Achuit K. Singh

Bio: Achuit K. Singh is an academic researcher from Indian Council of Agricultural Research. The author has contributed to research in topics: Begomovirus & Leaf curl. The author has an hindex of 18, co-authored 40 publications receiving 702 citations. Previous affiliations of Achuit K. Singh include Central University of Gujarat & Jawaharlal Nehru University.

Cultural, morphological, pathogenic and molecular variability amongst tomato isolates of Alternaria solani in India

Abstract: Early blight (Alternaria solani) is an important disease causing severe damage in tomato. The eleven isolates of A. solani designated as So, Dh, Sh, Va-5, Ka, Ma, Hy, Ba-1, My, Va-3 and Mi were collected from different agroclimatic conditions and these isolates were characterized for cultural, morphological, pathogenic and molecular variations. The pigmentation varied from yellow, brown, black, brownish to greenish black in isolates of A. solani on potato dextrose agar medium. In general, radial growth of all isolates ranged between 14.9 mm and 32.2 mm on PDA and 24.3 mm to 53.7 mm on three selective media i.e., ASM, V-8 juice agar and V-8 juice agar (synthetic) on the fourth day. The fastest radial growth was recorded in the So isolate and slowest in the Ka isolate on PDA, while isolates Dh, Ba-1 and Va-3 were recorded to be faster in growth on ASM, V-8 juice agar and V-8 juice agar (synthetic) medium. The thickness of conidiogenous hyphae varied between 1.17 μ and 9.56 μ, with maximum in the Va-5 and Ma isolates. Most of the isolates showed smooth mycelial growth with circular and irregular margin and without concentric zonation. Sporulation was not found in any of the isolates on four different nutrient media, whereas conidiogenous hyphal length was observed in V-8 juice agar medium only. Based on the pathogenicity, isolates of A. solani were rated as virulent or less virulent based on percentage disease incidence data. Molecular variability studies were also done to find out the best annealing temperature and eighty-six primers were screened to select for maximum polymorphism of DNA. The best annealing temperature was recorded between 32.5 °C and 34.0 °C for the pathogen, and most efficient amplification and polymorphism of DNA was found with random primer 5′-CGCGTTCCTG-3′.

Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India.

Abstract: Chilli, which encompasses several species in the genus Capsicum, is widely consumed throughout the world. In the Indian subcontinent, production of chilli is constrained due to chilli leaf curl disease (ChiLCD) caused by begomoviruses. Despite the considerable economic consequences of ChiLCD on chilli cultivation in India, there have been scant studies of the genetic diversity and structure of the begomoviruses that cause this disease. Here we report on a comprehensive survey across major chilli-growing regions in India. Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds. The associated betasatellites neither enhanced the accumulation of the begomovirus components nor reduced the incubation period in Nicotiana benthamiana. The ChiLCD-associated begomoviruses induced mild symptoms on Capsicum spp., but both the level of helper virus that accumulated and the severity of symptoms were increased in the presence of cognate betasatellites. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The betasatellites possess high nucleotide variability, and recombination among them was also evident. The nucleotide substitution rates were determined for the AV1 gene of begomoviruses (2.60 × 10- 3 substitutions site- 1 year- 1) and the βC1 gene of betasatellites [chilli leaf curl betasatellite (ChiLCB), 2.57 × 10- 4 substitution site- 1 year- 1; tomato leaf curl Bangladesh betasatellite (ToLCBDB), 5.22 × 10- 4 substitution site- 1 year- 1]. This study underscores the current understanding of Indian ChiLCD-associated begomoviruses and also demonstrates the crucial role of betasatellites in severe disease development in Capsicum spp.

CRISPR/Cas9 Mediated Genome Engineering for Improvement of Horticultural Crops.

Abstract: Horticultural crops are an important part of agriculture for food as well as nutritional security. However, several pests and diseases along with adverse abiotic environmental factors poses a severe threat to these crops by affecting their quality and productivity. This warrants the effective and accelerated breeding programmes by utilizing innovative biotechnological tools that can tackle aforementioned issues. The recent technique of genome editing by Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated 9 (CRISPR/Cas9) has greatly advanced the breeding for crop improvement due to its simplicity and high efficiency over other nucleases such as Zinc Finger Nucleases and Transcription Activator Like Effector Nucleases. CRISPR/Cas9 tool contains a non-specific Cas9 nuclease and a single guide RNA that directs Cas9 to the specific genomic location creating double strand breaks and subsequent repair process creates insertion or deletion mutations. This is currently the widely adopted tool for reverse genetics, and crop improvement in large number of agricultural crops. The use of CRISPR/Cas9 in horticultural crops is limited to few crops due to lack of availability of regeneration protocols and sufficient sequence information in many horticultural crops. In this review, the present status of applicability of CRISPR/Cas9 in horticultural crops was discussed along with the challenges and future potential for possible improvement of these crops for their yield, quality and resistance to biotic and abiotic stress

Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants

Abstract: Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been shown to possess extensive variations in the length, number and distribution of SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2) = 0.5, P < 0.05) and relative abundance (R (2) = 0.6, P < 0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants.

Infectivity of the cloned components of a begomovirus: DNA beta complex causing chilli leaf curl disease in India

Abstract: The full-length genome of a begomovirus and its cognate DNA-beta satellite component associated with chilli leaf curl disease (ChLCD), originating from Varanasi, India, were cloned. Sequence analysis revealed that the viral genome (EF190217) is 2,750 bp and the DNA-beta satellite (EF190215) is 1,361 bp in length. Agroinoculation with partial tandem repeats of the viral genome along with the satellite induced symptoms typical of ChLCD in chilli and Nicotiana benthamiana. However, symptom expression was delayed and milder when the viral genome was agroinoculated alone in these hosts. Sequence comparisons revealed that the genome had the highest sequence identity (95%) with that of chilli leaf curl virus-PK[PK:Mul:98]. The DNA-beta satellite shared maximum sequence identity (88%) with a DNA-beta satellite associated with tomato leaf curl disease from Rajasthan (ToLCBDB-[IN:Raj:03]). These results demonstrate that ChLCD is caused by a complex consisting of the monopartite chilli leaf curl virus and a DNA-beta satellite component. This is the first experimental demonstration of Koch's postulates using cloned DNA molecules associated with chilli leaf curl disease.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

CRISPR for Crop Improvement: An Update Review.

Abstract: The availability of genome sequences for several crops and advances in genome editing approaches has opened up possibilities to breed for almost any given desirable trait. Advancements in genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has made it possible for molecular biologists to more precisely target any gene of interest. However, these methodologies are expensive and time-consuming as they involve complicated steps that require protein engineering. Unlike first-generation genome editing tools, CRISPR/Cas9 genome editing involves simple designing and cloning methods, with the same Cas9 being potentially available for use with different guide RNAs targeting multiple sites in the genome. After proof-of-concept demonstrations in crop plants involving the primary CRISPR-Cas9 module, several modified Cas9 cassettes have been utilized in crop plants for improving target specificity and reducing off-target cleavage (eg. Nmcas9, Sacas9, Stcas9). Further, the availability of Cas9 enzymes from additional bacterial species has made available options to enhance specificity and efficiency of gene editing methodologies. This review summarizes the options available to plant biotechnologists to bring about crop improvement using CRISPR/Cas9 based genome editing tools and also presents studies where CRISPR/Cas9 has been used for enhancing biotic and abiotic stress tolerance. Application of these techniques will result in the development of non-genetically modified (Non-GMO) crops with the desired trait that can contribute to increased yield potential under biotic and abiotic stress conditions.

Advances in Understanding Begomovirus Satellites

Abstract: Begomoviruses are numerous and geographically widespread viruses that cause devastating diseases in many crops. Monopartite begomoviruses are frequently associated with betasatellites or alphasatellites. Both betasatellite and alphasatellite DNA genomes are approximately half the size of begomovirus DNA genomes. Betasatellites are essential for induction of typical disease symptoms. The βC1 genes encoded by the betasatellites have important roles in symptom induction, in suppression of transcriptional and posttranscriptional gene silencing, and they can affect jasmonic acid responsive genes. Host plants of begomoviruses have evolved diverse innate defense mechanisms against the βC1 protein to counter these challenges. Alphasatellites have been identified mainly in monopartite begomoviruses that associate with betasatellites and have no known contributions to pathogenesis of begomovirus-betasatellite disease complexes. Applications of current molecular tools are facilitating viral diagnosis and the discove...

Notes for genera: Ascomycota

Abstract: Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10–15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of Lalaria, which were invalidly published are transferred to Taphrina and validated as new combinations. Catenomycopsis Tibell & Constant. is reduced under Chaenothecopsis Vain., while Dichomera Cooke is reduced under Botryosphaeria Ces. & De Not. (Art. 59).