Biased gene expression reveals the contribution of subgenome to altitude adaptation in allopolyploid Isoetes sinensis.

Allopolyploids are believed to inherit the genetic characteristics of its progenitors and exhibit stronger adaptability and vigor. The allotetraploid Isoetes sinensis was formed by the natural hybridization and polyploidization of two diploid progenitors, Isoetes taiwanensis and Isoetes yunguiensis, and was believed to have the potential to adapt to plateau environments. To explore the expression pattern of homoeologous genes and their contributions to altitude adaptation, we transplanted natural allotetraploid I. sinensis (TnTnYnYn) along the altitude gradient for a long-term, and harvested them in summer and winter, respectively. One year after transplanting, it still lived well, even in the extreme environment of the Qinghai-Tibet Plateau. Then, we performed high-throughput RNA sequencing to measure their gene expression level. A total of 7801 homoeologous genes were expressed, among which 5786 were identified as shared expression in different altitudes and seasons. We further found that altitude variations could change the subgenome bias trend of I. sinensis, but season could not. Moreover, the functions of uniquely expressed genes indicated that temperature might be an important restrictive factor during the adaptation process. Through the analysis of DEGs and uniquely expressed genes, we found that Y subgenome provided more contributions to high altitude adaptation than T subgenome. These adaptive traits to high altitude may be inherited from its plateau progenitor I. yunguiensis. Through weighted gene co-expression network analysis, pentatricopeptide repeats gene family and glycerophospholipid metabolism pathway were considered to play important roles in high-altitude adaptation. Totally, this study will enrich our understanding of allopolyploid in environmental adaptation.

An in vivo anti-tumor effect of eckol from marine brown algae by improving the immune response.

The anti-cancer activities of brown algae and some active extracts or components from brown algae have been demonstrated. But the anti-tumor activities of eckol, a new natural phlorotannin derived from marine brown algae, are poorly understood. In order to investigate the in vivo anti-tumor effect and its potential mechanisms of eckol in a sarcoma 180 (S180) xenograft-bearing animal model, S180 xenograft-bearing mice were randomly divided into 4 groups: model control, and eckol low-dose (0.25 mg kg-1), middle-dose (0.5 mg kg-1) and high-dose (1.0 mg kg-1) groups. After eckol administration, the tumor inhibition, tumor tissue histology, thymus index and spleen index were measured. The apoptotic tumor cells were detected using the terminal deoxynucleotidyl transferase mediated dUTP nick end labelling (TUNEL) assay. The protein expression levels of cleaved Caspase-3 and Caspase-9 (two key apoptotic proteins), Bcl-2 and Bax (two key anti-apoptosis-related genes), as well as epidermal growth factor receptor (EGFR, a well-known cell proliferation-stimulating molecule in tumorigenesis) and p-EGFR in tumor tissues were determined by western blot. A carbon particle clearance test, measurement of serum cytokine levels, a splenic T lymphocyte proliferation test, and T lymphocyte subpopulation analysis were used to evaluate the effect of eckol on the immune function of tumor-bearing mice. Moreover, CD11c+-dendritic cell (DC) infiltration in tumor tissues was detected by immunohistochemistry, and the surface molecules on bone marrow-derived DCs were analyzed using flow cytometry. The pro-apoptosis and anti-proliferation activities of eckol were manifested by the increased TUNEL-positive apoptotic cells, the upregulated Caspase-3 and Caspase-9 expression, and the downregulated expression of Bcl-2, Bax, EGFR and p-EGFR in eckol-treated transplanted S180 tumors. Most importantly, eckol stimulated the mononuclear phagocytic system, recruited and activated DCs, promoted the tumor-specific Th1 responses, increased the CD4+/CD8+ T lymphocyte ratio, and enhanced cytotoxic T lymphocyte responses in the eckol-treated animals, suggesting its potent stimulatory property on innate and adaptive immune responses. This study suggested that eckol might act as a functional food constituent derived from marine brown algae with a potential in vivo anti-tumor effect achieved by improving the immune response.

Anti-inflammatory effect of external use of escin on cutaneous inflammation: possible involvement of glucocorticoids receptor.

Escin, as an internally applied anti-inflammatory agent, has been widely used in the treatment of inflammation and edema resulting from trauma or operation in the clinic. However, the effect of its external use on cutaneous inflammation and edema remains unexplored. In the present study, the anti-inflammatory and anti-edematous effects of external use of escin were studied in carrageenan-induced paw edema and histamine-induced capillary permeability in rats, paraxylene-induced ear swelling in mice, and cotton pellet-induced granuloma in rats. Effects of external use of escin gel on prostaglandin E2 (PGE2), tumor necrosis factor-α (TNF-α), and interleukin-1ß (IL-1ß) were determined by ELISA. The anti-inflammatory mechanism was explored by detecting the expression of glucocorticoid receptor (GR) with Western blotting and Real-time PCR analyses, with further exploration of nuclear factor-κB (NF-κB), p38 mitogen-activated protein kinase (P38MAPK) and activator protein-1 (AP-1) expressions. We demonstrated that external use of escin showed significant anti-inflammatory effects on acute and chronic inflammation in different animal models and its anti-inflammatory effects might be related to down-regulation of PGE2, TNF-α, and IL-1ß. The results also showed that escin exerted its anti-inflammatory effects by promoting the expression of GR, with the possible mechanism being inhibition of the expressions of GR-related signaling molecules such as NF-κB and AP-1.

Targeted eco-pharmacovigilance for ketoprofen in the environment: Need, strategy and challenge.

Implementing "targeted" eco-pharmacovigilance(EPV) which focuses on individual or specific pharmaceuticals on a prioritised basis is a feasible, economical and customized approach to reduce the environmental concentrations and risks of pharmaceuticals. Non-steroidal anti-inflammatory drugs(NSAIDs) remaining in environment are a kind of priority hazard substances, due to a notable case that diclofenac residues caused the loss of more than 99% of vultures across the Indian sub-continent. Ketoprofen, as another widely used NSAID with comparable or even higher global consumption than diclofenac, in the environment has been shown to present a potential risk to non-target terrestrial and aquatic species. Based on the review of 85 articles reporting the analyses of ketoprofen residues in environment since 2010, we found that this NSAID frequently present in various environmental compartments around the world. Therefore, it is urgent to implement EPV targeting ketoprofen pollution. Here, we provide some recommendations for implementing the targeted EPV for ketoprofen, including: Closely monitoring ketoprofen in the natural environment; Reducing the residues of ketoprofen through source control; Encouraging urine source separation and treatment; Limiting the application of veterinary ketoprofen; Designing and constituting a framework system of targeted EPV. But some challenges, such as ambiguity in the accountability of the main bodies responsible for continued monitoring of ketoprofen residues, the lack of optimized urine source separation scenarios and procedure, the need for detailed design and application schemes of the framework system of targeted EPV, etc. should be addressed.

Relationship between hepatitis B virus infection and chronic kidney disease in Asian populations: a meta-analysis.

PURPOSE: To evaluate the association of Chronic hepatitis B virus (HBV) infection and chronic kidney disease (CKD). METHODS: We searched Embase, Grateful Med, Ovid, PubMed, and the China Biological Medicine Database. A meta-analysis was performed to assess whether HBV infection plays an independent impact on the development of CKD in the general population. Relative risks of CKD (defined as reduced glomerular filtration rate or proteinuria) according to HBsAg serologic status were studied. RESULTS: Six eligible clinical studies (189,709 individuals in total) were included in the analysis. There was no association between HBsAg seropositive status and prevalence of CKD, the summary estimate for adjusted relative risk (RR) was 1.16 (95% confidence interval (CI), 0.78, 1.71; p = .46) according to the random-effects model, and between studies heterogeneity was noted (p values by Q test <0.001). Also, there were no significant associations between positive HBV serologic status and low eGFR (adjusted relative risk, 0.95; 95% CI, 0.72, 1.26; p = .72) or proteinuria (adjusted relative risk, 1.00; 95% CI, 0.83, 1.20; p = .99). CONCLUSIONS: This meta-analysis shows that there was no association between exposure to HBV and the risk of developing CKD in Asian populations.

The role of myocardin-related transcription factor-A in Aß25-35 induced neuron apoptosis and synapse injury.

Myocardin-related transcription factor-A (MRTF-A) highly expressed in brain has been demonstrated to promote neuronal survival via regulating the transcription of related target genes as a powerful co-activator of serum response factor (SRF). However, the role of MRTF-A in Alzheimer's disease (AD) is still unclear. Here, we showed that MRTF-A was significantly downregulated in cortex of the Aß25-35-induced AD rats, which played a key role in Aß25-35 induced cerebral neuronal degeneration in vitro. Bilateral intracerebroventricular injection of Aß25-35 caused significantly MRTF-A expression decline in cortex of rats, along with significant neuron apoptosis and plasticity damage. In vitro, transfection of MRTF-A into primary cultured cortical neurons prevented Aß25-35 induced neuronal apoptosis and synapses injury. And luciferase reporter assay determined that MRTF-A could bind to and enhance the transactivity of the Mcl-1 (Myeloid cell leukemia-1) and Arc (activity-regulated cytoskeletal-associated protein) promoters by activating the key CArG box element. These data demonstrated that the decreasing of endogenous MRTF-A expression might contribute to the development of AD, whereas the upregulation MRTF-A in neurons could effectively reduce Aß25-35 induced synapse injury and cell apoptosis. And the underlying mechanism might be partially due to MRTF-A-mediated the transcription and expression of Mcl-1 and Arc by triggering the CArG box.

BOAT: Basic Oligonucleotide Alignment Tool.

BACKGROUND: Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together. RESULTS: We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control. CONCLUSION: Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at http://boat.cbi.pku.edu.cn under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies.

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of transcripts are generated by large-scale cDNA and EST sequencing projects every year, there is a need for automatic methods to distinguish protein-coding RNAs from noncoding RNAs accurately and quickly. We developed a support vector machine-based classifier, named Coding Potential Calculator (CPC), to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features. Tenfold cross-validation on the training dataset and further testing on several large datasets showed that CPC can discriminate coding from noncoding transcripts with high accuracy. Furthermore, CPC also runs an order-of-magnitude faster than a previous state-of-the-art tool and has higher accuracy. We developed a user-friendly web-based interface of CPC at http://cpc.cbi.pku.edu.cn. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation.

Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).

MOTIVATION: The rapid accumulation of single amino acid polymorphisms (SAPs), also known as non-synonymous single nucleotide polymorphisms (nsSNPs), brings the opportunities and needs to understand and predict their disease association. Currently published attributes are limited, the detailed mechanisms governing the disease association of a SAP remain unclear and thus, further investigation of new attributes and improvement of the prediction are desired. RESULTS: A SAP dataset was compiled from the Swiss-Prot variant pages. We extracted and demonstrated the effectiveness of several new biologically informative attributes including the structural neighbor profiles that describe the SAP's microenvironment, nearby functional sites that measure the structure-based and sequence-based distances between the SAP site and its nearby functional sites, aggregation properties that measure the likelihood of protein aggregation and disordered regions that consider whether the SAP is located in structurally disordered regions. The new attributes provided insights into the mechanisms of the disease association of SAPs. We built a support vector machines (SVMs) classifier employing a carefully selected set of new and previously published attributes. Through a strict protein-level 5-fold cross-validation, we attained an overall accuracy of 82.61%, and an MCC of 0.60. Moreover, a web server was developed to provide a user-friendly interface for biologists. AVAILABILITY: The web server is available at http://sapred.cbi.pku.edu.cn/