Solution structure of the orphan PABC domain from Saccharomyces cerevisiae poly(A)-binding protein

We have determined the solution structure of the PABC domain from Saccharomyces cerevisiae Pab1p and mapped its peptide-binding site. PABC domains are peptide binding domains found in poly(A)-binding proteins (PABP) and are a subset of HECT-family E3 ubiquitin ligases (also known as hyperplastic discs proteins (HYDs)). In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail. PABC domains are highly conserved, with high specificity for peptide sequences of roughly 12 residues with conserved alanine, phenylalanine, and proline residues at positions 7, 10, and 12. Compared with human PABP, the yeast PABC domain is missing the first alpha helix, contains two extra amino acids between helices 2 and 3, and has a strongly bent C-terminal helix. These give rise to unique peptide binding specificity wherein yeast PABC binds peptides from Paip2 and RF3 but not Paip1. Mapping of the peptide-binding site reveals that the bend in the C-terminal helix disrupts binding interactions with the N terminus of peptide ligands and leads to greatly reduced binding affinity for the peptides tested. No high affinity or natural binding partners from S. cerevisiae could be identified by sequence analysis of known PABC ligands. Comparison of the three known PABC structures shows that the features responsible for peptide binding are highly conserved and responsible for the distinct but overlapping binding specificities.     

Disseminated rhinosporidiosis masquerading as soft tissue round cell tumour diagnosed by fine needle aspiration cytology

Rhinosporidium seeberi belongs to the eukaryotic class Mesomycetozoea and causes chronic granulomatous lesions known as rhinosporidiosis. Rhinosporidiosis frequently involves the nasal cavity and nasopharynx through transepithelial invasion. Atypical presentations of this disease at other body sites have been reported, including the subcutis, visceral organs, bones, and genitals. Only a few cases of cutaneous and subcutaneous involvement have been reported to date. This chronic granulomatous condition is known for its recurrence following autoinoculation unless the correct diagnosis and appropriate treatment are given. We describe a case of an immunocompetent adult who had undergone fine needle aspiration cytology (FNAC) of mass-like swellings in the right thigh and right calf at another healthcare centre and had been diagnosed with a small round blue cell tumour. FNAC at our centre confirmed a rare case of rhinosporidiosis that was clinically mimicking a soft tissue neoplasm of the lower extremity, and the erroneous interpretation of the prior cytology studies had resulted in misinterpretation of the individually dispersed pathogenic organisms as individual malignant cells. FNAC of rhinosporidiosis can lead to early diagnosis and prompt treatment of this pathogen when it presents at unanticipated body sites.     

Age and Growth of Spotted Snakehead,Channa punctata from the Ganga River

Journal of Ichthyology - The present study was undertaken to estimate age and growth of the spotted snakehead Channa punctata (Bloch, 1793) from the Ganga River, based on 390 fish samples collected...     

Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase

The C-terminal domain of poly(A)-binding protein (PABC) is a peptide-binding domain found in poly(A)-binding proteins (PABPs) and a HECT (homologous to E6-AP C-terminus) family E3 ubiquitin ligase. In protein synthesis, the PABC domain of PABP functions to recruit several translation factors possessing the PABP-interacting motif 2 (PAM2) to the mRNA poly(A) tail. We have determined the solution structure of the human PABC domain in complex with two peptides from PABP-interacting protein-1 (Paip1) and Paip2. The structures show a novel mode of peptide recognition, in which the peptide binds as a pair of beta-turns with extensive hydrophobic, electrostatic and aromatic stacking interactions. Mutagenesis of PABC and peptide residues was used to identify key protein-peptide interactions and quantified by isothermal calorimetry, surface plasmon resonance and GST pull-down assays. The results provide insight into the specificity of PABC in mediating PABP-protein interactions.     

"Distant spin trapping": a method for expanding the availability of spin trapping measurements

The technique of spin trapping is used to study a wide range of free radicals in various systems, including those generated in vitro and in vivo. But unfortunately, EPR spectrometers are not always immediately accessible at the site of experimentation, and therefore it is important to find a method that can preserve a radical adduct over longer periods of time. We describe here an alternative method in which the samples can be frozen and transported for EPR measurements at another site. Various spin adducts of DEPMPO were frozen and measured at 0 degrees C at various intervals after freezing to determine their stability in the frozen state. The radical adducts were generated by established methods and stored at two different temperatures; -196 degrees C (liquid nitrogen) and -80 degrees C (dry ice). The experiments were carried out in an aqueous solution with and without a model of reducing environment (2 mM ascorbate). The results indicate that it is feasible to store and transport spin adducts for subsequent analysis. We conclude that this approach, which we term "distant spin trapping", makes it feasible to transport samples to another site for EPR measurements. This should significantly expand the ability to use spin trapping in biology and medicine.     

Towards thermally stable cyclophanediene-dihydropyrene photoswitches

Cyclophanediene dihydropyrenes (CPD-DHP) are photochromic compounds because they change their color by irradiation with lights of different color. Potential use of CPD-DHP photoswitch in memory devices requires a very slow thermal return in the dark in the absence of any side reaction. Herein, thermal return of CPDs to DHPs, and an unwanted sigmatropic shift in DHP is studied through density functional theory calculations at (U)B3LYP/6-31+G(d). The thermal return occurs through symmetry forbidden conrotatory electrocyclic reaction. Dimethyl amino CPD-DHP photoswitch pair has the highest activation barrier for electrocyclization and sigmatropic shifts. The lowest activation barrier for symmetry forbidden electrocyclization is observed for GeBr₃ functionalized CPD. An unprecedented decomposition pathway involving elimination of the internal substituents is predicted for Cl, Br and SMe functionalized DHPs. This study shows great promise in understanding the Woodward Hoffmann forbidden processes and, in reducing the synthetic efforts toward robust photochromes for memory applications.     

Endothelial influences on cerebrovascular tone.

The cerebrovascular endothelium exerts a profound influence on cerebral vessels and cerebral blood flow. This review summarizes current knowledge of various dilator and constrictor mechanisms intrinsic to the cerebrovascular endothelium. The endothelium contributes to the resting tone of cerebral arteries and arterioles by tonically releasing nitric oxide (NO*). Dilations can occur by stimulated release of NO*, endothelium-derived hyperpolarization factor, or prostanoids. During pathological conditions, the dilator influence of the endothelium can turn to that of constriction by a variety of mechanisms, including decreased NO* bioavailability and release of endothelin-1. The endothelium may participate in neurovascular coupling by conducting local dilations to upstream arteries. Further study of the cerebrovascular endothelium is critical for understanding the pathogenesis of a number of pathological conditions, including stroke, traumatic brain injury, and subarachnoid hemorrhage.     

Periodontal Treatment for Preventing Adverse Pregnancy Outcomes: A Meta- and Trial Sequential Analysis

Objectives

Periodontal treatment might reduce adverse pregnancy outcomes. The efficacy of periodontal treatment to prevent preterm birth, low birth weight, and perinatal mortality was evaluated using meta-analysis and trial sequential analysis.

Methods

An existing systematic review was updated and meta-analyses performed. Risk of bias, heterogeneity, and publication bias were evaluated, and meta-regression performed. Subgroup analysis was used to compare different studies with low and high risk of bias and different populations, i.e., risk groups. Trial sequential analysis was used to assess risk of random errors.

Results

Thirteen randomized clinical trials evaluating 6283 pregnant women were meta-analyzed. Four and nine trials had low and high risk of bias, respectively. Overall, periodontal treatment had no significant effect on preterm birth (odds ratio [95% confidence interval] 0.79 [0.57-1.10]) or low birth weight (0.69 [0.43-1.13]). Trial sequential analysis demonstrated that futility was not reached for any of the outcomes. For populations with moderate occurrence (<20%) of preterm birth or low birth weight, periodontal treatment was not efficacious for any of the outcomes, and trial sequential analyses indicated that further trials might be futile. For populations with high occurrence (≥20%) of preterm birth and low birth weight, periodontal treatment seemed to reduce the risk of preterm birth (0.42 [0.24-0.73]) and low birth weight (0.32 [0.15-0.67]), but trial sequential analyses showed that firm evidence was not reached. Periodontal treatment did not significantly affect perinatal mortality, and firm evidence was not reached. Risk of bias, but not publication bias or patients’ age modified the effect estimates.

Conclusions

Providing periodontal treatment to pregnant women could potentially reduce the risks of perinatal outcomes, especially in mothers with high risks. Conclusive evidence could not be reached due to risks of bias, risks of random errors, and unclear effects of confounding. Further randomized clinical trials are required.     

Optimal and Numerical Solutions for an MHD Micropolar Nanofluid between Rotating Horizontal Parallel Plates

The present analysis deals with flow and heat transfer aspects of a micropolar nanofluid between two horizontal parallel plates in a rotating system. The governing partial differential equations for momentum, energy, micro rotation and nano-particles concentration are presented. Similarity transformations are utilized to convert the system of partial differential equations into system of ordinary differential equations. The reduced equations are solved analytically with the help of optimal homotopy analysis method (OHAM). Analytical solutions for velocity, temperature, micro-rotation and concentration profiles are expressed graphically against various emerging physical parameters. Physical quantities of interest such as skin friction co-efficient, local heat and local mass fluxes are also computed both analytically and numerically through mid-point integration scheme. It is found that both the solutions are in excellent agreement. Local skin friction coefficient is found to be higher for the case of strong concentration i.e. n=0, as compared to the case of weak concentration n=0.50. Influence of strong and weak concentration on Nusselt and Sherwood number appear to be similar in a quantitative sense.