Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.

Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794).

Ornithine decarboxylase of Leishmania donovani: biochemical properties and possible role of N-terminal extension.

Leishmaniasis is a wide spread tropical disease caused by protozoan parasite Leishmania which belongs to order kinetoplastida and family trypanosomatidae. Ornithine decarboxylase is key enzyme in polyamine biosynthesis in Leishmania donovani. Here, we report biochemical characterization of ornithine decarboxylase from L.

Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58.

The genome of Agrobacterium tumefaciens C58 encodes 12 members of the enolase superfamily (ENS), eight of which are members of the mandelate racemase (MR) subgroup and, therefore, likely to be acid sugar dehydratases. Using a library of 77 acid sugars for high-throughput screening, one protein (UniProt entry A9CG74; locus tag Atu4196) showed activity with both m-galactarate and d-galacturonate. Two families of galactarate dehydratases had been discovered previously in the ENS, GalrD/TalrD [Yew, W.

Huge Subchondral Cyst Communicating with Medulary Canal of Femur in OA Knee-Treated by Extension Stem and Bone Grafting.

Introduction: We report an osteoarthritic patient with huge sub-chondral cyst-like lesions in the Anterior part of distal femur. Deep and large bone defects and severe lateral laxity due to Advanced osteoarthritis was successfully treated with semi-constrained type total knee arthroplasty with long stem.

Case Report: A 70yrs old Female was admitted in our institution diagnosed with severe bilateral Osteoarthritis.

Replacing the axial ligand tyrosine 75 or its hydrogen bond partner histidine 83 minimally affects hemin acquisition by the hemophore HasAp from Pseudomonas aeruginosa.

Hemophores from Pseudomonas aeruginosa (HasAp), Serratia marcescens (HasAsm), and Yersinia pestis (HasAyp) bind hemin between two loops. One of the loops harbors conserved axial ligand Tyr75 (Y75 loop) in all three structures, whereas the second loop (H32 loop) contains axial ligand His32 in HasAp and HasAsm, but a noncoordinating Gln32 in HasAyp. Binding of hemin to the Y75 loop of HasAp or HasAsm causes a large rearrangement of the H32 loop that allows His32 coordination.

Gum Arabic enhances paracellular transport of water in amphibian everted small intestinal segments.

Gum Arabic (GA) is known for its proabsorbent activity in normal intestine as well as in animal models of diarrhea. The aim of the study was to find the effect of GA on intestinal transport of water and possible route of absorption in frog everted gut sacs. D-Mannitol was used as a marker of paracellular transport to find the route of absorption.

Penile metastasis secondary to bladder cancer: a report of two cases.

Penile metastasis secondary to primary bladder cancer is a rare entity and represents a challenging problem. The common mode of spread to the penis is by retrograde venous route. The overall outcome is dismal and most patients will die within 1 year even after optimum treatment.

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

Unlabelled: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway.

De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel).

The Korean black raspberry (Rubus coreanus Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits.

Surface-initiated polymerization from barium titanate nanoparticles for hybrid dielectric capacitors.

A phosphonic acid is used as a surface initiator for the growth of polystyrene and polymethylmethacrylate (PMMA) from barium titanate (BTO) nanoparticles through atom transfer radical polymerization with activators regenerated by electron transfer. This results in the barium titanate cores embedded in the grafted polymer. The one-component system, PMMA-grafted-BTO, achieves a maximum extractable energy density of 2 J/cm(3) at a field strength of ∼220 V/μm, which exhibits a 2-fold increase compared to that of the composite without covalent attachment or the neat polymer.

Auxin-callose-mediated plasmodesmal gating is essential for tropic auxin gradient formation and signaling.

In plants, auxin functions as a master controller of development, pattern formation, morphogenesis, and tropic responses. A sophisticated transport system has evolved to allow the establishment of precise spatiotemporal auxin gradients that regulate specific developmental programs. A critical unresolved question relates to how these gradients can be maintained in the presence of open plasmodesmata that allow for symplasmic exchange of essential nutrients and signaling macromolecules.

Electrical burns of the abdomen.

A 35-year-old male farmer came in contact with 11,000 volts high tension electric wire and sustained full thickness burn wounds over scapula, upper limb and anterior abdominal wall along with perforation of the intestine. Patient was initially managed conservatively in general surgery ward and was referred to us after 3 days with necrosis of the burned skin and muscles over the shoulder and abdomen. Patient was initially managed conservatively and then thorough debridement of the necrotic skin over the left shoulder and upper arm was done and the area was split skin grafted.

Dosimetric and clinical outcome in image-based high-dose-rate interstitial brachytherapy for anal cancer.

Purpose: To evaluate dosimetric and clinical outcome in patients of anal cancer treated with image-based interstitial high-dose-rate brachytherapy following chemoradiation.

Methods And Materials: Sixteen patients with anal cancer were treated with chemoradiation followed by brachytherapy boost with image-based high-dose-rate interstitial brachytherapy from January 2007 to June 2011. Two brachytherapy dose schedules were used: 21 Gy in seven fractions and 18 Gy in six fractions depending on response to chemoradiation.

Evaluation of outcome and prognostic factors in patients of glioblastoma multiforme: A single institution experience.

Aims: We present retrospective analysis of patients of glioblastoma multiforme (GBM) and discuss clinical characteristics, various treatment protocols, survival outcomes, and prognostic factors influencing survival.

Materials And Methods: From January 2002 to June 2009, 439 patients of GBM were registered in our department. The median age of patients was 50 years, 66.

Survival and failure outcomes in primary thyroid lymphomas: a single centre experience of combined modality approach.

Primary thyroid lymphoma (PTL) is a rare malignancy and represents 2%-5% of all thyroid malignancies and 1%-2.5% of all malignant lymphomas. We present our institute's experience in combined modality management of 16 successive patients of PTL treated from 2005 to 2010.

Discovery of new enzymes and metabolic pathways by using structure and genome context.

Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with 'metabolite docking' to experimentally derived or homology-based three-dimensional structures. Bacterial metabolic pathways often are encoded by 'genome neighbourhoods' (gene clusters and/or operons), which can provide important clues for functional assignment.

Paratesticular rhabdomyosarcoma in young adults: A tertiary care institute experience.

Introduction: Paratesticular rhabdomyosarcoma (RMS) is a rare tumor arising from the mesenchymal tissues of the spermatic cord, epididymis, testis and testicular tunics. It represents only 7% of all patients entered in the Intergroup Rhabdomyosarcoma Study (IRS) and 17% of all malignant intrascrotal tumors in children less than 15 years old. We present our experience in combined modality management of 10 successive patients of paratesticular RMS.

A retrospective analysis of clinicopathological characteristics, treatment, and outcome of 27 patients of primary intestinal lymphomas.

Purpose: Primary intestinal lymphomas comprise of a wide variety of histological subtypes with varied presentation. The objective of this study was to determine the presentation, histological type, treatment, and outcome of patients of primary intestinal lymphoma.

Methods: A retrospective analysis of 27 patients of primary intestinal lymphoma treated at our institute from 2004 to 2010 was carried out.

Low-grade myofibroblastic sarcoma of the larynx: a rare entity with review of literature.

Mesenchymal neoplasms of the larynx are rare and make up approximately 0.3% to 1.0% of all malignancies at this location.