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The most tedious and hectic job is to identify the tiny benthic animals by spending thousands of hour under the microscope, since all the fauna need to be counted, sorted, picked and permanently mounted on glass slides for taxonomic identification. All faunal identifications need a lot of preprocessing and it consumes a lot of time to identify a single specimen. Therefore, to reduce the complexity of many such procedures, combined with the desire to identify larger datasets, we came up with new software based on artificial intelligence which can automatically identify the benthic fauna through the microscopic images. In this paper, we propose a machine learning method for automatic visual identification through the images of the benthic fauna. To this end, we propose a neural network model, where we demonstrate that the proposed approach differentiates the fauna based on images. However, it works well with vast amounts of image data and significant computational resources.

Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explicates the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with ENC 50) possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus. The non-significant MELP and ENC correlation analysis suggested that expression of genes might not be associated with CUB. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping CUB. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all three species. In addition, the role of CUB regarding the predilection of fungal pathogens Aspergillus fumigatus and Fusarium oxysporum towards host plant C. sativus has also been expounded. We found a similar trend of codon usage pattern operative in plant and fungal pathogens as both the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus. Overall, different CUB indices reflected a weak codon bias in the C. sativus, F. oxysporum and A. fumigatus genome.

Bioinformatic approaches were utilized to investigate the pattern of codon usage in 109 epilepsy-related genes. The genes were found to be rich in G and C nucleotides, with GC usage 7% higher than AT. Preferred codon analysis confirmed the dominance of G and C at the wobble position of codons. CAG is the most frequently used codon. The ENc analysis, on the other hand, did not reveal any exceptional codon usage bias. Correlation of GC content at the first and second codon positions with the third codon position (neutrality plot) suggested the impact of selection pressure in shaping the GC enriched compositional pattern observed in epilepsy-related genes. It was further confirmed by correspondence analysis. Altogether, our findings imply that the pattern of evolutionary processes (especially selection pressure) operating on epilepsy-related genes. This might aid in identifying disease genes compositional signatures and deciphering the genetic mechanisms underlying epilepsy. Further this information would be useful in facilitating the existing epilepsy related therapies like gene therapy, cell therapy etc.

Plantagos are important economical and medicinal plants that possess several bioactive secondary metabolites, such as phenolics, iridoids, triterpenes, and alkaloids. Triterpenoids are the ubiquitous and dynamic secondary metabolites that are deployed by plants for chemical interactions and protection under biotic/abiotic stress. Plantago ovata, a cultivated species, is the source of psyllium, while Plantago major, a wild species, has significant therapeutic potential. Wild species are considered more tolerant to stressful conditions in comparison to their cultivated allies. In view of this, the present study aimed to decipher the terpenoid biosynthetic pathway operative in P. ovata and P. major using a comparative transcriptomics approach. Majority of terpenoid biosynthetic genes were observed as upregulated in P. major including rate limiting genes of MVA (HMGR) and MEP (DXR) pathways and genes (α-AS, BAS, SM, and CYP716) involved in ursolic acid biosynthesis, an important triterpenoid prevalent in Plantago species. The HPLC output further confirmed the higher concentration of ursolic acid in P. major as compared to P. ovata leaf samples, respectively. In addition to terpenoid biosynthesis, KEGG annotation revealed the involvement of differentially expressed unigenes in several metabolic pathways, aminoacyl-tRNA biosynthesis, biosynthesis of antibiotics, and biosynthesis of secondary metabolites. MYB was found as the most abundant transcription factor family in Plantago transcriptome. We have been able to generate valuable information which can help in improving terpenoid production in Plantago. Additionally, the present study has laid a strong foundation for deciphering other important metabolic pathways in Plantago.

Codon usage bias influences the genetic features prevalent in genomes of all the organisms. It also plays a crucial role in establishing the host-pathogen relationship. The present study elucidates the role of codon usage pattern regarding the predilection of fungal pathogens Aspergillus flavus, Aspergillus niger, Fusarium oxysporum and Colletotrichum gloeosporioides towards host plant Zingiber officinale. We found a similar trend of codon usage pattern operative in plant and fungal pathogens. This concurrence might be attributed for the colonization of fungal pathogens in Z. officinale. The transcriptome of both plant and pathogens showed bias towards GC-ending codons. Natural selection and mutational pressure seem to be accountable for shaping the codon usage pattern of host and pathogen. We also identified some distinctive preferred codons in A. flavus, F. oxysporum and Z. officinale that could be regarded as signature codons for the identification of these organisms. Knowledge of favored, avoided and unique codons will help to devise strategies for reducing spice losses due to fungal pathogens.

The present study entails the usefulness of thermophilic amidase-producing bacterium in the biotransformation of benzamide to benzohydroxamic acid (BHA). A bacterium Bacillus smithii IIIMB2907 was isolated from a soil sample collected from hot springs of Manikaran, Himachal Pradesh, India. The whole cells of the bacterium displayed versatile substrate specificity by exhibiting significant activity with a diverse range of amides. In addition, amidase from thermophilic bacterium was induced by adding Ɛ-caprolactam in the mineral base media. The optimum temperature and pH of acyltransferase activity of amidase enzyme were found to be 50 °C and 7.0, respectively. Interestingly, half-life (t(1/2)) of this enzyme was 17.37 h at 50 °C. Bench-scale production and purification of BHA was carried out at optimized conditions which resulted in the recovery of 64% BHA with a purity of 96%. Owing to this, the reported process in the present study can be considered of immense industrial significance for the production of BHA. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03109-2.

Circular RNAs (circRNAs) are endogenous RNA formed by the back splicing process. They are ubiquitous, stable, evolutionally conserved, and are tissue-specific. The biochemical and molecular features of circRNAs hold the potential to be used as biomarkers in various diseases to achieve pharmacological goals. CircRNAs have numerous latent modes of action, from acting as sponges for microRNAs and RNA binding proteins to serve as transcriptional regulators, epigenetic alterations, etc. Dysregulated functioning of several circular RNAs lead to the progression of a plethora of diseases. Due to their extremely stable nature and amazing tissue specificity, circRNAs have paved the way for advanced clinical studies as a novel method of early disease detection and treatment efficacy. Therefore, they have been recognized as a latent diagnostic biomarker for neurodegenerative diseases, diabetes, osteoarthritis, and cardiovascular diseases.

Technological advances have led to an increase in the number of investigations in the deep sea over the last two decades. However, despite a large number of scientific cruises, few published data on the nematode biodiversity and community structure are available from the abyssal nodule fields of the Central Indian Ocean Basin (CIOB). It is well known that CIOB harbors one of the largest high-grade nodule reservoirs and has therefore gained the most attention from industries and governments. Therefore, to adequately assess the potential environmental impacts of deep-sea polymetallic nodule mining in CIOB, more quantitative samples are needed to better understand trends in nematode diversity, abundance, and community structure in the nodule fields. Recently, on the basis of detailed surveys and analysis, a Test Mine Site (TMS) and Reference Mining Site (TRS) have been identified within the First Generation Mine Site (FGM) for further detailed studies. According to ISA guidelines, the TMS and TRS need to be similar in faunal abundance, composition and diversity, nodule abundances, metal grade and environmental data. As per the deep-sea environment conservation point of view, particularly to plan mining operations, the study has been done to check whether TMS and TRS have a similar type of faunal assemblage so that impacts and the ensuing loss of biota are minimized. To address this, we compared the composition and distribution of nematode communities at genus/species level from TMS and TRS. The average nematode density ranged from 71.68 ± 1.7 inds/10 cm2 in the TRS and 91.23 ± 1.3 inds/10 cm2 in the TMS. A total of 63 nematode genera belonging to 24 families were identified from TMS. The TRS samples supported 52 genera belonging to 20 families. A homogeneous community was observed at family/genus level from the TMS and TRS, particularly dominated by cosmopolitan nematode genera like Acantholaimus, Halalaimus, Thalasomonhystera and Leptolaimus. The TRS and TMS samples did exhibit a similar evenness (J'), and diversity (H’) suggesting a homogeneous nematode community throughout the area. Taxon diversity and richness estimators revealed that the current sampling design was able to characterize the majority of the nematode genera present. It can be suggested that the entire area of sampling is inhabited by a single, uniformly distributed, nematode assemblage at the genus level. This study also addresses whether or not nematode assemblages at genus/ species level inhabiting the bare sediment (soft sediment without nodules) in abyssal nodule fields are unique and differ from those found in the crevices of polymetallic nodules. As expected, there were fewer numbers of total genera recorded from the crevices with the differences being found in the dominant genera and families. Thalassomonhystera, Acantholaimus and Desmoscolex were noted as characteristic of the bare sediment while Leptolaimus and Camacolaimus showed the highest likelihood in nodule crevices. Hard nodule crevice substratum does favor some species level morphotypes of the genus Leptolaimus and Camacolaimus since these morphotypes were found exclusively in nodule crevices. However, owing to the still limited sampling effort in the deep sea, it is premature to suggest that these species are endemic to nodules. Implications of the present findings for environmental management and future research needs are provided.

Meloidogyne incognita (Root-knot nematode) and Alternaria alternata (fungus) were among the dominant parasites of the medicinal plant Withania somnifera. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation is lacking. The present study elucidates evolutionary and codon usage bias analysis of W. somnifera (host plant), M. incognita (root-knot nematode) and A. alternata (fungal parasite). The results of the present study revealed a weak codon usage bias prevalent in all the three organisms. Based on the nucleotide analysis, genome of W. somnifera and M. incognita was found to be A-T biased while A. alternata had GC biased genome. We found high similarity of CUB pattern between host and its nematode pathogen as compared to the fungal pathogen. Inclusively, both the evolutionary forces influenced the CUB in host and its associated pathogens. However, neutrality plot indicated the pervasiveness of natural selection on CUB of the host and its pathogens. Correspondence analysis revealed the dominant effect of mutation on CUB of W. somnifera and M. incognita while natural selection was the main force affecting CUB of A. alternata. Taken together the present study would provide some prolific insight into the role of codon usage bias in the adaptability of pathogens to the host’s environment for establishing parasitic relationship.

Codon usage bias influences the genetic features prevalent in genomes of all the organisms. It also plays a crucial role in establishing the host-pathogen relationship. The present study elucidates the role of codon usage pattern regarding the predilection of fungal pathogens Aspergillus flavus, Aspergillus niger, Fusarium oxysporum and Colletotrichum gloeosporioides towards host plant Zingiber officinale. We found a similar trend of codon usage pattern operative in plant and fungal pathogens. This concurrence might be attributed for the colonization of fungal pathogens in Z. officinale. The transcriptome of both plant and pathogens showed bias towards GC-ending codons. Natural selection and mutational pressure seem to be accountable for shaping the codon usage pattern of host and pathogen. We also identified some distinctive preferred codons in A. flavus, F. oxysporum and Z. officinale that could be regarded as signature codons for the identification of these organisms. Knowledge of favored, avoided and unique codons will help to devise strategies for reducing spice losses due to fungal pathogens.

Plantagos are important economical and medicinal plants that possess several bioactive secondary metabolites, such as phenolics, iridoids, triterpenes, and alkaloids. Triterpenoids are the ubiquitous and dynamic secondary metabolites that are deployed by plants for chemical interactions and protection under biotic/abiotic stress. Plantago ovata, a cultivated species, is the source of psyllium, while Plantago major, a wild species, has significant therapeutic potential. Wild species are considered more tolerant to stressful conditions in comparison to their cultivated allies. In view of this, the present study aimed to decipher the terpenoid biosynthetic pathway operative in P. ovata and P. major using a comparative transcriptomics approach. Majority of terpenoid biosynthetic genes were observed as upregulated in P. major including rate limiting genes of MVA (HMGR) and MEP (DXR) pathways and genes (α-AS, BAS, SM, and CYP716) involved in ursolic acid biosynthesis, an important triterpenoid prevalent in Plantago species. The HPLC output further confirmed the higher concentration of ursolic acid in P. major as compared to P. ovata leaf samples, respectively. In addition to terpenoid biosynthesis, KEGG annotation revealed the involvement of differentially expressed unigenes in several metabolic pathways, aminoacyl-tRNA biosynthesis, biosynthesis of antibiotics, and biosynthesis of secondary metabolites. MYB was found as the most abundant transcription factor family in Plantago transcriptome. We have been able to generate valuable information which can help in improving terpenoid production in Plantago. Additionally, the present study has laid a strong foundation for deciphering other important metabolic pathways in Plantago.

The biased usage of nucleotides in coding sequence and its correlation with gene expression has been observed in several studies. A complex set of interactions between genes and other components of the expression system determine the amount of proteins produced from coding sequences. It is known that the elongation rate of polypeptide chain is affected by both codon usage bias and specific amino acid compositional constraints. Therefore, it is of interest to review local DNA-sequence elements and other positional as well as combinatorial constraints that play significant role in gene expression.

The spread of COVID-19 is a global concern that has taken a toll on entire human health. Researchers across the globe has been working in devising the strategies to combat this dreadful disease. Studies focused on genetic variability helps design effective drugs and vaccines. Considering this, the present study entails the information regarding the genome-wide mutations detected in the 108 SARS CoV-2 genomes worldwide. We identified a few hypervariable regions localized in orf1ab, spike, and nucleocapsid gene. These nucleotide polymorphisms demonstrated their effect on both codon usage as well as amino acid usage pattern. Altogether the present study provides valuable information that would be helpful to ongoing research on 2019-nCoV vaccine development.

Codon usage bias (CUB) is a species-specific phenomenon where some codons are used more commonly than their synonymous partners. It helps to understand the effect of recombination on the evolution of genomes, gene discovery, transgene design and much more. Here, we have analyzed the nucleotide composition and CUB of Ancylostoma ceylanicum protein-coding sequences. Genes are AT-biased and have a narrow GC3 distribution. Analysis of parity rule 2 indicates mutation pressure while analysis of neutrality plot confirms the influence of both the evolutionary factors on codon usage pattern. Codon context analysis revealed the skewed use of certain homologous codon pairs. The lower values of codon usage bias that are acquired as a result of mutation and selection pressure may be involved in higher transcriptional adaptation for living in diverse host conditions.

This study addresses whether or not nematode assemblages inhabiting the soft sediment in abyssal nodule fields are unique and differ from those occurring in the nodule-free abyssal areas. This question is important for the evaluation of possible diversity losses caused by nodule mining operations. The analysis involved seven datasets at genus-level of nematode assemblages from three nodule-bearing abyssal areas in the Pacific (the Clarion-Clipperton Fracture Zone or CCFZ, and the Peru Basin) and the Indian Ocean (CIOB), and five datasets from nodule-free abyssal regions (the Atlantic Ocean). Only individuals identified to valid genera were used in the analysis. Overall, more than 20,000 nematode individuals from 90 samples were analysed. The analyses showed that the nematode communities in the nodule fields did differ from those in the nodule-free abyss. The nodule fields are characterized by a higher microhabitat heterogeneity, which resulted in a higher diversity of nematode communities inhabiting the nodule fields. However, one set of dominant taxa (Monhysteridae, Microlaimus, Acantholaimus, Theristus and Desmoscolex) was identical for both the nodule-bearing and nodule-free abyss, although some genera were strongly and significantly associated with either the nodule-free abyss (Microlaimus) or the nodule-bearing abyssal regions (Capsula). On the other hand, nematode assemblages at nodule-bearing and nodule-free sites within the nodule-bearing abyss proved to be similar at the genus level. This makes it possible for the nodule-free sites to serve as donors of colonizers for the mining-impacted nodule-bearing abyss. However, this suggestion has to be treated with caution, because the species-level differences have not been tested yet.

Commercial-scale mining for polymetallic nodules could have a major impact on the deep-sea environment, but the effects of these mining activities on deep-sea ecosystems are very poorly known. The first commercial test mining for polymetallic nodules was carried out in 1970. Since then a number of small-scale commercial test mining or scientific disturbance studies have been carried out. Here we evaluate changes in faunal densities and diversity of benthic communities measured in response to these 11 simulated or test nodule mining disturbances using meta-analysis techniques. We find that impacts are often severe immediately after mining, with major negative changes in density and diversity of most groups occurring. However, in some cases, the mobile fauna and small-sized fauna experienced less negative impacts over the longer term. At seven sites in the Pacific, multiple surveys assessed recovery in fauna over periods of up to 26 years. Almost all studies show some recovery in faunal density and diversity for meiofauna and mobile megafauna, often within one year. However, very few faunal groups return to baseline or control conditions after two decades. The effects of polymetallic nodule mining are likely to be long term. Our analyses show considerable negative biological effects of seafloor nodule mining, even at the small scale of test mining experiments, although there is variation in sensitivity amongst organisms of different sizes and functional groups, which have important implications for ecosystem responses. Unfortunately, many past studies have limitations that reduce their effectiveness in determining responses. We provide recommendations to improve future mining impact test studies. Further research to assess the effects of test-mining activities will inform ways to improve mining practices and guide effective environmental management of mining activities.

Patterns of macrofaunal distribution were studied along the western Indian continental margin to distinguish the role of habitat heterogeneity in generating and maintaining community structure. A transect perpendicular to the coast at 14°N latitude was selected for seabed sampling. Eight stations were sampled in the depth range 34–2546 m and characterized with respect to macrofaunal composition, abundance, biomass, diversity and feeding type. The sediments in the shelf region (34, 48, 100 m) and upper slope (525 m) were characterized by silty and sandy facies, whereas the mid slope (1001 m), lower slope (1524 m) and basin (2001, 2546 m) consisted of clayey silts. The highest value of sediment chlorophyll-a (Chl-a) and total organic carbon (Corg) were recorded from the mid slope areas. Faunal abundance and biomass increased from the shallow to deeper depths in the shelf region, and decreased in the slope region (525–1001 m) due to the reduced bottom-water oxygen. The community parameters showed an overall increase in both the lower slope and basin areas. A total of 81 macro-invertebrate species belonging to five major groups represented the macrofauna of the area. Polychaeta was the major group at all depths. Among polychaete families, species of the Spionidae, particularly Prionospio pinnata, predominated at the oxygen minimum zone (OMZ) core and Cossuridae dominated in the lower part of the OMZ in sediments of the mid slope region (1001 m depth). Species diversity was higher in the basin than in the slope region. Fluctuations in diversity appear to be partly due to the bottom-water dissolved oxygen (DO) gradient which includes values that are below the oxygen tolerance of many benthic species. Further, Margalef’s index (d) and Shannon–Wiener index (H′) showed a significant negative (P

The Central Indian Ocean Basin (CIOB) is an important area for prospective mining for polymetallic nodules. However, little is known about the biodiversity or community structure of abyssal benthic assemblages in the area. The aim of this study was to investigate nematode assemblages inhabiting nodule fields in the CIOB in terms of species composition, diversity, density, biomass, size spectra and sex ratio. Samples were collected by box corer from a depth of 5000–5100 m during the 39th cruise of RV Akademik Boris Petrov in 2009. In total, 1066 individuals were examined from 4 stations and 16 samples. The total average density of nematodes recorded in the CIOB was considerably lower than reported from other deep-sea regions (27.17 ± 2.7 inds/10 cm2). Nematode diversity was comparable with that of other deep-sea regions and the composition of the dominant taxa was typical for oceanic basins. A total of 284 morphotypes belonging to 113 genera and 30 families were identified. Chromadoridae (29.6%), Xyalidae (19.3%), Oxystominidae (6.6%) and Desmoscolecidae (5.0%) were the dominant families. Among the genera, Acantholaimus (23.2%), Halalaimus (5.7%), Desmoscolex (4.8%), Theristus (3.5%) and Daptonema (3.4%) were the most numerous. The majority of specimens had a body length in the range of 1000–1500 µm, which is also in accordance with other deep-sea studies. Females were three times more abundant than males at all CIOB stations. Average total nematode biomass (52.39 ± 10.0 mg/m2) was comparable with macrofauna biomass from the same area.

Life history of a free-living meiobenthic nematode Daptonema normandicum (DeMan, 1890) was studied in the laboratory. Live specimens were primarily collected from the sewage outlet site near the mouth of the Mandovi estuary, Goa This species was the most dominant (67%) among the meiobenthic nematodes. Vertically, nematode abundance was highest at the surface sediment and correlated with the organic carbon and sediment chlorophyll-a. Considering their dominance in the meiofauna, attempts were made to rear D. normandicum in laboratory. Salinity of the culture medium was maintained at 14 to 17 PSU (same as the collection site). All the culture experiments were conducted in semisolid nutrient agar media at 27 +/- 2 degrees C temperature for 12 hr dark: 12 hr light conditions. The food consists primarily of an unidentified bacterium and mixed algae, but diatom and ciliates were also observed in culture. Females produced first batch of eggs at the age of 23 days. Gravid female normally carry 8-10 eggs. Embryonic development is completed in -72 hr and entire life cycle (egg to adult) was completed in 22-24 days. Average size of juveniles at the hatching was 0.189 mm. Young individuals attains a maximum size of 1.23 mm (male) and 1.04 mm (female) in -21-23 days. Growth, in terms of length was augmented upto 23rd day and ceased thereafter. The daily growth increment for the first 5 days was 0.01-0.04 mm which increased upto 0.05-0.08 mm d(-1) during the maturation (10-18 days). Male : female ratio was 1:2. In this laboratory study, we provided information on the embryonic development, the life cycle and ecology Our results demonstrated that D. normandicum can be reared successfully under the controlled conditions, suggesting possible use of this species in toxicological and aquaculture studies. The culture method described is very handy and can be applicable for rearing other meiobenthic species particularly the nematodes with comparable feeding habits.

Suctorian epibionts Thecacineta calix attached on the cuticle of nematodes Desmodora sphaerica and D. pontica are reported here from the deep-sea hexactinellid sponge Pheronema sp. from the Andaman Sea (Indian Ocean). The epibiont T. calix is reported here for first time from the Andaman Sea.