Occupancy Modeling of Coverage Distribution for Whole Genome Shotgun Dna Sequencing

Expected-value models have long provided a rudimentary theoretical foundation for random DNA sequencing. Here, we are interested in improving characterization of genome coverage in terms of its underlying probability distributions. We find that the mathematical notion of occupancy serves as a good model for evolution of the coverage distribution function and reveals new insights related to sequence redundancy. Established concepts, such as “full shotgun depth,” have been assumed invariant, but actually depend on project size and decrease over time. For most microbial projects, the full shotgun milestone should be revised downward by about 30%. Accordingly, many already-completed genomes appear to have been over-sequenced. Results also suggest that read lengths for emerging high-throughput sequencing methods must be increased substantially before they can be considered as possible successors to the standard Sanger method. In particular, gains in throughput and sequence depth cannot be made to compensate for diminished read length. Limits are well approximated by a simple logarithmic equation, which should be useful in estimating maximum coverage-based redundancy for future projects.     

Foraminifera diversity changes and paleoenvironmental analysis: the Lower Cretaceous shallow-water carbonates of San Lorenzello, Campanian Apennines, southern Italy

A high-resolution stratigraphic study, carried out on the carbonate platform strata of the San Lorenzello section (Matese Mountains, southern Italy), Valanginian–Hauterivian in age, has allowed to: recognise lithofacies and their associations; assign the lithofacies associations to specific environments and individuate early meteoric diagenetic modifications, recurring at specific horizons. In this frame the vertical variation of benthic foram diversity has been analysed. On the whole, foraminiferal genera diversity decreases from open to restricted marine environments. Moreover, a climatic control on carbonate sedimentation is suggested by a Milankovitch cyclicity organised in elementary cycles, bundles and superbundles as well as by diagenetic characteristics testifying that humid and arid conditions alternated during the Early Cretaceous times. The orbital cyclicity is also documented by foraminiferal diversity changes, even if some discrepancies between the lithofacies and the diversity locally occur. Therefore, the above diversity changes do not appear to provide sufficient information for the sequence-stratigraphic interpretation of shallow-water carbonates.     

Sequence stratigraphy and carbonate platform organization of the Devonian Santa Lucia Formation, Cantabrian Mountains, NW-Spain

In this paper, the sedimentology and the stratigraphic architecture of the Devonian Santa Lucia Formation in the Cantabrian Mountains of NW-Spain are described. The Santa Lucia Formation consists of 11 different facies that can be attributed to peritidal/lagoonal, intertidal and subtidal facies associations. These facies associations are arranged in small-scale sedimentary cycles. Three different settings of small-scale sedimentary cycles are recognized: intertidal/supratidal, shallow subtidal/intertidal and subtidal cycles. These cycles reflect spatial differences in the reaction of the depositional system to small-scale relative sea-level changes. Small-scale stratigraphic cycles are stacked into seven medium-scale cycles that in turn are integral parts of three larger-scale cycles. Most of the Santa Lucia Formation (sequences 2–6) forms one major large-scale cycle, whereas sequences 1 and 7 are part of an underlying and an overlying cycle, respectively. Eustatic sea-level changes exerted major control on the formation of these large-scale sequences, whereas the medium-scale cycles seem to be co-controlled by regional tectonism and eustasy. Small-scale cycles seem to be the product of high frequency, eustatic sea-level changes. During the deposition of the Santa Lucia Formation, the morphology of the carbonate platform changed from a gently south-dipping ramp to a rimmed shelf and back to a gently dipping ramp.     

Aberrant expression of HLA-B*3565Q is associated with a disrupted disulfide bond

The identification of expression variants is a challenge in HLA diagnostics. We here describe the identification of the novel allele HLA-B*3565Q. The serological HLA class I type, as determined by a lymphocytotoxicity test, was A11,24; B38; Bw4; Cw−; whereas PCR-sequence-specific primers resulted in A*11,*24, B*35,*38; Cw*12, thus suggesting the presence of a nonexpressed B*35 allele. To clarify the lack of serological HLA-B35 reactivity, exons 2 and 3 were sequenced following haplotype-specific amplification. At position 564 from the beginning of the coding region (exon 3), a transversion (C→G) was observed, which, at the amino acid level, results in a substitution from cysteine to tryptophane at position 164 of the mature polypeptide. Because this position is essential for the formation of a disulfide bond linking the cysteine residues at positions 101 and 164, which is strongly conserved in functional class I molecules of vertebrates, the disruption of this bond is very likely to be the reason for the lack of serological detectability. We later found the same novel allele in a second unrelated individual, of whom we were able to establish a lymphoblastoid cell line (B-LCL). Serological testing of this B-LCL indicated a very low aberrant expression of HLA-B*3565Q, which cannot be expected to be detected by standard serology techniques. Holger-Andreas Elsner and Peter A. Horn contributed equally to this work. The nucleotide sequence data reported in this paper have been published in the European Molecular Biology Laboratory, GenBank, and DNA Data Bank of Japan Nucleotide Sequence Database under the accession numbers AJ278746, AJ278747, and AJ879892. The name B*3565Q was officially assigned by the WHO Nomenclature Committee in December 2005. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Marsh et al. 2005), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report.     

Photosynthesis in the Archean Era

The earliest reductant for photosynthesis may have been H₂. The carbon isotope composition measured in graphite from the 3.8-Ga Isua Supercrustal Belt in Greenland is attributed to H₂-driven photosynthesis, rather than to oxygenic photosynthesis as there would have been no evolutionary pressure for oxygenic photosynthesis in the presence of H₂. Anoxygenic photosynthesis may also be responsible for the filamentous mats found in the 3.4-Ga Buck Reef Chert in South Africa. Another early reductant was probably H₂S. Eventually the supply of H₂ in the atmosphere was likely to have been attenuated by the production of CH₄ by methanogens, and the supply of H₂S was likely to have been restricted to special environments near volcanos. Evaporites, possible stromatolites, and possible microfossils found in the 3.5-Ga Warrawoona Megasequence in Australia are attributed to sulfur-driven photosynthesis. Proteobacteria and protocyanobacteria are assumed to have evolved to use ferrous iron as reductant sometime around 3.0 Ga or earlier. This type of photosynthesis could have produced banded iron formations similar to those produced by oxygenic photosynthesis. Microfossils, stromatolites, and chemical biomarkers in Australia and South Africa show that cyanobacteria containing chlorophyll a and carrying out oxygenic photosynthesis appeared by 2.8 Ga, but the oxygen level in the atmosphere did not begin to increase until about 2.3 Ga.     

A new gene, sigG, encoding a putative alternative sigma factor of Streptomyces coelicolor A3(2)

An oligonucleotide probe encoding a peptide motif conserved in all sigma factors was used to isolate a new gene, sigG, from a Streptomyces coelicolor A3(2) genomic library. The deduced protein of 263 amino acids with an M(r) of 29,422 showed the greatest similarity to the previously identified sporulation sigma factor (sigma F) of Streptomyces coelicolor, and general stress response sigma factor (sigma B) of Bacillus subtilis, mostly in domains suggested to be involved in recognition of -10 and -35 promoter regions. Southern-blot hybridization with DNA from several Streptomyces spp. revealed the presence of a similar gene in all strains tested. Disruption of the S. coelicolor sigG gene appeared to have no obvious effect on growth, morphology, differentiation, and production of pigmented antibiotic actinorhodin and undecylprodigiosin.     

一株长春地区戊型肝炎病毒全基因cDNA序列测定

我国报道的戊型肝炎病毒(Hepatitis E virusHEV)基因组序列,大多数为散发型 HEV 部分基因序列的测定,仅少数为全基因序列的分析结果,而且,各实验室所分析的 HEV 片段不同,因此,很难确定新型变异株,远远不能满足中国基因分型的研究和临床诊断的需要。为此,我们对长春地区一株散发性HEV进行了全基因cDNA序列测定。1　材料和方法1.1　血清样品病例源于2000 年 6 月我院住院患者,女性,52岁,因腹痛、腹泻、发热 10d加重伴呕吐 2d入院,入院前曾有不洁饮食史。近期无外出旅游史。ALT25.9IU/L、GGT 110. 0IU/L、TBIL 36. 6μmol…     

不同致病型马立克氏病病毒1．8kb基因家族序列比较

为了分析鸡马立克氏病病毒(Marek′sdiseasevirus,MDV)的致病性与其1.8kb基因家族的关系,本研究比较了四个不同致病型12个毒株的该基因家族的同源性关系,即弱毒疫苗株、强毒株、超强毒株、特超强毒株和中国野毒株。结果表明:不同毒株间1.8kb基因家族的上游调控序列的同源性在1.8kb基因家族转录方向上大于92.5%,序列间有缺失突变,其中大多数突变发生在弱毒株上。CVI988在TATAbox和上游SP1位点间丢失小片段“5′CTCGG3′”。1.8kb基因家族中存在132bp串连重复序列,CVI988包含37个132bp串连重复序列拷贝,强毒株、超强毒株、特超强毒株通常只包含2个串连重复序列。但是已知的中国疫苗毒株814株也只有2个重复序列,表明重复序列的拷贝数不是引起病毒毒力变化的主要原因。各毒株的1.8kb基因家族同源性在97%以上。其中未剪切的1.69kbcDNA中有两个阅读框,分别编码63和64个氨基酸组成的多肽。不同毒株的这二个多肽都很保守,虽然也有一些氨基酸变异,但这些变异与病毒的致病型或地域分布没有明显的关系。     

鸡传染性支气管炎病毒变异株（793／B）核蛋白基因的克隆与序列分析

根据GenBank已经发表的传染性支气管炎病毒(IBV)N全基因组序列设计引物,对IBV793/B分离毒株N基因进行克隆与序列分析。结果表明,IBV793/B的N基因由1229bp组成,与GenBank已发表的11株IBV的N基因相比较,IBV793/B的N基因共有88处点突变,在第991位发生了一个核苷酸的缺失。N基因的核苷酸同源性为86.9%～91.4%,氨基酸同源性为75.8%～77.5%。表明IBV93/B的N基因存在着较大的变异性。     

侵染花生的辣椒褪绿病毒SRNA全序列分析

番茄斑萎病毒属(Tospovirus)是布尼亚病毒科(Bunyaviridae)中植物病毒组成的一个属,病毒粒子为球状,直径80~110nm,粒体外层由一层脂质包裹。基因组属于负单链RNA,由三个片段组成,分别被称为L RNA、M RNA、和S RNA。L RNA为负链、含单个开放阅读框架(ORF),M RNA和S RNA均为双义R