De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore.

Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The high-quality filtered RNA-seq raw reads were deposited in a public database which provides approximately 54 billion high-quality paired-end sequencing reads in total, with an average mapping rate of ~93.92%. Transcriptome databases represent valuable resources that can be used to study patterns of gene expression, and pathways that are related to key biological processes, including important economic traits in herbivores.

Physiological-biochemical responses and transcriptomic analysis reveal the effects and mechanisms of sulfamethoxazole on the carbon fixation function of Chlorella pyrenoidosa.

The occurrence of sulfamethoxazole (SMX) is characterized by low concentration and pseudo-persistence. However, the toxic effects and mechanisms of SMX, especially for low concentration and long-term exposure, are still not clear. This study investigated the effects and mechanisms of SMX on carbon fixation-related biological processes of Chlorella pyrenoidosa at population, physiological-biochemical, and transcriptional levels. Results showed that 1-1000 µg/L SMX significantly inhibited the dry weight and carbon fixation rate of C. pyrenoidosa during 21 d. The upregulation of superoxide dismutase (SOD) and catalase (CAT) activities, as well as the accumulation of malondialdehyde (MDA) demonstrated that SMX posed oxidative damage to C. pyrenoidosa. SMX inhibited the activity of carbonic anhydrase (CA), and consequently stimulated the activity of Rubisco. Principal component analysis (PCA) revealed that SMX concentration was positively correlated with Rubisco and CAT while exposure time was negatively correlated with CA. Transcriptional analysis showed that the synthesis of chlorophyll-a was stabilized by regulating the diversion of protoporphyrin IX and the chlorophyll cycle. Meanwhile, multiple CO2 compensation mechanisms, including photorespiratory, C4-like CO2 compensation and purine metabolism pathways were triggered in response to the CO2 requirements of Rubisco. This study provides a scientific basis for the comprehensive assessment of the ecological risk of SMX.

Unregistered Hexaphenoxycyclotriphosphazene and Its Metabolite Antagonize Retinoic Acid and Retinoic X Receptors and Cause Early Developmental Damage.

Hexaphenoxycyclotriphosphazene (HPCTP), an unregistered chemical, has been used as a substitute for triphenyl phosphate in flame retardants and plasticizers. Here, we identified its metabolite, pentaphenoxycyclotriphosphazene (PPCTP) in the liver of Japanese medaka exposed to HPCTP. When sexually mature female medaka were exposed to HPCTP at 37.0, 90.4, and 465.4 ng/L for 35 days, the HPCTP concentration (642.1-2531.9 ng/g lipid weight [lw]) in the embryos considerably exceeded that (34.7-298.1 ng/g lw) in the maternal muscle, indicating remarkable maternal transfer. During 0-9 days postfertilization, the HPCTP concentration in the embryos decreased continuously, while the PPCTP concentration increased. HPCTP and PPCTP antagonized the retinoic X receptor with 50% inhibitory concentrations (IC50) of 34.8 and 21.2 µM, respectively, and PPCTP also antagonized the retinoic acid receptor with IC50 of 2.79 µM. Such antagonistic activities may contribute to eye deformity (4.7% at 465.4 ng/L), body malformation (2.1% at 90.4 ng/L and 6.8% at 465.4 ng/L), and early developmental mortality (11.6-21.7% in all exposure groups) of the embryos. HPCTP was detected in a main tributary of the Yangtze River Basin. Thus, HPCTP poses a risk to wild fish populations, given the developmental toxicities associated with this chemical and its metabolite.

Melatonin disturbed rumen microflora structure and metabolic pathways in vitro.

IMPORTANCE: In in vitro studies, it has been found that the effects of MLT on rumen microorganisms and metabolites can change the rumen flora structure, significantly inhibit the relative abundance of harmful Acinetobacter, and improve the relative abundance of beneficial bacteria. MLT may regulate the "arginine-glutathione" pathway, "phenylalanine, tyrosine and tryptophan biosynthesis-tryptophan generation" branch, "tryptophan-kynurenine" metabolism, and "tryptophan-tryptamine-serotonin" pathway through microorganisms.

VEGF/Nrp1/HIF-1α promotes proliferation of hepatocellular carcinoma through a positive feedback loop.

To investigate the role of neuropilin1 (Nrp1) in glucose metabolism and proliferation of hepatocellular carcinoma (HCC) cells and to analyze its mechanism of action. The CRISPR gene knockout technique was used to knock out the Nrp1 gene in two HCC cell lines. The effect of Nrp1 on the proliferation of HCC cells was assessed in the CCK8 assay and plate cloning assay. The expression levels of glucose consumption, lactate production, and essential proteins of the glycolytic pathway were detected to explore the effect of Nrp1 on glucose metabolism in HCC cells. Using CoCl2 to revert the expression of hypoxia inducible factor-1α (HIF-1α), the role of HIF-1α in the pro-HCC cell metabolism of Nrp1 were demonstrated. The protein synthesis inhibitor CHX and proteasome inhibitor MG-132 was used to analyze the molecular mechanism of action of Nrp1 on HIF-1α. The Kaplan-Meier method was used to calculate survival rates and plot survival curves. Based on the CCK8 assay and plate cloning assay, we found that Nrp1 knockout significantly inhibited the proliferation of HCC cells. Nrp1 inhibitor suppressed lactate production and glucose consumption in HCC cells. Knockout of Nrp1 decreased the expression of glycolytic pathway-related proteins and HIF-1α protein. Furthermore, by joint use of CoCl2 and NRP1 knockout, we confirmed that reverting HIF-1α expression could reverse the effect of Nrp1 knockout on HCC cell metabolism in vitro. Mechanistically, Nrp1 showed a close correlation with the stability of HIF-1α protein in protein stability assay. Finally, we revealed that high expression of Nrp1 in HCC tissues was associated with poor overall survival and disease-free survival of the patients. Nrp1 accelerates glycolysis and promotes proliferation of HCC by regulating HIF-1α protein stability and through the VEGF/Nrp1/HIF-1α positive feedback loop.

Tryptophan improves antioxidant capability and meat quality by reducing responses to stress in nervous Hu sheep.

In sheep, the effect of tryptophan (Trp) on behavioural traits that are associated with temperament and any effects on production traits is unknown. The hypothesis of this study is that the supplementation of Trp would improve temperament by enhancing serotonin production, which is beneficial to meat production subsequently in sheep. Twelve ewes that had the lowest and 12 ewes that had the highest behavioural responses to human contact were selected into the calm and the nervous groups respectively. Then, the ewes from each group were equally assigned into two treatments that were treated with the basal diet and the diet with extra 90 mg/kg/d Trp for 30 d. The temperament traits, the growth performance, the biochemicals that are related to health the slaughter performance and meat quality were measured at the end of feeding experiment. The findings in this study suggested the Hu sheep with calm temperament would experience less stress during production, resulting in less oxidative stress, better growth performance, slaughter traits and carcass traits, compared to the nervous sheep. Meanwhile, the dietary supplementation of Trp reduced stress responses by enhancing production of 5-HT in sheep from the nervous group which is beneficial to improve the production traits that mentioned above.

Amniogenesis in Human Amniotic Sac Embryoids after Exposures to Organophosphate Flame Retardants.

BACKGROUND: Amniogenesis is a key event in biochemical pregnancy, and its failure may result in human embryonic death. However, whether and how environmental chemicals affect amniogenesis remain largely unknown. OBJECTIVES: The objective of the present study was to screen chemicals that may disrupt amniogenesis in an amniotic sac embryoid model and to investigate the potential mechanism of amniogenesis failure, with a focus on organophosphate flame retardants (OPFRs). METHODS: This study developed a high-throughput toxicity screening assay based on transcriptional activity of octamer-binding transcription factor 4 (Oct4). For the two positive OPFR hits with the strongest inhibitory activity, we used time-lapse and phase-contrast imaging to assess their effects on amniogenesis. Associated pathways were explored by RNA-sequencing and western blotting, and potential binding target protein was identified through a competitive binding experiment. RESULTS: Eight positive hits exhibiting Oct4 expression were identified, with 2-ethylhexyl-diphenyl phosphate (EHDPP) and isodecyl diphenyl phosphate (IDDPP) showing the strongest inhibitory activity. EHDPP and IDDPP were found to disrupt the rosette-like structure of the amniotic sac or inhibit its development. Functional markers of squamous amniotic ectoderm and inner cell mass were also found disrupted in the EHDPP- and IDDPP-exposed embryoids. Mechanistically, embryoids exposed to each chemical exhibited abnormal accumulation of phosphorylated nonmuscle myosin (p-MLC-II) and were able to bind to integrin ß1 (ITGß1). CONCLUSION: The amniotic sac embryoid models suggested that OPFRs disrupted amniogenesis likely by inhibiting the ITGß1 pathway, thus providing direct in vitro evidence associating OPFRs with biochemical miscarriage. https://doi.org/10.1289/EHP11958.

Facile Construction of Iron/Nickel Phosphide Nanocrystals Anchored on N-B-Doped Carbon-Based Composites with Advanced Catalytic Capacity for 4-Nitrophenol and Methylene Blue.

The search for a simple and effective method to remove organic dyes and color intermediates that threaten human safety from the water environment is urgent. Herein, we report a simple method for constructing iron/nickel phosphide nanocrystals anchored on N-B-doped carbon-based composites, using steam-exploded poplar (SEP) and graphene oxide (GO) as a carrier. The stability and catalytic activity of N-B-NixFeyP/SEP and GO were achieved by thermal conversion in a N2 atmosphere and modifying the Fe/Ni ratio in gel precursors. N-B-Ni7Fe3P/SEP was employed for the catalytic hydrogenation of 4-nitrophenol (4-NP) and methylene blue (MB), using sodium borohydride in aqueous media at room temperature. This showed much better catalytic performances in terms of reaction rate constant (0.016 S-1 and 0.041 S-1, respectively) and the activity factor, K (1.6 S-1·g-1 and 8.2 S-1·g-1, respectively) compared to the GO carrier (0.0053 S-1 and 0.035 S-1 for 4-NP and MB, respectively). The strong interaction between the carrier's morphology and structure, and the vertically grown bimetallic phosphide nanoclusters on its surface, enhances charge transfer, electron transfer kinetics at the interface and Ni-Fe phosphide dispersion on the nanoclusters, and prevents dissolution of the nanoparticles during catalysis, thereby improving stability and achieving catalysis durability. These findings provide a green and simple route to efficient catalyst preparation and provide guidance for the rational selection of catalyst carriers.

Arginine Alters miRNA Expression Involved in Development and Proliferation of Rat Mammary Tissue.

This study was designed to determine the effects of dietary arginine on development and proliferation in rat mammary tissue through changes in miRNA profiles. Twelve pregnant Wistar rats were allocated randomly to two groups. A basal diet containing arginine or the control diet containing glutamate on an equal nitrogen basis as the arginine supplemented diet were used. The experiment included a pre-experimental period of four days before parturition and an experimental period of 17 days after parturition. Mammary tissue was collected for histology, RNA extraction and high-throughput sequencing analysis. The greater mammary acinar area indicated that arginine supplementation enhanced mammary tissue development (p < 0.01). MicroRNA profiling indicated that seven miRNA (miR-206-3p, miR-133a-5p, miR-133b-3p, miR-1-3p, miR-133a-3p, miR-1b and miR-486) were differentially expressed in response to Arginine when compared with the glutamate-based control group. In silico gene ontology enrichment and KEGG pathway analysis revealed between 240 and 535 putative target genes among the miRNA. Further verification by qPCR revealed concordance with the differential expression from the sequencing results: 17 of 28 target genes were differentially expressed (15 were highly expressed in arginine and 2 in control) and 11 target genes did not have significant difference in expression. In conclusion, our study suggests that arginine may potentially regulate the development of rat mammary glands through regulating miRNAs.

Diverse effects of different Akkermansia muciniphila genotypes on Brown adipose tissue inflammation and whitening in a high-fat-diet murine model.

BACKGROUND: The purpose of this study was to investigate the differences in the metabolic protective effects of Akkermansia muciniphila (A.muciniphila) genotypes on high-fat diet mice and explore possible mechanisms. METHODS: Male C57BL/6 mice were randomly divided into 6 groups, including high-fat diet (HFD)+ A. muciniphila I/II/PBS group, normal control diet (NCD)+ A. muciniphila I/II/PBS group, respectively. Dietary intervention and A. muciniphila gavage were performed simultaneously. Blood glucose and lipid metabolism, brown adipose morphology and activities, and intestinal barrier function were examined after the mice were sacrificed. RESULTS: A.muciniphila gavage improved the impaired glucose tolerance, hyperlipidemia and liver steatosis in HFD mice, and that A. muciniphila II (Amuc_GP25) was not as effective as A. muciniphila I (Amuc_GP01). This phenomenon might be because Amuc_GP01 intervention significantly inhibited brown adipose tissue whitening and inflammation induced by HFD, by repairing the intestinal barrier and relieving endotoxemia. Amuc_GP25 did not display the same results as Amuc_GP01 in HFD mice but had stronger effects in the NCD mice. CONCLUSIONS: This study reveals the distinct functions of different A. muciniphila genotypes on diet-induced obesity, suggesting that different A. muciniphila genotypes may affect pathological conditions differently through distinct action pathways.

Protective effects of Akkermansia muciniphila on cognitive deficits and amyloid pathology in a mouse model of Alzheimer's disease.

OBJECTIVE: Alzheimer's disease (AD) is a global health problem without effective methods to alleviate the disease progression. Amyloid ß-protein (Aß) is widely accepted as a key biomarker for AD. Metabolic syndromes, including obesity and insulin resistance, are key high risk factors for AD. Akkermansia muciniphila (Akk), the only representative human gut microbe in the genus Verrucomicrobia, can prevent the weight gain caused by a high-fat diet, repair the damaged integrity of the intestinal epithelium barrier, reduce endotoxin levels in blood and improve insulin resistance. The aim of this study is to explore the impact of Akk administration in AD model mice in different diets. METHODS: APP/PS1 mice were fed either a normal chow diet or a high-fat diet and were treated with Akk by gavage each day for 6 months. The impacts of Akk on glucose metabolism, intestinal barrier and lipid metabolism in the mouse model of AD were determined. Changes in brain pathology and neuroethology were also analyzed. RESULTS: Akk effectively reduced the fasting blood glucose and serum diamine oxidase levels, and alleviated the reduction of colonic mucus cells in APP/PS1 mice. After treatment with Akk, the APP/PS1 mice showed obviously reduced blood lipid levels, improved hepatic steatosis and scapular brown fat whitening. Moreover, Akk promoted the reduction of Aß 40-42 levels in the cerebral cortex of APP/PS1 mice, shortened the study time and improved the completion rate in Y-maze tests. CONCLUSION: Akk effectively improved glucose tolerance, intestine barrier dysfunction and dyslipidemia in AD model mice. Our study results suggested that Akk could delay the pathological changes in the brain and relieve impairment of spatial learning and memory in AD model mice, which provides a new strategy for prevention and treatment of AD.

An Akkermansia muciniphila subtype alleviates high-fat diet-induced metabolic disorders and inhibits the neurodegenerative process in mice.

The prevalence of obesity and diabetes, and their complicating mental disorders, severely affect public health. This study aimed to investigate the long-term effects of an Akkermansia muciniphila subtype (A. muciniphilasub) on high-fat diet-induced obesity and diabetes, and to evaluate whether this subtype can alleviate their complicated mental disorders. Whole genome sequencing and short chain fatty acid production analysis in supernatant of pure culture were performed. Female adult C57BL/6 mice were fed a high-fat diet or a normal chow diet and were gavaged with A. muciniphilasub or phosphate-buffered saline daily for 10 months. Body weight, food consumption and blood glucose were measured. At the end of the treatment period, all mice were subjected to the Y-maze test, sucrose preference test, analyses of serum, fecal microbiota analysis and histological examination. This A. muciniphilasub had 278 unique genes compared to the type strain (A. muciniphila ATCC BAA-835) and produced short chain fatty acids both. A. muciniphilasub administration significantly reduced body weight gain and improved the spatial memory of high-fat diet-fed mice. A. muciniphilasub increased Nissl bodies in neurons of the hippocampus, and restored the high-fat diet-inhibited tryptophan metabolism. The high-fat diet led to decreased serum 5-hydroxytryptamine and induced depression, which were not alleviated by A. muciniphilasub. A. muciniphilasub increased the relative fecal abundance of Bifidobacterium, and was negatively correlated with the fecal abundance of Bacteroides. The present study demonstrated the beneficial effects of this A. muciniphilasub on body weight, blood glucose control and the alleviation of the memory decay caused by a high-fat diet in mice.

Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas.

BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content. RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer. CONCLUSIONS: The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium.

Phascolarctobacterium faecium abundant colonization in human gastrointestinal tract.

Phascolarctobacterium can produce short-chain fatty acids, including acetate and propionate, and can be associated with the metabolic state and mood of the host. The present study investigated the colonization characteristics of Phascolarctobacterium faecium in healthy individuals <1-80 years old in Southern China. A total of 150 fresh fecal samples were collected, and bacterial DNA was isolated from these samples for quantitative polymerase chain reaction analysis. Phascolarctobacterium faecium demonstrated a high colonization rate and abundant colonization in the human gastrointestinal tract. The colonization rate varied between 43.33-93.33%, and the abundance of Phascolarctobacterium faecium ranged between 3.22-5.76 log cells g-1 (<1 years old) and 3.06-9.33 log cells g-1 (>1 year old). The permillage of Phascolarctobacterium faecium in total bacteria ranged between 0.004-1.479. There was presence of Phascolarctobacterium faecium-like bacteria in younger individuals with a gradual increase in the number of bacteria maintained at a high level with increasing ages (between 1 and 60 years old), but with a decrease in elderly individuals (>60 years old). The results of the present study demonstrated that Phascolarctobacterium faecium is abundantly colonized in the human gastrointestinal tract.

The influence of dehydration on the prognosis of acute ischemic stroke for patients treated with tissue plasminogen activator.

BACKGROUND: Many studies have determined that dehydration is an independent predictor of outcome after ischemic stroke (IS); however, none have determined if the use of thrombolytic therapy modifies the negative impact of poor hydration. To inform the stroke registry established at our institution, we conducted a retrospective study to determine if dehydration remains a negative prognostic factor after IS patients treated with tissue plasminogen activator (tPA). METHODS: Between 2007 and 2012, we recruited 382 subjects; 346 had data available and were divided into 2 groups on the basis of their blood urea nitrogen/creatinine (BUN/Cr) ratio. Dehydrated subjects had a BUN/Cr ratio ≥ 15; hydrated subjects had a BUN/Cr < 15. The primary outcome was impairment at discharge as graded by the Barthel Index (BI) and the modified Rankin Scale (mRS). RESULTS: The dehydration group had a greater mean age; more women; lower mean levels of hemoglobin, triglycerides, and sodium; and higher mean potassium and glucose levels. A favorable outcome as assessed by the mRS (≤2) was significantly less frequent among dehydrated subjects, but a favorable outcome by the BI (≥60) was not. Logistic regression and multivariate models confirmed that dehydration is an independent predictor of poor outcome by both the mRS and the BI; however, it was not predictive when patients were stratified by Trial of Org 10,172 in Acute Stroke Treatment subtype. CONCLUSIONS: Our findings indicate that use of thrombolytic therapy does not eliminate the need to closely monitor hydration status in patients with IS.

[Rapid selection of recombinant orf virus expression vectors using green fluorescent protein].

OBJECTIVE: To construct a universal, highly attenuated orf virus expression vector for exogenous genes using green fluorescent protein (GFP) as the reporter gene. METHODS: The flanking regions of the ORFV132 of orf virus DNA were amplified by PCR to construct the shuttle plasmid pSPV-132LF-EGFP-132RF. The shuttle plasmid was transfected into OFTu cells and GFP was incorporated into orf virus IA82Delta 121 by homologous recombination. The recombinant IA82Delta121-V was selected by green fluorescent signal. The deletion gene was identified by PCR and sequencing. The effects of ORFV132 knockout were evaluated by virus titration and by observing the proliferation of the infected vascular endothelial cells in vitro. RESULTS: The recombinant orf virus IA82Delta121-V was obtained successfully and quickly, and the deletion of ORFV132 did not affect the replication of the virus in vitro but reduced its virulence. CONCLUSION: Green fluorescent protein is a selectable marker for rapid, convenient and stable selection of the recombinant viruses. Highly attenuated recombinant orf virus IA82Delta121-V can serve as a new expression vector for exogenous genes.