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A distinct mechanism of generating metagenome is metagenomics which includes sequencing the whole DNA extracted from an environmental sample, mapping it to a reference database followed by gene annotation. Advancement in sequence-based metagenomics has significantly reduced processing costs and has acquired a rapid pace. Metagenomics has been crucial in investigating “hidden” genetic characteristics and construction biotechnological processes through the discovery of novel genes, enzymes, pathways and bioactive molecules with entirely different or improved biochemical functions. Metagenomics is a fairly recent addition to the molecular toolbox and is the simplest, impartial way of challenging the adaptive ability of microbial populations. Metagenomics is beneficial in recognising the complex consortium of bacteria, protozoa, archaea, fungi, etc. and association amongst them resulting in higher feed utilization and productivity of animals. It allows formulating probiotics feed materials, as well as in immunomodulation in both livestock and poultry. This review emphasizes significant recent achievements in metagenomics, offers insights into the possibilities, modern-day challenges and its utility in livestock and poultry.

The lockdowns imposed to contain the COVID-19 spread had an indisputably cascading effect on the aquaculture industry across the globe. It has adversely impacted the Indian fisheries sector through changing purchaser demand, supply chain disruptions, trade restrictions, and also the livelihood of millions dependent on it. However, the consequential reduced fishing will also likely help in replenishment of the aquatic biodiversity and provide the balance needed in the long-term sustenance of the fisheries sector. The technological and policy interventions in pre- and post-harvest fisheries operations are anticipated to reduce some of these negative impacts in similar lockdown scenarios. [ABSTRACT FROM AUTHOR] Copyright of Current Science (00113891) is the property of Indian Academy of Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Climate change and pollution are the most vulnerable stressors that are anticipated increasingly to affect all living organisms including fishes. The aquatic ecosystems are the most affected ecosystem due to contamination and global increasing temperature. In view of the above, the present study delineates 96-h median lethal concentration of heavy metal, lead alone and in combination with high temperature (34 °C) by conducting static non-renewable acute toxicity bioassay in Pangasius hypophthalmus (average weight 3.65 ± 0.75 g). Further, the effect of different definitive doses (80, 82, 84, 86, 88 and 90 mg/L) of lead alone and high temperature on cellular metabolic response was probed. The LC50 of lead was found to be 84.93 mg/L, whereas in combination with high temperature it was 83.10 mg/L in P. hypophthalmus. Catalase, superoxide dismutase and glutathione-S-transferase were noticeably higher (p

Stress is the result of an organism's interaction with environmental challenges. Regulations of gene expression including translation modulations are critical for adaptation and survival under stress. Untranslated regions (UTRs) of the transcripts play significant roles in translation regulation and continue to raise many intriguing questions in our understanding of cellular stress physiology. IRES (Internal ribosome entry site) and uORF (upstream open reading frame) mediated alternative translation initiations are emerging as unique mechanisms. Recent studies have revealed novel means of mRNAs stabilization in stress granules and their reversible modifications. Differential regulation of select transcripts is possible by the interplay between the adenine/uridine-rich elements (AREs) in 3'UTR with their binding proteins (AUBP) and by microRNA-mediated effects. Coordination of these various mechanisms control translation and thereby enables appropriate responses to environmental stress. In this review, we focus on the role of sequence signatures both at 5' and 3'UTRs in translation reprogramming during cellular stress responses.

To establish normal values of blood biochemical indices for different indigenous local donkey population available in various agro-climatic zones, blood samples were collected from 233 adult and apparently healthy donkeys. The samples were analysed for metabolites (albumin, total serum protein, direct bilirubin, total bilirubin, cholesterol, HDL cholesterol, urea, uric acid, triglyceride, creatinine) and minerals (calcium, phosphorus) to evaluate significant difference within and between populations. Confidence limit of each biochemical indices showed a close range as compared to their actual range observed under varied geographic areas. All the metabolites and minerals showed significant variations in their levels within and between donkey populations which could possibly be due to the differences in the nutritional status of donkeys, their managemental aspects and biochemical metabolism. In agro-climatic zone 1 (Spiti and Leh areas), having low vegetation cover with poor nutritious grasses for a limited period, levels of most of the biochemical profiles in donkey populations belonging to these areas were significantly lower than those in other zones (VI, IX, XII, XIV). This study indicated that normal biochemical values of different indices for a particular population should not be used as such for disease prognosis, diagnosis and therapeutic monitoring of other donkey population belonging to other agro-climatic zone having different nutritional and managemental practices.

In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.

The aim of this work was to define the bioaccumulation mechanism of metals onto the non-living biomaterial prepared from an extensively available plant bark biomass of neem (Azadirachta indica). Based on maximum ultimate fixation capacities (mmol/g) of the product, metals ions could be arranged as Hg(2+) < Cd(2+) < Pb(2+) ≅ Cu(2+). Surface properties of the biomaterial were characterized by X-ray photoelectron spectroscopy and X-ray diffraction techniques for their sorption mechanism. Whewellite (C2CaO4 · H2O) was identified in the biomaterial, which indicated that calcium ions are electrovalently bonded with carboxylate ions facilitating the ion exchange mechanism with metal ions. Bioaccumulation of metal ions was also studied by Fourier transform infrared spectroscopy, which indicated the presence of functional groups implicated in adsorbing metal ions. Biomaterial did not adsorb anionic As(III), As(V) and Cr(VI), because of their electrostatic repulsion with carboxylic functional groups. Neem bark can be used as bioindicators, bioaccumulators and biomonitors while determining environmental pressures. Metal bioaccumulative properties and structural investigation of plant bark has potential in providing quantitative information on the metal contamination in the surrounding environment.

The authors have reported the use of nanopolymers for the inhibition of shrimp pathogenic bacteria for aquaculture use. The antimicrobial activity of polyethylene glycols based amphiphilic polymers have different linker molecules such as suberic acid, adipic acid, glutaric acid and dimethyl-5-hydroxyisophthalate on Vibrio harveyi. It was examined by drawing growth curves using optical density measurements. Concentration dependent antimicrobial effects of nanopolymers were tested against V. harveyi which were further confirmed by agar well diffusion for determining minimum inhibitory concentra- tions. The increased concentrations of nanopolymer ef- fectively reduced the bacterial growth and increased the diameter of inhibition zone. This study has important im- plications for disease management in coastal aquaculture.

Donkeys support rural livelihoods and low-income farmer’s family by providing economy at minimal maintenance cost. In India, donkeys constitute about 28% of total equine population but these are non-descript local donkeys without any breed characterization. This study describes phenotypic diversity among different donkey populations available in various agro-climatic regions in India including Gujarat, Rajasthan, Maharashtra, J&K, Haryana, Bihar and Himachal Pradesh for their phenotypic clustering as a distinct breed(s) by considering each population as a separate cluster. Biometric indices of seven local donkey populations were recorded and compared to French Poitou donkey breed which revealed that average body length of donkeys from Spiti, Gujarat, Rajasthan, Baramati, Bihar, Haryana and Leh areas was 97.09, 101.18, 97.60, 103.68, 96.31, 109 & 95.76 cm, respectively, while Poitou donkeys had significantly higher length (138.79 cm) than indigenous donkey populations. Further height at wither revealed that except leh donkey population, the rest of the donkeys prevalent throughout different agro-climatic regions met a “small standard’ pattern. Donkey populations from Leh were fitted in ‘Miniature’ donkey pattern. All local donkeys were well adapted to their agroclimatic environment and ecology as they were totally dependent upon the grass cover and roughages available within their reach for meeting their nutritional requirement. Coat colour varied across different regions. Black and brown colours were prevalent in donkeys from cold desert regions including Leh and Spiti region. Face length of donkeys from Spiti, Gujarat and Baramati were at par with each other while donkeys from Leh had smallest face length. Cluster analysis based on biometric indices revealed that exotic Poitou donkeys is an out-group as it formed a distinct cluster while Indigenous donkeys belonging to various agro-climatic zones were grouped in three clusters namely, C1-miniature or near miniature donkeys (Leh, Spiti and Bihar regions), C2- small standard ones including donkeys from Rajasthan and Gujarat while cluster C3 having donkeys from Baramati and Haryana region. Poitou cluster was phenotypically different from Cluster 1 as Eucledean cluster distance was maximum with donkeys of this cluster, followed by cluster 2 and cluster 3. This information will be useful for breed classification of these local non-descript donkeys.

Heat shock proteins (Hsp) play crucial role in cellular thermotolerance and heat stress response. In the present work, Allele specific PCR (AS-PCR) was standardized to detect the nucleotide polymorphism within the HSP90AB1 gene (SNP g.4338TC) in Indian breeds of dairy cattle. The identified genotypes were associated with relative thermotolerance in terms of physiological parameters and milk production traits. The results of the experiments revealed that the genotype frequency of CC, CT, and TT for Sahiwal were 0.05, 0.78, and 0.17, respectively, and in Frieswal, the frequencies were 0.20, 0.70, and 0.10, respectively. The average rectal temperature (ART) and average respiration rates (ARR) were recorded during peak summer stress and heat tolerance coefficient (HTC) was calculated. The association studies indicated that TT genotypes had significantly (P0.01) higher HTC and lower ARR values than CT and CC in both the breeds. The TT genotype animals also had better production parameter in terms of total milk yield (TMY) (P0.01). These findings may partly suggest the role of HSP90AB1 polymorphisms in the regulation of heat stress response and consequent effect on production traits. Nevertheless, involvement of other regulatory mechanisms cannot be overruled.

Determination of early life stages of fish for thermal tolerance, optimum temperature for growth, rate of oxygen consumption is becoming essential for aquaculture industry in the climate change scenario due to long-term and short term (seasonal and diurnal) variability in temperature. Emphasis was made to understand the response of early of rohu (0.09 to 0.1 g) to thermal acclimation. Three hundred early fry stage rohu, Labeo rohita (initial weight 0.097±0.01 g) were equally distributed at four different temperatures (28, 30, 32 and 34°C) each with three replicates for a period of 40 days. Highest body weight gain was between 30 and 32°C and lowest feed conversion ratio (FCR) was at 30°C. The percentage weight gain and specific growth rate at 30°C were 382±8.01 and 0.88±0.03% respectively, significantly higher than other acclimation temperatures. Thermal tolerance and oxygen consumption rate were analyzed to determine the temperature tolerance limits and metabolic activity at four acclimation temperatures. Critical thermal maxima (CTmax) was 42.86±0.04, 43.3±0.02, 44.45±0.02 and 45.42±0.03; critical thermal minima (CTmin) was 13.07±0.04, 14.35±0.02, 14.92±0.04 and 15.64±0.03 and oxygen consumption rate was 110.75±0.44, 126.57±0.60, 146.22±0.68, 166.47±0.86 mgO2 kg-1h-1 at 28, 30, 32 and 34°C respectively and increased with increasing acclimation temperatures. Oxygen consumption rate for four acclimatization temperatures increased significantly, 110.75±0.44, 126.57±0.60, 146.22±0.68, 166.47±0.86 mgO2 kg-1h-1 at 28, 30, 32 and 34°C respectively. Temperature preference of the early fry of rohu derived from relationship between acclimation temperatures and Q10 values for 28 to 30°C, 30 to 32°C, 32 to 34°C were 1.94, 2.05, and 1.91 respectively. The optimum temperature range for growth was 30 to 32°C and Q10 value was 32 to 34°C. Survival at different acclimation temperatures was between 98.7±2.31, 96.0±4.0, 93.3±2.31 and 94.7±4.62%, from lower to higher acclimation temperatures. Key words: Acclimation temperature, critical temperature, critical thermal maxima (CTmax), critical thermal minima (CTmin), Labeo rohita.

Heat shock proteins (Hsp) are known to play major role in protection of cells from thermal stress. Nucleotide polymorphisms within the promoter of Hsp affect degree of expression and inducibility of Hsp mRNA. The present study aimed to investigate the effect of polymorphism within promoter region on the cellular expression of Hsp70.1 mRNA and association of identified polymorphisms with the physiological parameters during summer stress and milk production traits in dairy cattle. Two hundred Frieswal cows were genotyped using double PCR-RFLP to identify deletion of cytosine within the Hsp70.1 promoter AP2 box at base position 895. Homozygous wild type genotypes (CC) were found in lower frequency (39.29, n=78) than heterozygous cytosine deletion mutant genotypes (C-) (60.71, n=122). In the observed physiological parameters (rectal temperature, respiration rate and heat tolerance coefficient), cows that were homozygous wild types had better significant (P

We used random amplification of polymorphic DNA (RAPD) to generate species-specific diagnostic fragment patterns for the molecular identification of the ornamental aquarium fish species Badis badis and Dario dario. Seven arbitrary oligodecamer primers produced a total of 116 bands of which 98.23% were polymorphic. The size of the amplified products was in the range 340 bp to 2170 bp. Intraspecies genetic similarity was 0.879 ± 0.023 for B. badis and 0.840 ± 0.014 for D. dario while interspecies genetic similarity was 0.602 ± 0.017, with cluster analysis displaying separate taxonomic and evolutionary status for these fish. The results show that RAPD was useful for the molecular identification of aquarium fish species, with morphological traits also being important.

RAPD was used to delineate the hilsa populations sampled from the Ganga, Yamuna, Hooghly, and Narmada Rivers at six different locations. Six degenerate primers were used to generate the fragment patterns from the samples collected. All primers were highly polymorphic and generated high numbers of amplification products. Nei's genetic distances were calculated between locations. The overall average genetic distance among all the six locations was 0.295. The Fst value within the Ganga was 0.469 and within the Hooghly it was 0.546. The overall Fst value for the six populations analyzed was 0.590. The UPGMA dendrogram clustered the hilsa into two distinct clusters: Ganga and Yamuna populations and the Hooghly and Narmada populations.

Aims: (i) To study the occurrence of Escherichia coli serotype O157 in cattle stool in West Bengal, India, and (ii) the virulence properties and antimicrobial resistance of the E. coli isolates. Methods and Results: Following enrichment in modified EC broth and plating onto HiCrome MS.O157 agar, a total of 14 strains of E. coli serotype O157 was isolated from faecal samples from two (2.04%) slaughtered cattle and six (7.59%) diarrhoeic calves. By multiplex PCR, Shiga toxin genes were detected in all the isolates. The enterohaemolysin phenotype was found in all, but one strain. Among 14 strains, ten were resistant to at least one of the antimicrobial agents tested. Multiple antibiotic resistance was frequent. Conclusions: The study showed that occurrence of Shiga toxin-producing and multiple antibiotic-resistant E. coli O157 among cattle population in this region of India is significant. Significance and Impact of the Study: Considering routine human contacts with cattle, a large human population in this region may be at risk for exposure to Shiga toxin-producing E. coli O157.