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HLA-C*17:78 differs from HLA-C*17:03:01:03 by one nucleotide change C>T in exon 3 (GCG>GTG)., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

HLA-A*33:33:02 differs from HLA-A*33:33:01 by one synonymous nucleotide change C>T in exon 3 (TCC>TCT)., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Background: A molecular approach for the identification of unknown species by the using mitochondrial cox1 gene is an effective and reliable as compared with morphological-based identification. Hirudinaria manillensis referred to as Asian Buffalo Leech, is found in South Asia and traditionally used as medicine owing to its medicinal properties., Methods and Results: The study aimed to isolate and identify the leech species using cox1 gene sequencing and their phylogenetic relationships. The nucleotide sequences of cytochrome c oxidase subunit I (cox1) mitochondrial genes were analyzed for species identification and the phylogenetic relationship of crucial therapeutic leech Hirudinaria manillensis. The isolated DNA from the leech sample was amplified with cox1 gene-specific primers. BLAST results with the H. manillensis sequence showed 89.24% homology with H. manillensis and phylogenetic tree analysis revealed the genetic relationship with other GenBank submitted sequences., Conclusion: The present study concluded that the cox1 gene could be an effective way to identify the leech H. manillensis and provided sufficient phylogenetic information to distinguish H. manillensis indicating a significant mtDNA-based approach to species identification., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

HLA-G*01:01:01:34 differs from HLA-G*01:01:01:01 by one nucleotide in intron 3 at position 1432 (G to A)., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Allele variants HLA-C*01:02:01:74Q and -C*15:02:01:63 differ from -C*01:02:01:01 and -15:02:01:01 by a single nucleotide, respectively., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

HLA-B*15:679 and HLA-C*15:02:01:61 differ from HLA-B*15:12:01 and HLA-C*15:02:01:01 by a single nucleotides., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

In this study, we investigated and confirmed natural lumpy skin disease virus (LSDV) infection in Himalayan yaks (Bos grunniens) in Himachal Pradesh, India, based on clinical manifestations and results of genome detection, antibody detection, virus isolation, and nucleotide sequencing. Subsequent phylogenetic analysis based on complete GPCR, RPO30, and EEV gene sequences revealed that the LSDV isolates from these yaks and local cattle belonged to LSDV subcluster 1.2.1 rather than the dominant subcluster 1.2.2, which is currently circulating in India, suggesting a separate recent introduction. This is the first report of natural LSDV infection in yaks in India, expanding the known host range of LSDV. Further investigations are needed to assess the impact of LSDV infection in yaks., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Camelpox is an important viral disease of dromedary camel in Rajasthan, India. In the present study, partial C18L gene sequences (n = 6) of camelpox virus (CMLV) obtained in an outbreak in Bikaner, Rajasthan, India in year 2022 were compared with other similar sequences obtained in the past in similar geographical location. Clinical and epidemiological features of the disease were also compared. Genomic study suggested variations in C18L gene sequences obtained in the present outbreak from those obtained during the past outbreaks. CMLV were genetically different from cowpox viruses, but appeared identical to CMLV causing disease in Israel, Egypt and Kazakhstan. Genomes of CMLV virus circulating in dromedary camel population of Rajasthan, India appeared diverse and changing, hence complete genome sequencing and identification of genomic changes altering infectivity and pathogenicity is warranted for designing control strategies., Competing Interests: Declaration of Competing Interest Authors declare no conflicts of interest., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

HLA-DPB1*1461:01 differs from DPB1*02:01:02:01 in exon 2, codon 51 CTG > CGG a Leucine to Arginine replacement., (© 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Water/drought stress experiments are frequently conducted under imposed stress or rainout shelters, while natural drought hot-spot investigations are rare. The "drought hot spot" in Anantapur, Andhra Pradesh, India, is appropriate for drought stress evaluation due to its hot, arid environment, limited rainfall, with over 50% rainfall variability. According to reports, 30 out of 200 groundnut cultivars in India are supposed to possess drought-tolerant characteristics. However, these cultivars are yet to be evaluated in areas that are prone to drought. This study tested these drought-tolerant genotypes in naturally drought-prone areas of Anantapur under rainfed conditions from Kharif 2017 to 2019. Pod yield and rainfall-use-efficiency (RUE) were measured for these genotypes. Genotype and genotype*environment interactions affected pod yield and RUE (GEI). The AMMI model exhibits significant season-to-season variability within the same area with environmental vectors > 90° angles. GGE biplot suggested the 2018 wet season for drought-resistant cultivar identification. Kadiri5 and GPBD5 were the most drought-tolerant cultivars for cultivation in Anantapur and adjacent regions. These types could also be used to generate drought-tolerant groundnut variants for drought-prone regions., (© 2023. Springer Nature Limited.)

Background: Scianna (Sc) antigens, seven high and two of low prevalence, are expressed on erythrocyte membrane-associated protein (ERMAP). We investigated SC (ERMAP) in individuals who made antibodies to high prevalence Scianna antigens, and propose a 3D model for ERMAP to precisely localize the residues associated with the known antigens., Methods: Serological testing and DNA sequencing was performed by standard methods. A 3D structural model was built using a multi-template homology approach. Protein structures representing missense variants associated with the loss or gain of an antigen were generated. Residue accessibility and intraprotein interactions were compared with the wild-type protein., Results: Two new SC alleles, one with c.349C > T (p.Arg117Cys) in a woman from South India with anti-Sc3 in her plasma, and a c.217_219delinsTGT (p.Arg73Cys) in an African-American woman with an antibody to a new high prevalence antigen, termed SCAC, were identified. Six structural templates were used to model ERMAP. 3D analysis showed that residues key for Scianna antigen expression were all exposed at the surface of the extracellular domain. The p.Arg117Cys change was predicted to abolish interactions between residues 93 and 117, with no compensating interactions., Conclusion: We confirm the extracellular location of Scianna residues responsible for antigen expression which predicts direct accessibility to antibodies. Loss of intraprotein interactions appear to be responsible for a Sc null and production of anti-Sc3 with p.117Cys, SC*01 N.03, and for loss of a high prevalence antigen with p.73Cys, termed SCAC for Sc Arg to Cys. Comparative modeling aids our understanding of new alleles and Scianna antigen expression., (© 2022 AABB.)

The novel allele HLA-DQB1*04:02:01:18 differs from HLA-DQB1*04:02:01:04 by a nucleotide change at position; gDNA 2789 A → G., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Background: Aconitum heterophyllum Wall. ex Royle and Aconitum balfourii Stapf, are two highly important, threatened medicinal plants of the Indian Himalayan Region. Root-tubers of Aconites have occupied an important place in Indian pharmacopoeia from very ancient times. India is a hub of the wild-collected medicinal herbs industry in Asia and these two aconites are known to have been heavily traded from the region in illicit manner. Prosecution of these illegal trading crimes is hampered by lack of pharma-forensic expertise and tools., Methods and Results: Present study was conducted to evaluate the discriminatory potential of rbcL, a Chloroplast based DNA barcode marker for the authentication of these two Himalayan Aconites. Fresh plant samples were collected from their natural distributional range as well as raw materials were procured from herbal market and a total of 32 sequences were generated for the rbcL region. Analysis demonstrated that rbcL region can successfully be used for authentication and importantly, both the aconites, were successfully discriminated by rbcL locus with high bootstrap support (> 50%)., Conclusion: Molecular markers could certainly be relied upon morphological and chemical markers being tissue specific, having a higher discriminatory power and not age dependent. Phylogenetic analysis using Maximum Likelihood Method revealed that the rbcL gene could successfully discriminate Himalayan Aconites to species level and have potential to be used in pharma-forensic applications as well as to curb illicit trade of these invaluable medicinal plants., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Golden trumpet (Allamanda cathartica) plants were observed to exhibit mottling and distortion symptoms on leaves. The genome of an associated begomovirus (Al-K1) was amplified by rolling-circle amplification, cloned, and sequenced. The viral genome consisted of two circular ssDNA molecules, and the organization of the ORFs was similar to those of DNA-A and DNA-B components of bipartite begomoviruses. The size of DNA-A (KC202818) and DNA-B (MG969497) of the begomovirus was 2772 and 2690 nucleotides, respectively. Sequence analysis revealed that the DNA-A and DNA-B components shared the highest sequence identity with duranta leaf curl virus (MN537564, 87.8%) and cotton leaf curl Alabad virus (MH760452, 81.0%), respectively. Interestingly, the Al-K1 isolate shared significantly less nucleotide sequence identity with allamanda leaf curl virus (EF602306, 71.6%), the only monopartite begomovirus reported previously in golden trumpet from China. Al-K1 shared less than 91% sequence identity with other begomoviruses, and hence, according to the latest ICTV guidelines for species demarcation of begomoviruses, Al-K1 is proposed to be a member of a new species, and we propose the name "allamanda leaf mottle distortion virus" (AllLMoDV-[IN-Al_K1-12]) for this virus. AllLMoDV was detected in various golden trumpet samples from different locations by PCR with specific primers based on the genome sequence determined in this study. Our study provides evidence of the occurrence of a new bipartite begomovirus in a perennial ornamental plant in India., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Coconut pollen has been documented to be a major contributor to the aeroallergen load in India, causing respiratory allergy in a large cohort of susceptible individuals. Here, we report the identification of the first major allergen from Coconut pollen, Coc n 1. The full-length sequence of the allergen was determined from previously identified peptides and overexpressed in E. coli. Recombinant Coc n 1 folded into a trimer and was found to possess allergenicity equivalent to its natural counterpart. Proteolytic processing of Coc n 1 led to the formation of an immunodominant ∼20 kDa C-terminal subunit and the site of cleavage was determined by amino acid microsequencing. Five linear IgE binding epitopes were predicted and mapped on the homology modelled structure of Coc n 1. Amongst three immunodominant epitopes, two were present towards the C-terminal end. Coc n 1 was found to belong to the highly diverse cupin superfamily and mimics its structure with known 7S globulin or vicilin allergens but lacks sequence similarity. Using sequence similarity networks, Coc n 1 clustered as a separate group containing unannotated cupin domain proteins and did not include known vicilin allergens except Gly m Bd 28 kDa, a Soybean major allergen. 7S globulins are major storage proteins and food allergens, but presence of such protein in pollen grains is reported for the first time. Further study on Coc n 1 may provide insights into its function in pollen grains and also in the development of immunotherapy to Coconut pollen allergy., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: Plasmodium falciparum erythrocyte membrane protein is encoded by a highly variable multicopy var gene family known to play a key role in malaria pathogenicity. Therefore, we investigated sequence variation, expression profile and immune response of the Duffy binding-like domain (DBLα) region of the var gene., Methods: Blood samples were collected from patients with cerebral, severe and mild malaria in Chhattisgarh, India, a region with endemic malaria. Polymerase chain reaction amplicons were cloned and sequenced to determine sequence variation. The expression level was analyzed targeting the upstream region of var gene using the Delta-Delta-Ct method. Immunoglobulin G (IgG) level was determined against the 6 synthetic peptides of the DBLα region., Results: The study identified that group 1 and group 5 sequences (cysteine/position of limited variability (cys/PoLV) classification) along with cys2/cys4 and MFK*/REY motifs and short amino acid length were significantly associated with malaria severity. The specific PoLV (MFKS, LREA, PTNL) were restricted to cerebral malaria. The expression level of var group A was higher than var groups B and C, demonstrating its prognostic characteristic. All peptides showed high-quality IgG response, while VAR P5 appeared to be a good marker for severity., Conclusions: The present study illustrates the presence of specific sequences of DBLα tags involved in severe malaria that could be targeted in future interventions for malaria control and elimination., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Pashmina goat (Capra hircus) is an economically important livestock species, which habitats the cold arid desert of the Ladakh region (India), and produces a princely animal fiber called Pashmina. The Pashmina goat has a double coat fleece as an adaptation to the very harsh cold winters the outer long coarse hair (guard hair) produced from primary hair follicles and the inner fine Pashmina fiber produced from secondary hair follicles. Pashmina fiber undergoes a circannual and synchronized growth cycle. In the present study, we analyzed transcriptome profiles from 10 different Pashmina goats during anagen and telogen to delineate genes and signaling pathways regulating active (anagen) and regressive (telogen) phases of the follicle growth. During anagen, 150 genes were expressed at significantly higher levels with log (FC) > 2 and p adj  < 0.05. The RNA seq results were subjected to qRT-PCR validation. Among the nine genes selected, the expression of HAS1, TRIB2, P2RX1. PRG4, CNR2, and MMP25 were significantly higher (p < 0.05) in the anagen phase, whereas MC4R, GIPC2, and CDO1 were significantly expressed (p < 0.05) in the telogen phase which supports and validates the gene expression pattern from the RNA-sequencing. Differentially expressed genes revealed that Pashmina fiber initiation is largely controlled by signaling pathways like Wnt, NF-Kappa, JAK-STAT, Hippo, MAPK, Calcium, and PI3K-Akt. Expression of genes from the Integrin family, Cell adhesion molecules, and ECM-receptors were observed to be at much higher levels during anagen. We identified key genes (IL36RN, IGF2, ITGAV, ITGA5, ITCCR7, CXCL5, C3, CCL19, and CXCR3) and a collagen cluster which might be tightly correlated with anagen-induction. The regulatory network suggests the potential role of RUNX3, NR2F1/2, and GATA family transcription factors in anagen-initiation and maintaining fiber quality in Pashmina goats.

The drug resistance of Plasmodium vivax in clinical cases remains largely unknown till date because of the difficulty in diagnosing the resistant P. vivax strains. The present study was undertaken to determine the prevalence of mutant alleles in drug resistance genes viz P. vivax multi-drug resistance (pvmdr-1), chloroquine resistance transporter (pvcrt-o), dihydrofolate reductase (pvdhfr) and dihydropteroate synthase (pvdhps) along with in vitro chloroquine (CQ) sensitivity in P. vivax clinical isolates. During August-October 2017 a total of 86 samples of the febrile patients were screened and 31 samples were found to be positive for P. vivax in Safdarjung hospital, New Delhi. Sequence genotyping of the drug resistance genes was carried out in these P. vivax samples and in vitro CQ susceptibility for 23 isolates was determined by the schizont maturation assay (SMA). The CQ inhibitory concentrations (IC 50 ) for the clinical isolates was found to be in the range of 25.6-176.7 nM. All the 31 clinical isolates analyzed for pvmdr-1 gene, showed mutant alleles and in only two isolates novel mutations at 861 and 898 codons were observed. Sequence analysis of pvcrt-o, pvdhfr and pvdhps genes revealed wild type genotypes in all the 31 studied isolates. The presence of mutations in pvmdr-1 gene and the increase in the CQ IC 50 value indicates the possibility of shift in drug tolerance where CQ with primaquine (PQ) is still the first line of treatment for P. vivax malaria in the country. The regular molecular surveillance in P. vivax would provide useful information for the policy makers of the malaria control programme., (Copyright © 2020. Published by Elsevier Inc.)

Purpose: To estimate the prevalence of Leber hereditary optic neuropathy (LHON) along with genetic screening at a tertiary eye care center in southern India., Methods: Patients with LHON were identified at the Neuro-Ophthalmology Clinic, Aravind Eye Hospital (AEH; Madurai, India) from 2015 to 2019. Clinical data were collected along with blood samples. Genetic testing was performed for the confirmation of LHON using a multiplex PCR restriction fragment length polymorphism (RFLP) approach to detect the primary mutations 3460A, 11778A, and 14484C in mitochondrial DNA (mtDNA)., Results: During the study period, 1,598,441 outpatients attended AEH of whom 40,527 were referred to the Neuro-Ophthalmology Clinic. Among them, 55 patients were diagnosed with LHON. The male to female ratio was 8.2:1.0, and the mean age at onset was 20.95 years (SD 8.940). The estimated prevalence was 1:737 or 13.57 per 10,000 (95% confidence intervals [CI] 10.23-17.66) at the Neuro-Ophthalmology Clinic. The frequency of primary mutations in the patients with LHON was determined as 43.6% (24/55), giving a prevalence of 1:1689 or 5.92 per 10,000 (95% CI 3.78-8.81)., Conclusions: The high prevalence of LHON observed at a single hospital highlights the impact of the disease in southern India. As the epidemiology of LHON remains unexplored in this region, these findings will pave the way to evaluate the national prevalence. Further, screening the whole mitochondrial genome may help to increase the detection of mutations to estimate the accurate prevalence of the disease., (Copyright © 2020 Molecular Vision.)

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first identified in Wuhan, China late in 2019. Nine months later (Sept. 23, 2020), the virus has infected > 31.6 million people around the world and caused > 971.000 (3.07 %) fatalities in 220 countries and territories. Research on the genetics of the SARS-CoV-2 genome, its mutants and their penetrance can aid future defense strategies. By analyzing sequence data deposited between December 2019 and end of May 2020, we have compared nucleotide sequences of 570 SARS-CoV-2 genomes from China, Europe, the US, and India to the sequence of the Wuhan isolate. During worldwide spreading among human populations, at least 10 distinct hotspot mutations had been selected and found in up to > 80 % of viral genomes. Many of these mutations led to amino acid exchanges in replication-relevant viral proteins. Mutations in the SARS-CoV-2 genome would also impinge upon the secondary structure of the viral RNA molecule and its repertoire of interactions with essential cellular and viral proteins. The increasing frequency of SARS-CoV-2 mutation hotspots might select for dangerous viral pathogens. Alternatively, in a 29.900 nucleotide-genome, there might be a limit to the number of mutable and selectable sites which, when exhausted, could prove disadvantageous to viral survival. The speed, at which novel SARS-CoV-2 mutants are selected and dispersed around the world, could pose problems for the development of vaccines and therapeutics., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)

The wave of COVID-19 is a big threat to the human population. Presently, the world is going through different phases of lock down in order to stop this wave of pandemic; India being no exception. We have also started the lock down on 23rd March 2020. In this current situation, apart from social distancing only a vaccine can be the proper solution to serve the population of human being. Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. This fast motivated us to analyze publicly available 566 Indian complete or near complete SARS-CoV-2 genomes to find the mutation points as substitution, deletion and insertion. In this regard, we have performed the multiple sequence alignment in presence of reference sequence from NCBI. After the alignment, a consensus sequence is built to analyze each genome in order to identify the mutation points. As a consequence, we have found 933 substitutions, 2449 deletions and 2 insertions, in total 3384 unique mutation points, in 566 genomes across 29.9 K bp. Further, it has been classified into three groups as 100 clusters of mutations (mostly deletions), 1609 point mutations as substitution, deletion and insertion and 64 SNPs. These outcomes are visualized using BioCircos and bar plots as well as plotting entropy value of each genomic location. Moreover, phylogenetic analysis has also been performed to see the evolution of SARS-CoV-2 virus in India. It also shows the wide variation in tree which indeed vivid in genomic analysis. Finally, these SNPs can be the useful target for virus classification, designing and defining the effective dose of vaccine for the heterogeneous population., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Lumpy skin disease (LSD) caused by lumpy skin disease virus (LSDV) inflicts significant economic losses in cattle production with impact on livelihoods of smallholders. This study reports the first occurrence of LSD in cattle in India and analyses epidemiological and genetic characterization data from LSD outbreaks in five districts of Odisha state in August 2019. In all, 182 of 2,539 cattle were affected with an apparent morbidity rate of 7.1% and no mortality. Out of 102 samples from 60 LSD suspected and 17 asymptomatic in-contact cattle tested, 29.87% cattle were positive by capripoxvirus generic PCR and 37.66% were positive by LSDV real-time PCR. All the in-contact cattle tested were negative for LSDV. Among affected cattle, LSDV genome was detected more in scabs (79.16%) than blood (31.81%) and frozen bull semen (20.45%). Differential diagnosis by PCR was negative for pseudo-LSD, buffalopox, cowpox, pseudo-cowpox and bovine papular stomatitis. Five selected PCR and real-time PCR-positive LSDV DNA were sequenced in three genomic regions, P32 (LSDV074), F (LSDV117) and RPO30 (LSDV036). Phylogenetic analysis based on partial P32 and F gene sequences and complete RPO30 gene sequences showed that all the five Indian LSDV strains were identical and clustered with other field strains of LSDV circulating globally. However, the F and RPO30 gene sequence analyses revealed that Indian LSDV strains are genetically closer to the South African NI2490/KSGP-like strains than the strains detected in Europe, which was rather surprising. The present study established the existence of LSDV in India and involvement of LSDV field strains in the outbreaks. Additionally, we provided evidence of LSDV shedding in semen of naturally infected bulls. Further studies are required to determine the source of LSD introduction, extent of spread, modes of transmission and impact on dairy cattle production in India and effective control measures must be undertaken urgently., (© 2020 Blackwell Verlag GmbH.)

HLA-DQB1*02:01:01:02 differs from HLA-DQB1*02:01:01:01 by one nucleotide change in intron 2 at position 3949 (G>C)., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest accessory protein in the SARS-CoV2 genome is ORF3a which modulates the host response to the virus infection and consequently it plays an important role in pathogenesis. In this study, an attempt is made to decipher the conservation of nucleotides, dimers, codons and amino acids in the ORF3a genes across thirty-two genomes of Indian patients. ORF3a gene possesses single and double point mutations in Indian SARS-CoV2 genomes suggesting the change of SARS-CoV2's virulence property in Indian patients. We find that the parental origin of the ORF3a gene over the genomes of SARS-CoV2 and Pangolin-CoV is same from the phylogenetic analysis based on conservation of nucleotides and so on. This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SARS-CoV2., Competing Interests: Declaration of Competing Interest The authors do not have any conflicts of interest to declare., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The soil nature and characterstics are directly related to the micro-organisms present, bio-mineralization process, plant type and thus having harmonius and interdependent relationships. Soil bacteria having antagonistic activity against phytopathogens, play an important role in root growth, overall plant growth and also their composition depends upon the plant species. Population explosion across globe has resulted in indiscriminate use of chemical fertilizers, fungicides and pesticides, thus posing serious risk to plant productivity and soil flora. Plant growth promoting rhizobacteria (PGPRs) are considered safer than chemical fertilizers as they are eco-friendly and sustain longer after colonization in rhizospheric soil. PGPRs are preferred as a green choice and acts as a superior biocontrol agents against phytopathogens. In the present study, a potential rhizobacteria, Pseudomonas aeruginosa (isolate-2) was isolated from the rhizosphere of a medicinal plant, Valeriana wallichi. The bacterial isolate exhibited qualitative tests for plant growth promoting determinatives. It was also subjected to in-vitro biocontrol activity against potential phytopathogens viz. Alternaria alternata, Aspergillus flavus and F. oxysporum. The antagonistic efficacy against F. oxysporum was 56.2% followed by Alternaria alternata to be 51.02%. The maximum inhibition of radial growth of F. oxysporum was 69.2%, Alternaria alternata (46.4%) and Aspergillus flavus (15%). The Pseudomonas aeruginosa exhibited plant growth promotion rhizobacterial activity which can be expoited as biofertilizers. This study deals with microbial revitalization strategy and offers promising solution as a biocontrol agent to enhance crop yield. Further, PGPRs research using the interdisciplinary approaches like biotechnology, nanotechnology etc. will unravel the molecular mechanisms which may be helpful for maximizing its potential in sustainable agriculture.

Deleterious mutations within the SLC45A2 gene, encoding membrane-associated transporter protein (MATP), are responsible for type 4 oculocutaneous albinism. The cytogenetic location of SLC45A2 is 5p13.2 and it comprises seven exons located over around 40 kb. Its encoded protein, MATP, is 530 amino acids long and has 12 putative transmembrane domains. MATP is synthesized within melanocytes. It is in these cells that melanogenesis takes place and the melanin is contained within specialized organelles called melanosomes. Previous studies have shown that when MATP expression was reduced using small interfering RNA in MNT-1 melanoma cells, pH was lowered within melanosomes, they became poorly melanized and tyrosinase activity within melanocytes was also reduced. This type of albinism produces a broad spectrum of phenotypes, ranging from complete absence of melanin to brown hair and brown irides. In the current study, blood was collected from a family in which four members had oculocutaneous albinism, showing a complete absence of melanin in skin, hair and eyes. Screening of the TYR gene using the extracted DNA showed no mutation and therefore whole exome sequencing analysis was performed. A novel deletion mutation c.579delG [p.(Gly194Valfs*7)] in the SLC45A2 gene, predicted to be pathogenic and to result in both frameshift and premature termination of the MATP chain, was identified. These data add to the information pertaining to the mutation spectrum of OCA4., (© 2019 British Association of Dermatologists.)

The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.

Recurrent infectious bursal disease (IBD) outbreaks were reported in different regions of Kerala, India. This paper reports the comparative genetic analysis of the hypervariable region of the VP2 gene of IBD virus isolates from the field outbreaks in Kerala. In phylogenetic analysis, the obtained field isolates fall into genogroup 1 and 3. In genogroup 3, all vvIBDV isolates shared a common ancestor with other south Indian isolates but isolates 9/CVASP/IBDV, 10/CVASP/IBDV, 12/CVASP/IBDV, 14/CVASP/IBDV and 17/CVASP/IBDV are most recently evolved and are diverged from the south Indian isolates. The amino acid sequence of 22 isolates was analysed, out of which 18 had conserved amino acids which were characteristic of vvIBDV. All the vvIBDV isolates obtained in the study had phenylalanine and valine at the position 240 and 294, respectively, similar to recently evolved Indian IBDV isolate (MDI14). But we observed T269A and S299N mutations in the isolate 6/CVASP/IBDV, and it is the first report of such mutations at these positions in India IBDV isolates. The isolate 11/CVASP/IBDV had a unique mutation of V225A which is not yet reported in IBDV isolates. Two isolates (15/CVASP/IBDV and 18/CVASP/IBDV) were 100% amino acid similar to intermediate plus vaccine strain. The isolates 8/CVASP/IBDV/VP2 and 19/CVASP/IBDV had amino acids unique for the intermediate vaccine with mutations observed at H253Q and V256I in 19/CVASP/IBDV, T270A and novel mutation N279Y in isolate 8/CVASP/IBDV. These two isolates had non-virulent classical heptapeptide sequence 'SWSARGS'; nevertheless, they produce field outbreaks of IBD. This is the first report of genetic characterisation of IBDV in Kerala, India.

Background & Objectives: Hepatitis A is prevalent worldwide and is among the leading cause of acute viral hepatitis in India. Major geographical differences in endemicity of hepatitis A are closely related to hygienic and sanitary conditions and other indicators of the level of socio-economic development. The present study was aimed to know the seropositivity prevalence and predominant circulating strain of HAV in a north India., Methods: Patients with acute viral hepatitis were enrolled. Blood samples were collected over a period of one year from June 2016 to May 2017. Serum samples were tested for anti-immunoglobulin M (IgM) HAV antibodies. The seropositive samples were analyzed for HAV-RNA by real-time reverse transcription-polymerase chain reaction (RT-PCR). Samples detected on molecular assay were subjected to conventional semi-nested RT-PCR for VP1 gene. Further sequencing of amplified RT-PCR products was done, and data were analyzed., Results: A total of 1615 patients were enrolled, and serum samples were collected and tested. The male:female ratio was 1.3:1 with a mean age of 24.31±17.02 yr (range 0-83 yr). Among these, 128 (7.93%) were positive for anti-HAV IgM antibodies; 41.63 per cent of seropositive patients were in their childhood or early adolescent age group. Of all seropositive samples, 59 (46.09%) were positive for HAV RNA. Genotyping sequencing of 10 representative strains was carried out, and the circulating genotype was found to be IIIA. The nucleotide sequences showed homology among the strains., Interpretation & Conclusions: Our results showed that hepatitis A was a common disease in children with IIIA as a circulating genotype in this region. In approximately 50 per cent of cases, HAV RNA could be detected. Higher number of HAV IgM-seropositive cases was observed during monsoon period., Competing Interests: None

The variants reported for mitochondrial DNA (mtDNA) and type 2 diabetes (T2D) may not be accountable for the disease in certain other populations and the risk depends upon numerous factors which may include genetics, environment as well as ethnicity. This leads to a challenge in identifying, exploring and comparing the variants between diabetic cases and healthy controls in a remote unexplored tribal population. To study the possible contribution of mtDNA variants, we sequenced the entire mitochondrial genomes and the frequencies of mtSNPs, their association with familial T2D and the potential impact of non-synonymous substitutions on protein functions were determined. The mtSNP 8584 G > A (ATP6: A20T) was detected in 14.28% of the diabetic patients and none in the control groups. The mitochondrial ND3 variant 10398A > G was found to be significantly associated with the risk of T2D (OR = 9.489, 95% CI = 1.161-77.54, P value = 0.036). A novel Frame-shift substitution ND5: 81&#95;81ins A at position 12,417 was observed in 53.57% of diabetic individuals. Majority of the variants lie in tRNA-Phe in the non-protein coding region of mtDNA for both diabetic cases and common cases. We concluded that mutations in the coding (synonymous or non-synonymous) and noncoding regions of the mitochondria might have contribution towards the development of T2D. Our study is the first to report the distinct mitochondrial variants which may be attributed to the susceptibility as well as development of type 2 diabetes in an ethnic tribe from northeast India., (Copyright © 2019 Elsevier B.V. and Mitochondria Research Society. All rights reserved.)

Background: Cryptococcus neoformans is the leading cause of cryptococcal meningitis in HIV/AIDS patients. As infections in humans are predominantly caused by the inhalation of basidiospores from environmental sources, therefore, analysing the population structure of both clinical and environmental populations of C neoformans can increase our understanding of the molecular epidemiology of cryptococcosis., Objective: To investigate the genotypic diversity and antifungal susceptibility profile of a large collection of C neoformans isolates (n = 523) from clinical and environmental sources in India between 2001 and 2014., Materials and Methods: Cryptococcus neoformans isolates were genotyped by AFLP, microsatellite typing (MLMT) and MLST. In vitro antifungal susceptibility for standard antifungals was undertaken using CLSI M27-A3., Results: All isolates were C neoformans, AFLP1/VNI and exhibited mating-type MATα. MLMT revealed that the majority of isolates belonged to microsatellite cluster (MC) MC3 (49%), followed by MC1 (35%), and the remaining isolates fell in 11 other MC types. Interestingly, two-thirds of clinical isolates were genotype MC3 and only 17% of them were MC1, whereas majority of environmental strains were MC1 (54%) followed by MC3 (16%). Overall, MLST assigned 5 sequence types (STs) among all isolates and ST93 was the most common (n = 76.7%), which was equally distributed in both HIV-positive and HIV-negative patients. Geometric mean MICs revealed that isolates in MC1 were significantly less (P < .05) susceptible to amphotericin B, 5-flucytosine, itraconazole, posaconazole and isavuconazole than isolates in MC3., Conclusions: The study shows a good correlation between MLMT and MLST genotyping methods. Further, environmental isolates were genetically more diverse than clinical isolates., (© 2019 Blackwell Verlag GmbH.)

The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish, Carinotetraodon travancoricus (dwarf pufferfish or Malabar pufferfish) endemic to southwest India. The genome is 16487 bp in length and consist of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region like all the other vertebrate mitogenomes. The protein-coding genes ranged from 165 bp (ATP synthase subunit 8) to 1812 bp (NADH dehydrogenase subunit 5) and comprised of 11310 bp in total, constituting 68.5% of the complete mitogenome. Some overlaps have been observed in protein-coding genes by a total of 7 bp. The AT skew (0.032166) and GC skew (-0.29746) of the mitogenome indicated that heavy strand consists equal amount of A and T, but the overall base composition was mainly C skewed. The noncoding D-loop region comprised 869 bp. The conserved motifs ATGTA and its complement TACAT associated with thermostable hairpin structure formation were identified in the control region. The phylogenetic analysis depicted a sister group relationship of C. travancoricus with euryhaline species Dichotomyctere nigroviridis and D. ocellatus with 100% bootstrap value rather than with the other freshwater members of Carinotetraodon species from Southeast Asia. The data from this study will be useful for proper identification, genetic differentiation, management and conservation of the dwarf Indian pufferfish.

The novel HLA allele HLA-B*38:75 differs from B*38:02:01 by nonsynonymous change in codon 50., (© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Artemisinin-based combination therapy (ACT) has been used to treat uncomplicated Plasmodium falciparum infections in India since 2004. Since 2008, a decrease in artemisinin effectiveness has been seen throughout the Greater Mekong Subregion. The geographic proximity and ecological similarities of northeastern India to Southeast Asia may differentially affect the long-term management and sustainability of ACT in India. In order to collect baseline data on variations in ACT sensitivity in Indian parasites, 12 P. falciparum isolates from northeast India and 10 isolates from southwest India were studied in vitro Ring-stage survival assay (RSA) showed reduced sensitivity to dihydroartemisinin in 50% of the samples collected in northeast India in 2014 and 2015. Two of the 10 assayed samples from the southwest region of India from as far back as 2012 also showed decreased sensitivity to artemisinin. In both these regions, kelch gene sequences were not predictive of reduced artemisinin sensitivity, as measured by RSA. The present data justify future investments in integrated approaches involving clinical follow-up studies, in vitro survival assays, and molecular markers for tracking potential changes in the effectiveness of artemisinin against P. falciparum throughout India., (Copyright © 2019 Chakrabarti et al.)

Background: Genetic changeability of hepatitis B virus (HBV) signifies a challenge for the sensitivity of immunologic and molecular diagnostics. Therefore, knowing the spread of HBV genotypes (GENs) and mutation has considerable impacts on treatment strategies, vaccination program, diagnosis, and prevention. The present study aimed to detect HBV GENs and mutants in HBsAg-positive patients., Methods: The study conducted on 4927 patients in Meerut, India, between March 2013 and April 2017. The blood specimens were analyzed for HBsAg using an ELISA kit, then the blood samples from HBsAg-positive patients were subjected to HBeAg assay and DNA isolation. Amplification of the HBV DNA of pre-S gene and pre-core or basal core promoter region were performed by RT-PCR and sequenced to analyze both GEN and mutation., Results: According to the results, 245 cases were positive for HBsAg, and 55 were HBeAg-positive. With regard to HBV DNA levels, 16 samples were found positive in PCR assay with 7 (43.8%) less than 2000 IU/mL, 4 (25%) between >2000 and 20,000 IU/mL, and 5 (3.25%) >20,000 IU/mL. No mutations were detected in GENs B and A. The prevalence of HBV GENs B and A were 68.8% (n = 11) and 31.25% (n = 6), respectively., Conclusion: GEN-B was more prevalent in comparison to GEN-A. The genetic diversity of HBV and distribution of its GENs and mutation improve the current knowledge of epidemiological, clinical and virological patterns of hepatitis B in this region, which help physicians to prescribe proper antiviral/interferon therapy according to current genotyping pattern.

Bacillus thuringiensis is a spore-forming bacterium that is pathogenic towards a range of insect and nematode species and had been widely used as a biopesticide. In this study, we present the morphological, molecular and genetic characteristics of an indigenous Bt isolate T414 which displayed an effective toxicity against Pectinophora gossypiella. Scanning electron microscopy revealed the presence of bipyramidal, spherical and cubic shaped protein crystals in its spore-crystal suspension. SDS-PAGE analysis of its spore-crystal mixture showed the presence of two major protein bands viz.130 and 65 kDa. Whole genome sequencing with MiSeq divulged that it contains a chromosome and many plasmids. The assembled genome finally contained 6493494bp. Automated annotation of this genome draft predicted 6877 coding sequences and 152 RNAs (rRNAs, tRNAs and ncRNAs). NCBI blast analysis showed that assembled genome was distributed in a chromosome and 15 different types of plasmids. Further analysis of draft sequence revealed it harbors parasporal crystal protein genes (cry1Aa, cry1Ab, cry1Ac, cry1IAa, cry2Aa, cry2Ab and cyt1), vegetative insecticidal protein gene (vip3Aa), all plasmid borne and various additional virulence factors such as chitinases, proteases, bacteriocins and hemolysins. From the analysis it is evident that all the Cry, Cyt or Vip toxins are plasmid borne and are present on two types of plasmids named as p414A and p414E in the present study. A cry2A type gene was cloned and sequenced. It was named as cry2Aa21 by Bt nomenclature committee., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The indian subcontinent has experienced numerous paleogeological and paleoclimatic events during the Cenozoic which shaped the biotic assembly over time in the subcontinent. The role of these events in governing the biotic exchange between Southeast Asia and Indian subregion is underexplored. We aimed to uncover the effects the collision of the Indian and Asian plate, marine transgression in the Bengal basin as well as the paleoclimatic changes in the subcontinent and adjoining regions, on the dispersal of freshwater snail family Viviparidae from Southeast Asia (SEA) to Indian subregion. Extensive sampling was carried out throughout the Indian subcontinent to capture the current diversity of the targeted lineages. Three mitochondrial and two nuclear markers were sequenced from these samples and combined with published sequences to reconstruct global phylogeny of Viviparidae. Molecular dating and ancestral range estimation were undertaken to obtain the time frame for the dispersal events. Results from these analyses were contrasted with paleoclimate and paleogeology to better understand the biogeography of Indian viviparids. Results support at least two dispersal events into India from Southeast Asia. The earlier event is likely to have occurred during a warm and humid Eocene period before a permanent land connection was established between the two landmasses. While the more recent dispersal occurred post-suturing and overlapped with a time in late Tertiary to Quaternary when arid climate prevailed. However, we could not firmly establish how the marine transgressions influenced the dispersal events. Even though most biotic exchange between India and SEA are noted to be post-suturing, our results add to a growing body of work that suggests faunal exchange pre-suturing probably mediated by intermittent land connections., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Background: Cytomegalovirus [CMV] is a causative agent of congenital infection worldwide and often leads to neurological deficits and hearing loss in newborns. Infants born with symptomatic congenital Cytomegalovirus infection [cCMV] are at significant high risk for developing adverse long-term outcomes. In this study, we look into the sequence variability of surface glycoprotein B [gB] encoding region in newborns with symptomatic CMV infection for the first time in Eastern region of India., Methods: 576 suspected newborns from seropositive mothers were subjected to the study and ELISA was used to confirm CMV infection. Different genotypes and their subtypes were determined using multiplex nested-PCR. Viral load of different glycoprotein B [gB] genotypes was measured using RT-PCR. Sequencing and phylogenetic analysis was then performed using Bayesian interference., Results: The overall frequency of cCMV infection was 18.4%, where 16.0% neonates were symptomatic. Among the different gB genotypes, gB1 had the highest frequency [23.5%] and gB4 showed the lowest occurrence [5.8%]. 23.5% of symptomatic neonates had mixed genotypes of gB, probably indicating matrenal reinfection with CMV strains in Indian population. Significant genotypic clades [gB1-gB2-gB3-gB5] were grouped closely based on gene sequences, but the gB4 sequence was in the outlier region of the phylogenetic tree indicating the genetic polymorphism., Conclusion: This is the first study on cCMV genotyping and its phylogenetic analysis from Eastern Indian neonatal population. The study holds importance in the assessment of cCMV seroprevalence in global perspective. gB protein can be used as a potential therapeutic target against CMV infection.

One nucleotide substitution in codon 46 of HLA-DQB1*05:01:01:01 results in a new allele, HLA-DQB1*05:115., (© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Information pertaining to parasitic fauna and parasitic diseases in Manipuri ponies in India is not available. Moreover, no systematic studies have been undertaken on cutaneous habronemosis in Manipuri ponies which is a common skin problem of Manipuri ponies as reported by pony owners. Keeping in the view of the importance of parasitic infections in veterinary health coverage particularly in Manipuri ponies, the present study was planned. A survey of natural cases of cutaneous habronemosis followed by molecular confirmation of species involved and treatments were done. Out of 200 ponies examined, nine cases (4.5%) of cutaneous habronemosis was recorded. Gross examination revealed raised and ulcerated wounds with necrotic tissues covered with yellowish-tan granulation. Histopathological study revealed eosinophilic granuloma and in the center of the granuloma with necrotic debris. Remnants of the Hebronema larvae with infiltrating neutrophils surrounded by proliferating fibrous tissue with numerous eosinophils, macrophages and lymphocytes were also observed. Molecular detection of Habronema sp. was confirmed by semi-nested PCR. Sequence analysis revealed larvae of H. muscae was the common spirurid species responsible for producing cutaneous habronemosis in Manipuri ponies. Subsequently, sequence submitted to NCBI GenBank and accession number obtained (MH038181). Surgical removal of necrotic tissue, ivermectin injection along with antibiotics successfully cured all the lesions in infected ponies.Results confirmed occurrence of cutaneous habronemosis in Manipuri ponies in India., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Objective: To characterize the in vitro replication fitness, viral diversity, and phylogeny of dengue viruses (DENV) isolated from Indian patients., Methods: DENV was isolated from whole blood collected from patients by passaging in cell culture. Passage 3 viruses were used for growth kinetics in C6/36 mosquito cells. Parallel efforts also focused on the isolation of DENV RNA from plasma samples of the same patients, which were processed for next-generation sequencing., Results: It was possible to isolate 64 clinical isolates of DENV, mostly DENV-2. Twenty-five of these were further used for growth curve analysis in vitro, which showed a wide range of replication kinetics. The highest viral titers were associated with isolates from patients with dengue with warning signs and severe dengue cases. Full genome sequences of 21 DENV isolates were obtained. Genome analysis mapped the circulating DENV-2 strains to the Cosmopolitan genotype., Conclusions: The replication kinetics of isolates from patients with mild or severe infection did not differ significantly, but the viral titers varied by two orders of magnitude between the isolates, suggesting differences in replication fitness among the circulating DENV-2., (Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

GABPB1, known as nuclear respiratory factor 2 (Nrf2), activates mitochondrial genes that are responsible for oxidative phosphorylation. Earlier studies on GABPB1 reported that two single nucleotide polymorphisms (SNPs) such as rs7181866 and rs8031031, to be associated with increased endurance in athletes. In the present study, a cohort of 302 South Indians, including normoglycemic healthy controls, T2DM with and without obesity were genotyped for the two SNPs by PCR-RFLP method and correlated with serum adipokines. The 'G' allele of rs7181866 was found to be associated with obesity whereas rs8031031 didn't show any significant association with obese individuals. The increased levels of adipokines such as Leptin, IL-6 and TNF-α and decreased adiponectin were found among obese-T2DM, when compared to non-obese T2DM subjects. Further, Factor analysis on metabolic components revealed four factors which accounts for 71.5% for non-obese control and 88.3% for obese T2DM of variance. The bias-corrected and accelerated bootstrap analysis revealed GG genotype to have significant positive and negative correlation with both TNF-α and adiponectin. In conclusion, the G allele of (rs7181866 A/G) was found to be significantly associated with risk for obesity among T2DM subjects., (Copyright © 2019. Published by Elsevier B.V.)

Neuronal ceroid lipofuscinosis (NCL) is a group of progressive neurodegenerative disorders characterized by intracellular accumulation of ceroid lipopigments. Based on gene defect of NCL-associated proteins, 14 types of NCL have been described till date. NCL type 11 was first described in 2014 in two siblings as adult-onset NCL and was found to be due to a homozygous progranulin gene mutation. These siblings had progressive retinopathy, recurrent generalized seizures, moderate ataxia and subtle cognitive dysfunction. Palinopsia was present and MRI showed selective and severe cerebellar atrophy which was progressive with age. There have been no further reports of NCL 11 in literature. We here present a 14-year old girl born to second degree consanguineous couple who presented with gradually increasing frequency of seizures for the past 1 year without any signs of visual abnormalities and dementia. She had an elder sister who had progressive seizures and dementia from 8 years of age and died after few years. Her electroencephalogram showed frequent generalized epileptiform discharges and magnetic resonance imaging (MRI) showed pure cerebellar atrophy mainly affecting the vermis. MRI findings suggested a neurodegenerative disorder like NCL and prompted us to go for whole exome screen which revealed NCL type 11 due to homozygous mutation c.912G>A (p.Trp304Ter) in exon 9 of GRN gene (OMIM#614706). To the best of our knowledge this is the third case of NCL 11 and the first from Asia., (Copyright © 2019 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.)

Wilson disease (WD) is an autosomal recessive disorder, characterized by excessive deposition of copper in various parts of the body, mainly in the liver and brain. It is caused by mutations in ATP7B. We report here the genetic analysis of 102 WD families from a south Indian population. Thirty-six different ATP7B mutations, including 13 novel ones [p.Ala58fs*19, p.Lys74fs*9, p.Gln281*, p.Pro350fs*12, p.Ser481*, p.Leu735Arg, p.Val752Gly, p.Asn812fs*2, p.Val845Ala, p.His889Pro, p.Ile1184fs*1, p.Val1307Glu and p.Ala1339Pro], were identified in 76/102 families. Interestingly, the mutation analysis of affected individuals in two families identified two different homozygous mutations in each family, and thus each affected individual from these families harbored two mutations in each ATP7B allele. Of 36 mutations, 28 were missense, thus making them the most prevalent mutations identified in the present study. Nonsense, insertion and deletion represented 3/36, 2/36 and 3/36 mutations, respectively. The haplotype analysis suggested founder effects for all the 14 recurrent mutations. Our study thus expands the mutational landscape of ATP7B with a total number of 758 mutations. The mutations identified during the present study will facilitate carrier and pre-symptomatic detection, and prenatal genetic diagnosis in affected families., Competing Interests: The authors have declared that no competing interests exist.

In the present study, two pod borer larvae were found to damage pods of the host plant Senna alata. As pods (seeds) are commercially important, it prompted the investigators to find out the adult of pod borer larvae by molecular sequencing and reported in this article for the first time from S. alata. Successful amplification was achieved for chloroplast DNA isolated from leaves of host plant S. alata and tissue DNA from unknown larvae and sequenced. The sequences were submitted to NCBI domain, and the taxonomic position of host plant of pod borer larvae was confirmed as S. alata (L.) Roxb. Of the two sequences belonging to pod borer larvae, specimen 1 (S1) matched with already available three sequences of Thylacoptila sp. AA. But, specimen 2 (S2) showed significant variation in its genetic distance in Neighborhood Joining tree and maximum likelihood tree; these factors imply that specimen 2 (S2) is distinct from Thylacoptila sp. AA. Therefore, it is reported that specimen 2 may be represented as Thylacoptila sp. BB where in BB indicates variant from other available sequences. Nonetheless, reporting species of Thylacoptila as insect pest in pods of S. alata is an important contribution to the annals of insect-pest-plant interaction more importantly in medicinally important plant species S. alata.

Striped snakehead (Channa striata) is a freshwater species of early Miocene period belonging to family Channidae. The genetic variability of the snakehead populations in India was not well known. Present study was undertaken using 149 sequences of control region of mitochondrial DNA from seven geographically distinct populations of Indian water, which resulted in 46 haplotypes with 137 variable nucleotide sites (60 singletons and 77 parsimony informative) and the nucleotide frequencies was: A = 33.0, T = 28.1, G = 15.4, and C = 23.5%. The presence of low-frequency of younger haplotypes with a large number of singletons indicates the absence of dominant haplotype. Hierarchical AMOVA showed highly significant genetic differentiation (F ST  = 0.56, p < .00) among the populations. The pattern of genetic differentiation was not consistent with geographical distributions. AMOVA identified three genetically heterogeneous clades. The significant finding of Imphal and Chaliyar was that they were found genetically close to each other, but geographically much isolated from each other. The inference of the study suggests that the hypothesis of the single panmictic population of C. striata in Indian waters is rejected.

A begomovirus isolate collected from bitter gourd plants showing yellowing, puckering and stunting symptoms from Coimbatore district, Tamil Nadu, India was characterized. The full-length genome of the virus isolate was amplified by rolling circle amplification using phi29 DNA polymerase. The virus isolate exhibited 98% identity in the nucleotide sequence of DNA-A component with the Coccinia mosaic Virudhunagar virus (GenBank accession no. KY860899). The DNA-B component was very distinct and shared only 60% identity with the begomovirus, Coccinia mosaic Tamil Nadu virus (GenBank accession no. KM244719). The virus renamed as new species Bitter gourd yellow mosaic virus (BgYMV) was detected in seeds from infected plants and in the grow-out test seedlings by ELISA and virus-specific PCR. The seed infectivity was 79.16% and transmission rate to seedling was 32.05%. The virus titre as indicated by A 405 absorption value was high (0.854-0.280) in different seed parts. Results clearly indicated seed transmission of the begomovirus, BgYMV., (Copyright © 2018. Published by Elsevier Ltd.)