Protozoan genomes: gene identification and annotation

The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture. Since the genomes vary greatly in size, GC-content, nucleotide composition, and degree of repetitiveness, genome structure is often a factor in choosing the methodology utilised for annotation. In addition, the approach taken is dictated, to a greater or lesser extent, by the particular reasons for carrying out genome-wide analyses and the level of funding available for projects. Nevertheless, these projects have provided a plethora of material that will aid in understanding the biology and evolution of these parasites, as well as identifying new targets that can be used to design urgently required drug treatments for the diseases they cause.     

A protein containing a serine-rich domain with vesicle fusing properties mediates cell cycle-dependent cytosolic pH regulation

Initial differentiation in Dictyostelium involves both asymmetric cell division and a cell cycle-dependent mechanism. We previously identified a gene, rtoA, which when disrupted randomizes the cell cycle-dependent mechanism without affecting either the underlying cell cycle or asymmetric differentiation. We find that in wild-type cells, RtoA levels vary during the cell cycle. Cytosolic pH, which normally varies with the cell cycle, is randomized in rtoA cells. The middle 60% of the RtoA protein is 10 tandem repeats of an 11 peptide-long serine-rich motif, which we find has a random coil structure. This domain catalyzes the fusion of phospholipid vesicles in vitro. Conversely, rtoA cells have a defect in the fusion of endocytic vesicles. They also have a decreased exocytosis rate, a decreased pH of endocytic/exocytic vesicles, and an increased average cytosolic pH. Our data indicate that the serine-rich domain of RtoA can mediate membrane fusion and that RtoA can increase the rate of vesicle fusion during processing of endoctyic vesicles. We hypothesize that RtoA modulates initial cell type choice by linking vegetative cell physiology to the cell cycle.     

Pleuston communities are buffered from regional flood pulses: the example of ostracods in the Paraná River floodplain, Brazil

1. It is widely acknowledged that sudden, large‐scale flood pulses are drivers of benthic and planktonic biodiversity change in floodplains. The impact of such pulses on pleuston (biotic communities associated with root systems of floating plants) remains to be demonstrated. Here, we investigate the effects of local and regional drivers on seasonal changes in abundance and diversity of ostracod communities in pleuston. 2. Temporal and spatial distribution patterns of species richness, abundance, diversity and evenness of ostracods associated with the floating water hyacinth, Eichhornia crassipes, in a lentic environment from the upper Paraná River floodplain, were investigated in relation to local, as well as regional, environmental factors. Ostracods were sampled monthly over an annual cycle (March 2004–February 2005). Twenty‐seven species were found, representing the families Cyprididae, Candonidae, Limnocytheridae and Darwinulidae. Both diversity and abundance of ostracod communities showed seasonal changes, although species turn‐over during the year was limited. 3. We tested two hypotheses concerning the causality of these fluctuations: seasonal recruitment and influx of allochthonous ostracods during the flood pulse. Our results indicate that seasonal recruitment is more likely to be the driver of fluctuations in relation to the flood pulse. We postulate that pleuston communities are buffered against possible detrimental effects of flood pulses.     

Mycobacterium tuberculosis Rv3651 is a triple sensor‐domain protein

The genome of the human pathogen Mycobacterium tuberculosis (Mtb) encodes ～4,400 proteins, but one third of them have unknown functions. We solved the crystal structure of Rv3651, a hypothetical protein with no discernible similarity to proteins with known function. Rv3651 has a three‐domain architecture that combines one cG MP‐specific phosphodiesterases, a denylyl cyclases and F hlA (GAF) domain and two P er‐A RNT‐S im (PAS) domains. GAF and PAS domains are sensor domains that are typically linked to signaling effector molecules. Unlike these sensor‐effector proteins, Rv3651 is an unusual sensor domain‐only protein with highly divergent sequence. The structure suggests that Rv3651 integrates multiple different signals and serves as a scaffold to facilitate signal transfer.     

Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia

Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with two anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two “gate-keeper” residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y?R) and 100 (V?D) and for Gl-MIF it is at position 100 (V?R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins.     

松香改性的研究进展

本文综述了近年来松香改性的研究进展情况,对其进行了分类阐述,即基于羧基的改性、基于双键的改性、基于羧基和双键的改性以及其它方面的改性,并展望了此领域的发展趋势和前景。     

大豆疫霉菌的EMS化学诱变

以甲基磺酸乙酯(ethylmethane sulfonate,EMS)为诱变剂,通过其对大豆疫霉菌Phytophthora sojae休止孢萌发的影响,确定化学诱变条件。通过收集单卵孢子,建立了包含640个单卵孢子系的突变体库,其中约有50%的诱变菌系在培养性状和菌落形态方面发生了明显变化,菌落形态多样,表现出较紧密或松散,近圆形或不规则;气生菌丝减少,生长速度较慢或快;在卵孢子产量方面,8.13%的菌系有增加,20.41%的菌系减少,27.82%的菌系极少或者没有卵孢子产生,43.64%的菌系卵孢子产量类似野生型。以质膜氢离子泵蛋白基因PsPMA1(plasma membrane H+-ATPase1)为对象,通过TILLING技术,从320个大豆疫霉菌突变体中获得9个突变体,进一步确认了EMS对大豆疫霉菌的诱变效果,并且估算EMS对大豆疫霉菌的诱变频率至多每115kb发生一个核苷酸变异。新构建的突变体库为开展大豆疫霉病菌的功能基因组研究奠定了遗传材料基础。     

肝细胞生长因子对主要器官/组织损伤的修复作用

肝细胞生长因子(HGF)是一种多功能的生长因子,它参与多种细胞的增殖、迁移和形态发生。HGF对多种成熟的器官／组织有营养修复作用,促进肝、肾、肺等损伤器官的再生,同时也是神经系统新的营养因子之一。本综合近年来有关献对HGF在主要器官或组织损伤中的修复作用作一概括性介绍。     

浑善达克沙地沙地榆种子雨的扩散规律

于2010年采用定点连续观测的方法,研究了浑善达克沙地不同树龄(23年生、40年生、56年生)沙地榆孤立木种子雨的数量、组成及散布过程,分析沙地榆种子雨的扩散规律及其与外界环境干扰因子的关系。结果表明:(1)孤立木种子雨的总量随其年龄增长而增加,其中56年生孤立木>40年生孤立木>23年生孤立木,其种子雨的总量分别为(7744±16.26)粒/m2、(5236±18.87)粒/m2、(2456±12.67)粒/m2;(2)40年生孤立木的种子质量较好,成熟种子的比例最高,未成熟、空粒和虫害种子的比例较低,56年生孤立木次之,23年生孤立木质量最差,56年生沙地榆和40年生沙地榆是自然更新种子的主要来源;(3)榆树种子于当年5月下旬开始成熟并于6月初开始脱落,6月中旬达到降落高峰期,落种持续到6月下旬结束,落种期持续近1个月;(4)种子雨的前扩散过程中种子集中降落在主风向的下风向50 m和树冠周围20 m的范围内;(5)在种子的后扩散过程中,种子沿下风向继续运动,散落在下风向50 m范围或更远处,后扩散对前扩散表现为"削锋"作用。     

北京市11种园林植物滞留大气颗粒物能力研究

测定了北京市11种园林植物叶面颗粒物附着密度,利用环境扫描电镜观察比较了各测试树种叶表面微形态,测量统计了滞留颗粒物的粒径分布.结果表明,植物主要通过叶片上表面滞留大气颗粒物,上表面滞留的大气颗粒物数量约为下表面的5倍;叶片上表面滞留大气颗粒物能力由高到低的微形态结构依次是沟槽>叶脉＋小室 >小室>条状突起,并且结构越密集、深浅差别越大,越有利于滞留大气颗粒物;测试树种叶片上、下表面PM_2.5和PM₁₀平均百分含量分别为66.7％和98.3％与 43.4％和92.9％.