Effect of Panax ginseng and Fructus Mume on Intestinal Barrier and Gut Microbiota in Rats with Diarrhea.

Panax ginseng and Fructus mume (Renshen Wumei in Chinese, RW) are natural medicines with high nutritional and pharmacological value. They have been widely used together in China to treat gastrointestinal diseases, especially persistent diarrhea, but the potential mechanisms remain elusive. In this study, a diarrhea model was established in rats using a 30% aqueous extract of senna. The therapeutic effects of RW were evaluated by recording the prevalence of loose stools, the diarrhea index, and histopathological changes in colon tissue. The levels of mucins, tight junction (TJ) proteins, inflammatory cytokines, and phosphoinositide 3-kinase/Akt/nuclear factor-κB (PI3K/Akt/NF-κB) signaling pathway proteins were measured. Metagenomic sequencing was used to analyze the gut microbiota. Treatment with RW alleviated injury to the intestinal barrier in rats with diarrhea and also upregulated levels of Muc2 and TJ proteins, such as occludin, zonula occludens-1, and claudin-1. Administration of RW regulated the structure of the gut microbiota in diarrheal rats. Furthermore, RW suppressed levels of interleukin (IL), tumor necrosis factor (TNF)-α, IL-1, PI3K, Akt, and p-NF-κB p65 and also increased IL-4 levels. Our study indicates that P. ginseng and Fructus mume help improve the symptoms of diarrhea, possibly by alleviating the intestinal barrier injury, regulating intestinal flora composition, and inhibiting the PI3K/Akt/NF-κB signaling pathway.

Isolation, identification and characterization of a novel antimicrobial peptide from Moringa oleifera seeds based on affinity adsorption.

This study aimed to characterize a novel antimicrobial peptide (AMP) obtained from Moringa oleifera seed protein hydrolysates. Cell membrane chromatography and live bacteria adsorption were combined into a single step to efficiently isolate the active fraction of the AMP. Five peptides were identified by LC-MS/MS, among which the MCNDCGA peptide (termed MOp3) showed the greatest inhibitory effect against Staphylococcus aureus [minimum inhibitory concentration (MIC): 2 mg/mL]. MOp3 was identified as a hydrophobic anionic AMP rich in ß-sheet structures with negligible hemolytic activity at 2.0 × MIC. MOp3 had good tolerance to salt solutions at 5 % and pH range 6.0-8.0, but was sensitive to high temperatures (>100 °C) and acid protease. Microscopic observation further revealed that MOp3 induced irreversible damage onto the cell membrane of S. aureus and interacted with dihydrofolate reductase and DNA gyrase by hydrogen bonding and hydrophobic interaction. These findings highlight the potential application of a new antimicrobial agent against S. aureus in the food industry.

Network pharmacology and molecular docking analysis on the mechanism of Baihe Zhimu decoction in the treatment of postpartum depression.

Baihe Zhimu decoction (BZD) has significant antidepressant properties and is widely used to treat mental diseases. However, the multitarget mechanism of BZD in postpartum depression (PPD) remains to be elucidated. Therefore, the aim of this study was to explore the molecular mechanisms of BDZ in treating PPD using network pharmacology and molecular docking. Active components and their target proteins were screened from the traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The PPD-related targets were obtained from the OMIM, CTD, and GeneCards databases. After overlap, the targets of BZD against PPD were collected. Protein-protein interaction (PPI) network and core target analyses were conducted using the STRING network platform and Cytoscape software. Moreover, molecular docking methods were used to confirm the high affinity between BZD and targets. Finally, the DAVID online tool was used to perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of overlapping targets. The TCMSP database showed that BZD contained 23 active ingredients in PPD. KEGG analysis showed that overlapping genes were mainly enriched in HIF-1, dopaminergic synapses, estrogen, and serotonergic synaptic signalling pathways. Combining the PPI network and KEGG enrichment analysis, we found that ESR1, MAOA, NR3C1, VEGFA, and mTOR were the key targets of PPD. In addition, molecular docking confirmed the high affinity between BZD and the PPD target. Verified by a network pharmacology approach based on data mining and molecular docking methods, the multi-target drug BZD may serve as a promising therapeutic candidate for PPD, but further in vivo/in vitro experiments are needed.

Characterization of a Novel Antimicrobial Peptide Isolated from Moringa oleifera Seed Protein Hydrolysates and Its Membrane Damaging Effects on Staphylococcus aureus.

The present study sought to identify and characterize a novel antimicrobial peptide, named MOp2 from Moringa oleifera seed protein hydrolysates, and elucidate its potential antimicrobial effects on Staphylococcus aureus. MOp2, with the amino acid sequence of His-Val-Leu-Asp-Thr-Pro-Leu-Leu (HVLDTPLL), was characterized as a hydrophobic anionic AMP of the ß-sheet structure. MOp2 exhibited negligible hemolytic activity at 2.0× MIC, suggesting its inhibitory effect on the growth of S. aureus (MIC: 2.204 mM). It maintained more than 90% of antimicrobial activity under 5% salt and about 78% of antimicrobial activity at a high temperature of 115 °C for 30 min. Protease, especially acid protease, reduced its antimicrobial activity to different extents. Moreover, MOp2 caused irreversible membrane damage to S. aureus cells by increasing the membrane permeability, resulting in the release of intracellular nucleotide pools. Additionally, molecular docking revealed that MOp2 could inhibit S. aureus growth by interacting with dihydrofolate reductase and DNA gyrase through hydrogen bonding and hydrophobic interactions. Overall, MOp2 could be a potential novel antimicrobial agent against S. aureus in food processing.

Response of carbon, nitrogen and phosphorus concentration and stoichiometry of plants and soils during a soybean growth season to O3 stress and straw return in Northeast China.

Carbon (C), nitrogen (N) and phosphorus (P) concentrations and stoichiometry play important roles in biogeochemical cycles of the ecosystems, yet it is still unclear how the allocations of C, N and P concentrations and stoichiometry among plant organs and soils related to O3 stress and straw return. Here, a pot experiment was conducted in open top chambers to monitor the response of C, N and P concentrations and stoichiometry of leaves, stems, roots and soils during a growing season (branching, flowering and podding stages) of soybean (Glycine max; a species highly sensitive to O3) to background O3 concentration (44.8 ± 5.6 ppb), O3 stress (79.7 ± 5.4 ppb) and straw treatment (no straw return and straw return). O3 stress significantly decreased root biomass. Straw return significantly increased root biomass under O3 stress at branching and flowering stages. Generally, O3 stress and straw return showed significant effects on the C, N and P concentrations of leaves and soils, and stoichiometric ratios of leaves, stems and microbial biomass. The C, N and P concentrations and stoichiometry of leaves, stems, roots and soils in response to O3 stress and straw return at the branching stage were inconsistent with the changes observed at the flowering and podding stages. The P conversion efficiency showed significant relationship with root P concentration under the combined effects of O3 stress and straw return. Altogether, the present study indicated that C, N and P concentrations of soybean might be more important than stoichiometric ratios as a driver of root defence against O3 stress in the case of straw return.

Modified Renshen Wumei Decoction Alleviates Intestinal Barrier Destruction in Rats with Diarrhea.

Modified Renshen Wumei decoction (MRWD), a famous traditional Chinese medicine, is widely used for treating persistent diarrhea. However, as the mechanism by which MRWD regulates diarrhea remains unknown, we examined the protective effects of MRWD on intestinal barrier integrity in a diarrhea model. In total, 48 male rats were randomly distributed to four treatment groups: the blank group (CK group), model group (MC group), Medilac-Vita group (MV group) and Chinese herb group (MRWD group). After a 21-day experiment, serum and colon samples were assessed. The diarrhea index, pathological examination findings and change in D-lactate and diamine oxidase (DAO) contents illustrated that the induction of diarrhea caused intestinal injury, which was ameliorated by MV and MRWD infusion. Metabolomics analysis identified several metabolites in the serum. Some critical metabolites, such as phosphoric acid, taurine, cortisone, leukotriene B4 and calcitriol, were found to be significantly elevated by MRWD infusion. Importantly, these differences correlated with mineral absorption and metabolism and peroxisome proliferator-activated receptor (PPAR) pathways. Moreover, it significantly increased the expression levels of TLR4, MyD88 and p-NF-κB p65 proteins and the contents of IL-1 and TNF-α, while the expression levels of occludin, claudin-1 and ZO-1 proteins decreased. These deleterious effects were significantly alleviated by MV and MRWD infusion. Our findings indicate that MRWD infusion helps alleviate diarrhea, possibly by maintaining electrolyte homeostasis, improving the intestinal barrier integrity, and inhibiting the TLR4/NF-κB axis.

Proteomics analysis of the bio-functions of Dregea sinensis stems provides insights regarding milk-clotting enzyme.

Dregea sinensis (D. sinensis) stems have traditionally been used as milk coagulant in Dali of Yunnan Province, China. In this study, proteomics was used to investigate the bio-functions of D. sinensis stem proteins, leading to the purification and identification of the milk-clotting enzyme. A total of 205 proteins mainly involved in the catalytic and metabolic processes were identified, of which 28 proteins exhibited hydrolase activity. Among the 28 proteins, we focused on two enzymes (M9QMC9 and B7VF65). Based on proteomics, a cysteine protease (M9QMC9) with a molecular weight of 25.8 kDa and milk-clotting activity was purified from D. sinensis stems using double ammonium sulfate precipitation and was confirmed using liquid chromatography-mass spectrometry (LC-MS/MS). The milk-clotting temperature using the purified enzyme was around 80 °C (specific activity at 314.38 U/mg), and it was found to be stable in the pH range of 6-9 in NaCl concentration of <0.8 mol/L. These findings indicated that the enzyme isolated from D. sinensis stems has potential in the dairy and food sectors, especially in the cheese-making industry.

Transcriptional Factor Yin Yang 1 Promotes the Stemness of Breast Cancer Cells by Suppressing miR-873-5p Transcriptional Activity.

Transcription factor Yin Yang 1 (YY1) is upregulated in multiple tumors and plays essential roles in tumor proliferation and metastasis. However, the function of YY1 in breast cancer stemness remains unclear. Herein, we found that YY1 expression was negatively correlated with the overall survival and relapse-free survival of breast cancer patients and positively correlated with the expression of stemness markers in breast cancer. Overexpression of YY1 increased the expression of stemness markers, elevated CD44+CD24- cell sub-population, and enhanced the capacity of cell spheroid formation and tumor-initiation. In contrast, YY1 knockdown exhibited the opposite effects. Mechanistically, YY1 decreased microRNA-873-5p (miR-873-5p) level by recruiting histone deacetylase 4 (HDAC4) and HDAC9 to miR-873-5p promoter and thus increasing the deacetylation level of miR-873-5p promoter. Sequentially, YY1 activated the downstream PI3K/AKT and ERK1/2 pathways, which have been confirmed to be suppressed by miR-873-5p in our recent work. Moreover, the suppressed effect of YY1/miR-873-5p axis on the stemness of breast cancer cells was partially dependent on PI3K/AKT and ERK1/2 pathways. Finally, it was found that the YY1/miR-873-5p axis is involved in the chemoresistance of breast cancer cells. Our study defines a novel YY1/miR-873-5p axis responsible for the stemness of breast cancer cells.

Altered leaf functional traits by nitrogen addition in a nutrient-poor pine plantation: A consequence of decreased phosphorus availability.

This study aimed to determine how specific leaf area (SLA) and leaf dry matter content (LDMC) respond to N addition and understory vegetation removal in a 13-year-old Mongolian pine (Pinus sylvestris var. mongolica) plantation. Traits (SLA, LDMC, individual needle dry weight, N and P concentrations) of different-aged needles and their crown-average values were measured, and their relationships with soil N and P availability were examined. N addition and understory removal reduced soil Olsen-P by 15-91%. At the crown level, N addition significantly reduced foliar P concentration (by 19%) and SLA (by 8%), and elevated N concentration (by 31%), LDMC (by 10%) and individual leaf dry weight (by 14%); understory removal did not have a significant effect on all leaf traits. At the needle age level, traits of the previous year's needles responded more strongly to N addition and understory removal than the traits of current-year needles, particularly SLA and N concentration. SLA and LDMC correlated more closely with soil Olsen-P than with soil inorganic N, and LDMC correlated more closely with soil Olsen-P than SLA did. These results indicate that aggravated P limitation resulting from N addition and understory removal could constrain Mongolian pine growth through their effects on the leaf traits.

Discovery and Mechanistic Study of Benzamide Derivatives That Modulate Hepatitis B Virus Capsid Assembly.

Chronic hepatitis B virus (HBV) infection is a global public health problem. Although the currently approved medications can reliably reduce the viral load and prevent the progression of liver diseases, they fail to cure the viral infection. In an effort toward discovery of novel antiviral agents against HBV, a group of benzamide (BA) derivatives that significantly reduced the amount of cytoplasmic HBV DNA were discovered. The initial lead optimization efforts identified two BA derivatives with improved antiviral activity for further mechanistic studies. Interestingly, similar to our previously reported sulfamoylbenzamides (SBAs), the BAs promote the formation of empty capsids through specific interaction with HBV core protein but not other viral and host cellular components. Genetic evidence suggested that both SBAs and BAs inhibited HBV nucleocapsid assembly by binding to the heteroaryldihydropyrimidine (HAP) pocket between core protein dimer-dimer interfaces. However, unlike SBAs, BA compounds uniquely induced the formation of empty capsids that migrated more slowly in native agarose gel electrophoresis from A36V mutant than from the wild-type core protein. Moreover, we showed that the assembly of chimeric capsids from wild-type and drug-resistant core proteins was susceptible to multiple capsid assembly modulators. Hence, HBV core protein is a dominant antiviral target that may suppress the selection of drug-resistant viruses during core protein-targeting antiviral therapy. Our studies thus indicate that BAs are a chemically and mechanistically unique type of HBV capsid assembly modulators and warranted for further development as antiviral agents against HBV.IMPORTANCE HBV core protein plays essential roles in many steps of the viral replication cycle. In addition to packaging viral pregenomic RNA (pgRNA) and DNA polymerase complex into nucleocapsids for reverse transcriptional DNA replication to take place, the core protein dimers, existing in several different quaternary structures in infected hepatocytes, participate in and regulate HBV virion assembly, capsid uncoating, and covalently closed circular DNA (cccDNA) formation. It is anticipated that small molecular core protein assembly modulators may disrupt one or multiple steps of HBV replication, depending on their interaction with the distinct quaternary structures of core protein. The discovery of novel core protein-targeting antivirals, such as benzamide derivatives reported here, and investigation of their antiviral mechanism may lead to the identification of antiviral therapeutics for the cure of chronic hepatitis B.

Cloning, expression, and nutritional regulation of the glutamine synthetase gene in Ctenopharyngodon idellus.

Glutamine synthetase (GS) is considered a master enzyme that catalyzes ATP-dependent biosynthesis of glutamine from glutamate. In the present study, the GS gene was cloned from the intestine of grass carp (Ctenopharyngodon idellus). The full-length cDNA sequence of GS encodes a 371-amino-acid polypetide. Phylogenetic analysis of the C. idellus GS sequence reveals common carp (Cyprinus carpio) as its closest neighbor. GS mRNA was differentially expressed in different tissues, with high to low gradient expression the intestine, brain, muscle, heart, gill, liver, pituitary gland, and spleen. Additionally, GS exhibited a dynamic pattern of expression during embryonic development, reaching maximal and minimal levels in the organ and hatching stages, respectively, and constant low levels from 7 to 28days post-hatching. We also assessed dietary protein levels and feed sources in diet-regulated fish, and the results suggested that low crude protein (CP) and fish meal stimulate GS gene expression. Furthermore, intestinal GS mRNA expression was significantly increased by 0.2, 0.4, 0.6, 0.8mM concentrations of glutamine dipeptide in vitro. This study provides valuable knowledge about the regulation of GS expression in teleosts.

MONENSIN SENSITIVITY1 (MON1)/CALCIUM CAFFEINE ZINC SENSITIVITY1 (CCZ1)-Mediated Rab7 Activation Regulates Tapetal Programmed Cell Death and Pollen Development.

Programmed cell death (PCD)-triggered degradation of plant tapetum is essential for microspore development and pollen coat formation; however, little is known about the cellular mechanism regulating tapetal PCD Here, we demonstrate that Rab7-mediated vacuolar transport of tapetum degradation-related cysteine proteases is crucial for tapetal PCD and pollen development in Arabidopsis (Arabidopsis thaliana), with the following evidence: (1) The monensin sensitivity1 (mon1) mutants, which are defective in Rab7 activation, showed impaired male fertility due to a combined defect in both tapetum and male gametophyte development. (2) In anthers, MON1 showed preferential high level expression in tapetal cell layers and pollen. (3) The mon1 mutants exhibited delayed tapetum degeneration and tapetal PCD, resulting in abnormal pollen coat formation and decreased male fertility. (4) MON1/CALCIUM CAFFEINE ZINC SENSITIVITY1 (CCZ1)-mediated Rab7 activation was indispensable for vacuolar trafficking of tapetum degradation-related cysteine proteases, supporting that PCD-triggered tapetum degeneration requires Rab7-mediated vacuolar trafficking of these cysteine proteases. (5) MON1 mutations also resulted in defective pollen germination and tube growth. Taken together, tapetal PCD and pollen development require successful MON1/CCZ1-mediated vacuolar transport in Arabidopsis.

Sodium selenate regulates the brain ionome in a transgenic mouse model of Alzheimer's disease.

Many studies have shown that imbalance of mineral metabolism may play an important role in Alzheimer's disease (AD) progression. It was recently reported that selenium could reverse memory deficits in AD mouse model. We carried out multi-time-point ionome analysis to investigate the interactions among 15 elements in the brain by using a triple-transgenic mouse model of AD with/without high-dose sodium selenate supplementation. Except selenium, the majority of significantly changed elements showed a reduced level after 6-month selenate supplementation, especially iron whose levels were completely reversed to normal state at almost all examined time points. We then built the elemental correlation network for each time point. Significant and specific elemental correlations and correlation changes were identified, implying a highly complex and dynamic crosstalk between selenium and other elements during long-term supplementation with selenate. Finally, we measured the activities of two important anti-oxidative selenoenzymes, glutathione peroxidase and thioredoxin reductase, and found that they were remarkably increased in the cerebrum of selenate-treated mice, suggesting that selenoenzyme-mediated protection against oxidative stress might also be involved in the therapeutic effect of selenate in AD. Overall, this study should contribute to our understanding of the mechanism related to the potential use of selenate in AD treatment.

Preclinical evaluation of perifosine as a potential promising anti-rhabdomyosarcoma agent.

Rhabdomyosarcoma (RMS) is a highly malignant and metastatic pediatric cancer that arises from the skeletal muscle. Recent studies have identified an important role of AKT signaling in RMS progression. In the current study, we investigated the activity of perifosine, an oral alkylphospholipid AKT inhibitor, against human RMS cells (RD and Rh-30 lines) both in vivo and in vitro, and studied the underlying mechanisms. We showed that perifosine significantly inhibited RMS cell growth in concentration- and time-dependent manners. Meanwhile, perifosine induced dramatic apoptosis in RMS cells. At the signaling level, perifosine blocked AKT activation, while inducing reactive oxygen species (ROS) production as well as JNK and P38 phosphorylations in RMS cells. Restoring AKT activation by introducing a constitutively active-AKT (CA-AKT) only alleviated (not abolished) perifosine-induced cytotoxicity in RD cells. Yet, the ROS scavenger N-acetyl cysteine (NAC) as well as pharmacological inhibitors against JNK (SP-600125) or P38 (SB-203580) suppressed perifosine-induced cytotoxicity in RMS cells. Thus, perifosine induces growth inhibition and apoptosis in RMS cells through mechanisms more than just blocking AKT. In vivo, oral administration of perifosine significantly inhibited growth of Rh-30 xenografts in severe combined immunodeficient (SCID) mice. Our data indicate that perifosine might be further investigated as a promising anti-RMS agent.

Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis).

BACKGROUND: Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth and development. Until now, little was known about the expression patterns of genes involved in secondary metabolic pathways or their regulatory mechanisms. This study aimed to generate expression profiles for C. sinensis tissues and to build a gene regulation model of the secondary metabolic pathways. RESULTS: RNA sequencing was performed on 13 different tissue samples from various organs and developmental stages of tea plants, including buds and leaves of different ages, stems, flowers, seeds, and roots. A total of 43.7 Gbp of raw sequencing data were generated, from which 347,827 unigenes were assembled and annotated. There were 46,693, 8446, 3814, 10,206, and 4948 unigenes specifically expressed in the buds and leaves, stems, flowers, seeds, and roots, respectively. In total, 1719 unigenes were identified as being involved in the secondary metabolic pathways in C. sinensis, and the expression patterns of the genes involved in flavonoid, caffeine, and theanine biosynthesis were characterized, revealing the dynamic nature of their regulation during plant growth and development. The possible transcription factor regulation network for the biosynthesis of flavonoid, caffeine, and theanine was built, encompassing 339 transcription factors from 35 families, namely bHLH, MYB, and NAC, among others. Remarkably, not only did the data reveal the possible critical check points in the flavonoid, caffeine, and theanine biosynthesis pathways, but also implicated the key transcription factors and related mechanisms in the regulation of secondary metabolite biosynthesis. CONCLUSIONS: Our study generated gene expression profiles for different tissues at different developmental stages in tea plants. The gene network responsible for the regulation of the secondary metabolic pathways was analyzed. Our work elucidated the possible cross talk in gene regulation between the secondary metabolite biosynthetic pathways in C. sinensis. The results increase our understanding of how secondary metabolic pathways are regulated during plant development and growth cycles, and help pave the way for genetic selection and engineering for germplasm improvement.

Oat ß-glucan inhibits lipopolysaccharide-induced nonalcoholic steatohepatitis in mice.

Nonalcoholic steatohepatitis (NASH) is part of the spectrum of nonalcoholic fatty liver disease. However, there are few suitable animal models to study the pathogenesis of NASH or very limited advances in the prevention. Our aims were to establish a mouse model of NASH by intraperitoneally injecting lipopolysaccharide (LPS) at a dose of 1.5 mg per kg body weight per day for 6 weeks and to investigate the potential inhibitory effects of oat ß-glucan (1%, 5%, or 10%) added to a specific pathogen-free diet. Intraperitoneal injection of LPS for 6 weeks increased serum LPS levels; decreased serum glucagon-like peptide-2 levels; triggered abnormal aminotransferase activity, glucose intolerance, and insulin resistance; and increased hepatic proinflammatory cytokines (tumor necrosis factor-α, interleukin-6, interleukin-1ß), triglyceride, and malonyl dialdehyde levels; but reduced hepatic superoxide dismutase activity. Histologic evaluation revealed evidence of hepatic steatosis, inflammation, and mild necrosis in LPS-treated mice. Dietary supplementation of oat ß-glucan prevented most of the LPS-induced metabolic disorders, and improved hepatic steatosis and inflammation, although a dose-dependent effect was not observed. In conclusion, oat ß-glucan could inhibit LPS-induced NASH in mice.

Global transcriptome profiles of Camellia sinensis during cold acclimation.

BACKGROUND: Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold acclimation, we employed RNA-Seq and digital gene expression (DGE) technologies to the study of genome-wide expression profiles during cold acclimation in tea plants. RESULTS: Using the Illumina sequencing platform, we obtained approximately 57.35 million RNA-Seq reads. These reads were assembled into 216,831 transcripts, with an average length of 356 bp and an N50 of 529 bp. In total, 1,770 differentially expressed transcripts were identified, of which 1,168 were up-regulated and 602 down-regulated. These include a group of cold sensor or signal transduction genes, cold-responsive transcription factor genes, plasma membrane stabilization related genes, osmosensing-responsive genes, and detoxification enzyme genes. DGE and quantitative RT-PCR analysis further confirmed the results from RNA-Seq analysis. Pathway analysis indicated that the "carbohydrate metabolism pathway" and the "calcium signaling pathway" might play a vital role in tea plants' responses to cold stress. CONCLUSIONS: Our study presents a global survey of transcriptome profiles of tea plants in response to low, non-freezing temperatures and yields insights into the molecular mechanisms of tea plants during the cold acclimation process. It could also serve as a valuable resource for relevant research on cold-tolerance and help to explore the cold-related genes in improving the understanding of low-temperature tolerance and plant-environment interactions.

Supplementation with oat protein ameliorates exercise-induced fatigue in mice.

Oat protein was purified from oat meal and its effects on swimming performance and related biochemical parameters were investigated. Thirty male Kun-ming mice were divided into the normal control, the oat meal and the oat protein group (n = 10). They were fed with a laboratory food for 30 days, then were subjected to swim to exhaustion. Their swimming endurance and the major metabolic substrates were measured from serum, liver and muscle. The results showed that no significant differences were observed in swimming endurance test between the normal control group and the oat protein group (P > 0.05). Mice in the oat meal group had significantly longer swimming endurance compared to the normal control group (P < 0.05). Furthermore, dietary oat protein increased the levels of liver glycogen, enhanced the activities of lactic dehydrogenase and superoxide dismutase, and decreased the levels of blood urea nitrogen and malondialdehyde in serum. These results suggested that oat protein was effective in improving the physiological condition of the mice.

[Effects of understory removal and nitrogen addition on the soil chemical and biological properties of Pinus sylvestris var. mongolica plantation in Keerqin Sandy Land].

A full factorial experiment was conducted to study the effects of understory removal and nitrogen addition (8 g x m(-2)) on the soil NO(3-)-N and NH(4+)-N concentrations, potential net nitrogen mineralization rate (PNM) and nitrification rate (PNN), microbial biomass C (MBC) and N (MBN), MBC/MBN, urease and acid phosphomonoesterase activities, and Olsen-P concentration in a Pinus sylvestris var. mongolica plantation in Keerqin Sandy Land during a growth season. Understory removal decreased the soil NH(4+)-N concentration, PNM, MBC, and MBN/MBN significantly, increased the soil Olsen-P concentration, but had little effects on the soil NO(3-)-N concentration, PNN, and urease and acid phosphomonoesterase activities. Nitrogen addition increased the soil NO(3-)-N concentration, PNM and PNN significantly, but had little effects on the other test properties. The interaction between understory removal and nitrogen addition had significant effects on the soil NH(4+)-N concentration, but little effects on the soil NO(3-)-N concentration. However, the soil NO(3-)-N concentration in the plots of understory removal with nitrogen addition was increased by 27%, compared with the plots of nitrogen addition alone, which might lead to the leaching of NO3-. It was suggested that understory vegetation could play an important role in affecting the soil chemical and biological properties in Mongolian pine plantations, and hence, the importance of understory vegetation should not be neglected when the forest management and restoration were implemented.

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.

BACKGROUND: With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected assembly outcomes, and there was no consensus on how to approach an optimal solution by selecting software tool and suitable strategy based on the properties of RNA-Seq data. RESULTS: To reveal the performance of different programs for transcriptome assembly, this work analyzed some important factors, including k-mer values, genome complexity, coverage depth, directional reads, etc. Seven program conditions, four single k-mer assemblers (SK: SOAPdenovo, ABySS, Oases and Trinity) and three multiple k-mer methods (MK: SOAPdenovo-MK, trans-ABySS and Oases-MK) were tested. While small and large k-mer values performed better for reconstructing lowly and highly expressed transcripts, respectively, MK strategy worked well for almost all ranges of expression quintiles. Among SK tools, Trinity performed well across various conditions but took the longest running time. Oases consumed the most memory whereas SOAPdenovo required the shortest runtime but worked poorly to reconstruct full-length CDS. ABySS showed some good balance between resource usage and quality of assemblies. CONCLUSIONS: Our work compared the performance of publicly available transcriptome assemblers, and analyzed important factors affecting de novo assembly. Some practical guidelines for transcript reconstruction from short-read RNA-Seq data were proposed. De novo assembly of C. sinensis transcriptome was greatly improved using some optimized methods.