Analysis of synonymous codon usage patterns of HPRT1 gene across twelve mammalian species.

Genetic changes in Hypoxanthine guanine phosphoribosyltransferace (HPRT1) gene can alter the expression of the dopamine neurotransmitter leads to abnormal neuron function, a disease called Lesch-Nyhan syndrome (LNS). Although different studies were conducted on LNS, information on codon usage bias (CUB) of HPRT1 gene is limited. The present study examines the genetic determinants of CUB in HPRT1 gene using twelve mammalian species. In the coding sequence of HPRT1 genes, A/T ending codons was most frequently used. A higher ENC value was observed indicating lower HPRT1 gene expression in the selected mammalian species. Correlation analysis indicates that compositional constraints under mutation pressure can involve in CUB of HPRT1 genes among the selected mammalian species. Relative synonymous codon usage (RSCU) value revealed that the codons such as ACT, AGG, ATT and AGC were over-represented in each of the mammalian species. Result from the analysis of the RSCU indicates that compositional constraint is a key driver for the variation in codon usage. Ratio of nonsynonymous (dN) and synonymous (dS) substitution further suggested that purifying selection occurs among the HPRT1 gene of studied mammals to maintain its protein function under the process of evolution. Our findings report an insight into the codon usage patterns of HPRT1 gene and will be useful for LNS management.

Brevibacillus as a biological tool: a short review.

The significance of Brevibacillus has been documented scientifically in the published literature and commercially in heterologous recombinant protein catalogs. Brevibacillus is one of the most widespread genera of Gram-positive bacteria, recorded from the diverse environmental habitats. The high growth rate, better transformation efficiency by electroporation, availability of shuttle vectors, production of negligible amount of extracellular protease, and the constitutive expression of heterologous proteins make some strains of this genus excellent laboratory models. Regarding biotechnological applications, this genus continues to be a source of various enzymes of great biotechnological interest due to their ability to biodegrade low density polyethylene, ability to act as a candidate bio-control agent, and more recently acknowledged as a tool for the overexpression. This article reviews the properties of Brevibacillus spp. as better biological tools with varied applications.

Nutritional analysis of rice landraces from southern Odisha, India.

Rice landraces conserved by tribal farmers are important for their nutritional richness. Landraces are rich in essential amino acids, vitamins, anthocyanins, and flavonoids useful to cure noncommunicable diseases and metabolic disorders. A study was carried out with 10 rice landraces from the tribal-dominated belt of Southern Odisha to investigate grain nutrition, proximate composition, and vitamin and mineral contents. The protein content of the landraces was higher (>6 g/100 g) and the fat content was lower (<0.6 g/100 g) than popular Indian rice varieties. The mean nutrient content of 10 rice landraces was as follows: protein 6.3 ± 0.313 g/100 g, total dietary fiber 1.6 ± 0.094 g/100 g, fat 0.536 ± 0.008 g/100 g, ash 10.514 ± 6.753%, and total sugar 77.18 ± 2.118 g/100 g. The high genotypic coefficient of variation (GCV) was observed for alkali spreading value (31.11%), capacity of grain hydration (52.705), index of hydration (171.439), moisture (46.343%), and vitamin B2 (23.994%) in rice landraces. Few landraces had superior iron content: Kalamalli (1.49 mg/100 g), Kandulakathi (1.42 mg/100 g), and Dudhamani (1.39 mg/100 g) compared to popular Indian rice varieties. Tikichudi had highest moisture (19%) and fat (0.53 g/100 g) content, which signifies the taste quality of rice. Kanakchudi exhibited the highest fiber content (1.8 g/100 g) and ash content (22.80%). Kalamalli contained higher zinc (0.49 mg/100 g), iron (1.49 mg/100 g), potassium (108.33 mg/100 g), magnesium (78.33 mg/100 g), and phosphorus (125.00 mg/100 g), whereas Muktabali was found to have higher Ca (3.88 mg/100 g) and Baunsidubraj exhibited higher niacin (4.9 mg/100 g). The indigenous landraces Kalamalli, Kandulakathi, and Dudhamani had considerably high iron content, whereas Kalamalli, Baunsidubraj, and Muktabali possessed less phytic acid in comparison with existing varieties and other landraces reported from various states of our country. Landraces Kalamalli, Kanakchudi, Tikichudi, and Muktabali from southern Odisha, India, represented nutritionally better genetic pool for future rice improvement.

Efficacy of Intraperitoneal 0.2% Ropivacaine With Dexmedetomidine Versus 0.2% Ropivacaine With Ketamine in Laparoscopic Surgeries: A Randomized Controlled Trial.

BACKGROUND: Effective pain management modalities are the armamentarium for enhanced recovery in laparoscopic surgeries. Intraperitoneal instillation of local anaesthetics with adjuvants is advantageous in minimizing pain. So, we designed this study with the aim to compare the analgesic effectiveness of intraperitoneal ropivacaine with adjuvants like dexmedetomidine versus ketamine for postoperative analgesia. OBJECTIVE:  The objective of this study is to assess the total duration of analgesia and total rescue analgesic dose requirements in the first 24 hours postoperatively. MATERIALS AND METHODS: A total of 105 consenting patients for elective laparoscopic surgeries were enrolled and divided into three groups by computer-generated randomization as follows: Group 1: 30 ml of 0.2% ropivacaine with ketamine 0.5 mg/kg diluted to 1 ml; Group 2: 30 ml of 0.2% ropivacaine with dexmedetomidine 0.5 mcg/kg diluted to 1 ml; Group 3: 30 ml of 0.2% ropivacaine with 1 ml of normal saline. The postoperative visual analogue scale (VAS) score, total duration of analgesia, and total analgesic dose were calculated and compared among the three groups. RESULTS: The postoperative analgesic duration after intraperitoneal instillation of Group 2 was longer as compared to Group 1. The total analgesic requirement was lower in Group 2 as compared to Group 1, and the p-value was significant (p ≤ 0.001) for both parameters. Demographic parameters and VAS scores among the three groups were not statistically significant. CONCLUSION: We conclude that intraperitoneal instillation of local anaesthetics with adjuvants is effective for postoperative analgesia in laparoscopic surgeries, and ropivacaine 0.2% with dexmedetomidine 0.5 mcg/kg is more effective when compared to ropivacaine 0.2% with ketamine 0.5 mg/kg.

Exploring the rare variants associated with Type 2 Diabetes Mellitus in Indian population and its disease-drug association studies: an in-silico approach.

The diversified eating habits and religious culture of Indian population may be one of the reasons they largely contribute to the global diabetes burden. In the present investigation, an in-silico approach was carried out to explore hub genes in the Indian population with Type 2 Diabetes Mellitus (T2DM) that are scantily reported in the GWAS catalogue and probable potential anti-diabetic drugs from plants. This computational approach unwrapped LEP (leptin) as the hub gene among 170 genes analyzed with 14 non-synonymous single nucleotide polymorphisms (nsSNPs) with MAF < 0.01. The mutation of the LEP gene leads to a decrease in leptin concentration, which increases the risk of obesity and T2DM. According to the DUET webserver, 11 of 14 mutations examined were found to destabilize the LEP protein. Among 14, four barely reported LEP variants rs781301976 (I45N), rs776443424 (S52F), rs200915360 (D76Y), and rs1191666811 (D162N) were unzipped to be associated with T2DM, which may be the probable potential drug targets. The virtual screening revealed Vescalagin as having the highest binding energy among 336 natural compounds. Molecular docking of Vescalagin depicted higher binding energy (-9.0 kcal/mol) against mutated LEP [rs200915360 (D76Y)] compared to wild (-8.9 kcal/mol) and LEP-Metformin complexes. The trajectory analysis of MD simulations revealed that Vescalagin was more effective than Metformin in stabilizing the system. The present study suggests that the associations of the investigated nsSNPs in LEP [rs200915360 (D76Y)] and others can be key factors in the predominant role of T2DM morbidity in the Indian population that can be used as potential markers and drug targets for T2DM therapeutics.Communicated by Ramaswamy H. Sarma.

Structure based virtual screening and molecular dynamics of natural anti-biofilm compounds against SagS response regulator/sensor kinase in Pseudomonas aeruginosa.

SagS sensor regulator plays a vital role in biofilm development of Pseudomonas aeruginosa which subsequently makes the cells more tolerant to various antimicrobials. The multidrug resistance (MDR) issue has risen substantially in recent years and is considered a global threat. Therefore, alternative compounds should be unearthed immediately to address the issues related to P. aeruginosa drug resistance for which SagS could be a candidate. The present study is an attempt to screen natural anti-biofilm compounds as the potent inhibitors of SagS. Twenty natural anti-biofilm/quorum sensing inhibiting compounds were retrieved from various literatures with significant inhibitory effects against P. aeruginosa biofilm from in-vitro experiments which were screened using various pharmacokinetic parameters. The screened and three standard drugs were docked against SagS-HisKA using AutoDock 4.2 tool, which were further analysed by MD simulations to understand the binding mode of compounds and dynamic behaviour of the complexes. Two potential anti-biofilm natural compounds, pinocembrin with binding affinity (-7.19 kcal/mol), vestitol (-7.18 kcal/mol) and the standard drug ceftazidime (-8.89 kcal/mol) were selected based on filtered parameters and better binding affinity. The trajectory analysis of MD simulations reflected Pinocembrin in stabilizing the system compared to ceftazidime. The existing reports state that the natural products represent promising source of therapy with least or almost nil adverse effect compared to synthetic drugs which is well collated with our in-silico findings. This investigation can save both time and cost required for in-vitro and in-vivo analysis for designing of a novel anti-biofilm agent against P. aeruginosa biofilm-associated infections.Communicated by Ramaswamy H. Sarma.

A Comparative Study of Hemodynamic Parameters Following Subarachnoid Block in Patients With and Without Hypertension.

Background Hypotension is common in patients receiving a subarachnoid block (SAB) and can decrease vital organ perfusion, causing increased morbidity and mortality. Patients may receive intraoperative intravenous (IV) fluids and rescue medications to avoid these adverse effects and maintain adequate hemodynamic parameters. We conducted this study to compare the hemodynamic parameters and heart rate following spinal anesthesia on patients receiving antihypertensive medications (e.g., calcium channel blockers with or without beta-blockers) with those without hypertension during surgical procedures requiring SAB. Methods We conducted this two-year, single-center, prospective observational study in patients with hypertension and blood pressure within reference ranges receiving elective surgical procedures that do not require a definitive airway. All participants were from the American Society of Anesthesiologists physical status I and II. We assigned patients into three groups. Group 1 consisted of patients with hypertension receiving calcium channel blockers. Group 2 consisted of patients with hypertension receiving calcium channel blockers with beta-blockers. Patients whose blood pressure was within reference range were assigned to group 3. We collected patient ages and body weights, and we compared heart rate (HR), systolic and diastolic blood pressure (SBP; DBP), and mean arterial pressure (MAP) between the groups. We also compared the use of intraoperative rescue medications, IV fluid administration, and patient outcomes. We used Epi Info version 7.1 (Atlanta, GA: Centers for Disease Control and Prevention) public domain software for statistical analysis. Results Seventy-eight patients were included in the study (41 men, 37 women); group 1, HR, SBP, DBP, and MAP significantly declined over time in all groups, but there were no significant differences when comparing parameters between groups. Hypotension occurred in significantly more patients in group 1 (p=0.02) than groups 2 and 3. Bradycardia was experienced by significantly more patients in group 2 (p<0.05) than group 1 and group 3. Twenty-four patients in group 3, 17 patients in group 1, and 14 patients in group 2 required IV fluid in the first 20 minutes of the procedure, and the differences between the groups were not significant. Likewise, 15 patients in group 3, 14 in group 1, and 10 in group 2 required ephedrine, but the differences were not significant. Conclusions We compared intraoperative hemodynamic parameters following spinal anesthesia on patients receiving antihypertensive medications with patients without hypertension following SAB. Our results showed no meaningful differences in hemodynamic parameters between patients receiving antihypertensive drugs (calcium channel blockers without or in combination with beta-blockers) and those not receiving antihypertensive drugs after SAB. Therefore, calcium channel blockers alone or in combination with beta-blockers can be used to control patient blood pressure prior to surgery.

Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach.

The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.

Antimicrobial Peptides: Novel Source and Biological Function With a Special Focus on Entomopathogenic Nematode/Bacterium Symbiotic Complex.

The rapid emergence of multidrug resistant microorganisms has become one of the most critical threats to public health. A decrease in the effectiveness of available antibiotics has led to the failure of infection control, resulting in a high risk of death. Among several alternatives, antimicrobial peptides (AMPs) serve as potential alternatives to antibiotics to resolve the emergence and spread of multidrug-resistant pathogens. These small proteins exhibit potent antimicrobial activity and are also an essential component of the immune system. Although several AMPs have been reported and characterized, studies associated with their potential medical applications are limited. This review highlights the novel sources of AMPs with high antimicrobial activities, including the entomopathogenic nematode/bacterium (EPN/EPB) symbiotic complex. Additionally, the AMPs derived from insects, nematodes, and marine organisms and the design of peptidomimetic antimicrobial agents that can complement the defects of therapeutic peptides have been used as a template.

Perioperative Obstetric Care in Coronavirus Infectious Disease 2019: Anesthetic Perspective.

BACKGROUND: The novel coronavirus infectious disease-2019 (COVID-19) is a global pandemic involving many countries and has affected more than seventy-nine million people worldwide, with greater than a million deaths in the current scenario. AIMS: The aim of the study is to improvise perioperative obstetric healthcare in a tertiary healthcare center. SETTINGS AND DESIGN: This is a retrospective case series of parturients infected with COVID-19. MATERIALS AND METHODS: We present a case series of COVID-19-infected parturients. There is no evidence that pregnant women are more likely to become seriously affected by coronavirus, yet these groups of patients are vulnerable to infection. Hence, the objectives in the management of such patients which includes caring for the range of the asymptomatic to critically ill women in the peripartum period and protection of healthcare providers from exposure to the disease while treating them while treating them is of paramount importance. RESULTS: There is limited literature available about the effect of this disease and the risk of complications in pregnancy. The variables affect the respiratory system and exacerbate the susceptibility to infections. This complicates or delays the diagnosis in COVID-19-infected parturients, which affect their clinical outcome. Thus, there is a need on focused and optimal management in a tertiary healthcare center. Of the total 109 lower segment cesarean section patients in our hospital, there were only two maternal and neonatal deaths among the 12 emergency cases performed. CONCLUSIONS: Collaborative efforts are imperative among experts such as anesthesiologists and obstetricians to tackle the impact of this disease. There must be surveillance systems in place for reporting maternal and fetal data during this pandemic.

Natural Anti-biofilm Agents: Strategies to Control Biofilm-Forming Pathogens.

Pathogenic microorganisms and their chronic pathogenicity are significant concerns in biomedical research. Biofilm-linked persistent infections are not easy to treat due to resident multidrug-resistant microbes. Low efficiency of various treatments and in vivo toxicity of available antibiotics drive the researchers toward the discovery of many effective natural anti-biofilm agents. Natural extracts and natural product-based anti-biofilm agents are more efficient than the chemically synthesized counterparts with lesser side effects. The present review primarily focuses on various natural anti-biofilm agents, i.e., phytochemicals, biosurfactants, antimicrobial peptides, and microbial enzymes along with their sources, mechanism of action via interfering in the quorum-sensing pathways, disruption of extracellular polymeric substance, adhesion mechanism, and their inhibitory concentrations existing in literature so far. This study provides a better understanding that a particular natural anti-biofilm molecule exhibits a different mode of actions and biofilm inhibitory activity against more than one pathogenic species. This information can be exploited further to improve the therapeutic strategy by a combination of more than one natural anti-biofilm compounds from diverse sources.

MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot.

Caves in Mizoram, Northeast India, are potential hotspot diversity regions due to the historical significance of the formation of the Indo-Burman plateau and also because of their unexplored and unknown diversity. High-throughput paired end Illumina sequencing of the V4 region of 16S rRNA was performed to study the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (OTUs) (based on 97 % cutoff) comprising of 21 major and 21 candidate phyla with a sequencing depth of 1,140,013 were found in this study. The overall taxonomic profile obtained by the RDP classifier and Greengenes OTU database revealed high diversity within the bacterial communities. Communities were dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of Archaea were less varied and mostly comprising of Eukaryoarchea. Analysis revealed that Farpuk (CFP) cave sediment has low microbial diversity and is mainly dominated by Actinobacteria (80 % reads), whereas different bacterial communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis also revealed that a major portion of the identified OTUs was classified under rare biosphere. Importantly, all these caves recorded a high number of unclassified OTUs, which might represent new species. Further analysis with whole genome sequencing is needed to validate the unknown species as well as to determine their functional role.

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India.

Bacterial and archaeal diversity of two alkaline Indian hot springs, Jakrem (Meghalaya) and Yumthang (Sikkim), were studied. Thirteen major bacterial phyla were identified of which Firmicutes, Chloroflexi and Thermi were dominant in Jakrem and Proteobacteria in Yumthang. The dominant genera were Clostridium, Chloroflexus and Meiothermus at Jakrem (water temperature 46 °C, pH 9) and Thiobacillus, Sulfuritalea at Yumthang (water temperature 39 °C, pH 8) hot springs. The four Euryarchaeota taxa that were observed in both the hot springs were Methanoculleus, Methanosaeta, Methanosarcina and Methanocorposculum. Elstera litoralis, Thiovirga sp., Turneriella sp. were observed for the first time in association with hot springs along with Tepidibacter sp., Ignavibacterium sp., Teribacillus sp. and Dechloromonas sp. Individual bacterial phyla were found to be specifically correlated with certain physico-chemical factors such as temperature, dissolved SiO2, elemental S, total sulphide, calcium concentrations in hot spring water. Bacterial reads involved in sulfur cycle were identified in both16S rRNA gene library and sulfur metabolism may play key physiological functions in this hot spring. Members within Desulfobacterales and Thermodesulfovibrionaceae were identified and hypothesized their role in regulating sulfur cycle. The presence of many taxonomically unsolved sequences in the 16S rRNA gene tag datasets from these hot springs could be a sign of novel microbe richness in these less known hot water bodies of Northeastern India.

Investigations on microbial diversity of Jakrem hot spring, Meghalaya, India using cultivation-independent approach.

Jakrem hot water spring is located in the West Khasi Hill District of the state of Meghalaya, and is one of the most popular hot springs of the state. There is a populist belief among the inhabitants and people that the hot spring water has got curative properties against various skin ailments. This is the first report on V3 hyper-variable region of 16S rDNA metagenome sequence employing Illumina platform to profile the microbial community of this less known hot spring from Meghalaya, India. Metagenome comprised of 10, 74,120 raw sequences with a sequence length of 151 bp and 56.35% G + C content. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP056897. A total of 8, 77, 364 pre-processed reads were clustered into 694 OTUs (operational taxonomical units) comprising of 14 bacterial phyla including unknown phylum demonstrating 49 families. Hot spring bacterial community is dominated by Firmicutes (61.60%), Chloroflexi (21.37%), Cyanobacteria (12.96%) and unclassified bacteria (1.2%) respectively.

Illumina-based analysis of bacterial community in Khuangcherapuk cave of Mizoram, Northeast India.

Bacterial community of the Khuangcherapuk cave sediment was assessed by Illumina amplicon sequencing. The metagenome comprised of 533,120 raw reads with an average base quality (Phred score) 36.75 and G + C content is 57.61%. A total of 18 bacterial phyla were detected with following abundant genus - Mycobacterium (21.72%), Rhodococcus (7.09%), Alteromonas (1.42%), Holomonas (0.7%) and Salinisphaera (0.20%). Majority portion of the sequences (68%) is unclassified at the genus level indicating the possibilities for the presence of novel species in this cave. This study reports the cave bacterial diversity from the biodiversity hotspot region of Eastern Himalayas. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. SRP056890.

Biochemical Characterization and 16S rRNA Sequencing of Few Lipase-Producing Thermophilic Bacteria from Taptapani Hot Water Spring, Orissa, India.

Three lipase-producing thermophilic bacteria (AK-P1, AK-P2, and AK-P3) were isolated from the Taptapani hot water spring in Orissa, India. The crude extra cellular lipases from cell-free culture supernatant were reacted in an olive oil mixture, and their lipolytic activities were compared. Identification of the bacteria was carried out using biochemical tests, 16SrRNA sequencing and sequences submitted to NCBI GenBank. Strain AK-P3, exhibited the highest lipolytic activity of 5.5 U/mL was identified as Porphyrobacter sp. The lipolytic activities of strains AK-P1 and AK-P 2 were 4.5 U/mL and 3.5 U/mL, respectively. Strains AK-P1 and AK-P2 were identified as Acinetobacter sp. and Brevibacillus spp. The GenBank accession numbers of the 16S rRNA gene sequences determined in this study for the strains AK-P1, AK-P2, and AK-P3 are HM359120, HM359119, and HM359118, respectively.