The kinase activity of the Helicobacter pylori Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase is sensitive to distal mutations in its putative ammonia tunnel

The Helicobacter pylori (Hp) Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase (AdT) plays important roles in indirect aminoacylation and translational fidelity. AdT has two active sites, in two separate subunits. Kinetic studies have suggested that interdomain communication occurs between these subunits; however, this mechanism is not well understood. To explore domain-domain communication in AdT, we adapted an assay and optimized it to kinetically characterize the kinase activity of Hp AdT. This assay was applied to the analysis of a series of point mutations at conserved positions throughout the putative AdT ammonia tunnel that connects the two active sites. Several mutations that caused significant decreases in AdT's kinase activity (reduced by 55-75%) were identified. Mutations at Thr149 (37 ? distal to the GatB kinase active site) and Lys89 (located at the interface of GatA and GatB) were detrimental to AdT's kinase activity, suggesting that these mutations have disrupted interdomain communication between the two active sites. Models of wild-type AdT, a valine mutation at Thr149, and an arginine mutation at Lys89 were subjected to molecular dynamics simulations. A comparison of wild-type, T149V, and K89R AdT simulation results unmasks 59 common residues that are likely involved in connecting the two active sites.     

Construction of a metagenomic library for the marine sponge Halichondria okadai

Symbionts of the marine sponge Halichondria okadai are promising as a source of natural products. Metagenomic technology is a powerful tool for accessing the genetic and biochemical potential of bacteria. Hence, we established a method of recovering bacterial-enriched metagenomic DNA by stepwise centrifugation. The metagenomic DNA was analyzed by ultrafast 454-pyrosequencing technology, and the results suggested that more than three types of bacterial DNA, Alphaproteobacteria, Actinobacteria, and Cyanobacteria, had been recovered, and that eukaryotic genes comprised only 0.02% of the metagenomic DNA. These results indicate that stepwise centrifugation and real-time quantitative PCR were effective for separating sponge cells and symbiotic bacteria, and that we constructed a bacteria-enriched metagenomic library from a marine sponge, H. okadai, selectively for the first time.     

N-terminal purification tag alters thermal stability of the carboxylesterase EstGtA2 from G. thermodenitrificans by impairing reversibility of thermal unfolding

The novel thermostable carboxylesterase EstGtA2 from G. thermodenitrificans (accession no. AEN92268) was functionally expressed and purified using an N-terminal fusion tag peptide. We recently reported general properties of the recombinant enzyme. Here we report preliminary data on thermal stability of EstGtA2 and of its tagged form. Conformational stability was investigated using circular dichroism and correlated with residual activity measurements using a colorimetric assay. The tag peptide had no considerable impact on the apparent melting temperature: T(m) value = 64.8°C (tagged) and 65.7°C (cleaved) at pH 8. After thermal unfolding, the tag-free enzyme rapidly recovered initial activity at 25°C (1.2 Umg(-1)), which was corroborated by substantial refolding (83%) as determined by far-UV CD transitions. However, after thermal unfolding, the purification tag drastically decreased specific activity at 25°C (0.07 Umg(-1)). This was corroborated by the absence of refolding transition. Although the purification tag has no undesirable impact on activity before thermal unfolding as well as on Tm, it drastically hinders EstGtA2 refolding resulting in a major loss of thermal stability.     

Spectroscopic identification of new ellagitannins and a trigalloyl-glucosylkaempferol from an extract of Euphorbia cotinifolia L. with antitumour and antioxidant activity

From an extract of leaves and small branches of Euphorbia cotinifolia L., 17 polyphenols were isolated including two new ellagitannins and a trigalloyl-glucosylkaempferol. Based on extensive spectral data (UV, ESI-MS, 1H NMR, DEPT and 1D/2D NMR) and chemical studies, their structures were characterized as 1-O-galloyl-3,6-hexahydroxydiphenoyl-D-B1,4-glucopyranose (5), 1-O-galloyl-3,6-valoneoyl-D-B1,4-glucopyranose (6), and kaempferol 3-O-(2",3",6"-tri-O-galloyl)-beta-D-glucopyranoside (13). Biological evaluation indicated that the 80% aqueous methanol extract (AME), chloroform extract (CE), and some pure compounds have potent scavenging activity in the DPPH assay with SC50 values lower than that of ascorbic acid, especially 5, 7-9, and a mixture of hyperin 6"-gallate (11) and isoquercitrin 6"-gallate (12). Moreover, using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) cell viability assay, 6 and 8 exhibited the highest inhibition of human hepatocellular carcinoma cells (Hep-G2), while AME, CE, 5, 7, 9, and the mixture of 11 and 12 were found to be moderate growth inhibitors according to their IC50 values. In addition, AME, 5, and 8 exhibited significant antiproliferative activity against colon carcinoma cells (HCT-116); however, CE and the other examined compounds displayed moderate to low antitumour activity against HCT-116 cells.     

Past and future trends in cancer and biomedical research: a comparison between Egypt and the World using PubMed-indexed publications

ABSTRACT: BACKGROUND: PubMed is a free web literature search service that contains almost 21 millions of abstracts and publications with almost 5 million user queries daily. The purposes of the study were to compare trends in PubMed-indexed cancer and biomedical publications from Egypt to that of the world and to predict future publication volumes. METHODS: The PubMed was searched for the biomedical publications between 1991 and 2010 (publications dates). Affiliation was then limited to Egypt. Further limitation was applied to cancer, human and animal publications. Poisson regression model was used for prediction of future number of publications between 2011 and 2020. RESULTS: Cancer publications contributed 23% to biomedical publications both for Egypt and the world. Egyptian biomedical and cancer publications contributed about 0.13% to their world counterparts. This contribution was more than doubled over the study period. Egyptian and world's publications increased from year to year with rapid rise starting the year 2003. Egyptian as well as world's human cancer publications showed the highest increases. Egyptian publications had some peculiarities; they showed some drop at the years 1994 and 2002 and apart from the decline in the animal: human ratio with time, all Egyptian publications in the period 1991-2000 were significantly more than those in 2001-2010 (P<0.05 for all). By 2020, Egyptian biomedical and cancer publications will increase by 158.7% and 280% relative to 2010 to constitute 0.34% and 0.17% of total PubMed publications, respectively. CONCLUSIONS: The Egyptian contribution to world's biomedical and cancer publications needs significant improvements through research strategic planning, setting national research priorities, adequate funding and researchers' training.     

Subterranean, herbivore-induced plant volatile increases biological control activity of multiple beneficial nematode species in distinct habitats

While the role of herbivore-induced volatiles in plant-herbivore-natural enemy interactions is well documented aboveground, new evidence suggests that belowground volatile emissions can protect plants by attracting entomopathogenic nematodes (EPNs). However, due to methodological limitations, no study has previously detected belowground herbivore-induced volatiles in the field or quantified their impact on attraction of diverse EPN species. Here we show how a belowground herbivore-induced volatile can enhance mortality of agriculturally significant root pests. First, in real time, we identified pregeijerene (1,5-dimethylcyclodeca-1,5,7-triene) from citrus roots 9-12 hours after initiation of larval Diaprepes abbreviatus feeding. This compound was also detected in the root zone of mature citrus trees in the field. Application of collected volatiles from weevil-damaged citrus roots attracted native EPNs and increased mortality of beetle larvae (D. abbreviatus) compared to controls in a citrus orchard. In addition, field applications of isolated pregeijerene caused similar results. Quantitative real-time PCR revealed that pregeijerene increased pest mortality by attracting four species of naturally occurring EPNs in the field. Finally, we tested the generality of this root-zone signal by application of pregeijerene in blueberry fields; mortality of larvae (Galleria mellonella and Anomala orientalis) again increased by attracting naturally occurring populations of an EPN. Thus, this specific belowground signal attracts natural enemies of widespread root pests in distinct agricultural systems and may have broad potential in biological control of root pests.     

Temporal similarity between Candida albicans genotypes in a Tunisian neonatal intensive care unit suggests several nosocomial cross-contamination episodes

The nosocomial transmission of Candida albicans in neonatal intensive care units (NICUs) is an increasing concern and understanding the route of this transmission is critical for adequate infection control measures. The aim of our study was to assess the likeliness of nosocomial acquisition of C. albicans in the NICU of Farhat Hached hospital in Sousse (Tunisia). We genotyped 82 isolates from 40 neonates and 7 isolates from 5 health care workers (HCWs) with onychomycosis, by using CDC3 microsatellite length polymorphism (MLP) and the high-resolution melting (HRM) analysis. Combined MLP and HRM CD3 analysis led to the delineation of 12 genotypes. Five temporal clustering caused by five genotypes occurred during the study period. Three of these genotypes were isolated in both neonates and HCWs. The first clustering included 28 isolates obtained between January 2003 and May 2004 from 16 neonates and 2 HCWs. The second clustering included three isolates collected in 2004 from three neonates and two HCWs. The third clustering included 11 isolates obtained from 6 neonates and 1 HCW in 2006. The two remaining clustering could not be associated with any HCW's contamination. These results argue for the nosocomial transmission of C. albicans in our NICU. The combined MLP and HRM analysis is a rapid first approach for tracking cross-contamination.     

The efficiency of in vitro isolation and myogenic differentiation of MSCs derived from adipose connective tissue,bone marrow,and skeletal muscle tissue

The objective of the study is to evaluate efficiency of in vitro isolation and myogenic differentiation of mesenchymal stem cells (MSCs) derived from adipose connective tissue (AD-MSCs), bone marrow (BM-MSCs), and skeletal muscle tissue (MC-MSCs). MSCs were isolated from adipose connective tissue, bone marrow, and skeletal muscle tissue of two adult 6-wk-old rats. Cultured MSCs were treated with 5-azacytidine (AZA) to induce myogenic differentiation. Isolated MSCs and differentiated cells were evaluated by immunocytochemistry (ICC), fluorescence-activated cell sorting (FACS), PCR, and RT-PCR. AD-MSCs showed the highest proliferation rate while BM-MSCs had the lowest one. In ICC, isolated MSCs had strong CD90- and CD44-positive expression and negative expression of CD45, CD31, and CD34, while AZA-treated MSCs had strong positive desmin expression. In FACS analysis, AD-MSCs had the highest percentage of CD90- and CD44-positive-expressing cells (99% and 96%) followed by BM-MSCs (97% and 94%) and MC-MSCs (92% and 91%).At 1 wk after incubation with AZA treatment, the peak of myogenin expression reached 93% in differentiated MC-MSCs, 83.3% in BM-MSCs, and 77% in AD-MSCs. MSCs isolated from adipose connective tissue, bone marrow, and skeletal muscle tissue have the same morphology and phenotype, but AD-MSCs were the most easily accessible and had the highest rate of growth on cultivation and the highest percentage of stem cell marker expression. Moreover, although MC-MSCs showed the highest rate of myogenic differentiation potential and expression of myoblast markers, AD-MSCs and BM-MSCs still can be valuable alternatives. The differentiated myoblastic cells could be an available new choice for myoblastic auto-transplantation in regeneration medicine.     

Prevalence and sociodemographic correlates of consanguineous marriages in Turkey

The aim of this study was to determine the prevalence and sociodemographic correlates of consanguineous marriages in Turkey using data derived from the 2003 Turkey Demographic and Health Survey (TDHS-2003). Demographic surveys conducted in the last 40 years consistently show that Turkey is a country with a high level of consanguinity. In the latest demographic survey (TDHS-2003), a nationally representative sample of 8075 ever-married women, consanguineous marriages accounted for 22% of the total, which is equivalent to a mean coefficient of inbreeding (alpha) of 0.011. There are changing secular profiles in the rates of consanguinity in general and of the specific sub-types of cousin marriages in particular in Turkey. The prevalence of first cousin marriages among all consanguineous marriages presents a steady decline from one marriage cohort to the next. The changes observed over time may be attributable to several factors such as the increase in educational level of women, the nuclearization of the family system, the mobility from rural to urban settings, a better socioeconomic status of families, an increase in women's labour force participation in formal sectors, lower fertility rates resulting in a smaller number of cousins available for marriage, and an increased awareness of the effects of consanguineous unions on child health in cases where there is an inherited recessive disease in the family. Any attempts to discourage consanguinity at the population level appear to be inappropriate and undesirable, especially when the consanguineous union remains an integral part of the cultural and social life of Turkey. Nevertheless the WHO-recommended approach to minimizing the negative effects of consanguinity on child health should be followed, i.e. the identification of families with a high risk of a genetic disease and the provision of prospective genetic counselling.