A genealogical approach to quantifying lineage divergence

We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.     

Decreased iPLA2gamma expression induces lipid peroxidation and cell death and sensitizes cells to oxidant-induced apoptosis

Our previous studies showed that renal proximal tubular cells (RPTC) express Ca(2+)-independent phospholipase A(2)gamma (iPLA(2)gamma) in endoplasmic reticulum (ER) and mitochondria and that iPLA(2)gamma prevents and/or repairs lipid peroxidation induced by oxidative stress. Our present studies determined the importance of iPLA(2)gamma in mitochondrial and cell function using an iPLA(2)gamma-specific small hairpin ribonucleic acid (shRNA) adenovirus. iPLA(2)gamma expression and activity were decreased in the ER by 24 h and in the mitochondria by 48 h compared with scrambled shRNA adenovirus-treated cells. Lipid peroxidation was elevated by 2-fold at 24 h and remained elevated through 72 h in cells with decreased iPLA(2)gamma. Using electrospray ionization-mass spectrometry, primarily phosphatidylcholines and phosphatidylethanolamines were increased in iPLA(2)gamma-shRNA-treated cells. At 48 h after exposure to the iPLA(2)gamma shRNA, uncoupled oxygen consumption was inhibited by 25% and apoptosis was observed at 72 and 96 h. RPTC with decreased iPLA(2)gamma expression underwent apoptosis when exposed to a nonlethal concentration of the oxidant tert-butyl hydroperoxide (TBHP). Exposure of control cells to a nonlethal concentration of TBHP induced iPLA(2)gamma expression in RPTC. These results suggest that iPLA(2)gamma is required for the prevention and repair of basal lipid peroxidation and the maintenance of mitochondrial function and viability, providing further evidence for a cytoprotective role for iPLA(2)gamma from oxidative stress.     

原核表达载体pOPE101-8E5的改构及单链抗体的表达鉴定

本研究利用基因重组技术将链亲和素(core-streptavidin)cDNA插入原核表达载体pOPE101-8E5的3′端,并用单链抗体scFv-C4的重链和轻链可变区cDNA取代其scFv-8E5,构建重组表达载体pOPE101-C4::core-streptavidin。将该表达载体转化入在大肠杆菌中进行诱导表达,用聚丙烯酰胺凝胶电泳和免疫印迹法分析表达产物的表达量和产物活性。结果提示我们成功地获得一个分子量约为45kDa的scFv-C4::core-streptavidin的融合蛋白,它可结合KG1a细胞裂解物中分子量约为60kDa、45kDa的蛋白带,且其结合功能可以通过融合蛋白中的链亲和素基因直接测定。     

Use of Tape‐Recorded Food Records in Assessing Children's Dietary Intake

Background: Dietary assessment among children is particularly problematic when techniques are dependent on memory skills or advanced cognitive development. Objective: The current study explored the use of self‐report by tape recorders to document children's dietary intake immediately upon consumption, and compared this method with the traditional, interviewer‐guided recall technique. In addition, the influence of body fatness and sociodemographic characteristics on the accuracy of recall and tape‐recorded food records was determined. Research Methods and Procedures: The sample included 30 black and white children aged 6.5 to 11.6 years (x¯ = 9.5). Energy intake (EI), measured by six 24‐hour food records (three for each method), was compared with total energy expenditure calculated by the doubly labeled water technique. Paired t tests, correlation analyses, and multiple re‐gression analyses were performed. Results: The analyses revealed poor validity of the tape recorder method (x¯ misreporting score = ?1.13 ± 2.62 MJ/day, r for total energy expenditure and EI = ?0.06, p = 0.74). Estimates of EI differed significantly between the tape recorder and recall methods (p < 0.01). The traditional recall method was confirmed as a valid estimate of energy intake (x¯ misreporting score = 0.04 ± 2.38 MJ/day), although demonstrating a modest correlation with TEE (r = 0.32, p = 0.08). Although no significant predictors of misreporting using the recall method were identified in the multivariate analyses, older children and children with higher adiposity were more likely to misreport using the tape recorder method. Discussion: The results suggest that the use of the tape recorder for estimating EI does not result in accurate assessments among children, although this techniquemay be useful for specific subgroups (i.e., younger and leaner children).     

The Diversity and Distribution of the Fruit Bat Fauna (Mammalia, Chiroptera, Megachiroptera) of Danjugan Island, Cauayan, Negros Occidental, Philippines (with Notes on the Microchiroptera)

Bats are the most diverse mammalian order in the Philippines and whilst many endemic and threatened species have been documented, they are also probably the least well-known order. Negros Island (central Visayas, Philippines) represents one of the ten highest-ranking sites globally for megachiropteran diversity, and is listed as a priority area for the establishment of protected areas for megachiropteran conservation. It is also listed as a priority site for survey work. The current study undertook mist-netting, roost and observation surveys of the bat fauna of Danjugan Island, off the west coast of Negros Occidental, to inventory the bat species present and to provide baseline ecological information to identify key areas of conservation concern. Eight species – five megachiropterans and three microchiropterans – were recorded over the course of the study, representing over 10% of the total Philippine bat fauna. Four of the species are new records for the island, and three are IUCN Red Listed. The results show that the island provides important cave- and tree-roosting areas for the local populations of several endemic and globally endangered species and sub-species. Already designated with reserve status, and with an environmental education programme established within the local communities, the island may be considered of national and global importance for bat conservation. Recommendations are given for future management.     

The Impact of Bioaugmentation on Metal Cyanide Degradation and Soil Bacteria Community Structure

Metal cyanides are significant contaminants of many soils found at the site of former industrial activity. In this study we isolated bacteria capable of degrading ferric ferrocyanide and K₂Ni(CN)₄. One of these bacteria a Rhodococcus spp. was subsequently used to bioaugment a minimal medium broth, spiked with K₂Ni(CN)₄, containing 1 g of either an uncontaminated topsoil or a former coke works site soil. Degradation of the K₂Ni(CN)₄ was observed in both soils, however, bioaugmentation did not significantly impact the rate or degree of K₂Ni(CN)₄ removal. Statistical analysis of denaturing gradient gel electrophoresis profiles showed that the topsoil bacterial community had a higher biodiversity, and its structure was not significantly affected by either K₂Ni(CN)₄ or bioaugmentation. In contrast, profiles from the coke works site indicated significant changes in the bacterial community in response to these additions. Moreover, in both soils although bioaugmentation did not affect rates of biodegradation the Rhodococcus spp. did become established in the communities in broths containing both top and coke works soil. We conclude that bacterial communities from contaminated soils with low biodiversity are much more readily perturbed through interventions such as contamination events or bioaugmentation treatments and discuss the implications of these findings for bioremediation studies.     

Gametogenesis in malaria parasites is mediated by the cGMP-dependent protein kinase

Malaria parasite transmission requires differentiation of male and female gametocytes into gametes within a mosquito following a blood meal. A mosquito-derived molecule, xanthurenic acid (XA), can trigger gametogenesis, but the signalling events controlling this process in the human malaria parasite Plasmodium falciparum remain unknown. A role for cGMP was revealed by our observation that zaprinast (an inhibitor of phosphodiesterases that hydrolyse cGMP) stimulates gametogenesis in the absence of XA. Using cGMP-dependent protein kinase (PKG) inhibitors in conjunction with transgenic parasites expressing an inhibitor-insensitive mutant PKG enzyme, we demonstrate that PKG is essential for XA- and zaprinast-induced gametogenesis. Furthermore, we show that intracellular calcium (Ca²⁺) is required for differentiation and acts downstream of or in parallel with PKG activation. This work defines a key role for PKG in gametogenesis, elucidates the hierarchy of signalling events governing this process in P. falciparum, and demonstrates the feasibility of selective inhibition of a crucial regulator of the malaria parasite life cycle.     

Characterization of a randomized FRET library for protease specificity determination

Protease specificity determination is an important first step when characterizing novel proteases. Given the large number of proteases that are known to exist from genomic sequencing efforts, we reason that sensitive, reliable, and high-throughput methods to determine protease specificity must be developed. This study describes the construction and initial characterization of a protein based FRET library using the fluorescent proteins GFP and DsRed for such a purpose. Using a DNA "cassette" that allowed for directional insertion of annealed oligonucleotides between the genes encoding the GFP and DsRed proteins, we constructed a library using a mixture of standard nucleotide bases at 27 positions in the center of the oligonucleotide cassette. This resulted in a randomized linker region between these fluorescent donor-acceptor pairs to produce substrates with varied amino acids located between the proteins. Kinetic assays were then performed and monitored using the increase in GFP fluorescence to arrive at relative reaction velocities for a set of enzymes. These results demonstrated the ability of the enzymes tested to discriminate between different substrates and the resistance of GFP and DsRed to proteolysis. Colony screening, using color development and restriction enzyme digests, were shown to help eliminate DNA samples in the library that contained stop codons and/or deletions and a flow plan for the efficient use of the library is presented.     

Sexual and social stimuli elicit rapid and contrasting genomic responses

Sensory physiology has been shown to influence female mate choice, yet little is known about the mechanisms within the brain that regulate this critical behaviour. Here we examine preference behaviour of 58 female swordtails, Xiphophorus nigrensis, in four different social environments (attractive and unattractive males, females only, non-attractive males only and asocial conditions) followed by neural gene expression profiling. We used a brain-specific cDNA microarray to identify patterns of genomic response and candidate genes, followed by quantitative PCR (qPCR) examination of gene expression with variation in behaviour. Our microarray results revealed patterns of genomic response differing more between classes of social stimuli than between presence versus absence of stimuli. We identified suites of genes showing diametrically opposed patterns of expression: genes that are turned 'on' while females interact with attractive males are turned 'off' when interacting with other females, and vice versa. Our qPCR results identified significant predictive relationships between five candidate genes and specific mate choice behaviours (preference and receptivity) across females exposed to males, with no significant patterns identified in female or asocial conditions or with overall locomotor activity. The identification of stimulus- and behaviour-specific responses opens an exciting window into the molecular pathways associated with social behaviour and mechanisms that underlie sexual selection.