National Center For Biotechnology Information Research Articles

SH3GL2 and MMP17 as lung adenocarcinoma biomarkers: a machine-learning based approach

ObjectiveUsing bioinformatics machine learning methods, our research aims to identify the potential key genes associated with Lung adenocarcinoma (LUAD). MethodsWe obtained two gene expression profiling microarrays (GSE68571 and GSE74706) from the public Gene Expression Omnibus (GEO) database at the National Centre for Biotechnology Information (NCBI). The purpose was to identify Differentially Expressed Genes (DEGs) between the lung adenocarcinoma group and the healthy control group. The limma R package in R was utilized for this analysis. For the differential gene diagnosis of lung adenocarcinoma, we employed the least absolute shrinkage and selection operator (LASSO) regression and SVM-RFE screening crossover. To evaluate the performance, ROC curves were plotted. We performed immuno-infiltration analysis using CIBERSORT. Finally, we validated the key genes through qRT-PCR and Western-blot verification, then downregulated MMP17 gene expression, upregulated SH3GL2 gene expression, and performed CCK8 experiments. ResultsA total of 32 Differentially Expressed Genes (DEGs) were identified. Two diagnostic marker genes, SH3GL2 and MMP17, were selected by employing LASSO and SVM-RFE machine learning methods. In Lung adenocarcinoma cells, the expression of MMP17 was observed to be elevated compared to normal lung epithelial cells in the control group (P < 0.05). In contrast, a down-regulation of SH3GL2 was found in Lung adenocarcinoma cells (P < 0.05). Finally, we downregulated MMP17 and upregulated SH3GL2 gene expression, then the CCK8 showed that the proliferation of both lung cancer cells was inhibited. ConclusionSH3GL2 and MMP17 are expected to be potential biomarkers for Lung adenocarcinoma.

Abstract 5377: Investigating human leukocyte antigen (HLA) class 1 leukemogenic pathways in acute myelogenous leukemia

Abstract Background: Aging, smoking and germline predisposition are known to accelerate leukemogenesis. However, the the ability for myeloid clonal pathogenic variants (MCPV) to elicit an antigen-driven host antileukemia immune response is not well characterized. A better understanding on how cellular immunity selectively discriminates leukemia-related “neopeptides” could uncover mechanisms supporting tumor genome evolution. Methods: 122 patients with acute myelogenous leukemia (AML) were included and 111 had available protein coding sequences. A neopeptide library was created using protein FASTA coding extracted for individual myeloid clonal mutations via National Center for Biotechnology Information (NCBI). Patient class 1 HLA typing was obtained through Tempus, and Genomic Testing Cooperative laboratories. Prediction of number and strength of AML neopeptide bindings to MHC class I molecules were obtained via NetMHCPan-1. Analysis was performed with K-means algorithm assigning age at diagnosis, detected MCPV, number of neopeptides binding (as continuous variable), overall survival (OS) and event-free survival (EFS) as variables. Unsupervised data input allowed 3 cluster partitions for differential survivals allowing HLA class 1 peptide binding aggregation with potential roles in leukemogenesis and patient outcome. Descriptive statistics were performed with SAS. Results: Sixty-six different MCPV were detected. Of 111 patients, 70 (63%) with available MCPV produced at least 1 MHC I neopeptide binding. Frequently observed variants were P53 (13%), FLT3 (9.2%), WT1 (7%), DNMT3A (6.5%), RAS (5%), ASXL1 (4.3%), RUNX1 (4.2%), NPM1 (4.2%) and IDH1/2 (2.6%). Cluster 2 demonstrated a lack of favorable and higher proportion of adverse ELN 2022 subgroups. Cluster 3 exhibited a higher of P53 [p=0.03] and MDS-related mutations. OS was 79, 239, and 1551 days for cluster 2,1 and 3, respectively [p=0.0001]. EFS was 134, 363 and 451 days for cluster 2,1 and 3, respectively [p=0.0001]. Interestingly, Cluster 2 and 3 assembled the highest probability for peptide binding [1 v 2 v 3 = 1.76% v 36.6% v 62%, p=0.01]. Lastly, albeit in low frequencies, higher diversity of DNA repairing enzymes was seen in cluster 2. Conclusions: Different MCPV arising in AML genome are variably immunogenic and leukemia-related neopeptide binding’s ability is differentially expressed in our 3 clusters. Frequent neopeptide bindings in clusters 2 and 3 may reflect higher AML immunogenicity resulting in genomic instability. It is possible that less “edited” genomes in cluster 1 preserve higher chemosensitivity resulting in better OS, while highly edited genomes in cluster 2 and 3 are less chemo-sensitive and circumvent host immunosurveillance. Further expansion of cluster 2 is necessary to better understand the role of DNA repairing enzymes in younger patients’ outcomes, especially when genomic instability is observed. Citation Format: Paul Sackstein, Sarah Mudra, Lacey Williams, Garrett Diltz, Rachel Zemel, Sravanti Teegavarapu, Martha Mims, Catherine Lai, Kimberley Doucette, Anne Renteria, Olga Timofeeva, Gustavo A. Rivero. Investigating human leukocyte antigen (HLA) class 1 leukemogenic pathways in acute myelogenous leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5377.

Association of single nucleotide polymorphisms in ITLN1 gene with ischemic stroke risk in Xi'an population, Shaanxi province.

Ischemic stroke (IS) is the main cause of death and adult disability. However, the pathogenesis of this complicated disease is unknown. The present study aimed to assess the relationship between ITLN1 single nucleotide polymorphisms (SNPs) and the susceptibility to IS in Xi'an population, Shaanxi province. In this study, we designed polymerase chain reaction (PCR) primers located at -3,308 bp upstream of the transcription initiation site within promoter region of the ITLN1 gene. The target fragment was amplified by PCR and identified by agarose gel electrophoresis. Sanger sequencing was then performed in the samples extracted from a cohort comprising 1,272 participants (636 controls and 636 cases), and the obtained sequences were compared with the reference sequences available on the National Center for Biotechnology Information (NCBI) website to detect SNPs in the ITLN1 gene promoter region. Logistic regression analysis was employed to assess the relationship between ITLN1 polymorphisms and IS risk, with adjustments for age and gender. Significant positive results were tested by false-positive report probability (FPRP) and false discovery rate (FDR). The interaction among noteworthy SNPs and their predictive relationship with IS risk were explored using the Multi-Factor Dimensionality Reduction (MDR) software. The results of Sanger sequencing were compared with the reference sequences on the NCBI website, and we found 14 SNPs in ITLN1 gene promoter satisfied Hardy-Weinberg equilibrium (HWE). Logistic regression analysis showed that ITLN1 was associated with a decreased risk of IS (rs6427553: Homozygous C/C: adjusted OR: 0.69, 95% CI [0.48-0.97]; Log-additive: adjusted OR: 0.83, 95% CI [0.70-0.98]; rs7411035: Homozygous G/G: adjusted OR: 0.66, 95% CI [0.47-0.94]; Dominant G/T-G/G: adjusted OR: 0.78, 95% CI [0.62-0.98]; Log-additive: adjusted OR: 0.81, 95% CI [0.69-0.96]; rs4656958: Heterozygous G/A: adjusted OR: 0.74, 95% CI [0.59-0.94]; Homozygous A/A: adjusted OR: 0.51, 95% CI [0.31-0.84]; Dominant G/A-A/A: adjusted OR: 0.71, 95% CI [0.57-0.89]; Recessive A/A: adjusted OR: 0.59, 95% CI [0.36-0.96]; Log-additive: adjusted OR: 0.73, 95% CI [0.61-0.88]), especially in people aged less than 60 years and males. In short, our study revealed a correlation between ITLN1 variants (rs6427553, rs7411035 and rs4656958) and IS risk in Xi'an population, Shaanxi province, laying a foundation for ITLN1 gene as a potential biomarker for predicting susceptibility to IS.

Detection of Bacteroides fragilis LuxR gene, involved in quorum sensing, among colitis patients in Mosul, Iraq

Bacteroides fragilis is the most anaerobic bacteria that infect humans, particularly in the abdominal cavity. Its pathogenesis is linked to numerous virulence factors. Understanding these factors and exploring alternative options for the use of antibiotics in the treatment of this bacterium, molecular techniques offer several advantages over traditional culture techniques because they are easier and more specific. The present study aimed to use specific primers for the 16sRNA and LuxR genes to identify B. fragilis. Genetic identification of the B. fragilis isolates was performed using the 16SrRNA gene, and the obtained sequences were submitted to National Centre for Biotechnology Information (NCBI) with accession numbers (OQ448827, OQ448828). Each strain was assigned a unique strain name, AS. AWB94 and AS. AWB79. From the total of all samples, it was found that the growth of various types of bacteria constituted ( 76%), and the samples that did not have growth formed (24%). It was noted that Bacteroidetes constituted only two isolates (2.7%), and these two isolates possessed the gene for quorum sensing (luxR gene), while the results confirmed that they do not possess the sialidase (nanH) enzyme gene. Both isolates possessed the quorum sensing gene (LuxR) out of one hundred samples. This suggests that the isolates have a quorum-sensing mechanism responsible for cell-to-cell communication, multidrug resistance, and biofilm formation.

Phylogenetic lineage dynamics of global parainfluenza virus type 3 post-COVID-19 pandemic.

During the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of parainfluenza virus type 3 (PIV-3) decreased due to infection control measures. However, a post-pandemic resurgence of PIV-3 has recently been observed. Nonetheless, the role of viral genetic epidemiology, possibly influenced by a genetic bottleneck effect, remains unexplored. We investigated the phylogenetic structure of the publicly available PIV-3 whole-genome and hemagglutinin-neuraminidase (HN) gene sequences spanning the last 65 years, including the COVID-19 pandemic. Sequences were retrieved from the nucleotide database of the National Center for Biotechnology Information using the search term "Human respirovirus 3." Sequence subsets covering all six genes of PIV-3 or the HN gene were designated as the whole-genome and HN surveillance data sets, respectively. Using these data sets, we constructed maximum-likelihood phylogenetic trees and performed a time-scaled analysis using a Bayesian SkyGrid coalescent prior. A total of 455 whole-genome and 1,139 HN gene sequences were extracted, revealing 10 and 11 distinct lineages, respectively, with >98% concurrence in lineage assignments. During the 2020 COVID-19 pandemic, only three single-lineage clusters were identified in Japan, Korea, and the USA. The inferred year of origin for PIV-3 was 1938 (1903-1963) for the whole-genome data set and 1955 (1930-1963) for the HN gene data set. Our study suggests that PIV-3 epidemics in the post-COVID era are likely influenced by a pandemic-driven bottleneck phenomenon and supports previous hypotheses suggesting s that PIV-3 originated during the early half of the 20th century.IMPORTANCEUsing publicly available parainfluenza virus type 3 (PIV-3) whole-genome sequences, we estimated that PIV-3 originated during the 1930s, consistent with previous hypotheses. Lineage typing and time-scaled phylogenetic analysis revealed that PIV-3 experienced a bottleneck phenomenon in Korea and the USA during the coronavirus disease 2019 pandemic. We identified the conservative hemagglutinin-neuraminidase gene as a viable alternative marker in long-term epidemiological studies of PIV-3 when whole-genome analysis is limited.

Identification of Dalbergiae Odoriferae Lignum active ingredients and potential mechanisms in the treatment of adriamycin-induced cardiotoxicity based on network pharmacology and experimental verification.

The purpose of this study is to investigate the ingredients and mechanisms through which Dalbergiae Odoriferae Lignum (DOL) reduces adriamycin-induced cardiotoxicity. DOL's ingredients and drug targets were acquired from Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), and adriamycin-induced cardiotoxicity disease targets were gathered from GeneCards and National Center for Biotechnology Information (NCBI). The therapeutic targets of DOL against adriamycin-induced cardiotoxicity were identified by intersecting drug and disease targets. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted using R. Subsequently, core targets were determined and used for molecular docking with DOL ingredients. In vitro and in vivo experiments validated DOL's primary ingredients against adriamycin-induced cardiotoxicity efficacy. Western blot and immunohistochemistry verified its impact on target protein. After intersecting 530 drug targets and 51 disease targets, 19 therapeutic targets for DOL alleviated adriamycin-induced cardiotoxicity were received. Molecular docking demonstrated that DOL primary ingredient formononetin had a robust binding affinity for nitric oxide synthase 3 (NOS3). Experimental results showed that formononetin effectively mitigated adriamycin-induced cardiotoxicity. Additionally, western blot and immunohistochemistry showed that formononetin improved NOS3 expression. The network pharmacology and experimentation suggest that the primary ingredient of DOL, formononetin, may target NOS3 to act as a therapeutic agent for adriamycin-induced cardiotoxicity.

Navigating the vestibular maze: text-mining analysis of publication trends over five decades.

The field of vestibular science, encompassing the study of the vestibular system and associated disorders, has experienced notable growth and evolving trends over the past five decades. Here, we explore the changing landscape in vestibular science, focusing on epidemiology, peripheral pathologies, diagnosis methods, treatment, and technological advancements. Publication data was obtained from the US National Center for Biotechnology Information (NCBI) PubMed database. The analysis included epidemiological, etiological, diagnostic, and treatment-focused studies on peripheral vestibular disorders, with a particular emphasis on changes in topics and trends of publications over time. Our dataset of 39,238 publications revealed a rising trend in research across all age groups. Etiologically, benign paroxysmal positional vertigo (BPPV) and Meniere's disease were the most researched conditions, but the prevalence of studies on vestibular migraine showed a marked increase in recent years. Electronystagmography (ENG)/ Videonystagmography (VNG) and Vestibular Evoked Myogenic Potential (VEMP) were the most commonly discussed diagnostic tools, while physiotherapy stood out as the primary treatment modality. Our study presents a unique opportunity and point of view, exploring the evolving landscape of vestibular science publications over the past five decades. The analysis underscored the dynamic nature of the field, highlighting shifts in focus and emerging publication trends in diagnosis and treatment over time.

Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.

As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit ( https://github.com/wyp1125/MCScanX ) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .

The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars-Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States.

The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.

Exploring the role of mitochondrial-associated and peripheral neuropathy genes in the pathogenesis of diabetic peripheral neuropathy

BackgroundDiabetic peripheral neuropathy (DPN) is a prevalent and serious complication of diabetes mellitus, impacting the nerves in the limbs and leading to symptoms like pain, numbness, and diminished function. While the exact molecular and immune mechanisms underlying DPN remain incompletely understood, recent findings indicate that mitochondrial dysfunction may play a role in the advancement of this diabetic condition.MethodsTwo RNA transcriptome datasets (codes: GSE185011 and GSE95849), comprising samples from diabetic peripheral neuropathy (DPN) patients and healthy controls (HC), were retrieved from the Gene Expression Omnibus (GEO) database hosted by the National Center for Biotechnology Information (NCBI). Subsequently, differential expression analysis and gene set enrichment analysis were performed. Protein–protein interaction (PPI) networks were constructed to pinpoint key hub genes associated with DPN, with a specific emphasis on genes related to mitochondria and peripheral neuropathy disease (PND) that displayed differential expression. Additionally, the study estimated the levels of immune cell infiltration in both the HC and DPN samples. To validate the findings, quantitative polymerase chain reaction (qPCR) was employed to confirm the differential expression of selected genes in the DPN samples.ResultsThis research identifies four hub genes associated mitochondria or PN. Furthermore, the analysis revealed increased immune cell infiltration in DPN tissues, particularly notable for macrophages and T cells. Additionally, our investigation identified potential drug candidates capable of regulating the expression of the four hub genes. These findings were corroborated by qPCR results, reinforcing the credibility of our bioinformatics analysis.ConclusionsThis study provides a comprehensive overview of the molecular and immunological characteristics of DPN, based on both bioinformatics and experimental methods.

Unveiling the impacts of land use on the phylogeography of zoonotic New World Hantaviruses

Billions of genomic sequences and records of species occurrence are available in public repositories (e.g. National Center for Biotechnology Information, NCBI and the Global Biodiversity Information Facility, GBIF). By implementing analytical tools from different scientific disciplines, data mining these databases can aid in the global surveillance of zoonotic pathogens that circulate among wildlife. We illustrate this by investigating the Hantavirus–rodent system in the Americas, i.e. New World Hantaviruses (NWH). First, we considered the circulation of pathogenic NWH among Cricetidae rodents, by inferring the phylogenetic links among 277 genomic samples of the S segment (N protein) of NWH found in 55 species. Second, we used machine learning to assess the impact of land use on the probability of presence of the rodent species linked with reservoirs of pathogenic Hantaviruses. Our results show that hosts are widely present across the Americas. Some hosts are present in the primary forest and agricultural land, but not in the secondary forest, whereas other hosts are present in secondary forest and agricultural land. The diversity of host species allows Hantavirus to circulate in a wide spectrum of habitats, in particular rural rather than urban. We highlight that public repositories of genomic data and species occurrence are very useful resources for monitoring potential enzootic transmission and spillover of zoonotic viruses in relation with the changes that humans produce in the biosphere.

Molecular approach for identification and validation of Eurycoma longifolia, Labisia pumila, and Orthosiphon stamineus in herbal products

BackgroundEurycoma longifolia (E. longifolia), Labisia pumila (L. pumila), and Orthosiphon stamineus (O. stamineus) are popular species known for their therapeutic properties. An increase in local demand for herbal products makes them susceptible to adulteration, which poses a risk to their safety and efficacy. Current identification methods, such as organoleptic, microscopic, and macroscopic analysis, need to be revised to identify plant species in highly processed herbal products due to their limited ability to detect morphological features and provide comprehensive plant taxonomy information.MethodsThis research objective was to develop a simple, reliable, and accurate DNA molecular identification method based on polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) for E. longifolia, L. pumila, and O. stamineus, used to validate the species identification for herbal products. PCR–RFLP was developed for rapid identification using restriction enzymes TaqI, BamH I, HinfI, EcoRI, EcoRV, Mbol, and Mspl.ResultsThe nuclear DNA internal transcribed spacer 2 (ITS2) sequences were identified and compared between plant specimens of E. longifolia, L. pumila, and O. stamineus and 101 samples of commercial herbal products. Plant specimens of E. longifolia, L. pumila, and O. stamineus were successfully identified with high similarity of 100%, 100%, and 99.33%, respectively, based on National Center for Biotechnology Information (NCBI) GenBank. The recovery of DNA sequences from the herbal products was 60.4%, of which 81.97% were identified, and 18.03% showed no sequence through Basic Local Alignment Search Tool (BLAST) identification.ConclusionA reliable approach for identifying and validating plant species in herbal products has been created using restriction enzymes. This simple and accurate PCR–RFLP approach efficiently identifies E. longifolia, L. pumila, and O. stamineus by analysing ITS2 sequences, assuring consumer health and safety.

Combined Plasma Olink Proteomics and Transcriptomics Identifies CXCL1 and TNFRSF12A as Potential Predictive and Diagnostic Inflammatory Markers for Acute Kidney Injury.

Acute kidney injury (AKI) poses a significant global public health challenge. Current methods for detecting AKI rely on monitoring changes in serum creatinine (Scr), blood urea nitrogen (BUN), urinary output and some commonly employed biomarkers. However, these indicators are usually neither specific nor sensitive to AKI, especially in cases of mild kidney injury. AKI is accompanied by severe inflammatory reactions, resulting in the upregulation of numerous inflammation-associated proteins in the plasma. Plasma biomarkers are a noninvasive method for detecting kidney injury, and to date, plasma inflammation-associated cytokines have not been adequately studied in AKI patients. The objective of our research was to identify novel inflammatory biomarkers for AKI. We utilized Olink proteomics to analyze the alterations in plasma inflammation-related proteins in the serum of healthy mice (n = 2) or mice treated with cisplatin (n = 6). Additionally, transcriptome datasets for the lipopolysaccharide (LPS), cisplatin, and ischemia‒reperfusion injury (IRI) groups were obtained from the National Center of Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. We calculated the intersection of differentially expressed proteins (DEPs) and genes (DEGs) from both datasets. In the Olink proteomics analysis, the AKI group had significantly greater levels of 11 DEPs than did the control group. In addition, 56 common upregulated DEGs were obtained from the transcriptome dataset. The expression of CXCL1 and TNFRSF12A overlapped across all the datasets. The transcription and protein expression levels of CXCL1 and TNFRSF12A were detected in vivo. The gene and protein levels of CXCL1 and TNFRSF12A were significantly increased in different AKI mouse models and clinical patients, suggesting that these genes and proteins could be potential specific biomarkers for the identification of AKI.

Telehealth for healthy gestational weight gain among overweight pregnant women: A systematic review

Introduction: Excessive Gestational Weight Gain (GWG) is associated with various complications during pregnancy and childbirth. In contrast, digital interventions like telehealth offer cost-effective solutions with broader accessibility. Therefore, our outcomes are to analyze the effectiveness of telehealth interventions for healthy GWG among overweight and obese pregnant women and to know which features are needed in telehealth for healthier GWG.Methods: We undertook a systematic review to address the objectives mentioned above. Initially, we employed the keywords telehealth, pregnant women, and overweight, which were subsequently refined using Medical Subject Headings provided by the National Center for Biotechnology Information. To identify relevant articles, we searched six databases—Scopus, SAGE Journals, Web of Science, PubMed, ScienceDirect, and ProQuest.Results: We included 15 articles in this review according to the criteria. Eleven papers show a positive effect of telehealth in promoting healthy GWG. Telehealth encompasses various functionalities, such as providing information, push notifications, self-monitoring, and feedback features related to gestational weight gain (GWG), maintaining a healthy diet, engaging in physical activity, receiving reminders, managing stress, and setting goals. On the other hand, four papers show no significant difference between telehealth and regular interventions.Conclusions: Telehealth is alternatively effective to use as an additional intervention to promote healthier GWG in overweight pregnant women. Keywords: gestational weight gain; overweight; pregnant women; telemedicine

Prognostic Factors Associated with the Severe Course of a New Coronavirus Infection

Introduction. Novel coronavirus infection (COVID-19) is a respiratory infectious disease caused by the novel severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2). It is characterized by a heterogeneous course of the disease from asymptomatic and mild forms to more severe and fatal outcomes. There are many risk factors for a severe course of a new coronavirus infection, in most cases, a severe course of the disease is associated with the individual characteristics of the patient, especially with dysregulation of the immune response. In this article, we reviewed the main prognostic factors for the severity of the disease.The aim of the study is to determine the unfavorable prognostic factors associated with the severe course of a new coronavirus infection caused by the SARS-CoV-2 virus in foreign and domestic literature sources.Materials and methods. To achieve this goal, scientific publications on the new coronavirus infection caused by the SARS-CoV-2 virus were analyzed in the scientometric databases PubMed, National Center for Biotechnological Information (NCBI), Cochrane, Web of Science, Scopus, MEDLINE (2019–2022), and Russian specialized journals on infectious diseases (2019–2022). Particular attention was paid to factors influencing the severe course of a new coronavirus infection.Results. Risk factors for a severe course of a new coronavirus infection include: lipid spectrum, advanced age, hemostasis system, changes in the leukocyte count, serum markers. Mathematical models of the course of a new coronavirus infection have also been developed.Discussion. In most studies, scientists note that the uncontrolled course of COVID-19 disease is associated with a dysregulated immune response. One of the main methods of influencing the immune system is vaccination.Conclusion. There are many factors that contribute to the development of severe forms of the disease of a new coronavirus infection. However, thanks to universal vaccination against a new coronavirus infection, the frequency of severe forms of the disease and deaths has significantly decreased. Novel coronavirus infection (COVID-19) is a respiratory infectious disease caused by the novel severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2).

ClinGen variant curation expert panel recommendations for classification of variants in GAMT, GATM and SLC6A8 for cerebral creatine deficiency syndromes

Cerebral creatine deficiency syndromes (CCDS) are inherited metabolic phenotypes of creatine synthesis and transport. There are two enzyme deficiencies, guanidinoacetate methyltransferase (GAMT), encoded by GAMT and arginine-glycine amidinotransferase (AGAT), encoded by GATM, which are involved in the synthesis of creatine. After synthesis, creatine is taken up by a sodium-dependent membrane bound creatine transporter (CRTR), encoded by SLC6A8, into all organs. Creatine uptake is very important especially in high energy demanding organs such as the brain, and muscle. To classify the pathogenicity of variants in GAMT, GATM, and SLC6A8, we developed the CCDS Variant Curation Expert Panel (VCEP) in 2018, supported by The Clinical Genome Resource (ClinGen), a National Institutes of Health (NIH)-funded resource. We developed disease-specific variant classification guidelines for GAMT-, GATM-, and SLC6A8-related CCDS, adapted from the American College of Medical Genetics/Association of Molecular Pathology (ACMG/AMP) variant interpretation guidelines. We applied specific variant classification guidelines to 30 pilot variants in each of the three genes that have variants associated with CCDS. Our CCDS VCEP was approved by the ClinGen Sequence Variant Interpretation Working Group (SVI WG) and Clinical Domain Oversight Committee in July 2022. We curated 181 variants including 72 variants in GAMT, 45 variants in GATM, and 64 variants in SLC6A8 and submitted these classifications to ClinVar, a public variant database supported by the National Center for Biotechnology Information. Missense variants were the most common variant type in all three genes. We submitted 32 new variants and reclassified 34 variants with conflicting interpretations. We report specific phenotype (PP4) using a points system based on the urine and plasma guanidinoacetate and creatine levels, brain magnetic resonance spectroscopy (MRS) creatine level, and enzyme activity or creatine uptake in fibroblasts ranging from PP4, PP4_Moderate and PP4_Strong. Our CCDS VCEP is one of the first panels applying disease specific variant classification algorithms for an X-linked disease. The availability of these guidelines and classifications can guide molecular genetics and genomic laboratories and health care providers to assess the molecular diagnosis of individuals with a CCDS phenotype.

First report of Hibiscus latent Singapore virus and Hibiscus latent Fort Pierce virus infecting Lantana camara in China.

Hibiscus latent Singapore virus (HLSV) and Hibiscus latent Fort Pierce virus (HLFPV) both belong to the genus Tobamovirus in the family Virgaviridae. The genomes of both HLSV and HLFPV consist of a linear positive sense single-stranded RNA of about 6.3 kb. HLSV is the causal agent of hibiscus leaf crinkle disease. Infections of HLSV in hibiscus (Hibiscus rosa-sinensis) have so far only been reported in Singapore, Japan and Malaysia (Srinivasan et al., 2002; Yoshida et al., 2018; Yusop et al., 2021). In 2017, leaf curling and chlorosis symptoms of lantana (Lantana camara) plants were found in Chenshan Botanical Garden, Shanghai, China. To detect potential virus(es) in these lantana samples, leaves from one lantana plant were collected and total RNA was extracted with RNAiso Plus (TaKaRa). A cDNA library was prepared by TruSeq RNA Sample Prep Kit (Illumina) after removing ribosomal RNA by Ribo-ZeroTM rRNA Removal Kit (Epicentre). The paired-end sequencing was then performed on an Illumina NovaSeq 6000. A total of 61,085,018 high quality reads were obtained and de novo assembly by StringTie revealed 124,516 contigs (greater than 50 bp, N50=719 bp) with an average length of 537 bp. BLASTx analyses in the National Center for Biotechnology Information (NCBI) database showed that 1 long contig of 6,305 bp, assembled of 1794 clean reads, shared significant nucleotide similarities with the genomic sequence of HLSV, and 1 contig of 6,271 bp, assembled of 3174 clean reads, shared significant similarities with the genomic sequence of HLFPV, yielding an average coverage of the whole genome at 42.65 and 75.83 per million reads, respectively. To obtain the complete genome of the viral RNA in this lantana sample, eleven overlapping regions covering the entire HLSV viral genome, and nine overlapping regions covering the entire HLFPV viral genome were amplified by reverse transcription-PCR (RT-PCR) and sequenced. In addition, the exact 5' and 3' ends of the genomic RNA of each virus were determined by rapid amplification of the cDNA ends (RACE) (Wang et al. 2020). The complete genome of the identified HLSV, deposited in GenBank: MZ020960, is 6,486 nt in length and shows 98.4% nucleotide sequence identity with HLSV Singapore isolate (GenBank: AF395898). Similar to other HLSV isolates, this virus isolate possesses an internal poly(A) tract of 87 nucleotides, which is crucial to virus replication (Niu et al., 2015). The complete genome of the Lantana HLFPV isolate is 6,463 nt (GenBank MZ020961) including a 73 nt internal poly(A) tract, and has 98.4% nt identity to HLFPV-Japan (AB917427). In two other lantana plants from the same site, the presence of HLSV and HLFPV was confirmed by RT-PCR using the primer pairs (5'-GCATCTGCATAACACGGTTG-3'/5'-ACGTTGTAGTAGACGTTGTTGTAG-3' and 5'-GGACCTTGCTAATCCGCTAAAGTTG-3'/5'-GGTCCATGTCCATCCAGATGCAATC-3'). In addition to the HLSV and HLFPV genomes, BLASTx analysis of three contigs of 3,006 bp, 2,845 bp and 2,200 bp, assembled of 1328, 352 and 2280 clean reads respectively, showed high identity to RNAs 1 (MG182148), 2 (DQ412731) and 3 (KY794710) of cucumber mosaic virus. To the best of our knowledge, this is the first report of L. camara as a new natural host of HLSV and HLFPV, and first identification of a mixed infection of HLSV and HLFPV.

Emergence of zoonotic sporotrichosis in Brazil: a genomic epidemiology study

Zoonotic sporotrichosis is a neglected fungal disease, whereby outbreaks are primarily driven by Sporothrix brasiliensis and linked to cat-to-human transmission. To understand the emergence and spread of sporotrichosis in Brazil, the epicentre of the current epidemic in South America, we aimed to conduct whole-genome sequencing (WGS) to describe the genomic epidemiology. In this genomic epidemiology study, we included Sporothrix spp isolates from sporotrichosis cases from Brazil, Colombia, and the USA. We conducted WGS using Illumina NovaSeq on isolates collected by three laboratories in Brazil from humans and cats with sporotrichosis between 2013 and 2022. All isolates that were confirmed to be Sporothrix genus by internal transcribed spacer or beta-tubulin PCR sequencing were included in this study. We downloaded eight Sporothrix genome sequences from the National Center for Biotechnology Information (six from Brazil, two from Colombia). Three Sporothrix spp genome sequences from the USA were generated by the US Centers for Disease Control and Prevention as part of this study. We did phylogenetic analyses and correlated geographical and temporal case distribution with genotypic features of Sporothrix spp isolates. 72 Sporothrix spp isolates from 55 human and 17 animal sporotrichosis cases were included: 67 (93%) were from Brazil, two (3%) from Colombia, and three (4%) from the USA. Cases spanned from 1999 to 2022. Most (61[85%]) isolates were S brasiliensis, and all were reported from Brazil. Ten (14%) were Sporothrix schenckii and were reported from Brazil, USA, and Colombia. For S schenckii isolates, two distinct clades were observed wherein isolates clustered by geography. For S brasiliensis isolates, five clades separated by more than 100 000 single-nucleotide polymorphisms were observed. Among the five S brasiliensis clades, clades A and C contained isolates from both human and cat cases, and clade A contained isolates from six different states in Brazil. Compared with Sbrasiliensis isolates, larger genetic diversity was observed among S schenckii isolates from animal and human cases within a clade. Our results suggest that the ongoing epidemic driven by S brasiliensis in Brazil represents several, independent emergence events followed by animal-to-animal and animal-to human transmission within and between Brazilian states. These results describe how S brasiliensis can emerge and spread within a country. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil; the São Paulo Research Foundation; Productivity in Research fellowships by the National Council for Scientific and Technological Development, and Ministry of Science and Technology of Brazil.

First report of wilt disease caused by Pythium myriotylum on peanut plants in Korea.

Peanut (Arachis hypogaea L.) has long been cultivated worldwide as an important crop for oil and protein production. Among the various diseases in peanut plants, wilt diseases caused by soil-borne pathogens such as Ralstonia solanacearum and Verticillium dahliae are especially destructive and substantially diminish both quantity and quality in peanut production (Kokalis-Burelle et al., 1997; Thiessen et al., 2012). In July 2022, wilt symptoms were observed in 1 to 3% of the area of peanut fields in Yeoju-si, Korea (37°23´04.0˝N; 127°33´43.0˝E). The xylem in the stems of the wilted plants was dark brown at the soil-surface, which is a representative symptom of vascular wilt pathogens (Yadeta et al. 2013). To isolate the causative pathogens, the stems exhibiting dark lesions were disinfected with 1% NaOCl for 1 min, rinsed with sterile distilled water, and placed on potato dextrose agar medium. The plates were incubated at 25℃ for 2 days, and white hyphae that grew out from the tissues were subcultured twice on V8 juice agar (V8A) medium. Among the 3 isolates, morphological characteristics of the representative strain YJ1-2 were observed under a microscope. The sporangia were terminal intercalary, filamentous, inflated lobulate, and ranging from 37.4 to 73.6 μm in diameter. The antheridia were diclinous, with clavate, elongate, and crook-necked shapes. The oogonia were mostly globose, with an average of 27.1 μm (range from 20.2 to 35.2 μm, n = 50) in diameter, and mated with one to several antheridia. Both plerotic or aplerotic oospores were observed. Overall, the morphological characteristics of the sporangia, antheridia, oogonia, and oospores indicated that YJ1-2 belongs to the genus Pythium. To genetically characterize YJ1-2, genomic DNA was extracted using cetyltrimethylammonium bromide buffer, and the internal transcribed spacer (ITS) region and cytochrome c oxidase subunit I (cox1) gene were amplified by PCR using primer sets ITS4/ITS5 and OomCoxI-Levlo/ OomCoxI-Levup, respectively (White et al., 1990; Robideau et al. 2011), sequenced, and identified using BLASTN (NCBI, National Center for Biotechnology Information). The ITS sequence (NCBI Acc. No. OR125595) of YJ1-2 has 99% similarity with that of P. myriotylum isolate PY39 (NCBI Acc. No. KX671096). A neighbor-joining phylogenetic tree was constructed from aligned cox1 sequence (NCBI Acc. No. OR224334) of the 10 Pythium species strains including YJ1-2 by CLUSTALW method was used as an outgroup. The YJ1-2 was most closely related to P. myriotylum isolate PM30 (NCBI Acc. No. MT823167). To substantiate the pathogenicity of YJ1-2, the crown roots of peanut plants grown in pots for 4 weeks were wounded using a sterile tweezer, and the mycelial plugs of YJ1-2 cultured for 5 days on V8A were inoculated on the wounds. The inoculated plants were cultivated in a growth chamber at 30℃ and 70% relative humidity with a 12-h photoperiod. The infected peanut plants exhibited wilt symptoms 11 days after inoculation, consistent with the initial observation, while uninoculated plants remained healthy. To satisfy Koch's postulates, white mycelia were re-isolated from the stems of inoculated plants and axenically cultured in V8A. The morphologies and ITS sequences of the re-isolates were consistent with those of YJ1-2. P. myriotylum has been reported as a causal pathogen of peanut pod rot in the United States and China. However, to the best of our knowledge, this is the first report of wilt disease in peanut plants caused by P. myriotylum in Korea. To prevent the incidence of wilt disease, we will continue our investigations to develop control strategies, including the selection of appropriate agrochemicals.

Diversity of species and geographic distribution of tick-borne viruses in China.

Tick-borne pathogens especially viruses are continuously appearing worldwide, which have caused severe public health threats. Understanding the species, distribution and epidemiological trends of tick-borne viruses (TBVs) is essential for disease surveillance and control. In this study, the data on TBVs and the distribution of ticks in China were collected from databases and literature. The geographic distribution of TBVs in China was mapped based on geographic locations of viruses where they were prevalent or they were detected in vector ticks. TBVs sequences were collected from The National Center for Biotechnology Information and used to structure the phylogenetic tree. Eighteen TBVs from eight genera of five families were prevalent in China. Five genera of ticks played an important role in the transmission of TBVs in China. According to phylogenetic analysis, some new viral genotypes, such as the Dabieshan tick virus (DTV) strain detected in Liaoning Province and the JMTV strain detected in Heilongjiang Province existed in China. TBVs were widely distributed but the specific ranges of viruses from different families still varied in China. Seven TBVs belonging to the genus Orthonairovirus of the family Nairoviridae such as Nairobi sheep disease virus (NSDV) clustered in the Xinjiang Uygur Autonomous Region (XUAR) and northeastern areas of China. All viruses of the family Phenuiviridae except Severe fever with thrombocytopenia syndrome virus (SFTSV) were novel viruses that appeared in the last few years, such as Guertu virus (GTV) and Tacheng tick virus 2 (TcTV-2). They were mainly distributed in the central plains of China. Jingmen tick virus (JMTV) was distributed in at least fourteen provinces and had been detected in more than ten species of tick such as Rhipicephalus microplus and Haemaphysalis longicornis, which had the widest distribution and the largest number of vector ticks among all TBVs. Parainfluenza virus 5 (PIV5) and Lymphatic choriomeningitis virus (LCMV) were two potential TBVs in Northeast China that could cause serious diseases in humans or animals. Ixodes persulcatus carried the highest number of TBVs, followed by Dermacentor nuttalli and H. longicornis. They could carry as many as ten TBVs. Three strains of Tick-borne encephalitis (TBEV) from Inner Mongolia Province clustered with ones from Russia, Japan and Heilongjiang Province, respectively. Several SFTSV strains from Zhejiang Province clustered with strains from Korea and Japan. Specific surveillance of dominant TBVs should be established in different areas in China.