This research communication screened and identified differentiated expressed genes in bovine mammary epithelial cells (BMECs) upon prolactin (PRL) stimulation. PRL of 5 μg/ml increased β-casein synthesis in BMECs with milk protein synthesis capacity. RNA sequencing (RNA-seq) was used to screen differentially expressed genes (DEGs). A total of 375 DEGs (165 up-regulated and 210 down-regulated) were identified between PRL-stimulated group and the control group. Gene ontology enrichment analysis showed that the up-regulated genes were primarily associated with cell functions, metabolic processes, and biological regulatory processes. Pathway enrichment analysis showed that the up-regulated genes were mainly enriched in JAK-STAT, Rap1, Ras and Notch signaling pathways, which are widely involved in cell proliferation, differentiation and milk component synthesis. This study provides an initial understanding of the changes in gene expression in BMECs with PRL-stimulation, as determined by RNA-seq transcriptomic analysis, thereby enhancing our knowledge of the molecular regulation of lactation metabolism.

Methionine (Met) can activate the mechanistic target of rapamycin (mTOR) to promote milk synthesis in mammary epithelial cells. However, it is largely unknown which G protein-coupled receptor can mediate the stimulation of Met on mTOR activation. In this study, we employed transcriptome sequencing to analyse which G protein-coupled receptors were associated with the role of Met and further used gene function study approaches to explore the role of G protein-coupled receptor 183 (GPR183) in Met stimulation on mTOR activation in HC11 cells. We identified nine G protein-coupled receptors including GPR183 whose expression levels were upregulated by Met treatment through RNA sequencing and subsequent quantitative real-time PCR analysis. Using GPR183 knockdown and overexpression technology, we demonstrate that GPR183 is a positive regulator of milk protein and fat synthesis and proliferation of HC11 cells. Met affected GPR183 expression in a dose-dependent manner, and GPR183 mediated the stimulation of Met (0·6 mM) on milk protein and fat synthesis, cell proliferation and mTOR phosphorylation and mRNA expression. The inhibition of phosphoinositide 3-kinase blocked the phosphorylation of mTOR and AKT stimulated by GPR183 activation. In summary, through RNA sequencing and gene function study, we uncover that GPR183 is a key mediator for Met to activate the phosphoinositide 3-kinase-mTOR signalling and milk synthesis in mouse mammary epithelial cells.

Waterhemp [Amaranthus tuberculatus (Moq.) Sauer] is one of the most troublesome weeds in the United States. An A. tuberculatus population (CHR) was identified in Illinois, USA, as resistant to herbicides from six different site-of-action groups. Recently, the same population was also recognized as dicamba resistant. This study aimed to identify key resistance genes and the putative dicamba resistance mechanism in A. tuberculatus via transcriptomics analysis. Multiple differentially expressed (DE) genes and co-expression gene modules were identified as associated with dicamba resistance. Specifically, genes encoding glutathione S-transferases (GSTs), ATP-binding cassette transporters, peroxidases, and uridine diphosphate (UDP)-glycosyltransferases (UGTs) were identified. Results indicated enhanced oxidative stress tolerance as the primary mechanism for reducing dicamba toxicity. Results also point to potential glycosylation via UGTs and conjugation via GSTs of dicamba and its by-products. This is the first transcriptomics characterization of dicamba resistance in A. tuberculatus. Multiple non-target-site resistance genes were identified, indicating a cross-resistance pattern in the CHR population leading to a putative-enhanced oxidative stress response. Regions of multiple DE genes (i.e., genomic hot spots) across the A. tuberculatus genome corroborate previous results and potentially add to the complexity of non-target-site resistance traits.

Fetal liver tissue collected from a nonhuman primate (NHP) baboon model of maternal nutrient reduction (MNR) at four gestational time points (90, 120, 140, and 165 days gestation [dG], term in the baboon is ∼185 dG) was used to quantify MNR effects on the fetal liver transcriptome. 28 transcripts demonstrated different expression patterns between MNR and control livers during the second half of gestation, a developmental period when the fetus undergoes rapid weight gain and fat accumulation. Differentially expressed transcripts were enriched for fatty acid oxidation and RNA splicing-related pathways. Increased RNA splicing activity in MNR was reflected in greater abundances of transcript splice variant isoforms in the MNR group. It can be hypothesized that the increase in splice variants is deployed in an effort to adapt to the poor in utero environment and ensure near-normal development and energy metabolism. This study is the first to study developmental programming across four critical gestational stages during primate fetal liver development and reveals a potentially novel cellular response mechanism mediating fetal programming in response to MNR.

The role of bees in the environment, economic, biodiversity and pharmaceutical industries is due to its social behavior, which is oriented from the brain and hypopharyngeal gland that is the center of royal jelly (RJ) production. Limited studies have been performed on the head gene expression profile at the RJ production stage. The aim of this study was to compare the gene expressions in 9 and 1-day-old (DO) honeybee workers in order to achieve better understanding about head gene expression pattern. After sequencing of RNAs, transcriptome and their networks were compared. The head expression profile undergoes various changes. 1662 gene transcripts had differential expressions which 1125 and 537 were up and down regulated, respectively, in 9_DO compared with 1_DO honey bees. The day 1th had more significant role in the expression of genes related to RJ production as major RJ protein 1, 2, 3, 5, 6 and 9 encoding genes, but their maximum secretion occurred at day 9th. All process related to hypopharyngeal glands activities as CYP450 gene, fatty acid synthase gene, vitamin B6 metabolism and some of genes involved in fatty acid elongation and degradation process had an upward trend from 1_DO and were age-dependent. By increasing the age, the activity of pathways related to immune system increased for keeping the health of bees against the chemical compound. The expression of aromatic amino acid genes involved in Phenylalanine, tyrosine and tryptophan biosynthesis pathway are essential for early stage of life. In 9_DO honeybees, the energy supplying, reducing stress, protein production and export pathways have a crucial role for support the body development and the social duties. It can be stated that the activity of honeybee head is focused on energy supply instead of storage, while actively trying to improve the level of cell dynamics for increasing the immunity and reducing stress. Results of current study identified key genes of certain behaviors of honeybee workers. Deeper considering of some pathways will be evaluated in future studies.

Cuscuta chinensis Lam. is a traditional medicinal herb used to treat female sterility and male reproductive system disorders. However, the anti-lung cancer properties of Cuscuta chinensis Lam. and possible molecular mechanisms have yet to be explored. Thus, the study’s main purpose was to evaluate in vitro and in vivo anti-lung cancer properties of C. chinensis water extract (CLW) in human lung adenocarcinomas and the underlying molecular mechanism involved. Our results demonstrated that CLW caused a significant inhibition of cell viability and induced G1 cycle arrest in lung cancer cells. Furthermore, RNA-seq transcriptome analysis revealed 602 common genes with a significant expression in A549 and H1650 cells under CLW treatment. Functional enrichment analysis suggested that these common genes regulated by CLW mainly involve lung cancer cell proliferation, metastases and apoptosis processes. In addition, forty-six common genes (> 2-fold change) regulated by CLW in A549 and H1650 cells were selected for further validation. In vitro quantitative real-time PCR results confirmed that twelve genes were up-regulated, and four genes were down-regulated in A549 and H1650 cells. The in vivo experiment demonstrated CLW could significantly decrease tumour volume and tumour weight of mice compared with the control group. Moreover, in vivo quantitative real-time PCR results revealed that C11orf96, FGFBP1, FOSB and NPTX1 genes were up-regulated and EGR1, GBP4 and MAP2K6 genes were down-regulated in tumour tissues compared with the control group. These data strongly suggest that CLW could be developed as an efficacious drug for lung cancer treatment.

Zinc (Zn) is an essential mineral and its deficiency manifests in non-specific clinical signs that require long time to develop. The response of swine intestine to Zn restriction was evaluated to identify early changes that can be indicative of Zn deficiency. Twenty-seven pigs (body weight = 77⋅5 ± 2⋅5 kg) were assigned to one of three diets: diet without added Zn (Zn-restricted diet, ZnR), and ZnR-supplemented with either 50 (Zn50) or 100 mg of Zn/kg of diet (Zn100) of Zn supplied by ZnCl2. After 32 d consuming the diets, serum Zn concentration in ZnR pigs was below the range of 0⋅59–1⋅37 μg/ml considered sufficient, thereby confirming subclinical Zn deficiency. Pigs showed no obvious health or growth changes. RNA-seq analysis followed by qPCR showed decreased expression of metallothionein-1 (MT1) (P < 0⋅05) and increased expression of Zn transporter ZIP4 (P < 0⋅05) in jejunum and ileum of ZnR pigs compared with Zn-supplemented pigs. Ingenuity pathway analysis revealed that Zn50 and Zn100 induced changes in genes related to nucleotide excision repair and integrin signalling pathways. The top gene network in the ZnR group compared with Zn100 was related to lipid and drug metabolism; and compared with Zn50, was related to cellular proliferation, assembly and organisation. Dietary Zn concentrations resulted in differences in genes related to immune pathways. Our analysis showed that small intestine presents changes associated with Zn deficiency after 32 d of Zn restriction, suggesting that the intestine could be a sentinel organ for Zn deficiency.

Global human activities, such as greenhouse emissions and pollution, are promoting global warming, environmental changes and biodiversity reduction. Pristine environments such as those of Antarctica are not immune to these phenomena, as is noticeable from the increasing pace of the temperature shift registered within the continent in recent decades. In this study, we describe the first de novo transcriptome analysis of the endemic Antarctic springtail (= collembolan) Cryptopygus terranovus and we evaluate its global gene expression response following a mid-term exposure of 20 days to 18°C. Expression data are compared with wild specimens sampled from their native environment to outline the molecular mechanisms triggered by the thermal exposure. Although individual plasticity in transcript modulation is assessed, several pathways appear to be differentially modulated in springtails subjected to the heat treatment vs wild specimens. Through enrichment analysis, we show that protein catabolism, fatty acid metabolism and a sexual response characterized by spermatid development are induced, while carbohydrate consumption, lipid catabolism and tissue development are downregulated in treated samples compared to controls.

In order to better understand the molecular mechanisms associated with salinity tolerance, transcriptome analysis of a local salt-tolerant wheat landrace (i.e. Roshan) was performed under salt stress. Transcriptome sequencing yielded 137,508,542 clean reads using the Illumina HiSeq 2000 platform. The results of two alignment programs, i.e. STAR and HISAT2, were used separately to perform the analysis of differentially expressed genes (DEGs) using DESeq2. Finally, a total of 17,897 DEGs were identified by DESeq2. Moreover, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses identified 108 GO terms and 62 significant KEGG pathways, of which ‘metabolic process’ and ‘metabolic pathways’ were the most abundant enriched term and pathway, respectively. Additionally, key salinity-tolerant genes, including asparagine synthetase, were also identified in the present study. Out of 87 identified families of transcription factors, GAI‐RGA ‐ and ‐SCR (GRAS) was one of the most important, which participates in signal transduction, and meristem maintenance and development. Eventually, to validate the gene expression levels, six DEGs were selected for a quantitative real-time polymerase chain reaction, and the results were in line with those of RNA-Seq. The findings of the current study can guide future genetic and molecular studies and allow a better understanding and improvement of salt tolerance in wheat.

The WSSA Group 15 (HRAC Group K3) herbicide flufenacet is a key compound in weed resistance management, primarily used for PRE control of grass weeds in winter cereal–based crop rotations in Europe. Although resistance to compounds of its mechanism of action (inhibition of the synthesis of very-long-chain fatty acids) generally evolves slowly, reduced flufenacet efficacy due to enhanced glutathione transferase (GST) activity has been described in several blackgrass (Alopecurus myosuroides Huds.) populations. The present study aimed to better understand of the mechanism of flufenacet detoxification in A. myosuroides. Therefore, we characterized four A. myosuroides populations with different levels of flufenacet sensitivity. Flufenacet degradation was significantly slowed down in a sensitive population and a population with reduced flufenacet sensitivity by the use of the GST inhibitors tridiphane and ethacrynic acid at sublethal rates. Finally, an RNA sequencing (RNA-seq) study with the four A. myosuroides populations was conducted. In total, six differentially expressed GSTs and nine transcription factors as well as a keto-acyl-CoA reductase involved in the biosynthesis of very-long-chain fatty acids were identified as candidate genes among a set of 319 significantly more highly expressed gene-associated contigs. Among a set of 218 contigs with significantly lower expression levels, receptor kinase activity was the most frequent annotation. In summary, the likely GST-mediated reduction in sensitivity evolves in A. myosuroides at a slow rate and can partially be reversed by an interaction between flufenacet and the GST inhibitors tridiphane and ethacrynic acid. This provides further evidence for enhanced GST activity as a key mechanism in flufenacet resistance in A. myosuroides and supports the hypothesis that the six differentially expressed GSTs detected in the present RNA-seq study are potentially involved in flufenacet resistance.

Parasites cause harm to their hosts and represent pervasive causal agents of natural selection. Understanding host proximate responses during interactions with parasites can help predict which genes and molecular pathways are targets of this selection. In the current study, we examined transcriptional changes arising from interactions between Drosophila melanogaster and their naturally occurring ectoparasitic mite, Gamasodes queenslandicus. Shifts in host transcript levels associated with behavioural avoidance revealed the involvement of genes underlying nutrient metabolism. These genetic responses were reflected in altered body lipid and glycogen levels in the flies. Mite infestation triggered a striking immune response, while male accessory gland protein transcript levels were simultaneously reduced, suggesting a trade-off between host immune responses to parasite challenge and reproduction. Comparison of transcriptional analyses during mite infestation to those during nematode and parasitoid attack identified host genes similarly expressed in flies during these interactions. Validation of the involvement of specific genes with RNA interference lines revealed candidates that may directly mediate fly–ectoparasite interactions. Our physiological and molecular characterization of the Drosophila–Gamasodes interface reveals new proximate mechanisms underlying host–parasite interactions, specifically host transcriptional shifts associated with behavioural avoidance and infestation. The results identify potential general mechanisms underlying host resistance and evolutionarily relevant trade-offs.

This study aimed to evaluate the transcriptional changes occurring in isolated perfused mammary alveolar tissue in response to inoculation with S. agalactiae and to identify the most affected biological functions and pathways after 3 h. Four udders taken at slaughter from cows with healthy mammary gland were perfused ex situ with warmed and gassed Tyrode's solution. Mammary alveolar tissue samples were taken from the left fore and rear quarters (IQ-inoculated quarters) before inoculation (hour 0) and at 3 h post inoculation (hpi) and at the same times from control right fore and rear quarters (not inoculated: NIQ). A total of 1756 differentially expressed genes (DEGs) were identified between IQ and NIQ at 3 hpi using edgeR package. Within this set of DEGs, 952 were up regulated and mainly involved with innate immune response and inflammatory response, e.g., CD14, CCL5, TLR2, IL-8, SAA3, as well as in transcriptional regulation such as FOS, STAT3 and NFKBIA. Genes down-regulated (804) included those involved with lipid synthesis e.g., APOC2, SCD, FABP3 and FABP4. The most affected pathways were chemokine signaling, Wnt signaling and complement and coagulation cascades, which likely reflects the early stage response of mammary tissue to S. agalactiae infection. No significant gene expression changes were detected by RNA-Seq in the others contrasts. Real time-PCR confirmed the increase in mRNA abundance of immune-related genes: TLR2, TLR4, IL-1β, and IL-10 at 3 hpi between IQ and NIQ. The expression profiles of Casp1 and Bax for any contrasts were unaffected whereas Bcl2 was increased in IQ, which suggests no induction of apoptosis during the first hours after infection. Results provided novel information regarding the early functional pathways and gene network that orchestrate innate immune responses to S. agalactiae infection. This knowledge could contribute to new strategies to enhance resistance to this disease, such as genomic selection.

Seed germination, the first and critical step of the plant's life cycle, is affected by salt stress. However, the underlying mechanism of salt tolerance during early seed germination remains elusive. Here, a comparative RNA-seq analysis was performed using early germinating seeds either under normal conditions or in 100 and 150 mM sodium chloride. A total of 575 genes were up-regulated and 913 genes were down-regulated in the presence of 100 mM NaCl. Under the 150 mM NaCl treatment 1921 genes were up-regulated and 3501 genes were down-regulated. A total of 379 or 863 genes were up-regulated or down-regulated in both 100 and 150mM NaCl. These co-regulated genes were further analysed by GO enrichment. Genes in the categories abscisic acid signaling and synthesis and nutrient reservoir activity were significantly enriched in the up-regulated genes. Transcription factors responsive to gibberellin and auxin were significantly down-regulated by salinity stress. Genes related to anti-oxidant activity were significantly enriched in the down-regulated gene clusters by NaCl treatment. Our results suggest that salt stress inhibits seed germination by activating ABA synthesis and signalling, and depressing GA and auxin signalling, while preserving nutrition and down-regulated anti-oxidant activity. Our study provides more insight into the molecular mechanism of salt tolerance during early seed germination.

Bradynema listronoti is a parasitic nematode described from infected specimens of the carrot weevil Listronotus oregonensis. Prevalence of infection by B. listronoti under field conditions was followed over a period of 16 years in an untreated carrot field. Susceptibility of different carrot weevil life stages was evaluated as well as the impact of infection on fecundity and mortality. Gene expression in infected and uninfected carrot weevils was also compared to evaluate the impact of the parasite on the host transcriptome. Prevalence of B. listronoti in carrot weevil populations was sustained over the years ranging from 20 to 63%. All the weevil stages exposed to B. listronoti inoculum were susceptible to infection, larvae being more vulnerable (59 ± 8% infected) compared with pupae (4 ± 3% infected) and adults (7 ± 3% infected). The fecundity of infected female weevils was greatly reduced (60-fold) due to an inhibition of the maturation of the reproductive system. Transcriptomic analyses revealed that this parasitic castration may have been triggered by the inhibition of reproductive hormone production. The B. listronoti–L. oregonensis interaction represents a case of parasitic castration with a unique potential for biological control of an important pest of carrots.

Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.

Herbicide resistance, and in particular multiple-herbicide resistance, poses an ever-increasing threat to food security. A biotype of junglerice [Echinochloa colona (L.) Link] with resistance to four herbicides, imazamox, fenoxaprop-P-ethyl, quinclorac, and propanil, each representing a different mechanism of action, was identified in Sunflower County, MS. Dose responses were performed on the resistant biotype and a biotype sensitive to all four herbicides to determine the level of resistance. Application of a cytochrome P450 inhibitor, malathion, with the herbicides imazamox and quinclorac resulted in increased susceptibility in the resistant biotype. Differential gene expression analysis of resistant and sensitive plants revealed that 170 transcripts were upregulated in resistant plants relative to sensitive plants and 160 transcripts were upregulated in sensitive plants. In addition, 507 transcripts were only expressed in resistant plants and 562 only in sensitive plants. A subset of these transcripts were investigated further using quantitative PCR (qPCR) to compare gene expression in resistant plants with expression in additional sensitive biotypes. The qPCR analysis identified two transcripts, a kinase and a glutathione S-transferase that were significantly upregulated in resistant plants compared with the sensitive plants. A third transcript, encoding an F-box protein, was downregulated in the resistant plants relative to the sensitive plants. As no cytochrome P450s were differentially expressed between the resistant and sensitive plants, a single-nucleotide polymorphism analysis was performed, revealing several nonsynonymous point mutations of interest. These candidate genes will require further study to elucidate the resistance mechanisms present in the resistant biotype.

In cattle early gastrulation-stage embryos (Stage 5), four tissues can be discerned: (i) the top layer of the embryonic disc consisting of embryonic ectoderm (EmE); (ii) the bottom layer of the disc consisting of mesoderm, endoderm and visceral hypoblast (MEH); (iii) the trophoblast (TB); and (iv) the parietal hypoblast. We performed microsurgery followed by RNA-seq to analyse the transcriptome of these four tissues as well as a developmentally earlier pre-gastrulation embryonic disc. The cattle EmE transcriptome was similar at Stages 4 and 5, characterised by the OCT4/SOX2/NANOG pluripotency network. Expression of genes associated with primordial germ cells suggest their presence in the EmE tissue at these stages. Anterior visceral hypoblast genes were transcribed in the Stage 4 disc, but no longer by Stage 5. The Stage 5 MEH layer was equally similar to mouse embryonic and extraembryonic visceral endoderm. Our data suggest that the first mesoderm to invaginate in cattle embryos is fated to become extraembryonic. TGFβ, FGF, VEGF, PDGFA, IGF2, IHH and WNT signals and receptors were expressed, however the representative members of the FGF families differed from that seen in equivalent tissues of mouse embryos. The TB transcriptome was unique and differed significantly from that of mice. FGF signalling in the TB may be autocrine with both FGFR2 and FGF2 expressed. Our data revealed a range of potential inter-tissue interactions, highlighted significant differences in early development between mice and cattle and yielded insight into the developmental events occurring at the start of gastrulation.