National Center For Biotechnology Information Research Articles

THE IMPORTANCE OF trnL/trnF IGS REGION IN THE TAXONOMY OF THE GENUS Potentilla L.

This study was performed to determine the phylogenetic relationships in the genus Potentilla L. and to assess the importance of the trnL/trnF intergenic spacer (IGS) region. The selection of DNA barcoding region to provide for more effective, accurate and consistent results in the analysis is one of the most important points in success of the study. For this purpose, 71 Potentilla taxa were examined based on trnL/trnF IGS sequence data of chloroplast DNA acquired from the National Center for Biotechnology Information (NCBI) and a Maximum Parsimony (MP) dendrogram was drawn. The trnL/trnF IGS region has the convenient sequence length for barcoding region, and it is also proposed the use of this region which has highly variable and parsimony informative sites. When the probabilities of substitutions from one base to another base for trnL/trnF IGS region were examined, it was assigned that the rate of transitional substitutions with 57.13% is higher than the transversional substitutions. The MP dendrogram revealed that the studies taxa were placed in six groups as Fragarioides, Reptans, Anserina, Alba, Himalayan and Argentea. Phylogenetic relationships within the Argentea clade, represented by the highest species number in this study, were observed as quite confusing compared to other clades. In order to get the most accurate results, it is necessary to determine the regions giving the best results, and then to use these regions together with as many taxa as possible. In conclusion, the using of trnL/trnF IGS sequence information that have high variable sites and grouping ability for studies taxa is strongly recommended.

Identification, Phytochemistry and Biological Activities of Paris polyphylla on Hepatocellular Carcinoma.

<b>Background and Objective:</b> Liver cancer is the common cause of cancer death. <i>Paris polyphylla</i> is used as a traditional folk medicine in Vietnam to treat pneumonia, mastitis, bruises and fractures but no study was available regarding its ability to treat liver cancer or slow its growth. In this study, <i>Paris polyphylla</i> samples were identified and evaluated cytotoxic activity against the liver cancer cells. <b>Materials and Methods:</b> <i>Paris polyphylla</i> species were collected from various areas in Yen Bai, Vietnam, which were identified by comparative morphological method and DNA barcoding for the <i>18S, matK</i> genes and <i>ITS</i> region. <i>Paris polyphylla</i> samples were dried until constant weight, ground into a fine powder and extracted in various solvents. The bioactivity of these extracts were done by the MTT assay. <b>Results:</b> The sequences of <i>18S, matK</i> genes and <i>ITS</i> region were high similarity to sequences of <i>P. polyphylla</i> in the National Center for Biotechnology Information. The N-hexane and ethyl acetate fractions were produced from the methanol extract of <i>P. polyphylla</i>. The TLC results showed that there was a significant difference in the component of n-hexane and ethyl acetate fraction. The N-hexane fraction contains mainly low-polarity and non-polarity substances. While ethyl acetate fraction consists mainly of polar substances. In addition, ethyl acetate fraction was shown the strongest cytotoxic activity on the cancer cell lines HepG2 and Huh7 with the evaluation of IC<sub>50</sub> = 115.11±2.77 μg mL<sup>1</sup> and IC<sub>50</sub> = 148.11±1.78 μg mL<sup>1</sup>. <b>Conclusion:</b> The extract of <i>Paris polyphylla</i> demonstrated strong potential to inhibit the growth of the liver cancer cell line. The ethyl acetate fraction has the highest ability for cytotoxicity on the liver and cell line at a concentration of 200 μg mL<sup>1</sup> through MTT.

Genetic characterization of infectious spleen and kidney necrosis virus in Banggai cardinalfish Pterapogon kauderni identified from eight separate cases between 2000 and 2017

The authors declare that there are no conflicts of interest associated with this publication. The data that support the findings of this study are openly available in National Center for Biotechnology Information at https://www.ncbi.nlm.nih.gov/, reference number MN432490, MT926123. Figure S1 Histologic appearance of a typical infected Banggai cardinalfish from the BCIV-2010 case. (a) and (b) Spleen: Basophilic inclusion bodies in megalocytic cells whose morphology is often obscured. Foci of necrosis within intervening pulp areas. (c) and (d) Kidney: Basophilic inclusion bodies in megalocytic cells within foci of interstitial haematopoietic necrosis. (e) and (f) Intestine: Basophilic inclusion bodies in megalocytic perivascular cells but minimal mucosal reaction. Pigmentation within normal limits. Original magnifications: (a, c) 100×, (d, e) 200×, (b, f) 400×; H&E stain. Figure S2 Conventional PCR results of the Banggai cardinalfish case from 2000 (BCIV-2000) using the MCV-F/R primers (Koda et al., 2018) and a 100 bp ladder. (a) a single positive band for BCIV-2000 at the 173 bp position. Samples (b) and (c) are negative and correspond to the extraction control and negative template control, respectively. (d) a single bright band at the 173 bp position, representing the positive control for the MCV assay. Table S1 Genome annotation of the Banggai cardinalfish iridovirus from 2012 (BCIV-2012). Table S2 Genome annotation of the Banggai cardinalfish iridovirus from 2017 (BCIV-2017). Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The trends in the spread of simple sequence repeats in the genomes of Schizophyllum commune

ABSTRACT Due to their high number and variety, simple sequence repeats in DNA are a valuable source of genetic markers widely used in population genetics, genetic diversity, and fingerprinting. Schizophyllum commune is a cosmopolitan basidiomycete and a valuable object for biotechnology and mycology. It is often used as a model organism in genetic and population studies. Numerous genome sequences of S. commune are available in the National Center for Biotechnology Information (NCBI) database, allowing for a meticulous study of the distribution of simple tandem nucleotide repeats in the genomes of different strains, based on their origin. Analysis of the average density of simple tandem repeats in the genomes of S. commune fungi reveals the division of cultures into groups based on the USA, Ru (Russian Federation), and EA (South Korea, Japan, China) populations. Intensive point mutations lead to the accumulation and dominance of mononucleotide (C)n and dinucleotide (CG)n motifs in fungal genomes. Results show that the GCT motif contributes more to the divergence of the Ru population, whereas CTC, GAG, and GGA motifs contribute to the divergence of the USA population. Strains MG53 (China) and IUM1114-SS01 (South Korea: Incheon) from the EA population occupy a separate position, mainly because of the CGA motif. The divergence in quantitative traits of motifs between populations provides evidence of the evolutionary transformation of fungal genomes under environmental factors.

Preliminary study to identify CXCR4 inhibitors as potential therapeutic agents for Alzheimer's and Parkinson's diseases.

Neurodegenerative disorders (NDDs) are known to exhibit genetic overlap and shared pathophysiology. This study aims to find the shared genetic architecture of Alzheimer's disease (AD) and Parkinson's disease (PD), two major age-related progressive neurodegenerative disorders. The gene expression profiles of GSE67333 (containing samples from AD patients) and GSE114517 (containing samples from PD patients) were retrieved from the Gene Expression Omnibus (GEO) functional genomics database managed by the National Center for Biotechnology Information. The web application GREIN (GEO RNA-seq Experiments Interactive Navigator) was used to identify differentially expressed genes (DEGs). A total of 617 DEGs (239 upregulated and 379 downregulated) were identified from the GSE67333 dataset. Likewise, 723 DEGs (378 upregulated and 344 downregulated) were identified from the GSE114517 dataset. The protein-protein interaction networks of the DEGs were constructed, and the top 50 hub genes were identified from the network of the respective dataset. Of the four common hub genes between two datasets, C-X-C chemokine receptor type 4 (CXCR4) was selected due to its gene expression signature profile and the same direction of differential expression between the two datasets. Mavorixafor was chosen as the reference drug due to its known inhibitory activity against CXCR4 and its ability to cross the blood-brain barrier. Molecular docking and molecular dynamics simulation of 51 molecules having structural similarity with Mavorixafor was performed to find two novel molecules, ZINC49067615 and ZINC103242147. This preliminary study might help predict molecular targets and diagnostic markers for treating Alzheimer's and Parkinson's diseases. Insight Box Our research substantiates the therapeutic relevance of CXCR4 inhibitors for the treatment of Alzheimer's and Parkinson's diseases. We would like to disclose the following insights about this study. We found common signatures between Alzheimer's and Parkinson's diseases at transcriptional levels by analyzing mRNA sequencing data. These signatures were used to identify putative therapeutic agents for these diseases through computational analysis. Thus, we proposed two novel compounds, ZINC49067615 and ZINC103242147, that were stable, showed a strong affinity with CXCR4, and exhibited good pharmacokinetic properties. The interaction of these compounds with major residues of CXCR4 has also been described.

MutaGAN: A sequence-to-sequence GAN framework to predict mutations of evolving protein populations.

The ability to predict the evolution of a pathogen would significantly improve the ability to control, prevent, and treat disease. Machine learning, however, is yet to be used to predict the evolutionary progeny of a virus. To address this gap, we developed a novel machine learning framework, named MutaGAN, using generative adversarial networks with sequence-to-sequence, recurrent neural networks generator to accurately predict genetic mutations and evolution of future biological populations. MutaGAN was trained using a generalized time-reversible phylogenetic model of protein evolution with maximum likelihood tree estimation. MutaGAN was applied to influenza virus sequences because influenza evolves quickly and there is a large amount of publicly available data from the National Center for Biotechnology Information's Influenza Virus Resource. MutaGAN generated 'child' sequences from a given 'parent' protein sequence with a median Levenshtein distance of 4.00 amino acids. Additionally, the generator was able to generate sequences that contained at least one known mutation identified within the global influenza virus population for 72.8 per cent of parent sequences. These results demonstrate the power of the MutaGAN framework to aid in pathogen forecasting with implications for broad utility in evolutionary prediction for any protein population.

Prospective Genomic Surveillance Reveals Cryptic MRSA Outbreaks with Local to International Origins among NICU Patients.

Methicillin-resistant Staphylococcus aureus (MRSA) infections cause substantive morbidity and mortality in neonates. Using publicly available resources from the National Center of Biotechnology Information (NCBI) and Food and Drug Administration's (FDA) GalaxyTrakr pipeline, we illustrate the dynamics of MRSA colonization and infection in neonates. Over 217 days of prospective surveillance, analyses revealed concurrent MRSA transmission chains affecting 11 of 17 MRSA-colonized patients (65%), with two clusters that demonstrated intervals of more than a month among the appearance of isolates. All MRSA infected neonates (n = 3) showed previous colonization with the infecting strain. GalaxyTrakr clustering of the NICU strains, in the context of 21,521 international isolates deposited in NCBI's Pathogen Detection Resource, revealed NICU isolates to be distinct from adult MRSA strains seen locally and internationally. Clustering of the NICU strains within an international context enhanced the resolution of strain clusters and supported the rule-out of suspected, local transmission events within the NICU. Analyses also identified sequence type 1535 isolates, emergent in the Middle East, carrying a unique SCCmec with fusC and aac(6')-Ie/aph(2'')-1a that provided a multidrug-resistant phenotype. NICU genomic pathogen surveillance, leveraging public repositories and outbreak detection tools, supports rapid identification of cryptic MRSA clusters, and can inform infection prevention interventions for this vulnerable patient population. Results demonstrate that sporadic infections in the NICU may be indicative of hidden chains of asymptomatic transmission best identified with sequenced-based approaches.

First Stranding Event of a Common Minke Whale (Balaenoptera acutorostrata Lacépède, 1804) Reported in the Gulf of Thailand

On 5 September 2022, a dead baleen whale was found stranded at Laem Phak Bia, Phetchaburi, the Gulf of Thailand, Thailand but could not be identified because it was in an advanced stage of decomposition. It was first suspected to be Omura’s whale (Balaenoptera Omurai), as that is a common species in the Gulf of Thailand. However, the cranium morphology was different from B. omurai and more similar to the common minke whale (Balaenoptera acutorostrata) from the North Pacific Ocean, which has never been reported in Thai territorial waters. The mitochondrial DNA control region (D-loop) was then used to identify the species through the Basic Local Alignment Search Tool (BLAST) available at the National Center for Biotechnology Information (NCBI) GenBank, which resulted in a high percent identity, 96.49 to 98.84, with B. acutorostrata. A Bayesian phylogenetic tree was further used to confirm the species, which grouped with B. acutorostrata from the North Pacific Ocean. This study provides evidence of the first stranding event of B. acutorostrata in the Gulf of Thailand. It is new information that extends previous knowledge on the distribution of the common minke whale and raises the need for more active surveys of cetaceans in the South China Sea going forward.

Integrative Analysis and Experimental Validation of Competing Endogenous RNAs in Obstructive Sleep Apnea

Obstructive sleep apnea (OSA) is highly prevalent yet underdiagnosed. This study aimed to develop a predictive signature, as well as investigate competing endogenous RNAs (ceRNAs) and their potential functions in OSA. The GSE135917, GSE38792, and GSE75097 datasets were collected from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. Weighted gene correlation network analysis (WGCNA) and differential expression analysis were used to identify OSA-specific mRNAs. Machine learning methods were applied to establish a prediction signature for OSA. Furthermore, several online tools were used to establish the lncRNA-mediated ceRNAs in OSA. The hub ceRNAs were screened using the cytoHubba and validated by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Correlations between ceRNAs and the immune microenvironment of OSA were also investigated. Two gene co-expression modules closely related to OSA and 30 OSA-specific mRNAs were obtained. They were significantly enriched in the antigen presentation and lipoprotein metabolic process categories. A signature that consisted of five mRNAs was established, which showed a good diagnostic performance in both independent datasets. A total of twelve lncRNA-mediated ceRNA regulatory pathways in OSA were proposed and validated, including three mRNAs, five miRNAs, and three lncRNAs. Of note, we found that upregulation of lncRNAs in ceRNAs could lead to activation of the nuclear factor kappa B (NF-κB) pathway. In addition, mRNAs in the ceRNAs were closely correlated to the increased infiltration level of effector memory of CD4 T cells and CD56bright natural killer cells in OSA. In conclusion, our research opens new possibilities for diagnosis of OSA. The newly discovered lncRNA-mediated ceRNA networks and their links to inflammation and immunity may provide potential research spots for future studies.

Identification of key genes and molecular pathways in type 2 diabetes mellitus and polycystic ovary syndrome via bioinformatics analyses.

Type 2 diabetes mellitus (T2DM) and polycystic ovary syndrome (PCOS) are highly prevalent endocrine system diseases. However, studies on the molecular mechanisms of T2DM and PCOS at the transcriptomic level are still few. Thus, we aimed to reveal the potential common genetic and molecular pathways between T2DM and PCOS via bioinformatics analyses. We downloaded the GSE10946 and GSE18732 datasets for T2DM and PCOS, respectively, from the National Center for Biotechnology Information's Gene Expression Omnibus (GEO) database. These datasets were subjected to integrated differential and weighted gene co-expression network analyses (WGCNA) to screen common genes. Thereafter, functional enrichment and disease gene association analyses were performed, transcription factor (TF)-gene and TF-miRNA-gene regulatory networks were constructed, and finally, the relevant target drugs were identified. We identified common genes (BIRC3, DEPTOR, TNNL3, ADRA2A) in T2DM and PCOS. Pathway enrichment analysis depicted that the common genes were enriched in smooth muscle contraction, channel inhibitor activity, apoptosis, and tumor necrosis factor (TNF) signaling pathways. TFs such as SP7, KLF8, HCFC1, IRF1, and MLLT1 played key roles in TF regulatory networks. Orlistat was indicated to be an important gene-targeting drug. This study is the first study to explore four diagnostic biomarkers and gene regulatory networks for T2DM and PCOS. The findings of our study provide novel insights into the diagnosis and treatment of T2DM and PCOS.

Differential Expression Factors in Radiation Induced Lung Injury and Immune Checkpoint Inhibitor associated Pneumonia in Lung Cancer

Radiotherapy and immune checkpoint inhibitors (ICIs) are both important treatments for lung cancer patients. However, radiation induced lung injury (RILI) and immune checkpoint inhibitor associated pneumonia (CIP) are severe dose-limited pulmonary inflammation. The prediction or early diagnosis of them can help improve the therapeutic effect and avoid lung injury, thus improve the quality of life (QOL) for patients with lung cancer. This study obtained datasets GSE41789 and GSE184000 from National Center for Biotechnology Information (NCBI), Gene Expression Omnibus (GEO). Using DEseq2 in R packages to analysis differential gene expression (DEGs). T-test and Fold Change were used to screen DEGs. By comparing the differential expressed genes between the two datasets, the contemporary DEGs were elected and analyzed. Four DEGs in both RILI high risk group and CIP high risk group were identified, including PER3, DBP, CXCL5 and SPON2, indicated that these gene may be potential biomarkers for RILI and CIP, during the radiation an ICIs treatment process. Molecular and clinical experiments will be conducted in the next stage to verify the results.

A Review of Crucial Radiological Investigations in the Management of COVID-19 Cases.

Chest X-ray, chest CT, and lung ultrasound are the most common radiological interventions used in the diagnosis and management of coronavirus disease 2019 (COVID-19) patients. The purpose of this literature review, which was performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, is to determine which radiological investigation is crucial for that purpose.PubMed, Medline, American Journal of Radiology (AJR), Public Library of Science (PLOS), Elsevier, National Center for Biotechnology Information (NCBI), and ScienceDirect were explored. Seventy-two articles were reviewed for potential inclusion, including 50 discussing chest CT, 15 discussing chest X-ray, five discussing lung ultrasound, and two discussing COVID-19 epidemiology. The reported sensitivities and specificities for chest CT ranged from 64 to 98% and 25 to 88%, respectively. The reported sensitivities and specificities for chest X-rays ranged from 33 to 89% and 11.1 to 88.9%, respectively. The reported sensitivities and specificities for lung ultrasound ranged from 93 to 96.8% and 21.3 to 95%, respectively. The most common findings on chest CT include ground glass opacities and consolidation. The most common findings on chest X-rays include opacities, consolidation, and pleural effusion. The data indicate that chest CT is the most effective radiological tool for the diagnosis and management of COVID-19 patients. The authors support the continued use of reverse transcription polymerase chain reaction (RT-PCR), along with physical examination and contact history, for such diagnosis. Chest CT could be more appropriate in emergency situations when quick triage of patients is necessary before RT-PCR results are available. CT can also be used to visualize the progression of COVID-19 pneumonia and to identify potential false positive RT-PCR results. Chest X-ray and lung ultrasound are acceptable in situations where chest CT is unavailable or contraindicated.

New Electrogenic Microorganism Citrobacter sp. Isolated from Microbial Fuel Cell and Bacterial Characteristics Determination

The generation of energy through the transformation of polluting waste is a widely explored field and offers advances in green technologies. One of the promising technologies is Microbial Fuel Cells (MFCs). These cells can contain electroactive microorganisms that transform organic waste into electricity by transferring electrons from their metabolism. In this study, a new bacterium capable of producing electricity from the waste of the poultry sector and using copper electrodes, called Av_G1, was identified and isolated. It is phylogenetically related to Citrobacter freundii and Citrobacter Murlinae. This new strain was identified molecularly, biochemically, and phylogenetically; its physiological and morphological characteristics were also studied through a Scanning Electron Microscope (SEM). Biochemical determination was performed using Simmons Citrate Agar, Lysine Iron Medium (L.I.A.), Motility/Ornithine Test, Methyl Red indicator, Enzymes: oxidase and catalase, and Gram stain test. The phylogenetic inference was deduced by bioinformatics tools (MEGA X, JalView, Clustal Omega) and the genetic databases The Ribosomal Database Project—RDP and the National Center for Biotechnology Information (NCBI). A maximum current potential of 0.645 V, a maximum current density of 168.72 ± 14.07 mA/m2, and a power density of 31.05 mW/m2 were recorded. During the monitoring, the physicochemical parameters were taken: pH, Oxide Reduction Potential (ORP), Dissolved Oxygen (DO), conductivity, Total Solids (TDS), and average temperature were recorded. Therefore, the present study shows a new Gram-negative electrogenic bacterium, which can be used for electrochemical processes and applied in MFC with copper electrodes.

Оценка биологической безопасности молочных продуктов, содержащих антибиотики

Antibiotics have traditionally been used to prevent and treat common diseases in farm animals. However, residual antibiotics in dairy products and meat remain a serious public health problem, which is associated with antibiotic resistance. The research objective was to assess the impact of antibiotic contamination on the quality and safety of dairy products, the microbiological composition of milk, and antibiotic-resistant bacteria.
 The study featured six years of Russian and foreign scientific articles registered in PubMed (National Center for Biotechnology Information, USA), Scopus and ScienceDirect (Elsevier, the Netherlands), Web of Science (Clarivate, USA), and eLibrary.ru.
 The analysis involved 63 foreign and domestic sources. Residual antibiotics in milk inhibits the vital activity of lactic acid bacteria, which, in its turn, disrupts the technological process of yogurts, cheeses, etc. After such processing as normalization, pasteurization, and homogenization, antibiotics accumulate in fermented dairy products and bind with milk proteins and fats. Antibiotics, in their initial amount, enter yoghurts from dairy raw materials. In cheese production, antibiotics usually pass into the whey, but aminoglycosides, quinolones, and tetracyclines remain in the finished product because they bind with the protein fraction.
 The problem of biological safety of dairy products is associated with antibiotic resistance developed by human intestinal microbiota. This problem remains understudied, and the number of scientific papers on the matter is limited.

The first genome sequence of Anopheles squamous from Macha, Zambia.

Despite efforts to minimize the impacts of malaria and reduce the number of primary vectors, malaria has yet to be eliminated in Zambia. Understudied vector species may perpetuate malaria transmission in pre-elimination settings. Anopheles squamosus is one of the most abundantly caught mosquito species in southern Zambia and has previously been found with Plasmodium falciparum sporozoites, a causal agent of human malaria. This species may be a critical vector of malaria transmission, however, there is a lack of genetic information available for An. squamosus. We report the first genome data and the first complete mitogenome (Mt) sequence of An. squamosus. The sequence was extracted from one individual mosquito from the Chidakwa area in Macha, Zambia. The raw reads were obtained using Illumina Novaseq 6000 and assembled through NOVOplasty alignment with related species. The length of the An. squamosus Mt was 15,351 bp, with 77.9 % AT content. The closest match to the whole mitochondrial genome in the phylogenetic tree is the African malaria mosquito, Anopheles gambiae. Its genome data is available through National Center for Biotechnology Information (NCBI) Sequencing Reads Archive (SRA) with accession number SRR22114392. The mitochondrial genome was deposited in NCBI GenBank with the accession number OP776919. The ITS2 containing contig sequence was deposited in GenBank with the accession number OQ241725. Mitogenome annotation and a phylogenetic tree with related Anopheles mosquito species are provided.

Panel of primers for evaluation of antibiotic resistance genes with real time detection of results

Introduction. The problem of the spread of antibiotic resistance among pathogens of nosocomial infections is becoming increasingly important. In order to improve microbiological monitoring, it is advisable to use methods that allow you to quickly determine the largest number of antibiotic resistance determinants. In this regard, it seems relevant to develop PCR test systems for detecting antibiotic resistance genes, in particular, for screening hospitalized patients and identifying cases of nosocomial infection.Purpose. Develop a panel of primers for detection of antibiotic resistance genes using PCR with real-time visualization of results. Materials and methods. For the design of specific primers and probes, reference sequences from the databases of the National Center for Biotechnology Information (NCBI) were used. Primer selection and specificity assessment were performed using the NCBI PrimerBlast and Primer3 programs. Primers for PCR amplification of a number of antibiotic resistance genes were tested on strains of Klebsiella pneumoniae. These strains were isolated from the clinical material of intensive care patients with COVID-19 and whole genome sequencing of the strains was carried out with a detailed assessment of the resistome, virulome. The results of whole genome sequencing and multiplex real-time PCR were compared.Results. We have developed a set of primers for the detection of antibiotic resistance genes, including carbapenemase, using real-time multiplex PCR.Conclusion. The developed panel of primers can be used to screen Klebsiella pneumoniae isolates for the presence of resistance genes; further expansion of the spectrum of detected genes and testing of the panel on clinical material is required.

Global Increase of Antibiotic Resistance Genes in Conjugative Plasmids.

Antibiotic resistance is propagating worldwide, but the predominant dissemination mechanisms are not fully understood. Here, we report that antibiotic resistance gene (ARG) abundance in conjugative plasmids that are recorded in the National Center for Biotechnology Information (NCBI) RefSeq plasmid database is increasing globally, which is likely a key factor in the propagation of resistance. ARG abundance in plasmids increased by 10-fold on a global scale from the year 2000 to the year 2020 (from 0.25 to 2.93 ARG copies/plasmid), with a more pronounced increase being observed in low-to-middle income countries. This increasing trend of plasmid-borne ARGs was corroborated by bootstrap resampling from each year of the NCBI RefSeq plasmid database. The results of a correlation analysis imply that if antibiotic consumption keeps growing at the current rates, a 2.7-fold global increase in the ARG abundance of clinically relevant plasmids may be reached by 2030. High sequence similarities of clinically relevant, conjugative plasmids that are isolated both from clinics and from the environment raise concerns about the environmental resistome serving as a potential ARG maintenance reservoir that facilitates transmission across these ecological boundaries. IMPORTANCE Antibiotic resistance propagation is a significant concern due to its projected impacts on both global health and the economy. However, global propagation mechanisms are not fully understood, including regional and temporal trends in the abundance of resistance plasmids that facilitate antibiotic resistance gene (ARG) dissemination. This unprecedented study reports that ARG abundance in the conjugative plasmids that are recorded in the National Center for Biotechnology Information (NCBI) database and harbor ARGs is increasing globally with antibiotic consumption, especially in low-to-medium income countries. Through network and comparative genomic analyses, we also found high sequence similarities of clinically relevant conjugative resistance plasmids that were isolated from clinical and environmental sources, suggesting transmission between these ecological boundaries. Therefore, this study informs the One Health perspective to develop effective strategies by which to curtail the propagation of plasmid-borne antibiotic resistance.

Mare-MAGE curated reference database of fish mitochondrial genes

Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.

Staying Informed of Best Evidence to Guide Practice

Staying Informed of Best Evidence to Guide Practice

Morphological, anatomical and molecular characterisation of the leaves of Isoberlinia doka Craib and Stapf and Isoberlinia tomentosa (Harms) Craib and Stapf

Background: Isoberlinia (Craib and Stapf) is a genus with high economic and pharmacological values.Aim: This study aimed at establishing the morphological, anatomical and molecular characterisation of the leaves of I. doka and I. tomentosa, which were conducted for proper authentication.Setting: The leaves of I. doka and I. tomentosa were obtained from Shika, kaduna State, Nigeria.Method: Morphological and anatomical characters were determined according to standard procedures, while molecular identifications were performed using ribulose-1,5-bisphosphate carboxylase (rbcl) gene and internal transcribed spacer (ITS) DNA barcode’s region.Result: Morphological studies revealed similar features for both species except for the shiny leaves of I. doka and rough abaxial surfaces of I. tomentosa because of the presence of trichomes. Variations were observed in their epidermal features, stomatal index, stomata frequency, presence or absence of trichomes, trichomes frequency and their quantitative anatomical features. The quantity and quality of DNA measured at A260/280 ratio using nanodrop spectrophotometer were 29.1 ng/μL and 1.74 ng/μL for I. doka, respectively, while the I. tomentosa concentration and purity were 71.1 ng/μL and 1.85 ng/μL, respectively. Agarose gel electrophoresis revealed two DNA bands with 700 bp (rbcl) and 600 bp (ITS). The sequence analysis revealed maximum identity with National Centre for Biotechnology Information (NCBI) GeneBank Isoberlinia species. Evolutionary analysis supported the monophyletic origin of the genus Isoberlinia. The morphological and anatomical characters of I. doka and I. tomentosa leaves have provided a significant taxonomy tool for proper authentication of this plant.Conclusion: The findings ascertained that ITS and rbcl served as an improved and efficient tool for species identification of these studied species and could serve as potential DNA barcodes for these taxa.Contribution: This article suggests that further studies the on screening of these plants, for various pharmacological potentials, might be useful for new drug development.