Isolation and molecular characterization of multidrug‑resistant Escherichia coli from chicken meat

Antibiotics in animal farms play a significant role in the proliferation and spread of antibiotic-resistant genes (ARGs) and antibiotic-resistant bacteria (ARB). The dissemination of antibiotic resistance from animal facilities to the nearby environment has become an emerging concern. The present study was focused on the isolation and molecular identification of Escherichia coli (E. coli) isolates from broiler chicken meat and further access their antibiotic-resistant profile against different antibiotics. Broiler chicken meat samples were collected from 44 retail poultry slaughter shops in Prayagraj district, Uttar Pradesh, India. Standard bacteriological protocols were followed to first isolate the E. coli, and molecular characterization was performed with genus-specific PCR. Phenotypic and genotypic antibiotic-resistant profiles of all confirmed 154 E. coli isolates were screened against 09 antibiotics using the disc diffusion and PCR-based method for selected resistance genes. In antibiotic sensitivity testing, the isolates have shown maximum resistance potential against tetracycline (78%), ciprofloxacin (57.8%), trimethoprim (54.00%) and erythromycin (49.35%). E. coli bacterial isolates have shown relative resistant to amoxicillin-clavulanic acid (43.00%) and against ampicillin (44.15%). Notably, 64.28% E. coli bacteria were found to be multidrug resistant. The results of PCR assays exposed that tetA and blaTEM genes were the most abundant genes harboured by 83 (84.0%) and 82 (82.0%) out of all 99 targeted E. coli isolates, followed by 48.0% for AmpC (CITM) gene and cmlA (23.00%) for chloramphenicol resistance. It is notable that most of the isolates collected from chicken meat samples were multidrug resistant (> 3 antibiotics), with more than 80% of them carrying tetracycline (tetA) and beta-lactam gene (blaTEM). This study highlights the high risk associated with poultry products due to MDR-E. coli and promote the limited use of antibiotics in poultry farms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03950-7.

Salivary microbiomes: a potent evidence in forensic investigations

Saliva components combine with oral cavity microorganisms, blood cells, and airway secretions after entering the oral cavity via salivary ducts; these factors provide relevant information about persons' health state, quality of life, and lifestyle, in addition to their age and gender due to which salivary microbiome has emerged as a subject of significant interest in the forensic domain. This study aims to provide an extensive review of the possible applications of the salivary microbiome in characterizing the habit-specific microbiomes. Thirty-three relevant articles were selected for inclusion in this study. The study highlighted the influence of habits on the salivary microbiome suggesting smokers have distinct bacteria like Synergistetes, Streptococcus, Prevotella, and Veillonella in relation to age; people of higher age have more Prevotella; further, dental plaque can be corelated with Streptococci and Actinomycetes. Likewise, dietary habits, alcoholism, and consumption of coffee also affect bacteria types in oral cavities. The study underscores the added benefits of salivary microbiome profiling in forensics, as it is evident that microbial DNA profiling holds substantial promise for enhancing forensic investigations; it enables the characterization of an individual's habits, such as smoking, alcohol consumption, and dietary preferences; bacteria specific to these habits can be identified, thereby helping to narrow down the pool of potential suspects. In conclusion, the salivary microbiome presents a valuable avenue for forensic science, offering a novel approach which not only enhances the prospects of solving complex cases but also underscores the rich potential of microbiome analysis in the realm of forensic investigation.

Identification of habit specific bacteria in human saliva through Next-Generation Sequencing

Characterization of human saliva through Next-Generation Sequencing has emerged as a valuable tool for understanding the complex microbial communities residing in the oral cavity. This study aims to investigate the habit-based variations in the salivary microbiome using Next-Generation Sequencing technology. Saliva samples were collected from a diverse population representing different habits, including smoking, alcohol consumption, and vegan diet. The DNA from the samples was extracted, and the V3-V4 region of the 16 S rRNA gene was amplified for Next-Generation Sequencing analysis. The obtained sequences were processed and analysed using bioinformatics tools to determine the microbial composition and diversity. Preliminary results revealed distinct microbial profiles associated with different habits, indicating the potential influence of different habits on the salivary microbiome. Smokers exhibited a higher abundance of certain pathogenic bacteria, while alcohol consumers showed alterations in microbial diversity compared to non-consumers. Furthermore, individuals with vegan diet demonstrated an increased prevalence of specific bacteria. These findings highlight the significance of habit-based characterization of the salivary microbiome and its potential implications in the presence of certain bacteria. Understanding the relationship between habits and the salivary microbiome could contribute to developing personalized approaches for estimating and identifying any particular individual. Further research is warranted to explore additional factors and expand the scope of habit-based analysis in saliva-based microbial characterization through Next-Generation Sequencing.

An in-silico insight into the predictive interaction of Apolipoprotein-E with Epstein-Barr virus proteins and their probable role in mediating Alzheimer's disease

Recent reports suggest that persistent Epstein-Barr virus (EBV) infection and its recurrent reactivation could instigate the formation of proteinaceous plaques in the brain: a hallmark of Alzheimer's disease (AD). Interestingly, a major genetic risk factor of AD, the apolipoprotein E (ApoE), could also influence the outcome of EBV infection in an individual. The ApoE is believed to influence the proteinaceous plaque clearance from the brain, and its defective functioning could result in the aggregate deposition. The persistent presence of EBV infection in a genetically predisposed individual could create a perfect recipe for severe neurodegenerative consequences. Therefore, in the present study, we investigated the possible interactions between ApoE and various EBV proteins using computational tools. Our results showed possibly stable de-novo interactions between the C-terminal domain of ApoE3 and EBV proteins: EBV nuclear antigen-1 (EBNA1) and BamHI Z fragment leftward open reading frame-1 (BZLF1). The EBNA1 protein of EBV plays a crucial role in establishing latency and replication of the virus. Whereas BZLF1 is involved in the lytic replication cycle. The proposed interaction of EBV proteins at the ligand-binding site of ApoE3 on CTD could interfere with- its capability to sequester amyloid fragments and, hence their clearance from the brain giving rise to AD pathology. This study provides a new outlook on EBV's underexplored role in AD development and paves the way for novel avenues of investigation which could further our understanding of AD pathogenesis.Communicated by Ramaswamy H. Sarma[Figure: see text].

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Signaling and crosstalk of rhizobacterial and plant hormones that mediate abiotic stress tolerance in plants

Agricultural areas exhibiting numerous abiotic stressors, such as elevated water stress, temperatures, and salinity, have grown as a result of climate change. As such, abiotic stresses are some of the most pressing issues in contemporary agricultural production. Understanding plant responses to abiotic stressors is important for global food security, climate change adaptation, and improving crop resilience for sustainable agriculture, Over the decades, explorations have been made concerning plant tolerance to these environmental stresses. Plant growth-promoting rhizobacteria (PGPR) and their phytohormones are some of the players involved in developing resistance to abiotic stress in plants. Several studies have investigated the part of phytohormones in the ability of plants to withstand and adapt to non-living environmental factors, but very few have focused on rhizobacterial hormonal signaling and crosstalk that mediate abiotic stress tolerance in plants. The main objective of this review is to evaluate the functions of PGPR phytohormones in plant abiotic stress tolerance and outline the current research on rhizobacterial hormonal communication and crosstalk that govern plant abiotic stress responses. The review also includes the gene networks and regulation under diverse abiotic stressors. The review is important for understanding plant responses to abiotic stresses using PGPR phytohormones and hormonal signaling. It is envisaged that PGPR offer a useful approach to increasing plant tolerance to various abiotic stresses. However, further studies can reveal the unclear patterns of hormonal interactions between plants and rhizobacteria that mediate abiotic stress tolerance.

Microsecond Isomer at the N=20 Island of Shape Inversion Observed at FRIB

Excited-state spectroscopy from the first experiment at the Facility for Rare Isotope Beams (FRIB) is reported. A 24(2)-μs isomer was observed with the FRIB Decay Station initiator (FDSi) through a cascade of 224- and 401-keV γ rays in coincidence with ^{32}Na nuclei. This is the only known microsecond isomer (1  μs≤T_{1/2}<1  ms) in the region. This nucleus is at the heart of the N=20 island of shape inversion and is at the crossroads of the spherical shell-model, deformed shell-model, and ab initio theories. It can be represented as the coupling of a proton hole and neutron particle to ^{32}Mg, ^{32}Mg+π^{-1}+ν^{+1}. This odd-odd coupling and isomer formation provides a sensitive measure of the underlying shape degrees of freedom of ^{32}Mg, where the onset of spherical-to-deformed shape inversion begins with a low-lying deformed 2^{+} state at 885 keV and a low-lying shape-coexisting 0_{2}^{+} state at 1058 keV. We suggest two possible explanations for the 625-keV isomer in ^{32}Na: a 6^{-} spherical shape isomer that decays by E2 or a 0^{+} deformed spin isomer that decays by M2. The present results and calculations are most consistent with the latter, indicating that the low-lying states are dominated by deformation.

Harnessing and bioprospecting botanical-based herbal medicines against potential drug targets for COVID-19: a review coupled molecular docking studies

Since the end of February 2020, the world has come to a standstill due to the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Since then, the global scientific community has explored various remedies and treatments against this virus, including natural products that have always been a choice because of their many benefits. Various known phytochemicals are well documented for their antiviral properties. Research is being carried out to discover new natural plant products or existing ones as a treatment measure for this disease. The three important targets in this regard are-papain like protease (PLpro), spike protein, and 3 chymotrypsin like proteases (3CLpro). Various docking studies are also being elucidated to identify the phytochemicals that modulate crucial proteins of the virus. The paper is simultaneously a comprehensive review that covers recent advances in the domain of the effect of various botanically derived natural products as an alternative treatment approach against Coronavirus Disease 2019 (COVID-19). Furthermore, the docking analyses revealed that rutin (inhibitor of the major protease of SARS-CoV-2), gallocatechin (e.g., interacting with 03 hydrogen bonds with a spike-like protein), lycorine (showing the best binding affinity with amino acids GLN498, THR500 and GLY446 of the spike-like protein), and quercetrin (inhabiting at its residues ASP216, PHE219, and ILE259) are promising inhibitors of SARS‑CoV‑2.Communicated by Ramaswamy H. Sarma.

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families

CRISPR-Cas is a widespread anti-viral adaptive immune system in the microorganisms. Viruses living in bacteria or some phages carry anti-CRISPR proteins to evade immunity by CRISPR-Cas. The anti-CRISPR proteins are prevalent in phages capable of lying dormant in a CRISPR-carrying host, while their orthologs frequently found in virulent phages. Here, we propose a probabilistic strategy of ancestral sequence reconstruction (ASR) and Hidden Markov Model (HMM) profile search to fish out sequences of anti-CRISPR proteins from environmental metagenomic, human microbiome metagenomic, human microbiome reference genome, and NCBI's non-redundant databases. Our results revealed that the metagenome database dark matter might contain anti-CRISPR encoding genes.

Cobalt-doped copper vanadate: a dual active electrocatalyst propelling efficient H2 evolution and glycerol oxidation in alkaline water

Strategically doped metal oxide nanomaterials signify a rapidly growing genre of functional materials with a wide range of practical applications. Copper vanadate (CuV) represents one such highly active system, which has been rarely explored following its doping with an abundant first-row transition metal. Here, we have developed a series of CuV samples with varying cobalt(ii) doping concentrations deploying a relatively simple solid state synthetic procedure. Among the samples, the 10% Co(ii)-doped CuV (Co_10%-CuV) exhibited excellent reactivity for both the H₂ evolution reaction (HER) and glycerol oxidation reaction (GOR) in an alkaline aqueous medium (pH 14.0) during cathodic and anodic scans, respectively. During this dual-active catalysis, surface-immobilized Co_10%-CuV operates at exceptionally low overpotentials of 176 mV and 160 mV for the HER and GOR, respectively, while achieving 10 mA cm² current density. The detailed spectroscopic analysis revealed the formation of formate as the major product during the GOR with a faradaic efficiency of >90%. Therefore, this Co_10%-CuV can be included on either side of a two-electrode electrolyzer assembly to trigger a complete biomass-driven H₂ production, establishing an ideal carbon-neutral energy harvest process.

Crossing N=28 Toward the Neutron Drip Line: First Measurement of Half-Lives at FRIB

New half-lives for exotic isotopes approaching the neutron drip-line in the vicinity of N∼28 for Z=12-15 were measured at the Facility for Rare Isotope Beams (FRIB) with the FRIB decay station initiator. The first experimental results are compared to the latest quasiparticle random phase approximation and shell-model calculations. Overall, the measured half-lives are consistent with the available theoretical descriptions and suggest a well-developed region of deformation below ^{48}Ca in the N=28 isotones. The erosion of the Z=14 subshell closure in Si is experimentally confirmed at N=28, and a reduction in the ^{38}Mg half-life is observed as compared with its isotopic neighbors, which does not seem to be predicted well based on the decay energy and deformation trends. This highlights the need for both additional data in this very exotic region, and for more advanced theoretical efforts.

Fighting Cancer around the World: A Framework for Action

Tackling cancer is a major challenge right on the global level. Europe is only the tip of an iceberg of cancer around the world. Prosperous developed countries share the same problems besetting Europe-and the countries and regions with fewer resources and less propitious conditions are in many cases struggling often heroically against a growing tide of disease. This paper offers a view on these geographically wider, but essentially similar, challenges, and on the prospects for and barriers to better results in this ceaseless battle. A series of panels have been organized by the European Alliance for Personalised Medicine (EAPM) to identify different aspects of cancer care around the globe. There is significant diversity in key issues such as NGS, RWE, molecular diagnostics, and reimbursement in different regions. In all, it leads to disparities in access and diagnostics, patients' engagement, and efforts for a better understanding of cancer.

Ethnodermatological use of medicinal plants in India: From ayurvedic formulations to clinical perspectives - A review

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional knowledge is a particular form of practice or skill set that was developed in ancient times and was sustained through generations via the passing of knowledge, essentially confined within a specific tribe, local people, or family lineages. Ethnodermatological use of medicinal plants in India is still a subject to conduct more studies to see if there is chemical, microbiological, and/or clinical evidence, from a scientific perspective, of their effectiveness for those skin disorders. Thus, this review can be the basis for further studies and may provide targets for drug development.

AIM OF THE STUDY

We compile and emphasize the most important part of ethnodermatology, namely, traditional knowledge of medicinal plants and their applications for several skin diseases in India. We also include a brief review and explanation on dermatology in Ayurvedic and Unani medicine. We review the pharmacological activity of extracts derived from some of the most cited plants against problem skin diseases as well.

MATERIALS AND METHODS

Different kinds of key phrases such as "Indian traditional ethnodermatology", "ethnodermatology", "ethnobotany", "skin diseases", "Ayurveda dermatology", "pharmacological activity" were searched in online search servers/databases such as Google Scholar (https://scholar.google.com/), ResearchGate (https://www.researchgate.net/), PubMed (https://pubmed.ncbi.nlm.nih.gov/), NISCAIR Online Periodicals Repository (NOPR) (http://nopr.niscair.res.in/). Based upon the analyses of data obtained from 178 articles, we formulated several important findings which are a summary shown in Tables. Tables. A total of 119 records of plants' uses have been found across India against 39 skin diseases. These are depicted with their localities of report, parts used, and preparation and administration methods against particular skin diseases.

RESULTS

The knowledge and utilisation of herbal medicine in the Indian subcontinent has great potential to treat different kinds of human skin disorders. The administration of extracts from most of the plant species used is topical and few only are administrated orally. We also investigated the pharmacological activity of the extracts of the most cited plants against mice, bacterial and fungal pathogens, and human cells.

CONCLUSIONS

Complementary therapy for dermatological problems and treatment remains the main option for millions of people in the Indian subcontinent. This review on the practices of ethnobotanical dermatology in India confirms the belief that their analysis will accelerate the discovery of new, effective therapeutic agents for skin diseases. However, more studies and clinical evidence are still required to determine if the identified species may contribute to skin condition treatment, particularly in atopic eczema. Today, ethnodermatology is a well-accepted international discipline and many new practices have been initiated in numerous countries. We hope this article will further accelerate the development of this area to identify a new generation of natural human skin treatments that will help meet the growing consumer demand for safe, sustainable, and natural treatments. In this context, research on plants utilised in ethnodermatology in India and elsewhere should be intensified.

Bacosides from Bacopa monnieri extract: An overview of the effects on neurological disorders

From ancient history, complementary and alternative medicines have played a significant role as holistic therapeutic treatments of various human diseases including cancer, diabetes, neurological diseases, and skin problems. One Indian medicinal plant (herb), Bacopa monnieri has been used in many parts of the world as such medicine, particularly for the treatment of various neurological disorders. It is well known as a potent "tonic for the human brain," which serves as a memory enhancer. Multiple studies proved that this herb contains a plethora of potential bioactive, phytochemical compounds with synergistic properties. The main purpose of the present review is to shed light on the use of Bacopa monnieri and its active principles (bacosides) in the management of neurological disorders. Furthermore, the signaling pathways modulated by bacosides have been critically discussed in this review. Moreover, we have critically summarized the present knowledge of this perennial creeping herb based upon the literature mining from different scientific engines.

Pharmacological properties, therapeutic potential, and legal status of Cannabis sativa L.: An overview

Marijuana, or Cannabis sativa L., is a common psychoactive plant used for both recreational and medicinal purposes. In many countries, cannabis-based medicines have been legalized under certain conditions because of their immense prospects in medicinal applications. With a comprehensive insight into the prospects and challenges associated with the pharmacological use and global trade of C. sativa, this mini-review focuses on the medicinal importance of the plant and its legal status worldwide; the pharmacological compounds and its therapeutic potential along with the underlying public health concerns and future perspective are herein discussed. The existence of major compounds including Δ⁹ -tetrahydrocannabinol (Δ⁹ -THC), cannabidiol, cannabinol, and cannabichromene contributes to the medicinal effects of the cannabis plant. These compounds are also involved in the treatment of various types of cancer, epilepsy, and Parkinson's disease displaying several mechanisms of action. Cannabis sativa is a plant with significant pharmacological potential. However, several aspects of the plant need an in-depth understanding of the drug mechanism and its interaction with other drugs. Only after addressing these health concerns, legalization of cannabis could be utilized to its full potential as a future medicine.

SARS-CoV-2 and other viruses in soil: An environmental outlook

In the present review, the authors shed light on the SARS-CoV-2 impact, persistence, and monitoring in the soil environment. With this purpose, several aspects have been deepened: i) viruses in soil ecosystems; ii) direct and indirect impact on the soil before and after the pandemic, and iii) methods for quantification of viruses and SARS-CoV-2 monitoring in soil. Viruses are present in soil (i.e. up to 417 × 10⁷ viruses per g TS^-1 in wetlands) and can affect the behavior and ecology of other life forms (e.g. bacteria), which are remarkably important for maintaining environmental equilibrium. Also, SARS-CoV-2 can be found in soil (i.e. up to 550 copies·g^-1). Considering that the SARS-CoV-2 is very recent, poor knowledge is available in the literature on persistence in the soil and reference has been made to coronaviruses and other families of viruses. For instance, the survival of enveloped viruses (e.g. SARS-CoV) can reach 90 days in soils with 10% of moisture content at ambient. In such a context, the possible spread of the SARS-CoV-2 in the soil was evaluated by analyzing the possible contamination routes.

Potential Therapeutic Targets and Vaccine Development for SARS-CoV-2/COVID-19 Pandemic Management: A Review on the Recent Update

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly pathogenic novel virus that has caused a massive pandemic called coronavirus disease 2019 (COVID-19) worldwide. Wuhan, a city in China became the epicenter of the outbreak of COVID-19 in December 2019. The disease was declared a pandemic globally by the World Health Organization (WHO) on 11 March 2020. SARS-CoV-2 is a beta CoV of the Coronaviridae family which usually causes respiratory symptoms that resemble common cold. Multiple countries have experienced multiple waves of the disease and scientific experts are consistently working to find answers to several unresolved questions, with the aim to find the most suitable ways to contain the virus. Furthermore, potential therapeutic strategies and vaccine development for COVID-19 management are also considered. Currently, substantial efforts have been made to develop successful and safe treatments and SARS-CoV-2 vaccines. Some vaccines, such as inactivated vaccines, nucleic acid-based, and vector-based vaccines, have entered phase 3 clinical trials. Additionally, diverse small molecule drugs, peptides and antibodies are being developed to treat COVID-19. We present here an overview of the virus interaction with the host and environment and anti-CoV therapeutic strategies; including vaccines and other methodologies, designed for prophylaxis and treatment of SARS-CoV-2 infection with the hope that this integrative analysis could help develop novel therapeutic approaches against COVID-19.

Photoluminescence with Peaked Structure: Inherent to Nanoparticles or Resulting From Impurities in Sample Vial Caps?

We show that fluorescence emission in the visible spectral range reported in the case of many nanoparticles, polymers, complexes and liquid crystals with molecular type signatures could originate from the organic impurities leaching from the caps of glass vials.

Novel coronavirus disease 2019 (COVID-19) pandemic: From transmission to control with an interdisciplinary vision

There a lot of review papers addressing specific COVID-19 research sectors, then devoted to specialists. This review provides an in-depth summary of the available information about SARS-CoV-2 and the corresponding disease (also known as COVID-19), with a multi-disciplinary approach. After the paper introduction, the first section treats the virological characteristics of SARS-CoV-2, the medical implications of the infection, and the human susceptivity. Great attention is devoted to the factor affecting the infection routes, distinguishing among the possible human-to-human, environmental-to-human, and pollution-to-human transmission mechanisms. The second section is devoted to reporting the impact of SARS-CoV-2 not only on the healthcare systems but also on the economy and society. The third section is devoted to non-pharmaceutical behaviours against COVID-19. In this context, this review section presents an analysis of the European second wave allowing not only to focalize the importance of some restrictions, but also the relevance of social acceptance of some measures. The data reassumed in this work are very useful for interdisciplinary researchers that work in a team to find the basic available information about all the aspects connected with this pandemic (from virus diffusion mechanism to health information, from economic and social impacts to measures to reduce the pandemic spread), with great attention to social acceptance of restriction measures and of vaccines (that currently results to be insufficient to achieve community immunity). Then, this review paper highlights the fundamental role of the trans-multi-disciplinary research that is devoted not only to understand the basics of the pandemic to propose solutions but has also the commitment to find strategies to increase population resilience. For this aim, the authors strongly suggest the establishment of an international health-care trans-multi-disciplinary workforce devoted to investigate, mitigate, and control also future viral events.

Novel coronavirus disease 2019 (COVID-19) pandemic: From transmission to control with an interdisciplinary vision

There a lot of review papers addressing specific COVID-19 research sectors, then devoted to specialists. This review provides an in-depth summary of the available information about SARS-CoV-2 and the corresponding disease (also known as COVID-19), with a multi-disciplinary approach. After the paper introduction, the first section treats the virological characteristics of SARS-CoV-2, the medical implications of the infection, and the human susceptivity. Great attention is devoted to the factor affecting the infection routes, distinguishing among the possible human-to-human, environmental-to-human, and pollution-to-human transmission mechanisms. The second section is devoted to reporting the impact of SARS-CoV-2 not only on the healthcare systems but also on the economy and society. The third section is devoted to non-pharmaceutical behaviours against COVID-19. In this context, this review section presents an analysis of the European second wave allowing not only to focalize the importance of some restrictions, but also the relevance of social acceptance of some measures. The data reassumed in this work are very useful for interdisciplinary researchers that work in a team to find the basic available information about all the aspects connected with this pandemic (from virus diffusion mechanism to health information, from economic and social impacts to measures to reduce the pandemic spread), with great attention to social acceptance of restriction measures and of vaccines (that currently results to be insufficient to achieve community immunity). Then, this review paper highlights the fundamental role of the trans-multi-disciplinary research that is devoted not only to understand the basics of the pandemic to propose solutions but has also the commitment to find strategies to increase population resilience. For this aim, the authors strongly suggest the establishment of an international health-care trans-multi-disciplinary workforce devoted to investigate, mitigate, and control also future viral events.

A review of the presence of SARS-CoV-2 RNA in wastewater and airborne particulates and its use for virus spreading surveillance

According to the WHO, on October 16, 2020, the spreading of the SARS-CoV-2, responsible for the COVID-19 pandemic, reached 235 countries and territories, and resulting in more than 39 million confirmed cases and 1.09 million deaths globally. Monitoring of the virus outbreak is one of the main activities pursued to limiting the number of infected people and decreasing the number of deaths that have caused high pressure on the health care, social, and economic systems of different countries. Wastewater based epidemiology (WBE), already adopted for the surveillance of life style and health conditions of communities, shows interesting features for the monitoring of the COVID-19 diffusion. Together with wastewater, the analysis of airborne particles has been recently suggested as another useful tool for detecting the presence of SARS-CoV-2 in given areas. The present review reports the status of research currently performed concerning the monitoring of SARS-CoV-2 spreading by WBE and airborne particles. The former have been more investigated, whereas the latter is still at a very early stage, with a limited number of very recent studies. Nevertheless, the main results highlights in both cases necessitate more research activity for better understating and defining the biomarkers and the related sampling and analysis procedures to be used for this important aim.

Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives

According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.

Phytotherapy and food applications from Brassica genus

Plants of the genus Brassica occupy the top place among vegetables in the world. This genus, which contains a group of six related species of a global economic significance, three of which are diploid: Brassica nigra (L.) K. Koch, Brassica oleracea L., and Brassica rapa L. and three are amphidiploid species: Brassica carinata A. Braun, Brassica juncea (L.) Czern., and Brassica napus L. These varieties are divided into oily, fodder, spice, and vegetable based on their morphological structure, chemical composition, and usefulness of plant organs. The present review provides information about habitat, phytochemical composition, and the bioactive potential of Brassica plants, mainly antioxidant, antimicrobial, anticancer activities, and clinical studies in human. Brassica vegetables are of great economic importance around the world. At present, Brassica plants are grown together with cereals and form the basis of global food supplies. They are distinguished by high nutritional properties from other vegetable plants, such as low fat and protein content and high value of vitamins, fibers along with minerals. In addition, they possess several phenolic compounds and have a unique type of compounds namely glucosinolates that differentiate these crops from other vegetables. These compounds are also responsible for numerous biological activities to the genus Brassica as described in this review.

Phenolic Composition, Antioxidant Capacity and Antibacterial Activity of White Wormwood (Artemisia herba-alba)

Artemisia herba-alba Asso. (Wormwood) is a wild aromatic herb that is popular for its healing and medicinal effects and has been used in conventional as well as modern medicine. This research aimed at the extraction, identification, and quantification of phenolic compounds in the aerial parts of wormwood using Soxhlet extraction, as well as characterizing their antimicrobial and anitoxidant effects. The phenolic compounds were identified in different extracts by column chromatography, thin layer chromatography (TLC), and high performance liquid chromatography. Five different fractions, two from ethyl acetate extraction and three from ethanolic extraction were obtained and evaluated further. The antimicrobial activity of each fractions was evaluated against two Gram-positive (Bacillus cereus and Staphylococcus aureus) and two Gram-negative microorganisms (Escherichia coli and Proteus vulgaris) using the disc-diffusion assay and direct TLC bioautography assay. Fraction I inhibited B. cereus and P. vulgaris, Fraction II inhibited B. cereus and E. coli, Fraction III inhibited all, except for P. vulgaris, while Fractions IV and V did not exhibit strong antimicrobial effects. Their antioxidant capabilities were also measured by calculating their ability to scavenge the free radical using DPPH method and the ferric reducing antioxidant power (FRAP) assay. Ethanolic fractions III and V demonstrated excellent antioxidant properties with IC50 values less than 15.0 μg/mL, while other fractions also had IC50 values less than 80.0 μg/mL. These antioxidant effects were highly associated with the number of phenolic hydroxyl group on the phenolics they contained. These extracts demonstrated antimicrobial effects, suggesting the different phenolic compounds in these extracts had specific inhibitory effects on the growth of each bacteria. The results of this study suggested that the A. herba-alba can be a source of phenolic compounds with natural antimicrobial and antioxidant properties which can be used for potential pharmaceutical applications.

Detecting antimicrobial peptides by exploring the mutual information of their sequences

The rise of antibiotic resistance in pathogenic bacteria is a growing concern for every part of the world. The present study shows the prediction efficiency of mutual information for the classification of antimicrobial peptides. The proven role of antimicrobial peptides (AMPs) to fight against multidrug-resistant pathogens and AMP's low toxic properties laid the foundation of computational methods to play their role in detecting AMPs from non-AMPs. Mutual information vectors (MIV) were created for AMP/non-AMP sequences and then fed to different machine learning classifiers out of which a random forest (RF) classifier showed best results for predicting AMPs. Random forest classifiers were evaluated on benchmark datasets by 10-fold cross-validation. The proposed MIV-RF method showed better prediction accuracy, MCC (Matthews correlation coefficient), and AUC-ROC (Area Under The Curve-Receiver Operating Characteristics) than available methods for detecting AMPs.Communicated by Ramaswamy H. Sarma.

Attitudes towards risk-reducing early salpingectomy with delayed oophorectomy for ovarian cancer prevention: a cohort study

OBJECTIVE

To determine risk-reducing early salpingectomy and delayed oophorectomy (RRESDO) acceptability and effect of surgical prevention on menopausal sequelae/satisfaction/regret in women at increased ovarian cancer (OC) risk.

DESIGN

Multicentre, cohort, questionnaire study (IRSCTN:12310993).

SETTING

United Kingdom (UK).

POPULATION

UK women without OC ≥18 years, at increased OC risk, with/without previous RRSO, ascertained through specialist familial cancer/genetic clinics and BRCA support groups.

METHODS

Participants completed a 39-item questionnaire. Baseline characteristics were described using descriptive statistics. Logistic/linear regression models analysed the impact of variables on RRESDO acceptability and health outcomes.

MAIN OUTCOMES

RRESDO acceptability, menopausal sequelae, satisfaction/regret.

RESULTS

In all, 346 of 683 participants underwent risk-reducing salpingo-oophorectomy (RRSO). Of premenopausal women who had not undergone RRSO, 69.1% (181/262) found it acceptable to participate in a research study offering RRESDO. Premenopausal women concerned about sexual dysfunction were more likely to find RRESDO acceptable (odds ratio [OR] = 2.9, 95% CI 1.2-7.7, P = 0.025). Women experiencing sexual dysfunction after premenopausal RRSO were more likely to find RRESDO acceptable in retrospect (OR = 5.3, 95% CI 1.2-27.5, P < 0.031). In all, 88.8% (143/161) premenopausal and 95.2% (80/84) postmenopausal women who underwent RRSO, respectively, were satisfied with their decision, whereas 9.4% (15/160) premenopausal and 1.2% (1/81) postmenopausal women who underwent RRSO regretted their decision. HRT uptake in premenopausal individuals without breast cancer (BC) was 74.1% (80/108). HRT use did not significantly affect satisfaction/regret levels but did reduce symptoms of vaginal dryness (OR = 0.4, 95% CI 0.2-0.9, P = 0.025).

CONCLUSION

Data show high RRESDO acceptability, particularly in women concerned about sexual dysfunction. Although RRSO satisfaction remains high, regret rates are much higher for premenopausal women than for postmenopausal women. HRT use following premenopausal RRSO does not increase satisfaction but does reduce vaginal dryness.

TWEETABLE ABSTRACT

RRESDO has high acceptability among premenopausal women at increased ovarian cancer risk, particularly those concerned about sexual dysfunction.

Next-Generation Sequencing: An Emerging Tool for Drug Designing

BACKGROUND

With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production.

METHOD

In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques.

DISCUSSIONS

The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day.

CONCLUSION

Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

Nanotechnological interventions for plant health improvement and sustainable agriculture

Agriculture is the source of food for both humans and animals. With the growing population demands, agricultural production needs to be scaled up where nanotechnology can play a significant role. The use of nanotechnology in agriculture can manage plant disease and growth for better and quality output. Therefore, this review focuses on the use of various nanoparticles for detection of nutrients and contaminants, nanosensors for monitoring the environmental stresses and crop conditions as well as the use of nanotechnology for plant pathogen detection and crop protection. In addition, the delivery of plant growth regulators and agrichemicals like nanopesticides and nanofertilizers to the plants along with the delivery of DNA for targeted genetic engineering and production of genetically modified (GM) crops are discussed briefly. Further, the future concerns regarding the use of nanoparticles and their possible toxicity, impact on the agriculture and ecosystem needs to be assessed along with the assessment of the nanoparticles and GM crops on the environment and human health.

Dynamics of gene expression of hormones involved in the growth of broiler chickens in response to the dietary protein and energy changes

The synergy between the genetic potential and the nutrient intake determines the growth performance of meat-type chicken and nutrigenomics approach helps us understand the response of candidate genes of growth in chicken to dietary manipulations. The current study aimed to assess the growth performance and expression of hepatic growth related genes in the naked neck broiler chicken in response to different dietary energy and protein levels with a hypothesis that high plane of nutrition enhances both of these positively. The results revealed that birds have shown significantly better growth performance under high protein (HP) and high energy (HE) dietary regime. The expression profiles of the genes studied revealed upregulation of IGF-1, IGF-2, and GH under dietary HP and HE regime relative to other protein and energy levels with greater upregulation at 3rd week than the 1st and 5th week of age of birds. The IGFR and GHR mRNA expression was significantly higher under HP and HE dietary regimen with an increasing and decreasing trend from 1st to 5th week of age, respectively. A consistent and significant downregulation of IGFBP-2 was observed under HP and HE regime throughout the feeding trial. The myostatin expression was higher at 3rd week of age followed by 1st week expression. The HP and HE as well as LP (Low protein) and HE diet resulted in significant upregulation of myostatin gene expression in liver. In support to the set hypothesis of this study the high protein and high energy diet resulted in better growth performance of broiler chickens with corresponding upregulation of IGF-1, IGF-2, IGFR, GH, GHR, and Myostatin gene expression and downregulation of IGFBP-2 in liver.

Microwave-induced electric discharges on metal particles for the synthesis of inorganic nanomaterials under solvent-free conditions

Microwave irradiation of metals generates electric discharges (arcs). These arcs are used to generate nanoparticles of Cu and Ni and one-dimensional nanorods of CuS, ZnF₂, and NiF₂ protected with fluorinated amorphous carbon. We have also synthesized reduced graphene oxide and partially rolled graphene by this method.

Recent Advances in the System Biology-based Target Identification and Drug Discovery

The enormous quantity of publicly available active chemical ligand and biological receptor data knowledge allows scientists to retreat several open questions by the analysis and systematic integration of these complex unique data. Systems biology plays a crucial role through the constructive alignment of bio-physiochemical monitoring of gene, protein along with metabolites from the complex data. Further, it integrates information within the data and responses (metabolic and signaling pathway) which lead to the formulation of computational models for the elucidation of structure and function of the molecular determinant. The system biology methods utilize big complex high throughput data for the identification of the whole drug target and for the mechanism of action to lead compound characterization. Nowadays, the system biology is one of the most popular approaches to characterize proteinligand interaction on a large scale and is vital to address a complex mode of the drug action to clinical indications. The network of protein-ligand interactions also reveals the correlation between molecular functions of the cell with their physiological processes which help to design safe and effective ligands for drug development. Here, we review recent attempts to apply system biology-based approaches with large-scale network analyses to predict novel interactions of ligand and targets. We also deliver an essential step involved in the discovery and development of such multi-target drugs by identifying the group of proteins targeted by a particular ligand, leading to innovation in therapeutic research.

Distribution of cyanobacteria and their interactions with pesticides in paddy field: A comprehensive review

Cyanobacteria, also known as blue green algae are one of the important ubiquitous oxygen evolving photosynthetic prokaryotes and ultimate source of nitrogen for paddy fields since decades. In past two decades, indiscriminated use of pesticides led to biomagnification that intensively harm the structure and soil functions of soil microbes including cyanobacteria. Cyanobacterial abundance biomass, short generation, water holding capacity, mineralizing capacity and more importantly nitrogen fixing have enormous potential to abate the negative effects of pesticides. Therefore, investigation of the ecotoxicological effects of pesticides on the structure and function of the tropical paddy field associated cyanobacteria is urgent and need to estimate the fate of interaction of pesticides over nitrogen fixations and other attributes. In this regard, comprehensive survey over cyanobacterial distribution patterns and their interaction with pesticides in Indian context has been deeply reviewed. In addition, the present paper also deals the molecular docking pattern of pesticides with the nitrogen fixing proteins, which helps in revealing the functional interpretation over nitrogen fixation process.

Vibrational spectroscopic study of cationic phosphorus dendrimers with aminoethylpiperidine terminal groups

Two generations of phosphoric dendrimers with piperidine functional groups were synthesized for use in biology and medicine. Neutral samples are soluble in organic solvents but after protonation these dendrimers become water soluble and can be used for biological experiments. The FTIR and FT Raman spectra of two generations of dendrimers G_i constructed from the cyclotriphosphazene core, repeating units OC₆H₄CHNN(CH₃)P(S)< and aminoethylpiperidine end groups NH(CH₂)₂C₅NH₁₁ were recorded. The study of the IR spectra shows that the NH groups form hydrogen bonds. The calculation of the molecular structure and vibrational spectra of the first generation dendrimer was performed by the method of DFT. This molecule has flat, repeating units and a plane of symmetry passing through the core. The calculation of the distribution of potential energy made it possible to classify the bands in the experimental spectra of dendrimers. Amine groups are manifested in the form of a band of NH stretching vibrations at 3389 cm^-1 in the IR spectrum of G₁. NH⁺ stretching bands located at 2646 and 2540 cm^-1 in the IR spectrum of G₂. The stretching vibrations of NH⁺ groups are noticeably shifted to low frequencies due to the formation of a hydrogen bond with the chlorine atom. The line at 1575 cm^-1 in the Raman spectrum of G₁ is characteristic for repeating units.

The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor

Dectin-1 is a recently discovered pattern-recognition receptor that plays an important role in antifungal innate immunity, which acts a specific receptor for β-glucan (BG). The present study, aimed at clarifying effect of BG and a new analog, maltotriose (MT) on Dectin-1 receptor. We implemented molecular docking of MT on Dectin-1 along with model-independent all-atom-molecular dynamics simulations. Simulations were carried out at three levels of complexity: (1) Apo-Dectin-1; (2) BG:Dectin-1; (3) MT:Dectin-1. All three system complexes were undergone stability check before showing a comparative analysis. A characteristic feature, noted for the MT:Dectin-1, is a shifting of loops (loop1 and loop2) orientation towards atoms of MT, a broad interaction suggested a robust and tight binding on comparison with BG:Dectin-1. Free energy estimation corroborated the observation, which furthermore, made a close agreement by revealing contribution of energy components of interacting residues. In addition, cluster analysis of complexes exhibit a smooth continuous transition to a new confirmation, represented by a series of clusters each having a longer lifetime. Principal component analysis revealed a broken pipe at binding site of BG:Dectin-1 during movement of atoms whereas in MT:Dectin-1 exhibited wide band and high amplitude motion of atoms in trajectory, was due to loop orientation toward MT. Observation was further shown by measuring distances and hydrogen binding calculation. Simulations of the BG:Dectin-1 and MT:Dectin-1 complex revealed first time the influence of BG and MT ligands. This study might extend the knowledge of the BG and MT interaction on Dectin-1 and proposed further potential bioassay of MT.

High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments

Integrons are extensively targeted as a proxy for anthropogenic impact in the environment. We developed a novel high-throughput amplicon sequencing pipeline that enables characterization of thousands of integron gene cassette-associated reads, and applied it to acquire a comprehensive overview of gene cassette composition in effluents from wastewater treatment facilities across Europe. Between 38 100 and 172 995 reads per-sample were generated and functionally characterized by screening against nr, SEED, ARDB and β-lactamase databases. Over 75% of the reads were characterized as hypothetical, but thousands were associated with toxin-antitoxin systems, DNA repair, cell membrane function, detoxification and aminoglycoside and β-lactam resistance. Among the reads characterized as β-lactamases, the carbapenemase bla_OXA was dominant in most of the effluents, except for Cyprus and Israel where bla_GES was also abundant. Quantitative PCR assessment of bla_OXA and bla_GES genes in the European effluents revealed similar trends to those displayed in the integron amplicon sequencing pipeline described above, corroborating the robustness of this method and suggesting that these integron-associated genes may be excellent targets for source tracking of effluents in downstream environments. Further application of the above analyses revealed several order-of-magnitude reductions in effluent-associated β-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.

Cardioprotective potential of curcumin against norepinephrine-induced cell death: a microscopic study

Cardiomyopathy and associated heart failure continues to be one of the most severe complications that threaten a large population. Curcumin, one of the three curcuminoids of the spice turmeric, is very well known for a multitude of health benefits and functions. Norepinephrine (NE), a catecholamine and also a stress hormone may cause the cardiomyocytes to develop increased sensitivity to death with its increasing concentrations. In this study, we investigated the cardioprotective effect of curcumin in NE-induced cardiac apoptosis using several fluorescent and nonfluorescent microscopic techniques like DAPI, PI, Giemsa, PicroSirius and TUNEL. The aim of the study was to assess the effect of curcumin in preventing the occurrence of features underlying apoptosis such as nuclear disruption, chromatin condensation, DNA fragmentation and alterations in mitochondrial membrane permeability. Our results show that curcumin protects the cardiomyocytes against apoptosis significantly and also helps them to revert to their normal physiological state. Hence, we propose that curcumin has the potential to act as a therapeutic agent for the attenuation of NE-induced cardiac cell death and modulation of apoptosis in H9c2 cardiomyocytes.

Novel Peptides Enhance the Production of Nitric Oxide and Inducible Nitric Oxide Synthase (iNOS) Gene Expression in Murine Macrophage

Bioactive novel polypeptide of Anurans skin has a wide range of antimicrobial properties against the infection and tumour cell. Macrophages are known to produce the Nitric oxide (NO) by a variety of cells upon activation. NO produced by the activated macrophages an important mediator for antimicrobial and tumoricidal activity. In-vitro macrophage exposed with medium alone, containing LPS, containing polypepeptides and LPS + polypeptides for 24 h showed enhanced production of NO with respect to control and LPS treated and significant increase in NO production in LPS + polypeptide. Western blot and PCR analysis also showed that increased production of protein expression and mRNA expression of inducible nitric oxide synthase (iNOS). These findings suggest that novel polypeptides are potent activating agent for enhanced production of NO through activation of iNOS gene.

Berry phase mechanism of the anomalous Hall effect in a disordered two-dimensional magnetic semiconductor structure

The anomalous Hall effect (AHE) arises from the interplay of spin-orbit interactions and ferromagnetic order and is a potentially useful probe of electron spin polarization, especially in nanoscale systems where direct measurement is not feasible. While AHE is rather well-understood in metallic ferromagnets, much less is known about the relevance of different physical mechanisms governing AHE in insulators. As ferromagnetic insulators, but not metals, lend themselves to gate-control of electron spin polarization, understanding AHE in the insulating state is valuable from the point of view of spintronic applications. Among the mechanisms proposed in the literature for AHE in insulators, the one related to a geometric (Berry) phase effect has been elusive in past studies. The recent discovery of quantized AHE in magnetically doped topological insulators - essentially a Berry phase effect - provides strong additional motivation to undertake more careful search for geometric phase effects in AHE in the magnetic semiconductors. Here we report our experiments on the temperature and magnetic field dependences of AHE in insulating, strongly-disordered two-dimensional Mn delta-doped semiconductor heterostructures in the hopping regime. In particular, it is shown that at sufficiently low temperatures, the mechanism of AHE related to the Berry phase is favoured.

A case of co-existing paraganglioma and thymoma

Background

Head and neck paragangliomas are rare tumours and can arise as a part of inherited syndromes. Their association with thymic tumour is not well known.

Case description

This report describes a female patient who presented with right sided neck paragangliomas. The histology of the tumour was consistent with paraganlioma. Few years later her MRI scan of the chest revealed presence of an anterior mediastinal mass that corresponded to the location of the thymus. Review of her previous scans showed that the mass was present all along and had gradually increased in size. Patient developed symptoms including fatigue, dyspnoea, migratory polyarthritis, Raynaud’s phenomenon and erythema nodosum. She had sternotomy and excision of mediastinal mass. The histology was consistent with cortical thymoma (WHO type B2) and she had radiotherapy. After treatment her constitutional symptoms improved. Her paraganglioma susceptibility genes are negative.

Discussion and evaluation

To our knowledge this is only the second case report in the literature of coexistence of carotid body tumour and thymoma. The first case reported was bilateral carotid body tumour, thyroid gland adenoma and thymoma. This case also highlights the importance of long term surveillance, multidisciplinary management and being aware of associated pathologies in patients with isolated paraganglioma.

Strong nucleosomes of yeasts

Yeast genome lacks visibly periodic sequences characteristic of strong nucleosomes (SNs) originally discovered in A. thaliana, C. elegans, and H. sapiens. Yet, the sequences with good match to the (RRRRRYYYYY)n consensus of the SNs do show preference to centromere regions of Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Cryptococcus neoformans - property characteristic of SNs of higher eukaryotes. Candida albicans is the first exception detected so far, where their SNs do not have any affinity to the centromeres, nor pericentromeric regions. Three of the four yeast genomes analyzed possess unique repeating centromere-specific SN sequences (C. albicans, again, is an exception). The results firmly indicate that centromeres of plants, animals, and yeasts in general have special chromatin structure, favoring SNs.

Statistical approach for lysosomal membrane proteins (LMPs) identification

Discrimination of Lysosomal membrane proteins (LMP's) from folding types of globular (GPs) and other membrane proteins (OtMPs) is an important task both for identifying LMPs from genomic sequences and for the successful prediction of their secondary and tertiary structures. We have systematically analyzed the amino acid frequencies as well as dipeptide count of GPs, LMPs and OtMPs. Based on the above calculated single amino acid frequency combined with dipeptide count information, we statistically discriminated LMPs from GPs and OtMPs. This approach correctly classified the LMPs with an accuracy of 95 %. On the other hand, the amino acid frequency alone can discriminate LMPs with an accuracy of only 79 %. Similarly dipeptide count alone has an accuracy of 87 % for the discrimination of LMPs. Thus the combined information of both amino acid frequencies and dipeptide composition gives us significant high accurate results.

Molecular phylogenetics and comparative modeling of MnSOD, an enzyme involved during environmental stress conditions in Oryza sativa

Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen. Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn (III) at the active site. The three dimensional structure of MnSOD of Oryza sativa is not yet available in protein data bank so we have predicted the structure model of O. sativa MnSOD using homology modeling. The predicted model can further be explored for identification of ligand binding sites which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated that the phylogenetic analysis of O. sativa MnSOD protein with distinct dicot and monocot plant species. The MnSOD protein of O. sativa has shown similarity with both monocot and as well as dicot plant species.

Strong nucleosomes of mouse genome including recovered centromeric sequences

Recently discovered strong nucleosomes (SNs) characterized by visibly periodical DNA sequences have been found to concentrate in centromeres of Arabidopsis thaliana and in transient meiotic centromeres of Caenorhabditis elegans. To find out whether such affiliation of SNs to centromeres is a more general phenomenon, we studied SNs of the Mus musculus. The publicly available genome sequences of mouse, as well as of practically all other eukaryotes do not include the centromere regions which are difficult to assemble because of a large amount of repeat sequences in the centromeres and pericentromeric regions. We recovered those missing sequences using the data from MNase-seq experiments in mouse embryonic stem cells, where the sequence of DNA inside nucleosomes, including missing regions, was determined by 100-bp paired-end sequencing. Those nucleosome sequences, which are not matching to the published genome sequence, would largely belong to the centromeres. By evaluating SN densities in centromeres and in non-centromeric regions, we conclude that mouse SNs concentrate in the centromeres of telocentric mouse chromosomes, with ~3.9 times excess compared to their density in the rest of the genome. The remaining non-centromeric SNs are harbored mainly by introns and intergenic regions, by retro-transposons, in particular. The centromeric involvement of the SNs opens new horizons for the chromosome and centromere structure studies.