Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.     

Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair

Background

The Beijing family is a successful group of M. tuberculosis strains, often associated with drug resistance and widely distributed throughout the world. Polymorphic genetic markers have been used to type particular M. tuberculosis strains. We recently identified a group of polymorphic DNA repair replication and recombination (3R) genes. It was shown that evolution of M. tuberculosis complex strains can be studied using 3R SNPs and a high-resolution tool for strain discrimination was developed. Here we investigated the genetic diversity and propose a phylogeny for Beijing strains by analyzing polymorphisms in 3R genes.

Methodology/Principal Findings

A group of 3R genes was sequenced in a collection of Beijing strains from different geographic origins. Sequence analysis and comparison with the ones of non-Beijing strains identified several SNPs. These SNPs were used to type a larger collection of Beijing strains and allowed identification of 26 different sequence types for which a phylogeny was constructed. Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by other genetic markers, such as Large Sequence Polymorphisms (LSPs). A recent Beijing genotype (Bmyc10), which included 60% of strains from distinct parts of the world, appeared to be predominant.

Conclusions/Significance

We found SNPs in 3R genes associated with the Beijing family, which enabled discrimination of different groups and the proposal of a phylogeny. The Beijing family can be divided into different groups characterized by particular genetic polymorphisms that may reflect pathogenic features. These SNPs are new, potential genetic markers that may contribute to better understand the success of the Beijing family.     

Abnormal brain default-mode network functional connectivity in drug addicts

Background

The default mode network (DMN) is a set of brain regions that exhibit synchronized low frequency oscillations at resting-state, and is believed to be relevant to attention and self-monitoring. As the anterior cingulate cortex and hippocampus are impaired in drug addiction and meanwhile are parts of the DMN, the present study examined addiction-related alteration of functional connectivity of the DMN.

Methodology

Resting-state functional magnetic resonance imaging data of chronic heroin users (14 males, age: 30.1±5.3 years, range from 22 to 39 years) and non-addicted controls (13 males, age: 29.8±7.2 years, range from 20 to 39 years) were investigated with independent component analysis to address their functional connectivity of the DMN.

Principal Findings

Compared with controls, heroin users showed increased functional connectivity in right hippocampus and decreased functional connectivity in right dorsal anterior cingulate cortex and left caudate in the DMN.

Conclusions

These findings suggest drug addicts'' abnormal functional organization of the DMN, and are discussed as addiction-related abnormally increased memory processing but diminished cognitive control related to attention and self-monitoring, which may underlie the hypersensitivity toward drug related cues but weakened strength of cognitive control in the state of addiction.     

免疫预防阻断乙型肝炎病毒母婴传播效果的观察

阻断乙型肝炎病毒(HBV)母婴传播是控制乙型肝炎的重大问题。为探讨免疫预防对阻断HBV母婴传播的效果及影响因素,对667例HBV表面抗原(HBsAg)阳性孕妇及其婴儿进行研究。这些孕妇按HBVe抗原(HBeAg)和HBVDNA检测结果,分为HBeAg阳性组及阴性组、DNA阳性组及阴性组;按是否于孕晚期注射乙型肝炎免疫球蛋白(HBIG),分为注射组及未注射组。婴儿于出生24h内均肌内注射HBIG100IU,并按0、1、6方案注射10μg重组酵母HBV疫苗;8～12月龄后随访婴儿,并进行HBV标志物(HBV-M)检测。667个婴儿中,20例感染HBV,免疫阻断失败率为3.0%。孕妇HBeAg阳性组免疫阻断失败率为8.7%,阴性组为0.2%,两组差异显著(P<0.001);两组婴儿对疫苗免疫应答率分别为83.0%和83.1%,无显著差异(P=0.988)。孕妇DNA阳性组免疫阻断失败率为8.1%,HBVDNA均≥6log10copies/ml。孕期注射与未注射HBIG组婴儿免疫阻断失败率分别为3.7%和2.7%,无显著差异(P=0.479);两组婴儿对疫苗免疫应答率分别为84.4%和82.4%,无显著差异(P=0.519)。孕妇HBeAg阳性注射HBIG组与未注射组的免疫阻断失败率分别为8.4%和8.9%,无显著差异(P=0.892)。孕妇HBeAg阴性注射与未注射HBIG组的免疫阻断失败率分别为0.0%和0.3%,也无显著差异(P=0.538)。11例免疫阻断失败的婴儿中,10例出生时血清HBsAg已为阳性;8～12个月后随访,HBsAg仍持续阳性,提示为宫内感染。本研究证实,孕期注射HBIG未能提高婴儿对HBV疫苗加HBIG的免疫阻断效果。宫内感染可能是疫苗加HBIG免疫阻断失败的主要原因。采用降低孕妇血清HBVDNA的措施,如对孕妇进行抗HBV治疗,也许能降低HBV宫内感染率。     

间歇性充气加压疗法对下肢深静脉血栓患者血液流变学的影响

目的:观察间歇性充气加压疗法(intermittent pneumatic compression,IPC)对下肢深静脉血栓形成(deep vein thrombosis of lower limbs,DVT)患者的治疗效果,并从血液流变学方面探讨间歇性充气加压的作用机理.方法:2003年3月-2010年9月我科收治的243例下肢深静脉血栓患者,将其中42例IPC治疗病例定为B组实验组,145例单纯药物治疗病例中选取60例定为A组对照组.观察两组患者血液流变学指标和小腿肿胀消退情况的对比.结果:两组患者全血粘度、红细胞聚集指数、红细胞电泳时间、红细胞变形性,在治疗第1天较入院时无差异,组间无差异(P＞0.05),第3天较入院时有差异(P＜0.05),组间第3天有差异(P＜0.05),两组患者下肢肿胀度均明显消退,但B组肿胀消退速度明显快于对照组(P＜0.05).结论:间歇性充气加压治疗仪可有效改变血液流变学状态,改善血液高凝状态,有效缓解肢体肿胀症状,缩短住院时间.且不增加治疗难度,使用简单,治疗依从性好.     

利用市政污水培养Chlorella vulgaris生产生物柴油

为了考察利用南昌市政污水规模化培养富油微藻生产生物柴油,同时达到净化污水的目的,取南昌市青山湖污水处理厂未经任何处理的市政污水作为普通小球藻(Chlorella vulgaris)生长的培养液。监测了C.vulgaris在市政污水中连续培养10 d的特定生长率、生物质产量以及与之相关的市政污水中氨氮(NH4+-N)、总磷(TP)、化学需氧量(COD)、总悬浮固体(TSS)和挥发性悬浮固体(VSS)的清除情况。实验表明:营养物质的水平显著地影响了C.vulgaris的生长。C.vulgaris的生长率在培养8 d后达到最大,OD680为2.856,总的生物质产量日均最大积累速率为0.01 g/L,油脂含量为干质量的18%,油脂的平均日产量为0.001 g/L。培养10 d内NH4+-N、TP和COD的去除率分别为50.0%、32.1%和26.0%,TSS和VSS的日平均去除速率分别为0.01 g/L和0.006 1 g/L。     

红光促进难治性创面愈合的研究

目的:探讨红光照射对难治性创面的创缘组织中血管内皮细胞生长因子(vascular endothelial growth factor,VEGF)的表达及治疗难治性创面的临床效果。方法:收集2008年6月-2010年12月因难治性创面入住笔者单位治疗的40例患者,按治疗方法分为红光照射治疗组20例和常规治疗组20例。常规治疗组患者创面以0.5%碘伏与水胶体敷料换药。治疗组在常规治疗的基础上加用红光照射。于治疗后第7天、14天、21天切取创缘组织,研究红光照射对创缘组织中VEGF的影响,并比较两组患者的创面愈合率和愈合时间。结果:临床实验中,治疗组创缘组织中的VEGF含量明显高于对照组(P<0.01);治疗组创面愈合率明显高于对照组(P<0.01);治疗组的愈合时间低于对照组(P<0.05)。结论:红光照射能显著提高创缘组织中VEGF含量,减少创面愈合时间,促进愈合。     

蛋白质分离纯化方法的研究进展

蛋白质作为生命物质基础之一,存在于自然界中复杂的混合体系中。蛋白质在细胞中的含量极低,将其从复杂体系中分离出来并保持其活性,难度较大,因此分离纯化蛋白质的方法受到生命科学领域广泛关注。本文首先阐述了蛋白质的预处理,其次阐述了蛋白质分离纯化的各种方法如沉淀、层析、离心等,重点阐述了蛋白质新纯化的各种原理,以及每种方法的适用范围。有助大家更全面、更彻底的了解蛋白纯化技术的发展,以期为今后开展蛋白质的制备及应用提供一定理论依据和实验指导。