Concept of Pathyapathya w.s.r. to Mutravaha Sroto Vikaras

Mutravaha Sroto Vikaras are the diseases of urinary tract including kidney, ureters, urinary bladder and urethra. Prevalence of the disease is on increasing trend every year. In Ayurveda classical texts Mutravaha Srotogata Vikaras are mainly compiled under Mutraghata, Mutrakriksha and Mutrashmari. The risk factors for these Vikaras can be broadly categorised under dietary and non dietary factors. Non dietary factors include age, gender, ethnic background, genetic predisposition, climate, economic status etc. Nothing much can be done with the Non dietary factors. Moreover, dietary factors and lifestyle plays a very important role in initiation, progression as well as regression of the disease. This is an attempt to review the Pathyapathya (Do’s & Don’ts of diet & lifestyle) related to Mutravaha Srotas

Drilling characteristics and properties analysis of fiber reinforced polymer composites: A comprehensive review

Fiber-reinforced polymer (FRP) composites play a vital role in the production of structural and semi-structural components for engineering applications. The drilling process is a commonly employed machining process for FRP composites to join the FRP structural elements. Usually, the FRP composites possess a heterogeneous nature because of their multi-layered structure, hybridization, and the presence of multi-phase materials. Hence, common problems like delaminations, fuzzing, buckling, cracking, matrix and fiber burning occur during the drilling operations. These problems cause dimensional inaccuracy, poor surface finish, and tool wear and reduce the mechanical strength of the composites. The optimum drilling parameters (drill geometry, speed, feed, and depth of cut) selection for the specific materials is good to achieve effective drilling performance and better surface quality of the holes. Yet, little study has been done on how all of these factors affect the size of the drilled hole. The majority of drilling studies on FRPCs in the past have focused on how to improve the hole quality by maximizing processing conditions, and there has been little discussion on the correlation between drilling conditions, physical properties, and production techniques. This is what motivated to review the characteristics and properties analysis of FRP composites. As a consequence of this research, it is anticipated that scientists and researchers would place a greater emphasis on the drilling characteristic of the workpieces made from FRPCs than on other attributes. This review clearly presents an overview of FRP composites drilling that had progressed from 2000 to 2021. The analysis of different drilling conditions and parameters like thrust force, drill geometry, temperature, speed, and feed also includes the post-drilling analysis through delaminations, thermal damage, and surface roughness. Furthermore, the recent developments in carbon, glass, and natural fiber reinforced polymer composites are studied with both conventional and nonconventional drilling techniques. Based on the above studies, some future challenges and conclusions are drawn from this review

Development and evaluation of high-density Axiom® CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea

To accelerate genomics research and molecular breeding applications in chickpea, a high-throughput SNP genotyping platform ‘Axiom®CicerSNP Array’ has been designed, developed and validated. Screening of whole-genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70 463 high-quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p-convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom®CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High-density genetic maps comprising 13 679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main-effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/ CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data

Mining of gene-based SNPs from publicly available ESTs and their conversion to cost-effective genotyping assay in sorghum [Sorghum bicolor (L.) Moench]

Single Nucleotide Polymorphisms (SNPs) are the commonest type of nucleotide variation distributed throughout the genome and have enormous potential to saturate genetic maps. However, their identification is constrained by the huge investment required for their detection. In this study, we used publicly available EST (Expressed Sequence Tag) sequences to identify SNPs in Sorghum bicolor. A total of 12,421 putative SNPs were identified from 2,921 contiguous transcripts leading to an average SNP interval of one putative SNP for every 275.26 bp. The proportion of transition type mutations (0.598) was larger than transversion types conforming to biological expectations. In order to demonstrate the utility of the SNPs for development of markers with relatively cheap assays, we experimentally validated SNPs using Single Strand Conformation Polymorphism (SSCP) technique in sorghum accessions, which are used as parents for development mapping populations. Genotyping these parents of mapping populations with SSCP markers showed up to 33% polymorphism in the markers suggesting that the SNPs can be used as potential resource for S. bicolor crop improvement programs

Preoperative quantification of aortic valve stenosis: comparison of 64-slice computed tomography with transesophageal and transthoracic echocardiography and size of implanted prosthesis

Precise measurements of aortic complex diameters are essential for preoperative examinations of patients with aortic stenosis (AS) scheduled for aortic valve (AV) replacement. We aimed to prospectively compare the accuracy of transthoracic echocardiography (TTE), transoesophageal echocardiography (TEE) and multi-slice computed tomography (MSCT) measurements of the AV complex and to analyze the role of the multi-modality aortic annulus diameter (AAd) assessment in the selection of the optimal prosthesis to be implanted in patients surgically treated for degenerative AS. 20 patients (F/M: 3/17; age: 69 ± 6.5 years) with severe degenerative AS were enrolled into the study. TTE, TEE and MSCT including AV calcium score (AVCS) assessment were performed in all patients. The values of AAd obtained in the long AV complex axis (TTE, TEE, MSCT) and in multiplanar perpendicular imaging (MSCT) were compared to the size of implanted prosthesis. The mean AAd was 24 ± 3.6 mm using TTE, 26 ± 4.2 mm using TEE, and 26.9 ± 3.2 in MSCT (P = 0.04 vs. TTE). The mean diameter of the left ventricle out-flow tract in TTE (19.9 ± 2.7 mm) and TEE (19.5 ± 2.7 mm) were smaller than in MSCT (24.9 ± 3.3 mm, P < 0.001 for both). The mean size of implanted prosthesis (22.2 ± 2.3 mm) was significantly smaller than the mean AAd measured by TTE (P = 0.0039), TEE (P = 0.0004), and MSCT (P < 0.0001). The implanted prosthesis size correlated significantly to the AAd: r = 0.603, P = 0.005 for TTE, r = 0.592, P = 0.006 for TEE, and r = 0.791, P < 0.001 for MSCT. Obesity and extensive valve calcification (AV calcium score ≥ 3177Ag.U.) were identified as potent factors that caused a deterioration of both TTE and MSCT performance. The accuracy of AAd measurements in TEE was only limited by AV calcification. In multivariate regression analysis the mean value of the minimum and maximum AAd obtained in MSCT-multiplanar perpendicular imaging was an independent factor (r = 0.802, P < 0.0001) predicting the size of implanted prosthesis. In patients with AS echocardiography remains the main diagnostics tool in clinical practice. MSCT as a 3-dimentional modality allows for accurate measurement of entire AV complex and facilitates optimal matching of prosthesis size

Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea

APETALA2/ethylene response factor (AP2/ERF) and heat-shock protein 90 (HSP90) are two significant classes of transcription factor and molecular chaperone proteins which are known to be implicated under abiotic and biotic stresses. Comprehensive survey identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 131 in Medicago, 179 in common bean and 140 in Lotus, whereas the number of HSP90 genes ranged from 5 to 7 in five legumes. Sequence alignment and phylogenetic analyses distinguished AP2, ERF, DREB, RAV and soloist proteins, while HSP90 proteins segregated on the basis of their cellular localization. Deeper insights into the gene structure allowed ERF proteins to be classified into AP2s based on DNA-binding domains, intron arrangements and phylogenetic grouping. RNA-seq and quantitative real-time PCR (qRT-PCR) analyses in heat-stressed chickpea as well as Fusarium wilt (FW)- and sterility mosaic disease (SMD)-stressed pigeonpea provided insights into the modus operandi of AP2/ERF and HSP90 genes. This study identified potential candidate genes in response to heat stress in chickpea while for FW and SMD stresses in pigeonpea. For instance, two DREB genes (Ca_02170 and Ca_16631) and three HSP90 genes (Ca_23016, Ca_09743 and Ca_25602) in chickpea can be targeted as potential candidate genes. Similarly, in pigeonpea, a HSP90 gene, C.cajan_27949, was highly responsive to SMD in the resistant genotype ICPL 20096, can be recommended for further functional validation. Also, two DREB genes, C.cajan_41905 and C.cajan_41951, were identified as leads for further investigation in response to FW stress in pigeonpea

CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/. It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes