Homology model of the human tRNA splicing ligase RtcB

RtcB is an essential human tRNA ligase required for ligating the 2',3'‐cyclic phosphate and 5'‐hydroxyl termini of cleaved tRNA halves during tRNA splicing and XBP1 fragments during endoplasmic reticulum stress. Activation of XBP1 has been implicated in various human tumors including breast cancer. Here we present, for the first time, a homology model of human RtcB (hRtcB) in complex with manganese and covalently bound GMP built from the Pyrococcus horikoshii RtcB (bRtcB) crystal structure, PDB ID 4DWQA. The structure is analyzed in terms of stereochemical quality, folding reliability, secondary structure similarity with bRtcB, druggability of the active site binding pocket and its metal‐binding microenvironment. In comparison with bRtcB, loss of a manganese‐coordinating water and movement of Asn226 (Asn202 in 4DWQA) to form metal‐ligand coordination, demonstrates the uniqueness of the hRtcB model. Rotation of GMP leads to the formation of an additional metal‐ligand coordination (Mn‐O). Umbrella sampling simulations of Mn binding in wild type and the catalytically inactive C122A mutant reveal a clear reduction of Mn binding ability in the mutant, thus explaining the loss of activity therein. Our results furthermore clearly show that the GTP binding site of the enzyme is a well‐defined pocket that can be utilized as target site for in silico drug discovery.     

Environmental isolates of Aeromonas spp. harboring the cagA-like gene of Helicobacter pylori

We investigated the presence of cagA-like gene of Helicobacter pylori in environmental isolates of Aeromonas spp. from different water samples of Calcutta, India, by colony hybridization using a cagA-specific DNA probe and by PCR with cagA-specific primers. Nucleotide sequencing of five PCR products revealed 97 to 98% homology to canonical cagA of H. pylori 26695 as well as to four clinical H. pylori strains from Calcutta. The cagA-like gene of the environmental isolates was unstable in laboratory conditions and tended to be lost upon subculturing.     

Individualizing breast cancer treatment—The dawn of personalized medicine

Identification of breast cancer not being a single disease but backed by multiple heterogeneous oncogenic subpopulations is of growing interest in developing personalized therapies to provide optimal outcomes. Through this review, we bring attention to evolution of tumor and microenvironment heterogeneity as a predominant challenge in stratifying therapies. Establishment of a ‘precancer niche’ serves as a prerequisite for genetically initiated cells to survive and promote neoplastic evolution towards clinically established cancer through development of tumor and its microenvironment. Additionally, continuous evolutionary interplay between tumor and recruited stromal cells along with many other components in the tumor microenvironment adds up to further complexity in developing targeted therapies. However, through continued excellence in developing high throughput technologies including the advent of single-nucleus sequencing, which makes it possible to sequence individual tumor cells, leads to improved abilities in decoding the heterogenic perturbations through reconstruction of tumor evolutionary lineages. Furthermore, simple liquid-biopsies in form of enumeration/characterization of circulating tumor cells and tumor microvesicles found in peripheral circulation, shed from distinct tumor lesions, show great promise as prospective biomarkers towards better prognosis in tailoring individualized therapies to breast cancer patients. Lastly, by means of network medicinal approaches, it is seemingly possible to develop a map of the cell's intricate wiring network, helping to identify appropriate interconnected protein networks through which the disease spreads, offering a more patient-specific outcome. Although these therapeutic interventions through designing personalized oncology-based trials are promising, owing to continuous tumor evolution, targeting genome instability survival pathways might become an economically viable alternative.     

Histochemical study on localization of adenosine triphosphatase and 5-nucleotidase in the olfactory bulb of the rat

Summary In the present paper, a histochemical study of the localization of adenosine triphosphatase and 5-nucleotidase in fixed frozen sections of rat olfactory bulb has been carried out by Wachstein and Meisel's method. The structures showing positive reaction are the neurons and blood vessels. The neurons show a wide range of variation of reaction in both intensity as well as distribution. The nucleolus shows an intense and variable reaction and the significance of these have been discussed. The reaction in the cytoplasm is diffuse when it is mild but tends to concentrate toward the cell wall as the intensity increases. It is suggested that the nucleolus may play an important role in the synthesis of the enzymes which can take part in providing the energy needed for the molecular transport concerned with the coduction of nerve impulses.     

Estradiol-induced expression of N(+)-K(+)-ATPase catalytic isoforms in rat arteries: gender differences in activity mediated by nitric oxide donors

We tested the hypothesis that previously demonstrated gender differences in ACh-induced vascular relaxation could involve diverse Na(+)-K(+)-ATPase functions. We determined Na(+)-K(+)-ATPase by measuring arterial ouabain-sensitive 86Rb uptake in response to ACh. We found a significant increase of Na+ pump activity only in aortic rings from female rats (control 206 +/- 11 vs. 367 +/- 29 nmol 86Rb/K.min(-1).g wt tissue(-1); P < 0.01). Ovariectomy eliminated sex differences in Na(+)-K(+)-ATPase function, and chronic in vivo hormone replacement with 17beta-estradiol restored the ACh effect on Na(+)-K(+)-ATPase. Because ACh acts by enhancing production of NO, we examined whether the NO donor sodium nitroprusside (SNP) mimics the action of ACh on Na(+)-K(+)-ATPase activity. SNP increased ouabain-sensitive 86Rb uptake in denuded female arteries (control 123 +/- 7 vs. 197 +/- 12 nmol 86Rb/K.min(-1).g wt tissue(-1); P < 0.05). Methylene blue (an inhibitor of guanylate cyclase) and KT-5823 (a cGMP-dependent kinase inhibitor) blocked the stimulatory action of SNP. Exposure of female thoracic aorta to the Na+/K+ pump inhibitor ouabain significantly decreased SNP-induced and ACh-mediated relaxation of aortic rings. At the molecular level, Western blot analysis of arterial tissue revealed significant gender differences in the relative abundance of catalytic isoforms of Na(+)-K(+)-ATPase. Female-derived aortas exhibited a greater proportion of alpha2-isoform (44%) compared with male-derived aortas. Furthermore, estradiol upregulated the expression of alpha2 mRNA in male arterial explants. Our results demonstrate that enhancement of ACh-induced relaxation observed in female rats may be in part explained by 1) NO-dependent increased Na(+)-K(+)-ATPase activity in female vascular tissue and 2) greater abundance of Na(+)-K(+)-ATPase alpha2-isoform in females.     

Primary structure, recombinant expression, and molecular characterization of Phl p 4, a major allergen of timothy grass (Phleum pratense)

Grass pollen allergy is one of the most important allergic diseases world-wide. Several meadow grasses, like timothy grass and rye grass, contribute to allergic sensitizations, but also allergens from extensively cultivated cereals, especially rye, make a profound contribution. The group 4 allergens are well known as important major allergens of grasses. We have cloned for the first time group 4 sequences from Phleum pratense, Lolium perenne, Secale cereale, Triticum aestivum, and Hordeum vulgare, and investigated the IgE-reactivity of recombinant Phl p 4 as a candidate for allergy diagnostic and therapeutic applications.     

Alkalinity and dissolved oxygen as controlling parameters for ammonia removal through partial nitritation and ANAMMOX in a single-stage bioreactor

The oxidation of ammonia to dinitrogen through partial nitritation and anaerobic ammonium oxidation (ANAMMOX) in a single-stage bioreactor is based on suppressing the nitratation process. The single-stage process operated on a laboratory-scale fixed film bioreactor achieved ammonia removal of 0.7 kg NH₄-N/(m³ day) at 4 h hydraulic retention time (HRT) by controlling the nitratation process through a ‘three-way control mechanism’ comprising control of electron donor (nitrite), electron acceptor (oxygen) and carbon source (bicarbonate). The control of alkalinity and dissolved oxygen (DO) concentrations in feed to maintain an alkalinity to ammonia ratio of less than 8 and DO loading of less than 0.06 mg O/(mg N day), respectively, was necessary for inhibiting nitratation and enhancing partial nitritation and ANAMMOX. Therefore, feed alkalinity along with DO concentrations are critical controlling parameters in a single-stage biological process for nitrogen removal.     

Photosynthesis and water-use efficiency of some mangroves from Sundarbans, India

We studied seasonal fluctuations in the rates of photosynthesis, transpiration, PAR, and stomatal conductance for 16 species of true mangroves from the Sundarbans region of West Bengal. Soil salinity and pH were also measured. Leaf temperatures were almost always higher than the ambient temperature. We observed considerable seasonal (summer vs winter) as well as interspecific variations in photosynthesis, with the highest rates occurring inHeritiera fomes (13.21 pmol m^-2s^-1) andAvicennia marina (11.8 mol m^-2s^-1), and the lowest inNypa fruticans (1.56 mol m^-2s^-1) andCeriops decandra (2.32 pmol m^-2s^-1), in many species, an abrupt rise in leaf temperature retarded the photosyn-thetic process. In winter, the rate of transpiration and stomatal conductance reached their maxima inA. marina (4.83 mmol ra^-2s^-1 and 124.23 m mol m^-2s^-1, respectively) and their mimima inExcoecaria agallocha (1.85 mmol m^-2s^-1 and 49.19 mmol m^-2s^-1, respectively). In contrast, the maximum summer readings were recorded in E.agallocha (6.07 mmol m^-2s^-1 and 192.74 mmol m^-2s^-1 respectively).     

EXPERIMENTAL EVOLUTION OF FEMALE TRAITS UNDER DIFFERENT LEVELS OF INTERSEXUAL CONFLICT IN DROSOPHILA MELANOGASTER

A number of studies have documented the evolution of female resistance to mate‐harm in response to the alteration of intersexual conflict in the populations. However, the life‐history consequence of such evolution is still a subject of debate. In this study, we subjected replicate populations of Drosophila melanogaster to different levels of sexual conflict (generated by altering the operational sex ratio) for over 45 generations. Our results suggest that females from populations experiencing higher level of intersexual conflict evolved increased resistance to mate‐harm, in terms of both longevity and progeny production. Females from the populations with low conflict were significantly heavier at eclosion and were more susceptible to mate‐harm in terms of progeny production under continuous exposure to the males. However, these females produced more progeny upon single mating and had significantly higher longevity in absence of any male exposure—a potential evidence of trade‐offs between resistance‐related traits and other life‐history traits, such as fecundity and longevity. We also report tentative evidence, suggesting an increased male cost of interacting with more resistant females.     

Synergistic Combinations of Nucleoside Analog Drugs with Other Drugs Induce Greater Apoptosis in Human Leukemic T-Cells

Abstract

Combinations of nucleoside analog drugs such as 6-MP. ara-C. or F-araA are synergistic against human leukemic T-cells and induce apoptotic cell death. Addition of Taxotere or PEG-ASNase to the synergistic combination of nucleoside analog drugs augments the synergism several fold by enhancing cellular apoptosis.