Molecular-based identification and phylogeny of genomic and proteomic sequences of mosquito-borne flavivirus

Mosquito-borne flaviviruses (MBFVs) are important cause of emerging and re-emerging human diseases nearly worldwide, transmitted by arthropod vectors (mostly aedes and culex mosquitoes), with particular reference to yellow fever virus, Japanese encephalitis virus, dengue fever virus, St. Louis encephalitis virus, Murray Valley encephalitis virus, etc. In over 100 countries, more than 2.5 billion people are at risk of infection, and approximately 20 million infections are reported annually. Through the analysis of gene sequence data of these virus populations it is possible to infer phylogenetic relationships, which in turn can yield important epidemiological information, including their demographic history. Early attempts to define the evolutionary relationships and origins of viruses in the genus flavivirus are hampered by the lack of genetic information particularly amongst the MBFVs. In this study, complete genome, translated polyprotein, structural and non-structural proteins of MBFVs have been targeted and revealed an extensive series of clades defined by their epidemiology and disease associations. The branching patterns of at the deeper nodes of the resultant trees were different from those reported in the previous study. The significance of these observations is discussed.     

The Association of the Triglyceride-to-HDL Cholesterol Ratio with Insulin Resistance in White European and South Asian Men and Women

Introduction

There is recent interest surrounding the use of the triglyceride-to-HDL cholesterol ratio as a surrogate marker of insulin resistance in clinical practice, as it may identify people at high risk of developing diabetes or its complications. However, it has been suggested using this lipid ratio may not be appropriate for measuring insulin resistance in African-Americans, particularly women. We investigated if this inconsistency extended to South Asian women in a UK multi-ethnic cohort of White Europeans and South Asians.

Methods

Cross-sectional analysis was done of 729 participants from the ADDITION-Leicester study from 2005 to 2009. The association between tertiles of triglyceride-to-HDL cholesterol ratio to fasting insulin, homeostatic model of assessment for insulin resistance (HOMA1-IR), quantitative insulin sensitivity check index (QUICKI) and glucose: insulin ratio was examined with adjustment for confounding variables.

Results

Incremental tertiles of the triglyceride-to-HDL cholesterol ratio demonstrated a significant positive association with levels of fasting insulin, HOMA1-IR, glucose: insulin ratio and a negative association with QUICKI in White European men (n = 255) and women (n = 250) and South Asian men (n = 124) (all p<0.05), but not South Asian women (n = 100). A significant interaction was demonstrated between sex and triglyceride-to-HDL cholesterol ratio tertiles in South Asians only (p<0.05). The area under the receiver operating characteristic curve for triglyceride-to-HDL cholesterol ratio to detect insulin resistance, defined as the cohort HOMA1-IR≥75^th percentile (3.08), was 0.74 (0.67 to 0.81), 0.72 (0.65 to 0.79), 0.75 (0.66 to 0.85) and 0.67 (0.56 to 0.78) in White European men and women, South Asian men and women respectively. The optimal cut-points for detecting insulin resistance were 0.9–1.7 in mmol/l (2.0–3.8 in mg/dl) for the triglyceride-to-HDL ratio.

Conclusion

In South Asian women the triglyceride-to-HDL cholesterol ratio was not associated with insulin resistance; therefore there may be limitations in its use as a surrogate marker in this group.     

Leishmaniasis Direct Agglutination Test: Using Pictorials as Training Materials to Reduce Inter-Reader Variability and Improve Accuracy

Background

The Direct Agglutination Test (DAT) has a high diagnostic accuracy and remains, in some geographical areas, part of the diagnostic algorithm for Visceral Leishmaniasis (VL). However, subjective interpretation of results introduces potential for inter-reader variation. We report an assessment of inter-laboratory agreement and propose a pictorial-based approach to standardize reading of the DAT.

Methodology

In preparation for a comparative evaluation of immunochromatographic diagnostics for VL, a proficiency panel of 15 well-characterized sera, DAT-antigen from a single batch and common protocol was sent to nine laboratories in Latin-America, East-Africa and Asia. Agreement (i.e., equal titre or within 1 titer) with the reading by the reference laboratory was computed. Due to significant inter-laboratory disagreement on-site refresher training was provided to all technicians performing DAT. Photos of training plates were made, and end-titres agreed upon by experienced users of DAT within the Visceral-Leishmaniasis Laboratory-Network (VL-LN).

Results

Pre-training, concordance in DAT results with reference laboratories was only 50%, although agreement on negative sera was high (94%). After refresher training concordance increased to 84%; agreement on negative controls increased to 98%. Variance in readings significantly decreased after training from 3.3 titres to an average of 1.0 titre (two-sample Wilcoxon rank-sum (Mann-Whitney) test (z = −3,624 and p = 0.0003)).

Conclusion

The most probable explanation for disagreement was subjective endpoint reading. Using pictorials as training materials may be a useful tool to reduce disparity in results and promote more standardized reading of DAT, without compromising diagnostic sensitivity.     

Biotechnological advances in pomegranate (Punica granatum L.)

Pomegranate (Punica granatum L.) is known for its nutritional, medicinal, and ornamental importance. It is conventionally propagated by hardwood and softwood cuttings, but about 1 yr is needed before the rooted cuttings can be transplanted to the field. Propagation by seed is undesirable as populations are heterozygous and seed propagation leads to wide variations in tree and fruit characteristics. Several studies have been conducted on in vitro culture of pomegranate, and protocols have been developed for plant regeneration through organogenesis and embryogenesis from various types of explants. Tissue culture has enabled mass propagation of superior genotypes of both wild and cultivated varieties. However, successful application of tissue culture systems for genetic engineering of pomegranate is still limited. Molecular markers are essential for identification and discrimination of genotypes for genetic conservation, crop improvement, breeding programs, and commercialization of superior genotypes. These techniques may also be applicable to rapid identification and indexing of disease-free planting material. This review focuses on the biotechnological approaches that are being used for pomegranate improvement.     

Transient Accumulation of Metabolic Intermediates of p-Cresol in the Culture Medium by a Pseudomonas sp. Strain A Isolated from a Sewage Treatment Plant

Summary Activated sludge from a sewage treatment plant in Kanpur, India, was screened for bacterial strains metabolizing p-cresol exclusively under aerobic conditions. One such isolate was identified to be belonging to the genus Pseudomonas based on morphological and physiological criteria as well as 16S ribosomal RNA gene sequence analysis. Two intermediates were identified from the culture medium during the growth phase of Pseudomonas sp. strain A that indicated that the strain degraded p-cresol via the protocatechuate (PCA) pathway. p-Cresol was rapidly converted into p-hydroxybenzaldehyde (PHB) during early growth phase, which was later utilized after p-cresol depletion. p-Hydroxybenzoate (PHBA) accumulation was observed during the later stages of exponential growth phase. Kinetic constants for the degradation of p-cresol were determined using Haldane’s model. High μ_max and inhibitory constant (K_I) values along with the observed accumulation of significant amounts of PHB in culture filtrates seem to indicate that the isolated Pseudomonas sp. strain A may be of potential use in biotransformations.     

Effects of add-on melatonin on sleep in epileptic children on carbamazepine monotherapy: A randomized placebo controlled trial

Sleep and Biological Rhythms - This double-blind, randomized, placebo controlled study in epileptic children, aged 3–12 years, evaluated the effect of add-on melatonin on the sleep behavior...     

GDP-mannose-4,6-dehydratase is a cytosolic partner of tankyrase 1 that inhibits its poly(ADP-ribose) polymerase activity

Tankyrase 1 is a poly(ADP-ribose) polymerase (PARP) that participates in a broad range of cellular activities due to interaction with multiple binding partners. Tankyrase 1 recognizes a linear six-amino-acid degenerate motif and, hence, has hundreds of potential target proteins. Binding of partner proteins to tankyrase 1 usually results in their poly(ADP-ribosyl)ation (PARsylation) and can lead to ubiquitylation and proteasomal degradation. However, it is not known how tankyrase 1 PARP activity is regulated. Here we identify GDP-mannose 4,6-dehydratase (GMD) as a binding partner of tankyrase 1. GMD is a cytosolic protein required for the first step of fucose synthesis. We show that GMD is complexed to tankyrase 1 in the cytosol throughout interphase, but its association with tankyrase 1 is reduced upon entry into mitosis, when tankyrase 1 binds to its other partners TRF1 (at telomeres) and NuMA (at spindle poles). In contrast to other binding partners, GMD is not PARsylated by tankyrase 1. Indeed, we show that GMD inhibits tankyrase 1 PARP activity in vitro, dependent on the GMD tankyrase 1 binding motif. In vivo, depletion of GMD led to degradation of tankyrase 1, dependent on the catalytic PARP activity of tankyrase 1. We speculate that association of tankyrase 1 with GMD in the cytosol sequesters tankyrase 1 in an inactive stable form that can be tapped by other target proteins as needed.     

Abrogation of Plasminogen Activator Inhibitor-1-Vitronectin Interaction Ameliorates Acute Kidney Injury in Murine Endotoxemia

Sepsis-induced acute kidney injury (AKI) contributes to the high mortality and morbidity in patients. Although the pathogenesis of AKI during sepsis is poorly understood, it is well accepted that plasminogen activator inhibitor-1 (PAI-1) and vitronectin (Vn) are involved in AKI. However, the functional cooperation between PAI-1 and Vn in septic AKI has not been completely elucidated. To address this issue, mice were utilized lacking either PAI-1 (PAI-1^−/−) or expressing a PAI-1-mutant (PAI-1^R101A/Q123K) in which the interaction between PAI-1 and Vn is abrogated, while other functions of PAI-1 are retained. It was found that both PAI-1^−/− and PAI-1^R101A/Q123K mice are associated with decreased renal dysfunction, apoptosis, inflammation, and ERK activation as compared to wild-type (WT) mice after LPS challenge. Also, PAI-1^−/− mice showed attenuated fibrin deposition in the kidneys. Furthermore, a lack of PAI-1 or PAI-1-Vn interaction was found to be associated with an increase in activated Protein C (aPC) in plasma. These results demonstrate that PAI-1, through its interaction with Vn, exerts multiple deleterious mechanisms to induce AKI. Therefore, targeting of the PAI-1-Vn interaction in kidney represents an appealing therapeutic strategy for the treatment of septic AKI by not only altering the fibrinolytic capacity but also regulating PC activity.     

Mechanistic studies on carboxypeptidase A from goat pancreas Part I: Role of tyrosine residue at the active site

Chemical modification of carboxypeptidase Ag₁ from goat pancreas with Nacetylimidazole or iodine led to loss of enzymic activity. This loss in activity could be prevented when chemical modification was carried out in the presence of Β-phenylpropionic acid or substrate NCbz-glycyl-L-phenylalanine, thus suggesting a tyrosine residue at the active site. Chemical modification of tyrosine was confirmed by spectral and kinetic studies. While tyrosine modification destroyed peptidase activity, esterase activity of the enzyme remained unchanged thus indicating non-involvement of tyrosine residue in ester hydrolysis     

Metabolism of (−)-trans-(3R,4R)-dihydroxy-3,4-dihydrochrysene to diol epoxides by liver microsomes

Metabolism of biosynthetic (?)-trans-(3R,4R)-dihydroxy-3,4-dihydrochrysene by liver microsomes from control, phenobarbital-treated and 3-methylcholanthrene-treated rats was investigated. Although previous studies of the metabolism of related benzo[a]pyrene and benzo[e]pyrene dihydrodiols which also prefer the diaxial conformation had indicated that diol epoxides were minor metabolites, the diastereomeric chrysene 3,4-diol-1,2-epoxides-$\text{1}$ and $\text{?2}$ were major metabolites (66–90%). All three types of microsomes metabolized the chrysene 3,4-dihydrodiol at low but essentially similar rates (0.5–0.7 nmol substrate/nmol cytochrome P-450/min).