Lineage-specific gene expansions in bacterial and archaeal genomes

Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (approximately 5%-33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size > or =20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.     

Autoimmunity,Infectious Immunity,and Atherosclerosis

Introduction  

Vascular inflammation is common in certain systemic autoimmune diseases and contributes to the oxidation of low-density lipoprotein (oxLDL) and oxLDL/β2-glycoprotein I (β2GPI) complex formation. These complexes have been implicated as proatherogenic autoantigens that participate in the development of atherosclerotic disease.     

Parkinson’s Disease–Associated Changes in the Expression of Neurotrophic Factors and their Receptors upon Neuronal Differentiation of Human Induced Pluripotent Stem Cells

Journal of Molecular Neuroscience - Parkinson’s disease (PD) is a neurodegenerative pathology resulting from the degeneration of dopaminergic (DA) neurons in the substantia nigra (SN)....     

Pegylated liposomal doxorubicin plus highly active antiretroviral therapy versus highly active antiretroviral therapy alone in HIV patients with Kaposi's sarcoma

Twenty-eight HIV patients either naive or failing highly active antiretroviral therapy (HAART)with moderate-advanced Kaposi's sarcoma (KS)were randomly chosen to initiate a new HAART regimen plus pegylated liposomal doxorubicin(PLD) or the new HAART regimen alone. After 48 weeks, better response rates were observed in the HAART plus PLD group (76% versus 20%).In HIV-infected patients with moderate-advanced KS, HAART alone may not be enough for KS response.     

Novel insight into the detailed myocardial motion and deformation of the rodent heart using high-resolution phase contrast cardiovascular magnetic resonance

Background

Phase contrast velocimetry cardiovascular magnetic resonance (PC-CMR) is a powerful and versatile tool allowing assessment of in vivo motion of the myocardium. However, PC-CMR is sensitive to motion related artifacts causing errors that are geometrically systematic, rendering regional analysis of myocardial function challenging. The objective of this study was to establish an optimized PC-CMR method able to provide novel insight in the complex regional motion and strain of the rodent myocardium, and provide a proof-of-concept in normal and diseased rat hearts with higher temporal and spatial resolution than previously reported.

Methods

A PC-CMR protocol optimized for assessing the motion and deformation of the myocardium in rats with high spatiotemporal resolution was established, and ten animals with different degree of cardiac dysfunction underwent examination and served as proof-of-concept. Global and regional myocardial velocities and circumferential strain were calculated, and the results were compared to five control animals. Furthermore, the global strain measurements were validated against speckle-tracking echocardiography, and inter- and intrastudy variability of the protocol were evaluated.

Results

The presented method allows assessment of regional myocardial function in rats with high level of detail; temporal resolution was 3.2 ms, and analysis was done using 32 circumferential segments. In the dysfunctional hearts, global and regional function were distinctly altered, including reduced global peak values, increased regional heterogeneity and increased index of dyssynchrony. Strain derived from the PC-CMR data was in excellent agreement with echocardiography (r = 0.95, p < 0.001; limits-of-agreement −0.02 ± 3.92%strain), and intra- and interstudy variability were low for both velocity and strain (limits-of-agreement, radial motion: 0.01 ± 0.32 cm/s and −0.06 ± 0.75 cm/s; circumferential strain: -0.16 ± 0.89%strain and −0.71 ± 1.67%strain, for intra- and interstudy, respectively).

Conclusion

We demonstrate, for the first time, that PC-CMR enables high-resolution evaluation of in vivo circumferential strain in addition to myocardial motion of the rat heart. In combination with the superior geometric robustness of CMR, this ultimately provides a tool for longitudinal studies of regional function in rodents with high level of detail.     

转录因子T-bet与哮喘大鼠气道炎症及川芎嗪的干预效应

目的:转录因子T-bet在支气管哮喘的发病中起重要作用,川芎嗪治疗哮喘有效。实验拟观察川芎嗪对哮喘大鼠气道炎症的影响和转录因子T-bet的调控作用。方法:实验于2005-11/2006-06在南京医科大学完成。①实验材料及分组:72只SPF级SD大鼠随机分为正常对照组、哮喘模型组、川芎嗪小剂量组(20mg/kg)、川芎嗪中剂量组(40mg/kg)、川芎嗪大剂量组(80mg/kg)和地塞米松组,每组12只。实验用磷酸川芎嗪注射液为丽珠集团利民制药厂生产)。②实验过程及评估:以卵蛋白腹腔注射并雾化吸入制备大鼠哮喘模型,末次雾化后24h内麻醉后处死大鼠。观察6组大鼠肺组织形态学变化;测定支气管壁厚度、支气管平滑肌厚度、嗜酸粒细胞和淋巴细胞数。采用免疫组织化学半定量法测定肺组织T-bet蛋白的表达;进行转录因子T-bet蛋白表达量与气道炎症的相关性分析。实验过程中对动物处置符合动物伦理学标准。结果:①哮喘模型组嗜酸粒细胞、淋巴细胞、支气管壁厚度和支气管平滑肌厚度,明显高于正常对照组相应指标(P均<0.01);与哮喘模型组比较,川芎嗪小、中、大剂量组和地塞米松组上述4项指标均减少(P均<0.01)。②哮喘模型组、川芎嗪小、中、大剂量组和地塞米松组的T-bet表达量低于正常对照组(P均<0.01);与哮喘模型组比较,川芎嗪小、中、大剂量组T-bet表达量增加(P均<0.01);随着川芎嗪剂量增加,T-bet表达量亦相应增加,川芎嗪小、中、大剂量组之间两两比较,差异均有统计学意义(P均<0.01)。③相关分析显示哮喘模型组T-bet蛋白表达量与嗜酸性粒细胞和淋巴细胞浸润数呈负相关(r=-0.81,-0.85,P<0.01),与支气管管壁厚度和支气管平滑肌厚度呈负相关(r=-0.77,-0.79,P<0.01)。结论:支气管哮喘大鼠存在T-bet低表达;川芎嗪可抑制气道炎症,增加转录因子T-bet蛋白的表达,纠正Th1/Th2失衡,从而治疗支气管哮喘。