Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities

Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as no surprise that organizing ISCB-SC-related activities sometimes interferes with day-to-day research and shakes up your priority list. However, we unanimously agree that the rewards, both in the short as well as the long term, make the time spent on these extracurricular activities more than worth it. In this article, we will explain what makes this so worthwhile: soft skills.     

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context.

Availability

MACBenAbim is available from the authors for non-commercial purposes.     

Transition of hemoglobin between two tertiary conformations: The transition constant differs significantly for the major and minor hemoglobins of the Japanese quail (Cortunix cortunix japonica)

We demonstrate that 5,5'-dithiobis(2-nitrobenzoate) - DTNB - reacts with only CysF9[93]beta and CysB5[23]beta among the multiple sulfhydryl groups of the major and minor hemoglobins of the Japanese quail (Cortunix cortunix japonica). K(equ), the equilibrium constant for the reaction, does not differ very significantly between the two hemoglobins. It decreases 430-fold between pH approximately 5.6 and pH approximately 9: from a mean of 7+/-1 to a mean of 0.016+/-0.003. Quantitative analyses of the K(equ) data based on published X-ray and temperature-jump evidence for a tertiary structure transition in liganded hemoglobin enable the calculation of K(rt), the equilibrium constant for the r<---->t tertiary structure transition. K(rt) differs significantly between the two hemoglobins: 0.744+/-0.04 for the major, 0.401+/-0.01 for the minor hemoglobin. The mean pK(a)s of the two groups whose ionizations are coupled to the DTNB reaction are about the same as previously reported for mammalian hemoglobins.     

Scavenging Rhodamine B dye using moringa oleifera seed pod

Moringa oliferia seed pod was modified using orthophosphoric acid (H₃PO₄) and used as adsorbent for sequestering Rhodamine B (Rh-B) dye from aqueous solution. The acid-modified adsorbent (MOSPAC) was characterized using Scanning Electron microscopy (SEM), Fourier Transform Infra Red (FTIR), Energy Dispersive X-ray (EDX), pH point of zero charge (pH_pzc) and Boehm Titration (BT) techniques, respectively. Operational parameters such as contact time, initial dye concentration, adsorbent dosage, pH and solution temperature were studied in batch process. Optimum dye adsorption was observed at pH 3.01. Equilibrium adsorption data was tested data using four different isotherm models: Langmuir, Freundlich, Temkin and Dubinin-Radushkevich. Langmuir isotherm model fitted most with maximum monolayer adsorption capacity of 1250 mg g^–1. Pseudo-second-order kinetic model provided the best correlation for the experimental data. Thermodynamic study showed that the process is endothermic, spontaneous and feasible. MOSPAC is an effective adsorbent for the removal of RhB dye from aqueous solutions.     

Catecholamines up integrates dopamine synthesis and synaptic trafficking

The highly reactive nature of dopamine renders dopaminergic neurons vulnerable to oxidative damage. We recently demonstrated that loss-of-function mutations in the Drosophila gene Catecholamines up (Catsup) elevate dopamine pools but, paradoxically, also confer resistance to paraquat, an herbicide that induces oxidative stress-mediated toxicity in dopaminergic neurons. We now report a novel association of the membrane protein, Catsup, with GTP cyclohydrolase rate-limiting enzyme for tetrahydrobiopterin (BH(4)) biosynthesis and tyrosine hydroxylase, rate-limiting enzyme for dopamine biosynthesis, which requires BH(4) as a cofactor. Loss-of-function Catsup mutations cause dominant hyperactivation of both enzymes. Elevated dopamine levels in Catsup mutants coincide with several distinct characteristics, including hypermobility, minimal basal levels of 3,4-dihydroxy-phenylacetic acid, an oxidative metabolite of dopamine, and resistance to the vesicular monoamine transporter inhibitor, reserpine, suggesting that excess dopamine is synaptically active and that Catsup functions in the regulation of synaptic vesicle loading and release of dopamine. We conclude that Catsup regulates and links the dopamine synthesis and transport networks.     

Spatial Patterns in the Distribution,Diversity and Abundance of Benthic Foraminifera around Moorea (Society Archipelago,French Polynesia)

Coral reefs are now subject to global threats and influences from numerous anthropogenic sources. Foraminifera, a group of unicellular shelled organisms, are excellent indicators of water quality and reef health. Thus we studied a set of samples taken in 1992 to provide a foraminiferal baseline for future studies of environmental change. Our study provides the first island-wide analysis of shallow benthic foraminifera from around Moorea (Society Archipelago). We analyzed the composition, species richness, patterns of distribution and abundance of unstained foraminiferal assemblages from bays, fringing reefs, nearshore and back- and fore-reef environments. A total of 380 taxa of foraminifera were recorded, a number that almost doubles previous species counts. Spatial patterns of foraminiferal assemblages are characterized by numerical abundances of individual taxa, cluster groups and gradients of species richness, as documented by cluster, Fisher α, ternary plot and Principal Component Analyses (PCA). The inner bay inlets are dominated by stress-tolerant, mostly thin-shelled taxa of Bolivina, Bolivinella, Nonionoides, Elongobula, and Ammonia preferring low-oxygen and/or nutrient-rich habitats influenced by coastal factors such as fresh-water runoff and overhanging mangroves. The larger symbiont-bearing foraminifera (Borelis, Amphistegina, Heterostegina, Peneroplis) generally live in the oligotrophic, well-lit back- and fore-reef environments. Amphisteginids and peneroplids were among the few taxa found in the bay environments, probably due to their preferences for phytal substrates and tolerance to moderate levels of eutrophication. The fringing reef environments along the outer bay are characterized by Borelis schlumbergeri, Heterostegina depressa, Textularia spp. and various miliolids which represent a hotspot of diversity within the complex reef-lagoon system of Moorea. The high foraminiferal Fisher α and species richness diversity in outer bay fringing reefs is consistent with the disturbance-mosaic (microhabitat heterogeneity) hypothesis.Calculations of the FORAM Index (FI), a single metric index to assess reef vitality, indicate that all fore- and most back-reef environments support active carbonate accretion and provide habitat suitability for carbonate producers dependent on algal symbiosis. Lowest suitability values were recorded within the innermost bays, an area where natural and increasing anthropogenic influences continue to impact the reefs. The presence of habitat specific assemblages and numerical abundance values of individual taxa show that benthic foraminifera are excellent recorders of environmental perturbations and good indicators useful in modern and ancient ecological and environmental studies.     

Impact of Diabetes Mellitus on the Outcome of Pancreatic Cancer

Introduction

Diabetes mellitus (DM) has the potential to impact the pathogenesis, treatment, and outcome of pancreatic cancer. This study evaluates the impact of DM on pancreatic cancer survival.

Methods

We conducted a retrospective cohort study from the Veterans Affairs (VA) Central Cancer Registry (VACCR) for pancreatic cancer cases between 1995 and 2008. DM and no-DM cases were identified from comorbidity data. Univariate and multivariable analysis was performed. Multiple imputation method was employed to account for missing variables.

Results

Of 8,466 cases of pancreatic cancer DM status was known in 4728 cases that comprised this analysis. Males accounted for 97.7% cases, and 78% were white. Overall survival was 4.2 months in DM group and 3.6 months in the no-DM group. In multivariable analysis, DM had a HR = 0.91 (0.849–0.974). This finding persisted after accounting for missing variables using multiple imputations method with the HR in DM group of 0.93 (0.867–0.997).

Conclusions

Our data suggest DM is associated with a reduction in risk of death in pancreatic cancer. Future studies should be directed towards examining this association, specifically impact of DM medications on cancer outcome.     

Dtorsin, the Drosophila ortholog of the early-onset dystonia TOR1A (DYT1), plays a novel role in dopamine metabolism

Dystonia represents the third most common movement disorder in humans. At least 15 genetic loci (DYT1-15) have been identified and some of these genes have been cloned. TOR1A (formally DYT1), the gene responsible for the most common primary hereditary dystonia, encodes torsinA, an AAA ATPase family protein. However, the function of torsinA has yet to be fully understood. Here, we have generated and characterized a complete loss-of-function mutant for dtorsin, the only Drosophila ortholog of TOR1A. Null mutation of the X-linked dtorsin was semi-lethal with most male flies dying by the pre-pupal stage and the few surviving adults being sterile and slow moving, with reduced cuticle pigmentation and thin, short bristles. Third instar male larvae exhibited locomotion defects that were rescued by feeding dopamine. Moreover, biochemical analysis revealed that the brains of third instar larvae and adults heterozygous for the loss-of-function dtorsin mutation had significantly reduced dopamine levels. The dtorsin mutant showed a very strong genetic interaction with Pu (Punch: GTP cyclohydrolase), the ortholog of the human gene underlying DYT14 dystonia. Biochemical analyses revealed a severe reduction of GTP cyclohydrolase protein and activity, suggesting that dtorsin plays a novel role in dopamine metabolism as a positive-regulator of GTP cyclohydrolase protein. This dtorsin mutant line will be valuable for understanding this relationship and potentially other novel torsin functions that could play a role in human dystonia.     

A soluble beta-cyanoalanine synthase from the gut of the variegated grasshopper Zonocerus variegatus (L.)

Beta-cyanoalanine synthase (beta-cyano-l-alanine synthase; l-cysteine: hydrogen sulphide lyase (adding hydrogen cyanide (HCN)); EC 4. 4.1.9) was purified from the cytosolic fraction of the gut of grasshopper Zonocerus variegatus (L.) by ion-exchange chromatography on DEAE-Cellulose and gel filtration on Sephadex G-100 columns. The crude enzyme had a specific activity of 2.16nmol H2S/min/mg. A purified enzyme with a specific activity, which was seventeen times higher than that of the crude extract, was obtained. A molecular weight of about 55.23+/-1.00Kd was estimated from its elution volume on Sephadex G-100. The fraction when subjected to sodium dodecyl sulphate-polyacrylamide elel electrophoresis revealed the presence of a protein band with Mr of 23.25+/-0.25Kd. The enzyme exhibited Michaelis-Menten kinetics having Km of 0.38mM for l-cysteine and Km of 6.25mM for cyanide. The optimum temperature and pH for activity were determined to be at 30 degrees C and pH 9.0, respectively. This enzyme might be responsible for the ability to detoxify cyanide in this insect pest and hence its tolerance of the cyanogenic cassava plant. Biophysical, biochemical and kinetic properties of this enzyme, which will reveal how this ability can possibly be compromised by enzyme inhibition, may lead, in the long term, to the potential use of this enzyme as drug target for pest control.