Identification and Characterization of a Novel Prokaryotic Peptide: N-GLYCOSIDASE FROM ELIZABETHKINGIA MENINGOSEPTICA*

Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. Since its discovery in 1984, PNGase F has remained as the sole prokaryotic PNGase. Recently, a novel gene encoding a protein with a predicted PNGase domain was identified from a clinical isolate of Elizabethkingia meningoseptica. In this study, the candidate protein was expressed in vitro and was subjected to biochemical and structural analyses. The results revealed that it possesses PNGase activity and has substrate specificity different from that of PNGase F. The crystal structure of the protein was determined at 1.9 Å resolution. Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. These structural and functional analyses indicated that the candidate protein is a novel prokaryotic N-glycosidase. The protein has been named PNGase F-II.     

经直肠前列腺穿刺活检术后败血症的相关因素分析

目的:虽然前列腺穿刺活检术前预防及术后治疗都有了很大的创新,但术后的并发症仍可能发生,本文通过对前列腺穿刺术后感染性并发症的前瞻性检测,对其致病菌进行描述,探讨经直肠前列腺穿刺活检术后败血症的发生率、致病菌、发病相关因素,为临床上败血症的治疗和预防提供理论依据。方法:对2008年1月-2012年11月在兰州军区总医院经直肠前列腺穿刺活检术后238例患者中6例尿路败血症患者进行回顾性分析及术后随访。结果:经直肠前列腺穿刺活检术后并发败血症占2.52%(6/238),8例败血症患者中感染性休克患者3例。血培养阳性6例,5例为大肠埃希菌,1例为耐甲氧西林金葡菌。结论:经直肠前列腺穿刺是简单有效的活检方式,但仍有发生败血症的可能,致病菌多为大肠埃希菌。术前适当准备及术后合理预防可减少并发症的发生。如患者前列腺穿刺活检术后48 h内出现败血症的症状,则应立即入院给予碳青霉烯类治疗。多重耐药大肠埃希菌感染要引起足够重视,早期的直肠及尿液耐药大肠埃希菌检查可有助于败血症的早期预防。     

中华真地鳖若虫肠道细菌的研究

中华真地鳖是一种传统中药资源昆虫,从人工饲养种群的正常取食及蜕皮若虫肠道环境中分离、纯化,好氧和厌氧培养获得11个细菌菌株,对其形态、染色反应、培养性状和生理生化反应进行了系统研究。鉴定结果表明,上述11个细菌菌株依次分别属于:不动杆菌属(Acinetobacter)、柠檬酸杆菌属(Citobacter)、沙门菌属(Sal-monella)、芽胞乳酸杆菌属(Sporolacillus)、节杆菌属(Arthrobacter)、肠杆菌属(Enterobacter)、地杆菌属(Terrabacter)、放线杆菌属(Actinobacillus)、克雷伯菌属(Klebsiella)、沙雷菌属(Serratia)、预研菌属(Yokenella)。中华真地鳖正常取食和蜕皮若虫肠道环境细菌种类不同。分离未获得真菌和放线菌。     

慢性肾盂肾炎L型细菌感染及耐药分析

目的了解L型细菌在慢性肾盂肾炎的感染及耐药状况。方法对71例患者清洁中段尿做普通细菌培养(B型)、L型细菌培养(L型)及耐药分析。结果细菌阳性率为77.5%,其中单独L型阳性率为49.3%、B型与L型混合感染为15.5%,而B型阳性率仅为12.7%。主要是大肠埃希菌,其次是葡萄球菌;青霉素及头孢噻肟均有较高的耐药率(88.9%及73.6%)。结论L型细菌在慢性肾盂肾炎感染中占主导,β-内酰胺类药物有较高的耐药性,临床治疗应据药敏结果合理选择及时调整抗生素。     

Benzene oxidation under sulfate-reducing conditions in columns simulating in situ conditions

The oxidation of benzene under sulfate-reducing conditions was examined in column and batch experiments under close to in situ conditions. Mass balances and degradation rates for benzene oxidation were determined in four sand and four lava granules filled columns percolated with groundwater from an anoxic benzene-contaminated aquifer. The stoichiometry of oxidized benzene, produced hydrogen carbonate and reduced sulfate correlated well with the theoretical equation for mineralization of benzene with sulfate as electron acceptor. Mean retention times of water in four columns were determined using radon (²²²Rn) as tracer. The retention times were used to calculate average benzene oxidation rates of 8–36 μM benzene day⁻¹. Benzene-degrading, sulfide-producing microcosms were successfully established from sand material of all sand filled columns, strongly indicating that the columns were colonized by anoxic benzene-degrading microorganisms. In general, these data indicate a high potential for Natural Attenuation of benzene under sulfate-reducing conditions at the field site Zeitz. In spite of this existing potential to degrade benzene with sulfate as electron acceptor, the benzene plume at the field site is much longer than expected if benzene would be degraded at the rates observed in the column experiment, indicating that benzene oxidation under sulfate-reducing conditions is limited in situ.     

Activity of bacteria in water of hot springs from Southern and Central Kamchatskaya geothermal provinces, Kamchatka Peninsula, Russia

The hot-spring waters of numerous hot springs at the Kamchatka Peninsula, Russia differ in their chemical characteristics and elemental composition. Total bacterial abundance (TBA) as well as enzymatically active and respiring bacteria was enumerated in water samples collected from the Nalychevskie, Oksinskie, Apapelskie, and Dachnye hot springs. 5-Carboxyfluorescein diacetate activity was detected in all water samples and comprised 29-65% of the TBA as determined by 4',6-diamidino-2-phenylindol staining. The respiratory activity of iron-oxidizing bacteria was assayed by 5-cyano-2,3-ditolyltetrazolium chloride reduction. Respiring cells accounted for 9-14% of the TBA, indicating a positive correlation with the number of iron-oxidizing bacteria from the hot-spring biomats. Enumeration of heterotrophic bacteria revealed a high-density bacterial population only in the water of the Apapelskie hot spring, which has a temperature of 36 degrees C. Therefore, it appears that heterotrophic and iron-oxidizing bacteria inhabiting the hot-spring waters are essential for the geochemical processes occurring in hydrothermal systems.     

Phylotype diversity of deep-sea hydrothermal vent prokaryotes trapped by 0.2- and 0.1-μm-pore-size filters

Eleven 16S rRNA gene clone libraries including 34 archaeal and 72 bacterial phylotypes were constructed from total 708 clones of hydrothermal vent prokaryotes trapped by 0.2- and 0.1-μm-pore-size filters. Crenarchaeota and Proteobacteria phylotypes dominated the archaeal and bacterial populations, respectively. Novel unaffiliated phylotypes occurred only in the 0.1-μm-trapped populations.     

中国南海沉积环境可培养细菌多样性研究

【目的】探索海洋沉积环境中可培养细菌的多样性。【方法】采用纯培养分离及16S rRNA基因序列鉴定的方法,对我国南海海域20个沉积物样品进行细菌多样性分析。【结果】共获得200株细菌,分属于47个属,99个种。经系统进化分析,可培养菌株主要分布于4个类群:厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和拟杆菌门(Bacteroidetes),优势类群为Firmicutes,其中芽孢杆菌属(Bacillus)所占比例为55.6%;而Actinobacteria和Bacteroidetes两个类群获得菌株较少;在Firmicutes和Actinobacteria两个类群中发现8个潜在新种和3个潜在新属级类群。【结论】初步研究结果表明,南海海洋沉积环境可培养微生物资源丰富,新物种资源多样;其中,芽孢杆菌为海洋沉积环境中的优势类群,随着样品深度的增加,细菌多样性呈现递减的趋势,深度可能是影响细菌多样性的一个重要因素;其次,分离培养基和分离方法直接关系到样品中可培养微生物多样性的发现,有待深入研究。     

Lateral genomics

More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.