The Making of the Women in Biology Forum (WiB) at Bioclues

The Women in Biology forum (WiB) of Bioclues (India) began in 2009 to promote and support women pursuing careers in bioinformatics and computational biology. WiB was formed in order to help women scientists deprived of basic research, boost the prominence of women scientists particularly from developing countries, and bridge the gender gap to innovation. WiB has also served as a platform to highlight the work of established female scientists in these fields. Several award-winning women researchers have shared their experiences and provided valuable suggestions to WiB. Headed by Mohanalatha Chandrasekharan and supported by Dr. Reeta Rani Singhania and Renuka Suravajhala, WiB has seen major progress in the last couple of years particularly in the two avenues Mentoring and Research, off the four avenues in Bioclues: Mentoring, Outreach, Research and Entrepreneurship (MORE).In line with the Bioclues vision for bioinformatics in India, the WiB Journal Club (JoC) recognizes women scientists working on functional genomics and bioinformatics, and provides scientific mentorship and support for project design and hypothesis formulation. As a part of Bioclues, WiB members practice the group''s open-desk policy and its belief that all members are free to express their own thoughts and opinions. The WiB forum appreciates suggestions and welcomes scientists from around the world to be a part of their mission to encourage women to pursue computational biology and bioinformatics.     

AB0 blood group incompatibility and inbreeding effects: Evidence for an interaction

Summary It is known that consanguinity reduces the chances of maternal-foetal incompatibility but it is not known whether inbreeding influences the expression of the effects of such incompatibility. This paper investigates and finds evidence for an interaction between inbreeding and AB0 blood group incompatibility on the expression of neonatal mortality, sibship precocious mortality, neonatal jaundice, asphyxia, and sex ratio, through screening of 3923 consecutive newborns. Inbreeding and incompatibility individually showed variable effects on the above parameters, but their interaction was such that, in the presence of inbreeding, incompatibility reduced the incidence/relative risk of all the above factors. Such a uniform negative interaction was presumed to be due to homozygosity of some pleiotropic genes caused by inbreeding.     

Microalgae as multi-functional options in modern agriculture: current trends,prospects and challenges

Algae are a group of ubiquitous photosynthetic organisms comprising eukaryotic green algae and Gram-negative prokaryotic cyanobacteria, which have immense potential as a bioresource for various industries related to biofuels, pharmaceuticals, nutraceuticals and feed. This fascinating group of organisms also has applications in modern agriculture through facilitating increased nutrient availability, maintaining the organic carbon and fertility of soil, and enhancing plant growth and crop yields, as a result of stimulation of soil microbial activity. Several cyanobacteria provide nitrogen fertilization through biological nitrogen fixation and through enzymatic activities related to interconversions and mobilization of different forms of nitrogen. Both green algae and cyanobacteria are involved in the production of metabolites such as growth hormones, polysaccharides, antimicrobial compounds, etc., which play an important role in the colonization of plants and proliferation of microbial and eukaryotic communities in soil. Currently, the development of consortia of cyanobacteria with bacteria or fungi or microalgae or their biofilms has widened their scope of utilization. Development of integrated wastewater treatment and biomass production systems is an emerging technology, which exploits the nutrient sequestering potential of microalgae and its valorisation. This review focuses on prospects and challenges of application of microalgae in various areas of agriculture, including crop production, protection and natural resource management. An overview of the recent advances, novel technologies developed, their commercialization status and future directions are also included.     

Deletion of the putative effector region of Era, an essential GTP-binding protein in Escherichia coli, causes a dominant-negative phenotype

Abstract era is an essential gene in E. coli , encoding a GTP-binding protein of unknown function. In the present work, a mutant designated Era-dE, for deletion of effector region is described. This is the first and only known era allele that confers a dominant-negative phenotype. Phenotypic analysis of the mutant showed that overproduction of Era-dE caused a dominant inhibition of growth when TCA cycle intermediates such as succinate, pyruvate, malate, α-ketoglutarate, and fumarate were provided as the sole carbon source. Examination of the macromolecular composition of cells overexpressing the mutant showed protein, DNA, and ATP levels expected for cells growing at slow rates. The response of cells expressing Era-dE to different stress conditions was studied by examining the rates of synthesis of stress-inducible proteins. Interestingly, when subjected to succinate starvation, cells expressing Era-dE showed a defective carbon starvation response, whereas response to glucose starvation was similar to that seen in control cells. Taken together with previous results, these studies indicate that Era is perhaps involved in multiple cellular processes and Era-dE disrupts more than one of these functions. Furthermore, it appears that some possible functions of Era include regulation of the TCA cycle and response to carbon starvation.     

Development of a fluorescent transgenic zebrafish biosensor for sensing aquatic heavy metal pollution

We report a transgenic zebrafish (Danio rerio) designed to respond to heavy metals using a metal-responsive promoter linked to a fluorescent reporter gene (DsRed2). The metallothionein MT-Ia1 promoter containing metal-responsive elements was derived from the Asian green mussel, Perna viridis. The promoter is known to be induced by a broad spectrum of heavy metals. The promoter-reporter cassette cloned into the Tol2 transposon vector was microinjected into zebrafish embryos that were then reared to maturity. A transgene integration rate of 28 % was observed. The confirmed transgenics were mated with wild-type counterparts, and pools of F₁ embryos were exposed to sub-lethal doses of Cd²⁺, Cu²⁺, Hg²⁺, Pb²⁺ and Zn²⁺. The red fluorescence response of zebrafish embryos was observed 8 h post- exposure to these sub-lethal doses of heavy metals using a fluorescence microscope. Reporter expression estimated by real-time PCR revealed eightfold, sixfold and twofold increase on exposure to highest concentrations of Hg²⁺, Cd²⁺ and Cu²⁺, while Pb²⁺ and Zn²⁺ had no effect. This biosensor could be a first-level screening method for confirming aquatic heavy metal bio-toxicity to eukaryotes.     

Alteration of the acyl chain composition of free fatty acids,acyl coenzyme A and other liPids by dietary polyunsaturated fats

Dietary alterations were used to demonstrate selective handling of fatty acids during their redistributionin vivo. Differences in the mol Per cent of individual acyl chains in the non-esterified fatty acid, acyl-coenzyme A and PhosPholiPid fractions reflected a result of relative Precursor abundance combined with enzymic selectivities. Selective distributions were observed in the utilization of individual acyl chains between 16:0 and 18:0, 18:1 and 18:2, and among 20:3, 20:4 and 20:5, 22:6 by ligase(s), hydrolase(s) and acyl-transferases. The variations in the mol Per cent of linoleate Present in the acyl-coenzyme A fraction of liver relative to that in the non-esterified fatty acids suggested anin vivo regulation of the level of linoleoyl-coenzyme A that influenced the synthesis of both arachidonoyl-coenzyme A and lipids. The greater abundance of eicosaPentaenoic acid in the free fatty acid fraction relative to that in the acyl-coenzyme A fraction may increase the ability of dietary 20: 5n-3 to be an effective inhibitor of the synthesis of Prostaglandins derived from 20:4n-6.     

A possible regulatory role for ethylene in the pollen-pistil interaction in a sporophytic self-incompatible system

The sporophytic type of self-incompatibility exhibited by Ipomoea cairica Sweet (Convolvulaceae) was partially overcome in vitro by treating the pollen and/or stigma with 10^–6 to 10^–1 M methionine, a precursor of ethylene. The implications of these observations are discussed in relation to other experiments involving use of the ethylene antagonist AgNO₃, individually and in combination with methionine and an optimum level of indole-3-acetic acid (10^–2 M). The results suggest a role for ethylene (which could also be IAA-induced) in regulating pollen germination and further tube growth in sporophytic self-incompatible systems. A hypothesis on the action of hormones in pollen germination and tube growth in a sporophytic self-incompatible (SSI) system is presented.     

Exact Tests using Two Correlated Binomial Variables in Contemporary Cancer Clinical Trials

New therapy strategies for the treatment of cancer are rapidly emerging because of recent technology advances in genetics and molecular biology. Although newer targeted therapies can improve survival without measurable changes in tumor size, clinical trial conduct has remained nearly unchanged. When potentially efficacious therapies are tested, current clinical trial design and analysis methods may not be suitable for detecting therapeutic effects. We propose an exact method with respect to testing cytostatic cancer treatment using correlated bivariate binomial random variables to simultaneously assess two primary outcomes. The method is easy to implement. It does not increase the sample size over that of the univariate exact test and in most cases reduces the sample size required. Sample size calculations are provided for selected designs.