Appropriate models for the management of infectious diseases

BackgroundMathematical models have become invaluable management tools for epidemiologists, both shedding light on the mechanisms underlying observed dynamics as well as making quantitative predictions on the effectiveness of different control measures. Here, we explain how substantial biases are introduced by two important, yet largely ignored, assumptions at the core of the vast majority of such models.ConclusionThis work aims to highlight that, when developing models for public health use, we need to pay careful attention to the intrinsic assumptions embedded within classical frameworks.     

Diversity and evolutionary history of plastids and their hosts

By synthesizing data from individual gene phylogenies, large concatenated gene trees, and other kinds of molecular, morphological, and biochemical markers, we begin to see the broad outlines of a global phylogenetic tree of eukaryotes. This tree is apparently composed of five large assemblages, or "supergroups." Plants and algae, or more generally eukaryotes with plastids (the photosynthetic organelle of plants and algae and their nonphotosynthetic derivatives) are scattered among four of the five supergroups. This is because plastids have had a complex evolutionary history involving several endosymbiotic events that have led to their transmission from one group to another. Here, the history of the plastid and of its various hosts is reviewed with particular attention to the number and nature of the endosymbiotic events that led to the current distribution of plastids. There is accumulating evidence to support a single primary origin of plastids from a cyanobacterium (with one intriguing possible exception in the little-studied amoeba Paulinella), followed by the diversification of glaucophytes, red and green algae, with plants evolving from green algae. Following this, some of these algae were themselves involved in secondary endosymbiotic events. The best current evidence indicates that two independent secondary endosymbioses involving green algae gave rise to euglenids and chlorarachniophytes, whereas a single endosymbiosis with a red algae gave rise to the chromalveolates, a diverse group including cryptomonads, haptophytes, heterokonts, and alveolates. Dinoflagellates (alveolates) have since taken up other algae in serial secondary and tertiary endosymbioses, raising a number of controversies over the origin of their plastids, and by extension, the recently discovered cryptic plastid of the closely related apicomplexan parasites.     

小鼠BTB/锌指结构新基因Bsg6的克隆及表达谱分析

Bsg6 (brain specific gene 6) 是用消减差异筛选的方法克隆的小鼠头部特异表达 新基因. Bsg6基因cDNA长3 871 bp,编码一个670个氨基酸残基的蛋白,GenBank 登录号AY635051,位于小鼠第4号染色体,由2个外显子构成. Bsg6蛋白含有一个N端BTB（Broad complex, Tramtrack, and Bric a brac）结构域和两个C端C２Ｈ２型锌指结构域. 小鼠Bsg6蛋白与其在人类和鸡中同源蛋白的同源性分别为86.2%和79.1%. Bsg6在小鼠胚胎中的表达具有一定动态性,在E8.5的小鼠胚胎中,Bsg6主要在前脑和神经管表达. 在E9.5的小鼠胚胎中,Bsg6的表达明显增强并主要集中在前脑的端脑部. Bsg6在E10.5小鼠胚胎端脑的表达出现了下降,但是在中脑和后脑的表达增加,此外,Bsg6 mRNA的表达还出现在肢芽和尾部. 在HH10期的鸡胚中,Bsg6主要在头部和神经管前端表达. Northern杂交结果显示,Bsg6在很多小鼠成体组织中没有表达,但是在破骨细胞瘤中高表达. Bsg6的表达谱提示,Bsg6可能是在器官形成期对脑的发育起到重要作用的转录因子,而且其表达受到严格的调控,此外Bsg6还能与肿瘤的发生有关.     

Evidence from SSU rRNA phylogeny that Octomitus is a sister lineage to Giardia

Octomitus intestinalis is a diplomonad flagellate inhabiting the digestive tract of rodents and amphibians. Octomitus is of evolutionary interest because, based on ultrastructural characteristics, it is thought to be closely related to the morphologically derived genus Giardia, and together they have been proposed to make up the Giardiinae. In molecular trees of diplomonads, Giardia is the deepest branching lineage, so identifying a sister group to Giardia that is less derived would be informative. Octomitus is a logical candidate for this position, but unfortunately there are no molecular data from it, and it is not available in culture. To determine the position of Octomitus, and specifically test whether it is more closely related to Giardia than other diplomonads, we have isolated it directly from the caecum of wild mice and characterized its small subunit ribosomal RNA (SSU rRNA) gene. Phylogenetic analysis showed Octomitus to be the sister to Giardia with strong support, together occupying one side of the deepest split in the diplomonad tree.     

Diterpene resin acids in conifers

Diterpene resin acids are a significant component of conifer oleoresin, which is a viscous mixture of terpenoids present constitutively or inducibly upon herbivore or pathogen attack and comprises one form of chemical resistance to such attacks. This review focuses on the recent discoveries in the chemistry, biosynthesis, molecular biology, regulation, and biology of these compounds in conifers.     

Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture

In photosynthetic eukaryotes, relative silent-site nucleotide substitution rates (which can be used to approximate relative mutation rates) among mitochondrial, plastid, and nuclear genomes (mtDNAs, ptDNAs, and nucDNAs) are estimated to be 1:3:10 respectively for seed plants and roughly equal for green algae. These estimates correlate with certain genome characteristics, such as size and coding density, and have therefore been taken to support a relationship between mutation rate and genome architecture. Plants and green algae, however, represent a small fraction of the major eukaryotic plastid-bearing lineages. Here, we investigate relative rates of mutation within the model red algal genus Porphyra. In contrast to plants, we find that the levels of silent-site divergence between the Porphyra purpurea and Porphyra umbilicalis mtDNAs are three times that of their ptDNAs and five times that of their nucDNAs. Moreover, relative mutation rates do not correlate with genome architecture: despite an estimated three-fold difference in their mutation rate, the mitochondrial and plastid genome coding densities are equivalent - an observation that extends to organisms with secondary red algal plastids. These findings are supported by within-species silent-site polymorphism data from P. purpurea.     

Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker

Background

DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.

Methodology/Principal Findings

The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name.

Conclusions/Significance

The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.     

人类新基因WDR70的克隆及初步研究

运用基于基因组数据库的特定基因同源新基因的克隆策略得到一个人类新基因WDR70 ,该基因编码一个包含 12个WD4 0结构域的蛋白。WDR70的cDNA序列长 2 2 6 6bp ,预测编码蛋白含 6 30个氨基酸 ,理论分子量为 70× 10 3 u ,染色体定位为 17p13.1。以小鼠胚胎为模型进行整体原位杂交 ,结果显示WDR70基因在 8.5d小鼠胚胎中没有表达 ,而在 9.5d和 10 .5d的小鼠胚胎的脑部有特异表达。由此推断该基因对胚胎期脑部的发育有重要的影响。     

小麦叶片β-1,3-葡聚糖酶的诱导、纯化与抗菌活性

三个小麦品种331、抗倒680和鲁麦23经氯化汞、水杨酸或核黄素处理后,叶片中的β-1,3-葡聚糖酶活性均有不同程度的升高.氯化汞处理24h对品种331该酶活性的诱导作用最强.因此取用氯化汞处理24 h的331小麦叶片研磨得到粗酶液.将粗酶液经硫酸铵分级沉淀、Phenyl-Sepharose Fast Flow疏水层析、DEAE-Sepharose Fast Flow阴离子交换层析和Sephacryl S-100分子筛层析,得到了SDS-PAGE凝胶电泳谱带单一的β-1,3-葡聚糖酶样品.经SDS-PAGE(12%)和凝胶过滤层析,测得其分子量约为52.0～53.6 kD.抗菌试验测定显示,纯化的β-1,3-葡聚糖酶对供试的4种病原真菌的生长、孢子萌发或芽管伸长都有一定程度的抑制作用.