Fast-HBR: Fast hash based duplicate read remover

The Next-Generation Sequencing (NGS) platforms produce massive amounts of data to analyze various features in environmental samples. These data contain multiple duplicate reads which impact the analyzing process efficiency and accuracy. We describe Fast-HBR, a fast and memory-efficient duplicate reads removing tool without a reference genome using de-novo principles. It uses hash tables to represent reads in integer value to minimize memory usage for faster manipulation. Fast-HBR is faster and has less memory footprint when compared with the state of the art De-novo duplicate removing tools. Fast-HBR implemented in Python 3 is available at https://github.com/Sami-Altayyar/Fast-HBR.     

Rational design of biodegradable sulphonamide candidates treating septicaemia by synergistic dual inhibition of COX-2/PGE2 axis and DHPS enzyme

A new series of co-drugs was designed based on hybridising the dihydropteroate synthase (DHPS) inhibitor sulphonamide scaffold with the COX-2 inhibitor salicylamide pharmacophore through biodegradable linkage to achieve compounds with synergistic dual inhibition of COX-2/PGE2 axis and DHPS enzyme to enhance antibacterial activity for treatment of septicaemia. Compounds 5 b, 5j, 5n and 5o demonstrated potent in vitro COX-2 inhibitory activity comparable to celecoxib. 5j and 5o exhibited ED₅₀ lower than celecoxib in carrageenan-induced paw edoema test with % PGE2 inhibition higher than celecoxib. Furthermore, 5 b, 5j and 5n showed gastric safety profile like celecoxib. Moreover, in vivo antibacterial screening revealed that, 5j showed activity against S.aureus and E.coli higher than sulfasalazine. While, 5o revealed activity against E.coli higher than sulfasalazine and against S.aureus comparable to sulfasalazine. Compound 5j achieved the target goal as potent inhibitor of COX-2/PGE2 axis and in vivo broad-spectrum antibacterial activity against induced septicaemia in mice.     

1,3-Dipropyl-8-(1-phenylacetamide-1H-pyrazol-3-yl)-xanthine derivatives as highly potent and selective human A(2B) adenosine receptor antagonists

A new series of 1,3-dipropyl-8-(1-phenylacetamide-1H-pyrazol-3-yl)-xanthine derivatives has been identified as potent A(2B) adenosine receptor antagonists. The products have been evaluated for their binding affinities for the human A(2B), A(1), A(2A), and A(3) adenosine receptors. N-(4-chloro-phenyl)-2-[3-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-5-methyl-pyrazol-1-yl] (11c) showed a high affinity for the human A(2B) adenosine receptor K(i)=7nM and good selectivity (A(1), A(2A), A(3)/A(2B)>140). Synthesis and SAR of this novel class of compounds is presented herein.     

Angiotensin II and its receptors in human endocardial endothelial cells: role in modulating intracellular calcium

The aims of the present study are to investigate the presence and distribution of angiotensin II (Ang II), as well as AT1 and AT2 receptors, in endocardial endothelial cells (EECs) and to determine if the effect of Ang II on intracellular calcium in these cells is mediated via the AT1 or the AT2 receptor. Immunofluorescence and 3D confocal microscopy techniques were used on 20-week-old fetal human EECs. Our results showed that Ang II and its receptors, the AT1 and the AT2 types, are present and exhibit a different distribution in human EECs. Ang II labelling is found throughout the cell with a fluorescence signal higher in the cytosol when compared with the nucleus. Like Ang II, the AT1 receptor fluorescence signal is also homogeneously distributed in human EECs but with a preferential labelling at the level of the nucleus, while the AT2 receptor labelling is solely present in the nucleus. Using fluo-3 and 3D confocal microscopy technique, superfusion of human EECs with increasing concentration of Ang II induced a dose-dependent sustained increase in free cytosolic and nuclear Ca2+ levels. This effect of Ang II on human EEC's intracellular Ca2+ ([Ca2+]) was completely prevented by losartan, an AT1 receptor antagonist. Our results suggest that Ang II, as well as AT1 and AT2 receptors, is present but differentially distributed in EECs of 20-week-old fetal human hearts, and that the AT1 receptor mediates the effects of Ang II on [Ca2+]i in these cells.     

Growth stimulation and inhibition by salt in relation to Na<Superscript>+</Superscript> manipulating genes in xero-halophyte <Emphasis Type="Italic">Atriplex halimus</Emphasis> L.

In the present study, Na⁺ manipulating genes could contribute not only to ion homeostasis but also to growth stimulation with exposing the halophyte Atriplex halimus L. to moderate NaCl concentration. The stimulation of growth was attributed to Na⁺ accumulation inside the vacuole leading to increase leaf cell size as well as accelerate leaf cell division. Increasing the assimilatory surface could result in enhancing the photosynthetic rate. The reduction of A. halimus growth compared to optimum growth at 50 and 200 mM NaCl could be attributed to osmotic effect rather than the ionic one of salt stress. The inhibition of photosynthesis seemed to be resulted from limitation of CO₂ due to the osmotic effect on stomatal conductance rather than the activity loss of photosynthetic machinery. The depletion of starch content along with the increase in sucrose content could imply that photosynthesis may be a limiting for A. halimus growth. The fast coordinate induction of Na⁺ manipulating genes could reveal that the tolerance of A. halimus to high concentrations evolved from its ability to regulate and control Na⁺ influx and efflux. V-H ⁺-PPase may play a vital role in A. halimus tolerance to osmotic and/or ionic stress due to its kinetics of induction. It seemed that H⁺-ATPase plays a pivotal role in A. halimus tolerance to stress due to the increase in its protein level was detected with all NaCl concentrations as well as with PEG treatments. Both of these genes might be useful in improving stress tolerance in transgenic crops.     

Gadopentatic acid affects in vitro proliferation and doxorubicin response in human breast adenocarcinoma cells

Contrasting agents (CAs) that are administered to patients during magnetic resonance imaging to facilitate tumor identification are generally considered harmless. However, gadolinium (Gd) based contrast agents can be retained in the body, inflicting specific cell line cytotoxicity. We investigate the effect of Gadopentatic acid (Gd-DTPA) on human breast adenocarcinoma MCF-7 cells. These cells exhibit a toggle switch response: exposure to 0.1 and 1 mM concentrations of Gd-DTPA enhances proliferation, which is hindered at a higher 10 mM concentration. Proliferation is enhanced when cells transition to 3D morphologies in post confluent conditions. The proliferation dependence on the concentration of CA is absent for Hs 578T and MDA-MB-231 triple negative cell lines. MCF-7 cells reveal a double toggle switch related to the expression of VEGF, which goes through high–low–high downregulation when cells are exposed to 0.1, 1, and 10 mM Gd-DTPA, respectively. Finally, doxorubicin drug response is assessed, which also reveals a double toggle switch behavior, where drug cytotoxicity exhibits a nonlinear dependence on the CA concentration. A toggle switch in cell characteristics that are exposed to 1 mM of Gd-DTPA amplifies the importance of this threshold, affecting several cell behaviors if surpassed. This work emphasizes the important effects that CAs can have on cells, specifically Gd-DTPA on MCF-7 cells, and the implications for cell growth and drug response during clinical and synthetic biology procedures.     

Fast and efficient alkaline peroxide treatment to enhance the enzymatic digestibility of steam-exploded softwood substrates.

The enzymatic digestibility of steam-exploded Douglas-fir wood chips (steam exploded at 195 degrees C, 4.5 min, and 4.5% (w/w) SO(2)) was significantly improved using an optimized alkaline peroxide treatment. Best hydrolysis yields were attained when the steam-exploded material was post-treated with 1% hydrogen peroxide at pH 11.5 and 80 degrees C for 45 min. This alkaline peroxide treatment was applied directly to the water-washed, steam-exploded material eliminating the need for independent alkali treatment with 0.4% NaOH, which has been traditionally used to post-treat wood samples to try to remove residual lignin. Approximately 90% of the lignin in the original wood was solubilized by this novel procedure, leaving a cellulose-rich residue that was completely hydrolyzed within 48 h, using an enzyme loading of 10 FPU/g cellulose. About 82% of the originally available polysaccharide components of the wood could be recovered. The 18% of the carbohydrate that was not recovered was lost primarily to sugar degradation during steam explosion.