A Vitamin D-RelB/NF-κB Pathway Limits Chandipura Virus Multiplication by Rewiring the Homeostatic State of Autoregulatory Type 1 IFN-IRF7 Signaling.

Besides its functions in the skeletomuscular system, vitamin D is known to alleviate viral-inflicted pathologies. However, the mechanism underlying protective vitamin D function remains unclear. We examined the role of vitamin D in controlling cellular infections by Chandipura virus, an RNA virus implicated in human epidemics. How immune signaling pathways, including those regulating NF-κB and IFN regulatory factors (IRFs), are activated in virus-infected cells has been well studied. Our investigation involving human- and mouse-derived cells revealed that vitamin D instructs the homeostatic state of these antiviral pathways, leading to cellular resilience to subsequent viral infections. In particular, vitamin D provoked autoregulatory type 1 IFN-IRF7 signaling even in the absence of virus infection by downmodulating the expression of the IFN-inhibitory NF-κB subunit RelB. Indeed, RelB deficiency rendered vitamin D treatment redundant, whereas IRF7 depletion abrogated antiviral vitamin D action. In sum, immune signaling homeostasis appears to connect micronutrients to antiviral immunity at the cellular level. The proposed link may have a bearing on shaping public health policy during an outbreak.

In vitro and in silico analysis unravelled clinically desirable attributes of Bacillus altitudinis L-asparaginase.

AIMS: To identify a marine L-asparaginase with clinically desirable attributes and characterize the shortlisted candidate through in silico tools. METHODS AND RESULTS: Marine bacterial strains (number = 105) isolated from marine crabs were evaluated through a stepwise strategy incorporating the crucial attributes for therapeutic safety. The results demonstrated the potential of eight bacterial species for extracellular L-asparaginase production. However, only one isolate (Bacillus altitudinis CMFRI/Bal-2) showed clinically desirable attributes, viz. extracellular production, type-II nature, lack of concurrent L-glutaminase and urease activities, and presence of ansZ (functional gene for clinical type). The enzyme production was 22.55 ± 0.5 µM/mg protein/min within 24 h without optimization. The enzyme also showed good activity and stability in pH 7-8 and temperature 37°C, predicting the functioning inside the human body. The Michealis-Menten constant (Km) was 14.75 µM. Detailed in silico analysis based on functional gene authenticating the results of in vitro characterization and predicted the nonallergenic characteristic of the candidate. Docking results proved the higher affinity of the shortlisted candidate to L-asparagine than L-glutamine and urea. CONCLUSION: Comprehensively, the study highlighted B. altitudinis type II asparaginase as a competent candidate for further research on clinically safe asparaginases.

Unraveling the spawning and reproductive patterns of tomato hind grouper, Cephalopholis sonnerati (Valenciennes, 1828) from south Kerala waters.

The objective of this study is to provide information on the reproductive biology of tomato hind grouper, Cephalopholis sonnerati (Valenciennes, 1828) for conservation and management purposes. Fish caught by artisanal fishermen from September 2019 to August 2021 were analysed. A total of 280 females, 31 males, and 4 transitional and 178 sex-undetermined fish were analysed. The female to male sex proportion was 9:1, and the fish reached a maximum total body length of 38.5 and 54.5 cm for females and males, respectively. The following microscopic stages were identified: immature, developing, ripe, running ripe/releasing, and spent in both males and females. Several asynchronous development patterns were observed in the studied gonads, including multiple oocyte stages and early and advanced stages of sexual transition. High gonadosomatic index (GSI) for both males and females was recorded in March, May, and November. Running ripe and releasing stages in females were identified in the months from March to June, which indicates the spawning season. The absolute and relative fecundity of the species ranged from 162,723 ± 207,267 and 239 ± 285, respectively. An exponential relationship was found between fecundity and total body length (TL), fecundity and total body weight (TW), and fecundity and gonad weight (GW).

A Global-Scale Ecological Niche Modeling of the Emerging Pathogen Serratia marcescens to Aid in its Spatial Ecology.

Serratia marcescens is a big emerging concern for human health and coral biodiversity. Spatial ecology and the influencing factors on pathogen ecology, however, remain unknown. The study forms the first global risk assessment of S. marcescens. MaxEnt niche modeling was applied using two biotic and sixteen abiotic variables. The world was classified into five risk-level categories based on the pathogen ecology, and the world population exposed to S. marcescens infection was then quantified. The prepared model showed an area under the curve value of 0.918 ± 0.028, implying excellent prediction ability. The highly and moderately suitable areas occupied around 0.52% and 17.9% of the total global land area. The order of probability of having S. marcescens-related infections was Asia > North America > South America > Europe > Africa > Australia. Human population density and temperature were the most influential factors in the distribution. The moderate to high transmission risk zones contained 0.20% (1.61 billion people) of the human population. In brief, these results give novel insights into its spatial ecology and provide the risk maps that can be utilized to plan targeted strategic control measures against future invasions of this emerging pathogen.

Ajay Kumar Parida (1963-2022), an eminent plant biotechnologist with a passion for mangrove biology.

We remember Dr Ajay Parida, a leading plant biotechnologist, whose premature passing has deprived the Indian plant science community of a committed scientist and an able administrator. Born on 12 December 1963 in Bhagabanpur, Cuttack District (now Jajpur district), Odisha, he passed away in Guwahati on 19 July 2022. A collegial scientist, his down-to-earth and approachable nature, as well as his resourcefulness were instrumental in advancing the cause of Indian science and harnessing frontier biotechnological tools as vehicles of social consciousness. His expertise in quantitative DNA variation and molecular marker analysis, paved the way for subsequent research on mangrove molecular diversity at the M. S. Swaminathan Research Foundation (MSSRF), Chennai. His contributions to mangrove biology, genetics and genomics as well as extremophile plant species in the Indian context over two decades are a benchmark in his field. He also provided commendable leadership in his capacity as Director, Institute of Life Sciences (ILS), Bhubaneshwar during the COVID-19 pandemic.

Comparative mitogenomics of Clupeoid fish provides insights into the adaptive evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes and codon usage in the heterogeneous habitats.

Clupeoid fish can be considered excellent candidates to understand the role of mitochondrial DNA in adaptive evolution, as they have colonized different habitats (marine, brackish, freshwater, tropical and temperate regions) over millions of years. Here, we investigate patterns of tRNA location, codon usage bias, and lineage-specific diversifying selection signals to provide novel insights into how evolutionary improvements of mitochondrial metabolic efficiency have allowed clupeids to adapt to different habitats. Based on whole mitogenome data of 70 Clupeoids with a global distribution we find that purifying selection was the dominant force acting and that the mutational deamination pressure in mtDNA was stronger than the codon/amino acid constraints. The codon usage pattern appears evolved to achieve high translational efficiency (codon/amino acid-related constraints), as indicated by the complementarity of most codons to the GT-saturated tRNA anticodon sites (retained by deamination-induced pressure) and usage of the codons of the tRNA genes situated near to the control region (fixed by deamination pressure) where transcription efficiency was high. The observed shift in codon preference patterns between marine and euryhaline/freshwater Clupeoids indicates possible selection for improved translational efficiency in mitochondrial genes while adapting to low-salinity habitats. This mitogenomic plasticity and enhanced efficiency of the metabolic machinery may have contributed to the evolutionary success and abundance of Clupeoid fish.

Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research.

Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.

The signals of selective constraints on the mitochondrial non-coding control region: insights from comparative mitogenomics of Clupeoid fishes.

The vertebrate mitochondrial genome is characterized by an exceptional organization evolving towards a reduced size. However, the persistence of a non-coding and highly variable control region is against this evolutionary trend that is explained by the presence of conserved sequence motifs or binding sites for nuclear-organized proteins that regulate mtDNA maintenance and expression. We performed a comparative mitogenomic investigation of the non-coding control region to understand its evolutionary patterns in Clupeoid fishes which are widely distributed across oceans of the world, exhibiting exemplary evolutionary potential. We confirmed the ability of sequence flanking the conserved sequence motifs in the control region to form stable secondary structures. The existence of evolutionarily conserved secondary structures without primary structure conservation suggested the action of selective constraints towards maintaining the secondary structure. The functional secondary structure is maintained by retaining the frequency of discontinuous AT and TG repeats along with compensatory base substitutions in the stem forming regions which can be considered as a selective constraint. The nucleotide polymorphism along the flanking regions of conserved sequence motifs can be explained as errors during the enzymatic replication of secondary structure-forming repeat elements. The evidence for selective constraints on secondary structures emphasizes the role of the control region in mitogenome function. Maintenance of high frequency of discontinuous repeats can be proposed as a model of adaptive evolution against the mutations that break the secondary structure involved in the efficient regulation of mtDNA functions substantiating the efficient functioning of the control region even in a high nucleotide polymorphism environment.

Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus lepturus (Trichiuridae): Insights into Special Characteristics.

Mitochondrial genomes are valuable for making inferences regarding population genetics, phylogenetics and recently in understanding adaptive variation in OXPHOS genes. Ribbon fish, Trichiurus lepturus is distributed in the Indian Ocean and contributes to a major share of pelagic fish landings. Considering the importance, we characterized the complete mitogenome of large head hairtail T. lepturus from Indian waters by PCR amplification and sequencing. The entire mitogenome is 16,840 bp in length, with 13 protein coding genes, 2 subunit ribosomal RNA genes, and 1 control region similar to other vertebrates. Genome contains only 21 tRNAs (tRNAPro is absent) as against 22 tRNAs reported in other vertebrates. The putative origin of L-strand replication (OL) was located in a cluster of five tRNA genes (WANCY region) and may not be functional due to the variation of conserved motif (5'-GCCGG-3') and loop. These two unusual features are common for Trichiurus mitogenomes. Phylogenetic analysis supported the monophyly of Trichiuridae. This study will provide information for further studies on taxonomy, phylogeny and patterns of adaptive evolution in the mitogenome of Trichiurus species.

Influence of weather patterns and air quality on ecological population dynamics of ectoparasites in goats.

Ectoparasitism has a damaging impact on the economy of goat production in India, but the factors influencing its distribution and dynamics are less explored. The present study was designed to investigate the influence of environmental factors like weather and air quality parameters on the occurrence of different types of ectoparasites in goats of two agro-climatic regions of India, viz. the Upper Gangetic Plain (UGP) and the Western Himalayas (WH). The prevalence survey for ectoparasitism among goats was conducted during the four distinct climatic seasons (winter, summer, monsoon, autumn) in both regions. The season-wise data of weather parameters (maximum and minimum temperature, relative humidity in morning and evening, sunrise and sunset time, mean daily temperature and relative humidity, daily variation in temperature and relative humidity, and day length) and air quality parameters (air quality index (AQI), particulate matter 2.5 µm (PM2.5), particulate matter 10 µm (PM10)) of both regions were analyzed in relation with the ectoparasitic prevalence pattern of corresponding regions. The results depict a noticeable correlation between the studied parameters and seasonal variation in the occurrence of each type of ectoparasites. This outcome on the interaction of studied parameters and ectoparasitism is intriguing and it opens a huge scope for future studies on the biometeorological aspects of host-parasite ecological interplay and evolutionary biology. The better understanding of climatological aspects of ectoparasite occurrences helps goat farmers in formulating appropriate timely intervention strategies for the economic control of ectoparasites, which in turn tackles ectoparasiticidal drug resistance and reduces threat of vector-borne diseases.

New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.

Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ±â€¯0.02) and the expected heterozygosity (He = 0.73 ±â€¯0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.

Contemporary and historic patterns of intraspecific diversity in Indian anchovy, Stolephorus indicus, from Indian peninsular waters.

We analyzed intraspecific diversity of Indian anchovy, Stolephorus indicus, a commercially and ecologically important species, using mitochondrial DNA markers so as to derive insights into population structuring and historical demography. Analyses were carried out on 128 and 138 individuals collected from 5 locations along the range of distribution using mitochondrial ATPase (843 bp) and COI (663 bp) sequences respectively. Significant connectivity and gene flow was detected among fishes collected from all the geographic locations as indicated by lack of structuring in Bayesian clustering analysis along with insignificant ΦST values. Oceanographic features of the Bay of Bengal, Arabian Sea and Andaman Sea may be favorable for the dispersal of anchovy larvae and subsequent gene flow. Historical demographic analyses indicated a demographic and spatial expansion taken place approximately during 125,000 years before present, the Pleistocene epoch. Indian Ocean witnessed emergence of upwelling events and consequent increase in productivity during the Pleistocene epoch causing a demographic and spatial expansion of anchovies. Management measures for this species should be devised considering it as a single stock along its entire range of distribution.

Isolation and characterization of Aquaporin 1 (AQP1), sodium/potassium-transporting ATPase subunit alpha-1 (Na/K-ATPase α1), Heat Shock Protein 90 (HSP90), Heat Shock Cognate 71 (HSC71), Osmotic Stress Transcription Factor 1 (OSTF1) and Transcription Factor II B (TFIIB) genes from a euryhaline fish, Etroplus suratensis.

The present study reports the complete sequences of Aquaporin 1 (AQP1) gene and partial sequences of genes, Sodium/potassium-transporting ATPase subunit alpha-1 (Na/K-ATPase α1 subunit), Osmotic Stress Transcription Factor 1 (OSTF1), Transcription Factor II B (TFIIB), Heat Shock Cognate 71 (HSC71) and Heat Shock Protein 90 (HSP90) obtained from mRNA and genomic DNA of Etroplus suratensis. They are candidate genes involved in stress responses of fishes. AQP1 gene was 2163 bp long. Its mRNA sequence has 55 bp 5' UTR, 783 bp open reading frame (ORF), 119 bp 3' UTR, three intronic regions and 90% identity with AQP1 of Oreochromis niloticus. The partial Na/K-ATPase α1subunit gene obtained 5998 bp length with an ORF of 2213 bp and 12 intronic regions. The partial OSTF1, TF IIB, HSC71 and HSP90 mRNA sequences obtained were 1473 bp, 587 bp, 1708 bp and 151 bp in length respectively. All the genes showed a high sequence similarity with respective genes reported from fishes. Comparison of AQP1 and Na/K-ATPase α1 genomic DNA sequence of E. suratensis collected from different water system showed two type of AQP1 with one synonymous mutation in exon-1 and higher sequence difference in intronic regions (including addition, deletion, transition and transversion mutations) with few synonymous and non-synonymous mutations in the exons of Na/K-ATPase α1. The sequence information of these major candidate genes involved in stress responses will help in further studies on population genetics, adaptive variations and genetic improvement programs of this cichlid species having aquaculture, ornamental and evolutionary importance.

Molecular based phylogenetic species recognition in the genus Pampus (Perciformes: Stromateidae) reveals hidden diversity in the Indian Ocean.

Pomfrets (Genus Pampus) are commercially important fishes in the Indo Pacific region. The systematics of this genus is complicated due to morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. The objective of the study was to utilize the mitochondrial COI gene to establish the molecular identity of the silver pomfret distributed in Indian waters and to resolve the phylogenetic relationships among Pampus species in the world based on sequence data in the NCBI database. Seven valid Pampus species are identified in this study. The mean genetic divergence value calculated between clades representing these species was 7.9%. The mean genetic distance between the so-called Pampus argenteus from Indian waters and sequences attributed to P. argenteus from the South China Sea, where the neotype of this species was collected, was found to be greater than 12%, strongly supporting the likelihood of the Indian species being distinct. The Indian Pampus species show very close affinity to P. cinereus, with inter species differences less than 2%. The taxonomic identity of the silver pomfret in India is also discussed here, in light of molecular and morphological evidence.

Th1/Th2 immune responses and oxidative stress in caprine flea allergy dermatitis.

Flea allergy dermatitis (FAD) is the common, often neglected skin disease of goats caused mainly by Ctenocephalides felis. This study aimed to evaluate the immuno-oxidative pathobiology of FAD in goats. Twelve goats from the same herd were divided into two groups of six animals each. The group I (FAD) included animals with natural flea infestation and severe dermatitis lesions. The group II (Healthy control) animals were free from any parasitic infestation. To assess the pathological changes, the markers of oxidative stress (lipid peroxidation, reduced glutathione and total antioxidant capacity), and immune status (Tumour necrosis factor alpha, Interleukin 10, Transforming growth factor beta 1 and Th1/Th2 cytokine ratio) were evaluated from the blood and the serum samples. Remarkable oxidative stress and severe inflammatory response with Th2 cytokine dominance were observed in flea infested animals. Highly antigenic agents of fleas, either secretory or excretory or structural, induced severe inflammatory responses and significant oxidative stress in caprine FAD. Massive release of cytokines may be responsible for severe skin inflammation and lesions in FAD in contrast to other Th2 dominant ectoparasitic skin conditions of goats'.

Oral neoplasms in pickhandle barracuda Sphyraena jello from India.

We report the spontaneous occurrence of oral neoplasms in pickhandle barracuda Sphyraena jello Cuvier, 1829 from Parangipettai, on the southeast coast of India. A total of 11736 fish were examined, of which 43 were affected with oral tumours, with an overall prevalence of 0.37%. Gross and clinical symptoms included reddish to grayish-white distended tumourous growths on the gingiva, intra-oral bones and tongue. The tumours exhibited delayed eruption and intra- or extra-oral swelling, varied in consistency from extremely firm to fleshy and released mucinous material. The majority of tumours consisted of numerous clumped toothlets, but some included hardened tissues. Local area invasion/transmission was observed in most cases; however, necropsy examination revealed no gross evidence of distant metastasis into visceral organs. Radiographic examination of compound odontomas revealed distinct unilocular radio-opaque mini-toothlets surrounded by defined radiolucency, whereas complex odontomas exhibited unilocular and indistinct radio-opaque masses within a much more extensive radiolucent zone. Histopathologically, the intra-oral tumour lesions were characterized by numerous imperfect (germ) toothlets consisting of a disorganized combination of dental tissues: pulp tissues with manifested and predominantly mixed hard dental tissues of immature dentine and enamel, numerous small to large and round to polyhedral ossicles embedded in hypocellular fibrous stromal tissues and sparsely spaced bland spindloid cells with cleft-like spaces of loose mucoid stroma. Histochemically, the neoplastic lesions stained positive for periodic acid-Schiff and Masson's trichrome. Based on the clinical and histological findings, the tumours were diagnosed as compound odontomas, complex odontomas, odontogenic myxomas, lingual myxomas and psammomatoid ossifying fibromas.

Histological profiling of gonads depicting protandrous hermaphroditism in Eleutheronema tetradactylum.

The fourfinger threadfin Eleutheronema tetradactylum is reported as a protandrous hermaphrodite from Australian waters, while being a gonochorist in reports from Singapore and India, with a single report of protandrous hermaphroditism from the latter. Histological analysis of gonads of fish from Indian waters confirms protandrous hermaphroditism in E. tetradactylum. The study was based on 480 fish examined from eight locations along the Indian coast. Mean total length (LT ) of male fish was 240 mm with the transition to female starting from 280 mm LT . Specimens confirmed as mature females were >380 mm LT .

Immunomodulatory basis of antioxidant therapy and its future prospects: an appraisal.

Antioxidants are agents which can modulate oxidant-antioxidant profile of body system by neutralizing pro-oxidant molecules. The current scientific knowledge on mechanisms of antioxidant activity of biomolecules was critically reviewed with a special emphasis on immunomodulation. The immuno-oxidative wreckage of animals in various disease conditions and the role of biomodulators in curbing the oxidative stress through immune pathways were analyzed. The critical role of immunomodulatory mechanisms in controlling oxidative damage was identified. Selection of antioxidant therapy considering the immunopharmacology of the drug as well as immunological basis of disease may reduce treatment failure and adverse health effects. Hence, it is suggested that future studies on antioxidants may focus on the immuno-oxidative pathobiology to better understand its clinical effects and effective disease management.

Adenoviral vector encoding soluble Flt-1 engineered human endometrial mesenchymal stem cells effectively regress endometriotic lesions in NOD/SCID mice.

This study was undertaken to study the efficiency of Adsflt-1 engineered human eutopic mesenchymal stem cells (MSCs) secreting anti-angiogenic sFlt-1 as a targeted cell-based therapy for endometriosis (EM). Eutopic MSCs were transduced with Adsflt-1/AdV0 viral vectors and were evaluated for expression and secretion of sFlt-1. EM was created in NOD/SCID mice using subcutaneous implantation techniques. Four doses of 10(6) MSC-Adsflt-1/MSC-AdV0 were administered to the model and therapeutic anti-angiogenic ability was analyzed by lesion size measurement, microvessel density, immunohistochemistry and real-time reverse transcriptase-PCR analysis. Approximately 86% of transduced MSCs expressed and secreted sFlt-1. MSC-Adsflt-1-treated animals exhibited significant reduction (52.8±1.8%) in size of endometriotic lesions. We observed a 2.3-fold decrease in the number and a 10-fold decrease in the size of endometrial glands in MSC-Adsflt-1-treated animals. A two-fold decrease in stromal cell densities was also observed in MSC-Adsflt-1-treated animals compared with the MSC-AdV0 group. Specific positive immunostaining for MSC marker, CD146 and sFlt-1 in the lesion sites of the MSC-Adsflt-1 group suggests possible homing of transduced MSCs, their survival and secretion of sFlt-1 at the target sites. A marked reduction in size of microvessels and microvessel density within endometriotic lesions and surrounding host subcutaneous layers was observed in MSC-Adsflt-1 group along with significantly downregulated expression of transcripts for vascular endothelial growth factor, fetal liver kinase 1 and matrix metalloproteinases (2 and 9). Our findings indicate the efficacy of a novel eutopic MSC-Adsflt-1 therapy in EM study models. Evaluating long-term effects of genetically modified MSCs in vivo is essential in translating MSC-Adsflt-1 therapy to the clinics.