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Imputation techniques provide means to replace missing measurements with a value and are used in almost all downstream analysis of mass spectrometry (MS) based proteomics data using label-free quantification (LFQ). Here we demonstrate how collaborative filtering, denoising autoencoders, and variational autoencoders can impute missing values in the context of LFQ at different levels. We applied our method, proteomics imputation modeling mass spectrometry (PIMMS), to an alcohol-related liver disease (ALD) cohort with blood plasma proteomics data available for 358 individuals. Removing 20 percent of the intensities we were able to recover 15 out of 17 significant abundant protein groups using PIMMS-VAE imputations. When analyzing the full dataset we identified 30 additional proteins (+13.2%) that were significantly differentially abundant across disease stages compared to no imputation and found that some of these were predictive of ALD progression in machine learning models. We, therefore, suggest the use of deep learning approaches for imputing missing values in MS-based proteomics on larger datasets and provide workflows for these. Imputation in mass spectrometry-based proteomics is a recurrent step of importance for downstream analysis. Here, the authors offer an extensive comparison workflow of 27 established with three new scalable, fast and performant methods from deep learning for large and high-dimensional data. [ABSTRACT FROM AUTHOR]

Cruciferae brassica oilseed rape is the third largest oilseed crop in the world and the first in China, as well as a fertilizer-dependent crop. With the increased application of organic fertilizers from livestock manure in agricultural production in recent years, the resulting antibiotic pollution and its ecological health effects have attracted widespread attention. In this study, typical tetracycline and sulfonamide antibiotics tetracycline (TC) and sulfamethoxazole (SMZ) were used to investigate the effects of antibiotics on rapeseed quality and oxidative stress at the level of secondary metabolism on the basis of examining the effects of the two drugs on the growth of soil-cultivated rapeseed seedlings. The results showed that both plant height and biomass of rapeseed seedlings were significantly suppressed and ROS were significantly induced in rapeseed by exposure to high concentrations (2.5 mg/kg) of TC and SMZ. Carotenoids, tocopherols, and SOD enzymes were involved in the oxidative stress response to scavenge free radicals in rapeseed, but phenolic acids and flavonoids contents were decreased, which reduced the quality of the seeds to some extent. [ABSTRACT FROM AUTHOR]

Although the use of polychlorinated biphenyls has been restricted worldwide for several decades, these pollutants are still occurring in the environment due to their persistency and their anthropogenic production. So far, there is limited knowledge on their long-distance transport, and on the associated health risk following air inhalation, notably in Chinese rural areas. Here we studied polychlorinated biphenyls in tree bark across China to estimate the atmospheric concentrations of dioxin-like polychlorinated biphenyls and to calculate toxic equivalents. We found that the 12 dioxin-like polychlorinated biphenyls accounted for up to 34.7% of the total concentration of polychlorinated biphenyls. 41% of the sites showed carcinogenic risks. Polychlorinated biphenyl-126 and polychlorinated biphenyl-169 appear as convenient indicators of toxicity and risk. [ABSTRACT FROM AUTHOR]

Immobilized microbial technology has been widely used in wastewater treatment, but it has been used less frequently for soil remediation, particularly in sites that are co-contaminated with organic compounds and heavy metals. In addition, there is limited knowledge on the efficiency of remediation and microbial preferences to colonize the immobilized carriers. In this study, biochar immobilized with Sphingobium abikonense was introduced to remediate soils that were co-contaminated with phenanthrene (PHE) and copper (Cu), and the mechanisms of microbial assemblage were investigated. The immobilized microbial biochar maintained a degradation rate of more than 96% in both the first (0–6 d) and second (6–12 d) contamination periods. The addition of biochar increased the proportion of Cu bound to organic matter, and Fe–Mn oxide bound Cu in the soil. In addition, both Cu and PHE could be adsorbed into biochar pellets in the presence or absence of immobilized S. abikonense. The presence of biochar significantly increased the abundance of bacteria, such as Luteibacter, Bordetella and Dyella, that could degrade organic matter and tolerate heavy metals. Notably, the biochar could specifically select host microbes from the soil for colonization, while the presence of S. abikonense affected this preference. The autonomous selection facilitates the degradation of PHE and/or the immobilization of Cu in the soil. These results provide a green approach to efficiently and sustainably remediate soil co-contaminated with PHE and Cu and highlight the importance of microbial preference colonized in immobilized carriers. Highlights: Biochar immobilized with S. abikonense could degrade PHE efficiently and sustainably. Pellets of biochar immobilized with S. abikonense adsorbed more Cu on its surface. Biochar had a selective preference for its colonized microbial communities. [ABSTRACT FROM AUTHOR]

The multi-functional properties of lactic acid bacteria (LAB) on host health have been a popular research topic. The aim of present study was to assess the multi-functional potential of five LAB strains isolated from giant panda. In this study, we analyzed five giant panda LAB strains (Weissella confuse WJ202003 (W3), WJ202009 (W9), WJ202021 (W21), BSP201703 (X3); Lactiplantibacillus plantarum BSGP201683 (G83)) and found that they exhibited rapid growth as well as strong acid production capacity. The five LAB strains possessed high cell surface hydrophobicity to the four tested solvents (xylene, hexadecane, chloroform, ethyl acetate; except strain W9), auto-aggregation ability, co-aggregation ability with three pathogens (Escherichia coli, Enterotoxigenic Escherichia coli, Salmonella), adhesion ability to Caco-2 cell line, and strongly biofilm formation ability, suggesting an adhesion property. As investigated for their antioxidative potential, all the strains showed good tolerance to H2O2, high scavenging ability against 1, 1-diphenyl-2-picrylhydrazyl (DPPH), and hydroxyl (OH−), and reduction ability. Furthermore, the five LAB strains could produce multiple probiotic substances, including exopolysaccharide (EPS), gamma-aminobutyric acid (GABA), bile salt hydrolase (BSH), cellulase (only strain G83), and protease (except strain X3), which was the first to report the production of EPS, GABA, BSH, cellulase, and protease in giant panda-derived LAB strain. These results demonstrated that strains W3, W9, W21, X3, and G83 had multi-functional potential and could be utilized as potential probiotics for giant panda. [ABSTRACT FROM AUTHOR]

A novel endophytic fungus producing beta-glucosidase was isolated and characterized from pigeon pea (Cajanus cajan [L.] Millsp.), which has excellent properties in converting ginsenoside Rb1 to ginsenoside Rd in Panax notoginseng. According to the 16S rDNA gene sequence, the G11-7 strain was identified as Fusarium proliferatum, and the accession number KY303906 was confirmed in GenBank. The G11-7 immobilized spores, in which the activity of beta-glucosidase could reach 0.95 U/mL, were co-cultured with P. notoginseng plant material to obtain a continuous beta-glucosidase supply for the biotransformation of ginsenoside Rb1 to Rd. Under the liquid–solid ratio (20:1), initial pH (6.0), and temperature (30 °C) constituents, the maximum ginsenoside Rd yield was obtained as 9.15 ± 0.65 mg/g, which was 3.67-fold higher than that without fungal spore co-culture (2.49 ± 0.98 mg/g). Furthermore, immobilized G11-7 spores showed significant beta-glucosidase producing ability which could be recovered and reused for 6 cycles. Overall, these results suggested that immobilized G11-7 offered a promising and effective approach to enhance the production of ginsenoside Rd for possible nutraceutical and pharmaceutical uses. [ABSTRACT FROM AUTHOR]

Sex selection technologies have immensely impacted swine production globally. Conventional earlier embryo sex identification methods require professional technicians and sophisticated laboratory instruments. Rapid on-site gender identification of porcine embryos and pork products remains challenging. In this study, we developed a CRISPR/Cas12a-based fluorescence visualization point-of-care sex determination test that is rapid, accurate and easy to implement on-site. The CRISPR/Cas12a assay coupled with either the polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP) employs precisely designed primers and single-guide RNAs targeting the sex-determining region Y (SRY) and the zinc finger protein X-linked (ZFX) genes. PCR and LAMP amplicons were cleaved with the subsequent generation of fluorescing products detectable with portable blue and ultraviolet light transilluminators. Approximately two copies per microliter of the ZFX and SRY genes were detected using the RApid VIsual CRISPR (RAVI-CRISPR) assay. This method is a sensitive, inexpensive, versatile, and point-of-care test. The technology has other potential applications like determining the sex of diverse livestock species, detecting livestock disease-causing pathogens and evaluating the quality of meat products. [ABSTRACT FROM AUTHOR]

Accelerated soil erosion and trace metal pollution in aquatic environments have become a pervasive aspect of global environmental changes during the Anthropocene, threatening food security and ecosystem viability. Long-term records of these processes can promote an improved understanding of their timing, amplitude, and environmental impacts. Here we present a sedimentary record from Lake Jian in Yunnan Province, southwestern China, which shows that land-use changes affected the lake watershed by at least 1200 CE, and that the intensity of soil erosion increased from 1450 CE onwards, as evidenced by increases in magnetic susceptibility and high concentrations of trace metals. The timing of the increase in atmospheric lead (Pb) transport, which was possibly related to the growth of metallurgical activity in the region, occurred ~250 years earlier than the anthropogenic soil erosion. Pb emissions resulting from the mining and smelting industry, coal burning, and the use of leaded gasoline led to enhanced Pb pollution in the area since the 1950s CE. Comparison of the results with geochemical records from lakes in northwestern Yunnan reveals that environmental disturbances were relatively limited during the intervals of the Nanzhao and Dali Kingdoms. However, enhanced human disturbances of lake watersheds in Yunnan occurred from the Yuan dynasty onwards, as a result of population increases caused by immigration to the area, which was followed by the changes in the type and intensity of human activity, with an enhanced anthropogenic impact after the middle twentieth century. Overall, our study provides a case study for understanding the historical background of the Anthropocene. [ABSTRACT FROM AUTHOR]

Implementing precision medicine hinges on the integration of omics data, such as proteomics, into the clinical decision-making process, but the quantity and diversity of biomedical data, and the spread of clinically relevant knowledge across multiple biomedical databases and publications, pose a challenge to data integration. Here we present the Clinical Knowledge Graph (CKG), an open-source platform currently comprising close to 20 million nodes and 220 million relationships that represent relevant experimental data, public databases and literature. The graph structure provides a flexible data model that is easily extendable to new nodes and relationships as new databases become available. The CKG incorporates statistical and machine learning algorithms that accelerate the analysis and interpretation of typical proteomics workflows. Using a set of proof-of-concept biomarker studies, we show how the CKG might augment and enrich proteomics data and help inform clinical decision-making. A knowledge graph platform integrates proteomics with other omics data and biomedical databases. [ABSTRACT FROM AUTHOR]

In the recent years, luminescent phosphor materials have contributed much to reduce the serious environmental problems such as environmental pollution, greenhouse effect, and energy crisis, but most of them commercially used for fabricating white LEDs are rare earth (RE) ions doped materials. Here, the non-RE Bi3+-doped Ba2(Y,Sc)NbO6 solid solution nanocrystals are prepared using a high temperature solid state route followed by a ball milling and griddle selection. Our experiments show that when the Y3+ ions are replaced by the Sc3+ ions, the obtained solid solution nanocrystals show a shift of X-ray reflection positions to higher angle, and the emission peaks from blue to blue-green. At the same time, a 1.35 time of PL intensity enhancement under 365 nm excitation is achieved in the Ba2(Y0.58,Sc0.4)NbO6:0.02Bi sample when compared to the Ba2Y0.98NbO6:0.02Bi sample. In addition, this optimal sample shows the quantum efficiency of 76% and good thermal stability with T50% value of 205 °C. By depositing the Ba2(Y0.58,Sc0.4)NbO6:0.02Bi and commercial red Sr2Si5N8:Eu2+ phosphors on a 365 nm UV LED chip at a driving current of 30 mA, a white LED device, with a CIE coordinates at (0.364, 0.379), a high color rendering index of 76.8 and luminous efficiency of 67 lm, and a low color temperature of 3469 K, is achieved. [ABSTRACT FROM AUTHOR]

Long non-coding RNA (lncRNA) represents a new direction to identify expression profiles and regulatory mechanisms in various organisms. Here, we report the first dataset of lncRNAs of the golden snub-nosed monkey (GSM), including 12,557 putative lncRNAs identified from seven organs. Compared with mRNA, GSM lncRNA had fewer exons and isoforms, and longer length. LncRNA showed more obvious tissue-specific expression than mRNA. However, for the top ten most abundant genes in each organ, mRNAs expression was more tissue-specific than lncRNAs. By identification of specifically expressed lncRNAs and mRNAs in each organ, it indicates that the expression of SEG-lncRNA (specifically expressed lncRNA) and SEG-mRNA (specifically expressed mRNA) had high correlation. In particular, combined our lncRNA and mRNA data, we identified 92 heart SEG-lncRNAs targeted ten mRNA genes in the oxidative phosphorylation pathway and upregulated the expression of these target genes such as ND4, ATP6, and ATP8. These may contribute to GSM adaption to its high-elevation environment. We also identified 171 liver SEG-lncRNAs, which targeted 27 genes associated with the metabolism of xenobiotics and leaded to high expression of these target genes in liver. These lncRNAs may play important roles in GSM adaptation to a folivory diet. [ABSTRACT FROM AUTHOR]

Main conclusion: Thirty CcMYB were identified to involve in flavonoid and lignin biosynthesis in pigeon pea genome. A comprehensive analysis of gene structure, phylogenetic relationships, distribution on chromosomes, gene duplication, and expression patterns was performed. MYB transcription factor is one of the largest gene families in plants and plays critical roles in plant growth and development, as well as resistance to biotic and abiotic stress. However, the function of MYB genes in pigeon pea (Cajanus cajan) remains largely unknown. Here, 30 R2R3-MYB which involved flavonoid and lignin biosynthesis were identified in the pigeon pea genome and were classified into five groups based on phylogenetic analysis. Simultaneously, another 122 key enzyme genes from biosynthetic pathways of flavonoid and lignin were identified and all of them were mapped on 11 chromosomes with the co-linearity relationship. Among these genes, the intron/exon organization and motif compositions were conserved and they have undergone a strong purifying selection and tandem duplications during evolution. Expression profile analysis demonstrated most of these genes were expressed in different tissues and responded significantly to MeJA, RNA-seq analysis revealed clear details of genes varied with time of induction. Ten key genes from the phenylpropanoid pathway were selected to further verify whether they responded to induction under different abiotic stress conditions (UV-B, cold, heat, salt, drought, and GA3). This study elaborates on potential regulatory relationships between R2R3-MYB genes and some key genes involved in flavonoid and lignin biosynthesis under MeJA treatment, as well as adding to the understanding of improving abiotic stress tolerance and regulating the secondary metabolism in woody crops. A simplified discussion model for the different regulation networks involved with flavonoid and lignin biosynthesis in pigeon pea is proposed. [ABSTRACT FROM AUTHOR]

Giant pandas often suffered from gastrointestinal disease, especially the captive sub-adult one. Our study aims to investigate whether L. plantarum G83, a good panda-derived probiotic, can improve the intestinal barrier against the enterotoxigenic Escherichia coli K88 (E. coli K88) infection in giant panda microbiota-associated mice (GPAM). We treated SPF mice with antibiotics cocktail and transplanted the giant panda intestinal microbiota to set up a GPAM. Our results demonstrated that the microbiota of GPAM changed over time and was relatively stable in the short-term experiment (2–4 weeks). Whereafter, the GPAM pretreated with L. plantarum G83 for 15 days and infected with enterotoxigenic E. coli K88. The result indicated that the number of Bifidobacteria spp. increased in GPAM-G and GPAM-GE groups; the Lactobacillus spp. only increased in the GPAM-G group. Although the abundance of Enterobacteriaceae spp. only decreased in the GPAM-G group, the copy number of Escherichia coli in the GPAM-E group was significantly lower than that in the other groups. Meanwhile, the L. plantarum G83-induced alteration of microbiota could increase the mRNA expression of Claudin-1, Zo-1, and Occludin-1 in the GPAM-G group in the ileum; only Occludin-1 was increased in the GPAM-GE group. The sIgA in the ileum showed a positive response, also the result of body weight and histology in both the GPAM-G and GPAM-GE group. These results indicated that the L. plantarum G83 could improve the intestinal barrier to defense the enterotoxigenic E. coli K88 invasion. [ABSTRACT FROM AUTHOR]

Cataracts are a common cause of visual impairment and blindness in mammals. They are usually associated with aging, but approximately one third of cases have a significant genetic component. Cataracts are increasingly prevalent among aging populations of captive giant pandas (Ailuropoda melanoleuca) and it is therefore important to identify genetic determinants that influence the likelihood of cataract development in order to distinguish between congenital and age-related disease. Here we screened for cataract-related genetic effects using a functional candidate gene approach combined with bioinformatics to identify the underlying genetic defect in a giant panda with congenital cataracts. We identified a missense mutation in exon 10 of the HSF4 gene encoding heat shock transcription factor 4. The mutation causes the amino acid substitution R377W in a highly conserved segment of the protein between the isoform-specific and downstream hydrophobic regions. Predictive modeling revealed that the substitution is likely to increase the hydrophobicity of the protein and disrupt interactions with spatially adjacent amino acid side chains. The mutation was not found in 13 unaffected unrelated animals but was found in an unrelated animal also diagnosed with senile congenital cataract. The novel missense mutation in the HSF4 gene therefore provides a potential new genetic determinant that could help to predict the risk of cataracts in giant pandas. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are key in the post-transcriptional regulation of gene expression and thus characterization of miRNAs and investigation of the relative abundance and specificity of tissue expression are essential for understanding gene expression in the golden snub-nosed monkey (GSM, Rhinopithecus roxellanae). Here, we report the first dataset of GSM miRNAs where we identified 460 miRNAs in seven tissues, with 246 conserved known mature miRNAs and 214 novel mature miRNAs. We determined miRNA abundance and expression in the seven tissues using a Tissue Specificity Index score and found that most novel GSM miRNAs showed a highly tissue-specific expression pattern. In particular, 67 novel miRNAs and the miR-34 family were expressed in abundance only in the lung. Five known miRNAs were highly abundant in digestive organs such as the pancreas and liver, and four novel miRNAs were highly expressed in the heart and muscle. Annotation of target genes of GSM miRNAs indicated that target genes were enriched in many important pathways, such as the HIF-1 signaling pathway and xenobiotic biodegradation-related pathways. Collectively, these results emphasize that miRNAs play important roles in GSM diet and high-elevation adaptation regulation. In summary, this study provides essential information on GSM miRNAs and will benefit further investigations of the function and mechanism of miRNAs in controlling gene expression in the GSM. [ABSTRACT FROM AUTHOR]

Ultrasound stimulation is an emerging noninvasive option in treating neuropsychiatric disorders. The present study investigates the behavioral alterations resulting from ultrasound stimulation on the nucleus accumbens (NAc) in freely moving mice. Our results show that an acute ultrasound stimulation on the NAc, rather than the visual cortex or auditory cortex, led to a pronounced avoidance behavior, while repeated NAc ultrasound stimulation resulted in an obvious conditioned place aversion with changes in synaptic protein (GluA1/2 subunit) expression. Notably, NAc ultrasound stimulation suppressed the morphine-induced conditioned place preference. The results provide evidence that NAc ultrasound stimulation can be applied as a potential noninvasive therapeutic option in treating psychiatric disorders. [ABSTRACT FROM AUTHOR]

Golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered primate endemic to China. The lack of standardized genetic markers limits its conservation works. In the present study, a total of 1,400,552 perfect STRs was identified in the reference genome of R. roxellana. By comparing it with the 12 resequencing genomes of four geographical populations, a total of 1,927 loci were identified as perfect tetranucleotides and shared among populations. We randomly selected 74 loci to design primer pairs. By using a total of 64 samples from the Chengdu Zoo captive population and the Pingwu wild population, a set of 14 novel STR loci were identified with good polymorphism, strong stability, high repeatability, low genotyping error rate that were suitable for non-invasive samples. These were used to establish a standardized marker system for golden snub-nosed monkeys. The genetic diversity analysis showed the average HO, HE, and PIC was 0.477, 0.549, and 0.485, respectively, in the Chengdu Zoo population; and 0.516, 0.473, and 0.406, respectively, in Pingwu wild population. Moreover, an individual identification method was established, which could effectively distinguish individuals with seven markers. The paternity tests were conducted on seven offspring with known mothers from two populations, and their fathers were determined with high confidence. A genotyping database for the captive population in the Chengdu Zoo (n = 25) and wild population in Pingwu country (n = 8) was acquired by using this marker system. [ABSTRACT FROM AUTHOR]

Currently, the definitive diagnosis in breast cancer requires biopsy and histopathology, such the most effective markers are tissue-based. However, the advantages of saliva in collection and storage make it possible for assessing human pathology and contributing to the development of cancer-related biomarkers for clinical application. The present study validated alteration of salivary protein glycopatterns recognized by Bandeiraea simplicifolia lectin I (BS-I) in the saliva of patients with breast diseases using saliva microarrays, and the N/O-glycan profiles of their salivary glycoproteins isolated by the BS-I-magnetic particle conjugates from 259 female subjects (66 healthy volunteers (HV), 65 benign breast cyst or tumor patients (BB), 66 patients with breast cancer in stage I (BC-I) and 62 patients with breast cancer in stage II (BC-II)) were analyzed by MALDI-TOF/TOF-MS. The results showed that the expression level of galactosylated glycans recognized by BS-I was significantly increased in patients with breast cancer compared with HV (p < 0.05). Totally, there were 11/10, 10/19, 7/24 and 7/9 galactosylated N-/O-linked glycans were identified and annotated from the pooled salivary samples of HV, BB, BC-I and BC-II, respectively. One galactosylated N-glycan peak (m/z 2773.977), and 4 galactosylated O-glycan peaks (m/z 868.295, 882.243, 884.270 and 1030.348) were found only in BC-I. These findings could provide pivotal information on galactosylated N/O-linked glycans related to breast cancer, and promote the study of biomarkers for early-stage breast cancer based on precise alterations of galactosylated N/O-glycans in saliva. [ABSTRACT FROM AUTHOR]

Phosphatase and the tensin homologue deleted on chromosome ten (PTEN) has pleiotropic effects on cell growth, organ development, glucose metabolism and insulin resistance in mammals. In the present study, we investigated the molecular characteristics, phylogeny and expression profile of the PTEN gene in different tissues of Jianzhou Daer goats. In this study, eight different tissues from E90, E135 and D90 female goats were collected to quantify the expression pattern of the PTEN gene using quantitative real-time PCR (qPCR), western blotting and FISH. In addition, the dynamic expression of PTEN was also determined during the differentiation of goat precursor adipose cells. A 1212-bp fragment (accession number MG923848), encoding a 403-amino acid protein with a putative molecular weight of 47.14 kDa, was identified in Jianzhou Daer goats by reverse-transcription polymerase chain reaction (RT-PCR). The phylogenetic tree showed that caprine PTEN had a relatively close relationship with ovine PTEN and bovine PTEN. qPCR revealed that PTEN was highly expressed in the liver, lung and spleen, while the lowest expression levels were observed in muscle tissues (P < 0.05). Moreover, the expression of the PTEN gene showed a decreasing trend during the differentiation of goat precursor adipose cells. RNA in situ hybridization yielded a consistent result with the qPCR data. Indeed, low protein expression was found in psoas major muscle and longissimus dorsi muscle, as well as in kidney and liver. However, PTEN protein was expressed at the highest level in the brain. The expression levels of PTEN mRNA and protein were inconsistent with each other, possibly because of post-transcriptional regulation. The findings obtained in our study lay a foundation for further investigations examining the caprine PTEN gene in embryo and organ development. [ABSTRACT FROM AUTHOR]

Key message: In this study, we have identified 120 UGT genes in pigeonpea and performed a bioinformatics analysis, which showed their tissue-specific and stress-induced expression patterns. Family 1 UDP-glycosyltransferases (UGTs; EC 2.4.1.x) are enzymes that glycosylate aglycones into glycoside-associated compounds. They play an important role in plant resistance to abiotic stresses by regulating the synthesis of plant hormones and secondary metabolites. However, in pigeonpea, the UGT family has not yet been reported. Here, 120 CcUGT genes were identified from the pigeonpea genome, which all contained the plant secondary product glycosyltransferase motif (PSPG). According to the phylogenetic relationship, 120 CcUGTs can be classified into 11 major groups. The CcUGTs are distributed on 10 chromosomes except chromosome 5. Homology modeling of CcUGT proteins and conserved motif search were used to predict the structure of 120 UGTs. Most protein structures can be predicted with high accuracy. After that, 11 representative CcUGT genes were selected for further analysis. We measured their specific expression in different tissues and the changes in transcription levels after stress. The results show that 11 genes are specific in different tissues and the expression of genes in leaves is higher than that of other tissues. In roots, CcUGT69 genes were highly expressed in salt and osmotic stresses, and CcUGT110 was up-regulated in low temperature injury. In leaves, most of the genes were up-regulated after stress treatment, and only CcUGT6, 37, 56 had little change in transcription levels. Overall, this study systematically analyses the UGT gene family in pigeonpea for the first time and provides some useful clues for further functional studies of UGT genes. [ABSTRACT FROM AUTHOR]

Objective: MiR-499 has been reported to be expressed only in cardiomyocytes, and its expression would increase after acute myocardial infarction (AMI). miR-499 plays a role in the process of cardiomyocytes injury induced by hypoxia/reoxygenation (H/R), however, it still remains unclear. Results: Hypoxia inhibited miR-499-5p expression and H/R induced apoptosis. SOX6 was a target gene of miR-499-5p, and high expression of miR-499-5p inhibited the expression of SOX6. MiR-499-5p reduced H9c2 cells injury by inhibiting the expression of SOX6, overexpression of which could reverse the effect of miR-499-5p on H9c2 cells. MiR-499-5p inhibited the levels of LDH and MDA, while overexpression of miR-499-5p inhibited H/R-induced cell apoptosis. MiR-499-5p could up-regulate the level of Bcl-2 and down-regulate the expression levels of Bax and caspase-3. However, SOX6 partially reversed these effects of miR-499-5p. Conclusion: We proved that miR-499-5p inhibited H/R-induced cardiomyocytes injury by targeting SOX6. Our results suggested that miR-499-5p/SOX6 pathway may present a potential therapeutic target for the treatment of AMI. [ABSTRACT FROM AUTHOR]

Weissella confusa has recently received attention for its probiotic potential. Some W. confusa and Weissella cibaria strains isolated from fermented foods show favorable probiotic effects. However, the probiotic properties of W. confusa isolated from giant panda remain unreported to date. Thus, this study isolated a W. confusa strain from giant panda feces and then investigated its characteristics and probiotic properties. A lactic acid bacteria strain was isolated from giant panda fecal samples. The isolated strain was screened by in vitro probiotic property tests, including in vitro antimicrobial test, antioxidant test, surface hydrophobicity, and stress resistance. On the basis of biochemical identification and 16S rDNA sequencing, the W. confusa strain was identified as BSP201703. This Weissella confusa strain can survive at pH 2 and 0.3% (w/v) concentration of bile salt environment and inhibit common intestinal pathogens. It also possesses an in vitro antioxidant capacity, a high auto-aggregation ability, and a high surface hydrophobicity. BSP201703 might serve as a probiotic to giant pandas. [ABSTRACT FROM AUTHOR]

The present study aimed to isolate an optimal lactic acid bacterial strain from the feces of healthy giant pandas. The strain exhibited good stability at low pH and high bile salt concentrations, activity against pathogens relevant to pandas, and antibiotic susceptibility. In the current study, 25 isolates were obtained from de Man, Rogosa, and Sharpe agar. Two (E21 and G83) and eight (E1, E2, E16, E18, E21, E69, E70, and G83) isolates demonstrated good performance at pH 2.0 and bile 2% (w/v), respectively. Three isolates (G83, G88, and G90) possessed better antimicrobial effect on enterotoxigenic Escherichia coli CVCC196 (ETEC) than the rest. One isolate (G83) strongly affected Salmonella, whereas three (G83, G87, and G88) exhibited inhibitory activity against Staphylococcus aureus. All isolates were multi-drug resistant. These isolates were identified as Lactobacillus (5 isolates) and Enterococcus (20 isolates) by 16S rRNA sequencing. Virulence genes were detected in Enterococcus isolates. Isolate G83 was identified as Lactobacillus plantarum and was considered as the best probiotic candidate among all of the experimental isolates. This study provided necessary and important theoretical guidance for further experiments on G83 in vivo. [ABSTRACT FROM AUTHOR]

Ecotoxicological studies have revealed the association between synthetic pyrethroid (SP) exposure and aquatic toxicity in fish; however, research on the toxic effects of SP metabolites is still limited. In this study, the toxicity of two SPs (permethrin (PM) and β-cypermethrin (β-CP)) and their three metabolites (3-phenoxybenzoic alcohol (PBCOH), 3-phenoxybenzaldehyde (PBCHO), and 3-phenoxybenzoic acid (PBCOOH)) towards zebrafish embryos and larvae was evaluated. Both SPs and their metabolites exhibited significant developmental toxicities, caused abnormal vascular development, and changed locomotor activities in larvae. The alteration of gene expression involved in the thyroid system and the innate immune system indicated that SPs and their three metabolites have the potency to induce thyroid disruption and trigger an immune response. The results from the present study suggest that SP metabolites could induce multiple toxic responses similar to parent compounds, and their toxicity should be considered for improving the understanding of environmental risks of SPs. [ABSTRACT FROM AUTHOR]

Hexachlorocyclohexane (HCH) isomers and dichlorodiphenyltrichloroethane (DDT) metabolites were analyzed in sediments of three different depths (0-10, 10-20 and 20-30 cm) collected from Kabul River, Pakistan, in February 2014. The occurrence levels, enantiomer fractions and potential ecological risk of these organochlorine pesticides (OCPs) were evaluated. The total concentrations of ∑HCHs and ∑DDTs in surface sediments ranged from 4.9-23.9 ng g and from 6.4-18.8 ng g (dry weight basis), respectively. The vertical contamination profile of DDTs was found in order of 20-30 cm >10-20 cm >0-10 cm, indicated that the residue levels of DDTs gradually decreased after it was banned. The ratios of β-HCH/HCHs ranged from 0.04 to 0.73 (69 % of samples below 0.5) suggesting the fresh input of HCHs, while isomeric ratios of α-HCH/γ-HCH (ranged from 0.02 to 7.94), with 76 % of samples less than 3, indicating the cocktail use of technical grade HCH and lindane in the study area. The ratio of (DDE + DDD)/DDTs (ranged from 0.42 to 0.90) indicated long-term biodegradation of parent DDT. The enantiomer of α-HCH was generally racemic or close to racemic for most of the samples, with enantiomeric fraction (EF) value <0.5 for some of the samples indicated the preferential biodegradation of (+)-α-HCH enantiomer, while for o, p′-DDT the EF values >0.5 indicated the depletion of (-)- o, p′-DDT enantiomer in most of the samples. According to sediment quality guidelines (SQGs), HCH contamination is the main concern for ecotoxicological risk in Kabul River. Graphical Abstract: [ABSTRACT FROM AUTHOR]

Owning to advantages over traditional species identification methods, DNA barcoding is suggested to be a promising tool in conservation research. However, the use of DNA barcoding to accurately identify unknown samples in conservation practices has not been well documented in the literature. To illustrate this issue, we implemented a survey of endangered birds and mammals in China based on mitochondrial Cytochrome c Oxidase subunit I (COI) gene. We included mostly confiscated specimens and non-invasive samples while concealing species information to simulate real-world scenarios of identification. In total, 47 avian and 39 mammalian specimen were re-identified by sequential analyses of online species assignment, genetic distances, phylogenetic reconstruction, and diagnostic nucleotide method. With this multiple analyses approach, 82 individuals were accurately assigned to the species level and four individuals to the genus level. 78.72% of the avian specimen and 87.18% of mammalian specimen identifications were consistent with morphological classification. Among those inconsistent with morphological classification, we identified several potential errors including misidentification based on morphology and mislabelling that may have occurred while combining results from different analytical methods. Our case study not only enriches the barcode database, but also reports a successful application of DNA barcoding identification to conservation practices, which could effectively facilitate species identification of unknown samples in conservation practices in the future. [ABSTRACT FROM AUTHOR]

Nornicotine is a natural alkaloid produced by plants in the genus Nicotiana and is structurally related to nicotine. Importantly, nornicotine is the direct precursor of tobacco-specific nitrosamine N′-nitrosonornicotine, which is a highly potent human carcinogen. Microbial detoxification and degradation of nicotine have been well characterized; however, until now, there has been no information on the molecular mechanism of nornicotine degradation. In this study, we demonstrate the transformation of nornicotine by the nicotine-degrading strain Shinella sp. HZN7. Three transformation products were identified as 6-hydroxy-nornicotine, 6-hydroxy-myosmine, and 6-hydroxy-pseudooxy-nornicotine by UV spectroscopy, high-resolution mass spectrometry, nuclear magnetic resonance, and Fourier transform-infrared spectroscopy analyses. The two-component nicotine dehydrogenase genes nctA1 and nctA2 were cloned, and their product, NctA, was confirmed to be responsible for the conversion of nornicotine into 6-hydroxy-nornicotine as well as nicotine into 6-hydroxy-nicotine. The 6-hydroxy-nicotine oxidase, NctB, catalyzed the oxidation of 6-hydroxy-nornicotine to 6-hydroxy-myosmine, and it spontaneously hydrolyzed into 6-hydroxy-pseudooxy-nornicotine. However, 6-hydroxy-pseudooxy-nornicotine could not be further degraded by strain HZN7. This study demonstrated that nornicotine is partially transformed by strain HZN7 via nicotine degradation pathway. [ABSTRACT FROM AUTHOR]

To research the molecular characteristics, expression pattern and phylogeny of the Delta- like 1 homolog gene ( Dlk1) in goats. Dlk1 transcripts were identified in the Jianyang Da'er goats by reverse-transcription polymerase chain reaction (RT-PCR). Phylogenetic trees were constructed by Bayesian inference and neighbor-joining methods. Quantitative real-time PCR (qPCR), western blotting and in situ hybridization were performed to analyze the expression pattern of Dlk1. Five alternatively transcripts were identified in different tissues and designated as Dlk1- AS1, 2, 3, 4 and 5. Compared with the normal transcript Dlk1- AS1, Dlk1- AS4 and Dlk1- AS5 retained the identical open reading frame (ORF) and encoded proteins with truncated epidermal-growth-factor like repeats of 121 and 83 amino acids, respectively. Using the Bayesian inference method, the consensus phylogenetic tree indicated that caprine Dlk1 had a closer relationship with bovine Dlk1 than with Dlk1 from pigs, humans and mice. qPCR revealed high expression levels of Dlk1 in the kidney ( P < 0.01). However, mRNA and protein levels presented an inconsistent correlation, possibly because of post-transcriptional regulation. RNA in situ hybridization indicated that Dlk1 mRNA was localized in the interlobular bile duct and alongside the hepatocyte nuclei, in the epithelial cells of proximal and distal convoluted tubules and in the connective region between the mesothelium and myocardium in the heart. The Dlk1 gene in goats produces alternatively spliced transcripts, with specific expression and cellular localization patterns. These findings would lay the foundation for further study. [ABSTRACT FROM AUTHOR]

It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics ( p < 0.05), but not significant compared to the subadults ( p > 0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults ( p < 0.05), while other bacterial groups and species detected did not significantly differ among the three age groups ( p > 0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition. [ABSTRACT FROM AUTHOR]

Intravenous and intratracheal implantation of mesenchymal stem cells (MSCs) may offer ameliorating effects on pulmonary hypertension (PH) induced by monocrotaline (MCT) in rats. The aim of this study was to examine the anti-remodeling effect of intravenous MSCs (VMSCs) and intratracheal MSCs (TMSCs) in rats with PH, and the underlying mechanisms. MSCs were isolated from rat bone marrow and cultured. PH was induced in rats by intraperitoneal injection of MCT. One week after MCT administration, the rats were divided into 3 groups in terms of different treatments: VMSCs group (intravenous injection of MSCs), TMSCs group (intratracheal injection of MSCs), PH group (no treatment given). Those receiving saline instead of MCT served as negative control (control group). Pulmonary arterial structure was pathologically observed, pulmonary arterial dynamics measured, and remodeling-associated cytokines Smad2 and Smad3 detected in the lungs, three weeks after MCT injection. The results showed that PH group versus control group had higher pulmonary arterial pressure (PAP) and wall thickness index (WTI) 21 days after MCT treatment. The expression of phosphorylated (p)-Smad2 and the ratio of p-Smad2/Smad2 were much higher in PH group than in control group. Fluorescence-labeled MSCs were extensively distributed in rats' lungs in VMSCs and TMSCs groups 3 and 14 days after transplantation, but not found in the media of the pulmonary artery. WTI and PAP were significantly lower in both VMSCs and TMSCs groups than in PH group three weeks after MCT injection. The p-Smad2 expression and the ratio of p-Smad2/Smad2 were obviously reduced in VMSCs and TMSCs groups as compared with those in PH group. In conclusion, both intravenous and intratracheal transplantation of MSCs can attenuate PAP and pulmonary artery remodeling in MCT-induced PH rats, which may be associated with the early suppression of Smad2 phosphorylation via paracrine pathways. [ABSTRACT FROM AUTHOR]

Human skin provides both physical integrity and immunological protection from the external environment using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combine advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantify 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe the quantitative distribution of structural proteins, known and previously undescribed proteins specific to cellular subsets and those with specialized immunological functions such as cytokines and chemokines. We anticipate that this proteomic atlas of human skin will become an essential community resource for basic and translational research (https://skin.science/). The human skin is a highly complex organ comprising multiple tissue layers and diverse cell types. Here, the authors present a spatially-resolved quantitative proteomic atlas of the healthy human skin, characterizing the protein profiles of four skin layers and nine cell types. [ABSTRACT FROM AUTHOR]

Due to the adverse impact of DDTs on ecosystems and humans, a full fate assessment deems a comprehensive study on their occurrence in soils over a large region. Through a sampling campaign across China, we measured the concentrations, enantiomeric fractions (EFs), compound-specific carbon isotope composition of DDT and its metabolites, and the microbial community in related arable soils. The geographically total DDT concentrations are higher in eastern than western China. The EFs and δ13C of o,p'-DDT in soils from western China show smaller deviations from those of racemic/standard compound, indicating the DDT residues there mainly result from atmospheric transport. However, the sources of DDT in eastern China are mainly from historic application of technical DDTs and dicofol. The inverse dependence of o,p'-DDT and p,p'-DDE on temperature evidences the transformation of parent DDT to its metabolites. Initial usage, abiotic parameters and microbial communities are found to be the main factors influencing the migration and transformation of DDT isomers and their metabolites in soils. In addition, a prediction equation of DDT concentrations in soils based on stepwise multiple regression analysis is developed. Results from this study offer insights into the migration and transformation pathways of DDTs in Chinese arable soils, which will allow data-based risk assessment on their use. [ABSTRACT FROM AUTHOR]