showed a lower relative abundance of gene transcripts encoding igf1 in the liver, but higher hepatic mRNAs for IGF binding proteins igfbp1a and igfbp1b. Fasting similarly decreased the abundance of igf1 mRNAs in the liver of fish reared under both the 9% and 3% rations, while concurrently increasing mRNAs encoding the IGF binding proteins igfbp1a, -1b, and -3a. Hepatic mRNAs for igfbp2b, -5a, and -5b were lower with long-term ration variation (3% ration) and fasting. Fish that experienced long-term reduced rations also had higher mRNA levels for igfbp3a, -3b, and IGF receptors isoforms A (igf1rA) and B (igf1rB) in skeletal muscle, but lower mRNA levels for igf1. Fasting increased muscle mRNA abundance for igfbp3a, igf1rA, and igf1rB, and decreased levels for igfbp2a and igf1. These data show that a positive relationship between circulating IGF-1 and individual growth rate is maintained in copper rockfish even when that growth variation relates to differences in food consumption across varying time scales, but that long- and short-term variation in food quantity can shift basal concentrations of circulating IGF-1 in this species.

Tetranins: new putative spider mite elicitors of host plant defense.

The two-spotted spider mite (Tetranychus urticae) is a plant-sucking arthropod herbivore that feeds on a wide array of cultivated plants. In contrast to the well-characterized classical chewing herbivore salivary elicitors that promote plant defense responses, little is known about sucking herbivores' elicitors. To characterize the sucking herbivore elicitors, we explored putative salivary gland proteins of spider mites by using an Agrobacterium-mediated transient expression system or protein infiltration in damaged bean leaves. Two candidate elicitors (designated as tetranin1 (Tet1) and tetranin2 (Tet2)) triggered early leaf responses (cytosolic calcium influx and membrane depolarization) and increased the transcript abundances of defense genes in the leaves, eventually resulting in reduced survivability of T. urticae on the host leaves as well as induction of indirect plant defenses by attracting predatory mites. Tet1 and/or Tet2 also induced jasmonate, salicylate and abscisic acid biosynthesis. Notably, Tet2-induced signaling cascades were also activated via the generation of reactive oxygen species. The signaling cascades of these two structurally dissimilar elicitors are mostly overlapping but partially distinct and thus they would coordinate the direct and indirect defense responses in host plants under spider mite attack in both shared and distinct manners.

Mutation of a Conserved Alanine Residue in Transcription Factor AraR Leads to Hyperproduction of α‐l‐Arabinofuranosidases in Penicillium oxalicum

α-l-Arabinofuranosidases are important in the degradation of plant polysaccharides and are used in several industrial processes. Although the use of filamentous fungi for the production of α-l-arabinofuranosidases is widely reported, there are few reports on strain engineering for enhanced production of these enzymes by fungi. In this study, the function of transcription factor AraR in l-arabinose release and catabolism by the fungus Penicillium oxalicum (P. oxalicum) is investigated. Also, a mutant of AraR, AraRA731V , is constructed to improve the production of α-l-arabinofuranosidases on the basis of the sequence homology between AraR and the xylanolytic gene activator XlnR. The AraRA731V -overexpressing strain can synthesize α-l-arabinofuranosidase in the absence of an inducer and shows a 54.1-fold increase in α-l-arabinofuranosidase production and a 7.4-fold increase in α-galactosidase production in the medium containing wheat bran. Determination of the transcript abundances of lignocellulolytic enzyme genes reveals significant upregulation of multiple α-l-arabinofuranosidase genes and downregulation of some cellulolytic and xylanolytic enzyme genes in the engineered strain relative to its parent. Taken together, the results suggest the conserved regulatory function of AraR in the family Trichocomaceae and provide a strategy for engineering fungal strains for enhanced α- l-arabinofuranosidase production.

Fine-tuned adaptation of embryo-endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus.

Interactions between embryo and endometrium at implantation are critical for the progression of pregnancy. These reciprocal actions involve exchange of paracrine signals that govern implantation and placentation. However, it remains unknown how these interactions between the conceptus and the endometrium are coordinated at the level of an individual pregnancy. Under the hypothesis that gene expression in endometrium is dependent on gene expression of extraembryonic tissues and genes expressed in extraembryonic tissues are dependent of genes expressed in the endometrium, we performed an integrative analysis of transcriptome profiles of paired extraembryonic tissue and endometria obtained from cattle (Bos taurus) pregnancies initiated by artificial insemination. We quantified strong dependence (|r| > 0.95, empirical false discovery rate [eFDR] < 0.01) in transcript abundance of genes expressed in the extraembryonic tissues and genes expressed in the endometrium. The profiles of connectivity revealed distinct coexpression patterns of extraembryonic tissues with caruncular and intercaruncular areas of the endometrium. Notably, a subset of highly coexpressed genes between extraembryonic tissue (n = 229) and caruncular areas of the endometrium (n = 218, r > 0.9999, eFDR < 0.001) revealed a blueprint of gene expression specific to each pregnancy. Gene ontology analyses of genes coexpressed between extraembryonic tissue and endometrium revealed significantly enriched modules with critical contribution for implantation and placentation, including “in utero embryonic development,” “placenta development,” and “regulation of transcription.” Coexpressing modules were remarkably specific to caruncular or intercaruncular areas of the endometrium. The quantitative association between genes expressed in extraembryonic tissue and endometrium emphasize a coordinated communication between these two entities in mammals. We provide evidence that implantation in mammalian pregnancy relies on the ability of the extraembryonic tissue and the endometrium to develop a fine-tuned adaptive response characteristic of each pregnancy.

Functional Analysis of Sesame Diacylglycerol Acyltransferase and Phospholipid: Diacylglycerol Acyltransferase Genes Using In Silico and In Vitro Approaches

Sesamum indicum L. is one of the major oilseed crops of India. Sesame oil is stable with a good source of unsaturated fatty acids. To know the mechanism of oil accumulation in sesame, genes coding for the key enzymes involved in triacylglycerol (TAG) synthesis pathway, namely diacylglycerol acyltransferase (DGAT; EC 2.3.1.20) and phospholipid:diacylglycerol acyltransferase (PDAT; EC 2.3.1.158), were retrieved from sesame full genome sequences by comparative analysis using Arabidopsis genes. All isoforms of SiDGAT and SiPDAT genes were analyzed in silico for their sequence and structural similarity with the existing members from other plants. Phylogenetic analysis delineated the sesame DGAT and PDAT genes into four separate clades. Most of the members had several transmembrane domains except SiDGAT1 A1, SiDGAT1 A2, SiDGAT1 B1, and SiPDAT2 which do not have any transmembrane domain suggesting a soluble function. In vitro gene isolation followed by mRNA expression analysis of SiDGAT1, SiDGAT2, SiPDAT1, and SiPDAT2 were carried out. Expression of these genes at the transcription level at the leaf, stem, root, flower, developing seeds, and mature seeds were examined by quantitative real-time PCR experiments. Functional analysis of these sesame genes was performed in a yeast quadruple mutant lacking TAG synthesis genes. Transcript abundance of SiDGAT1 and SiDGAT2 genes was highest in mature seeds, SiPDAT1 at flowering stage and developing seeds, and SiPDAT2 in stem and developing seeds. Heterologous expression of sesame genes in the yeast system indicated higher oil content in both SiDGAT and SiPDAT gene–transformed mutants. In addition, SiPDAT1-expressing mutants had higher polyunsaturated (C18:1; C18:2) fatty acid content. The present study indicates both sesame DGAT and PDAT genes are good candidates for not only oil yield increase but also for higher PUFA content.

Bovine pregnancy associated glycoproteins can alter selected transcripts in bovine endometrial explants

This study was designed to examine changes in target transcript abundance in endometrial explants exposed to pregnancy-associated glycoproteins (PAGs). Endometrial explants from pregnant and non-pregnant heifers collected on day18 (day 0: day of insemination) were incubated in the absence or presence of PAGs (15 μg/ml). The PAGs represented a mixture comprised of approximately equal amounts of bovine PAGs 4, 6, and 9. Samples were harvested for RNA extraction after 24 h or 96 h of incubation. Transcript abundance for target genes related to prostaglandin synthesis (PTGES), a chemokine (CXCL5) and tissue remodeling (EMMPRIN; MMPs 1, 2, 3, 7, 8, and 9; PLAU; SPP1; TIMP1 and TIMP2) were analyzed by quantitative PCR. Changes in relative transcript abundance for MMP1, MMP3, MMP7, PLAU, EMMPRIN and SPP1 were observed after PAG exposure in both non-pregnant and pregnant endometrium (P < 0.05). However, some of the transcripts associated with tissue remodeling were altered only at certain time points (either 24 h or 96 h). The transcript for bovine CXCL5 was increased in non-pregnant endometrium four- and six-fold at 24 h and 96 h of PAG exposure, respectively (P < 0.05); in pregnant endometrium, only the 24 h incubation period exhibited an elevation in CXCL5 (P < 0.05). In non-pregnant endometrium, both PTGES and MMP9 were elevated after exposure to PAGs for 24 h (P < 0.05) but not in the other samples. Some interferon-responsive transcripts (IFI6, ISG15) were found to be more abundant (P < 0.05) in pregnant endometrium after 96 h exposure to PAGs compared to endometrium that had not been exposed to the PAGs. Likewise, ISG15 message was elevated (P = 0.06) in non-pregnant endometrium after 24 h incubation with PAGs. These results indicate that the PAGs used in this experiment were able to induce changes in endometrial transcripts encoding for proteins associated with matrix remodeling as well as chemokine production and prostaglandin release.

Profiling RNA‐Associated Proteins for Vasopressin‐Mediated Translation in Kidney Collecting Duct Cells

Vasopressin‐mediated gene expression changes in the renal collecting duct has been intensively studied over the last decade. Prior studies were focused on transcriptional regulation as a mechanism of regulation of transport by vasopressin. However, post‐transcriptional regulation at the RNA level has not been studied. To identify vasopressin‐mediated RNA modulators, 1) a comprehensive list of RNA‐associated proteins was curated, and 2) vasopressin‐regulated genes from this list were identified using RNA‐seq in mouse mpkCCD cells exposed to vasopressin for various times.The curated database of RNA‐associated proteins was generated by mining information from multiple databases as follows. RNA processing‐related proteins were identified from Gene Ontology (GO) ‘Molecular Function’ and ‘Biological Process’, KEGG pathway, RNA modification database and Reactome. In addition, proteins that have RNA‐binding domains were identified from five different databases (RBPDB, ATtRACT, RBPmap, InterPro and UniProt). A total of 1369 proteins are listed in the current database of RNA‐associated proteins (https://hpcwebapps.cit.nih.gov/ESBL/Database/RNAprocessing_Proteins/). Among these proteins, 646 proteins have known RNA‐binding domain structures and 723 proteins were identified with annotated molecular functions related to RNA processing. 371 proteins were identified by both criteria.RNA‐seq was carried out in mpkCCD cells treated with the vasopressin analog dDAVP (10−10 M) for 3, 6 and 12 h. Relative transcript abundance was estimated using transcripts per million (TPM) and change of transcript abundance was presented as Log2 of the dDAVP:vehicle TPM ratio at each time point. Interestingly, we found that transcript abundance of genes coding for ribosomal proteins (60S ribosomal proteins and 40S ribosomal proteins) and translation initiation proteins (eukaryotic translation initiation factors) were extensively changed by dDAVP at all time points. These results indicate that vasopressin‐mediated gene expression includes changes mediated by abundance changes of translation‐associated proteins. Beyond this, the current study provides new resources for further study of RNA‐associated processes in the kidney.Support or Funding InformationThe work was supported by the Division of Intramural Research, National Heart, Lung, and Blood Institute projects ZIA‐HL001285 (to MAK) and ZIA‐HL006129 (to MAK).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

AtU2AF65b functions in abscisic acid mediated flowering via regulating the precursor messenger RNA splicing of ABI5 and FLC in Arabidopsis.

In mammalians and yeast, the splicing factor U2AF65/Mud2p functions in precursor messenger RNA (pre-mRNA) processing. Arabidopsis AtU2AF65b encodes a putative U2AF65 but its specific functions in plants are unknown. This paper examines the function of AtU2AF65b as a negative regulator of flowering time in Arabidopsis. We investigated the expression and function of AtU2AF65b in abscisic acid (ABA)-regulated flowering as well as the transcript abundance and pre-mRNA splicing of flowering-related genes in the knock-out mutants of AtU2AF65b. The atu2af65b mutants show early-flowering phenotype under both long-day and short-day conditions. The transcript accumulation of the flowering repressor gene FLOWERING LOCUS C (FLC) is reduced in the shoot apex of atu2af65b, due to both increased intron retention and reduced transcription activation. Reduced transcription of FLC results, at least partially, from the abnormal splicing and reduced transcript abundance of ABSCISIC ACID-INSENSITIVE5 (ABI5), which encodes an activator of FLC in ABA-regulated flowering signaling. Additionally, the expression of AtU2AF65b is promoted by ABA. Transition to flowering and splicing of FLC and ABI5 in the atu2af65b mutants are compromised during ABA-induced flowering. ABA-responsive AtU2AF65b functions in the pre-mRNA splicing of FLC and ABI5 in shoot apex, whereby AtU2AF65b is involved in ABA-mediated flowering transition in Arabidopsis.

Comparative Metabonomic Investigations of Schistosoma japonicum From SCID Mice and BALB/c Mice: Clues to Developmental Abnormality of Schistosome in the Immunodeficient Host.

The growth and development of schistosome has been affected in the immunodeficient hosts. But it remains unresolved about the molecular mechanisms involved in the development and reproduction regulation of schistosomes. This study tested and compared the metabolic profiles of the male and female Schistosoma japonicum worms collected from SCID mice and BALB/c mice at 5 weeks post infection using liquid chromatography tandem mass spectrometry (LC-MS/MS) platform, in which the worms from SCID mice were the investigated organisms and the worms from BALB/c mice were used as the controls. There were 1015 ion features in ESI+ mode and 342 ion features in ESI- mode were identified after filtration by false discovery rate. Distinct metabolic profiles were found to clearly differentiate both male and female worms in SCID mice from those in BALB/c mice using multivariate modeling methods including the Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). There were more differential metabolites in female worms than in male worms between SCID mice and BALB/c mice. And common and uniquely perturbed metabolites and pathways were identified among male and female worms from SCID mice when compared with BALB/c mice. The enriched metabolite sets of the differential metabolites in male worms between SCID mice and BALB/c mice included bile acid biosynthesis, taurine and hypotaurine metabolism, sphingolipid metabolism, retinol metabolism, purine metabolism, etc. And the enriched metabolite sets of differential metabolites in female worms included retinol metabolism, alpha linolenic acid and linoleic acid metabolism, purine metabolism, sphingolipid metabolism, glutamate metabolism, etc. Further detection and comparison in transcript abundance of genes of the perturbed retinol metabolism and its associated meiosis process in worms identified clues suggesting accumulated retinyl ester and perturbed meiotic process. These findings suggested an association between the schistosome with retarded growth and development in SCID mice and their perturbed metabolites and metabolic pathways, and provided a new insight into the growth and development regulation of S. japonicum worms from the metabolic level, which indicated great clues for discovery of drugs or vaccines against the parasites and disease with more researches.

Transcript abundance of stromal and thecal cell related genes during bovine ovarian development.

Movement and expansion of mesonephric-derived stroma appears to be very important in the development of the ovary. Here, we examined the expression of 24 genes associated with stroma in fetal ovaries during gestation (n = 17; days 58–274) from Bos taurus cattle. RNA was isolated from ovaries for quantitative RT-PCR. Expression of the majority of genes in TGFβ signalling, stromal transcription factors (NR2F2, AR), and some stromal matrix genes (COL1A1, COL3A1 and FBN1, but not FBN3) showed a positive linear increase with gestational age. Expression of genes associated with follicles (INSL3, CYP17A1, CYP11A1 and HSD3B1), was low until mid-gestation and then increased with gestational age. LHCGR showed an unusual bimodal pattern; high levels in the first and last trimesters. RARRES1 and IGFBP3 also increased with gestational age. To relate changes in gene expression in stromal cells with that in non stromal cells during development of the ovary we combined the data on the stromal genes with another 20 genes from non stromal cells published previously and then performed hierarchical clustering analysis. Three major clusters were identified. Cluster 1 genes (GATA4, FBN3, LHCGR, CYP19A1, ESR2, OCT4, DSG2, TGFB1, CCND2, LGR5, NR5A1) were characterised by high expression only in the first trimester. Cluster 2 genes (FSHR, INSL3, HSD3B1, CYP11A1, CYP17A1, AMH, IGFBP3, INHBA) were highly expressed in the third trimester and largely associated with follicle function. Cluster 3 (COL1A1, COL3A1, FBN1, TGFB2 TGFB3, TGFBR2, TGFBR3, LTBP2, LTBP3, LTBP4, TGFB1I1, ALDH1A1, AR, ESR1, NR2F2) had much low expression in the first trimester rising in the second trimester and remaining at that level during the third trimester. Cluster 3 contained members of two pathways, androgen and TGFβ signalling, including a common member of both pathways namely the androgen receptor cofactor TGFβ1 induced transcript 1 protein (TGFB1I1; hic5). GATA4, FBN3 and LHCGR, were highly correlated with each other and were expressed highly in the first trimester during stromal expansion before follicle formation, suggesting that this could be a critical phase in the development of the ovarian stroma.

Moderate nutrient restriction of beef heifers alters expression of genes associated with tissue metabolism, accretion, and function in fetal liver, muscle, and cerebrum by day 50 of gestation.

We hypothesized that a moderate maternal nutrient restriction during the first 50 d of gestation in beef heifers would affect transcript abundance of genes associated with tissue metabolism, accretion, and function in fetal liver, muscle, and cerebrum. Angus-cross heifers were estrus synchronized and assigned at breeding to one of two dietary treatments (CON- 100% of nutrient requirements to gain 0.45 kg/d; RES- 60% of CON). At day 50 of gestation, 14 heifers were ovariohysterectomized, and fetal liver, muscle, and cerebrum were collected. Transcriptome analysis via RNA-seq was conducted on the Illumina HiSeq 2500 platform using 50-bp paired-end reads at a depth of 2 × 10.4M reads/sample. Bioinformatic analysis was performed using the Tuxedo Suite and ontological analysis with DAVID 6.8. For fetal liver, muscle, and cerebrum, a total of 548, 317, and 151 genes, respectively (P < 0.01) were differentially expressed, of which 201, 144, and 28 genes, respectively were false discovery rate protected (FDR; q < 0.10). Differentially expressed genes were screened for fit into functional categories of pathways or ontologies associated with known impacts on tissue metabolism, accretion, and function. In fetal liver, five functional categories of interest (n = 125 genes) were affected by nutritional treatment: metabolic pathways, protein kinase, nucleosome core, mRNA splicing, and complement/coagulation cascades, of which 105 genes were upregulated in RES. In fetal muscle, three functional categories of interest (n = 106 genes) were affected by nutritional treatment: skeletal muscle, embryogenesis, and signaling cascades, of which 64 genes were upregulated in RES. In fetal cerebrum, three functional categories of interest (n = 60 genes) were affected by nutritional treatment: hippocampus and neurogenesis, metal-binding, and cytoskeleton, of which 58 genes were upregulated in RES. These results demonstrate that a moderate maternal nutrient restriction during the first 50 d of gestation in beef heifers alters transcript abundance of genes potentially impacting tissue metabolism, accretion, and function in fetal liver, muscle, and cerebrum. Furthermore, these results indicate that affected categories are tissue-specific and moderate maternal nutrient restriction generally increases expression of genes in fetuses from RES fed dams. Finally, these data lay the foundation upon which further research that identifies phenotypic responses to changes in these pathways may be elucidated.

Mulberry EIL3 confers salt and drought tolerances and modulates ethylene biosynthetic gene expression.

Ethylene regulates plant abiotic stress responses and tolerances, and ethylene-insensitive3 (EIN3)/EIN3-like (EIL) proteins are the key components of ethylene signal transduction. Although the functions of EIN3/EIL proteins in response to abiotic stresses have been investigated in model plants, little is known in non-model plants, including mulberry (Morus L.), which is an economically important perennial woody plant. We functionally characterized a gene encoding an EIN3-like protein from mulberry, designated as MnEIL3. A quantitative real-time PCR analysis demonstrated that the expression of MnEIL3 could be induced in roots and shoot by salt and drought stresses. Arabidopsis overexpressing MnEIL3 exhibited an enhanced tolerance to salt and drought stresses. MnEIL3 overexpression in Arabidopsis significantly upregulated the transcript abundances of ethylene biosynthetic genes. Furthermore, MnEIL3 enhanced the activities of the MnACO1 and MnACS1 promoters, which respond to salt and drought stresses. Thus, MnEIL3 may play important roles in tolerance to abiotic stresses and the expression of ethylene biosynthetic genes.

Transcriptional profiling and localization of GUL-1, a COT-1 pathway component, in Neurospora crassa

Impairment of theNeurospora crassaCOT-1 kinase results in defects in hyphal polarity. Some of these effects are partially suppressed by inactivation of gul-1 (encoding an mRNA-binding protein involved in translational regulation). Here, we report on the transcriptional profiling of cot-1 inactivation and demonstrate that gul-1 affects transcript abundance of multiple genes in the COT-1 pathway, including processes such as cell wall remodeling, nitrogen and amino acid metabolism. The GUL-1 protein itself was found to be distributed within the entire hyphal cell, along with a clear presence of aggregates that traffic within the cytoplasm. Live imaging of GUL-1-GFP demonstrated that GUL-1 transport is microtubule-dependent. Cellular stress, as imposed by the presence of the cell wall biosynthesis inhibitor Nikkomycin Z or by nitrogen limitation, resulted in a 2–3-fold increase of GUL-1 aggregate association with nuclei. Taken together, this study demonstrates that GUL-1 affects multiple processes, its function is stress-related and linked with cellular traffic and nuclear association.