High-throughput method for Peptide mapping and Amino acid sequencing for Calcitonin Salmon in Calcitonin Salmon injection using Ultra High Performance Liquid Chromatography - High Resolution Mass Spectrometry (UHPLC-HRMS) with the application of Bioinformatic tools.

BACKGROUND: Tandem mass spectrometry (MS/MS) can provide direct and accurate sequence characterization of synthetic peptide drugs, and peptide drug products including side chain modifications in the Peptide drugs. This article explains a step-by-step guide to developing a high-throughput method using high resolution mass spectrometry for characterization of Calcitonin Salmon injection containing high proportion of UV-active excipients. METHODS: The major challenge in the method development of Amino acid sequencing and Peptide mapping was presence of phenol in drug product. Phenol is a UV-active excipient and reacts with both Dithiothreitol (DTT) and Trypsin. Hence Calcitonin Salmon was extracted from the Calcitonin Salmon injection using solid phase extraction after the extraction, Amino acid sequencing and peptide mapping study was performed. Upon incubation of Calcitonin Salmon with Trypsin and DTT, digested fragments were generated which were separated by mass compatible reverse phase chromatography and the molecular mass of each fragment was determined using HRMS. RESULTS: A reverse phase chromatographic method was developed using UHPLC-HRMS for the determination of direct mass, peptide mapping and to determine the amino acid sequencing in the Calcitonin Salmon injection. The method was found Specific and fragments after trypsin digest are well resolved from each other and the molecular mass of each fragment was determined using HRMS. Sequencing was performed using automated identification of b and y ions annotation and identifications based on MS/MS spectra using Biopharma finder and Proteome discoverer software. CONCLUSION: Using this approach 100% protein coverage was obtained and protein was identified as Calcitonin Salmon and the observed masses of tryptic digest of peptide was found similar with theoretical masses. The method can be used for both UV and MS based Peptide mapping and whereas the UV based peptide mapping method can be used as identification test for Calcitonin Salmon drug substance and drug product in quality control.

Imperatorin from the aerial parts of Cleome viscosa L.: a characterization study and evaluation of the antibacterial activity.

Cleome viscosa L., a member of the family Cleomaceae, is a potential medicinal plant, known for several bioactive properties such as: anticancer, antidiabetic, antioxidant, anti-inflammatory, antimicrobial, wound healing, etc. Our study aimed to isolate a bioactive compound and assess its antibacterial activity. The crystal compound imperatorin was isolated and reported for the first time from the aerial parts of C. viscosa. The isolation was made using silica gel (100-200 mesh) column chromatography. The structure of imperatorin was investigated through single-crystal XRD, unit cell molecules, FTIR, and ESI-MS spectral analysis. The results validated imperatorin's triclinic crystal structure and P2i/c distance group. The electronic structure was also calculated (4.28/6.21 D) along with the frontier molecular orbital, dipole moment, atomic charges, and electrostatic map of particles in gaseous stage and active site. Imperatorin showed highest activity at 40 µg/mL concentration against Gram + ve bacteria: Staphylococcus aureus (3 ± 0.2 mm), Bacillus subtilis (3 ± 0.6 mm), and Gram -ve bacteria: Klebsiella pneumoniae (3 ± 0.2 mm), Escherichia coli (5 ± 0.2 mm). The study highlights that the compound can be isolated in larger quantities as the plant is easily available across the tropics.

Enhancement in the electrical transport properties of CaMnO3via La/Dy co-doping for improved thermoelectric performance.

The untiring endeavour towards green energy is a trending research among the research community. Thermoelectric materials are of vital importance here owing to their emission-free operation. As a righteous candidate, calcium manganate materials are being explored to increase its figure of merit. In this study, the structural, microstructural, electrical transport, and high-temperature thermoelectric measurements of LaxDyxCa1-2xMnO3 {x = 0.025 (L25D25), 0.05 (L50D50), 0.075 (L75D75), and 0.1 (L100D100)} were systematically performed. The structural confirmation of the synthesised sample was validated using X-ray diffraction, which also revealed the orthorhombic (space group: Pnma) crystallisation of co-doped samples with no traces of secondary peaks. A significant increase in the unit cell volume was observed with rare earth substitutions. The morphological studies revealed that the prepared samples were highly dense and the grain size was reduced with rare earth concentration. The substitution of La and Dy enhanced the conductivity values of pristine CMO by two orders of magnitude due to the high concentration of charge carriers and the presence of Mn3+ ions due to rare earth doping. The conductivity increased with rare earth concentrations but diminished for x = 0.1 due to the localization of charges. The Seebeck coefficient values were negative for all the prepared samples, indicating electrons as the predominant carriers over the entire operating range. A minimum κ of 1.8 W m-1 K-1 was achieved for La0.1Dy0.1Ca0.8MnO3 and the maximum value zT obtained was 0.122 at 1070 K for La0.075Dy0.075Ca0.85MnO3.

Advancement of targeted protein degradation strategies as therapeutics for undruggable disease targets.

Targeted protein degradation (TPD) aids in developing novel bifunctional small-molecule degraders and eliminates proteins of interest. The TPD approach shows promising results in oncological, neurogenerative, cardiovascular and gynecological drug development. We provide an overview of technology advancements in TPD, including molecular glues, proteolysis-targeting chimeras (PROTACs), lysosome-targeting chimeras, antibody-based PROTAC, GlueBody PROTAC, autophagy-targeting chimera, autophagosome-tethering compound, autophagy-targeting chimera and chaperone-mediated autophagy-based degraders. Here we discuss the development and evolution of the TPD field, the variety of proteins that PROTACs target and the biological repercussions of their degradation. We particularly highlight the recent improvements in TPD research that utilize autophagy or the endolysosomal pathway, which enables the targeting of undruggable targets.

Greater efficiency of polyherbal drug encapsulated biosynthesized chitosan nano-biopolymer on diabetes and its complications.

Diabetes is a highly complex disease that has an adverse impact on the lives of individuals, and the current medicines used to manage diabetes have obvious side effects. Medicinal plants, on the other hand, may serve as an alternate source of anti-diabetic drugs. A polyherbal combination has a higher and more extensive therapeutic potential than a single herb. Yet, due to deterioration during the absorption process, the usage of this drug still yields inadequate results. Encapsulation of polyherbal drug with chitosan nanoparticles is one of the key ways to solve this problem due to its biocombatibilty, slow and targeted drug delivery characteristics. In the present study, the chitosan was derived from prawn shell and the chitosan nanoparticles had been prepared by ionic-gelation method. The anti-diabetic polyherbal drug (Andrographis paniculata, Andrographis alata, Adhatoda zeylanica, Gymnema sylvestre, Syzygium cumini, and Justicia glabra) was encapsulated with a bio-derived chitosan biopolymer. The drug loading efficiency was about 85 %. The chemical and physical properties of the chitosan and drug-loaded chitosan nanoparticles had been analyzed by FT-IR absorption, XRD, SEM, TEM and EDAX analysis. The antidiabetic efficiency, hepatoprotective activity and antihyperlipedimic activity of the chitosan nanoparticles, polyherbal drug and polyherbal drug encapsulated with chitosan nanoparticles were assessed in a group of rats. The polyherbal drug reduced the serum glucose level from 306.4 mg/dL to 134.47 mg/dL, while the polyherbal drug encapsulated with chitosan nanoparticles reduced to 127.017 mg/dL. This was very close to the serum glucose level of non-diabetic rat (124.65 mg/dL). Further, it considerably increased the insulin level close to that of non-diabetic rat. Thus, the polyherbal drug encapsulated with chitosan nanoparticles showed superior efficiency in antidiabetic and also diabetic complications.

Ant Colony Optimization-Enabled CNN Deep Learning Technique for Accurate Detection of Cervical Cancer.

Cancer is characterized by abnormal cell growth and proliferation, which are both diagnostic indicators of the disease. When cancerous cells enter one organ, there is a risk that they may spread to adjacent tissues and eventually to other organs. Cancer of the cervix of the uterus often initially manifests itself in the uterine cervix, which is located at the very bottom of the uterus. Both the growth and death of cervical cells are characteristic features of this condition. False-negative results provide a significant moral dilemma since they may cause women to get an incorrect diagnosis of cancer, which in turn can result in the woman's premature death from the disease. False-positive results do not raise any significant ethical concerns; but they do require a patient to go through an expensive and time-consuming treatment process, and they also cause the patient to experience tension and anxiety that is not warranted. In order to detect cervical cancer in its earliest stages in women, a screening procedure known as a Pap test is often performed. This article describes a technique for improving images using Brightness Preserving Dynamic Fuzzy Histogram Equalization. To individual components and find the right area of interest, the fuzzy c-means approach is applied. The images are segmented using the fuzzy c-means method to find the right area of interest. The feature selection algorithm is the ACO algorithm. Following that, categorization is carried out utilizing the CNN, MLP, and ANN algorithms.

The Nicobarese tribes and their coastal fishing activities during the COVID-19 pandemic-related restrictions- preliminary findings.

We interviewed the Nicobarese tribal community (N = 95) of Car Nicobar Island situated in the Andaman and Nicobar archipelago, India to analyze the impact of COVID-19-related restrictions on their coastal fishing activities. Our surveys revealed a significant reduction (p < 0.001) in the average monthly income and fish catches during pre and post-COVID-19 scenarios. Constraints faced during the pandemic-related restrictions and the possible solutions to reinforce the fishing activities were highlighted for sustainable resource management in Car Nicobar Island.

Genome-wide detection of copy number variations in Tharparkar cattle.

Copy number variations (CNVs) are major forms of genetic variation with an increasing importance in animal genomics. This study used the Illumina BovineSNP 50 K BeadChip to detect the genome-wide CNVs in the Tharparkar cattle. With the aid of PennCNV software, we noticed a total of 447 copy number variation regions (CNVRs) across the autosomal genome, occupying nearly 2.17% of the bovine genome. The average size of detected CNVRs was found to be 122.2 kb, the smallest CNVR being 50.02 kb in size, to the largest being 1,232.87 Kb. Enrichment analyses of the genes in these CNVRs gave significant associations with molecular adaptation-related Gene Ontology (GO) terms. Most CNVR genes were significantly enriched for specific biological functions; signaling pathways, sensory responses to stimuli, and various cellular processes. In addition, QTL analysis of CNVRs described them to be linked with economically essential traits in cattle. The findings here provide crucial information for constructing a more comprehensive CNVR map for the indigenous cattle genome.

Biological methylation: redefining the link between genotype and phenotype.

The central dogma of molecular biology is responsible for the crucial flow of genetic information from DNA to protein through the transcription and translation process. Although the sequence of DNA is constant in all organs, the difference in protein and variation in the phenotype is mainly due to the quality and quantity of tissue-specific gene expression and methylation pattern. The term methylation has been defined and redefined by various scientists in the last fifty years. There is always huge excitement around this field because the inheritance of something is beyond its DNA sequence. Advanced gene methylation studies have redefined molecular genetics and these tools are considered de novo in alleviating challenges of animal disease and production. Recent emerging evidence has shown that the impact of DNA, RNA, and protein methylation is crucial for embryonic development, cell proliferation, cell differentiation, and phenotype production. Currently, many researchers are focusing their work on methylation to understand its significant role in expression, disease-resistant traits, productivity, and longevity. The main aim of the present review is to provide an overview of DNA, RNA, and protein methylation, current research output from different sources, methodologies, factors responsible for methylation of genes, and future prospects in animal genetics.

Progress and future perspectives of livestock genomics in India: a mini review.

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data.

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Trajectory of livestock genomics in South Asia: A comprehensive review.

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data.

Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.

Role of genomics in combating COVID-19 pandemic.

The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-19. Genomic technologies have been employed by researchers all over the world to better understand the biology of SARS-CoV-2 and its origin, genomic diversity, and evolution. Worldwide genomic resources have greatly aided in the investigation of the COVID-19 pandemic. The pandemic has ushered in a new era of genomic surveillance, wherein scientists are tracking the changes of the SARS-CoV-2 genome in real-time at the international and national levels. Availability of genomic and proteomic information enables the rapid development of molecular diagnostics and therapeutics. The advent of high-throughput sequencing and genome editing technologies led to the development of modern vaccines. We briefly discuss the impact of genomics in the ongoing COVID-19 pandemic in this review.

Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India.

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.

Policy framework and development strategy for freshwater aquaculture sector in the light of COVID-19 impact in Andaman and Nicobar archipelago, India.

The present study was aimed at understanding the impact of COVID-19 pandemic related restrictions on the freshwater aquaculture sector of Andaman and Nicobar archipelago (ANI). We interviewed the freshwater fish farmers (N = 211) covering all the three districts (North and Middle, South Andaman, Nicobar district) of the archipelago. The results revealed the critical issues faced by the stakeholders such as fish seed unavailability, limitations in feeding, insufficient logistical support, movement related restrictions, lack of inputs, manpower shortages, etc. as the important constraints during lockdown. Our surveys also revealed that there was a significant reduction in the income of the farmers post COVID-19 outbreak (p < 0.001). Possible reform strategies that could promote the sector development and resilience were outlined to recover from the COVID-19 impacts. The study also highlights the significance of effective networking among the stakeholders and necessary preparedness measures to be undertaken by the fish farmers to deal with the exigencies. The study also recommends a policy framework to strengthen the planning and management of freshwater aquaculture sector towards the path of sustainability.

Validation of crystal structure of 2-acetamidophenyl acetate: an experimental and theoretical study.

In this present study, we have determined the crystal structure of 2-acetamidophenyl acetate (2-AAPA) commonly used as influenza neuraminidase inhibitor, to analyze the polymorphism. Molecular docking and molecular dynamics have been performed for the 2-AAPA-neuraminidase complex as the ester-derived benzoic group shows several biological properties. The X-ray diffraction studies confirmed that the 2-AAPA crystals are stabilized by N-H···O type of intermolecular interactions. Possible conformers of 2-AAPA crystal structures were computationally predicted by ab initio methods and the stable crystal structure was identified. Hirshfeld surface analysis of both experimental and predicted crystal structure exhibits the intermolecular interactions associated with 2D fingerprint plots. The lowest docking score and intermolecular interactions of 2-AAPA molecule against influenza neuraminidase confirm the binding affinity of the 2-AAPA crystals. The quantum theory of atoms in molecules analysis of these intermolecular interactions was implemented to understand the charge density redistribution of the molecule in the active site of influenza neuraminidase to validate the strength of the interactions.Communicated by Ramaswamy H. Sarma.

Hydrogeochemical characteristics and risk evaluation of potential toxic elements in groundwater from Shanmughanadhi, Tamilnadu, India.

Hydrogeochemical and Health Risk Assessments of trace elements are integral to groundwater resource assessment, utilization, and human health. Investigation of groundwater chemistry and trace elemental impact on local inhabitants were attempted in Shanmuganadhi basin, Tamilnadu, India. About 60 groundwater samples were collected during the pre-monsoon period and analyzed for hydrochemical composition, including major and trace elements (Fe, Cr, Ni, Cu Pb, Mn, and As) to isolate chemical characteristics and human health risk assessment. Groundwater geochemistry is prejudiced by geochemical reactions uniting cation exchange, dissolution and precipitation, adsorption, and anthropogenic contributions. About thirty-two percent of groundwater samples recorded higher F-(>1.5 mg/L) than the prescribed limit suggests sources from rock weathering and silicate dissolution. Nitrates (>45.0 mg/L) suggest sources from agricultural influences. Water types indicate alkalis (Na+ + K+) dominating alkali earth (Ca2+ - Mg2+) and strong acids (Cl- and SO42-) looming weak acid (CO32- and HCO3-) irrespective of water samples. The geochemical stability diagram suggests precipitation of silica, carbonate, and magnesium and dissolution of sulphate minerals along the groundwater flow path. Significant correlation between major ions and trace elements (Pb, Mn, Ni, and Cu) suggests origin from rock weathering, human impacts, and cultivation practices. Non-carcinogenic human risk for trace elements was higher in children compared with adults via ingestion and dermal exposure. The carcinogenic result suggests that Cr in CHK (7.1 × 10-2) and HBG (4.3 × 10-2) have the most excellent chance of cancer risk. The environmental risk category attempted using Comprehensive risk factor (CRI) suggests Pb (3.2-CHK, 2.6-HBG) with potential cancer risk. The comprehensive evaluation index recommends environmental damage between mild to moderate, indicating continuous exposure of traceable elements might result in cancer cause to the inhabitants. The study suggests water quality seems to be prejudiced by various geological and anthropogenic causes and endorses counteractive measures and proper execution of existing laws to protect groundwater resources in the study area.

Comparison of vaginal gauze packing technique with or without balloon in high-dose-rate brachytherapy of uterine cervical cancer: A crossover randomized controlled trial.

Purpose: To compare the rectal and bladder doses using two different vaginal packing techniques among uterine cervical cancer patients receiving high-dose-rate (HDR) intracavitary brachytherapy (ICBT). Material and methods: Forty-five patients with cervical cancer were randomized to receive two sessions of ICBT using tandem and ring applicator (Varian©), following completion of pelvic external beam radiotherapy treatment. The procedure was performed with vaginal balloon plus gauze packing or vaginal gauze packing alone, each of which was used in one of two sessions. Sequence of the type of vaginal packing was chosen with computer-generated block randomization. A HDR dose of 8.5 Gy was prescribed to point A in all patients. Volumetric dose parameters, such as D0.1cc, D0.5cc, D1cc, and D2cc of the rectum and bladder were compared between the two techniques of vaginal packing. Results: The mean age of patients was 51 years. Majority (88%) of patients had locally advanced stages of cancer at baseline (stage IIB or more). Rectal doses were significantly less in combined packing technique (D0.1cc: 7.52 Gy vs. 9.02 Gy, p = 0.01; D0.5cc: 6.46 Gy vs. 7.42 Gy, p < 0.01; D1cc: 5.91 Gy vs. 6.7 Gy, p < 0.01; D2cc: 5.29 Gy vs. 5.97 Gy, p < 0.01). Bladder doses were higher in the combined packing technique (D0.1cc: 11.20 Gy vs. 10.76 Gy, p = 0.18; D0.5cc: 9.64 Gy vs. 9.32 Gy, p = 0.56; D1cc: 8.64 Gy vs. 8.36 Gy, p = 0.55; D2cc: 7.56 vs. 7.33 Gy, p = 0.55). Conclusions: Combined vaginal packing resulted in statistically significant reduction in rectal radiation dose compared with standard vaginal gauze packing in high-dose-rate brachytherapy of cervix cancer using tandem and ring applicators.

Baseline assessment of marine debris with soil, sediment, and water quality characteristics from the fish landing centres of South Andaman, Andaman archipelago, India.

The present study investigates the issue of marine debris and the associated soil, sediment, water quality, and microbial load from the fish landing centres (Junglighat, Chatham, Wandoor, and Guptapara) of South Andaman. The results revealed that significantly (P < 0.05) higher number and weight of marine debris was found in urban landing centres such as Chatham (21.26 ± 1.03 numbers/m2) and Junglighat (268.16 ± 27.00 g/m2), respectively. Plastic debris was found to be the most abundant type of debris, among which plastic bags were dominant. Better soil, sediment, and water quality parameters were observed in rural landing centres such as Wandoor and Guptapara, whereas microbial load was found to be higher in urban landing centres. The study recommends the imperative need to generate awareness on better management practices among the stakeholders to deal with the issue of marine debris and to aim sustainable management of the coastal environment.