De novo genome assembly of rice bean (Vigna umbellata) - A nominated nutritionally rich future crop reveals novel insights into flowering potential, habit, and palatability centric - traits for efficient domestication.

Rice bean is a less-known underutilized legume crop with a high nutritional value among members of the Vigna family. As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimated identification of 31,276 high confidence index genes via 15,521 scaffolds generated from Illumina and PacBio platform 30X coverage data has achieved 96.08% functional coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to Vigna angularis (experimental control/outgroup), Vigna radiata, and Vigna unguiculata, however, Vigna angularis being the closest. The assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete coding sequence (CDS) alignment. In contrast, 17 medically influential genomes from the National Institute of General Medical Sciences-National Institutes of Health NIGMS-NIH, when compared to rice bean assembly for LCB clusters, led to the identification of more than 18,000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Significantly, we found deserving late-flowering genes, palatably indexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Therefore, the findings from this report address the genomic value of rice bean to be escalated via breeding by allied and applied approaches.

Development and standardization of the DALI-DAB (dyslexia assessment for languages of India - dyslexia assessment battery).

A majority of Indian schoolchildren are biliterate in that they acquire literacy in at least two language systems, necessitating dyslexia assessment in both. The DALI-DAB assesses risk for dyslexia by evaluating reading ability and literacy-learning potential through a battery including literacy tests (letter and word reading, spelling, nonword reading, reading comprehension), and mediator skills (phonological awareness, processing automaticity and executive fluency, oral language) in multiple languages. DALI-DAB was developed in three languages - English, Hindi, and Marathi - and standardized on a sample of 1013 children. Reliability analyses revealed high internal consistency (α > 0.8) in most tests in all three languages. Low standard error of measurement values supported DALI-DAB score stability over repeated testing. Construct validity was variously reinforced through, (i) selection of culture-referenced, research-based tests, (ii) approval of test materials by schoolteachers (face validity) and (iii) grade-correlated performance increases on all DALI-DAB tests, besides robust correlations between (iv) literacy and mediator skill test scores (p < .001, concurrent validity), (v) equivalent tests across languages (p < .01, convergent validity), and (vi) DALI-DAB and WJ III ACH literacy scores (p < .01, criterion validity), in contrast to (vii) low correlation between DALI-DAB and WJ III ACH math scores (p > .05, discriminant validity). Overall, the DALI-DAB represents the first standardized dyslexia assessment tool for bilingual-biliterate children.

Genotype-Independent Regeneration and Transformation Protocol for Rice Cultivars.

Developing an efficient and reproducible plant transformation protocol relies on callus induction and plant regeneration, which is prerequisite for genetic enhancement of crops, especially rice. The present study has been carried out in order to establish a genotype-independent regeneration and biolistic transformation protocol for rice varieties. Putative transgenic rice lines were confirmed by PCR analysis, DNA sequencing, and Southern analysis. The transformation protocol reported here is relatively simple and consistent and can be exploited in future biotechnological investigations particularly for gene transformation studies.

Probing the effect of a plus 1bp frameshift mutation in protein-DNA interface of domestication gene, NAMB1, in wheat.

Transcription factor NAM-B1 has a major role in the process of senescence, which results in higher Fe and Zn concentrations in grains of wild wheat (T. durum; Td). The absence of the wild type NAMB1 in T. aestivum (Ta), one of the cardinal crops essential for more than 1/3rd of the global population, affects Fe and Zn remobilisation to the maturing grain from the flag leaf resulting in lesser micronutrient bioavailability. The cardinal difference in the NAMB1 gene between the two species is the absence of +1 bp allele in Ta. Insilico studies using NAMB1 from Td and Ta was performed to explore the variation in the interaction with the conserved cis-element DNA motif (CATGTG) as both the proteins share the same domain, but there are no in silico studies reported of these proteins. The secondary structure, 3D-modelling of the proteins, DNA-protein docking and dynamics have computed by Schrodinger Prime Suite. Predicted secondary structures were energy minimised using Macromodel and docking was performed based on binding energy and hydrogen bonds. Molecular dynamics simulation of NAMB1-Ta and NAMB1-Td individually and with the cis-element motif, performed for 100 ns, revealed significant variations in the protein-DNA interaction in Ta. This work provides the modelled 3D-interaction profile caused by a single bp frameshift mutation in understanding the difference in function between NAMB1 orthologs due to lack of NAC domain. The overall computational analysis reveals that NAMB1-Ta and NAMB1-Td proteins display a good amount of dissimilarity in their structure, dynamics and DNA-binding characteristics.Communicated by Ramaswamy H. Sarma.

Data Mining by Pluralistic Approach on CRISPR Gene Editing in Plants.

Genome engineering by site-specific nucleases enables reverse genetics and targeted editing of genomes in an efficacious manner. Contemporary revolutionized progress in targeted-genome engineering technologies based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-related RNA-guided endonucleases facilitate coherent interrogation of crop genome function. Evolved as an innate component of the adaptive immune response in bacterial and archaeal systems, CRISPR/Cas system is now identified as a versatile molecular tool that ensures specific and targeted genome modification in plants. Applications of this genome redaction tool-kit include somatic genome editing, rectification of genetic disorders or gene therapy, treatment of infectious diseases, generation of animal models, and crop improvement. We review the utilization of these synthetic nucleases as precision, targeted-genome editing platforms with the inherent potential to accentuate basic science "strengths and shortcomings" of gene function, complement plant breeding techniques for crop improvement, and charter a knowledge base for effective use of editing technology for ever-increasing agricultural demands. Furthermore, the emerging importance of Cpf1, Cas9 nickase, C2c2, as well as other innovative candidates that may prove more effective in driving novel applications in crops are also discussed. The mined data has been prepared as a library and opened for public use at www.lipre.org.

Drosophila melanogaster as a model to study virulence and azole treatment of the emerging pathogen Candida auris.

OBJECTIVES: Candida auris is an emerging, often MDR, yeast pathogen. Efficient animal models are needed to study its pathogenicity and treatment. Therefore, we developed a C. auris fruit fly infection model. METHODS: TollI-RXA/Tollr632 female flies were infected with 10 different C. auris strains from the CDC Antimicrobial Resistance bank panel. We used three clinical Candida albicans strains as controls. For drug protection assays, fly survival was assessed along with measurement of fungal burden (cfu/g tissue) and histopathology in C. auris-infected flies fed with fluconazole- or posaconazole-containing food. RESULTS: Despite slower in vitro growth, all 10 C. auris isolates caused significantly greater mortality than C. albicans in infected flies, with >80% of C. auris-infected flies dying by day 7 post-infection (versus 67% with C. albicans, P < 0.001-0.005). Comparison of C. auris isolates from different geographical clades revealed more rapid in vitro growth of South American isolates and greater virulence in infected flies, whereas the aggregative capacity of C. auris strains had minimal impact on their growth and pathogenicity. Survival protection and decreased fungal burden of fluconazole- or posaconazole-fed flies infected with two C. auris strains were in line with the isolates' disparate in vitro azole susceptibility. High reproducibility of survival curves for both non-treated and antifungal-treated infected flies was seen, with coefficients of variation of 0.00-0.31 for 7 day mortality. CONCLUSIONS: Toll-deficient flies could provide a fast, reliable and inexpensive model to study pathogenesis and drug activity in C. auris candidiasis.

School-based language screening among primary school children using telepractice: A feasibility study from India.

Purpose: This study explored the feasibility of conducting school-based language screening using telepractice to expand its scope for providing speech-language pathology services in India. Method: Thirty-two primary school children underwent language screenings through in-person and telemethods. Screening through telemethod was conducted by a Speech-Language Pathologist (SLP) using digitised picture stimuli presented through videoconferencing and remote computing with assistance of a facilitator at school site. Technology and child-related factors influencing screening were documented using an inventory. Result: Language outcomes through in-person and telemethods revealed no significant differences in both receptive and expressive domains, suggesting absence of bias due to testing method used. Use of multiple internet options at both sites helped overcome technical challenges related to connectivity during screening through telemethod. The trained facilitator played a crucial role in overcoming child related factors such as poor speech intelligibility, poor audibility of voice, motivation, interaction with SLP and need for frequent breaks. Conclusion: Feasibility of conducting school-based language screening using multiple internet options and help of a facilitator at school demonstrates promise for delivery of services by SLP in resource constrained contexts such as India.

Genetic validation and spectroscopic detailing of DHN-melanin extracted from an environmental fungus.

Accurate characterization of melanin using analytical methodologies has proved to be difficult due to its heterogeneity, insolubility in wide pH and broad range of solvents. The present study was undertaken to characterize melanin extracted from an environmental Aspergillus fumigatus AFGRD105 by studying its genes, chemical properties and spectral data. A gene based approach to confirm the type of melanin carried out indicated the extracted melanin to be of the dihydroxynaphthalene type. On comparison with synthetic melanin, UV-Vis and IR spectra of the extracted melanin revealed characteristic peaks that can be further used for confirmation of DHN-melanin extracted from any source. Solid state 13C NMR spectroscopy established the presence of the hydroxyl-naphthalene moiety and validated the results obtained by genetic analysis. The correct assignment of the observed spectral frequency characteristic of functional groups can be further adapted in future works that deal with binding capacities and biomolecule systems involving melanin.

School entry level tele-hearing screening in a town in South India - Lessons learnt.

INTRODUCTION: School screening is warranted in developing countries that do not have newborn hearing screening as schools provide access to a large number of young children between 3 and 5 years of age. Due to scarcity of technical manpower and equipment, hearing screening programs are not often conducted in developing countries. In these circumstances, telehealth services appear to be a reasonable solution. Consequently, the purpose of this study was to assess the feasibility of school hearing screening using telehealth technology operated by a practitioner located 400 kms away at a distant hospital. METHOD: Thirty one children received hearing screening procedures in their school. Each child was screened for both in-person and telehealth conditions to assess screening results. Remote computing software was employed for the telehealth condition in order for the practitioner to remotely operate an audiometer, DPOAE system and a video otoscope interfaced to a personal computer at the school site.Teamviewer version 10 was used to provide encrypted videoconferencing and synchronous hearing screening services between the hospital and school sites. All screening was conducted using a mobile phone hotspot or dongle device based internet connection to insure reliable connectivity. RESULTS: The outcome revealed no significant difference between PTA and DPOAE performed in-person and tele-hearing screening methods. Concurrence of greater than 87% was achieved between in-person and tele-video-otoscopy. Strengths and challenges were documented for tele-hearing screening in three different dimensions: technical issues, child related and school related. Understanding these challenges may provide more effective tele-audiology services. DISCUSSION: The results of the study indicate synchronous hearing screening services can be provided in a school setting using mobile hotspot or dongle connectivity in locations where Internet bandwidth is otherwise restricted.

Improved production of melanin from Aspergillus fumigatus AFGRD105 by optimization of media factors.

Melanins are indolic polymers produced by many genera included among plants, animals and microorganisms and targeted mainly for their wide range of applications in cosmetics, agriculture and medicine. An approach to analyse the cumulative effect of parameters for enhanced melanin production was carried out using response surface methodology. In this present study, optimization of media and process parameters for melanin production from Aspergillus fumigatus AFGRD105 (GenBank: JX041523; NFCCI accession number: 3826) was carried out by an initial univariate approach followed by statistical response surface methodology. The univariate approach was used to standardise the parameters that can be used for the 12-run Plackett-Burman design that is used for screening for critical parameters. Further optimization of parameters was analysed using Box-Behnken design. The optimum conditions observed were temperature, moisture and sodium dihydrogen phosphate concentration. The yield of every run of both designs were confirmed to be melanin by laboratory tests of analysis in the presence of acids, base and water. This is the first report confirming an increase in melanin production A. fumigatus AFGRD105 without the addition of costly additives.