Transcript Abundance Research Articles

Inferring post-transcriptional regulation within and across cell types in human testis.

Single-cell tissue atlases commonly use RNA abundances as surrogates for protein abundances. Yet, protein abundance also depends on the regulation of protein synthesis and degradation rates. To estimate the contributions of such post transcriptional regulation, we quantified the proteomes of 5,883 single cells from human testis using 3 distinct mass spectrometry methods (SCoPE2, pSCoPE, and plexDIA). To distinguish between biological and technical factors contributing to differences between protein and RNA levels, we developed BayesPG , a Bayesian model of transcript and protein abundance that systematically accounts for technical variation and infers biological differences. We use BayesPG to jointly model RNA and protein data collected from 29,709 single cells across different methods and datasets. BayesPG estimated consensus mRNA and protein levels for 3,861 gene products and quantified the relative protein-to-mRNA ratio (rPTR) for each gene across six distinct cell types in samples from human testis. About 28% of the gene products exhibited significant differences at protein and RNA levels and contributed to about 1, 500 significant GO groups. We observe that specialized and context specific functions, such as those related to spermatogenesis are regulated after transcription. Among hundreds of detected post translationally modified peptides, many show significant abundance differences across cell types. Furthermore, some phosphorylated peptides covary with kinases in a cell-type dependent manner, suggesting cell-type specific regulation. Our results demonstrate the potential of inferring protein regulation in from single-cell proteogenomic data and provide a generalizable model, BayesPG , for performing such analyses.

Developmental and Molecular Effects of C-Type Natriuretic Peptide Supplementation in In Vitro Culture of Bovine Embryos.

The use of C-type natriuretic peptide (CNP) in the interaction with the oocyte and in the temporary postponement of spontaneous meiosis resumption has already been well described. However, its action in pre-implantation developmental-stage embryos is yet to be understood. Thus, our study aimed to detect the presence of the canonical CNP receptor (natriuretic peptide receptor, NPR2) in germinal vesicle (GV)-, metaphase II (MII)-, presumptive zygote (PZ)-, morula (MO)-, and blastocyst (BL)-stage embryos and, later, to observe possible modulations on the embryos when co-cultured with CNP. In Experiment I, we detected and quantified NPR2 on the abovementioned embryo stages. Further, in Experiment II, we intended to test different concentrations (100, 200, or 400 nM of CNP) at different times of inclusion in the in vitro culture (IVC; inclusion from the beginning, i.e., day 1, or from day 5). In Experiment III, 400 nM of CNP was used on day 1 (D1) in the IVC, which was not demonstrated to be embryotoxic, and it showed potentially promising results in the blastocyst production rate when compared to the control. Thus, we analyzed the embryonic development rates of bovine embryos (D7) and hatching kinetics (D7, D8, and D9). Subsequently, morula and blastocyst were collected and evaluated for transcript abundance of their competence and quality (apoptosis, oxidative stress, proliferation, and differentiation) and lipid metabolism. Differences with probabilities less than p < 0.05, and/or fold change (FC) > 1.5, were considered significant. We demonstrate the presence of NPR2 until the blastocyst development stage, when there was a significant decrease in membrane receptors. There was no statistical difference in the production rate after co-culture with 400 nM CNP. However, when we evaluated the abundance of morula transcripts, there was an upregulated transcription in ADCY6 (p = 0.057) and downregulated transcripts in BMP15 (p = 0.013), ACAT1 (p = 0.040), and CASP3 (p = 0.082). In addition, there was a total of 12 transcriptions in morula that presented variation FC > 1.5. In blastocysts, the treatment with CNP induced upregulation in BID, CASP3, SOX2, and HSPA5 transcripts and downregulation in BDNF, NLRP5, ELOVL1, ELOVL4, IGFBP4, and FDX1 transcripts (FC > 1.5). Thus, our study identified and quantified the presence of NPR2 in bovine pre-implantation embryos. Furthermore, 400 nM of CNP in IVC, a concentration not previously described in the literature, modulated some transcripts related to embryonic metabolism, and this was not embryotoxic morphologically.

Delayed endometrial preparation for the induction of luteolysis as a potential factor for improved reproductive performance in Angus beef heifers with high antral follicle counts.

Antral Follicle Count (AFC) and anti-Müllerian hormone (AMH) concentrations are reflective for ovarian reserve and have been associated with improved reproductive performance in cattle. Key events for regulation of uterine receptivity are orchestrated by progesterone. As progesterone concentrations are greater in animals with high than low AFC, we tested the hypothesis, if the resulting improved uterine environment will lead to improved conceptus elongation and endometrial response to interferon tau. For four years, 10 heifers with lowest and highest AFC, respectively, were selected from 120 heifers. Reproductive tracts and blood samples for progesterone and AMH analysis were collected after synchronization and insemination. For a recovered conceptus, length was determined, and interferon tau (IFNT) transcript abundance was analyzed. Endometrial transcript abundance of interferon-stimulated gene 15 (ISG15) and oxytocin receptor (OXTR) were analyzed. Progesterone concentrations did not differ between Low and High AFC Group (P= 0.1). A difference in conceptus length was not observed. Endometrial abundance of ISG15 did not differ between Pregnant Low and High AFC heifers. Abundance of OXTR was greater in Open Low AFC than Open High AFC heifers (P< 0.01). Interaction of AMH and Pregnancy Status was determined, with greater AMH in Pregnant than Open High AFC heifers (P< 0.05). Improved uterine environment in High vs. Low AFC heifers did not result in longer conceptuses or improved endometrial response. As the increase in OXTR transcript abundance was only detected in Low AFC heifers, reported differences in reproductive performance might be associated with earlier initiation of luteolysis.

Melatonin Alleviates Albumin-Induced Tubular Cell Injury by Activating Clock-Controlled Nuclear Enriched Abundant Transcript 1-Mediated Proliferation

Melatonin Alleviates Albumin-Induced Tubular Cell Injury by Activating Clock-Controlled Nuclear Enriched Abundant Transcript 1-Mediated Proliferation

IDEIS: a tool to identify PTPRC/CD45 isoforms from single-cell transcriptomic data.

Single-cell RNA sequencing (scRNA-seq) methods are widely used in life sciences, including immunology. Typical scRNA-seq analysis pipelines quantify the abundance of particular transcripts without accounting for alternative splicing. However, a well-established pan-leukocyte surface marker, CD45, encoded by the PTPRC gene, presents alternatively spliced variants that define different immune cell subsets. Information about some of the splicing patterns in particular cells in the scRNA-seq data can be obtained using isotype-specific DNA oligo-tagged anti-CD45 antibodies. However, this requires generation of an additional sequencing DNA library. Here, we present IDEIS, an easy-to-use software for CD45 isoform quantification that uses single-cell transcriptomic data as the input. We showed that IDEIS accurately identifies canonical human CD45 isoforms in datasets generated by 10× Genomics 5' sequencing assays. Moreover, we used IDEIS to determine the specificity of the Ptprc splicing pattern in mouse leukocyte subsets.

Alteration of N-glycosylation of CDON promotes H2O2-induced DNA damage in H9c2 cardiomyocytes

Protein glycosylation is involved in DNA damage. Recently, DNA damage has been connected with the pathogenesis of heart failure. Cell adhesion associated, oncogene regulated (CDON), considered as an N-linked glycoprotein, is a transmembrane receptor for modulating cardiac function. But the role of CDON and its glycosylation in DNA damage remains unknown. In this study, we found that the knockdown of CDON caused DNA double-strand breaks as indicated by an increase in phosphorylated histone H2AX (γH2AX) protein level, immunofluorescent intensity of γH2AX and tail DNA moment in H9c2 cardiomyocytes. Conversely, overexpression of CDON led to decreasing DNA damage induced by hydrogen peroxide (H2O2) and upregulating the expression of genes related to DNA repair pathways-homologous recombination (HR) and non-homologous end joining (NHEJ). Moreover, we expressed nine predicted N-glycosylation site mutants in H9c2 cells prior to treatment with H2O2. The results showed that mutation of N-glycosylation sites (N99Q, N179Q, and N870Q) increased the accumulation of DNA damage and downregulated the expression of HR-related genes, demonstrating that CDON N-glycosylation on DNA damage is site-specific and these specific N-glycan sites may regulate HR repair-related transcript abundance of genes. Our data highlight that N-glycosylation of CDON is critical to cardiomyocyte DNA lesion. It may uncover the potential strategies targeting DNA damage pathway in heart disease.

Single-cell sequencing analysis revealed that NEAT1 was a potential biomarker and therapeutic target of prostate cancer.

Prostate cancer (PCa) usually manifests atypical symptoms in the early stage, and once symptoms appear, most PCa patients have developed to the advanced stage, failing to undergo radical surgery. In this study, PCa occurrence-related biomarkers were explored based on single-cell RNA sequencing (scRNA-seq) data. scRNA-seq data of prostate normal (Normal), benign prostatic hyperplasia (BPH), and PCa (Tumor) samples were acquired from the Gene Expression Omnibus (GEO). Cellular subsets associated with PCa occurrence were obtained using cell annotation. Additionally, the mRNA expression of nuclear enriched abundant transcript 1 (NEAT1) was detected by quantitative real-time PCR (qRT-PCR). The effects of NEAT1 on cell proliferation and apoptosis were analyzed by 5-ethynyl-2-deoxyuridine (EdU) and flow cytometry. Subsequently, cell-derived xenograft (CDX) models were constructed and divided into the LV-NC and LV-shNEAT1 groups. After the tumor tissues of CDX model mice in each group were extracted, the cell growth and Ki67 expression were observed separately using hematoxylin-eosin (H&E) staining and immunohistochemistry (IHC). Ten cellular subsets were obtained via cell annotation, and significantly differential changes were observed between Basal intermediate and Luminal during the course of BPH to PCa. NEAT1-Luminal was highly recruited in the Tumor group with low stemness and high malignancy scores. Matrix metallopeptidase 7 (MMP7)- keratin 17 (KRT17)-Basal intermediate had high ratios in the Tumor group with low stemness and high malignancy scores. The results of pseudotime analysis revealed that NEAT1-Luminal in the Tumor group were consistently distributed with tumor stage cells. In vitro assays showed that NEAT1 expression was elevated in PCa cells, and NEAT1 knockdown could inhibit cell proliferation and induce apoptosis. CDX assays indicated that silencing NEAT1 could reduce the growth rate of PCa tumor volume in CDX model mice. H&E staining results showed that nuclei of tumor cells were reduced and exhibited lighter color in the LV-shNEAT1 group compared with the LV-NC group. IHC results showed that Ki67 positivity was significantly lower in the LV-shNEAT1 group than in the LV-NC group. NEAT1 expression is increased in PCa, and NEAT1 can be a potential biomarker and therapeutic target for PCa.

CLN3 transcript complexity revealed by long-read RNA sequencing analysis

BackgroundBatten disease is a group of rare inherited neurodegenerative diseases. Juvenile CLN3 disease is the most prevalent type, and the most common pathogenic variant shared by most patients is the “1-kb” deletion which removes two internal coding exons (7 and 8) in CLN3. Previously, we identified two transcripts in patient fibroblasts homozygous for the 1-kb deletion: the ‘major’ and ‘minor’ transcripts. To understand the full variety of disease transcripts and their role in disease pathogenesis, it is necessary to first investigate CLN3 transcription in “healthy” samples without juvenile CLN3 disease.MethodsWe leveraged PacBio long-read RNA sequencing datasets from ENCODE to investigate the full range of CLN3 transcripts across various tissues and cell types in human control samples. Then we sought to validate their existence using data from different sources.ResultsWe found that a readthrough gene affects the quantification and annotation of CLN3. After taking this into account, we detected over 100 novel CLN3 transcripts, with no dominantly expressed CLN3 transcript. The most abundant transcript has median usage of 42.9%. Surprisingly, the known disease-associated ‘major’ transcripts are detected. Together, they have median usage of 1.5% across 22 samples. Furthermore, we identified 48 CLN3 ORFs, of which 26 are novel. The predominant ORF that encodes the canonical CLN3 protein isoform has median usage of 66.7%, meaning around one-third of CLN3 transcripts encode protein isoforms with different stretches of amino acids. The same ORFs could be found with alternative UTRs. Moreover, we were able to validate the translational potential of certain transcripts using public mass spectrometry data.ConclusionOverall, these findings provide valuable insights into the complexity of CLN3 transcription, highlighting the importance of studying both canonical and non-canonical CLN3 protein isoforms as well as the regulatory role of UTRs to fully comprehend the regulation and function(s) of CLN3. This knowledge is essential for investigating the impact of the 1-kb deletion and rare pathogenic variants on CLN3 transcription and disease pathogenesis.

Transcriptomic and Proteomic Insights into Host Immune Responses in Pediatric Severe Malarial Anemia: Dysregulation in HSP60-70-TLR2/4 Signaling and Altered Glutamine Metabolism.

Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.

Functional characterization of CCHamides and deorphanization of their receptors in the yellow fever mosquito, Aedes aegypti

As a widely distributed anthropophilic mosquito species and vector of various arboviruses, Aedes aegypti poses a significant threat to human health on a global scale. Investigating mosquito neuropeptides allows us to better understand their physiology. The neuropeptides CCHamide1 (CCHa1) and CCHamide2 (CCHa2) along with their associated G protein-coupled receptors (CCHa1R and CCHa2R) were recently identified and studied across insects. However, expression profiles and physiological roles of CCHamides and their receptors in many other insects, including A. aegypti, remain unclear. This research aimed to quantify and localize the expression of CCHamides along with their receptors and gain insight on their physiological function in the yellow fever mosquito. RT-qPCR analysis revealed transcript abundance of CCHamides and receptors changes over development. Differential expression was also observed in tissues/organs of adult mosquitoes indicating CCHa1 and CCHa2 transcripts are enriched in the midgut, while receptors are expressed across various tissues. CCHamide immunoreactivity was observed in neurons in the brain and ventral nerve cord along with enteroendocrine cells in the posterior midgut adjacent to the midgut-hindgut junction, corroborating their transcript expression profiles. Using different mass spectrometrical approaches, presence of CCHamides were confirmed in the brain of both sexes, including the pars intercerebralis of female mosquitoes, as well as in the gut of adult mosquitoes. For chemical identification of predicted CCHamides, we analyzed brain and gut extracts by ESI-Q Exactive Orbitrap MS and resulting fragmentations confirmed CCHa1 and CCHa2 in brain and midgut samples of both male and female mosquitoes. A heterologous functional assay was used to confirm the specificity and sensitivity of the two CCHamide receptors by assessing their activation in response to diverse mosquito peptides, which confirmed CCHa1 and CCHa2 as natural ligands. Finally, using a capillary feeder (CAFE) bioassay, our results suggest that CCHa2 modulates feeding behaviour in female mosquitoes.

Stocking density affects growth, feed utilisation, metabolism, welfare and associated mRNA transcripts in liver and muscle of rainbow trout more pronouncedly than dietary fish meal inclusion level

In aquaculture, stocking density and diet composition are critical factors that influence the performance and welfare of the farmed animal. However, there is limited information on their interactive effects. In this context, applying a 2 × 2 factorial design, we conducted a 12-week feeding trial to evaluate the effect of stocking density (low, LSD: 3.3–15 kg m−3 and high, HSD: 5.8–25 kg m−3; initial-final values) and dietary fish meal content (high, HFM: 30 % and low, LFM: 15 %) on growth, feed utilisation, metabolic oxygen consumption, tissue indices, carcass composition, plasma metabolites, and transcriptional regulation of growth, metabolism and welfare-related biomarker mRNAs in liver and muscle of the juvenile rainbow trout. At the whole-animal level, the HSD group showed significantly higher routine metabolic rate and feed intake indicating higher energy demand; but growth and feed efficiency was lower in HSD than the LSD group. Morpho-anatomically, HSD fish had lower relative gut length and higher intra-peritoneal fat index than LSD fish. Lower plasma free amino acids and glucose levels reiterated high energy expenditure in HSD, and elevated albumin levels indicated potential oxidative stress in the HSD group. Correspondingly, at the transcriptional level, hepatic mRNA levels of antioxidative enzymes (sod, cat, gst, g6pd) and stress-related molecular chaperone hsp90 were up-regulated in HSD; while the transcript abundance of growth-axis markers (ghr, igf1 igf2) and nutrient-sensor mtor were decreased. In muscle, proteolytic pathway components fbx32 and murf1 were upregulated in HSD, and concurrently mtor was also upregulated suggesting higher protein turnover in this group. With respect to the effect of dietary fish meal inclusion levels, LFM showed decrease in growth, hepatic igf2 expression, and lower plasma triglycerides and free amino acid levels than HFM group. However, the sensory appearance of flesh was found to be slightly better in LFM. Significant diet-husbandry interactions were not observed phenotypically, but the mRNA abundance of hepatic markers (ampk1, hsp70, mhc1 and tnfa) linked to energy-sensing, stress and immune response were differentially regulated. Overall, the study shows that high stocking density has a greater degree of impact on fish growth and welfare than reduction in dietary fishmeal inclusion, with limited interactional effects.

A Next-Generation Combinatorial Genomic Strategy Scans Genomic Loci Governing Heat Stress Tolerance in Chickpea.

In the wake of rising earth temperature, chickpea crop production is haunted by the productivity crisis. Chickpea, a cool season legume manifests tolerance in several agro-physiological level, which is complex quantitative in nature, and regulated by multiple genes and genetic networks. Understanding the molecular genetic basis of this tolerance and identifying key regulators can leverage chickpea breeding against heat stress. This study employed a genomics-assisted breeding strategy utilizing multi-locus GWAS to identify 10 key genomic regions linked to traits contributing to heat stress tolerance in chickpea. These loci subsequently delineated few key candidates and hub regulatory genes, such as RAD23b, CIPK25, AAE19, CK1 and WRKY40, through integrated genomics, transcriptomics and interactive analyses. The differential transcript accumulation of these identified candidates in contrasting chickpea accessions suggests their potential role in heat stress tolerance. Differential ROS accumulation along with their scavengers' transcript abundance aligning with the expression of identified candidates in the contrasting chickpea accessions persuade their regulatory significance. Additionally, their functional significance is ascertained by heterologous expression and subsequent heat stress screening. The high confidence genomic loci and the superior genes and natural alleles delineated here has great potential for swift genomic interventions to enhance heat resilience and yield stability in chickpea.

Synchronously improving intracellular electron transfer in electron-donating bacteria and electron-accepting methanogens for facilitating direct interspecies electron transfer during anaerobic digestion of kitchen wastes

Two major issues generally limit the effectiveness of direct interspecies electron transfer (DIET) during anaerobic digestion: 1) lack of essential electrical connection component, electrically conductive pili (e-pili) or multi-heme c-type cytochrome (MHC); 2) the thermodynamic limitations of combining electrons with protons for reducing carbon dioxide to methane. To address both issues, a strategy for facilitating DIET via combining ethanol-type fermentation pretreatment (EFP) with NaCl addition during anaerobic digestion of kitchen wastes was proposed. Combining EFP with NaCl addition dramatically increased methane yield rates (531.3 ± 11.4 vs 410.5 ± 8.7 mL/gVSadded/d) and efficiencies of conversion of organic substrates to methane (571.2 ± 13.8 vs 488.7 ± 11.7 mL/gVSremoval). The increased performances by combining EFP with NaCl addition were higher than that by independent EFP or NaCl addition. Paludibacter sp., Petrimonas sp. and Syntrophomonas wolfei were the predominant and metabolically active electron-donating bacteria, and their expression of genes for e-pili/MHCs by combining EFP with NaCl addition was higher than that by independent EFP or NaCl addition. Methanothrix soehngenii and Methanoculleus bourgensis were the predominant and metabolically active electron-accepting methanogens, and their expression of genes for carbon dioxide reduction pathway for methanogenesis by combining EFP with NaCl addition was higher than that by independent EFP or NaCl addition. In addition, EFP specifically increased the transcript abundance of genes for NAD+/NADH transformation closely associated with the formation of e-pili/MHCs, while NaCl addition specifically increased the transcript abundance of genes for coenzyme F420/F420H2 transformation known to participate in reduction of carbon dioxide to methane.

Pyometra alters uterine aquaporins related with lipopolysaccharide concentrations and antioxidant enzyme activities in bitches

Pyometra is a common life-threatening inflammatory disease with a complex etiopathogenesis that develops during the diestrus stage and can be observed in elderly intact bitches. The present study evaluated five aquaporin (AQP1, AQP2, AQP3, AQP5, and AQP9) transcript abundances and immunolocalization in the uterine tissue, and investigated their relationship with uterine tissue and blood lipopolysaccharide (LPS) concentration, superoxide dismutase (SOD) and glutathione peroxidase (GPX) activity, and nitric oxide (NO) production in dogs suffering from pyometra. The study sampled 36 client-owned intact bitches from different breeds, of which 24 cases were diagnosed with pyometra. Twelve of these bitches in the diestrus stage that presented for elective ovariohysterectomy were used as the control group. Blood samples were collected into tubes without anticoagulant for serum progesterone, LPS concentration, and antioxidant activities at the time of diagnosis. Bacteriological and tissue samples from the uteri were collected after the ovariohysterectomy. The tissue samples were used to determine antioxidant activity, and hormone and toxin concentrations. Transcript abundance of uterine AQPs were determined by qPCR, and their presence and localization were determined by by immunohistochemistry. For all pyometra samples, the bacteria isolated from the uterine swabs were Escherichia coli. Compared to the control group, AQP1, AQP2, and AQP5 were downregulated more than 2-fold, whereas AQP9 was upregulated nearly 3-fold and AQP3 was upregulated more than 4-fold in the pyometra affected uteri (P<0.05). Uterine AQP1 was moderately negatively correlated with serum LPS concentration (r=-0.568, P<0.01) and tissue NO production (r=-0.407, P<0.05). AQP5 was positively correlated with serum SOD activity (r=0.485, P<0.05) and negatively correlated with serum LPS concentration (r=-0.512, P<0.05). AQP9 was negatively correlated with tissue SOD and serum GPx activity. This is the first study to identify AQP9 transcript abundance and immunolocalization in canine uterine tissue. Uterine AQP1, AQP2, AQP3, AQP5, and AQP9 transcript abundances were altered in spontaneously developed canine pyometra while AQP transcript abundance was negatively related to serum toxin concentration, NO production, and antioxidant enzyme activity. Further studies should be conducted to determine the role of altered abundances of AQPs transcripts in pyometra pathogenesis.

Transcriptome-based prediction for polygenic traits in rice using different gene subsets

BackgroundTranscriptome-based prediction of complex phenotypes is a relatively new statistical method that links genetic variation to phenotypic variation. The selection of large-effect genes based on a priori biological knowledge is beneficial for predicting oligogenic traits; however, such a simple gene selection method is not applicable to polygenic traits because causal genes or large-effect loci are often unknown. Here, we used several gene-level features and tested whether it was possible to select a gene subset that resulted in better predictive ability than using all genes for predicting a polygenic trait.ResultsUsing the phenotypic values of shoot and root traits and transcript abundances in leaves and roots of 57 rice accessions, we evaluated the predictive abilities of the transcriptome-based prediction models. Leaf transcripts predicted shoot phenotypes, such as plant height, more accurately than root transcripts, whereas root transcripts predicted root phenotypes, such as crown root length, more accurately than leaf transcripts. Furthermore, we used the following three features to train the prediction model: (1) tissue specificity of the transcripts, (2) ontology annotations, and (3) co-expression modules for selecting gene subsets. Although models trained by a gene subset often resulted in lower predictive abilities than the model trained by all genes, some gene subsets showed improved predictive ability. For example, using genes expressed in roots but not in leaves, the predictive ability for crown root diameter was improved by more than 10% (R2 = 0.59 when using all genes; R2 = 0.66, using 1,554 root-specifically expressed genes). Similarly, genes annotated as “gibberellic acid sensitivity” showed higher predictive ability than using all genes for root dry weight.ConclusionsOur results highlight both the possibility and difficulty of selecting an appropriate gene subset to predict polygenic traits from transcript abundance, given the current biological knowledge and information. Further integration of multiple sources of information, as well as improvements in gene characterization, may enable the selection of an optimal gene set for the prediction of polygenic phenotypes.

Taste receptor T1R3 regulates testosterone synthesis via the cAMP-PKA-SP1 pathway in testicular Leydig cells

Taste receptor type 1 subunit 3 (T1R3) is a G protein-coupled receptor encoded by the TAS1R3 gene that can be specifically activated by certain sweeteners or umami agents for sweet/umami recognition. T1R3 is a potential target for regulating male reproduction. However, studies on the impact of non-nutritive sweeteners on reproduction are limited. In the present study, we evaluated the impact of the non-nutritive sweeteners (saccharin sodium, sucralose and acesulfame-K) on testosterone synthesis in testicular Leydig cells of Xiang pigs by comparing the relative abundance of mRNA transcripts and protein expression of T1R3, steroidogenic related factors, and intracellular cyclic adenosine monophosphate (cAMP), protein kinase A (PKA), as well as testosterone levels using Western blotting, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). To clarify the specific mechanism, a dual luciferase assay was used to uncover the relationship between the transcription factors and steroidogenic enzyme. The acute intratesticular injection of a typical non-nutritive sweeteners was conducted to verify this impact in mouse. The results showed that saccharin sodium not only enhanced T1R3 expression in Leydig cells of Xiang pigs, but also caused significant increases in testosterone, cAMP, PKA, phosphorylation of specificity protein 1 (p-SP1), total protein of specificity protein 1 (SP1), steroidogenic acute regulatory protein (StAR), and 3β-hydroxysteroid dehydrogenase type 1 (3β-HSD1) (P<0.05). Similarly, treatment of Leydig cells with sucralose and acesulfame-K also increased testosterone level, protein expression of T1R3, 17-α-hydroxylase/17, 20-lyase (CYP17A1), and 3β-HSD1 (P<0.05). Treatment with SQ22536 (an adenylate cyclas inhibitor) or H89 (a PKA inhibitor) significantly reduced saccharin sodium-induced protein levels of p-SP1, StAR, CYP17A1, and 3β-HSD1 (P<0.05). In addition, a dual luciferase assay further demonstrated that SP1 significantly increased the promoter activity of CYP17A1 (P<0.05). When mouse testes were injected with saccharin sodium, T1R3, p-SP1, CYP17A1, and 3β-HSD1 were upregulated, leading to a significant testicular increase in testosterone and cAMP levels (P<0.05). These results suggest a mechanism by which the taste receptor T1R3 regulates testosterone production, and this mechanism may be linked to the cAMP-PKA pathway. Understanding the interrelationship between T1R3 and the cAMP-PKA-SP1 pathway contributes to clarify the regulatory mechanisms of male reproduction.

Pgmiox mediates stress response and plays a critical role for pathogenicity in Pyrenophora graminea，the agent of barley leaf stripe

Barley leaf stripe is an important disease caused by Pyenophora graminea that affects barley yields in the world. Ascorbic acid (AsA) interacts with key elements of a complex network orchestrating plant defense mechanisms, thereby influencing the outcome of plant-pathogen interaction. Myo-inositol oxygenase (MIOX) is a pivotal enzyme involved in plants development and environmental stimuli. However, MIOX has described functions in plants but has not been characterized in fungi. In this study, we characterized the Pgmiox gene in P. graminea pathogenesis through annotated on the metabolic pathway of ascorbic acid aldehyde. Our analysis suggested that the Pgmiox protein had a typical conserved MIOX domain. Multiple alignment analysis indicated that the P. graminea MIOX orthologue clustered with MIOX proteins of Pyrenophora species. RNA interference successfully reduced transcript abundance of Pgmiox in six transformant lines compared to wild type, and the transformants were further less virulent on the host plant barley. Transformants of Pgmiox had significant reductions in vegetative growth and pathogenicity, which had increased resistance to tebuconazole and carbendazim. In addition, Pgmiox is associated with ionic, drought, osmotic, oxidative, and heavy metal stress tolerance in P. graminea. In conclusion, our findings reveal that Pgmiox may be widely utilized by fungi to enhance pathogenesis and holds significant potential for the development of durable P. graminea resistance through genetic modifications.

Lack of effect of cAMP modulation during pre-maturation in vitro on development to the blastocyst stage and expression of specific genes associated with lineage commitment

Pharmacological elevation of cAMP of cultured cumulus-oocyte complexes (COC) before or coincident with initiation of maturation has been reported to improve outcomes for various systems for in vitro production of embryos. Here it was hypothesized that artificial elevation of cAMP in the oocyte for a 2-h period of pre-maturation would improve developmental competence of matured oocytes and result in increased blastocyst yield and alter expression of genes important for embryonic differentiation. Treated COC were cultured for 2 h with dibutyryl cAMP (dbcAMP), a membrane-permeable form of cAMP, and 3-isobutyl-1-methylxanthine (IBMX), which inhibits phosphodiesterases that convert cAMP to ATP. Subsequently, oocytes were matured and fertilized and the resultant embryos cultured for 7.5 d. There was no effect of treatment on the percent of oocytes or cleaved embryos becoming blastocysts or on transcript abundance of EOMES, GATA4, NANOG, SOX2, or SOX17 in the blastocyst. Results do not support the use of pharmacological enhancers of cAMP concentrations in the oocyte for improving the blastocyst yield following in vitro oocyte maturation, fertilization, and embryo culture.

Multi-omic analysis of a mucolipidosis II neuronal cell model uncovers involvement of pathways related to neurodegeneration and drug metabolism

Defining the molecular consequences of lysosomal dysfunction in neuronal cell types remains an area of investigation that is needed to understand many underappreciated phenotypes associated with lysosomal disorders. Here we characterize GNPTAB-knockout DAOY medulloblastoma cells using different genetic and proteomic approaches, with a focus on how altered gene expression and cell surface abundance of glycoproteins may explain emerging neurological issues in individuals with GNPTAB-related disorders, including mucolipidosis II (ML II) and mucolipidosis IIIα/β (ML IIIα/β). The two knockout clones characterized demonstrated all the biochemical hallmarks of this disease, including loss of intracellular glycosidase activity due to impaired mannose 6-phosphate-dependent lysosomal sorting, lysosomal cholesterol accumulation, and increased markers of autophagic dysfunction. RNA sequencing identified altered transcript abundance of several neuronal markers and genes involved in drug metabolism and transport, and neurodegeneration-related pathways. Using selective exo-enzymatic labeling (SEEL) coupled with proteomics to profile cell surface glycoproteins, we demonstrated altered abundance of several glycoproteins in the knockout cells. Most striking was increased abundance of the amyloid precursor protein and apolipoprotein B, indicating that loss of GNPTAB function in these cells corresponds with elevation in proteins associated with neurodegeneration. The implication of these findings on lysosomal disease pathogenesis and the emerging neurological manifestations of GNPTAB-related disorders is discussed.

Luteolin Mitigates Dopaminergic Neuron Degeneration and Restrains Microglial M1 Polarization by Inhibiting Toll Like Receptor 4.

Luteolin is a natural flavonoid and its neuroprotective and anti-inflammatory effects have been confirmed to mitigate neurodegeneration. Despite these findings, the underlying mechanisms responsible for these effects remain unclear. Toll-like receptor 4 (TLR4) is widely distributed in microglia and plays a pivotal role in neuroinflammation and neurodegeneration. Here studies are outlined that aimed at determining the mechanisms responsible for the anti-inflammatory and neuroprotective actions of luteolin using a rodent model of Parkinson's disease (PD) and specifically focusing on the role of TLR4 in this process. The mouse model of PD used in this experiment was established through a single injection of lipopolysaccharide (LPS). Mice were then subsequently randomly allocated to either the luteolin or vehicle-treated group, then motor performance and dopaminergic neuronal injury were evaluated. BV2 microglial cells were treated with luteolin or vehicle saline prior to LPS challenge. MRNA expression of microglial specific marker ionized calcium-binding adapter molecule 1 (IBA-1) and M1/M2 polarization markers, as well as the abundance of indicated pro-inflammatory cytokines in the mesencephalic tissue and BV2 were quantified by real time-polymerase chain reaction (RT-PCR) and Enzyme-linked Immunosorbent Assay (ELISA), respectively. Cell viability and apoptosis of neuron-like PC12 cell line co-cultured with BV2 were detected. TLR4 RNA transcript and protein abundance in mesencephalic tissue and BV2 cells were detected. Nuclear factor kappa-gene binding (NF-κB) p65 subunit phosphorylation both in vitro and in vivo was evaluated by immunoblotting. Luteolin treatment induced functional improvements and alleviated dopaminergic neuronal loss in the PD model. Luteolin inhibited apoptosis and promoted cell survival in PC12 cells. Luteolin treatment shifted microglial M1/M2 polarization towards an anti-inflammatory M2 phenotype both in vitro and in vivo. Finally, it was found that luteolin treatment significantly downregulated both TLR4 mRNA and protein expression as well as restraining NF-κB p65 subunit phosphorylation. Luteolin restrained dopaminergic degeneration in vitro and in vivo by blocking TLR4-mediated neuroinflammation.