GenomeGems: evaluation of genetic variability from deep sequencing data

ABSTRACT: BACKGROUND: Detection of disease-causing mutations using Deep Sequencing technologies possesses great challenges. In particular, organizing the great amount of sequences generated so that mutations, which might possibly be biologically relevant, are easily identified is a difficult task. Yet, for this assignment only limited automatic accessible tools exist. Findings: We developed GenomeGems to gap this need by enabling the user to view and compare Single Nucleotide Polymorphisms (SNPs) from multiple datasets and to load the data onto the UCSC Genome Browser for an expanded and familiar visualization. As such, via automatic, clear and accessible presentation of processed Deep Sequencing data, our tool aims to facilitate ranking of genomic SNP calling. GenomeGems runs on a local Personal Computer (PC) and is freely available at http://www.tau.ac.il/~nshomron/GenomeGems.     

Novel N-Acylethanolamide Derivatives Affect Body Weight and Energy Balance

Introduction – The obesity pandemic is multifactorial. Nutritional, pharmacologic and surgical interventions are limited in reach and efficacy, raising need for new therapeutics. Aims – Characterization of anorexigenic and cognitive effect and central mechanism of action of novel N-acylethanolamide derivatives. Methods – Sabra mice divided to similar experimental groups, injected IP with: oleyl-L-leucinolamide ( 1 A ), linoleyl-L-leucinolamide ( 4 A ), linoleyl-L-valinolamide ( 5 A ), oleyl-oxycarbonyl-L-valinolamide ( 1 B ), oleyl-oxycarbonyl-D-valinolamide ( 2 B ), oleylamine-carbonyl-L-valinolamide ( 3 B ), oleylamine-carbonyl-D-valinolamide ( 4 B ), and oleyl-L-hydroxyvalineamide ( 5 B ). Control group with vehicle. Body weight and food consumption followed for 39 days. Motor activity and cognitive function by open field test and eight-arm maze. Mice sacrificed and mechanism of action investigated by qPCR. The genes analyzed involved in energy balance and regulation of appetite. Catecholamines and serotonin evaluated. Results – Compounds 1 A , 5 A , 1 B – 4 B , caused significant weight loss of 4.2–5.6 % and 5 A , 1 B – 4 B , improved cognitive function following 8 i. p. injections of 1 mg/kg during 39 days, by different mechanisms. 5 A , 3 B and 4 B decreased food consumption, whereas 1 A , 5 A and 2 B increased motor activity. 1 A , 4 A , 1 B and 3 B elevated SIRT-1, associated with survival. POMC upregulated by 1 B and 2 B , CART by 1 B , 2 B and 1 A . NPY and CAMKK2 downregulated by 5 A . 4 B enhanced 5-HT levels. 4 A , 5 A , 1 B , 4 B , 5 B decreased FAAH, showing long lasting effect. Conclusions – These new compounds might be developed for the treatment of obesity and for improved cognitive function.     

Newly Synthesized and Preformed Acetylcholine Are Released from Torpedo Synaptosomes by Different Pathways

In this study, we investigated the mechanisms underlying the release of preformed and of newly synthesized acetylcholine (ACh) from isolated Torpedo nerve terminals (synaptosomes). This was pursued by examining and comparing the effects of anticytoskeletal and anticalmodulin drugs and of activating the presynaptic muscarinic ACh receptors on the release of preformed endogenous ACh and of newly synthesized radiolabeled ACh. The anticytoskeletal drugs vinblastine, cytochalasin B, and colchicine inhibit the Ca2+-dependent K+-mediated release of newly synthesized radiolabeled ACh, but have no effect on the release of preformed ACh. By contrast, the muscarinic agonist oxotremorine markedly inhibits the release of preformed ACh, but has little effect on the release of newly formed ACh. Treatment of the synaptosomes with the calmodulin antagonist trifluoperazine inhibits the release of both ACh pools concomitantly. These findings show that preformed and newly synthesized ACh are released by different routes and suggest that their secretion is mediated by converging pathways. The significance of these results in view of the previously demonstrated preferential release of newly synthesized ACh is discussed.     

Testing the growth rate and translation compensation hypotheses in marine bacterioplankton

Two different hypotheses have been raised as to how temperature affects resource allocation in microorganisms. The translation-compensation hypothesis (TCH) predicts that the increase in enzymatic efficiency with temperature results in fewer required ribosomes per cell and lower RNA:protein ratio. In contrast, the growth rate hypothesis (GRH) predicts that increasing the growth rate with temperature requires more ribosomes and hence a higher cellular RNA:protein. We tested these two hypotheses in laboratory cultures of Prochlorococcus and Alteromonas as well as over an annual cycle in the Eastern Mediterranean Sea. The RNA:protein of Alteromonas mostly decreased with temperature in accordance with the TCH, while that of Prochlorococcus increased with temperature, as predicted by the GRH. No support was found for either hypothesis in surface waters from the Eastern Mediterranean, whereas the fraction of phosphorus in RNA was positively correlated with per-cell bacterial production in the deep chlorophyll maximum, supporting the GRH in this niche. A considerable part of the cellular phosphorus was not allocated to RNA, DNA, phospholipids or polyphosphate, raising the question which cellular molecules contain these P reserves. While macromolecular quotas differed significantly between laboratory cultures and field samples, these were connected through a power law, suggesting common rules of resource allocation.     

Bi-directional electron transfer between H2 and NADPH mitigates light fluctuation responses in green algae

The metabolism of green algae has been the focus of much research over the last century. These photosynthetic organisms can thrive under various conditions and adapt quickly to changing environments by concomitant usage of several metabolic apparatuses. The main electron coordinator in their chloroplasts, nicotinamide adenine dinucleotide phosphate (NADPH), participates in many enzymatic activities and is also responsible for inter-organellar communication. Under anaerobic conditions, green algae also accumulate molecular hydrogen (H₂), a promising alternative for fossil fuels. However, to scale-up its accumulation, a firm understanding of its integration in the photosynthetic apparatus is still required. While it is generally accepted that NADPH metabolism correlates to H₂ accumulation, the mechanism of this collaboration is still vague and relies on indirect measurements. Here, we investigated this connection in Chlamydomonas reinhardtii using simultaneous measurements of both dissolved gases concentration, NADPH fluorescence and electrochromic shifts at 520–546 nm. Our results indicate that energy transfer between H₂ and NADPH is bi-directional and crucial for the maintenance of redox balance under light fluctuations. At light onset, NADPH consumption initially eventuates in H₂ evolution, which initiates the photosynthetic electron flow. Later on, as illumination continues the majority of NADPH is diverted to the Calvin–Benson–Bassham cycle. Dark onset triggers re-assimilation of H₂, which produces NADPH and so, enables initiation of dark fermentative metabolism.

Energy transfer between H₂ and NADPH is bi-directional and crucial for the maintenance of redox balance under light fluctuations.