A Rapid, Sensitive and Type-Specific Detection of High-Risk HPV-16 and HPV-18.

Human papillomavirus (HPV) infection, particularly infection with HPVs 16 and 18, is a major cause of cervical cancer. The current high-risk HPV screening or diagnosis tests use cytological or molecular techniques that are primarily based on qualitative HPV DNA detection. Comparative studies, however, revealed that different assays have varying sensitivities for detecting specific HPV types. Here, we developed and optimized a sensitive PCR (Polymerase Chain Reaction) assay for detection of high-risk HPV-16 and HPV-18. The PCR parameters were optimized, and analytical specificities were validated. Performance of developed PCR assay was evaluated in clinical samples (n = 100) which showed 100% specificity for both the assays and 96.97% and 94.12% sensitivity for HPV-16 and HPV-18, respectively. The developed assay demonstrated high sensitivity and specificity for detection of high-risk HPV-16 and HPV-18, making it applicable to routine HPV detection practices.

Hyperthermophilic Clostridium sp. N-4 produced a glycoprotein biosurfactant that enhanced recovery of residual oil at 96 °C in lab studies.

Biosurfactant producing hypethermophilic microorganisms are essentially required for Microbial Enhanced Oil Recovery (MEOR) from high temperature oil reservoirs (above 90 °C). In the present study, biosurfactant producing Clostridium sp. N-4, optimally growing at 96 °C was isolated from a high temperature oil reservoir. Effect of pH, temperature and salinity on production and activity of N-4 biosurfactant was investigated. Biosurfactant produced by N-4 was partially purified by acid precipitation, characterized using FT-IR spectroscopy; and evaluated for its ability to enhance oil recovery in sand pack studies. The strain N-4 produced biosurfactant over a wide range of pH (5.0-9.0) and salinity (0-13%) at high temperature (80-100 °C) and optimally at pH 7, 96 °C and 4% salinity. N-4 biosurfactant was active at 37-101 °C; pH, 5-10 and salinity of 0-12 % (w/v). N-4 biosurfactant, characterized as glycoprotein reduced the surface tension of water by 32 ± 0.4 mN/m at critical micelle concentration of 100 µg/ml. N-4 biosurfactant mobilized 17.15% of residual oil saturation in sand pack studies. Similarly, the strain N-4 also recovered 36.92% of the residual oil in sand pack studies under the conditions mimicking the environment of depleted high temperature oil reservoir. Thus, the biosurfactant producing Clostridium sp. N-4 was identified as a suitable agent for enhanced oil recovery from high temperature oil reservoirs.

Oral Health Behavior and Treatment Needs among Drug Addicts and Controls in Amritsar District: A Case-controlled Study.

BACKGROUND: Substance and drug abuse is associated with severe psychosocial problems, violence and health complications. AIMS: The aim of the study was to evaluate and compare the oral hygiene status and sugar eating patterns among drug addicts with their age, gender and socio-economic status matched controls. SETTINGS AND DESIGN: The present study comprised of two groups-Group A comprised of 100 drug addicts and Group B included 100 controls. The study sample were interviewed and subjected to a comprehensive intra-oral examination. METHODS AND MATERIAL: Standardized methods of evaluation were performed using mouth mirror, dental probe, explorer and WHO probe. STATISTICAL ANALYSIS: The data was subjected to statistical analysis using Chi Square test and student t-test. RESULTS AND CONCLUSIONS: CPITN index revealed bleeding in 56% addicts and calculus in 20% addicts. The mean DMFT of group A was 5.71 as compared to 2.45 in group B. The frequency of sugar consumption was found to be high in addicts as compared to the controls. Significant P values (< 0.001) of DMFT index, periodontal status and frequency of sugar consumption were obtained on statistical analysis. The caries status was found to be poor in addicts, but the periodontal treatment needs were similar for both group A and B. Oral health promotion should be undertaken in drug rehabilitation centers for overall success of withdrawl treatment.

A randomised controlled trial comparing the efficacy of micellised and fat-soluble vitamin D3 supplementation in healthy adults.

Nanoemulsion formulation of vitamin D3 have been shown to have better bioavailability than the coarse emulsion preparation in vitro and in vivo animal studies. In the absence of randomised trial in humans, comparing the efficacy of nanotechnology-based miscellised vitamin D3 over conventional vitamin D3, we undertook this study. A total of 180 healthy adults were randomised to receive either micellised (DePura, group A) or conventional vitamin D3 (Calcirol, group B) at a monthly dose of 60 000 IU (1500µg) for 6 months. The outcome parameters were serum 25-hydroxyvitamin D (25(OH)D), parathyroid hormone (PTH), Ca, phosphate, alkaline phosphatase and urinary Ca:creatinine ratio. A total of eighty-nine subjects in group A and seventy-seven in group B completed the trial. Subjects in both the groups had a significant increase in their serum 25(OH)D levels following supplementation (group A: 21·5 (sd 10·9) to 76·7 (sd 18·8) nmol/l (P<0·001); group B: 22·8 (sd 10·4) to 57·8 (sd 16·0) nmol/l (P<0·001)). Participants in micellised group had an additional increase of 20·2 (95 % CI 14·0, 26·4) nmol/l in serum 25(OH)D levels (P<0·001). The difference between the groups was 17·5 (95 % CI 11·8, 23·1) nmol/l, which remained statistically significant (P<0·001) even after adjustment for age and sex. Significant decline in mean serum PTH was observed in both the groups. No hypercalcaemia or hypercalciuria was noted. Although supplementation with both the preparations resulted in a significant rise in serum 25(OH)D levels, micellised vitamin D3 appeared to be more efficacious in achieving higher levels of serum 25(OH)D.

Impact of three different daily doses of vitamin D3 supplementation in healthy schoolchildren and adolescents from North India: a single-blind prospective randomised clinical trial.

In India, there is a lack of information about the adequate daily dose of vitamin D3 supplementation in school children. Hence, we undertook this study to evaluate the adequacy and efficacy of different doses of vitamin D3 in schoolchildren. A total of 1008 vitamin D-deficient (VDD) children, aged 6-16 years with serum 25-hydroxyvitamin D (25(OH)D) levels <50nmol/l, were cluster randomised into three groups (A-344, B-341 and C-232) for supplementation (600, 1000 and 2000 IU daily) of vitamin D3 under supervision for 6 months. Of the 1008 subjects who completed the study, 938 (93 %) were compliant. Baseline and post-supplementation fasting blood and urine samples were evaluated for Ca, phosphates, alkaline phosphatase, 25(OH)D and parathormone and urine Ca:creatinine ratio. The mean age of the subjects was 11·7 (sd 2·4) years, and the overall mean baseline serum 25(OH)D level was 24·3 (SD 9·5)nmol/l. Post-supplementation rise in serum 25(OH)D in compliant group was maximum with 2000 IU (70·0 (SD 30·0)nmol/l), followed by 1000 IU (46·8 (SD 22·5)nmol/l) and 600 IU (36·5 (SD 18·5)nmol/l), and serum 25(OH)D levels of ≥50nmol/l were achieved in 71·5, 81·8 and 92·9 % by groups A, B and C, respectively. Secondary hyperparathyroidism decreased from 31·7 to 8·4 % post-supplementation. Two participants developed hypercalciuria, but none developed hypercalcaemia. Children with VDD benefit maximum with the daily supplementation of 2000 IU of vitamin D3. Whether recommendations of 400 IU/d by Indian Council of Medical Research or 600 IU by Indian Academy of Pediatrics or Institute of Medicine would suffice to achieve vitamin D sufficiency in children with VDD remains debatable.

Recurrent intestinal obstruction in a patient of Peutz-Jeghers syndrome.

Peutz-Jeghers syndrome is a rare hamartomatous polyposis syndrome characterized by the presence of intestinal polyps and mucocutaneous melanotic pigmentations. It is associated with various gastrointestinal and extraintestinal malignancies. This case report deals with the clinical presentation, investigations, operative findings, and outcome of a patient harboring this disease. A 45-year-old female presented to us with intermittent colicky abdominal pain for the last 6 months and a single episode of melena 1 month back. She had a previous history of resection of a jejunal growth 22 years back. The histopathology report was suggestive of papillary adenocarcinoma. On examination, hyperpigmented macules were seen on her lips and buccal mucosa. Laparotomy revealed multiple polyps mainly in the proximal small intestine and a focus of ileoileal intussusception. A limited resection was done.

Association of insulin-like growth factor-1 and IGF binding protein-3 with 25-hydroxy vitamin D in pre-pubertal and adolescent Indian girls.

BACKGROUND: There is a high prevalence of vitamin D deficiency (VDD) in India. Molecular mechanisms suggest a strong relationship between vitamin D and growth factors. However, there is a paucity of literature with regard to a relationship between insulin-like growth factor-1 (IGF-1), insulin-like growth factor binding protein-3 (IGFBP-3) and vitamin D particularly in subjects with VDD. The objective of the study was to assess the relationship between growth factors and serum vitamin D-parathormone (PTH) status in school girls and study the impact of vitamin D supplementation on growth factors in pre-pubertal girls with VDD. METHODS: Our study subjects were apparently healthy school girls aged 6-18 years. The baseline height, weight, body mass index (BMI), pubertal status, serum 25-hydroxy vitamin D (25OHD), PTH, IGF-1 and IGFBP-3 were assessed in 847 girls aged 6-18 years and in 190 pre-pubertal girls with VDD following supplementation. RESULTS: The mean age, BMI and serum 25OHD of girls were 11.5±3.2 years, 18.7±4.8 kg/m2 and 9.9±5.6 ng/mL, respectively. VDD was observed in 94.6% of girls. Unadjusted serum IGF-1 levels and IGF-1/IGFBP-3 molar ratio were significantly higher in girls with severe VDD as compared to girls with mild-to-moderate VDD. However, these differences disappeared when adjusted for age, height or sexual maturation. The serum IGF-1 and IGFBP-3 levels increased significantly post supplementation with vitamin D. CONCLUSIONS: There were no differences in serum IGF-1 levels and the IGF-1/IGFBP-3 molar ratio among VDD categories when adjusted for age, height and sexual maturation in girls. Vitamin D supplementation resulted in a significant increase in serum IGF-1 levels in VDD pre-pubertal girls.

Assessment of insulin like growth factor-1 and IGF binding protein-3 in healthy Indian girls from Delhi and their correlation with age, pubertal status, obesity and thyroid hormonal status.

BACKGROUND: Population specific data and influence of sub-clinical hypothyroidism on insulin like growth factor-1 (IGF-1) and its binding protein-3 (IGFBP-3) in Indian children is lacking. This study was undertaken to evaluate serum IGF-1 and IGFBP-3 and their correlation with age, gender, pubertal status and thyroid functions. METHODS: A total of 840 apparently healthy school girls aged 6-18 years, were recruited for the study and underwent assessment of height, weight, body mass index, pubertal status and serum T3, T4, TSH, IGF-1, IGFBP-3 and IGF-1/IGFBP-3 molar ratio. RESULTS: The mean serum levels of IGF-1, IGFBP-3 levels and IGF-1/IGFBP-3 molar ratio were 381.8±240.5 ng/mL, 4.19±2.08 µg/mL and 40.5±37.2%, respectively. The serum IGF-1 and IGF-1/IGFBP-3 molar ratio increased significantly (p<0.0001) at 11 years followed by a steady yet non-significant rise till 16 years of age. A similar pattern was observed for IGFBP-3 showing a steep rise at 12 years and peaking at 16 years. Likewise, serum levels of IGF-1 and molar ratio of IGF-1/IGFBP-3 increased significantly with pubertal maturation from stage 1 to 3 and were higher in overweight girls compared to normal weight and obese girls. The growth factors were no different in girls with or without subclinical hypothyroidism. CONCLUSIONS: There was no significant impact of age on IGF-1 and IGFBP-3 in pre-pubertal girls. A sudden marked increase at 11 years followed by a gradual rise in growth factors till 16 years is indicative of pubertal initiation and maturation. Subclinical hypothyroidism did not influence growth factors in girls.

Metagenome changes in the biogas producing community during anaerobic digestion of rice straw.

The present investigation was undertaken to study the microbial community succession in a sour and healthy digester. Ion torrent next-generation sequencing (NGS)-based metagenomic approach indicated abundance of hydrolytic bacteria and exclusion of methanogens and syntrophic bacteria in sour digester. Functional gene analysis revealed higher abundance of enzymes involved in acidogenesis and lower abundance of enzymes associated with methanogenesis like Methyl coenzyme M-reductase, F420 dependent reductase and Formylmethanofuran dehydrogenase in sour digester. Increased abundance of methanogens (Methanomicrobia) and genes involved in methanogenesis was observed in the restored/healthy digester highlighting revival of pH sensitive methanogenic community.

Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field.

Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph.

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches.

Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.

Draft Genome Sequence of Halostagnicola sp. A56, an Extremely Halophilic Archaeon Isolated from the Andaman Islands.

The first draft genome of Halostagnicola sp. A56, isolated from the Andaman Islands is reported here. The A56 genome comprises 3,178,490 bp in 26 contigs with a G+C content of 60.8%. The genome annotation revealed that A56 could have potential applications for the production of polyhydroxyalkanoate or bioplastics.

Draft genome of Elstera litoralis, a freshwater epilithic biofilm associated bacterium from littoral zone of Lake Constance.

Elstera litoralis, is a Rhodospirillaceae member which was isolated from the littoral zone of Lake Constance from a stone biofilm using diatom extracellular polymeric substances (EPS) as C source. We present here the draft genome of E. litoralis which has a genome size of 3.83 Mb and 61.2% G+C content. Genome analysis indicated utilization of multiple C substrates explaining its heterotrophic lifestyle as a bacterium present in natural biofilms. Further comparative genome analysis of Elstera with other members of Rhodospirillaceae would be helpful to understand the evolutionary relationships and divergence of hydrobacteria from terrabacteria.

Draft genome sequence of Clostridium sulfidigenes 113A isolated from sub-seafloor sediments associated with methane hydrate deposits.

Clostridium sulfidigenes 113A is a strictly anaerobic, rod shaped, gram positive bacterium isolated from sub-seafloor sediments associated with methane hydrates. Here, we report the first draft genome of C. sulfidigenes strain 113A, which comprises 3,717,420 bp in 96 contigs with the G+C content of 30.1%. A total of 3148 protein coding sequences were predicted. The genome annotation revealed that 113A could play an important role in biogeochemical cycles and have potential biotechnological applications such as production of organic acids and butanol.

Draft genome sequence of Clostridium celerecrescens 152B isolated from sub-seafloor methane hydrate deposits.

Clostridium celerecrescens 152B is an obligate anaerobic, Gram positive rod shaped bacterium isolated from sub-seafloor methane hydrate sediments of Krishna Godavari basin, India. Here, we report the first draft genome sequence of C. celerecrescens 152B, which comprises 5,050,495bp in 92 contigs with the G+C content of 43.5%. The whole genome of C. celerecrescens 152B was sequenced for further biotechnological exploitation of its genome features especially regarding the production of secondary metabolites as well as for environmental bioremediation and production of industrially valuable enzymes.

Draft genome of Cryobacterium sp. MLB-32, an obligate psychrophile from glacier cryoconite holes of high Arctic.

Obligate psychrophilic, Cryobacterium sp. MLB-32, was isolated from cryoconite holes of high Arctic glaciers. Here, we report the first draft genome sequence of the putative novel species of the genus Cryobacterium, providing opportunities for biotechnological and agricultural exploitation of its genome features.

Draft genome sequence of Methanoculleus sp. MH98A, a novel methanogen isolated from sub-seafloor methane hydrate deposits in Krishna Godavari basin.

Members of the genus Methanoculleus are among the most prevalent methanogens in biomethanation processes especially in marine and brackish environments. A methanogen, identified as a novel species of the genus Methanoculleus, was isolated from deep sub-seafloor sediment obtained from the Krishna Godavari Basin off the eastern coast of India. This methanogen is thought to be the supplier of the methane in the submarine methane hydrate deposits. Further study of this microorganism could possibly help to revolutionize the energy industry. The draft genome of Methanoculleus sp. MH98A is presented.