Topology independent protein structural alignment

Background  

Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps.     

我国巴拉巴按蚊形态描述

白踝按蚊种团是由很多形态近似的蚊种组成,其中巴拉巴按蚊和白踝按蚊均为东南亚一带的重要传疟媒介。我国过去资料均记载为白踝按蚊,但未从形态上详细鉴定。为了确定该种的分类地位,1963年作者等在海南岛万宁县兴隆附近山林区采集“白踝按蚊”全套标本10批共150多套,1971年后从云南省采集少数标本进行形态鉴定,发现其与Colless(1956,1957)所描述的白踝按蚊Anopheles leucosphyrus leucosphyrus Donitz(1901)有很明显的差别,而与巴拉巴按蚊A.balabacensis balabacensis Balsas(1936)除某些特征略有差异外,余均完全一致。按Colless的分类法,过去我国记载的“白踝按蚊”,应鉴定为巴拉巴按蚊A.balabacensis balabacensis Baisas。     

Ghrelin在小鼠体内早期胚胎发育中的表达

为了探讨Ghrelin是否在昆明系小白鼠(Mus musculus)体内早期胚胎发育中发挥作用。运用激素超排卵技术及动物解剖学方法获取小鼠体内不同发育阶段的早期胚胎,应用实时定量PCR技术检测了Ghrelin mRNA的相对表达量。结果表明,Ghrelin mRNA在小鼠各期胚胎中均有表达;同时,GhrelinmRNA的表达量呈现一定规律性变化,2-细胞期表达量最低,8-细胞期表达量达到最高值,总体趋势是先降低后升高之后又降低。研究结果揭示,Ghrelin可能在小鼠早期胚胎发育中发挥一定的作用。     

The whole mitochondrial genome sequence of the zebra finch (Taeniopygia guttata)

Here we describe the complete nucleotide sequence of the mitochondrial genome (16 583/4 bp) of the zebra finch (Taeniopygia guttata). Primers were designed based on highly conserved regions of an alignment of three passerine complete mitochondrial DNA (mtDNA) sequences. A combination of overlapping long polymerase chain reaction (PCR) purification, followed by fully nested PCR and sequencing was used to determine the complete mtDNA genome. Six birds, from distinct maternal lineages of a pedigreed population were sequenced. Five novel haplotypes were identified. These sequences provide the first data for sequence variation across the whole mitochondrial genome of a passerine bird species.     

SNP‐SCALE: SNP scoring by colour and length exclusion

Here we present SNP‐SCALE, a new single nucleotide polymorphism genotyping protocol based on allele‐specific polymerase chain reaction (AS‐PCR), but with two critical modifications designed to maximize accuracy, efficiency and throughput and minimize costs. The first is the addition of a locked nucleic acid (LNA) at the 3′‐SNP position of each of the two allele‐specific forward primers. The second is the addition of size‐differentiating M13 tails at the 5′ end of each primer, which facilitates the use of universal fluorescent primers. The use of LNAs makes SNP‐SCALE significantly more sensitive and specific than standard AS‐PCR. Moreover, SNP‐SCALE is ideally suited to a touchdown‐like PCR protocol, such that PCRs can be standardized, PCR optimization is straightforward, and medium‐high throughput can be readily achieved. We anticipate that the SNP‐SCALE protocol will be useful to molecular ecologists for a broad range of studies.     

Effects of environmental conditions on the fixation and transfer of nitrogen from alfalfa to associated timothy

Nitrogen fixation (NF) by alfalfa and nitrogen transfer (NT) from alfalfa to associated timothy was studied under different environmental conditions in controlled growth chambers, using the¹⁵N dilution technique. Evidence was obtained of NT from alfalfa to the associated timothy. Conditions that favored NF by alfalfa resulted in an increase in its NT. Of 3 different temperature regimes (25/20, 16/14, and 12/9°C day/night), 16–25/14–20°C was the best range for NF by alfalfa and resulted in the greatest NT. High light intensity (550 uE.m⁻².sec⁻¹) and long days (16–20 h) also caused increased NF by alfalfa and benefitting timothy more than in a regime of low light intensity (by shading 50% or 75%) or short days (12/12 or 16/8 h day/night). When the inoculated (Rhizobium meliloti) root systems of plants were kept free from other microorganisms (axenic condition) to minimize possible decomposition of dead tissues, lower NT from alfalfa was observed, especially at later cuts, compared to non-axenic plants. This suggests that both direct excretion and decomposition of dead alfalfa tissues are sources of N benefit from alfalfa to associated timothy. Contribution no 1065 of the Plant Research Centre.     

黄地老虎核型多角体病毒的一些特性

黄地老虎核型多角体病毒(Agrotis segetum Nulear Polyhedrosis Virus简称AsNPV)的国内分离株(AsNPV^C),多角体呈六边形,大小1.7—2.6μm,为多粒包埋类型.每个病毒束内有2—7个核衣壳,大小约52nm×308nm.感染烟青虫(Heliothis assttlta)后分离到的多角体(As-HaNPV)其形状不规则,大小0.7—2.6μm,亦为多粒包埋类型.核衣壳2—6个不等,大小约40nm×300nm.EcoR1和HindⅢ限制性内切酶电泳图谱分析表明,AsNPV^CDNA和As-HaNPV DNA的EcoRI、HindIII酶切图谱一致,两者与HaNPV DNA的EcoRI,HindⅢ酶切图谱存在明显差异,AsNPV^C DNA的EcoRI酶切图谱共有15个片段,分子量在12.74×10⁶—1.18×10⁶道尔顿之间,总分子量约88.6×10⁶道尔顿,相当于134.25kbp.HaNPV DNA的EcoRI酶切图谱共有19个片段,分子量在13.89×10⁶—1.10×10⁶道尔顿之间,总分子量约93.86×10⁶道尔顿,相当于142.25kbp.AsNPV对黄地老虎2龄和4龄幼虫以及对烟青虫4龄幼虫的LD_{50分别为:1.4×10⁵pIB、7.4×10⁴PIB和2.61×10⁴PIB.}     

Regulation of Na,K-pump-mediated transport by prolactin in cultured human prostate epithelial cells.

The prostate gland is unique in its ability to secrete large amounts of zinc and citrate, suggesting that it employs unusual transport mechanisms. Intracellular ionic homeostasis in prostate is likely to be mediated by the Na,K-pump, yet there have been few studies of its regulation in this tissue. Accordingly, we explored the expression of the Na,K-pump in PC3 cells, an established cell line of human prostate epithelial cells. Total RNA from confluent monolayers of PC3 cells was isolated, reverse transcribed, and the resulting complementary DNA was amplified by polymerase chain reaction using primers specific for each of the pump's constituent subunits. The amplification revealed a complex pattern of Na,K-pump expression, with detection of mRNAs encoding the alpha1-, alpha3-, alpha4-, betal-, beta2- and beta3-isoforms. We next examined the effect on pump activity of prolactin, an important mediator of cell proliferation in prostate cancer. Monolayers exposed to 10 nM prolactin for 24 hr revealed an inhibition of 40% in ouabain-sensitive 86Rb+ uptake, a sensitive measure of pump-mediated transport. These experiments suggest that the unique transport properties of prostate may depend, at least in part, on a complicated pattern of Na,K-pump expression and regulation.