E2-mediated Small Ubiquitin-like Modifier (SUMO) Modification of Thymine DNA Glycosylase Is Efficient but Not Selective for the Enzyme-Product Complex

Thymine DNA glycosylase (TDG) initiates the repair of G·T mismatches that arise by deamination of 5-methylcytosine (mC), and it excises 5-formylcytosine and 5-carboxylcytosine, oxidized forms of mC. TDG functions in active DNA demethylation and is essential for embryonic development. TDG forms a tight enzyme-product complex with abasic DNA, which severely impedes enzymatic turnover. Modification of TDG by small ubiquitin-like modifier (SUMO) proteins weakens its binding to abasic DNA. It was proposed that sumoylation of product-bound TDG regulates product release, with SUMO conjugation and deconjugation needed for each catalytic cycle, but this model remains unsubstantiated. We examined the efficiency and specificity of TDG sumoylation using in vitro assays with purified E1 and E2 enzymes, finding that TDG is modified efficiently by SUMO-1 and SUMO-2. Remarkably, we observed similar modification rates for free TDG and TDG bound to abasic or undamaged DNA. To examine the conjugation step directly, we determined modification rates (k_obs) using preformed E2∼SUMO-1 thioester. The hyperbolic dependence of k_obs on TDG concentration gives k_max = 1.6 min⁻¹ and K_1/2 = 0.55 μm, suggesting that E2∼SUMO-1 has higher affinity for TDG than for the SUMO targets RanGAP1 and p53 (peptide). Whereas sumoylation substantially weakens TDG binding to DNA, TDG∼SUMO-1 still binds relatively tightly to AP-DNA (K_d ∼50 nm). Although E2∼SUMO-1 exhibits no specificity for product-bound TDG, the relatively high conjugation efficiency raises the possibility that E2-mediated sumoylation could stimulate product release in vivo. This and other implications for the biological role and mechanism of TDG sumoylation are discussed.     

Phenotypic and Molecular Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Bangladesh

Background

Resistance to cephalosporins in Enterobacteriaceae is mainly due to the production of extended-spectrum beta-lactamase (ESBL). Little is known about ESBL-producing bacteria in Bangladesh. Therefore, the study presents results of phenotypic and molecular characterization of ESBL-producing Escherichia coli from hospitals in Bangladesh.

Methods

A total of 339 E. coli isolated from patients with urinary tract and wound infections attending three different medical hospitals in urban and rural areas of Bangladesh between 2003–2007 were screened for ESBL-production by the double disk diffusion test. Isolates with ESBL-phenotype were further characterized by antibiotic susceptibility testing, PCR and sequencing of different β-lactamase and virulence genes, serotyping, and XbaI-macrorestriction followed by pulsed-field gel electrophoresis (PFGE).

Results

We identified 40 E. coli with ESBL phenotype. These isolates were resistant to ceftriaxone, ceftazidime, cefotaxime, aztreonam, cefepime, and nalidixic acid but remained susceptible to imipenem. All but one isolate were additionally resistant to ciprofloxacin, and 3 isolates were resistant to cefoxitin. ESBL genes of blaCTX-M-1-group were detected in all isolates; blaTEM-type and blaOXA-1-type genes were detected in 33 (82.5%) and 19 (47.5%) isolates, respectively. Virulence genes that are present in diarrhoeagenic E. coli were not found. Class-1 integron was present in 20 (50%) isolates. All the ESBL-producing E. coli isolates harbored plasmids ranging between 1.1 and 120 MDa. PFGE-typing revealed 26 different pulsotypes, but identical pulsotype showed 6 isolates of serotype O25:H4.

Conclusion

The prevalence of multidrug-resistant ESBL-producing E. coli isolates appears to be high and the majority of the isolates were positive for bla _CTX-M. Although there was genetic heterogeneity among isolates, presence of a cluster of isolates belonging to serotype O25:H4 indicates dissemination of the pandemic uropathogenic E. coli clone in Bangladesh.     

Dengue 2 virus inhibits in vitro megakaryocytic colony formation and induces apoptosis in thrombopoietin-inducible megakaryocytic differentiation from cord blood CD34+ cells

Thrombocytopenia is frequently associated with dengue virus infection in humans. Although antiplatelet immunopathogenic processes have been implicated in the origin of dengue-associated thrombocytopenia, the effect of dengue viruses on megakaryocyte differentiation remains incompletely understood. In this study, we examined the effect of human dengue 2 virus isolates on the in vitro growth and differentiation of thrombopoietin-induced megakaryopoiesis of cord blood CD34+ cells. Dengue 2 viruses, but not Japanese encephalitis virus, showed a dose-dependent inhibition of CFU-Mk. Viral antigens could be detected by an immunohistochemical technique in 3-5% of the early megakaryocytic progenitors by the 5th postexposure day in liquid cultures with cell loss, increased annexin V binding and active caspase-3 expression. In summary, dengue 2 viruses can inhibit in vitro megakaryopoiesis, as well as infect and induce apoptotic cell death in a subpopulation of early megakaryocytic progenitors. These events might contribute towards the origin of thrombocytopenia in dengue disease.     

Dengue virus infection of SK Hep1 cells: inhibition of in vitro angiogenesis and altered cytomorphology by expressed viral envelope glycoprotein

Dengue virus (DENV) infection of human endothelial cells has been implicated in the pathobiology of dengue hemorrhagic fever and dengue shock syndrome. However, the mechanisms by which DENV infections alter the functional physiology of endothelial cells remain incompletely understood. In the present study, we examined the susceptibility of a human liver sinusoidal endothelial cell line SK Hep1 to all four serotypes of DENV and studied the effect of the virus on in vitro angiogenesis. All four serotypes of DENV could infect the SK Hep1 cells, but showed variable cytopathic effects, the most pronounced being that of DENV-2. Electron microscopy of the infected cells showed significant ultrastructural changes. In vitro angiogenesis assays on DENV-2 exposed SK Hep1 cells in the matrigel system showed inhibition compared with the controls. Importantly, transfection and transient expression of the DENV-2 envelope glycoprotein (E) in these cells showed drastic alterations in cell shapes and the E protein could be localized by fluorescence microscopy in terminal knob-like structures. Therefore, SK Hep1, a human hepatic sinusoid-derived endothelial cell line, may constitute a potential model to study DENV-endothelial cell interactions in vitro, especially towards understanding the possible virus-induced changes in hepatic endothelium and its role in disease pathogenesis.     

Comparison of Soil Quality Index Using Three Methods

Assessment of management-induced changes in soil quality is important to sustaining high crop yield. A large diversity of cultivated soils necessitate identification development of an appropriate soil quality index (SQI) based on relative soil properties and crop yield. Whereas numerous attempts have been made to estimate SQI for major soils across the World, there is no standard method established and thus, a strong need exists for developing a user-friendly and credible SQI through comparison of various available methods. Therefore, the objective of this article is to compare three widely used methods to estimate SQI using the data collected from 72 soil samples from three on-farm study sites in Ohio. Additionally, challenge lies in establishing a correlation between crop yield versus SQI calculated either depth wise or in combination of soil layers as standard methodology is not yet available and was not given much attention to date. Predominant soils of the study included one organic (Mc), and two mineral (CrB, Ko) soils. Three methods used to estimate SQI were: (i) simple additive SQI (SQI-1), (ii) weighted additive SQI (SQI-2), and (iii) statistically modeled SQI (SQI-3) based on principal component analysis (PCA). The SQI varied between treatments and soil types and ranged between 0–0.9 (1 being the maximum SQI). In general, SQIs did not significantly differ at depths under any method suggesting that soil quality did not significantly differ for different depths at the studied sites. Additionally, data indicate that SQI-3 was most strongly correlated with crop yield, the correlation coefficient ranged between 0.74–0.78. All three SQIs were significantly correlated (r = 0.92–0.97) to each other and with crop yield (r = 0.65–0.79). Separate analyses by crop variety revealed that correlation was low indicating that some key aspects of soil quality related to crop response are important requirements for estimating SQI.     

A 23-kDa, root exudate polypeptide co-segregates with aluminum resistance in Triticum aestivum

We previously reported that treatment with aluminum (Al) leads to the accumulation of several polypeptides (12-, 23-, and 43.5-kDa) in root exudates of an Al-resistant cultivar of Triticum aestivum. In this report, we examine the segregation of the 23-kDa, Al-induced polypeptide and the Al-resistant phenotype in single F₂ plants arising from a cross between Al-resistant and Al-sensitive doubled-haploid (DH) lines. Single plants and plant populations were screened for sensitivity/resistance to Al using synthesis of 1,3-β-glucans (callose) as a sensitive marker for Al injury. Callose production in the Al-sensitive cv. Katepwa was approximately 3-fold higher than observed in the Al-resistant cv. Maringa, or a near-isogenic line derived from Katepwa and Maringa (Alikat), over a broad range of Al concentrations (0–100 μM). Similar results were observed with DH lines developed from cv. Katepwa, which produced two–four times more callose than DH lines developed from cv. Alikat. When single plants from F₁ and F₂ populations derived from a cross between DH Katepwa and DH Alikat were scored for Al-induced callose production after 4 days exposure to 100 μM Al, all F₁ plants were Al-resistant and F₂ plants segregated approximately 3:1 for Al-resistance/sensitivity. A backcross population derived from crossing Al-resistant F₁ with Al-sensitive Katepwa, segregated 1:1 for Al-resistance/sensitivity. Thus, the Al-resistant phenotype is inherited in a monogenic, dominant fashion in our DH lines. Enhanced accumulation of the Al-induced, 23-kDa polypeptide in root exudates was a trait which co-segregated with the Al-resistant phenotype in F₂ populations. This polypeptide was strongly labeled with S-methionine after 3 days of Al exposure and 6 h labeling. When root exudate polypeptides were separated by immobilized metal ion affinity chromatography, the 23-kDa polypeptide demonstrated significant Al-binding capacity. This polypeptide has been purified to near-homogeneity, providing an opportunity to isolate the gene(s) encoding this polypeptide.     

Genetic analysis of a Minute mutation in the distal region of the second chromosome ofDrosophila melanogaster

Genetic organization of a proximal region of the second chromosome inDrosophila melanogaster has been analysed by saturation mutagenesis. Seven alleles were uncovered in this region in addition to the one previously known. Besides this, quite a few mutations were isolated that non-complemented more than one group of lethals and looked very much like deletions of varying extent. Except one, all the lethals complemented M(2)z.     

Interaction of phosphorus and molybdenum in relation to uptake and utilization of molybdenum,phosphorus, zinc,copper and manganese by rice

Summary The effect of phosphorus and molybdenum alone and combined, on the uptake and utilization of Mo, Mn, Zn, Cu and P by rice (Var. IR-579) was studied in the greenhouse at varying levels of Mo (0, 2.5 and 5.0 ppm) and (0,100 and 200 ppm). Application of P increased the dry matter yield of shoot and root. Combined application of P and Mo increased the dry matter yield of shoot. Application of Mo increased the concentration of Mo and P in shoot. Applied P caused an increase in the concentration of Mo, Zn and P in shoot. Combined application of P and Mo resulted in an increase in concentration and uptake of Mo in shoot.     

Bayesian adaptive biased-coin designs for clinical trials with normal responses

Adaptive designs are used in phase III clinical trials for skewing the allocation pattern toward the better treatments. We use optimum design theory to derive a skewed Bayesian biased-coin procedure for sequential designs with continuous responses. The skewed designs are used to provide adaptive designs, the performance of which is studied numerically and theoretically. Important properties are loss and the proportion of allocation to the better treatment.