Improved meta-analysis pipeline ameliorates distinctive gene regulators of diabetic vasculopathy in human endothelial cell (hECs) RNA-Seq data.

Enormous gene expression data generated through next-generation sequencing (NGS) technologies are accessible to the scientific community via public repositories. The data harboured in these repositories are foundational for data integrative studies enabling large-scale data analysis whose potential is yet to be fully realized. Prudent integration of individual gene expression data i.e. RNA-Seq datasets is remarkably challenging as it encompasses an assortment and series of data analysis steps that requires to be accomplished before arriving at meaningful insights on biological interrogations. These insights are at all times latent within the data and are not usually revealed from the modest individual data analysis owing to the limited number of biological samples in individual studies. Nevertheless, a sensibly designed meta-analysis of select individual studies would not only maximize the sample size of the analysis but also significantly improves the statistical power of analysis thereby revealing the latent insights. In the present study, a custom-built meta-analysis pipeline is presented for the integration of multiple datasets from different origins. As a case study, we have tested with the integration of two relevant datasets pertaining to diabetic vasculopathy retrieved from the open source domain. We report the meta-analysis ameliorated distinctive and latent gene regulators of diabetic vasculopathy and uncovered a total of 975 i.e. 930 up-regulated and 45 down-regulated gene signatures. Further investigation revealed a subset of 14 DEGs including CTLA4, CALR, G0S2, CALCR, OMA1, and DNAJC3 as latent i.e. novel as these signatures have not been reported earlier. Moreover, downstream investigations including enrichment analysis, and protein-protein interaction (PPI) network analysis of DEGs revealed durable disease association signifying their potential as novel transcriptomic biomarkers of diabetic vasculopathy. While the meta-analysis of individual whole transcriptomic datasets for diabetic vasculopathy is exclusive to our comprehension, however, the novel meta-analysis pipeline could very well be extended to study the mechanistic links of DEGs in other disease conditions.

Tinospora cordifolia modulates the seminal parameters, leakage of intracellular enzymes and seminal antioxidants in equilibrated and cryopreserved semen of Sahiwal bulls.

The present study was undertaken to assess the effects of stem extract of Tinospora cordifolia (Giloy or Guduchi) in the semen extender on seminal parameters, leakage of intracellular enzymes and antioxidants in semen of Sahiwal bull. A total of 48 ejaculates from four bulls were selected for the study. Spermatozoa of 25 × 106 were incubated in 100, 300 and 500 µg of stem extract of Guduchi as Gr II, III and IV, respectively, and pre-freeze and post-thaw semen samples were analysed for seminal parameters [motility, viability, total sperm abnormality (TSA), plasma membrane integrity (PMI) and acrosomal integrity (AcI)], intracellular enzymes [aspartate aminotransferase (AST) and lactate dehydrogenase (LDH)] and seminal antioxidants [superoxide dismutase (SOD) and catalase] in comparison with an untreated control group (Gr I). The results revealed that stem extract-treated semen had significantly (p < .05) higher motility, viability, PMI, AcI, SOD and catalase and had significantly (p < .05) lower TSA, AST and LDH compared to those in untreated control group at pre-freeze and post-thaw stages. Semen treated with 100 µg stem extract/25 × 106 spermatozoa had significantly (p < .05) higher motility, viability, PMI, AcI, SOD and catalase and had significantly (p < .05) lower TSA, AST and LDH compared to those in control, 300- and 500-µg-treated groups at pre-freeze and post-thaw stages. Further, these seminal parameters and antioxidants were showing decreasing trend and TSA and leakage of intracellular enzymes were showing increasing trend from Gr II to Gr IV at pre-freeze and post-thaw stages. Thus, 100 µg/25 × 106 spermatozoa were optimum or suitable dose for cryopreservation of Sahiwal bull semen. The study concluded that T. cordifolia stem extract 100 µg/25 × 106 spermatozoa in the semen extender can be effectively utilized to reduce the oxidative stress and improve the pre-freeze and post-thaw seminal parameters in Sahiwal bull. However, further studies on effects of different concentrations of stem extract on in vitro or in vivo fertility trials are to be conducted to assess the impact of the stem extract supplementation in the semen extender on field pregnancy outcomes in bovine species.

A scoping review on deep learning for next-generation RNA-Seq. data analysis.

In the last decade, transcriptome research adopting next-generation sequencing (NGS) technologies has gathered incredible momentum amongst functional genomics scientists, particularly amongst clinical/biomedical research groups. The progressive enfoldment/adoption of NGS technologies has incited an abundance of next-generation transcriptomic data harbouring an opulence of new knowledge in public databases. Nevertheless, knowledge discovery from these next-generation RNA-Seq. data analysis necessitates extensive bioinformatics know-how besides elaborate data analysis software packages consistent with the type and context of data analysis. Several reliability and reproducibility concerns continue to impede RNA-Seq. data analysis. Characteristic challenges comprise of data quality, hardware and networking provisions, selection and prioritisation of data analysis tools, and yet significantly implementing of robust machine learning algorithms for maximised exploitation of these experimental transcriptomic data. Over the years, numerous machine learning algorithms have been implemented for improved transcriptomic data analysis executing predominantly shallow learning approaches. More recently, deep learning algorithms are becoming more mainstream, and enactment for next-generation RNA-Seq. data analysis could be revolutionary in the coming years in the biomedical domain. In this scoping review, we attempt to determine the existing literature's size and potential nature in deep learning and NGS RNA-Seq. data analysis. An analysis of the contemporary topics of next-generation RNA-Seq. data analysis based on deep learning algorithms is critically reviewed, emphasising open-source resources.

Lactation stages modulate the hematological, serum biochemical, and endocrinological profiles and oxidative stress markers in crossbred cows under tropical humid island ecosystem of Andaman and Nicobar Islands.

The present study was designed to assess the interrelationship between hematological, serum biochemical, and endocrinological profiles and oxidative stress markers and lactational stages in crossbred (CB) dairy cows of Andaman and Nicobar Islands (ANI). Healthy (n = 6) CB cows (50-62.50% exotic inheritance; Holstein Friesian × Andaman local) of 4th parity with age of 7-9 years and body weight of 350-400 kg were selected from Cattle Breeding Farm, ICAR-Central Island Agricultural Research Institute (ICAR-CIARI), Port Blair, ANI. These experimental cows were synchronized with Ovsynch protocol, and parturition was planned to happen in the month of May-June. Lactation was allowed for 305 days. Hematological profiles, serum biochemical profiles, oxidative stress markers and endocrinological profiles were measured at a 15-day interval from day 07 to 305 of lactation (after 6 days of colostrum). The lactation period was divided into first (day 07 to 90), second (day 91 to 180), and third (day 181 to 305) stage of lactation. Average daily milk yield (L) did not vary among the stages of lactations; however, first (8.56 ± 1.26) and second (9.79 ± 0.87) stages had higher milk yield compared to third (7.93 ± 0.79) stage of lactation. Hematological profiles did not vary among the stages of lactation; however, these values were within the range of bovine species at lactation. Serum glucose, triglyceride, total cholesterol, total protein, globulin, and blood urea nitrogen (BUN) increased (P < 0.05) and albumin and creatinine decreased (P < 0.05) gradually as lactation stages advanced. Activity of aspartate aminotransferase (AST), alanine aminotransferase (ALT), and alkaline phosphatase (ALP) and concentration of calcium, phosphorous, and magnesium were nearly similar among the stages of lactation. Similarly, triiodothyronine (T3), and thyroxine (T4) increased and prolactin and cortisol decreased (P < 0.05) gradually as stages of lactation advanced. Total antioxidant capacity (TAC) increased and malondialdehyde (MDA) decreased (P < 0.05) as lactation stages advanced. The results of the present study indicated that the lactating CB cows suffered nutritional stress (deficiency of protein, carbohydrate, lipids, and minerals), physiological stress (higher cortisol), oxidative stress (higher MDA and deficiency of total antioxidant capacity), and hormonal imbalance (higher prolactin and cortisol and deficiency of thyroid hormones) during the early stages of lactation. Thus, the first and second stages are more stressful events compared to the third stage of lactation in the CB cows in ANI. Therefore, regular monitoring of blood components and accordingly suitable feeding strategies with balanced nutrients and minerals, supplementation of suitable antioxidants, and appropriate management practices need to be implemented to mitigate these stresses and to prevent metabolic disorders with maximum milk production during different stages of lactation in CB cows under humid tropical island ecosystem of Andaman and Nicobar Islands.

Assisted reproductive technologies (ARTs) in Mithun (Bos frontalis): What progress has been made so far? An overview.

Mithun, a unique bovine species, endemic to parts of North East India and plays an important role in the socioeconomic, cultural and religious fabrics of the local tribal population. To date, Mithuns are reared in a traditional free-range system by communities and increased deforestation, agricultural commercialization, disease outbreaks and indiscriminate slaughtering of elite Mithun for table purposes have significantly decreased its habitat and the elite Mithun population. Greater genetic gain is achieved with the implementation and effective use of assisted reproductive technologies (ARTs); however, presently it is limited to organized Mithun farms. At a slow pace, Mithun farmers are adopting semi-intensive rearing systems and interest in the use of ARTs is gradually escalating in Mithun husbandry. This article reviews the current status of ARTs such as semen collection and cryopreservation, estrus synchronization and timed artificial insemination (TAI), multiple ovulation and embryo transfer and in vitro embryo production and future perspectives in Mithun. Mithun semen collection and cryopreservation have been standardized, and estrus synchronization and TAI are suitable technologies that can be easily implemented under field conditions in near future. The establishment of an open nucleus-breeding system under community participatory mode along with the introduction of the ARTs is an alternative to the traditional breeding system for rapid genetic improvement of Mithun. Finally, the review considers the potential benefits of ARTs in Mithun and future research should include the use of these ARTs which will provide additional opportunities for improved breeding regimens in Mithun.

Improved downstream functional analysis of single-cell RNA-sequence data using DGAN.

The dramatic increase in the number of single-cell RNA-sequence (scRNA-seq) investigations is indeed an endorsement of the new-fangled proficiencies of next generation sequencing technologies that facilitate the accurate measurement of tens of thousands of RNA expression levels at the cellular resolution. Nevertheless, missing values of RNA amplification persist and remain as a significant computational challenge, as these data omission induce further noise in their respective cellular data and ultimately impede downstream functional analysis of scRNA-seq data. Consequently, it turns imperative to develop robust and efficient scRNA-seq data imputation methods for improved downstream functional analysis outcomes. To overcome this adversity, we have designed an imputation framework namely deep generative autoencoder network [DGAN]. In essence, DGAN is an evolved variational autoencoder designed to robustly impute data dropouts in scRNA-seq data manifested as a sparse gene expression matrix. DGAN principally reckons count distribution, besides data sparsity utilizing a gaussian model whereby, cell dependencies are capitalized to detect and exclude outlier cells via imputation. When tested on five publicly available scRNA-seq data, DGAN outperformed every single baseline method paralleled, with respect to downstream functional analysis including cell data visualization, clustering, classification and differential expression analysis. DGAN is executed in Python and is accessible at https://github.com/dikshap11/DGAN .

Flaxseed oil modulates testicular biometrics, hormone, libido, antioxidant and semen profiles in endangered Teressa goat of Andaman and Nicobar Islands.

Teressa goat is a unique goat breed in Andaman and Nicobar Islands (ANI) of India. Effects of Flaxseed oil (FSO) supplementation in body weight (BW), scrotal circumference (SC), testicular volume (TV) and testicular weight (TW), endocrinological profiles, sex behavioural profiles (SBPs), oxidative stress markers and semen production and its quality profiles in rainy and dry summer season were studied in Teressa goat. Male goats (n = 12) of 3-4 years old were equally divided into control and treated groups. Treated animals received 25 mL FSO per day. Oral drenching of FSO was done in the morning before feeding the concentrate ration. Body weight, scrotal circumference, TV and TW were measured in bucks of FSO treated and untreated during rainy and dry summer seasons. Blood follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone, thyroid stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), cortisol and prolactin, total antioxidant capacity (TAC), superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and malondialdehyde (MDA) were measured in bucks of FSO treated and untreated during rainy and dry summer seasons. Libido score (LS), mating ability score (MAS) and sex behavioural score (SBS) were estimated at time of semen collection in bucks of FSO treated and untreated during rainy and dry summer seasons. Semen samples (n = 100; 50 semen samples from each season; each 25 semen samples from control and treatment groups per season) were collected and analysed for semen quality profiles. One-way ANOVA (control rainy, control dry, treated rainy and treated dry) revealed that BW, SC, TV and TW, FSH, LH, testosterone, TSH, T3 and T4 were higher (P < 0.05) and cortisol and prolactin were lower (P < 0.05) in FSO treated bucks of rainy season followed by untreated bucks of rainy season, FSO treated bucks of dry summer season and were lower (P < 0.05) in untreated bucks of dry summer season. Similarly, TAC, CAT, SOD and GSH, LS, MAS and SBS, and volume, pH, sperm concentration, mass activity, total motility (TM), viability, acrosomal integrity (AcI), plasma membrane integrity (PMI) and nuclear integrity (NI) were higher (P < 0.05) and MDA and TSA were lower (P < 0.05) in FSO treated bucks of rainy season followed by FSO treated bucks of dry summer season, untreated bucks of rainy season and were lower (P < 0.05) in untreated bucks of dry summer season. The results of the present study indicated that the breeding bucks suffered physiological stress (higher cortisol), oxidative stress (higher MDA and deficiency of antioxidants), hormonal imbalance (higher prolactin and cortisol and deficiency of gonadotropins, gonadal hormone and thyroid hormones) and infertility due to poor libido and poor semen production and its quality profiles during dry summer season. Thus, dry summer was more stressful season compared to rainy season for the goat bucks. FSO supplementation mitigated these stresses and improved the scrotal and testicular biometrics, libido, antioxidants, hormones and semen quality profiles in Teressa goat bucks. The current study concluded that FSO effectively improved the hormones, libido, antioxidant profiles, and scrotal and testicular biometrics with cascading beneficial effects on semen quality profiles in Teressa goat bucks under humid tropical island ecosystem of Andaman and Nicobar Islands.

Platyphylloside, a potential inhibitor from epicarp of B. aegyptiaca against CYP450 protein in T. rubrum - In vitro and in silico approaches.

Trichophyton rubrum is one of the major disease causing pathogens in human; mainly it causes tinea pedis, tinea cruris and tinea corporis. Cytochrome P450 which considered to be an important protein that can impact ergosterol biosynthesis pathway. B. aegyptiaca is rich source of secondary metabolites with tremendous medicinal values and it has sweet pulp, leaves with spine, strong seed and oily kernel. The epicarp of the fruit was taken for this study to inhibit T. rubrum using in vitro and in silico techniques. The epicarp portion was extracted using various solvents and water. The anti-dermatophytic activity on T. rubrum of these extracts was assessed utilizing poison plate technique with 5 individual concentrations. The fractioned chloroform extract of epicarp had fully inhibited the growth of T. rubrum at 3 mg/ml. Further, the chloroform extract was subjected to LC-MS analysis, in total, 40 compounds were elucidated. Then, the derived compounds were included for predicting ADMETox properties using Qikprop module. From the analysis 40 compounds were identified to be eligible for docking process. Then the desirable compounds, drug Ketoconazole were subjected to docking analysis using Glide module of Schrödinger. It shows that Platyphylloside has better docking result than other compounds and drug Ketoconazole. Further, MD simulation was carried out for Ketoconazole-Cyp450 and Platyphylloside-CYP450 complexes using Desmond, Schrödinger. MD simulation study also confirmed that the Platyphylloside-CYP450 complex more stable. This study suggests that Platyphylloside may act as potential inhibitor and it could be further subjected to experimental analysis to inhibit the T. rubrum growth.

Impact of polystyrene microplastics on major marine primary (phytoplankton) and secondary producers (copepod).

The effect of microplastic adsorption on marine microalgae Tetraselmis suecica, Amphora subtropica, and copepod Pseudodiaptomus annandalei was investigated in the present study. Fluorescence microscopic images were used to evaluate MP interactions with algae and copepods. T. suecica growth rate decreased with effects of 0.1 µm polystyrene exposure to 75 µl/100 ml (0.899 to 0.601 abs), 50 µl/100 ml (0.996 to 0.632 abs) and 25 µl/100 ml (0.996 to 0.632 abs), respectively. On the other hand, at 10th day of experiment, the control T. suecica showed the highest growth rate (0.965 abs), chlorophyll concentration (Chl-'a' = 21.36 µg/L; Chl-'b' = 13.65 µg/L), and cell density (3.3 × 106 cells/ml). A marine diatom A. subtropica absorbed 2.0 µm microplastics, and the maximal inhibition rate increased at higher MP concentration until 10th day. The highest MPs (75 µl/100 ml) treatment resulted in decreased growth rate of A. subtropica from 0.163 to 0.096 abs. A. subtropica (without MPs) had the highest lipid concentration of 27.15%, whereas T. suecica had the lowest lipid concentration of 11.2% (without MP). The maximum survival (80%) of P. annandalei was found in control on 15th day whereas on 12th day, the microplastics ingested copepod had the lowest survival rate (0%). On 15th day, the maximum Nauplii Production Rate (NPR) (19.33) female-1 was observed in control, whereas the minimum (17.33) female-1 NPR was observed in copepod ingested with MPs. The maximum lipid production (17.33% without MPs) was reported in control, whereas MPs fed copepods had the lowest lipid production (16%). Long-term exposure to polystyrene microplastics significantly reduced algae growth and chlorophyll concentration and also NPR and lipid concentration rate of copepod. We inferred that microplastic exposure of algae and copepods might results in persistent decreases in ingested carbon biomass over time.

Biodegradation of low-density polyethylene and polypropylene by microbes isolated from Vaigai River, Madurai, India.

The present study aimed to evaluate the microplastic degradation efficiency of bacterial isolates collected from Vaigai River, Madurai, India. The isolates were processed with proper methods and incorporated in to the UV-treated polyethylene (PE) and polypropylene (PP) degradation. Based on preliminary screening, four bacterial isolates such as Bacillus sp. (BS-1), Bacillus cereus (BC), Bacillus sp. (BS-2), and Bacillus paramycoides (BP) were proceed to further degradation experiment for 21 days. The microplastics were filled with bacterial isolates which is use microplastic (PE, PP) as carbon source for their growth and proceed for shake flask experiment were carried out by two approaches with control. The microplastic degradation was confirmed through their weight loss, increasing fragmentations and changes of surface area against control experiments (microplastic without isolates) also confirms degrading efficiency of isolated bacterial strains through non-changes in their weight and surface area. The highest degradation of PP and PE were observed in BP (78.99 ± 0.005%), and BC (63.08 ± 0.009%) in single approach, while in combined approach BC & BP recorded the highest degradation in both PP (78.62 ± 2.16%), and PE (72.50 ± 20.53%). The formation of new functional groups is confirming the biofilm formation in the surface area of microplastics by isolates and proving their efficiency in degrade the microplastics. The degradation of microplastic experiments should be cost effective and zero waste which is helpful to save the environment and the present findings could reveal the way to degrade the microplastics and prevent the microplastic pollution in aquatic environment.

Gibberellic acids promote growth and exopolysaccharide production in Tetraselmis suecica under reciprocal nitrogen concentration: an assessment on antioxidant properties and nutrient removal efficacy of immobilized iron-magnetic nanoparticles.

The present study was aimed to assess the effect of gibberellic acids to enhance the growth, biomass, pigment, and exopolysaccharides production in Tetraselmis suecica under reciprocal nitrogen concentrations. For this study, the seven types of experimental media (N-P, NL-P/2GA3, N0-P/2GA3, NL-P/4GA3, N0-P/4GA3, NL-P/6GA3, and N0-P/6GA3) were prepared with the addition of gibberellic acids under various nitrogen concentrations. The experiment lasted for 15 days and the cell density, biomass, chlorophyll 'a', and exopolysaccharides (EPS) concentration of T. suecica were estimated for every 3 days. Then the EPS was subjected to the analyses of chemical (carbohydrate, protein, sulfate, and uronic acid), and antioxidant activity. In addition, nutrient removal efficiency was evaluated using different concentration of EPS. The highest DPPH (2,2-diphenyl-1-picrylhydrazyl) (86.7 ± 0.95%) and hydroxyl radical activity (85.7 ± 2.48%) were observed at the EPS concentrations 2.5 and 1.2 mg/mL, respectively. The immobilized magnetic Fe3O4-EPS (ferric oxide-exopolysaccharides) nanoparticles (5.0 and 10.0 g/L) have efficiently removed the excessive phosphate (89.5 ± 1.65%) and nitrate (73.5 ± 1.72%) from the Litopenaeus vannamei cultured wastewater. Thus, the application of gibberellic acids combined with limited nitrogen concentration could produce higher EPS that could exhibit excellent antioxidant activity, and nutrient removal efficacy in the form of Fe3O4-EPS magnetic nanoparticles.

Daily and seasonal rhythmic secretary pattern of endocrinological profiles in mithun bull.

Mithun (Bos frontalis) is a unique domestic free-range bovine species available in North Eastern hilly (NEH) regions of India and is reared for its protein rich meat. Mithun suffers severe non-cyclical population fluctuations; however, it is not yet declared as endangered species. Mithun follows some sort of seasonality based on the calving trend and semen production, although it is a perennial breeder. However, there is need to study the rhythmic changes of endocrine profiles to understand the hormone flow pattern in mithun to select the suitable time for blood collection to assess the exact endocrine profiles and to select the suitable time for natural breeding or semen collection by artificial methods for further research, conservation and propagation of its germplasm. Therefore, the present study was designed to evaluate the reproductive as well as metabolic endocrinological profiles in 24:00 h in intact adult mithun bulls during different seasons (winter, spring, summer and autumn) to know the rhythmic changes and flow pattern of the endocrinological profiles to improve its reproductive efficiency. Experimental mithun bulls (n = 6; age: 5-6 years; body condition score: 5-6 out of 10, classified as good) were selected for the study. Endocrinological profiles, follicle stimulating hormone (FSH), luteinizing hormone/interstitial cell stimulating hormone (LH/ICSH), testosterone, cortisol, thyroxine (T4), insulin like growth factor-1 (IGF-1), prolactin and melatonin (MT) were estimated at 04:00 h interval for one whole day in four seasons. The analysis was completed in two different ways as different times of collection (08:00, 12:00, 16:00, 20:00, 24:00 and 04:00 h) and day (08:00 to 16:00 h) & night time (20:00 to 04:00 h) collections. Repeated measures ANOVA analysis revealed that the bulls in winter and spring had significantly (p < 0.05) higher FSH, LH, testosterone, T4, IGF-1 and MT than those in summer whereas the bulls in summer had significantly higher cortisol and prolactin than those in winter and spring seasons. Similarly FSH, LH, testosterone, T4, IGF-1 and MT were significantly (p < 0.05) higher in night than in day time collections whereas cortisol and prolactin were significantly (p < 0.05) higher in day than in night time collections in different seasons. Correlation analysis revealed that FSH, LH, testosterone, T4, IGF-1 and MT had significant (p < 0.05) positive correlation with each other whereas these had significant (p < 0.05) negative correlation with cortisol and prolactin. The study concludes that season and time of blood collection had significant effect on the endocrinological profiles in mithun bulls. Estimation of FSH, LH, testosterone, T4, IGF-1 and MT during night time and cortisol and prolactin during day time was more appropriate to get correct value of the endocrinological profiles. Spring and winter have significantly greater beneficial effects than summer on reproduction and artificial breeding programs in mithun species in the semi-intensive management in the present location.

Role of seminal MDA, ROS, and antioxidants in cryopreservation and their kinetics under the influence of ejaculatory abstinence in bovine semen.

Despite many cryopreservation techniques in bovine semen, various stressors' detrimental effects remain a significant issue. The present study targeted to assess the role of semen quality parameters, sperm function tests, lipid peroxidation, reactive oxygen species (ROS), and different antioxidants in the cryopreservation of bovine semen. Further, the kinetics of lipid peroxidation, ROS, and antioxidants on repeated semen collection under short ejaculatory abstinence were studied. We designed a comparative study where bulls were grouped into good and low freezable semen groups (Freeze-groups) based on their post-thaw motility. All the bulls included had similar initial motility and qualified minimum standards for initial semen parameters viz. semen volume and sperm concentration. The present study detected a higher lipid peroxidation and ROS viz. superoxide anions (•O2-) and a lower total antioxidant capacity (TAC) in the low freeze-group compared to the good freeze-group. The ROS and antioxidants showed unique kinetics on repeated semen collection at short intervals, and no significant change was detected in semen volume, sperm motility, and sperm concentration. This study detected higher head abnormalities and poor acrosome integrity in the low freeze-groups. The present study results indicated that the sperm head might be the most vulnerable part of the sperm to cryopreservation stress. The present study finds significantly higher lipid peroxidation and ROS levels and reduced antioxidant capacity as the primary reasons for low cryopreservability. Further, repeated semen collection with a shorter or lack of abstinence does not impose any significant change in the semen volume and sperm concentration; moreover, it could be beneficial for higher antioxidant levels and lower lipid peroxidation levels. As seminal plasma has both inhibitory and stimulatory roles in sperm function and cryopreservation, identifying the critical role players of seminal plasma and identifying sperm related changes in cryopreservation could predict the cryopreservability potential of semen.

Design, synthesis, spectral characterization and molecular docking studies of novel pyranoquinolinyl dihydropyridine carboxylates as potential antibacterial agents including Vibrio cholerae with minimal cytotoxity towards fibroblast cell line (L-929).

Novel pyranoquinolinyl dihydropyridine carboxylate (PDC) derivatives were designed by incorporating the multi-drug resistance modulating effects of 1,4 dihydropyridines along with potential antibacterial activity of quinolines in the molecular design. The designed PDC derivatives were synthesized by multi-step synthesis involving Michael addition, reduction followed by inverse electro demand Diels-Alder reaction to produce pyranoquinolinyl dihydropyridine carboxylates in good yields. All the PDC derivatives were characterized by 1H NMR, 13C NMR, FT-IR, Mass spectral and CHN analysis. The Quinolinyl dihydropyridine carboxylate derivatives were evaluated for in vitro antibacterial activity by agar well diffusion method. Molecular docking studies revealed that the exo diethyl 4-(4aR,5S,10bR)-5-(4-chlorophenyl)-3,4,4a,5,6,10b-hexahydro-2H-pyrano[3,2-c]quinolin-8-yl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate diastereomer (5c) forms four hydrogen bonds with the cell wall protein of vibrio cholerae in comparison to the endo diethyl 4-((4aR,5R,10bR)-5-(4-chlorophenyl)-3,4,4a,5,6,10b-hexahydro-2H-pyrano[3,2-c]quinolin-8-yl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate diastereomer (4c) which forms two hydrogen bonds with the cell wall protein of vibrio cholerae and hence leading to better anchorage, enhanced gold score and relatively good antibacterial activity for the exo PDC derivatives. Minimum inhibitory concentration (MIC) of the active compounds was evaluated by macro dilution method. The mechanism of antibacterial action of the PDC derivatives was investigated by SEM studies. The cytotoxicity of PDC derivatives were evaluated against fibroblast cells (L-929).

Baseline assessment of water quality and ecological indicators in Penaeus vannamei farm wastewater along the Southeast coast of India.

The present study aimed to investigate the water quality characteristics and the ecological indicators of wastewater of white legged shrimp Penaeus vannamei ponds along the Southeast coast of India. The wastewater samples were collected from 15 shrimp farms covering 11 districts located along the coastal line of Tamil Nadu and Puducherry, India. By adopting standard methods, the collected samples were subjected to analyses of physico-chemical and biological characteristics, especially the microbial load and metal and plankton composition. The nitrate-nitrogen, ammonia-nitrogen, THB, TCB, and Cu concentrations of the samples were found to exceed the permissible limit as recommended by WHO, USEPA, CPCB, and CAA. Principal component analysis and canonical correspondence analysis have suggested that the phosphate, nitrate, silicate, ammonia, and total phosphorus are the important chemical factors. The generated data would be of interest to farmers for their shrimp crop management vis-à-vis culture pond wastewater treatment.

Slow release exogenous melatonin modulates scrotal circumference and testicular parameters, libido, endocrinological profiles and antioxidant and oxidative stress profiles in mithun.

Mithun (Bos frontalis) is a unique domestic free-range bovine species available in North Eastern hilly (NEH) regions of India and is reared for its protein rich meat. Although, mithun suffers from severe non-cyclical population fluctuations, it is not yet declared as endangered. Therefore, present study was conducted to assess the effect of slow release subcutaneous exogenous melatonin (MT) implant on sexual behaviour, scrotal circumference (SC) and testicular parameters, endocrinological profiles and antioxidant and oxidative stress profiles in mithun during different seasons (winter, spring, summer and autumn) to improve its reproductive efficiency. Experimental mithun bulls (5-6 years of age) were selected and divided randomly into two groups, Gr I: Control (n = 6) and Gr II: Treatment (n = 6; melatonin implant @ 18mg/50 kg B. Wt). Scrotal circumference and testicular parameters [total testicular volume and weight], endocrinological profiles [follicle stimulating hormone (FSH), luteinizing hormone/interstitial cell stimulating hormone (LH/ICSH), testosterone, thyroxine (T4), cortisol, prolactin and melatonin (MT)], sex behaviour profiles [libido score, mating ability score and sexual behaviour score], antioxidant profiles [total antioxidant capacity (TAC), catalase (CAT), glutathione (GSH), glutathione reductase (GSHRx) and superoxide dismutase (SOD)] and oxidative stress profile [malondialdehyde (MDA)] were estimated. Statistical analysis revealed that these experimental profiles differed between treatment and control groups within the seasons and among the seasons within the experimental groups. FSH, LH, testosterone, T4 and MT were higher and cortisol and prolactin were lower in spring and winter than in summer season. Concentration of FSH, LH, testosterone and MT were higher and concentration of T4, cortisol and prolactin were lower in MT treated than in untreated control group. Similarly, sexual behavioural scores, SC, testicular parameters and antioxidant profiles were higher and oxidative stress profile was lower in MT treated than in untreated control group and in winter and spring than in summer season. The study concluded that exogenous slow-release melatonin implantation and spring and winter seasons had significant beneficial effects in improvement of the antioxidant profiles, minimization of oxidative stress with cascading beneficial effects on endocrinological profiles, SC, testicular parameters and libido, which will improve the semen production, higher sperm cryo-survivability and fertility rate in mithun species.

Tracing the genetic root of Trinket cattle: an endangered cattle population of a small isolated island of Nicobar group of islands.

Trinket cattle are the inhabitant of a small island called Trinket, which is one of the picturesque islands of Andaman. This herd is thought to be of Danish leftover during their dynasty in Nicobar archipelago. When the island was abandoned by foreign invaders, indigenes utilized the animals for the purpose of meat. As a result, the cattle became semi-feral in nature. After the Great Sumatra earthquake and tsunami of Indian Ocean in 2004, Trinket island was left abandoned by indigenes and the cattle became totally feral in nature. To trace the genetic root of the cattle, this study has been undertaken based on the sequence information of the mitochondrial D-loop and cytochrome b gene. The genomic DNA was extracted from the blood samples of the Trinket cattle and was used for amplification of mitochondrial markers, and the sequence information was generated by Sanger sequencing. The analysis of sequence information revealed that the Trinket cattle belongs to Bos indicus (I) haplotype, sub-haplotype I2. The presence of I2 sub-haplotype in Trinket cattle may be due to the expansion of this I2 haplotype towards Southeast Asian countries. This is a novel input for the formulation of breeding strategy towards conservation of eco-friendly sustainable livestock in the isolated island ecosystem.

Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers.

For proteome analyses, the tissue samples are mostly preserved either snap frozen or formalin-fixed, paraffin-embedded form. Use of RNAlater-a non-toxic solution primarily used to stabilize the RNA content of samples-in tissue preservation for proteome analysis recently described equally reliable with snap-frozen preservation in human tissues. Even though RNALater storage has great potential in the preservation of Peripheral Blood Mononuclear Cells (PBMC), its impact on the results of proteome analysis is poorly described at qualitative and quantitative measures. The present study investigated protein profiles of RNAlater preserved and fresh PBMCs using three extraction buffers viz. Triton X-100, RIPA and SDS. Proteins are separated in SDS-PAGE and quantified using densitometry. On an average 19.3 bands from fresh and 15.6 bands from RNAlater storage cells were obtained with a molecular weight ranging from 25 to > 250 kDa. RNAlater storage generated a fewer number and lesser quantity of low molecular weight proteins while yielded a similar or high quantity of high molecular weight protein fractions. The principal component analysis showed that Triton X-100 is inferior as compared to SDS and RIPA with respect to their protein bands and quantity yielded. While RNAlater is effective in preserving PBMC for proteome analysis, our findings warrant caution in its use in proteomics experiments especially if the target is low molecular weight proteins.

Variability of the EG95 antigen-coding gene of Echinococcus granulosus in animal and human origin: implications for vaccine development.

In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated thatthere is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had α-turns and ß-turns, and α-amphipathic regions up to 129, 138-156 and 151-155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima's D value was negative (-2.404165), indicative of negative selection pressure.

Flaxseed oil modulates semen production and its quality profiles, freezability, testicular biometrics and endocrinological profiles in mithun.

Mithun (Bos frontalis) is a unique domestic free range bovine species of North Eastern Hilly (NEH) regions of India. Effect of feed supplementation of Flaxseed oil (FSO) on semen production and its quality profiles, freezability, oxidative stress, apoptotic sperm percentage and subsequently on endocrinological profiles & scrotal and testicular biometrics in different seasons was studied in mithun. The experimental animals were divided into two groups, Gr I: Control (n = 3) and Gr II: Treatment (n = 3; Flaxseed oil @ 150 mL/day). FSO was supplemented through oral drench in the morning hours just before concentrate feeding. A total of 80 semen samples (n = 80; 20 semen samples from each season; each 10 semen samples from control and treatment groups per season) were collected, not more than twice per week in winter, spring, autumn and summer seasons. Semen quality profiles (SQPs) such as volume, sperm concentration, motility (forward progressive and total), motility & velocity profiles by computer assisted sperm analyser (CASA), viability, total sperm abnormality, acrosome integrity, plasma membrane & nuclear abnormality and apoptotic sperm percentage were estimated in fresh semen. Along with SQPs measured in fresh semen, motility in estrus bovine cervical mucus (bovine cervical mucus penetration test; BCMPT) and mitochondrial membrane potential (MMP) by JC-1 stain were determined in the post-thawed semen samples. Biochemical profiles (aspartate aminotransferase; AST, alanine aminotransferase; ALT, total cholesterol; CHO), antioxidant profiles (superoxide dismutase; SOD, catalase; CAT, glutathione; GSH, total antioxidant capacity; TAC) and oxidative stress profile (malondialdehyde; MDA) were estimated in fresh semen whereas AST, ALT, lactate dehydrogenase (LDH), TAC and MDA were estimated in the frozen thawed semen samples. Endocrinological profiles such as follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone, cortisol and thyroxin and scrotal circumference (SC) & testicular biometrics were measured in both groups in different seasons. Result revealed a significant (p < 0.05) improvement in motility (total & forward progressive, motility & velocity by CASA and vanguard distance in cervical mucus), viability, intactness of acrosome & plasma membrane, MMP, antioxidant profiles and reduction in total sperm and nuclear abnormalities, reduction in leakage of intracellular enzymes and reduction in oxidative stress profile and reduction of apoptotic sperm percentage were observed in FSO supplemented than in un-supplemented control group accordingly in fresh and post thawed semen samples. Blood FSH, LH, testosterone and thyroxin concentration were significantly (p < 0.05) increased and cortisol concentration was significantly (p < 0.05) decreased in FSO supplemented group than in unsupplemented control group. Similarly, SC and testicular biometrics were increased significantly (p < 0.05) in supplemented than unsupplemented group for different seasons and significantly (p < 0.05) higher in winter and spring than in summer season in the experimental groups. It can be concluded from the study that supplementation of FSO can effectively be utilized to improve the antioxidant profiles, reduction of oxidative stress with cascading beneficial effects on SQPs and fertility status of the mithun bull.