Assessment of genetic fidelity in microclones of curry leaf plants [Murrayakoenigii (L.) Spreng.]using ISSR markers

286-291Murrayakoenigii (L.) Spreng., commonly called Indian curry leaf, is an aromatic shrub highly valued for its medicinal potentialviz. anticonvulsant, antitumor, anti-inflammatory, antidiabetic, antiviral and diuretic.Its leaves, locally known as curry patta, are used widely for culinary purpose, particularly in India. However, M. koenigii,due to poor rate of fruit set and seeds with short viability period and poor rate of germination, are sparsely distributedin wild, and has attractedresearchers for propagation through biotechnological approaches. In this context, maintaining genetic fidelity is a vital for assessing genetic uniformity in micropropagated plantlets as variations within the progeny can result in serious losses to the end users.Therefore, it is necessary to screen them for their genetic makeup whether they are true-to-type or not. Molecular techniques like Inter Simple Sequence Repeat (ISSR) that are not influenced by environmental factors are appropriate tools to analyse genetic fidelity of in vitro propagated plantsas, and generate reliable and reproducible results. In this study, we tried to evaluate genetic fidelity of micro-clones of tissue culture raised M. koenigii using ISSR technique. Twenty five ISSR primers were used to amplify genomic DNA from in vitro raised field grown plants and mother plant. Out of 25 primers screened, a total 465 amplified products were obtained from 10 ISSR primers. Out of which, 55 were monomorphic across the mother plant and its micropropagated progenies of 10 ISSR primers 05 showed profiles identical to mother plant. Similarity matrix based on Jaccard’s coefficient and pair-wise values between mother plant and tissue cultured plant ranged from 0.91 to 1.00, indicating a high degree of genetic fidelity

Three-dimensional alignment and merging of confocal microscopy stacks

pre-printWe describe an efficient, robust, automated method for image alignment and merging of translated, rotated and flipped confocal microscopy stacks. The samples are captured in both directions (top and bottom) to increase the SNR of the individual slices. We identify the overlapping region of the two stacks by using a variable depth Maximum Intensity Projection (MIP) in the z dimension. For each depth tested, the MIP images gives an estimate of the angle of rotation between the stacks and the shifts in the x and y directions using the Fourier Shift property in 2D. We use the estimated rotation angle, shifts in the x and y direction and align the images in the z direction. A linear blending technique based on a sigmoidal function is used to maximize the information from the stacks and combine them. We get maximum information gain as we combine stacks obtained from both directions

Segmentation of haematopoeitic cells in bone marrow using circle detection and splitting techniques

pre-printBone marrow evaluation is indicated when peripheral blood abnormalities are not explained by clinical, physical, or laboratory findings. In this paper, we propose a novel method for segmentation of haematopoietic cells in the bone marrow from scanned slide images. Segmentation of clumped cells is a challenging problem for this application. We first use color information and morphology to eliminate red blood cells and the background. Clumped haematopoietic cells are then segmented using circle detection and a splitting algorithm based on the detected circle centers. The Hough Transform is used for circle detection and to find the number and positions of circle centers in each region. The splitting algorithm is based on detecting the maximum curvature points, and partitioning them based on information obtained from the centers of the circles in each region. The performance of the segmentation algorithm for haematopoietic cells is evaluated by comparing our proposed method with a hematologist's visual segmentation in a set of 3748 cells

Pretreated rice straw as an improved fodder for ruminants-An overview

Rice straw, a by-product of the rice production is mainly used as a source of feed for ruminant livestock is the major forage in rice-producing areas in India. The disposal of the rice straw is a serious problem in areas where it is the major agricultural product. It is rich in polysaccharides and has a high lignin and silica content, limiting voluntary intake and reducing degradability by rumen microbes. By rice straw treatment, its quality and digestibility can be improved and enhanced the protein content. Several methods have been used to improve the utilization of rice straw by ruminants or supplemented by other ingredients to increase digestibility and nutrient value before it can be considered a suitable animal feed. In recent years, biological treatments have been investigated for improvement in nutritional value of rice straw. The use of ligninolytic fungi and their extracellular ligninolytic enzymes for treatment of rice straw results in degrading cellulose and hemicelluloses contents which improve its nutritional value. The use of fungi and enzyme treatments is expected to be a practical, cost-effective and environmental-friendly approach for enhancing the nutritive value and digestibility of rice straw. Therefore, the treated rice straw has a good potential as feed for ruminants

Disjunctive normal shape models

A novel implicit parametric shape model is proposed for segmentation and analysis of medical images. Functions representing the shape of an object can be approximated as a union of N polytopes. Each polytope is obtained by the intersection of M half-spaces. The shape function can be approximated as a disjunction of conjunctions, using the disjunctive normal form. The shape model is initialized using seed points defined by the user. We define a cost function based on the Chan-Vese energy functional. The model is differentiable, hence, gradient based optimization algorithms are used to find the model parameters

Experimental Generation of SNP Haplotype Signatures in Patients with Sickle Cell Anaemia

Sickle cell anemia is caused by a single type of mutation, a homozygous A→T substitution in the ß globin gene. Clinical severity is diverse, partially due to additional, disease-modifying genetic factors. We are studying one such modifier locus, HMIP (HBS1L-MYB intergenic polymorphism, chromosome 6q23.3). Working with a genetically admixed patient population, we have encountered the necessity to generate haplotype signatures of genetic markers to label genomic fragments with distinct genealogical origin at this locus. With the goal to generate haplotype signatures from patients experimentally, we have investigated the suitability of an existing nanofluidic assay platform to perform phase alignment with single-nucleotide polymorphism alleles.Patient DNA samples were loaded onto Fluidigm Digital Arrays and individual DNA molecules were assayed with allele-specific probes for SNP markers. Here we present data showing the utility of the nanofluidic approach, yielding haplotype data identical to those obtained with a family-based method. We then determined haplotype composition in a group of patients with sickle cell disease, including in those where a mathematical inference approach gave ambiguous or misleading results. Experimental phasing of genotypes across 3.8 kb for rs9399137, rs9402685, and rs11759553 created unequivocal haplotype signatures for each of the patients. In 68 patients, we found 8 copies of a haplotype signature ('C-C-T'), which is known to be prevalent in Europeans but to be absent in West African populations. We have confirmed the identity of our phased allele pairs by single-molecule sequencing and have demonstrated, in principle, that three-allele phasing (using three colors) is a potential extension to this method.Phased haplotypes yield more information than the individual marker genotypes. Procedures such as the one described here would therefore benefit genetic mapping and functional studies as well as diagnostic procedures where the identity or parental origin of short genetic fragments is of importance

The role of hydropower in South Asia’s energy future

With rising energy demand in Asia, the high potential for hydropower development and the need for low-carbon energy development, hydropower would seem to have a significant role in South Asia’s energy future. However, the extent of hydropower development will depend on several risk factors, including the cost of alternative energy sources, the environmental sustainability of hydropower and social issues of equitable development. Using a risk-analysis framework, it is concluded that the future of hydropower will depend on how well policies and institutions manage the risks, facilitate efficient financial markets, and promote fair and friendly cross-border electricity trade

Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens.

The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequencing (mNGS) to elucidate etiologies of meningitis in Bangladesh. This RNA mNGS study was performed on cerebrospinal fluid (CSF) specimens from patients admitted in the largest pediatric hospital, a World Health Organization sentinel site, with known neurologic infections (n = 36), with idiopathic meningitis (n = 25), and with no infection (n = 30), and six environmental samples, collected between 2012 and 2018. We used the IDseq bioinformatics pipeline and machine learning to identify potentially pathogenic microbes, which we then confirmed orthogonally and followed up through phone/home visits. In samples with known etiology and without infections, there was 83% concordance between mNGS and conventional testing. In idiopathic cases, mNGS identified a potential bacterial or viral etiology in 40%. There were three instances of neuroinvasive Chikungunya virus (CHIKV), whose genomes were >99% identical to each other and to a Bangladeshi strain only previously recognized to cause febrile illness in 2017. CHIKV-specific qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 (n = 472) revealed 17 additional CHIKV meningitis cases, exposing an unrecognized meningitis outbreak. Orthogonal molecular confirmation, case-based clinical data, and patient follow-up substantiated the findings. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis, conduct surveillance, and predict outbreaks. The improved patient- and population-level data can inform evidence-based policy decisions.IMPORTANCE Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based treatment and prevention strategies. We report here the results of a validation and application study of using unbiased metagenomic sequencing to determine etiologies of idiopathic (of unknown cause) cases. This included CSF from patients with known neurologic infections, with idiopathic meningitis, and without infection admitted in the largest children's hospital of Bangladesh and environmental samples. Using mNGS and machine learning, we identified and confirmed an etiology (viral or bacterial) in 40% of idiopathic cases. We detected three instances of Chikungunya virus (CHIKV) that were >99% identical to each other and to a strain previously recognized to cause systemic illness only in 2017. CHIKV qPCR of all remaining stored 472 CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital uncovered an unrecognized CHIKV meningitis outbreak. CSF mNGS can complement conventional diagnostic methods to identify etiologies of meningitis, and the improved patient- and population-level data can inform better policy decisions

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Effects of antiplatelet therapy after stroke due to intracerebral haemorrhage (RESTART): a randomised, open-label trial

Background: Antiplatelet therapy reduces the risk of major vascular events for people with occlusive vascular disease, although it might increase the risk of intracranial haemorrhage. Patients surviving the commonest subtype of intracranial haemorrhage, intracerebral haemorrhage, are at risk of both haemorrhagic and occlusive vascular events, but whether antiplatelet therapy can be used safely is unclear. We aimed to estimate the relative and absolute effects of antiplatelet therapy on recurrent intracerebral haemorrhage and whether this risk might exceed any reduction of occlusive vascular events. Methods: The REstart or STop Antithrombotics Randomised Trial (RESTART) was a prospective, randomised, open-label, blinded endpoint, parallel-group trial at 122 hospitals in the UK. We recruited adults (≥18 years) who were taking antithrombotic (antiplatelet or anticoagulant) therapy for the prevention of occlusive vascular disease when they developed intracerebral haemorrhage, discontinued antithrombotic therapy, and survived for 24 h. Computerised randomisation incorporating minimisation allocated participants (1:1) to start or avoid antiplatelet therapy. We followed participants for the primary outcome (recurrent symptomatic intracerebral haemorrhage) for up to 5 years. We analysed data from all randomised participants using Cox proportional hazards regression, adjusted for minimisation covariates. This trial is registered with ISRCTN (number ISRCTN71907627). Findings: Between May 22, 2013, and May 31, 2018, 537 participants were recruited a median of 76 days (IQR 29–146) after intracerebral haemorrhage onset: 268 were assigned to start and 269 (one withdrew) to avoid antiplatelet therapy. Participants were followed for a median of 2·0 years (IQR [1·0– 3·0]; completeness 99·3%). 12 (4%) of 268 participants allocated to antiplatelet therapy had recurrence of intracerebral haemorrhage compared with 23 (9%) of 268 participants allocated to avoid antiplatelet therapy (adjusted hazard ratio 0·51 [95% CI 0·25–1·03]; p=0·060). 18 (7%) participants allocated to antiplatelet therapy experienced major haemorrhagic events compared with 25 (9%) participants allocated to avoid antiplatelet therapy (0·71 [0·39–1·30]; p=0·27), and 39 [15%] participants allocated to antiplatelet therapy had major occlusive vascular events compared with 38 [14%] allocated to avoid antiplatelet therapy (1·02 [0·65–1·60]; p=0·92). Interpretation: These results exclude all but a very modest increase in the risk of recurrent intracerebral haemorrhage with antiplatelet therapy for patients on antithrombotic therapy for the prevention of occlusive vascular disease when they developed intracerebral haemorrhage. The risk of recurrent intracerebral haemorrhage is probably too small to exceed the established benefits of antiplatelet therapy for secondary prevention