AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors

We report here a robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures. The active site finder identifies all cavities in a protein and scores them based on the physicochemical properties of functional groups lining the cavities in the protein. The accuracy realized on 620 proteins with sizes ranging from 100 to 600 amino acids with known drug active sites is 100% when the top ten cavity points are considered. These top ten cavity points identified are then submitted for an automated docking of an input ligand/candidate molecule. The docking protocol uses an all atom energy based Monte Carlo method. Eight low energy docked structures corresponding to different locations and orientations of the candidate molecule are stored at each cavity point giving 80 docked structures overall which are then ranked using an effective free energy function and top five structures are selected. The predicted structure and energetics of the complexes agree quite well with experiment when tested on a data set of 170 protein-ligand complexes with known structures and binding affinities. The AADS methodology is implemented on an 80 processor cluster and presented as a freely accessible, easy to use tool at http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp .

The prognostic significance of MRI-detected extramural venous invasion in rectal carcinoma

AIM

To assess whether there is a significant difference in the incidence of patients with metastases of rectal carcinoma at 1 year follow-up between magnetic resonance imaging (MRI)-detected extramural venous invasion (EMVI) and those without.

MATERIALS AND METHODS

A search of our institution's cancer registry revealed 788 patients with rectal carcinoma between January 2007 and April 2012. Those who were initially staged using MRI and computed tomography (CT) chest/abdomen/pelvis, and followed-up with a CT chest/abdomen/pelvis examination at 1 year were included in this retrospective study. Patients with synchronous metastases were excluded, leaving a cohort of 202 cases. Two consultant radiologists reviewed all MRI images and gave a consensus opinion regarding EMVI grade and vessel size involved. All CT images were reviewed for metastases. Results were analysed using chi-squared and Fisher's exact tests.

RESULTS

There were 53 cases (26.2%) of EMVI-positive rectal carcinoma. Of the patients with EMVI, 24.5% developed metastases at 1 year follow-up, compared to 6.7% of those without. There is a significant difference in prognosis between those patients with and those without MRI-detected EMVI (χ(2) = 12.29, p < 0·001). Those with EMVI have a 3.7 times increased relative risk of developing metachronous metastases within 1 year of diagnosis.

CONCLUSION

MRI-detected EMVI-positive rectal carcinomas are associated with an increased risk of metachronous metastases within 1 year of diagnosis. Currently, EMVI status does not directly influence the initial management of rectal carcinoma. This available and potentially prognostic feature could be used to guide treatment pathways to increase disease-free survival.

Ubiquitous formation of bulk Dirac cones and topological surface states from a single orbital manifold in transition-metal dichalcogenides

Transition-metal dichalcogenides (TMDs) are renowned for their rich and varied bulk properties, while their single-layer variants have become one of the most prominent examples of two-dimensional materials beyond graphene. Their disparate ground states largely depend on transition metal d-electron-derived electronic states, on which the vast majority of attention has been concentrated to date. Here, we focus on the chalcogen-derived states. From density-functional theory calculations together with spin- and angle-resolved photoemission, we find that these generically host a co-existence of type-I and type-II three-dimensional bulk Dirac fermions as well as ladders of topological surface states and surface resonances. We demonstrate how these naturally arise within a single p-orbital manifold as a general consequence of a trigonal crystal field, and as such can be expected across a large number of compounds. Already, we demonstrate their existence in six separate TMDs, opening routes to tune, and ultimately exploit, their topological physics.

Uptake pathways of clinical and healthy animal isolates of Campylobacter jejuni into INT-407 cells

Campylobacter jejuni isolates obtained from human and animal sources showed different invasion levels into human embryonic intestinal (INT-407) cells. There was no significant relation between the degree of invasion and cytotoxins production. The depolymerization of both microfilaments by cytochalasin-D and microtubules by colchicine, demecolcine and nocodazole or stabilization of microtubules by paclitaxel reduced the invasiveness of C. jejuni, although microfilament depolymerization showed greater inhibition than microtubule depolymerization. Interference with receptor-mediated endocytosis by G-strophanthin and monodansylcadaverine and inhibition of endosome acidification by monensin reduced the number of viable intracellular C. jejuni cells. Furthermore inhibition of only host protein kinases by staurosporine, but not phosphoinositide 3-kinase by wortmannin or protein kinase-C by calphostin-C, significantly reduced invasion of epithelial cells by C. jejuni. These data suggest that the internalization mechanism triggered by C. jejuni is strikingly different from the microfilament-dependent invasion mechanism exhibited by many of the well-studied enteric bacteria such as enteroinvasive strains of Escherichia coli, Salmonella typhimurium, Shigella flexneri, Yersinia enterocolitica and Yersinia pseudotuberculosis.

Anti-allergic activity of German chamomile (Matricaria recutita L.) in mast cell mediated allergy model

ETHNOPHARMACOLOGICAL RELEVANCE

Chamomile is most popular used medicinal plant and extensively consumed as a tea or tisanes. Traditionally this plant was used for treatment of many ailments such as allergy disorders and inflammatory mediated diseases.

AIM OF THE STUDY

We investigated the effects of anti-allergic activity of Matricaria recutita L. on mast cell mediated allergic models.

MATERIALS AND METHODS

The protective effect of methanol extract of Matricaria recutita against compound 48/80 induced anaphylaxis and pruritis models for acute phase of hypersensitivity reactions were carried out. The late phase hypersensitivity reactions by compound 48/80 induced mast cell degranulation and histamine release from blood along with serum nitric oxide (NO), rat peritoneal fluid nitric oxide (NO) and bronchoalveolar fluid nitric oxide (NO) levels were measured.

RESULTS

The methanol extract of Matricaria recutita L. showed inhibitory effects on anaphylaxis induced by compound 48/80 and significant dose dependent anti-pruritis property was observed by inhibiting the mast cell degranulation. Mast cell membrane stabilization activity was also observed in compound 48/80 induced mast cell activation. Dose dependent reduction in the histamine release, along with decreased release of serum, rat peritoneal and BAL fluid nitric oxide (NO) levels were observed.

CONCLUSION

These results suggest that the methanol extract of Matricaria recutita showed potent anti-allergic activity by inhibition of histamine release from mast cells.

Histopathology of Trypanosoma (Trypanozoon) evansi infection in bandicoot rat. I. visceral organs

Experimental infection of Trypanosoma (Trypanozoon) evansi in Bandicota bengalensis produces an acute disease course leading to untimely death of the bandicoot rat. The sequential alteration of liver, spleen, lung, kidney, and heart was studied on the 5th, 8th, 12th, and 14th days postinoculation. The rats showed inflammatory, degenerative, and necrotic changes in these organs. In liver, pseudolobule formation, necrosis and hemorrhage within the sinusoids, and fatty degeneration of hepatic cells were the predominant histopathological changes. The changes were destructive and irreversible. In spleen giant cells aggregation and granulomatous lesion, i.e., accumulation of histiocytes, were the protective changes, whereas tissue and cell damage indicated irreversible degeneration. The gradual development of intrabronchus inflammation, aggregation of inflammatory cells around the alveoli, congestion of bronchioles, septal edema, atrophy of alveolar walls, migration of macrophages, and emphysema were the histopathological changes noticed in the lungs of the infected rats. The affected kidney showed infiltration of lymphocytes, hemorrhage in the interlobular space, and glomerulitis as the irreversible and destructive changes in the rats. There was degeneration of myocardium in the hearts of the rats. The histopathological changes in these organs are compared with those studied in surra, human sleeping sickness disease, and African trypanosomiasis. Possible mechanisms for these histological changes in the visceral organs are discussed.

Serosurvey of five viruses in chickens on smallholdings in Bangladesh

A serologic survey was undertaken in chickens in smallholdings in Bangladesh for avian influenza A virus (AIV), egg drop syndrome '76 virus (EDS'76V), infectious bronchitis virus (IBV), Newcastle disease virus (NDV) and reovirus (RV) in three phases: January 2002-May 2003, September 2003-August 2004, and August 2005-March 2006. Four hundred thirty-six sera collected in the 2nd phase, 295 in the first phase, 755 in the 1st plus 2nd phases and 295 in the 1st phase were investigated for AIV, EDS'76V, IBV and RV, respectively, using enzyme linked immunosorbent assays. All 854 sera collected in the three phases were screened for NDV using hemagglutination inhibition test. In chickens 20% were seropositive to AIV, 3% to EDS'76V, 74% to IBV, 88% to NDV, and 47% to RV. The seroprevalence in flocks was 23% to AIV, 6% to EDS'76V, 79% to IBV, 89% to NDV and 56% to RV. Twenty-five percent chickens had > or = 10log(2)HI titers to NDV.

Molecular epidemiology of measles in India, 2005-2010

Measles is a childhood disease that causes great morbidity and mortality in India and worldwide. Because measles surveillance in India is in its infancy, there is a paucity of countrywide data on circulating Measles virus genotypes. This study was conducted in 21 of 28 States and 2 of 7 Union Territories of India by MeaslesNetIndia, a national network of 27 centers and sentinel practitioners. MeaslesNetIndia investigated 52 measles outbreaks in geographically representative areas from 2005 through June 2010. All outbreaks were serologically confirmed by detection of antimeasles virus immunoglobulin M (IgM) antibodies in serum or oral fluid samples. Molecular studies, using World Health Organization (WHO)-recommended protocols obtained 203 N-gene, 40 H-gene, and 4 M-gene sequences during this period. Measles genotypes D4, D7, and D8 were found to be circulating in various parts of India during the study period. Further phylogenetic analysis revealed 4 lineages of Indian D8 genotypes: D8a, D8b, D8c, and D8d. This study generated a large, countrywide sequence database that can form the baseline for future molecular studies on measles virus transmission pathways in India. This study has created support and capabilities for countrywide measles molecular surveillance that must be carried forward.

Serotypes of Streptococcus pneumoniae causing invasive childhood infections in Bangladesh, 1992 to 1995

One hundred sixty-five invasive Streptococcus pneumoniae strains were isolated from children under five at Dhaka Shishu (Children's) Hospital during the period 1992 to 1995. Ninety-four strains were from cerebrospinal fluid, and 71 were from blood. More than 91% of the strains were isolated from patients aged 24 months or less. Predominant serotypes were, in descending order 7F, 12F, 14, 15B, 18, 5, and 22A. These comprised 70% of all isolates. The marked differences in serotype distribution in different countries indicate the need for a sentinel surveillance study for the countries of South Asia, particularly Bangladesh, China, India, and Pakistan.

The increasing burden of disease in Bangladeshi children due to Haemophilus influenzae type b meningitis

A laboratory-based study of diagnosed bacterial meningitis in the national paediatric hospital identified 852 cases of meningitis in the 8-year period 1987-1994. There were 587 culture-positive cases, of which Haemophilus influenzae (47%) and Streptococcus pneumoniae (32%) accounted for 80%. H. influenzae showed a remarkable increase of 700% during the study period. Most of the H. influenzae cases (90%) occurred in the 1st 2 years of life. Analysis of culture-negative specimens by antigen detection in the last 2 years also revealed the predominance of H. influenzae (71.4%) and S. pneumoniae (22.4%). Typing of H. influenzae isolates during this time showed that 98% of the strains were type b. This retrospective hospital-based study indicated a pronounced increase in the incidence of H. influenzae meningitis and strongly supports the need for large-scale Hib vaccination for young children. However, such nationwide intervention will probably need to be based on a prospective on a prospective and population-based surveillance of H. influenzae infections.

Correlation Between In Vitro Secretion of Virulence-Associated Proteins of Campylobacter jejuni and Colonization of Chickens

The mechanisms used by Campylobacter jejuni to colonize the (chicken) intestinal tract have not been defined. In this study, we obtained evidence that in the presence of chicken serum and mucus, C. jejuni secreted proteins that may play a role in the colonization of chicken gut (Campylobacter invasion antigen = Cia). C. jejuni strains NCTC11168V1 and 81-176, as well as an NCTC11168V1 flaA mutant, were found to colonize intestinal tract and secrete proteins in the presence of chicken mucus, chicken serum, or fetal bovine serum in cell culture-conditioned medium. C. jejuni strain NCTC11168V26, which was observed to be a poor colonizer compared with the other C. jejuni isolates, did not secrete Cia proteins. Secreted proteins were also recognized by Western immunoblot using sera from birds that had been colonized by C. jejuni. These data suggest that C. jejuni secretes Cia proteins during colonization of chicken gut and that these Cia proteins play an important role in colonization.

Serum fetuin-A concentration predicts glycaemic outcomes in people with prediabetes: a prospective study from eastern India

AIM

To evaluate the role of fetuin-A levels in predicting glycaemic outcomes (progression to diabetes or reversion to normoglycaemia) in people with prediabetes.

METHODS

A total of 2119 people were screened, of whom 144 people with prediabetes, 50 people with normoglycaemia and 66 people with newly diagnosed diabetes underwent estimation of fasting insulin, fetuin-A, interleukin-6, interleukin-1β, tumour necrosis factor-α, lipid and 25-hydroxyvitamin-D levels and assessment of non-alcoholic fatty liver disease using ultrasonography and the fatty liver index. People with prediabetes were followed and analysed according to glycaemic outcome and quartile of fetuin-A level.

RESULTS

Fetuin-A, interleukin-1β, interleukin-6, tumour necrosis factor-α and triglyceride levels and presence of non-alcoholic fatty liver disease increased across the glycaemic spectrum and were highest in people with diabetes. A total of 32 people with prediabetes reverted to normoglycaemia, 23 progressed to diabetes and 65 remained with prediabetes over a mean ± sd follow-up of 32.12 ± 8.4 months. People progressing to diabetes had higher baseline glycaemia rates, fetuin-A levels, interleukin-1β levels, fatty liver index scores and prevalence of non-alcoholic fatty liver disease and lower 25-hydroxyvitamin-D levels. People with prediabetes in the highest fetuin-A quartile had the highest risk of progression to diabetes (relative risk 2.68, 95% CI 0.95-7.55; P = 0.06) and the lowest rate of reversion to normoglycaemia (relative risk 0.27, 95% CI 0.08-0.85; P = 0.03). Fetuin-A levels correlated with interleukin-1β levels (r = 0.420; P < 0.001), interleukin-6 levels (r = 0.231; P = 0.022) and fatty liver index scores (r = 0.319; P < 0.001). Cox regression showed that higher fetuin-A levels and higher BMI and lower 25-hydroxyvitamin-D levels were predictive of lower rates of reversion to normoglycaemia. Age, triglyceride levels, and interleukin-6 and interleukin-1β levels were predictive of progression to diabetes.

CONCLUSIONS

Increased fetuin-A level has an adverse impact on glycaemic outcomes in prediabetes. This study highlights the importance of fetuin-A as a predictor of glycaemic outcomes in prediabetes.

Role of a large plasmid of Salmonella typhi encoding multiple drug resistance

Twenty isolates of Salmonella typhi from cases of typhoid during the 1989-1990 epidemic in Calcutta were examined. Most isolates (84% of all isolates in the epidemic) were resistant to chloramphenicol, ampicillin, tetracycline and streptomycin but were sensitive to nalidixic acid and ciprofloxacin. Plasmids of 120 kb and 14 kb were identified amongst the multi-drug resistant isolates of S. typhi. However, there was no plasmid in the antibiotic-sensitive isolates. The 120-kb plasmid was transferable and transconjugants were resistant to chloramphenicol, ampicillin, tetracycline and streptomycin. Restriction endonuclease analysis patterns after EcoRI digestion of the 120-kb antibiotic-resistance plasmids from the S. typhi isolates and transconjugants were similar.

A longitudinal study of the incidence of major endemic and epidemic diseases affecting semi-scavenging chickens reared under the Participatory Livestock Development Project areas in Bangladesh

A 17-month (from January 2002 to May 2003) longitudinal study was undertaken to elucidate the epidemiology of important endemic and epidemic diseases affecting semi-scavenging chickens reared in the Participatory Livestock Development Project area in Bangladesh. This project was implemented in 17 northern and north-central districts of Bangladesh, under which 361 839 rural poor people were assisted to undertake poultry-rearing activity as a tool of poverty reduction. Of the total beneficiaries 93% were "key rearers". A key rearer is defined as a beneficiary who generally rears 10 to 13 hens in a semi-scavenging system with little additional feed supply. Households of 650 key rearers and some chick rearers were observed. During the study period 1227 birds, which belonged to different age, breed and sex categories, were found dead as a result of disease occurrence. From every dead bird organ samples such as the liver, heart, spleen, brain lung, trachea and bursa of Fabricius were collected. The incidence rate of mortality was 0.01976 per bird-months at risk. Of the total deaths 58.44% had single or mixed type of infections. Newcastle disease had the highest proportional mortality rate (15.81%). The proportional mortality caused by fowlpox, fowl cholera, salmonellosis, colibacillosis, aspergillosis, infectious bursal disease, mixed infections and undiagnosed cases were 8.96%, 6.76%, 7.09%, 6.93%, 0.33%, 2.04%, 10.51% and 41.56%, respectively. Newcastle disease affected a significant higher proportion (18.81%) of birds older than 60 days of age (P=0.00). Younger birds (age < or = 60 days) had a higher proportional mortality due to fowlpox and infectious bursal disease than older birds (P=0.00). Sonali (male Rhode Island Red x female Fayoumi) birds reared under the semi-scavenging system had a higher infection rate with Newcastle disease virus compared with indigenous and Fayoumi birds (P=0.00). Fowlpox was more prevalent in Fayoumi birds compared with Sonali. Surprisingly, Newcastle disease was more common in the vaccinated birds rather than the unvaccinated birds.

A novel HBV recombinant (genotype I) similar to Vietnam/Laos in a primitive tribe in eastern India

Genotyping of 20 strains of Hepatitis B virus (HBV) from the Idu Mishmi primitive tribe of northeast India identified multiple genotypes and the presence of a unique cluster grouping with strains from Vietnam and Laos identified as novel recombinants/genotype I. Sequence analysis (similarity and bootscan plots) of three complete HBV genomes from the tribe provided evidence of recombination. Phylogenetic analyses supported recombination between genotypes A, G and C. The Pre-S gene between nt 2943 and 397 was clearly of genotype A origin, whereas nt 397-1397 represented genotype G and nt 1397-2943 represented genotype C. Percentage divergence from genotypes B, D, E, F, G and H varied from 9.2 +/- 0.45% to 13.8 +/- 0.53%, whereas genotype A and C differed by 7.9 +/- 0.42% and 7.4 +/- 0.39% respectively. The identification of similar recombinant viruses in three countries, especially in a primitive tribe with no contact with the outside world suggests that these viruses do not represent recent recombination events, but circulation of closely related viruses highly divergent from known HBV genotypes and should be classified as members of genotype 'I'.

Causes of loss of Sonali chickens on smallholder households in Bangladesh

In a 1-year-long prospective longitudinal study, we determined the causes of loss of 'Sonali' (male symbol Rhode Island Red x female symbol Fayoumi) chickens at key-rearers' households of the smallholder livestock development project-2 (SLDP-2) area in Bangladesh. A key rearer is a smallholder of chickens in the 'village poultry-production chain' (undertaken by SLDP-2 under the financial assistance of the DANIDA) who rears at least five Sonali and some 'Deshi' (non-descriptive and indigenous) chickens in their homesteads based on semi-scavenging system. The aim of this program is to ameliorate poverty, especially among women. Two co-ordination centers (set at the Potuakhali and Noakhali districts) supervised the development activities. We selected two upazilas (lower administration units) randomly from each of the two districts and in every selected upazila, we selected at random 125 key-rearer households. Incidence rates of loss of Sonali chickens from disease, predation, selling and slaughtering were 0.025, 0.023, 0.081 and 0.039 per bird-month at risk, respectively. The major predators of Sonali chickens in the study area were foxes, a kind of wild cat (Felis chaus), mongooses and human thieves. Colibacillosis (both single and mixed infections) had a contributory role in the death of 28% of dead Sonali birds collected for diagnosis; salmonellosis, Newcastle disease and internal parasites contributed to the next highest (14, 11and 10%) proportional mortalities.