Mitochondrial autophagy is an HIF-1-dependent adaptive metabolic response to hypoxia

Autophagy is a process by which cytoplasmic organelles can be catabolized either to remove defective structures or as a means of providing macromolecules for energy generation under conditions of nutrient starvation. In this study we demonstrate that mitochondrial autophagy is induced by hypoxia, that this process requires the hypoxia-dependent factor-1-dependent expression of BNIP3 and the constitutive expression of Beclin-1 and Atg5, and that in cells subjected to prolonged hypoxia, mitochondrial autophagy is an adaptive metabolic response which is necessary to prevent increased levels of reactive oxygen species and cell death.     

Solution NMR in structural genomics

Structural genomics (also known as structural proteomics) aims to generate accurate three-dimensional models for all folded, globular proteins and domains in the protein universe to understand the relationship between protein sequence, structure and function. NMR spectroscopy of small (<20 kDa) proteins has been used successfully within several large-scale structural genomics projects for more than six years now. Recent advances coming from traditional NMR structural biology laboratories as well as large scale centers and consortia using NMR for structural genomics promise to facilitate NMR analysis making it even a more efficient and increasingly automated procedure.     

基于遗传多样性构建金针菇的核心种质群体及分子身份证

金针菇Flammulina filiformis是我国产量最高的工厂化栽培食用菌。为提高优良工厂化栽培金针菇种质的育种效率,本研究以国内外收集的105份金针菇种质为材料,开展体细胞不亲和评价,并采用SSR分子标记的方法对所有种质进行遗传多样性分析和聚类分析。20对SSR引物在105份种质中共扩增得到209个等位基因位点,所有种质间的遗传相似系数为0.71-1.00,在遗传距离0.76处可分为5个大类群。105份金针菇种质共包含67种不同的遗传背景,野生金针菇种质比栽培种质具有更丰富的遗传多样性。基于SSR的聚类分析结果和体细胞不亲和评价结果既相互印证,又可互为借鉴。本研究构建了包含44份金针菇种质的核心种质群体,占所有供试材料的41.90%,保留了100%等位基因。核心种质群体覆盖区域广泛,最大限度地保留了原始群体的遗传多样性和表型变异,可为育种的亲本选择提供参考。进一步构建了能同时反映每份金针菇种质SSR分子标记指纹图谱、收集地区、子实体颜色和栽培性状的分子身份证编码,并转换成可视二维码,为金针菇种质的高效标识和快速溯源提供了科学依据。     

KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis

Mass spectrometry (MS)‐based quantitative phosphoproteomics has become a key approach for proteome‐wide profiling of phosphorylation in tissues and cells. Traditional experimental design often compares a single treatment with a control, whereas increasingly more experiments are designed to compare multiple treatments with respect to a control. To this end, the development of bioinformatic tools that can integrate multiple treatments and visualise kinases and substrates under combinatorial perturbations is vital for dissecting concordant and/or independent effects of each treatment. Here, we propose a hypothesis driven kinase perturbation analysis (KinasePA) to annotate and visualise kinases and their substrates that are perturbed by various combinatorial effects of treatments in phosphoproteomics experiments. We demonstrate the utility of KinasePA through its application to two large‐scale phosphoproteomics datasets and show its effectiveness in dissecting kinases and substrates within signalling pathways driven by unique combinations of cellular stimuli and inhibitors. We implemented and incorporated KinasePA as part of the “directPA” R package available from the comprehensive R archive network (CRAN). Furthermore, KinasePA also has an interactive web interface that can be readily applied to annotate user provided phosphoproteomics data ( http://kinasepa.pengyiyang.org ).     

Paeoniae Radix,a Chinese herbal extract,inhibit hepatoma cells growth by inducing apoptosis in a p53 independent pathway

Paeoniae Radix (PR) is the root of traditional Chinese Herb named Paeonia lactiflora Pallas, which is commonly used to treat liver diseases in China for centuries. Several earlier studies have indicated that PR has anticancer growth activities, however the mechanism underlying these activities was unclear and remained to be elucidated. In this study, we evaluated the molecular mechanism of the effect of PR on human hepatoma cell lines, HepG2 and Hep3B. Our results showed that the water-extract of Paeoniae Radix (PRE) had inhibitory effect on the growth of both HepG2 and Hep3B cell lines. The induction of internucleosomal DNA fragmentation and chromatin condensation appearance, and accumulation of sub-G1 phase of cell cycle profile in PRE treated hepatoma cells evidenced that the cytotoxicity of PRE to the hepatoma cells is through activation of the cell death program, apoptosis. The activation of apoptosis by PRE is independent of the p53 pathway as Hep3B cell is p53-deficient. In addition, the differential gene expression of PRE treated HepG2 was examined by cDNA microarray technology and RT-PCR analysis. We found that the gene expression of BNIP3 was up-regulated while ZK1, RAD23B, and HSPD1 were down-regulated during early apoptosis of the hepatoma cell mediated by PRE. The elucidation of the drug targets of PR on inhibition of tumor cells growth should enable further development of PR for liver cancer therapy.     

Short-term rescue by RNA injection of a mitotic arrest mutation that affects the preimplantation mouse embryo

The mutation oligosyndactyly results in syndactyly, abnormal fusion and insertion of certain limb muscles, and diabetes insipidus in heterozygous mice. When homozygous the mutation is lethal; beginning at the blastocyst stage, the homozygous cells arrest in metaphase with intact spindles. The mutant phenotype cannot be corrected by forming aggregation chimeras with wild-type cells, suggesting that the mutation results in a cell autonomous lethal condition. Short-term rescue of the homozygous-induced mitotic arrest can be achieved, however, by cytoplasmic injection of polyadenylated RNA obtained from a rapidly dividing embryo-derived stem cell line.     

Epitope insertion into the human hypoxanthine phosphoribosyltransferase protein and detection of the mutant protein by an anti-peptide antibody

The translational stop codon TAA of the human hypoxanthine phosphoribosyltransferase (HPRT) cDNA has been changed to GAA by site-specific mutagenesis. This modification extends the open reading frame to a downstream stop codon and results in the addition of a unique negatively charged hexapeptide to the C terminus of human HPRT protein. The mutated cDNA was transferred into HPRT-deficient rodent cells by retroviral vector infection, and the expressed enzyme was found to be fully active. An antibody against a synthetic octapeptide corresponding to the mutated HPRT C terminus precipitated the HPRT protein specifically from cells infected with the mutant virus and not infected with the wild-type HPRT virus. The technique of inserting a novel epitope into a protein by site-directed mutagenesis should be generally applicable in studies of the regulation of gene expression in vitro and in vivo.     

Ferredoxin-thioredoxin reductase, an iron-sulfur enzyme linking light to enzyme regulation in oxygenic photosynthesis: purification and properties of the enzyme from C3, C4, and cyanobacterial species

Ferredoxin-thioredoxin reductase (FTR), an enzyme involved in the light regulation of chloroplast enzymes, was purified to homogeneity from leaves of spinach (a C3 plant) and corn (a C4 plant) and from cells of a cyanobacterium (Nostoc muscorum). The enzyme is a yellowish brown iron-sulfur protein, containing four nonheme iron and labile sulfide groups, that catalyzes the activation of NADP-malate dehydrogenase and fructose 1,6-bisphosphatase in the presence of ferredoxin and of thioredoxin m and f, respectively. FTR is synonymous with the protein earlier called ferralterin. FTR showed an Mr of about 30,000 (determined by sedimentation equilibrium ultracentrifugation, amino acid composition, gel filtration, and gradient gel electrophoresis) and was composed of two dissimilar subunits (as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis). One of the FTR subunits from each source was similar both in Mr (about 13,000) and immunological properties, while the other subunit (of variable molecular weight) was characteristic of a particular organism. The similar subunit contained a disulfide group that was rapidly reduced by a dithiol (dithiothreitol) but not by monothiols (2-mercaptoethanol or reduced glutathione). Homogeneous FTR formed a tight noncovalent complex with ferredoxin on affinity columns. The basis for the structural variation in the different FTR enzymes remains to be determined.     

Evaluation of growth rate and semi‐refined carrageenan properties of tissue‐cultured Kappaphycus alvarezii (Rhodophyta,Gigartinales)

This study aimed to evaluate and compare the quality of κ‐carrageenan obtained from tissue‐cultured and field‐cultured Kappaphycus alvarezii. Carrageenan properties including yield, viscosity, gel strength and sulfate content were studied. After 60 days of cultivation, tissue‐cultured K. alvarezii showed a higher growth rate (6.3 ± 0.01% day^?1) than field‐cultured seedlings (3.4 ± 0.3% day^?1). The obtained carrageenan yield from tissue‐cultured (67.3 ± 16.4%) was higher than field‐cultured K. alvarezii (51.5 ± 21.0%). Gel viscosity of carrageenans from tissue‐cultured K. alvarezii (1280.0 ± 25.0 cP) was found significantly higher than field‐cultured samples (87.8 ± 20.9 cP). The 1.5% gel solution of tissue‐cultured and field‐cultured K. alvarezii exhibited gel strengths of 703.5 ± 14.1 and 288.3 ± 19.3 g cm^?2, respectively. The average sulfate content of carrageenans was found to be significantly different between tissue‐cultured and field‐cultured K. alvarezii with 34.2 ± 10.9 and 7.5 ± 6.7%, respectively. Tissue culture is recommended to produce high quality seedlings by providing optimized culture conditions to the seaweed. This approach can serve as an alternative way to solve the seedling shortage problems currently faced by the seaweed industry.     

Impact of Metarhizium brunneum (Hypocreales: Clavicipitaceae) on pre-imaginal Rhagoletis indifferens (Diptera: Tephritidae) within and on the surface of orchard soil

When last instar laboratory-reared Rhagoletis indifferens were allowed to pupate within non-sterile orchard soil containing incorporated Metarhizium brunneum isolate F52 conidia, a dose-related proportion died from developmental abnormalities and mycosis. When larvae entered soil superficially treated with M. brunneum, over 80% of the pupae died of developmental abnormalities.