基因芯片数据分析方法研究进展

基因芯片技术的出现改变了生物医学研究的前景,其产生的海量数据是限制其发展的瓶颈问题。为提取其中所隐含的有价值的信息,在基因芯片数据分析的复杂计算工具和方法方面近年来有很多尝试。本文对近5年来基因芯片表达数据的分类分析方法进行综述,既分类比较了以聚类分析为基础的分类方法,也吸收了当前应用数据挖掘、信息融合等系统生物学思路的研究技术,并对数据的分析结果进行评价。     

北极苔原土壤中可培养细菌的分离及其抗菌活性测定

【目的】北极地区具有高纬度、低温、高辐射等独特的环境条件。北冰洋及周围大面积的陆地区域鲜有人类踪迹,其中微生物数量不可低估。本研究旨在了解北极土壤中的可培养微生物的多样性及其抗菌活性。【方法】对来源于北极黄河站附近的7份不同植物根下苔原土壤进行直接涂布和富集培养后涂布。【结果】共获得细菌菌株721株,对其中608株进行细菌16S rRNA基因序列测定,归属于86个属,229个种,主要分布于变形菌门(Proteobacteria,54.3%)、放线菌门(Actinobacteria,21.2%)、拟杆菌门(Bacteroidetes,12.8%)、厚壁菌门(Firmicutes,10.0%)和奇异球菌门(Deinococcus-Thermus,1.6%)。其中从16S rRNA基因序列同源性推测有22株细菌菌株为潜在新种/属。从分离菌株中筛选出16株可抑制金黄色葡萄球菌(Staphylococcusaureus)或鲍氏不动杆菌(Acinetobacterbaumannii)生长的拮抗菌。【结论】获得了北极土壤地区特有的微生物菌株资源,为进一步筛选拮抗菌的活性物质提供了菌株基础。     

单克隆人胰腺干细胞分化特性的研究

研究1例来源于4月龄男性流产胎儿胰腺组织的单克隆人胰腺干细胞（monoclonal human pancreatic stem cell,mhPSC）系的体内外分化特性。将mhPSCs接种在铺有0．1％明胶的培养皿内,扩增培养3d后,加高糖DMEM诱导液诱导培养25d。相差显微镜下．观察细胞生长状况。采用双硫腙染色法、RT—PCR及葡萄糖刺激释放胰岛素和C肽实验．对体外定向诱导mhPSCs分化为功能性胰岛进行检测。将mhPSCs悬液注射在成年雄性裸鼠腹股沟皮下．注射30d时,取出移植物,采用SP法进行免疫组织化学反应,以检测mhPSCs的体内自然分化潜能。体外扩增培养,mhPSCs贴壁生长,呈多角形上皮样。生长至单层．呈“铺路石”状。体外定向诱导,细胞逐渐由多角形变成圆形,并聚集成类胰岛。诱导培养15d时．形成的类胰岛中少数细胞分化为B细胞,双硫腙染色阳性。诱导培养25d时,多数细胞分化为8细胞,双硫腙染色阳性,转录表达胰岛素的mRNA。用不同浓度葡萄糖刺激．诱导胰岛不仅释放胰岛素和C肽,而且其释放量随糖刺激浓度升高显著增加（0．01〈P〈0．05）。体内分化实验显示,mhPSCs在裸鼠背部形成类畸胎瘤。类畸胎瘤易与裸鼠分离,色白,血管丰富。显著表达pdx1、胰岛素、胰高血糖素、CK、MBP及NF蛋白。该研究结果证实单克隆人胰腺干细胞系体外定向诱导分化为包含大量β细胞的功能性类胰岛,在体内自然分化为胰岛、上皮及神经组织细胞。     

The importance of being kinked: role of Pro residues in the selectivity of the helical antimicrobial peptide P5

Antimicrobial peptides (AMPs) are promising compounds for developing new antibiotic drugs against drug‐resistant bacteria. Many of them kill bacteria by perturbing their membranes but exhibit no significant toxicity towards eukaryotic cells. The identification of the features responsible for this selectivity is essential for their pharmacological development. AMPs exhibit few conserved features, but a statistical analysis of an AMP sequence database indicated that many α‐helical AMPs surprisingly have a helix‐breaking Pro residue in the middle of their sequence. To discriminate among the different possible hypotheses for the functional role of this feature, we designed an analogue of the antimicrobial peptide P5, in which the central Pro was deleted (analogue P5Del). Pro removal resulted in a dramatic increase of toxicity. This was explained by the observation that P5Del binds both charged and neutral membranes, whereas P5 has no appreciable affinity towards neutral bilayers. CD and simulative data provided a rationalization of this behavior. In solution P5, due to the presence of Pro, attains compact conformations, in which its apolar residues are partially shielded from the solvent, whereas P5Del is more helical. These structural differences reduce the hydrophobic driving force for association of P5 to neutral membranes, whereas its binding to anionic bilayers can still take place because of electrostatic attraction. After membrane binding, the Pro residue does not preclude the attainment of a membrane‐active amphiphilic helical conformation. These findings shed light on the role of Pro residues in the selectivity of AMPs and provide hints for the design of new, highly selective compounds. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Activation characteristics of transient receptor potential ankyrin 1 and its role in nociception

Transient receptor potential (TRP) ankyrin 1 (TRPA1) is a Ca(2+)-permeant, nonselective cationic channel. It is predominantly expressed in the C afferent sensory nerve fibers of trigeminal and dorsal root ganglion neurons and is highly coexpressed with the nociceptive ion channel transient receptor potential vanilloid 1 (TRPV1). Several physical and chemical stimuli have been shown to activate the channel. In this study, we have used electrophysiological techniques and behavioral models to characterize the properties of TRPA1. Whole cell TRPA1 currents induced by brief application of lower concentrations of N-methyl maleimide (NMM) or allyl isothiocyanate (AITC) can be reversed readily by washout, whereas continuous application of higher concentrations of NMM or AITC completely desensitized the currents. The deactivation and desensitization kinetics differed between NMM and AITC. TRPA1 current amplitude increased with repeated application of lower concentrations of AITC, whereas saturating concentrations of AITC induced tachyphylaxis, which was more pronounced in the presence of extracellular Ca(2+). The outward rectification exhibited by native TRPA1-mediated whole cell and single-channel currents was minimal as compared with other TRP channels. TRPA1 currents were negatively modulated by protons and polyamines, both of which activate the heat-sensitive channel, TRPV1. Interestingly, neither protein kinase C nor protein kinase A activation sensitized AITC-induced currents, but each profoundly sensitized capsaicin-induced currents. Current-clamp experiments revealed that AITC produced a slow and sustained depolarization as compared with capsaicin. TRPA1 is also expressed at the central terminals of nociceptors at the caudal spinal trigeminal nucleus. Activation of TRPA1 in this area increases the frequency and amplitude of miniature excitatory or inhibitory postsynaptic currents. In behavioral studies, intraplantar and intrathecal administration of AITC induced more pronounced and prolonged changes in nociceptive behavior than those induced by capsaicin. In conclusion, the characteristics of TRPA1 we have delineated suggest that it might play a unique role in nociception.     

Palaeoctopus pelagicus from the Turonian of Mexico reinterpreted as a coelacanth (Sarcopterygian) gular plate

Abstract: The supposed vestige of a cephalopod gladius from Turonian platy limestones at Vallecillo, north‐east Mexico, named Palaeoctopus pelagicus by Fuchs et al. in 2008, is reinterpreted and shown to be a gular plate of a coelacanth fish, possibly of the genus Megacoelacanthus. In addition to the gular plate, two extrascapulars and fin rays of all fins are preserved on one slab and its counterpart. This is the first record of a coelacanth from these lower Turonian strata at Vallecillo, which are rich in fish.     

Food‐web structure and mercury dynamics in a large subarctic lake following multiple species introductions

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Identification and characterization of a novel salt‐tolerant esterase from a Tibetan glacier metagenomic library

A salt‐tolerant esterase, designated H9Est, was identified from a metagenomic library of the Karuola glacier. H9Est gene comprised 1071 bp and encoded a polypeptide of 357 amino acids with a molecular mass of 40 kDa. Sequence analysis revealed that H9Est belonged to the family IV of bacterial lypolitic enzyme. H9Est was overexpressed in Escherichia coli and the purified enzyme showed hydrolytic activity towards p‐nitrophenyl esters with carbon chain from 2 to 8. The optimal esterase activity was at 40°C and pH 8.0 and the enzyme retained its activity towards some miscible organic solvents such as polyethylene glycol. A three‐dimensional model of H9Est revealed that S200, D294, and H324 formed the H9Est catalytic triad. Circular Dichroism spectra and molecular dynamic simulation indicated that the esterase had a wide denaturation temperature range and flexible loops that would be beneficial for H9Est performance at low temperatures while retaining heat‐resistant features. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:890–899, 2015     

纤维素降解菌L-06的筛选、鉴定及其产酶条件的分析

从用于堆肥的水稻秸秆中初筛出一株高效纤维素降解菌L-06, 根据18S rRNA基因序列和菌株形态分析, 初步鉴定该菌为斜卧青霉(Penicillium decumbens)。研究了液体发酵培养基中氮源、碳源、表面活性剂、培养温度、起始pH以及接种量对该菌株各纤维素酶活力的影响。在最适条件下, 该菌的b-葡萄糖苷酶(BGL)、外切纤维素酶(CBH)于培养第3天酶活力分别达到1662 u/mL和2770 u/mL; 内切纤维素酶(EG)、滤纸糖化力(FPase)于培养第4天酶活力分别达到18064 u/mL和4035 u/mL。在产酶优化实验中, 该菌的EG和CBH在pH10的培养条件下分别保持了70%和43%的酶活性; 在50oC培养条件下EG和CBH分别保持了68%和59%的酶活性。表现出了耐热, 耐碱的特性。