Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins

Interferon-gamma is an immunomodulatory substance that induces the expression of many genes to orchestrate a cellular response and establish the antiviral state of the cell. Among the most abundant antiviral proteins induced by interferon-gamma are guanylate-binding proteins such as GBP1 and GBP2. These are large GTP-binding proteins of relative molecular mass 67,000 with a high-turnover GTPase activity and an antiviral effect. Here we have determined the crystal structure of full-length human GBP1 to 1.8 A resolution. The amino-terminal 278 residues constitute a modified G domain with a number of insertions compared to the canonical Ras structure, and the carboxy-terminal part is an extended helical domain with unique features. From the structure and biochemical experiments reported here, GBP1 appears to belong to the group of large GTP-binding proteins that includes Mx and dynamin, the common property of which is the ability to undergo oligomerization with a high concentration-dependent GTPase activity.

Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism

The interferon-gamma-induced guanylate-binding protein 1 (GBP1) belongs to a special class of large GTP- binding proteins of 60-100 kDa with unique characteristics. Here we present the structure of human GBP1 in complex with the non-hydrolysable GTP analogue GppNHp. Basic features of guanine nucleotide binding, such as the P-loop orientation and the Mg(2+) co-ordination, are analogous to those of Ras-related and heterotrimeric GTP-binding proteins. However, the glycosidic bond and thus the orientation of the guanine base and its interaction with the protein are very different. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein cannot approach. This has consequences for the GTPase mechanism of hGBP1 and possibly of other large GTP-binding proteins.

Haemorrhage into pituitary adenomas

Seventy cases of pituitary adenoma were analysed for evidence of haemorrhage. It was present in 18 cases. These are classified into four groups, acute, acute on chronic, chronic, and late sequelae of pituitary apoplexy, and an example of a patient in each group is given. The diagnosis and management are discussed.

Analysis of the amino acid sequences of plant Bowman-Birk inhibitors

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that of Macrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.

Effect of Supplementing Organic Forms of Zinc, Selenium and Chromium on Performance, Anti-Oxidant and Immune Responses in Broiler Chicken Reared in Tropical Summer

Two experiments were conducted to study the effect of supplementing organic forms of zinc (Zn), selenium (Se) and chromium (Cr) on performance, anti-oxidant activities and immune responses in broiler chickens from 1 to 21 days of age, which were reared in cyclic heat-stressed condition under tropical summer in open-sided poultry house. A total of 200 (experiment I) and 450-day-old (experiment II) broiler male chicks (Cobb 400) were randomly distributed in stainless steel battery brooders (610 mm × 762 mm × 475 mm) at the rate of five birds per pen. A maize-soybean meal-based control diet (CD) containing recommended (Vencobb 400, Broiler Management Guide) concentrations of inorganic trace minerals and other nutrients was prepared. The CD was supplemented individually with organic form of selenium (Se, 0.30 mg/kg), chromium (Cr, 2 mg/kg) and zinc (Zn, 40 mg/kg) in experiment I. In experiment II, two concentrations of each Zn (20 and 40 mg/kg), Se (0.15 and 0.30 mg/kg) and Cr (1 and 2 mg/kg) were supplemented to the basal diet in 2 × 2 × 2 factorial design. A group without supplementing inorganic trace minerals was maintained as control group in both experiments. Each diet was allotted randomly to ten replicates in both experiments and fed ad libitum from 1 to 21 days of age. At 19th day of age, blood samples were collected for estimation of anti-oxidant and immune responses. Supplementation of Se, Cr and Zn increased (P < 0.05) body mass gain (BMG) and feed intake compared to those fed the CD in experiment I. The feed efficiency (FE) in Cr-fed group was higher (P < 0.05) compared to the CD-fed group. Se or Cr supplementation reduced lipid peroxidation (LP) compared to broilers fed the CD. In experiment II, BMG was not affected (P > 0.05) by the interaction between levels of Zn, Se and Cr in broiler diet. The FE improved (P < 0.05) with supplementation of the trace minerals tested at both concentrations except in group fed 40 mg Zn, 0.5 mg Se and 1 mg Cr/kg. Reduction in lipid peroxidation (LP, P < 0.05) and increased (P < 0.05) activity of superoxide dismutase were observed in broiler fed organic Zn, Se and Cr compared to the CD-fed group. The dietary concentrations of Zn, Se and Cr did not influence (P > 0.05) the immune responses (Newcastle disease titre and cell-mediated immune response to phytohaemagglutinin-P) in both the experiments. Based on the results, it is concluded that supplementation of organic form of Se, Cr and Zn (0.30, 2 and 40 mg/kg, respectively) either alone or in combination significantly improved performance and anti-oxidant responses (reduced LP and increased superoxide dismutase) in commercial broiler chicks (21 days of age) reared in cyclic heat stress conditions in open-sided poultry house during summer.

Non-cytotoxic effect of green synthesized silver nanoparticles and its antibacterial activity

Silver nanoparticles (AgNPs) were green synthesized using ethanolic extract of fenugreek leaves and characterized using UV-Vis spectroscopy, Fourier transform infra-red spectroscopy (FTIR), X-ray diffraction (XRD), high resolution transmission electron microscopy HRTEM and energy dispersive X-ray analysis (EDX) techniques. The HRTEM results revealed the formation of highly stable, mono dispersed, spherical shaped AgNPs with the size ranging from 20 to 30nm. The presence of flavonoids and their interaction with the AgNPs were confirmed using FTIR. Antibacterial activities of the AgNPs were studied against pathogenic gram-positive Staphylococcus aureus (S. aureus) and gram negative Escherichia coli (E. coli) bacteria. The synthesized AgNPs displayed the enhancement of antibacterial activity against E. coli. The morphological changes in the bacterial cell membrane was observed using SEM analysis. Leakage of protein from the bacterial cells increased at every time intervals (2 and 4h). MTT assay was carried out for the AgNPs against human skin cell line (HaCaT). Interestingly, cytotoxicity of the synthesized AgNPs was less toxic to HaCaT cells as compared to bacteria cells, which suggests that the synthesized AgNPs by this method is eco-friendly in nature.

Schwannoma of the brain stem: case report

A case of intramedullary schwannoma of the brain stem is reported, and its possible origin discussed. The importance of a biopsy in brain-stem tumors is emphasized.

Vertebral and epidural hemangioma with paraplegia in Klippel-Trenaunay-Weber syndrome. Case report

A patient with a rare case of Klippel-Trenaunay-Weber syndrome presented with paraplegia due to compression by a vertebral and epidural cavernous hemangioma. The metameric distribution of the large cutaneous vascular nevus provided the clinical clue to the nature of the spinal lesion. The association of the two lesions is explained in the basis of developmental anomaly.

Hemicraniectomy for large middle cerebral artery territory infarction: outcome in 19 patients

BACKGROUND

Large space-occupying middle cerebral artery infarction accounts for 10-15% of all supratentorial infarctions and carries a mortality of 50% to 80%. Hemicraniectomy may be useful when optimal medical management has failed.

METHODS

Between June 1997 and June 2000, 19 patients who fulfilled the clinical and imaging criteria for large middle cerebral artery infarction underwent hemicraniectomy because of impending herniation despite best medical therapy. The National Institute of Health Stroke Scale (NIHSS) assessed neurological status on admission and at one week after surgery. At 3 month follow up, The Barthel Index (BI) and Rankin Scale (RS) were used to assess the functional outcome among survivors.

RESULTS

There were 15 males and 4 females with a mean age of 46.5 years (range 27-76 years). Ten patients (53%) had dominant hemisphere stroke. The mean interval between stroke onset and surgery was 60.3 hours (range 20-103 hours). The mean NIHSS score before surgery was 20.5 (range 17-26) and 10.5 (range 6-22) after surgery. One patient (5.2%) died due to post-operative meningitis. At follow up, mean BI was 56.4 (range 25-90) and RS revealed severe handicap in 4 patients (21%). Patients under 50 years of age had a significantly better outcome with mean BI of 60.7 as compared to only 41.3 (p=<0.048) in older patients. Speech function, especially comprehension improved in all patients with dominant hemisphere infarction.

CONCLUSION

These findings add to previous studies suggesting hemicraniectomy may be a useful procedure in patients with large middle cerebral artery territory infarction. The functional outcome is good in younger patients. A randomised controlled trial is required to substantiate these findings.

Computer assisted analysis of wound infection in neurosurgery

The effect of 10 variables on the development of postoperative infection in 536 clean elective neurosurgery patients was calculated using correlational, regression and discriminant analyses. The time of shaving the operation site, type of theatre ventilation and duration of operation were found to have a highly significant effect on the infection rate. The influence of season and age of patient was not evident on simple analysis, but both were found to be significant factors using regression analysis. The sex of patient, carriage of Staphylococcus aureus, airborne bacterial count, presence of bacteria in the wound and the use of prophylactic antibiotics did not have a significant effect on infection rates.

Application of a Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cow Components Adulterated in Buffalo Milk/Meat

Loop-mediated isothermal amplification (LAMP) is a diagnostic method for amplification of DNA with rapid and minimal equipment requirement. In the present study, we applied the LAMP assay for rapid detection of cow components adulteration in buffalo milk/meat samples. The test can be completed within around 1 h 40 min starting from DNA extraction and can be performed in water bath without requirement of thermocycler. The cow DNA in buffalo samples were identified in the developed LAMP assay by either visualizing with SYBR Green I/HNB dyes or observing the typical ladder pattern on gel electrophoresis. The test can detect up to 5 % level of cow milk/meat mixed in buffalo counterparts. Due to the simplicity and specificity, the developed LAMP test can be easily adapted in any laboratory for rapid detection of cow species identification in livestock by products.

Tuberculous abscess of the brain stem

Three cases of tuberculous abscess of the brain stem were treated with excision of the abscess supplemented with antitubercular therapy for 12 to 18 months. The lesions were frankly purulent and tubercle bacilli were demonstrated in the pus. A computed tomography scan demonstrated the site and extent of the lesion. Two of three patients developed the abscess during the course of antitubercular therapy for associated tubercular lesions. In spite of modern antitubercular treatment the abscess did not resolve and surgical excision had to be employed as a curative treatment.

Genetic analysis of river, swamp and hybrid buffaloes of north-east India throw new light on phylogeography of water buffalo (Bubalus bubalis)

This study analysed buffaloes from north-east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South-East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north-east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp-type buffaloes of north-east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D-loop region of 530-bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of north-east India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise FST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median-joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north-east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north-east India to South-East Asia.

Sellar tuberculoma

Images

Magnetic resonance evaluation of spinal dysraphism in children

Magnetic resonance (MR) imaging of the spine was performed as the initial imaging technique in 20 children when spinal dysraphism was suspected clinically and plain radiographs showed spina bifida. The correlation with surgical findings indicated that MR provided accurate information preoperatively in all the cases. Some unusual observations in cases with spina bifida cystica and occulta are discussed. It is concluded that plain radiograph and MR complete the preoperative radiologic evaluation of cases with spinal dysraphism.

Role of magnetic resonance imaging in the assessment of perianal fistulas

OBJECTIVE

This study was carried out to evaluate the role of magnetic resonance imaging (MRI) in preoperative assessment of fistula-in-ano.

SUBJECTS AND METHODS

Twenty-six patients (21 male and 5 female, age 19-65 years) were prospectively studied from July 1999 to December 2001 using a 1.0-tesla superconducting magnet. T(1)-weighted fast spin echo (T1W FSE) images before and after gadolinium injection and fat suppressed T2-weighted fast spin echo (T2W FSE) images were obtained in transverse and coronal planes. MRI findings were correlated with surgical findings.

RESULTS

Twenty-one of the 26 patients demonstrated active fistulas. The MRI findings were in accordance with the examination findings under anesthesia and/or surgery in 15 of 16 cases. Both coronal and transverse planes were useful in assessing the location and direction of tracts and abscesses. Both contrast-enhanced T1W FSE and fat-suppressed T2W FSE images were useful in assessing the activity of lesions and the course of tracts.

CONCLUSION

MRI showed accurate correlation with surgical findings and aided in preoperative management and planning for surgery.

Effect of plant growth-promoting Streptomyces sp. on growth promotion and grain yield in chickpea (Cicer arietinum L)

The physiological and molecular responses of six strains of Streptomyces sp. (CAI-13, CAI-85, CAI-93, CAI-140, CAI-155 and KAI-180), with their proven potential for plant growth-promotion (PGP) in rice were studied to understand the mechanisms causing the beneficial effects. In this investigation, those six strains were evaluated for their PGP capabilities in chickpea in the 2012-13 and 2013-14 post-rainy seasons. All of the Streptomyces sp. strains exhibited enhanced nodule number, nodule weight, root weight and shoot weight at 30 days after sowing (DAS) and pod number, pod weight, leaf area, leaf weight and stem weight at 60 DAS in both seasons over the un-inoculated control. At chickpea crop maturity, the Streptomyces strains had enhanced stover yield, grain yield, total dry matter, pod weight, seed number and seed weight in both seasons over the un-inoculated control. In the rhizosphere, at crop maturity, the Streptomyces strains also significantly enhanced soil biological and mineral nutrient traits including microbial biomass carbon, dehydrogenase activity, total nitrogen, available phosphorous and organic carbon in both seasons over the un-inoculated control. Of the six strains of Streptomyces sp., CAI-85, CAI-93 and KAI-180 were found superior to CAI-155, CAI-140 and CAI-13, in terms of their effects on root and shoot development, nodule formation and crop productivity. Scanning electron microscopy micrographs had revealed the success in colonization of the chickpea roots by all six strains. This investigation further confirms the broad-spectrum of PGP activities by the selected Streptomyces sp.

Low flow (cryptic) arteriovenous malformation and spontaneous haematoma

The authors emphasize the meticulous search for microangioma under magnification in cases of spontaneous haematoma. Two cases of low flow (cryptic) arteriovenous malformations are described. The CT scan and angiography are non-contributory in detecting such lesions. These small-sized angiomas are buried in the wall of the haematoma cavity. Histologically there is evidence of thrombosis in arteriovenous malformation.

T-ARMS PCR genotyping of SNP rs445709131 using thermostable strand displacement polymerase

OBJECTIVES

In a recent publication, we reported the successful use of tetra primer-amplification refractory mutation system based polymerase chain reaction (T-ARMS-PCR) for genotyping of rs445709131-SNP responsible for the bovine leukocyte adhesion deficiency (BLAD) in cattle. The SNP is characterized by higher GC content of the surrounding region, hence, the previous protocol utilized dimethyl sulfoxide as PCR enhancer. Here, the reaction cocktail was modified with the use of thermostable strand displacement polymerase (SD polymerase) instead of commonly used Taq DNA Polymerase. The amplification efficiency, reaction sensitivity, specificity, and need of PCR enhancer in reactions containing SD polymerase and Taq polymerase were compared.

RESULTS

T-ARMS-PCR assay is influenced by multiple factors for the correct genotyping necessitating extensive optimization at the initial stages. The described modification enabled generation of all amplicons by 25 cycles whereas the assay with Taq polymerase needed a minimum of 35 cycles. The modified assay amplified all amplicons at a wider range of annealing temperature (50-60 °C), without the addition of dimethyl sulfoxide. The replacement of Taq polymerase with SD polymerase may be beneficial in the T-ARMS assay for development of user-friendly, faster assay which is less affected by the reaction and cyclic conditions.