Evaluation of high-throughput genomic assays for the Fc gamma receptor locus

Cancer immunotherapy has been revolutionised by the use of monoclonal antibodies (mAb) that function through their interaction with Fc gamma receptors (FcγRs). The low-affinity FcγR genes are highly homologous, map to a complex locus at 1p23 and harbour single nucleotide polymorphisms (SNPs) and copy number variation (CNV) that can impact on receptor function and response to therapeutic mAbs. This complexity can hinder accurate characterisation of the locus. We therefore evaluated and optimised a suite of assays for the genomic analysis of the FcγR locus amenable to peripheral blood mononuclear cells and formalin-fixed paraffin-embedded (FFPE) material that can be employed in a high-throughput manner. Assessment of TaqMan genotyping for FCGR2A-131H/R, FCGR3A-158F/V and FCGR2B-232I/T SNPs demonstrated the need for additional methods to discriminate genotypes for the FCGR3A-158F/V and FCGR2B-232I/T SNPs due to sequence homology and CNV in the region. A multiplex ligation-dependent probe amplification assay provided high quality SNP and CNV data in PBMC cases, but there was greater data variability in FFPE material in a manner that was predicted by the BIOMED-2 multiplex PCR protocol. In conclusion, we have evaluated a suite of assays for the genomic analysis of the FcγR locus that are scalable for application in large clinical trials of mAb therapy. These assays will ultimately help establish the importance of FcγR genetics in predicting response to antibody therapeutics

Spike proliferation in black pepper (

Introduction. Black pepper (P. nigrum L.), the major world spice, is a climbing vine of historical, religious and economic importance. Landraces or farmer’s cultivars constitute the major component of this tropical vine's diversity. Normal spike formation. Berries of P. nigrum are produced in solitary, unbranched, axillary spikes. The apical bud of the plagiotropic branches transforms into an inflorescence (spike). Spike variant. Mutation in the floral meristem of black pepper could result in inflorescence proliferation. A variant with 100% of proliferating spikes was collected from a farmer’s plot, and then propagated by cuttings. The proliferating spikes are of indeterminate growth habit. Benefits. This natural mutant of Piper nigrum resulted in improved socioeconomic status of the farmer through sale of the rooted cuttings at a premium price. The variant can also be used as a donor for improvement of black pepper, besides as a novelty in potted pepper culture. Since berries of varying maturity are produced due to indeterminate growth, and since immature berries are rich in oleoresin, a single harvest will be yielding matured berries, which can be traded as black pepper of commerce, and half-matured berries suited to the value-added industry. Discussion. Mutations in the floral organ identity genes and their effect on altered flower/inflorescence development have been reported in the literature. In the case of spike proliferation, the transformation of the floral primordia in the mutant spike into inflorescence primordia has resulted in the modified spike architecture

Nutrient chemistry and seasonal variation in the groundwater quality of a Riverine Island on the west coast of Kerala, India

This study attempted to evaluate the groundwater quality, with a special emphasis on nutrients, of a riverine coastal island near Kodungallur, Kerala. Water quality parameters were analyzed in the collected samples over pre- and post-monsoon seasons. A considerable variation in groundwater chemistry was observed in the two periods. During pre-monsoon season, many wells were contaminated with TDS, Cl, Fe, Ca and Mg in certain locations. Whereas, post-monsoon water was relatively fresh, indicating the dilution process as well as aquifer recharge by the monsoon rain and consequent regression of saline water. A higher concentration of Fe was observed in the pre-monsoon season (41%) than in the post-monsoon season (24%). Nitrate and phosphates were analyzed to assess the nutrients and the observed concentration was below their corresponding permissible limits. Results show that overexploitation of the aquifer as well as the decreased flow of the River Periyar during the pre-monsoon period increased the threat from seawater intrusion and groundwater contamination. An interesting groundwater recharge mechanism locally known as backwashing—the diversion of rainwater from rooftops to dug wells—is being practiced in the study area and has been found to be effective in raising water levels and improving water quality

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Not AvailableBlack pepper (Piper nigrum), the “King of Spices,” is an economically important spice in India and is known for its medicinal and cultural values. SSRs, the tandem repeats of small DNA sequences, are often polymorphic in nature with diverse applications. For population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative to have their location specificity. The existing PinigSSRdb catalogs ∼70K putative SSR markers but these are anonymous (unknown chromosomal location), based on 916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD sequence data of 29 black pepper genotypes from all over India, being low-cost and most efficient technique for the identification of polymorphicmarkers. Themajor limitation of ddRAD with compromised/non-uniform coverage has been successfully overcome by taking advantage of chromosome-wise data availability. The latest black pepper genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic SSRs were mined distributed over 26 chromosomes, with relative density of 362.88 SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out of which 2015 were found to be hypervariable. The developed web-genomic resource, BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first reported web resource for genomic and polymorphic SSRs of black pepper, which is useful to develop varietal signature, coreset, physical map, QTL/gene identification, and MAS in endeavor of black pepper production.Not Availabl

Information-Driven Systems Engineering Study of a Formation Flying Demonstration Mission using Six CubeSats

Small satellites are suitable for formation flying missions where a large number of spacecraft serve as distributed sensors for applications like synthetic aperture radar, interferometry, etc. A survey of existing or proposed small satellite missions concludes that there is a dearth of formation flying missions using four or more spacecraft that require formation maintenance. This paper presents a systems engineering based design of a formation flying technology demonstration mission that requires precise formation maintenance and reconfigurations and highlights the challenges that need to be overcome for its successful implementation. The goal of this paper is to provide directions for future research and development in spacecraft formation flying technologies

Standard preanalytical coding for biospecimens: Review and implementation of the sample PREanalytical Code (SPREC)

The first version of the Standard PREanalytical Code (SPREC) was developed in 2009 by the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group to facilitate documentation and communication of the most important preanalytical quality parameters of different types of biospecimens used for research. This same Working Group has now updated the SPREC to version 2.0, presented here, so that it contains more options to allow for recent technological developments. Existing elements have been fine tuned. An interface to the Biospecimen Reporting for Improved Study Quality (BRISQ) has been defined, and informatics solutions for SPREC implementation have been developed. A glossary with SPRECrelated definitions has also been added