Marker assisted selection and F6 generation characterization of Katarni rice (Oryza sativa L.) derived lines

292-298Characterisation of promising progenies in the advanced generations of breeding schemes is essential to know about their distinctness from the parents as well as other existing cultivars. This also requires for developing them as a variety or pre-breeding line. In this study, an attempt was made for establishing distinctness of twenty five F6 families of Katarni x Rajendra Sweta, Katarni x IR64 and Katarni X MTU7029 along with 14 rice genotypes. The genotypes were characterised with the help of thirty simple sequence repeat (SSR) markers. The markers generated 107 polymorphic alleles with an average of 3.56 alleles per locus. The values polymorphic information content (PIC), expected heterozygosity (H) and discriminating power (D) of markers varied from 0.41 to 0.48, 0.32 to 0.50 and 0.75 to 0.96, respectively. At 0.38 similarity coefficient four distinct clusters were formed and cluster I had highest number accessions of F6 families. The study advocated use of (SSR) markers as a complementary tool to morphological descriptors to decipher the distinctiveness of the promising lines in advanced generations of a breeding programme

Forest Vegetation and Dynamics Studies in India

Forests across the globe have been exploited for resouces, and over the years the demand has increased, and forests are rather exploited instead of sustainable use. Focussed research on vegetation and forerst dynamics is necessary to preserve biodiversity and functioning of forests for sustanence of human life on Earth.This article emphasis that the India has a long history of traditional knowledge on forest and plants, and explorations from 17th century on forests and provided subsequent scientific approach on classification of forests. This also explains the developments of quantitative approach on the understanding of vegetation and forest diversity. Four case studies viz., Mudumalai, Sholayar, Uppangala, Kakachi permanent plots in the forests of Western Ghats has been explained in detail about their sampling methods with a note on the results of forest monitoring. In the case of deciduous forests, the population of plant species showed considerable fluctuations but basal area has been steadily increasing over time, and this is reflecting carbon sequestration. In Sholayar, a total of 25390 individuals of 106 woody species was recorded for < 1 cm diameter at breast height in the first census of the 10 ha plot in the tropical evergreen forest. In Uppangala, 1) a 27- year long investigation revealed that residual impact of logging in the evergreen forests and such forests would take more time to resemble unlogged forests in terms of composition and structure; 2) across a similar temporal scale, the unlogged plots trees < 30 cm gbh showed a more or less similar trend in mortality (an average of 0.8% year-1) and recruitment (1%). The Kakachi plot study revealed that 1) endemic species showed least change in stem density and basal area whereas widely distributed species showed greater change in both; 2) The overall recruitment of trees was 0.86 % per year and mortality 0.56% per year resulting in an annual turnover of 0.71% ; 3) majority of the gap species had high levels of recruitment and mortality resulting in a high turnover.Such studies can be used as early warning system to understand how the response of individual plants, species and forests with the climatic variability. In conclusion, the necessity of implementation of national level projects, the way forward of two such studies: 1) impact of climate change on Indian forests through Indian Council of Forestry Research and Education (ICFRE) colloborations and 2) Indian long term ecological observatorion, including the sampling protocols of such studies. This will be the first of its kind in India to address climate change issues at national and international level and helps to trace footprints of climate change impacts through vegetation and also reveals to what extent our forests are resilient to changes in the climate

Climatic Variation and Its Impacts on Yield and Water Requirement of Crops in Indian Central Himalaya

Climate is most important factor affecting agriculture, and issues related to climate and its implications have attracted attention of policy makers globally. The farm sector, particularly marginal ecosystems in mountains are vulnerable because of unpredictable variation and severe sink limitations. Efforts to impart resilience to farm and its allied sector are an urgent need. The climatic parameters play very important role to determine type of crops, cattle rearing and the life style adopted by the people. Moreover, weather has a significant impact on crop growth and development. Weather plays a vital role and affects the production and productivity of the crops. According to an estimate, weather contributes 67% variation in productivity and rest of the factors (soil, nutrient and management practices etc.) accounts for 33%. Therefore, there is a need of in-depth analysis of each meteorological parameters and identification of their trend over the years in order to identify and adapt suitable agriculture practices, better adaptable crops, varieties and their duration, time of field preparation, sowing time and irrigation as per the climatic conditions of the region. This will lead farming community to plan strategies of agriculture operation to obtain optimum yield. The climatic data from the meteorological observatory of ICAR-VPKAS, Hawalbagh located at mid hill condition (1250 m amsl) were analyzed for different periods (annual, seasonal, monthly, weekly). It was revealed that rainfall is decreasing over the years but significant (P < 0.05) decrease was recorded at mid hills. The maximum temperature is increasing significantly (P < 0.05) during post-monsoon and winter season however decreasing in monsoon season whereas minimum temperature is decreasing round the year. These changes in rainfall and temperatures are affecting production and productivity of the crops, as hills are largely rainfed. In terms of crop water demand, there is no need to apply irrigation during the rainy season except the transplanted rice. However, during the winter season as there is more than 60% of water deficit to irrigate the crops. The proper understanding of climate is necessary to bring sustainability in hill agriculture by adjusting crop sowing window and other operations as per suitability of the climate

In-Depth Molecular Characterization of Mycobacterium tuberculosis from New Delhi – Predominance of Drug Resistant Isolates of the ‘Modern’ (TbD1−) Type

BACKGROUND: India has the highest estimated burden of tuberculosis in the world, accounting for 21% of all tuberculosis cases world-wide. However, due to lack of systematic analysis using multiple markers the available information on the genomic diversity of Mycobacterium tuberculosis in India is limited. METHODOLOGY/PRINCIPAL FINDINGS: Thus, 65 M. tuberculosis isolates from New Delhi, India were analyzed by spoligotyping, MIRU-VNTR, large deletion PCR typing and single nucleotide polymorphism analysis (SNP). The Central Asian (CAS) 1 _DELHI sub-lineage was the most prevalent sub-lineage comprising 46.2% (n = 30) of all isolates, with shared-type (ST) 26 being the most dominant genotype comprising 24.6% (n = 16) of all isolates. Other sub-lineages observed were: East-African Indian (EAI)-5 (9.2%, n = 6), EAI6_BGD1 (6.2%, n = 4), EAI3_IND, CAS and T1 with 6.2% each (n = 4 each), Beijing (4.6%, n = 3), CAS2 (3.1%, n = 2), and X1 and X2 with 1 isolate each. Genotyping results from five isolates (7.7%) did not match any existing spoligopatterns, and one isolate, ST124, belonged to an undefined lineage. Twenty-six percent of the isolates belonged to the TbD1+ PGG1 genogroup. SNP analysis of the pncA gene revealed a CAS-lineage specific silent mutation, S65S, which was observed for all CAS-lineage isolates (except two ST26 isolates) and in 1 orphan. Mutations in the pncA gene, conferring resistance to pyrazinamide, were observed in 15.4% of all isolates. Collectively, mutations in the rpoB gene, the katG gene and in both rpoB and katG genes, conferring resistance to rifampicin and isoniazid, respectively, were more frequent in CAS1_DELHI isolates compared to non-CAS_DELHI isolates (OR: 3.1, CI95% [1.11, 8.70], P = 0.045). The increased frequency of drug-resistance could not be linked to the patients' history of previous anti-tuberculosis treatment (OR: 1.156, CI95% [0.40, 3.36], P = 0.79). Fifty-six percent of all new tuberculosis patients had mutations in either the katG gene or the rpoB gene, or in both katG and rpoB genes. CONCLUSION: CAS1_DELHI isolates circulating in New Delhi, India have a high frequency of mutations in the rpoB and katG genes. A silent mutation (S65S) in the pncA gene can be used as a putative genetic marker for CAS-lineage isolates

NetPath: a public resource of curated signal transduction pathways

NetPath, a novel community resource of curated human signaling pathways is presented and its utility demonstrated using immune signaling data

Bronchiectasis in India:results from the European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) and Respiratory Research Network of India Registry

BACKGROUND: Bronchiectasis is a common but neglected chronic lung disease. Most epidemiological data are limited to cohorts from Europe and the USA, with few data from low-income and middle-income countries. We therefore aimed to describe the characteristics, severity of disease, microbiology, and treatment of patients with bronchiectasis in India. METHODS: The Indian bronchiectasis registry is a multicentre, prospective, observational cohort study. Adult patients ( 6518 years) with CT-confirmed bronchiectasis were enrolled from 31 centres across India. Patients with bronchiectasis due to cystic fibrosis or traction bronchiectasis associated with another respiratory disorder were excluded. Data were collected at baseline (recruitment) with follow-up visits taking place once per year. Comprehensive clinical data were collected through the European Multicentre Bronchiectasis Audit and Research Collaboration registry platform. Underlying aetiology of bronchiectasis, as well as treatment and risk factors for bronchiectasis were analysed in the Indian bronchiectasis registry. Comparisons of demographics were made with published European and US registries, and quality of care was benchmarked against the 2017 European Respiratory Society guidelines. FINDINGS: From June 1, 2015, to Sept 1, 2017, 2195 patients were enrolled. Marked differences were observed between India, Europe, and the USA. Patients in India were younger (median age 56 years [IQR 41-66] vs the European and US registries; p&lt;0\ub70001]) and more likely to be men (1249 [56\ub79%] of 2195). Previous tuberculosis (780 [35\ub75%] of 2195) was the most frequent underlying cause of bronchiectasis and Pseudomonas aeruginosa was the most common organism in sputum culture (301 [13\ub77%]) in India. Risk factors for exacerbations included being of the male sex (adjusted incidence rate ratio 1\ub717, 95% CI 1\ub703-1\ub732; p=0\ub7015), P aeruginosa infection (1\ub729, 1\ub710-1\ub750; p=0\ub7001), a history of pulmonary tuberculosis (1\ub720, 1\ub707-1\ub734; p=0\ub7002), modified Medical Research Council Dyspnoea score (1\ub732, 1\ub725-1\ub739; p&lt;0\ub70001), daily sputum production (1\ub716, 1\ub703-1\ub730; p=0\ub7013), and radiological severity of disease (1\ub703, 1\ub701-1\ub704; p&lt;0\ub70001). Low adherence to guideline-recommended care was observed; only 388 patients were tested for allergic bronchopulmonary aspergillosis and 82 patients had been tested for immunoglobulins. INTERPRETATION: Patients with bronchiectasis in India have more severe disease and have distinct characteristics from those reported in other countries. This study provides a benchmark to improve quality of care for patients with bronchiectasis in India. FUNDING: EU/European Federation of Pharmaceutical Industries and Associations Innovative Medicines Initiative inhaled Antibiotics in Bronchiectasis and Cystic Fibrosis Consortium, European Respiratory Society, and the British Lung Foundation

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far

Ultrasonic intensification as a tool for enhanced microbial biofuel yields

peer-reviewedUltrasonication has recently received attention as a novel bioprocessing tool for process intensification in many areas of downstream processing. Ultrasonic intensification (periodic ultrasonic treatment during the fermentation process) can result in a more effective homogenization of biomass and faster energy and mass transfer to biomass over short time periods which can result in enhanced microbial growth. Ultrasonic intensification can allow the rapid selective extraction of specific biomass components and can enhance product yields which can be of economic benefit. This review focuses on the role of ultrasonication in the extraction and yield enhancement of compounds from various microbial sources, specifically algal and cyanobacterial biomass with a focus on the production of biofuels. The operating principles associated with the process of ultrasonication and the influence of various operating conditions including ultrasonic frequency, power intensity, ultrasonic duration, reactor designs and kinetics applied for ultrasonic intensification are also described

Neurodevelopmental disorders in children aged 2-9 years: Population-based burden estimates across five regions in India.

BACKGROUND: Neurodevelopmental disorders (NDDs) compromise the development and attainment of full social and economic potential at individual, family, community, and country levels. Paucity of data on NDDs slows down policy and programmatic action in most developing countries despite perceived high burden. METHODS AND FINDINGS: We assessed 3,964 children (with almost equal number of boys and girls distributed in 2-<6 and 6-9 year age categories) identified from five geographically diverse populations in India using cluster sampling technique (probability proportionate to population size). These were from the North-Central, i.e., Palwal (N = 998; all rural, 16.4% non-Hindu, 25.3% from scheduled caste/tribe [SC-ST] [these are considered underserved communities who are eligible for affirmative action]); North, i.e., Kangra (N = 997; 91.6% rural, 3.7% non-Hindu, 25.3% SC-ST); East, i.e., Dhenkanal (N = 981; 89.8% rural, 1.2% non-Hindu, 38.0% SC-ST); South, i.e., Hyderabad (N = 495; all urban, 25.7% non-Hindu, 27.3% SC-ST) and West, i.e., North Goa (N = 493; 68.0% rural, 11.4% non-Hindu, 18.5% SC-ST). All children were assessed for vision impairment (VI), epilepsy (Epi), neuromotor impairments including cerebral palsy (NMI-CP), hearing impairment (HI), speech and language disorders, autism spectrum disorders (ASDs), and intellectual disability (ID). Furthermore, 6-9-year-old children were also assessed for attention deficit hyperactivity disorder (ADHD) and learning disorders (LDs). We standardized sample characteristics as per Census of India 2011 to arrive at district level and all-sites-pooled estimates. Site-specific prevalence of any of seven NDDs in 2-<6 year olds ranged from 2.9% (95% CI 1.6-5.5) to 18.7% (95% CI 14.7-23.6), and for any of nine NDDs in the 6-9-year-old children, from 6.5% (95% CI 4.6-9.1) to 18.5% (95% CI 15.3-22.3). Two or more NDDs were present in 0.4% (95% CI 0.1-1.7) to 4.3% (95% CI 2.2-8.2) in the younger age category and 0.7% (95% CI 0.2-2.0) to 5.3% (95% CI 3.3-8.2) in the older age category. All-site-pooled estimates for NDDs were 9.2% (95% CI 7.5-11.2) and 13.6% (95% CI 11.3-16.2) in children of 2-<6 and 6-9 year age categories, respectively, without significant difference according to gender, rural/urban residence, or religion; almost one-fifth of these children had more than one NDD. The pooled estimates for prevalence increased by up to three percentage points when these were adjusted for national rates of stunting or low birth weight (LBW). HI, ID, speech and language disorders, Epi, and LDs were the common NDDs across sites. Upon risk modelling, noninstitutional delivery, history of perinatal asphyxia, neonatal illness, postnatal neurological/brain infections, stunting, LBW/prematurity, and older age category (6-9 year) were significantly associated with NDDs. The study sample was underrepresentative of stunting and LBW and had a 15.6% refusal. These factors could be contributing to underestimation of the true NDD burden in our population. CONCLUSIONS: The study identifies NDDs in children aged 2-9 years as a significant public health burden for India. HI was higher than and ASD prevalence comparable to the published global literature. Most risk factors of NDDs were modifiable and amenable to public health interventions