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.

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.

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.

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.

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.

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.

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.

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).

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.

Cu-mediated synthesis of differentially substituted diazepines as AChE inhibitors; validation through molecular docking and Lipinski's filter to develop novel anti-neurodegenerative drugs.

A highly efficient Cu-mediated route for the synthesis of fused [1,2,3]triazolo[1,4]diazepines has been developed by azidation-cyclization of 2-bromo-N-propargylamines in a one-pot fashion. The key highlight of the present work is that the 2-bromo-N-propargylamines are prepared through the A3-reaction of cyclic amines such as isoquinoline and decarboxylative coupling of proline and pipecolinic acid with 2-bromo benzaldehyde and alkyne. As preliminary, these compounds were analyzed for their most probable bioactivity using various in silico tools. The recognized anti-neurodegenerative activity potential was assessed by molecular docking, AChE inhibition activity in erythrocytes and DPPH radical scavenging activity potentials possessed by the compounds. With a relative AChE inhibition activity of 97% (IC50 0.25 ±â€¯0.02 µM), compound 5d identified as the most active compound. Druggability of these compounds also evaluated through Lipinski's filter and other ADMET tools for the betterment of selective execution of in vitro and in vivo activities of the screened compounds cautiously.

Evaluation of Stress-Induced Microbial Siderophore from Pseudomonas aeruginosa Strain S1 as a Potential Matrix Metalloproteinase Inhibitor in Wound Healing Applications.

Matrix metalloproteinases (MMPs) are zinc-dependent proteolytic enzymes capable of causing various inflammatory and various degenerative diseases if over-expressed. The active site of these enzymes is a zinc binding motif which binds to the specific site on the substrate and induce degradation. Hence an inhibitor is required to form a complex with zinc motif which hampers the binding ability of MMPs. To obtain novel MMPs inhibitor for wound healing, the chelating activity of siderophore from the microbial source was focused. During screening for siderophore production, strain S1 produced the highest amount of siderophore in the minimal salts medium. The isolate was confirmed as Pseudomonas aeruginosa strain S1 based on 16S rRNA gene sequencing and phylogenetic analysis. The activity of the siderophore was assayed using chrome azurol sulphonate and purified by the chromatographic techniques. The structural evidence through Fourier transform infrared and nuclear magnetic resonance spectra revealed that the isolated siderophore is a catecholate type with the distinctive characters. The positive results of calcein and fluozin-3 assays indicate that siderophore could bind to divalent metal ions, namely Fe(2+) and Zn(2+). As the siderophore compound focused on wound healing property, the in vitro studies revealed the viability of NH3T3 fibroblast cells and its efficiency in matrix modulating was confirmed through gelatin zymogram.

Effects of low-density lipoproteins as additive on quality parameters and oxidative stress following cryopreservation of mithun (Bos frontalis) spermatozoa.

Artificial breeding of mithun poses several challenges including lack of standard protocol for cryopreservation of spermatozoa. This is further complicated by harmful effects of hen's egg yolk (EY) as additive in extender. Purified low-density lipoproteins (LDL) extracted from EY have been shown as beneficial over EY extender for long-term semen storage in several species. This investigation explored use of LDL versus EY on semen quality and oxidative stress following freezing-thawing of spermatozoa. A total of 25 of 50 ejaculates based on biophysical parameters were selected for the experiment. After diluting with the Tris-citrate-glycerol (TCG) extender, each sample was split into three equal aliquots: Group I, control, EY; Group II and Group III contained 8% and 10% purified LDL, respectively. Frozen-thawed samples were evaluated for motility parameters (progressive, and in the bovine cervical mucus penetration test [BCMPT]), viability, sperm and nuclear abnormality, acrosome integrity, and enzymatic (leakage of intracellular contents) and biochemical (oxidative stress) profiles and in vitro fertility (IVF) assay. Study revealed a significant (p < .05) improvement in viability, sperm and nuclear abnormality, acrosome integrity, motility (progressive and in cervical mucus), cholesterol content, and reduction in the leakage of intracellular enzymes in Group II. Moreover, intactness of acrosome and biochemical membranes was protected significantly (p < .05) in addition to significant (p < .05) improvement in binding per cent and binding index in IVF assay in extender containing 8% LDL. These results demonstrate that although cryopreservation of mithun's spermatozoa in EY was comparable with other species, addition of 8% LDL holds a clear advantage over EY or 10% LDL.

Synthesis of BF3 catalyzed Mannich derivatives with excellent ee from phenylpropanolamine, study of their antimicrobial activity and molecular docking.

Antimicrobial agents 4a-g and 5a-g with very good potency were synthesized with 100% ee from phenylpropanolamine (norephedrine) by BF3 catalyzed three components one pot Mannich reaction in good yields. Obtained compounds were characterized using spectral techniques. Antimicrobial study of these compounds revealed a good to very high potential activity against tested microbes when compared to standard antimicrobial drugs streptomycin and ketoconazole. These synthesized compounds exhibited significant minimum inhibitory concentration (MIC) values against Gram positive and Gram negative bacteria. Amongst compound 4b, 4c, 4d, 4e, 5a, and 5e exhibited very high potent MIC values against tested twelve bacteria and three fungi when compared to control. When subjected to molecular docking, in silico studies revealed significant binding energies ranging from -7.06 to -8.90 kcal/mol for all obtained compounds towards target receptor DNA topoisomerase IV and amongst compounds 4b and 4d have shown maximum binding energies 8.70 and 8.90 kcal/mol, respectively.

The prevalence of abnormal ECG in trained sportsmen.

BACKGROUND: Competitive sports training causes structural and conductive system changes manifesting by various electrocardiographic alterations. We undertook this study to assess the prevalence of abnormal ECG in trained Indian athletes and correlate it with the nature of sports training, that is endurance or strength training. METHODS: We evaluated a standard resting, lying 12 lead Electrocardiogram (ECG) in 66 actively training Indian athletes. Standard diagnostic criteria were used to define various morphological ECG abnormalities. RESULTS: 33/66 (50%) of the athletes were undertaking endurance training while the other 33 (50%) were involved in a strength-training regimen. Overall 54/66 (81%) sportsmen had significant ECG changes. 68% of these changes were considered as normal training related features, while the remaining 32% were considered abnormal. There were seven common training related ECG changes-Sinus Bradycardia (21%), Sinus Arrhythmia (16%), 1st degree Atrioventricular Heart Block (6%), Type 1 2nd-degree Atrioventicular Heart Block (3%), Incomplete Right bundle branch block (RBBB) (24%), Early Repolarization (42%), Left Ventricular Hypertrophy (LVH) (14%); while three abnormal ECG changes--T-wave inversion (13%), RBBB(4%), Right ventricular hypertrophy (RVH) with strain (29%) were noted. Early repolarization (commonest change), sinus bradycardia, and incomplete RBBB were the commoner features noticed, with a significantly higher presence in the endurance trained athletes. CONCLUSION: A high proportion of athletes undergoing competitive level sports training are likely to have abnormal ECG recordings. Majority of these are benign, and related to the physiological adaptation to the extreme levels of exertion. These changes are commoner during endurance training (running) than strength training (weightlifting).

Synthesis, antimicrobial and molecular docking studies of enantiomerically pure N-alkylated ß-amino alcohols from phenylpropanolamines.

Enantiomerically pure N-alkylated ß-amino alcohols 1a, 1a', 1c, 1c', 1d, 1d', 1e and 1e', with ee 100% have been synthesized from phenylpropanolamines 2. Effect of the neighboring chiral environment on the newly formed chiral center has been studied experimentally and concluded that the newly formed chiral center's absolute configuration is opposite to the adjacent (α- or ß-) chiral environment. The antimicrobial activity of the synthesized ß-amino alcohols were screened using in vitro disc diffusion method and variable antimicrobial activities were shown for 1a, 1a', 1c, 1c', 1d, 1d', 1e &1e' and amongst them 1d &1d' exhibited significant activity against bacteria and fungi. In silico studies revealed all the synthesized ß-amino alcohols 1a-e and 1a'-e' have shown good binding energies ranging from -7.38 to -6.09 kJ/mol towards the target receptor DNA topoisomerase IV and 1d' has shown maximum binding energy -7.38 kJ/mol.

Discovery of novel inhibitors for Nek6 protein through homology model assisted structure based virtual screening and molecular docking approaches.

Nek6 is a member of the NIMA (never in mitosis, gene A)-related serine/threonine kinase family that plays an important role in the initiation of mitotic cell cycle progression. This work is an attempt to emphasize the structural and functional relationship of Nek6 protein based on homology modeling and binding pocket analysis. The three-dimensional structure of Nek6 was constructed by molecular modeling studies and the best model was further assessed by PROCHECK, ProSA, and ERRAT plot in order to analyze the quality and consistency of generated model. The overall quality of computed model showed 87.4% amino acid residues under the favored region. A 3 ns molecular dynamics simulation confirmed that the structure was reliable and stable. Two lead compounds (Binding database ID: 15666, 18602) were retrieved through structure-based virtual screening and induced fit docking approaches as novel Nek6 inhibitors. Hence, we concluded that the potential compounds may act as new leads for Nek6 inhibitors designing.

Oral epidermoid cyst. A case report.

BACKGROUND: Paediatric epidermoid cysts are the rare lesions in the oral cavity, especially under the age of 10 years. They appear in the midline of the mouth usually as a result of residual ectodermal tissue of the first and second branchial arches, which fuse during the third and fourth weeks of intra-uterine life. CASE REPORT: We present a case of a male patient aged 8 years with swelling of the floor of the mouth, complaining of difficulty in swallowing. The ultrasonographic finding was infected ranula with a differential diagnosis of foregut duplication cyst and dermoid cyst. The cyst was surgically enucleated and was diagnosed as epidermoid cyst after histopathology. At the 18-month follow-up the cyst had not recurred.

Methyl 4-(4-bromo-anilino)-2',5-dioxo-5H-spiro-[furan-2,3'-indoline]-3-carboxyl-ate.

In the title compound, C19H13BrN2O5, the spiro furan ring is almost planar with a maximum deviation of 0.034 (2) Å. The indole unit and the furan ring are normal to each other, making a dihedral angle of 87.82 (8) °. The mol-ecular structure is stabilized by an intra-molecular N-H⋯O hydrogen bond, which generates an S(6) ring motif. In the crystal, mol-ecules are linked via pairs of N-H⋯O hydrogen bonds, forming inversion dimers enclosing R (2) 2(8) ring motifs.

Facile one-pot synthesis of novel dispirooxindole-pyrrolidine derivatives and their antimicrobial and anticancer activity against A549 human lung adenocarcinoma cancer cell line.

Novel dispirooxindole-pyrrolidine derivatives have been synthesized through 1,3-dipolar cycloaddition of an azomethine ylide generated from isatin and sarcosine with the dipolarophile 3-(1H-indol-3-yl)-3-oxo-2-(2-oxoindolin-3-ylidene)propanenitrile, and also spiro compound of acenaphthenequinone obtained by the same optimized reaction condition. Synthesized compounds were evaluated for their antimicrobial activity and all the compounds shown significant activity. Anticancer activity was evaluated against A549 human lung adenocarcinoma cancer cell lines. Compounds 7b, 7g, 7i and 7r exhibit very good anticancer activity 62.96%, 62.03%, 67.67% and 60.22%, respectively, at the dose of 200µg/mL and compound 7i shows IC50 value in 50µg/mL.

Cu(OTf)2 catalyzed three component reaction: efficient synthesis of spiro[indoline-3,4'-pyrano[3,2-b]pyran derivatives and their anticancer potency towards A549 human lung cancer cell lines.

Cu(OTf)2 catalyzed efficient synthesis of spiropyrano[3,2-b]pyran-4(8H)-ones is accomplished via one-pot three component reaction between isatin, kojic acid and active methylenes. This synthetic protocol is operationally simple and affords product with good to excellent yields at a short reaction time. The synthesized compounds were evaluated for their tumor cell growth inhibitory activity against the human lung cancer cell line (A549) and found that 13 compounds exhibited moderate to good anticancer potency. Molecular docking studies were performed for all the synthesized compounds and the results showed that compound 4e showed greater affinity for anaplastic lymphoma kinase (ALK) receptor.