Protein Processing In Endoplasmic Reticulum Research Articles

Abstract 4120290: Sex-specific Impact of Early to Mid-gestational Testosterone Excess on Sheep Fetal and Adult Offspring Lungs

Using the translationally relevant sheep model of prenatal testosterone (T) excess, we previously reported intrauterine growth retardation (IUGR) in both sexes, adverse sex specific programming of fetal heart and cardiometabolic dysfunction in adult female offspring. Because of the intricate reciprocal relationship between the heart and lungs, we hypothesized that gestational T excess will have detrimental sex-specific effects on offspring lungs beginning as early as fetal life and extending into adulthood. Pregnant ewes were intramuscularly injected with 100 mg of testosterone propionate twice weekly from gestational days (GD) 30-90 (term 147 days) and offspring lungs were harvested at GD120, 30 days after cessation of T treatment; (n=4-7/group) and in adulthood (n=4-6/group) and processed for molecular and histological analyses. Data was analyzed by student T test within each sex and Cohen (d) effect size was calculated (Cohens d>0.8 represents large effect size. Lung collagen was significantly increased in T-male fetuses (TM) vs control males (CM) (p=0.01, d=1.99) that persisted into adulthood (TM vs CM: p=0.01, d=1.83). The effects of gestational T excess was evidenced as an increase in collagen only in the lungs of adult T-female fetuses (TF) relative to control females (CF) (p=0.003, d=2.38), but not during fetal life. Gestational T excess induced significant parallel increases in TUNEL positive nuclei/frame in TM fetuses relative to CM (n=3/group, p=0.01, d=3.35) persisting as a large magnitude increase of TUNEL positive nuclei/frame in adult TM (p=0.12, d=0.96). In TF females, apoptotic changes were not noted in fetal lungs but an increase of TUNEL positive nuclei/frame was evidenced in adult TF (p=0.08, d=1.14). At the molecular level prenatal T excess induced an increase in histone deacetylase 1 (HDAC1) expression in fetal TM vs CM (p=0.04, d=1.50), and decrease in HDAC1 in TF vs CF (p=0.10, d=1.09) suggestive of T-induced epigenetic alteration. Transcriptomic analysis of fetal lungs revealed upregulation of pathways associated with estrogen signaling and neuroactive ligand receptor interaction, and downregulation of pathways associated with protein processing in endoplasmic reticulum and antigen processing&presentation (unadjusted p< 0.05, log FC>1.5) in both sexes. Overall, early to mid-gestational exposure to testosterone adversely reprograms the lungs in sex specific fashion as early as fetal life extending into postnatal adult life.

Integrated Transcriptomic and Proteomic Analysis of Nutritional Quality-Related Molecular Mechanisms in "Longjia", "Yangpao", and "Niangqing" Walnuts (Juglans sigillata).

In this study, "Longjia (LJ)" and "Yangpao (YP)"exhibited higher contents of major nutrients compared to "Niangqing (NQ)" walnuts. The combination of transcriptome and proteome by RNA sequencing and isotope labeling for relative and absolute quantification techniques provides new insights into the molecular mechanisms underlying the nutritional quality of the three walnut species. A total of 4146 genes and 139 proteins showed differential expression levels in the three comparison groups. Combined transcriptome and proteome analyses revealed that these genes and proteins were mainly enriched in signaling pathways such as fatty acid biosynthesis, protein processing in endoplasmic reticulum, and amino acid metabolism, revealing their relationship with the nutritional quality of walnut kernels. This study identified key genes and proteins associated with nutrient metabolism and accumulation in walnut kernels, provided transcriptomic and proteomic information on the molecular mechanisms of nutrient differences in walnut kernels, and contributed to the elucidation of the mechanisms of nutrient differences and the selection and breeding of high-quality walnut seedlings.

Transcriptome Sequencing Analysis of Genes Associated with Different Developmental Periods of the Ovarian Follicle in the Duolang Sheep

Background: The ovaries are crucial reproductive organs in female mammals, directly influencing the reproductive efficiency and productivity of these animals. The Duolang sheep, native to Xinjiang, is known for its rapid growth and high fertility. However, the mechanisms underlying ovarian follicle development and regulation in sheep remain unclear. Methods: Employing transcriptome sequencing technology, this study methodically analyzed ovaries from sheep across various estrous cycles to uncover key genes and signaling pathways that play a role in the development of ovarian follicles. Results: The results indicated that a total of 130, 183, and 175 differentially expressed genes were identified in the DTA/DTB, DTB/DTC, and DTA/DTC groups, respectively. Key genes like BAG3, GDF5, RHOB, RUNX2, LGALS3, and CDH1, along with pathways such as endoplasmic reticulum protein processing, the NOTCH signaling pathway, and the MAPK signaling pathway, were found to be involved. RT-qPCR confirmed the differential expression of BAG3, RHOB, and RUNX2. Conclusions: This research provides insights into the molecular mechanisms of ovarian follicle development and a basis for enhancing the reproductive performance of Duolang sheep.

Identification and validation of circulating microRNAs as biomarkers for heart failure with preserved ejection fraction

Abstract Background Heart failure (HF) is a syndrome due to cardiac insufficiency, manifested by excessive volume overload, increased sympathetic activity, and circulatory redistribution [1]. Heart failure with preserved ejection fraction (HFpEF) accounts for approximately 40%-50% of the total HF events, and its development is often accompanied by various complications, including hypertension, obesity, and metabolic syndrome. Biomarker associations in heart failure with reduced ejection fraction were mostly cardiac stretch based, while many biomarkers of HFpEF are also associated with inflammation [2]. To date, treatments that effectively improve the clinical prognosis of HFpEF are relatively limited, thus HFpEF remains one of the challenges that needs to be further explored. A full understanding of the molecular mechanisms of HFpEF is essential to improve the early diagnosis, treatment and prognosis of these patients. Purpose The study aims to explore key circulating miRNAs and related molecular pathways in HFpEF patients through bioinformatics analysis and machine learning, and to further validate them using a double-hit HFpEF mouse model. Methods We downloaded HF datasets including circulating miRNA expression profiles from the GEO database. LASSO regression, SVM-RFE, Random Forest and XGboost algorithm were conducted to identify key miRNAs for diagnostic model construction. We used R software, GO, KEGG and Cytoscape to better understand the functions of key miRNA targets. Besides, the mRNA-miRNA interaction networks were predicted by starbase. We also constructed a HFpEF mouse model subjected to high fat diet and L-NAME (0.5 g/L) in drinking water to discover the correlation between the screened circulating miRNA and HFpEF. Results After differential expression analysis of the combined HFpEF dataset, we identified 37 differentially circulating miRNAs, of which 15 were down-regulated and 22 were up-regulated. Subsequently, we screened by machine learning and identified 4 key miRNAs that may be involved in the progression of HFpEF, including hsa-miR-645, hsa-miR-296-5p, hsa-miR-199b-5p, and hsa-miR-509-3-5p. We validated these miRNAs based on their expression, and the ROC plots suggest that these miRNAs may have diagnostic capability in HFpEF. The results of GO and KEGG enrichment analyses showed that the target genes of the differentiated miRNAs were mainly enriched in the MAPK signaling pathway, mTOR signaling pathway, protein processing in endoplasmic reticulum, hippo signaling pathway, cell cycle, Foxo signaling pathway, hypertrophic cardiomyopathy, dilated cardiomyopathy, and circadian rhythm. The mRNA-miRNA interaction networks suggested that TMEM135 was regulated by both has-miR-199b-5p and hsa-miR-296-5p. The RT-PCR results also suggested that miR-199b-5p was upregulated in the HFpEF mice. Conclusion We validated 4 circulating miRNAs with strong correlation to HFpEF, which provide a more reliable basis for pre-symptomatic diagnosis.

Transcriptome-wide analysis reveal dynamic expression changes during endoplasmic reticulum stress in tomato

Endoplasmic reticulum (ER) stress is a cellular condition induced by environmental stressors. Transcriptomic approaches reveal the response of plants to ER stress and provide a broadened view. Tomato plants were treated with tunicamycin, and total RNA isolated from the tomato leaves was sequenced on an RNA-sequencing platform to be analyzed for differential expressions. A total of 856 differentially expressed genes (DEGs) were discovered in tunicamycin-treated tomato leaves. Upregulation of ER stress marker gene expressions was detected after 2h, while a prolonged ER stress downregulated most of the protein-coding genes. Pathways such as: response to stress, jasmonic acid mediated signaling, signal transduction regulation, plant hormone signal transduction, and protein processing in ER were enriched. Prolonged stress mostly resulted in reduced transcript levels, possibly related to a mechanism functioning to lower the load of nascent transcripts in the ER. Our findings emphasize the key role of JA-regulated signaling in tomato ER stress responses due to the differential expressions of the pathway components, along with other plant hormones and signaling-related or regulatory genes. ER stress being a common response to many stressors in plants, transcriptome data obtained here will provide for further studies of understanding plant stress tolerance or generating stress-resistant tomato plants.

Asparagine614 Determines the Transport and Function of the Murine Anti-Aging Protein Klotho.

Klotho is an anti-aging protein whose deletion significantly reduces lifespan in mice, while its over-expression increases lifespan. Klotho is a type-I transmembrane protein that is N-glycosylated at eight positions within its ectodomain. Our study demonstrates that N-glycosylation or mutation at position N614, but not at N161, N285, or N346 in mouse Klotho, is critically involved in the transport of Klotho out of the endoplasmic reticulum (ER). Consequently, while wild-type Klotho-EGFP as well as the N-glycosylation mutants N161Q, N285Q, and N346Q were present at the plasma membrane (PM), only small amounts of the N614Q Klotho-EGFP were present at the PM, with most of the protein accumulating in the ER. Protein interactome analysis of Klotho-EGFP N614Q revealed increased interactions with proteasome-related proteins and proteins involved in ER protein processing, like heat shock proteins and protein disulfide isomerases, indicative of impaired protein folding. Co-immunoprecipitation experiments confirmed the interaction of Klotho-EGFP N614Q with ER chaperons. Interestingly, despite the low amounts of Klotho-EGFP N614Q at the PM, it efficiently induced FGF receptor-mediated ERK activation in the presence of FGF23, highlighting its efficacy in triggering downstream signaling, even in limited quantities at the PM.

A transcriptomics-based analysis of mechanisms involved in the neurobehavioral effects of 6PPD-quinone on early life stages of zebrafish

As an emerging pollutant frequently detected in aquatic ecosystems, the toxicity of N-(1,3-dimethylbutyl)-N’-phenyl-p-phenylenediamine-quinone (6PPD-quinone) on fish has been confirmed, but insight into the mechanisms underlying those adverse effects is still limited. Thus, we exposed zebrafish embryos to 6PPD-quinone at 0, 0.25, 2.5, and 25 μg/L until 120 h post-fertilization (hpf), and investigated the variations in their development, behavior, monoamine neurotransmitter levels, and transcriptional profile. Exposure to 6PPD-quinone notably elevated the heart rate of zebrafish at 48 hpf (at 2.5 and 25 μg/L) and 72 hpf (at 0.25, 2.5, and 25 μg/L). In the dark-light transition test, the locomotor activity of zebrafish larvae exposed to 6PPD-quinone significantly increased, especially in the dark periods. Exposure to 6PPD-quinone also altered the dopamine level and its turnover in zebrafish, which exhibited significant correlations to their locomotor activity. RNA sequencing identified 394 differentially expressed genes (DEGs), most of which have the molecular function of binding and catalytic activity. Five DEGs were predicted as the key driver genes in the protein-protein interaction networks associated with circadian rhythm (i.e., npas2), protein processing in endoplasmic reticulum (i.e., hsp90b1 and pdia4), and estrogen signaling pathway (i.e., hsp90aa1.1 and hsp90aa1.2). Our findings provide more insights into mechanisms underlying the toxicity of 6PPD-quinone to teleosts and highlight the necessity to assess its potential risks to aquatic ecosystems.

Identification of the effects of hypoxia on the liver tissues of Nile tilapia Oreochromis Niloticus

BackgroundHypoxia stress resulted in mortality during the fish aquaculture program, affecting the sustainable development of the aquaculture industry. The Egyptian strain of O. niloticus showed a strong ability to hypoxia. In this study, a Nile tilapia strain that was kept and selected for 45 years by the author’s team was used to elucidate the mechanism of the hypoxia response in the liver, including the identification of metabolic pathways and genes, involved in the hypoxia response of this strain.ResultsThe effects of hypoxia stress were detected at 0-hour, 6-hour, and 72-hour time points (0 h, 6 h, 72 h) on tilapia liver at 1 mg/L dissolved oxygen conditions. The blood triglyceride, blood glucose and cholesterol values exhibited significantly different change trends, but the hemoglobin content showed no significant differences between 0 h, 6 h and 72 h (P > 0.05). The activities of catalase (CAT), glutathione peroxidase (GSH-PX), total antioxidant capacity (T-AOC), lactate dehydrogenase (LDH), and acid phosphatase (ACP) in the liver tissue gradually increased at 0 h, 6 h and 72 h (P < 0.05). Histological analyses revealed structural changes in intracellular lipid droplets, nuclear migration and dissolution, and cell vacuolization in liver tissues. Six pathways were identified as the main enriched metabolic pathways according to the transcriptome profiling analysis, which were protein processing in endoplasmic reticulum, steroid biosynthesis, peroxisome, PPAR signaling pathway, glycolysis/gluconeogenesis and Insulin signaling pathway. The expressions of the important differentially expressed genes were verified by qPCR analysis, including erola, LOC100692144, sqle, cratb, pipox, cpt1a2b, hik and acss2l, ehhadh, prkcz, fasn and plaa, which showed the same expressions trends as those of RNA-Seq.ConclusionsThe Nile tilapia strain improves the abilities of hypoxia response through energy metabolism. Antioxidant enzyme measurements in the liver indicate that these five antioxidant enzymes play important roles in protecting the body from hypoxic damage. The histological changes in liver cells indicate that the damage caused by hypoxia stress. The immune-related metabolic pathways and energy metabolism-related pathways were obtained by transcriptome profiling, and these metabolic pathways and the differentially expressed genes selected from these metabolic pathways may be involved in the mechanism of hypoxia tolerance in this strain. These findings provide a better understanding of the hypoxia response mechanism of fish, and represent a useful resource for the genetic breeding of O. niloticus.

Identification of function modules in the co-expression protein–protein interaction network of Bombyx mori in response to Beauveria bassiana infection

Beauveria bassiana (B. bassiana) is a common fungal disease in sericulture. Previous research has primarily focused on investigating genes involved in innate immunity. However, the response of Bombyx mori (B. mori) to B. bassiana requires the coordination of other biological processes in addition to the immune system. We measured protein expression profile of B. mori after inoculating B. bassiana using iTRAQ technology in previous. Here we constructed a co-expression protein–protein interaction network of B. mori in response to B. bassiana infection. Subnetworks and modules were analyzed, and the functions of these modules were annotated. The results revealed the identification of numerous proteins associated with cellular immunity, including those involved in phagosomes, lysosomes, mTOR signaling, sugar metabolism, and the ubiquitin–proteasome pathway. Meanwhile, we observed that the pathways involved in protein synthesis were activated, including pyruvate and purine metabolism, RNA transport, ribosome, protein processing in endoplasmic reticulum, and protein export pathways, during B. bassiana infection. Based on this analysis, we selected six candidate genes (shock protein, ribosome, translocon, actin muscle-type A2, peptidoglycan recognition protein, and collagenase) that were found to be related to the response to B. bassiana. Further verification experiments demonstrated significant changes in their expression levels after inoculation with B. bassiana. These research findings provide new insights into the molecular mechanism of insect immune response to fungal infection.

A Proteomic Study on Seed Germination of Nitraria roborowskii Kom.

Owing to the dormancy of the seeds of Nitraria roborowskii Kom., which results in a low germination rate in nature, germination takes a long time, and natural regeneration is difficult. Therefore, there is a need to study the molecular mechanism by which the seeds of N. roborowskii release dormancy. In this study, the differentially expressed proteins of N. roborowskii seeds before and after dormancy and germination were quantitatively and qualitatively analyzed via two-dimensional high-performance liquid chromatography tandem mass spectrometry (LC–MS) and TMTTM. Differentially expressed proteins from dormant and germinated seeds were characterized and enriched via bioinformatics to determine the functions and pathways of the differentially expressed proteins. The results revealed that seed dormancy was regulated by multiple metabolic pathways, including protein synthesis, nutrient utilization and phytohormone signal transduction pathways. A comparison of the dormant and germinated N. roborowskii seed samples revealed 1082 differentially expressed proteins with FC ≥ 1.5 and p values ≤ 0.05, among which 191 proteins were upregulated and 891 proteins were downregulated in the seeds of the germinated group, and proteins more closely related to the key genes of the germinated N. roborowskii seeds were involved in the activity of D-threo-aldose 1-dehydrogenase. Four proteins (WD40, cystatin, AMP binding protein, and helicase) were involved in the positive regulation of seed germination. The release of N. roborowskii seed dormancy is a complex biological process involving cell differentiation, formation, cellular transport, signaling and resistance, etc. The interactions of multiple metabolic pathways, such as carbon fixation, glycolysis/gluconeogenesis, the pentose phosphate pathway, endoplasmic reticulum protein processing and pyruvic acid metabolism in photosynthetic organisms, constitute a complex regulatory mechanism for dormancy release.

Integrated transcriptomics and proteomics analyses reveal the ameliorative effect of hepatic damage in tilapia caused by polystyrene microplastics with chlorella addition

Fish exhibit varying responses to polystyrene microplastics (MPs) depending on particle size. Previous studies suggested that microorganisms adhering to the surface of MPs can induce toxic effects. In this study, Tilapia were exposed to MPs of control (group A), 75 nm (B), 7.5 μm (C), 750 μm (D), as well as combinations of all sizes (E) and 75 nm MPs with Chlorella vulgaris addition (F) for 7, 10 and 14 days. Histopathological changes in liver of tilapia were assessed using enzyme activities, transcriptomics and proteomics. The results showed that in groups combined MPs of different particle sizes and those supplemented with chlorella, MPs were localized on the surface of goblet cells, leading to vacuoles, constricted hepatic sinuses and nuclei displacement. Exposure to 7.5 and 750 μm MPs significantly increased the contents of fatty acid synthase (FAS), adenosine triphosphate (ATP), acetyl-CoA carboxylase (ACC), lipoprotein lipase (LPL), total cholesterol (TC), total triglyceride (TG) contents at 7 and 10 days. In particular, cytochrome p450 1a1 (EROD), reactive oxygen species (ROS) and superoxide dismutase (SOD) were markedly elevated following exposure to MPs. Apoptotic markers caspase-3, and inflammatory markers, including tumor necrosis factor α (TNF-α) and interleukin-1β (IL-1β), had a similar upward trend in comparisons of group C vs A at 7 d, group D vs A at 14 d. The peroxisome proliferator activated receptor (PPAR) signaling pathway, spliceosome, was highly enriched during the 7-day exposure of medium sized MPs, while largest MPs in the comparison of group D vs A at 14 d activated pathways such as phagosome, apoptosis, salmonella infection. Transcriptomic analysis revealed that after 14 days, the kyoto encyclopedia of genes and genomes (KEGG) pathways associated with protein processing in endoplasmic reticulum and the PPAR signaling has been significantly enriched in the Chlorella-supplemented group, which was further confirmed via the proteomic analysis. Overall, the findings highlight the size-dependent effects of MPs on histopathological changes, gene and protein expression in the liver of tilapia, and C. vulgaris effectively attenuated liver damages, likely through modulation of endoplasmic reticulum protein processing and PPAR signaling pathways.

Enhanced ER protein processing gene expression increases rAAV yield and full capsid ratio in HEK293 cells

The recombinant adeno-associated virus (rAAV) vector is among the most promising viral vectors in gene therapy. However, the limited manufacturing capacity in human embryonic kidney (HEK) cells is a barrier to rAAV commercialization. We investigated the impact of endoplasmic reticulum (ER) protein processing and apoptotic genes on transient rAAV production in HEK293 cells. We selected four candidate genes based on prior transcriptomic studies: XBP1, GADD34 / PPP1R15A, HSPA6, and BCL2. These genes were stably integrated into HEK293 host cells. Traditional triple-plasmid transient transfection was used to assess the vector production capability and the quality of both the overexpressed stable pools and the parental cells. We show that the overexpression of XBP1, HSPA6, and GADD34 increases rAAV productivity by up to 100% and increases specific rAAV productivity by up to 78% in HEK293T cells. Additionally, more prominent improvement associated with ER protein processing gene overexpression was observed when parental cell productivity was high, but no substantial variation was detected under low-producing conditions. We also confirmed genome titer improvement across different serotypes (AAV2 and AAV8) and different cell lines (HEK293T and HEK293); however, the extent of improvement may vary. This study unveiled the importance of ER protein processing pathways in viral particle synthesis, capsid assembly, and vector production.Key points• Upregulation of endoplasmic reticulum (ER) protein processing (XBP1, HSPA6, and GADD34) leads to a maximum 100% increase in rAAV productivity and a maximum 78% boost in specific rAAV productivity in HEK293T cells• The enhancement in productivity can be validated across different HEK293 cell lines and can be used for the production of various AAV serotypes, although the extent of the enhancement might vary slightly• The more pronounced improvements linked to overexpressing ER protein processing genes were observed when parental cell productivity was high, with minimal variation noted under low-producing conditions

Toxicological effects, absorption and biodegradation of bisphenols with different functional groups in Chromochloris zofingiensis

Bisphenols (BPs) are recognized as endocrine disrupting compounds and have garnered increasing attention due to their widespread utilization. However, the varying biological toxicities and underlying mechanisms of BPs with different functional groups remain unknown. In the present study, the toxic effects of four BPs (BPA, BPS, BPAF, and TBBPA) on a photosynthetic microalgae Chromochloris zofingiensis were compared. Results showed that halogen-containing BPs exhibited higher cellular uptake, leading to more severe oxidative stress, lower photosynthetic efficiency, and greater accumulation of starch and lipids. Specifically, TBBPA with bromine groups showed a greater toxicity than BPAF with fluorine groups, possibly due to the incomplete debromination in C. zofingiensis. Transcriptomic analysis revealed that halogen-containing BPs triggered greater number of differentially expressed genes (DEGs), and only 64 common DEGs were found among different BPs, indicating that the effects of BPs with different functional groups varied greatly. Genes involved in endocytosis, peroxisomes, and endoplasmic reticulum protein processing pathways were mostly upregulated across different BPs, while photosynthesis-related genes showed varied expression, possibly due to their distinct functional groups. Additionally, SIN3A, ZFP36L, CHMP, and ATF2 emerged as potential key regulatory genes. Overall, this study thoroughly explained how functional groups impact the toxicity and biodegradation of BPs in C. zofingiensis.

The development of silk glands and transcriptome aberration induced by cyantraniliprole in Bombyx mori

Bombyx mori is an insect species of great economic importance, and its silk gland is a vital organ for the synthesis and secretion of silk protein. However, long-term artificial domestication of B. mori has resulted in high sensitivity to chemical toxins, especially insecticides. Cyantraniliprole (Cya), a second-generation ryanodine receptor modulator insecticide, is widely utilized in agriculture for pest control. In this study, the impact of Cya toxicity on the development of silk glands in the 5th instar larvae of B. mori was assessed using Cya LC5, LC10 and LC20, as well as a starvation treatment group for comparison. Short-term exposure (24 h) to different concentrations of Cya resulted in delayed development of silk glands in B. mori. Meanwhile, the body weight, silk gland weight, silk gland index and cocoon quality were significantly reduced in a concentration-dependent manner, except for the Cya LC5 treatment. Histopathological and ultrastructural analysis revealed that Cya LC10 induced disruption of the nuclear membrane and endoplasmic reticulum in the posterior silk gland (PSG) cells, leading to the formation of intracellular vacuoles. Transcriptome sequencing of PSGs identified 2152 genes that were differentially expressed after exposure to Cya LC10, with 1153 down-regulated genes and 999 up-regulated genes. All differentially expressed genes were subjected to functional annotation using gene ontology and Kyoto encyclopedia of genes and genomes database, and it was found that protein synthesis-related pathways were significantly enriched, with the majority of genes being down-regulated. Furthermore, the transcription levels of genes involved in “protein processing in endoplasmic reticulum”, “protein export”, “proteasome” and “DNA replication” were quantified using qRT-PCR. Our findings suggested that short-term exposure to Cya LC10 resulted in disruption of DNA replication, as well as protein transport, processing and hydrolysis in the PSG cells of B. mori. The results of this study provide a theoretical foundation for the safe utilization of Cya in sericulture production.

Tandem mass tag (TMT)-based quantitative proteomics analysis reveals the different responses of contrasting alfalfa varieties to drought stress

BackgroundDrought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs).ResultsIn total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were ‘Translation, ribosomal structure and biogenesis’ and ‘Posttranslational modification, protein turnover, chaperones’. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in ‘photosynthesis’ and ‘ribosome’. The pathways of ‘linoleic acid metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘RNA transport’ in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment.ConclusionsThe differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments.

Extracellular microRNAs associated with psychiatric symptoms in the Normative Aging Study

Earlier studies have revealed microRNAs (miRNAs) as potential biomarkers for neurological conditions, however, such evidence on psychiatric outcomes is limited. We utilized the Normative Aging Study (NAS) cohort to investigate the associations between extracellular miRNAs (ex-miRNA) and psychiatric symptoms among a group of older male adults, along with the targeted genes and biological pathways. We studied 569 participants with miRNA profile primarily measured in extracellular vesicles isolated from plasma, and psychiatric symptoms reported over 1996–2014 with repeated measures. Global and dimension scales of psychiatric symptoms were measured via the administration of Brief Symptom Inventory (BSI) per visit covering nine aspects of psychiatric health, such as anxiety, depression, hostility, psychoticism, etc. Ex-miRNAs were profiled using small RNA sequencing. Associations of expression of 395 ex-miRNAs (present in >70% samples) with current mental status were assessed using single-miRNA as well as Least Absolute Shrinkage and Selection Operator (LASSO)-based multi-miRNAs linear mixed effects models adjusting for key demographic and behavioral factors. Biological functions were explored using pathway analyses. We identified ex-miRNAs associated with each BSI scale. In particular, hsa-miR-320d was consistently identified for two global scales. Similar overlapping miRNAs across global and dimension scores included hsa-miR-379-3p, hsa-miR-1976, hsa-miR-151a-5p, hsa-miR-151b, hsa-miR-144-3p, etc. Top KEGG pathways for identified miRNAs included p53 signaling, Hippo signaling, FoxO signaling, protein processing in endoplasmic reticulum and several pathways related with cancer and neurological diseases. This study provided early evidence supporting the associations between extracellular miRNAs and psychiatric conditions. MiRNAs may serve as biomarkers of subclinical psychiatric illness in older adults.

Effect of heat exposure on histology, transcriptomics and co-expression network: A synthetic study in Japanese flounder (Paralichthys olivaceus)

Water temperature has continued to increase as part of global warming. The heart of fish is the center that participates in the physiological limitations of thermal performance. However, only a few studies have focused on the response mechanisms of fish hearts to heat stress. Therefore, the economically important cold-water aquaculture fish, Japanese flounder (Paralichthys olivaceus) was chosen to explore the mechanisms of the heart in response to heat stress. Histological observations indicated that heat stress could widen the sarcoplasmic distance and deepen chromatin staining. Further transcriptome analysis identified 958 differentially expressed genes (DEGs), and significantly enriched “Protein processing in endoplasmic reticulum” pathway and related terms in functional enrichment analysis. Weighted gene co-expression network analysis (WGCNA) showed that different tissues had different response modules and hub genes, and calcium ions (Ca2+) related genes and pathways were noteworthy in the heart specific module. Functional identification of key Ca2+ regulatory hub genes illuminated that caveolin-3 (cav3) was an important gene that participates in controlling the Ca2+ into and out of cells. Meanwhile, overexpression of cav3 could reduce heat stress induced apoptosis. This study could not only be a crucial resource for the response mechanisms underlying heat stress in Japanese flounder, but also provide valuable insights into genetic improvement for heat-resistance.

Identification of Key Toxic Substances Considering Metabolic Activation: A Combination of Transcriptome and Nontarget Analysis.

There have been numerous studies using effect-directed analysis (EDA) to identify key toxic substances present in source and drinking water, but none of these studies have considered the effects of metabolic activation. This study developed a comprehensive method including a pretreatment process based on an in vitro metabolic activation system, a comprehensive biological effect evaluation based on concentration-dependent transcriptome (CDT), and a chemical feature identification based on nontarget chemical analysis (NTA), to evaluate the changes in the toxic effects and differences in the chemical composition after metabolism. Models for matching metabolites and precursors as well as data-driven identification methods were further constructed to identify toxic metabolites and key toxic precursor substances in drinking water samples from the Yangtze River. After metabolism, the metabolic samples showed a general trend of reduced toxicity in terms of overall biological potency (mean: 3.2-fold). However, metabolic activation led to an increase in some types of toxic effects, including pathways such as excision repair, mismatch repair, protein processing in endoplasmic reticulum, nucleotide excision repair, and DNA replication. Meanwhile, metabolic samples showed a decrease (17.8%) in the number of peaks and average peak area after metabolism, while overall polarity, hydrophilicity, and average molecular weight increased slightly (10.3%). Based on the models for matching of metabolites and precursors and the data-driven identification methods, 32 chemicals were efficiently identified as key toxic substances as main contributors to explain the different transcriptome biological effects such as cellular component, development, and DNA damage related, including 15 industrial compounds, 7 PPCPs, 6 pesticides, and 4 natural products. This study avoids the process of structure elucidation of toxic metabolites and can trace them directly to the precursors based on MS spectra, providing a new idea for the identification of key toxic pollutants of metabolites.

A Comparative Analysis of the Gene Expression Profiles in the Mammary Glands of Lactating and Nonlactating Mares at the Second Month of Gestation.

To investigate molecular regulation involved in lactation during pregnancy, this study focused on the transcriptomic profiles of mammary tissue from lactating and non-lactating Mongolian mares at the second month of gestation. A total of 4197 differentially expressed genes were identified by comparing mammary tissues from pregnant mares at two different states, including 1974 differentially expressed genes such as the milk protein-related genes a-s1-casein (CSN1S1), k-casein (CSN3), lactalbumin (LALBA), and lactoferrin (LTF), which were highly expressed in the lactating mares group, and overall, these differentially expressed genes were mainly associated with biological processes such as endoplasmic reticulum protein processing, the Toll-like receptor signaling pathway, steroid biosynthesis, cytokine-cytokine receptor interactions, and amino sugar and nucleotide glycolysis. These findings serve as a foundation for investigating the molecular underpinnings of lactation in pregnant equids.

Molecular Responses to Drought and Waterlogging Stresses of Kiwifruit (Actinidia chinensis var. deliciosa) Potted Vines

Environmental extremes, such as drought and flooding, are becoming increasingly common, resulting in significant crop losses. The aim of the present study was to understand the molecular response induced by drought and waterlogging conditions, and to link these responses to the physiological adaptation of plants. For this purpose, leaf RNA expression was analyzed in potted kiwifruit plants by Illumina Next Generation Sequences. Stressed plants showed an impairment of all physiological parameters (leaf-gas exchange and stem-water potential) with a more evident effect in waterlogging condition than in drought condition. However, the impact on the transcriptome in waterlogged plants was less intense than in drought stress. Drought affected several metabolic pathways, among which “plant hormone signal transduction”, “protein processing in endoplasmic reticulum”, and “mitogen-activated protein kinase signaling pathway” were the most representative in terms of number of genes involved. The genes involved in the biosynthesis of phenylpropanoids were positively influenced by both drought and waterlogging. Finally, waterlogging stimulated secondary metabolisms by upregulating the genes responsible for the biosynthesis of terpenoids and flavonoids, such as stilbenoids. The obtained results show that the two contrasting stress conditions share several common physiological responses and molecular mechanisms.