Complete genome sequence of Bacillus cereus bacteriophage PBC1

Bacillus cereus is a ubiquitous, spore-forming bacterium associated with food poisoning cases. To develop an efficient biocontrol agent against B. cereus, we isolated lytic phage PBC1 and sequenced its genome. PBC1 showed a very low degree of homology to previously reported phages, implying that it is novel. Here we report the complete genome sequence of PBC1 and describe major findings from our analysis.     

Pyrosequencing of a short fragment of the amelogenin gene for gender identification

We report a pyrosequencing method for detecting a short amelogenin fragment to aid the gender identification. The PCR products (44/45 bp), including primers and target sequence (4/5 bp) consisting of three point mutations and one indel mutation, were sequenced by the pyrosequencing method. 100 randomly chosen DNA samples of healthy donors were analyzed with this method, and all of them were correctly typed. The sensitivity of the technique was 0.5 ng template DNA. No specific peak was found in any detected animals or organisms except for monkey. For blood samples that were left outside for 26 weeks and DNA degraded artificially by digesting with DNaseI, this method gave more accurate results than the conventional method. Moreover, four bone samples analyzed using the method gave clear pyrograph. This method is easy, quick, cheap and suitable for high-throughput analysis, especially for identifying the gender of highly-degraded DNA samples.     

香鱼补体成分C9基因的克隆、序列分析及表达

补体成分C9是构成膜攻击复合体引起靶细胞溶解破坏的重要组成成分。该文测定了香鱼C9(aC9)基因的cDNA全序列,序列全长2125个核苷酸,编码一个由592个氨基酸组成、相对分子质量为6.56×104的前体蛋白,N端22个氨基酸为信号肽序列。序列分析表明,aC9与虹鳟C9的氨基酸同源性最高,达56.8%,与其它鱼类C9的同源性介于40.9%~53.8%之间。aC9在健康香鱼肝、脾、肠、鳃和肌肉有表达,其中在肝内的表达量最高。实时荧光定量PCR的结果显示,鳗利斯顿氏菌侵染4h后,肝中aC9mRNA表达量显著上调,并随着时间的推移在16h时达到峰值。Westernblotting分析的结果显示,鳗利斯顿氏菌侵染后香鱼血清中的aC9蛋白随着时间的推移呈显著上调。以上结果表明,香鱼肝组织C9基因表达变化与鳗利斯顿氏菌的侵染密切相关,揭示了C9在鱼类抗细菌免疫反应中具有重要的作用。     

Centromere mapping in the Pacific abalone (Haliotis discus hannai) through half-tetrad analysis in gynogenetic diploid families

Centromere mapping is an essential prerequisite for our understanding of the composition and structure of genomes. For centromere mapping, in two meiogynogenetic families of the Pacific abalone (Haliotis discus hannai), we screened 97 microsatellite markers that cover all linkage groups from a currently available abalone linkage map. Microsatellite analysis showed that no unique paternal allele was found in all gynogenetic progeny, which confirmed 100% success of induction of gynogenesis. In the control crosses, all 97 microsatellite loci were compatible with Mendelian inheritance, while in meiogynogenetic progeny, 5.2% of the microsatellite loci showed segregation distortions from an expected 1:1 ratio of two homozygote classes. The second division segregation frequency of the microsatellites ranged from 0.037 to 0.950 with a mean of 0.399, indicating the existence of interference. Heterogeneity among linkage groups in the crossover distribution was observed. Centromere location was mostly in accordance with the abalone karyotype, but differences in marker order between linkage and centromere maps occurred. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards assembly of genetic maps in the commercially important abalone species.     

Osteopontin increases the expression of β1, 4-Galactosyltransferase-I and promotes adhesion in human RL95-2 cells

Beta1, 4-Galactosyltransferase-I (β1, 4-GalT-I), which transfers galactose from UDP-Gal to N-acetylglucosamine and N-acetylglucosamine-terminated oligosaccharides of N- and O-linked glycans in a β(1-4) linkage, plays a critical role in cell adhesion, sperm-egg recognition, neurite growth, and tumor cell migration and invasion. Our previously experiments also show that β1, 4-GalT-I was up-regulated by estrogens and some important cytokines of embryo implantation especially Interleukin-1 (IL-1), TGF-α and Leukemia Inhibitory Factor (LIF) in endometrial cells. In the receptive phase human uterus, osteopontin (OPN) is the most highly up-regulated extracellular matrix/adhesion molecule/cytokine. In this study, we demonstrated the correlated expression of OPN and β1, 4-GalT-I in endometrium during early pregnancy, and recombinant human OPN (rhOPN) protein induced the β1, 4-GalT-I up-regulation in RL95-2 cells. Inhibition of MEK/ERK, PI3K/AKT and NF-κB suppressed rhOPN-induced β1, 4-GalT-I expression. In addition, rhOPN promoted the adhesion of blastocysts cells in vitro in β1, 4-GalT-I-dependent manner. Moreover, the adhesion is greatly inhibited when β1, 4-GalT-I was blocked with the specific antibody. Taken together, our data suggest that β1, 4-GalT-I provides a mechanism to bridge embryo to endometrium during implantation.     

The intra-S phase checkpoint targets Dna2 to prevent stalled replication forks from reversing

When replication forks stall at damaged bases or upon nucleotide depletion, the intra-S phase checkpoint ensures they are stabilized and can restart. In intra-S checkpoint-deficient budding yeast, stalling forks collapse, and ～10% form pathogenic chicken foot structures, contributing to incomplete replication and cell death (Lopes et al., 2001; Sogo et al., 2002; Tercero and Diffley, 2001). Using fission yeast, we report that the Cds1(Chk2) effector kinase targets Dna2 on S220 to regulate, both in vivo and in vitro, Dna2 association with stalled replication forks in chromatin. We demonstrate that Dna2-S220 phosphorylation and the nuclease activity of Dna2 are required to prevent fork reversal. Consistent with this, Dna2 can efficiently cleave obligate precursors of fork regression-regressed leading or lagging strands-on model replication forks. We propose that Dna2 cleavage of regressed nascent strands prevents fork reversal and thus stabilizes stalled forks to maintain genome stability during replication stress.     

The activity of plasma membrane hyperpolarization-activated Ca<Superscript>2+</Superscript> channels during pollen development of <Emphasis Type="Italic">Pyrus pyrifolia</Emphasis>

Calcium (Ca²⁺) plays crucial roles in regulation of pollen tube growth. The influx of Ca²⁺ into the pollen tube is mediated by ion channels, and the density and activity of Ca²⁺ channels in pollen plasma membranes critically determines their electrical properties. In this report, using whole-cell and single-channel patch-clamping techniques, we investigated developmental changes of hyperpolarization-activated Ca²⁺ channel activity in pear (Pyrus pyrifolia) pollen and its relationship with pollen viability. For both pollen and pollen tubes, hyperpolarization-activated Ca²⁺ channels had the same conductance and cAMP sensitivity, indicating that they were the same channels. However, the Ca²⁺ current density in pollen tube protoplasts was greater than that in pollen protoplasts. Compared with day-3 flowers’ pollen, hyperpolarization-activated Ca²⁺ current density was significantly lower in day 0 and day 3 flowers’ pollen, which was consistent with the pollen germination and pollen tube growth, indicating that pollen protoplasts’ increased Ca²⁺ current density may have enhanced the pollen viability. During pollen tube elongation, pollen tube plasma membrane Ca²⁺ current density increased with increased length pollen tubes up to 300 μm. All of these results indicated that hyperpolarization-activated Ca²⁺ channel activity was associated with in pear pollen development and may have a causal link between Ca²⁺ channel activity and pollen viability.     

Genome sequences of five Salmonella enterica serovar Heidelberg isolates associated with a 2011 multistate outbreak in the United States

Salmonella enterica serovar Heidelberg has caused numerous outbreaks in humans. Here, we report draft genomes of five isolates of serovar Heidelberg associated with the recent (2011) multistate outbreak linked to ground turkey in the United States. Isolates 2011K-1110 and 2011K-1132 were recovered from humans, while isolates 2011K-1138, 2011K-1224, and 2011K-1225 were recovered from ground turkey. Whole-genome sequence analysis of these isolates provides a tool for studying the short-term evolution of these epidemic clones.     

Impact of warm ischemia on gene expression analysis in surgically removed biosamples

Surgically removed samples of high quality provide more accurate and reliable results in downstream molecular assays. Some factors, including the type of anesthesia, surgical manipulation, transport time and mode, preservation method, storage length, and number of freeze-thaw cycles, can affect biosample quality and the subsequent gene expression analysis. Warm ischemia resulting from these factors has a substantial effect on biosample quality and is the focus of this mini review. We classified the effects of warm ischemia on gene expression as (i) warm ischemia-induced metabolic activity (WIMA) in living cells and (ii) warm ischemia-induced RNA degradation (WIRD). The differential effects of WIMA and WIRD on gene expression analysis appear to depend on the period after surgical removal. WIMA predominantly affects gene expression during the early stage after surgery, whereas WIRD has a more significant effect after tissue thawing. By a literature review, we also found that RNA isolated from surgically removed biopsies is stable, and high-quality RNA can be obtained for most nonfixed human tissue maintained at room temperature during the early period after surgery. Understanding these characteristics of gene expression variation should help biomedical researchers to avoid misleading gene expression results.