A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone.

Background: Genomic aberrations have been identified in metastatic castration-resistant prostate cancer (mCRPC), but molecular predictors of resistance to abiraterone acetate/prednisone (AA/P) treatment are not known. Patients and methods: In a prospective clinical trial, mCRPC patients underwent whole-exome sequencing (n = 82) and RNA sequencing (n = 75) of metastatic biopsies before initiating AA/P with the objective of identifying genomic alterations associated with resistance to AA/P. Primary resistance was determined at 12 weeks of treatment using criteria for progression that included serum prostate-specific antigen measurement, bone and computerized tomography imaging and symptom assessments. Acquired resistance was determined using the end point of time to treatment change (TTTC), defined as time from enrollment until change in treatment from progressive disease. Associations of genomic and transcriptomic alterations with primary resistance were determined using logistic regression, Fisher's exact test, single and multivariate analyses. Cox regression models were utilized for determining association of genomic and transcriptomic alterations with TTTC. Results: At 12 weeks, 32 patients in the cohort had progressed (nonresponders). Median study follow-up was 32.1 months by which time 58 patients had switched treatments due to progression. Median TTTC was 10.1 months (interquartile range: 4.4-24.1). Genes in the Wnt/ß-catenin pathway were more frequently mutated and negative regulators of Wnt/ß-catenin signaling were more frequently deleted or displayed reduced mRNA expression in nonresponders. Additionally, mRNA expression of cell cycle regulatory genes was increased in nonresponders. In multivariate models, increased cell cycle proliferation scores (≥ 50) were associated with shorter TTTC (hazard ratio = 2.11, 95% confidence interval: 1.17-3.80; P = 0.01). Conclusions: Wnt/ß-catenin pathway activation and increased cell cycle progression scores can serve as molecular markers for predicting resistance to AA/P therapy.

Culture-independent metagenomic approach to characterize the surface and subsurface soil bacterial community in the Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot.

Soil bacterial communities, which contain the highest level of prokaryotic diversity of any natural environment, are important for ecosystem functioning. A culture-independent metagenomic approach was employed in the present investigation to characterize the diversity of soil bacterial community composition in five geochemically and hydrologically different surface and subsurface soil habitats of Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot. The diversity of soil bacterial community was determined through sequence analysis of 16S-23S intergenic spacer regions (ISR). Polymerase chain reaction (PCR) universal primers, 1406F (5'-TGYACACACCGCCCGT-3') and 155r (5'-GGGTTBCATTCRG-3') were used for amplification of 16S-23S ribosomal DNA intergenic spacers of bacteria. Amplification resulted in an intense array of PCR products approximately ranging in size from 200 to 900 bp. Clear banding patterns were observed in analysed samples using the primer set in combination. A clear change in microbial ISR profile was observed on visual analysis of gel electrophoresis profiles. Fast alignment database searches of PCR amplicons of 16S-23S ISR sequence data revealed that the isolated sequences resembled five major phylogenetic groups of bacteria, namely α-, ß- and γ-subdivisions of Proteobacteria, Acidobacterium and Comamonadaceae.

Retinoic acid syndrome--cardiac complication.

Retinoic acid syndrome is a novel complication of therapy with all-trans retinoic acid (ATRA) in patients with acute promyelocytic leukemia (APML). Primarily the syndrome consists of fever and respiratory distress. Additional features include weight gain, oedema over lower extremities, pleural or pericardial effusion and hypotension. We report electrophysiological changes in a 16 year old patient with acute promyelocytic leukemia following treatment with ATRA. Such an unusual complication is a rarity and to the best of our knowledge has not been previously reported.

QTc interval in survivors of out of hospital cardiac arrest.

BACKGROUND: QTc interval (QTc) prolongation is seen on the post-arrest electrocardiogram (ECG) of many out of hospital cardiac arrest (OHCA) survivors. It remains unclear whether this is a transient phenomenon or a manifestation of an underlying arrhythmic substrate. This observational study assessed the trend of QTc in an unselected group of patients presenting with OHCA. We sought to identify any relationship between QTc, gender and aetiology of arrest. We observed whether targeted temperature management (TTM) is associated with malignant arrhythmia. METHOD: We analysed 60 patients presenting with OHCA to the Bristol Heart Institute during a 20-month period. We measured QTc on admission and assessed for persistence, development and resolution of prolongation at up to 5 time points post-OHCA. Aetiology of arrest was divided into coronary, non-coronary or primary arrhythmic to investigate for patterns in QTc behaviour. RESULTS: 81.7% (49/60) of arrests were attributed to an acute coronary event. 55% (33/60) had QTc prolongation on admission, of which 79% resolved. There were no significant differences in QTc behaviour by aetiology. One patient presenting with a normal QTc, developed prolongation during admission and received a genetic diagnosis of Long QT Syndrome. TTM was employed in 57/60, with no increased incidence of malignant arrhythmia. CONCLUSIONS: Prolonged QTc on admission does not imply a primary arrhythmic aetiology and resolves in the majority pre-discharge. However, an initial normal QTc post-OHCA does not preclude a diagnosis of Long QT syndrome, highlighting the importance of thorough investigations in these patients. TTM appears safe from a cardiac perspective.

Corroboration and efficacy of Magneto-Fluorescent (NiZnFe/CdS) Nanostructures Prepared using Differently Processed Core.

The selected and controlled preparation of core@shell nanostructures, which unite the multiple functions of ferromagnetic Ni-Zn ferrite core and CdS shell in a single material with tuneable fluorescence and magnetic properties, have been proposed by the seed mediated aqueous growth process. The shell particle thickness and core of nanostructures were precisely tuned. Current work exhibits the comparative study of core@shell multifunctional nanostructures where core being annealed at two different temperatures. The core@shell nanostructure formation was confirmed by complementary structural, elemental, optical, magnetic and IR measurements. Optical and magnetic characterizations were performed to study elaborative effects of different structural combinations of core@shell nanostructures to achieve best configuration with high-luminescence and magnetic outcomes. The interface of magnetic/nonmagnetic NiZnFe2O4/CdS nanostructures was inspected. Unexpectedly, in some of the core@shell nanostructures presence of substantial exchange-bias was observed in spite of the non-magnetic nature of CdS QDs which is clearly an "optically-active" and "magnetically-inactive" material. Presence of "exchange-bias" was confirmed by the change in "magnetic-anisotropy" as well as shift in susceptibility derivative. Finally, successful formulation of stable and efficient core@shell nanostructures achieved, which shows no exchange-bias and shift. Current findings suggest that these magneto-fluorescent nanostructures can be used in spintronics; and drug delivery-diagnosis-imaging applications in nanomedicine field.

Variations in antibiotic use across India: multi-centre study through Global Point Prevalence survey.

The aim of the study was to assess antimicrobial prescribing patterns, and variation in practice, in India. A point prevalence survey (PPS) was conducted in October to December 2017 in 16 tertiary care hospitals across India. The survey included all inpatients receiving an antimicrobial on the day of PPS and collected data were analysed using a web-based application of the University of Antwerp. In all, 1750 patients were surveyed, of whom 1005 were receiving a total of 1578 antimicrobials. Among the antimicrobials prescribed, 26.87% were for community-acquired infections; 19.20% for hospital-acquired infections; 17.24% for medical prophylaxis; 28.70% for surgical prophylaxis; and 7.99% for other or undetermined reasons. Antibiotic prescribing quality indicators, such as reason in notes and post-prescription review score, were low. This PPS showed widespread antibiotic usage, underlining the need for antibiotic stewardship to promote evidence-based practice.

Changing pattern of human group A rotaviruses: emergence of G12 as an important pathogen among children in eastern India.

BACKGROUND: Rotavirus genotypes, G1-G4 and G9 are associated with childhood diarrhoea throughout the world. In our previous study, we detected G1, G2, G4 and three G12 strains from Kolkata, India. OBJECTIVES: To study the prevalence of G- and P-genotypes of rotaviruses associated with dehydrating diarrhoea in children admitted to two leading hospitals in eastern India. STUDY DESIGN: An active surveillance was conducted for elucidation of rotavirus infection in two leading hospitals in Kolkata, West Bengal and Berhampur (GM), Orissa, India, separated by 603km from January 2003 to April 2005. The rotaviruses were detected by RNA electrophoresis in polyacrylamide gels. G- and P-typing of the positive samples were accomplished by amplifying VP7 and VP4 genes by RT-PCR and genotyped by seminested multiplex PCR methods. Sequencing, sequence analysis and phylogenetic analysis of VP7 genes of G12 strains were carried out to understand the variations between the strains isolated from different parts of the world. RESULTS: The genotypic distribution varied remarkably from our earlier study period (1998-2001) with G1 (53.8%) being the most predominant strain followed by G2 (22.5%), G12 (17.1%), G9 (2.1%) and not a single G3 or G4 isolate was detected separately. 35.2% samples exhibited mixed P-types followed by P[4] (31.7%), P[8] (21.8%) and P[6] (9.8%). The phylogenetic analysis of G12 strains revealed that the G12 strains detected from different parts of the world clustered into three different lineages. Though VP7 sequences of G12 strains isolated from Kolkata and Berhampur are conserved, their P-types were different. CONCLUSION: During this study period we reported emergence of G12 strains as an important pathogen among children in eastern India, thus necessitating its inclusion in future polyvalent vaccine to control rotavirus diarrhoea.

RT-PCR based diagnosis revealed importance of human group B rotavirus infection in childhood diarrhoea.

BACKGROUND: Human group B rotavirus was first identified as causative agent of a large outbreak of severe gastroenteritis affecting more than 1 million people, predominantly adults in China in 1982-1983. In spite of serological evidences for the presence of group B rotavirus in many countries of the world, the virus has been detected only from China, India and Bangladesh, where most of the cases were from adults. OBJECTIVES: To ascertain the role of group B rotavirus as an aetiological agent of diarrhoea among children in Kolkata, India. STUDY DESIGN: An active surveillance was conducted for rotavirus infection in children in a leading referral paediatric hospital and a few samples were also collected from adults of another hospital in Kolkata, India over a period of 3 years (2002-2004). After primary screening of rotaviruses by RNA electrophoresis in polyacrylamide gel, 200 of 412 samples negative by PAGE were screened by reverse transcription polymerase chain reaction for group B rotaviruses. The group B rotavirus positives samples were also confirmed by dot-blot hybridization. RESULT: During the study period, we detected 37 (18.5%) sporadic cases of human group B rotavirus infection in children below 3 years of age of which 15 (7.5%) showed mixed infection with group A rotaviruses by RT-PCR. In dot-blot hybridization studies the RNA of all rotavirus positive samples hybridized with the nonisotopic psoralen-biotin labeled total RNA probe generated from a human group B rotavirus CAL-1 strain confirming the samples as group B rotaviruses. CONCLUSION: The shift in age preference of group B rotavirus infection from adult to children and mixed infection of group B and group A rotaviruses reveals the importance of group B rotavirus as an etiological agent of childhood diarrhoea. Therefore, future vaccination strategy should include both group A and B rotaviruses to control rotavirus diarrhoea.

Chitohexaose protects against acetaminophen-induced hepatotoxicity in mice.

Acetaminophen (N-acetyl-para-aminophenol (APAP)) toxicity causes acute liver failure by inducing centrilobular hepatic damage as a consequence of mitochondrial oxidative stress. Sterile inflammation, triggered by hepatic damage, facilitates gut bacterial translocation leading to systemic inflammation; TLR4-mediated activation by LPS has been shown to have a critical role in APAP-mediated hepatotoxicity. In this study, we demonstrate significant protection mediated by chitohexaose (Chtx) in mice challenged with a lethal dose of APAP (400 mg/kg b.w.). Decreased mortality by Chtx was associated with reduced hepatic damage, increased peritoneal migration of neutrophils, decreased mRNA expression of IL-1ß as well as inhibition of inflammasome activation in liver. Further, an alternate mouse model of co-administration of a sublethal doses of APAP (200 mg/kg b.w.) and LPS (5 mg/kg b.w.) operating synergistically and mediating complete mortality was developed. Overwhelming inflammation, characterized by increased inflammatory cytokines (TNF-α, IL-1ß and so on) in liver as well as in circulation and mortality was demonstrable in this model. Also, Chtx administration mediated significant reversal of mortality in APAP+LPS co-administered mice, which was associated with reduced IL-1ß in liver and plasma cytokines in this model. In conclusion, Chtx being a small molecular weight linear carbohydrate offers promise for clinical management of liver failure associated with APAP overdose.

The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response.

Response to treatment with selective serotonin reuptake inhibitors (SSRIs) varies considerably between patients. The International SSRI Pharmacogenomics Consortium (ISPC) was formed with the primary goal of identifying genetic variation that may contribute to response to SSRI treatment of major depressive disorder. A genome-wide association study of 4-week treatment outcomes, measured using the 17-item Hamilton Rating Scale for Depression (HRSD-17), was performed using data from 865 subjects from seven sites. The primary outcomes were percent change in HRSD-17 score and response, defined as at least 50% reduction in HRSD-17. Data from two prior studies, the Pharmacogenomics Research Network Antidepressant Medication Pharmacogenomics Study (PGRN-AMPS) and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, were used for replication, and a meta-analysis of the three studies was performed (N=2394). Although many top association signals in the ISPC analysis map to interesting candidate genes, none were significant at the genome-wide level and the associations were not replicated using PGRN-AMPS and STAR*D data. The top association result in the meta-analysis of response represents SNPs 5' upstream of the neuregulin-1 gene, NRG1 (P = 1.20E - 06). NRG1 is involved in many aspects of brain development, including neuronal maturation and variations in this gene have been shown to be associated with increased risk for mental disorders, particularly schizophrenia. Replication and functional studies of these findings are warranted.

An automated annotation tool for genomic DNA sequences using GeneScan and BLAST.

Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

Early onset primary pulmonary cryptococcosis in a renal transplant patient.

We report a case of primary pulmonary cryptococcosis in a post-renal transplant patient. A 65-year-old male renal transplant patient was admitted to the hospital with a low grade fever of 1 month, radiologically mimicking tuberculosis (TB). Broncho-alveolar fluid (BAL) shows capsulated yeast, and Cryptococcus neoformans was grown on culture supported by cytology and histopathological examination. Cryptococcal antigen was positive (32-fold) in serum and was negative in cerebrospinal fluid (CSF). The patient was given amphotericin B and 5-flucytosine and clinical improvement was seen on a weekly follow up. The serum cryptococcal antigen test might contribute to the early detection and treatment of pulmonary cryptococcosis. The results of antifungal susceptibility were aid in selecting the drug of choice for treatment.

A rare case of diphyllobothriasis from Pondicherry, South India.

Diphyllobothriasis is an intestinal parasitic infection caused by the ingestion of raw fresh-water fish containing the infectious larvae of Diphyllobothrium spp. This infection is uncommon in India. We report a case of diphyllobothriasis that occurred in Pondicherry, India, in a 5-year-old boy hailing from a fishing community. He attended the Pediatric OPD with spontaneous discharge of segments of the adult parasite. The segments (macroscopically and microscopically) were identified as those of Diphyllobothrium latum. The stool examination also revealed characteristic oval eggs.

A simple method of changing clotted intra-arterial catheters.

A simple technique for changing a clotted catheter is presented which has been frequently useful during percutaneous transfemoral coronary angiography. A guide wire is passed through a punched hole in the clotted catheter and a new catheter is inserted over the guide wire after the clotted catheter has been taken out.

Sequencing and sequence analysis of VP7 and NSP5 genes reveal emergence of a new genotype of bovine group B rotaviruses in India.

Three bovine group B rotavirus strains were detected from diarrheic calves during a surveillance study of rotaviral diarrhea in West Bengal, India. The sequence analysis of VP7 and NSP5 genes of these strains demonstrates a high degree of sequence variation from other group B rotavirus strains, indicating the emergence of a new genotype.

Emergence of novel human group A rotavirus G12 strains in India.

Three rare human G12 strains were detected from diarrheic clinical samples of children (<8 months of age) in Calcutta during a routine surveillance study of rotaviral diarrhea in India. The VP7 genes of G12 strains and their products showed maximum homology (97 to 99% at the nucleotide level and 98% at the amino acid level, respectively) with those of two recently reported G12 strains (from the United States and Thailand) but lesser homology with those of prototype G12 strain L26.