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Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture.

Mol Phylogenet Evol 2021 Jun 12:107232. Epub 2021 Jun 12.

Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China. Electronic address:

Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g. Read More

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Informatics Methods and Infrastructure Needed to Study Factors Associated with High Incidence of Pediatric Brain and Central Nervous System Tumors in Kentucky.

J Registry Manag 2020 ;47(3):127-134

Pediatric brain and central nervous system tumors (PBCNSTs) are the most common solid tumors and are the leading cause of disease-related death in US children. PBCNST incidence rates in Kentucky are significantly higher than in the United States as a whole, and are even higher among Kentucky's Appalachian children. To understand and eventually eliminate such disparities, population-based research is needed to gain a thorough understanding of the epidemiology and etiology of the disease. Read More

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January 2020

DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid.

mSystems 2021 Jun 15:e0061921. Epub 2021 Jun 15.

Department of Food Science, Cornell University, Ithaca, New York, USA.

Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering of primary material, laboratory methods, data analysis, and interpretation. Read More

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Intragenomic sequence variations in the second internal transcribed spacer (ITS2) ribosomal DNA of the malaria vector Anopheles stephensi.

PLoS One 2021 14;16(6):e0253173. Epub 2021 Jun 14.

National Institute of Malaria Research, New Delhi, India.

Second Internal Transcribed Spacer (ITS2) ribosomal DNA (rDNA) sequence is a widely used molecular marker for species-identification or -delimitation due to observed concerted evolution which is believed to homogenize rDNA copies in an interbreeding population. However, intra-specific differences in ITS2 of Anopheles stephensi have been reported. This study reports the presence of intragenomic sequence variation in the ITS2-rDNA of An. Read More

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Phylogenetic delimitation of and .

Fungal Syst Evol 2021 Jun 12;7:197-221. Epub 2021 Feb 12.

ALVALAB, Dr. Fernando Bongera st., Severo Ochoa Bldg. S1.04, 33006 Oviedo, Spain.

In the present study six species of (including a new taxon, ) are described and subjected to phylogenetic analysis. The analysis of ITS and 28S rDNA, as well as sequences of and exons suggests that and represent independent lineages within . Morphologically, and do not seem to have clear diagnostic features, although species of often produce variously shaped conidia (navicular, fusoid, curved, polygonal, rounded), while most species of have rounded (face view) / lenticular (side view) conidia. Read More

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Time-Dependent Analysis of pAO1 Nicotine-Related Proteome.

ACS Omega 2021 Jun 25;6(22):14242-14251. Epub 2021 May 25.

Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699-5810, United States.

is a soil Gram-positive nicotine-degrading microorganism (NDM) that harbors a 165 kb pAO1 catabolic megaplasmid. The nicotine catabolic genes on pAO1 have been sequenced, but not all the details on the regulation and interplay of this pathway with the general metabolism of the cell are available. To address this issue at the protein level, a time-based shotgun proteomics study was performed. Read More

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The complete chloroplast genome of .

Mitochondrial DNA B Resour 2021 Jun 4;6(7):1855-1856. Epub 2021 Jun 4.

Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China.

is one of the Agave cultivars for sisal fiber production around the tropical areas of the world. In the present study, we successfully sequenced and assembled its chloroplast genome. The full size of the genome is 157,268 bp with a GC content at 37. Read More

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Characterization of the complete chloroplast genome of L. var. with phylogenetic analysis.

Mitochondrial DNA B Resour 2021 Jun 3;6(7):1852-1854. Epub 2021 Jun 3.

Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industralization, School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China.

In the present study, the complete chloroplast genome of L. var. was sequenced, assembled and compared with closely related species. Read More

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The complete chloroplast genome sequence of (Benth.) S. Moore. (Asteraceae).

Mitochondrial DNA B Resour 2021 Jun 3;6(7):1834-1836. Epub 2021 Jun 3.

Kunming Medical University Haiyuan College, Kunming, China.

The complete chloroplast (cp) genome of was sequenced and assembled for the first time. In this study, the total genome size is 150,596 bp in length and demonstrates a typical quadripartite structure containing a large single copy (LSC, 82,575 bp) and a small single copy (SSC, 18,293 bp), separated by a pair of inverted repeats (IRa, IRb) of 24,864 bp. The G + C content of this cp genome was 37. Read More

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The complete chloroplast genome and phylogenetic analysis of subsp. (Rupr.) P.S.Green & M.C.Chang from Qinghai Province, China.

Mitochondrial DNA B Resour 2021 Jun 3;6(7):1829-1831. Epub 2021 Jun 3.

Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.

subsp. (Rupr.) P. Read More

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The complete chloroplast genome of 'Yulinglong' ( var. ) with double-petaled in southeast of China.

Mitochondrial DNA B Resour 2021 Jun 2;6(6):1765-1767. Epub 2021 Jun 2.

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.

In this study, the complete chloroplast (cp) genome of var. cv 'Yulinglong' was sequenced and assembled by next-generation sequencing. The complete cp genome is 159,376 in length and contained 137 genes, consisting of 91 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. Read More

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Characterization of the complete mitochondrial genome of (Decapoda: Hippolytidae).

Mitochondrial DNA B Resour 2021 Jun 2;6(6):1718-1720. Epub 2021 Jun 2.

Food and Drug College, Qingyuan Polytechnic, Qingyuan, China.

is widely distributed in the Indian and Pacific oceans. In this study, we sequenced the mitochondrial genome of using Illumina HiSeq. The complete mitochondrial genome of was 20,837 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. Read More

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Exosomes Isolated From Bone Marrow Mesenchymal Stem Cells Exert a Protective Effect on Osteoarthritis via lncRNA LYRM4-AS1-GRPR-miR-6515-5p.

Front Cell Dev Biol 2021 28;9:644380. Epub 2021 May 28.

Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, China.

Objectives: The aim of this study was to investigate the effects of exosomes isolated from human bone marrow mesenchymal stem cells (BMSCs) on osteoarthritis (OA) and a competitive endogenous RNA (ceRNA) network.

Methods: Exosomes were isolated from human BMSCs and characterized by transmission electron microscopy (TEM), Nanosight (NTA), and western blotting. Chondrocytes were treated with interleukin-1β (IL-1β) and then transfected with exosomes. Read More

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Construction and Identification of New Molecular Markers of Triple-Negative Breast Cancer Stem Cells.

Front Oncol 2021 28;11:647291. Epub 2021 May 28.

Department of Breast Surgery, Breast Cancer Center, Tai'an Central Hospital, Tai'an, China.

We screened the TNBC stem cells using phage display (PD) and acquired the specific binding clones; and then the positive phage DNAs were amplified and extracted, synthesized with specific polypeptides, and labeled with fluorescein isothiocyanate (FITC). Finally, we identified the specificity of the polypeptides and . Human breast cancer cell line MDA-MB-231 and human mammary gland cell line hs578bst were chosen in our study, and MDA-MB-231 breast cancer stem cells (BCSCs) were cultured and identified by flow cytometry. Read More

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× Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs.

Front Plant Sci 2021 28;12:643137. Epub 2021 May 28.

Institute of Bioengineering, Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, Russia.

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant × . Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled . Read More

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Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast : Intron Evolution, Gene Rearrangement, and Its Phylogeny.

Front Microbiol 2021 28;12:646567. Epub 2021 May 28.

Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.

In this study, the mitogenome of was sequenced by next-generation sequencing (NGS) and successfully assembled. The mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of partially deleted the tRNA gene transferring cysteine. Read More

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Molecular characterization and expression analysis of gene in (L.) R. Br.

Saudi J Biol Sci 2021 Jun 19;28(6):3585-3593. Epub 2021 Mar 19.

Biology Department, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box: 83, Al-kharj 11942, Saudi Arabia.

Ribosomal L18/L5e (RL18/L5e) is a member of the ribosomal L18/L5e protein family, which has an essential function in translation of mRNA into protein in the large ribosomal subunit. In this study, was isolated and sequenced from local (L.) R. Read More

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Molecular Characterization and Haplotype Analyses of Lung Hydatid Cyst Isolates of Cattle and First Report of Echinococcus canadensis (G6/G7) in Cattle Isolates in Turkey.

Acta Parasitol 2021 Jun 14. Epub 2021 Jun 14.

Department of Parasitology, Faculty of Veterinary Medicine, Bingol University, Bingol, Turkey.

Purpose: Cystic echinococcosis (CE) is a zoonotic disease, caused by parasite known as Echinococcus granulosus sensu lato complex, leading to substantial economic losses in rural areas with public health problems. This study was carried out to understand the haplotypic profiles of the partial mitochondrial cytochrome c oxidase (mt-CO1) gene of cattle lung hydatid cyst samples which were obtained from two provinces in Turkey.

Methods: In this study, forty (n = 40) hydatid cyst samples from the lungs of slaughtered cattle were obtained. Read More

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Identification of potential SLA-I-restricted CTL epitopes within the M protein of porcine reproductive and respiratory syndrome virus.

Vet Microbiol 2021 May 26;259:109131. Epub 2021 May 26.

School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. Electronic address:

CD8+ cytotoxic T lymphocytes (CTLs), are essential for clearance of porcine reproductive and respiratory syndrome virus (PRRSV) infection and regulation of host immune responses. Identification of SLA I-restricted CD8+ CTL epitopes would facilitate PRRSV vaccine development. Here, cells isolated from peripheral blood mononuclear cells (PBMCs) of PRRSV-immunized Large White pigs (JXA1-R strain) were screened for immunodominant PRRSV-2 M protein T cell epitopes via ELISPOT assay. Read More

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Anopheles (Nyssorhynchus) tadei: A New Species of the Oswaldoi-konderi Complex (Diptera, Anophelinae) and its Morphological and Molecular Distinctions from An. konderi sensu stricto.

Acta Trop 2021 Jun 10:106004. Epub 2021 Jun 10.

Laboratório de Genética de Populações e Evolução de Mosquitos Vetores de Malária e Dengue. Instituto Nacional de Pesquisas da Amazônia, Manaus, CEP 69.067-375, Amazonas, Brazil. Electronic address:

The Oswaldoi-konderi Complex (Anopheles, Nyssorhynchus) is composed of five species that have been distinguished and delimited using DNA sequences of mitochondrial and nuclear genes. At least two species of the complex have been formally described, namely Anopheles oswaldoi s.s. Read More

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Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding.

Food Microbiol 2021 Oct 25;99:103836. Epub 2021 May 25.

Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece; Department of Food Science and Nutrition, University of the Aegean, Myrina, 81400, Lemnos, Greece.

Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Read More

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October 2021

Genome sequence of the cardiopulmonary canid nematode Angiostrongylus vasorum reveals species-specific genes with potential involvement in coagulopathy.

Genomics 2021 Jun 9. Epub 2021 Jun 9.

Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland.

Angiostrongylus vasorum is an emerging parasitic nematode of canids and causes respiratory distress, bleeding, and other signs in dogs. Despite its clinical importance, the molecular toolbox allowing the study of the parasite is incomplete. To address this gap, we have sequenced its nuclear genome using Oxford nanopore sequencing, polished with Illumina reads. Read More

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Description of the Metacercaria of Cardiocephaloides sp. (Digenea, Diplostomoidea), Newly Recorded from the Brain of Gangetic Leaffish (Nandus nandus) and Its Genetic Characterization in India.

Acta Parasitol 2021 Jun 12. Epub 2021 Jun 12.

Molecular Taxonomy Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut, 250004, UP, India.

Purpose: Cardiocephaloides comprises strigeid trematodes that represent a small genus. In this study, metacercaria identified as Cardiocephaloides sp. was collected from the Gangetic leaffish Nandus nandus from the Ganga River at Bairaj, Bijnor (29º01'N, 77º45'E) in the state of Uttar Pradesh (U. Read More

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Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study.

NPJ Breast Cancer 2021 Jun 11;7(1):76. Epub 2021 Jun 11.

Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.

Breast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. Read More

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Molecular characterization of decreased susceptibility to ceftriaxone and genotyping of Neisseria gonorrheae isolates in New Delhi, India.

Diagn Microbiol Infect Dis 2021 May 11;101(1):115423. Epub 2021 May 11.

Department of Dermatology & Venereology, All India Institute of Medical Sciences, New Delhi, India.

Data on genetic characteristics of Neisseria gonorrhoeae isolates exhibiting decreased susceptibility to extended-spectrum cephalosporins in India is deficient. In this study, we have sequenced penA, porB, mtrR and ponA and bla genes in 70 clinical isolates of NG with varying ceftriaxone MICs. Amongst these, 22 (31. Read More

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The role of Mobile phones as a possible pathway for pathogen movement A CROSS-SECTIONAL, MICROBIAL ANALYSIS.

Travel Med Infect Dis 2021 Jun 8:102095. Epub 2021 Jun 8.

Faculty of Health Sciences and Medicine, Bond University, Robina, QLD, Australia (AU); Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia (AU); General Department of Forensic Science and Criminology, Dubai Police, Dubai, United Arab Emirates (UAE); Dubai Future Council on Community Security, Dubai, United Arab Emirates (UAE); Dubai Police Scientists Council, Dubai Police, Dubai, United Arab Emirates (UAE).

Introduction: Mobile phones are used the world over, including in healthcare settings. This study aimed to investigate the viable microbial colonisation of mobile phones used by healthcare personnel.

Methods: Swabs collected on the same day from 30 mobile phones belonging to healthcare workers from three separate paediatric wards of an Australian hospital were cultured on five types of agar plate, then colonies from each phone were pooled, extracted and sequenced by shotgun metagenomics. Read More

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Etiology and prevalence of ESBLs in adult community-onset urinary tract infections in East China: a prospective multicenter study.

J Infect 2021 Jun 8. Epub 2021 Jun 8.

Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China. Electronic address:

Objectives: Community onset urinary tract infections (COUTIs) drew attention recently owing to their increased prevalence and associations with resistant pathogens. The study is aimed at investigating the etiology of COUTIs as well as prevalence and the related risk factors of extended-spectrum β-lactamase (ESBL) in COUTIs in China.

Methods: The prospective study was performed in nineteen hospitals during November 1, 2017 and August 31, 2019. Read More

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Sickle-trait hemoglobin reduces adhesion to both CD36 and EPCR by Plasmodium falciparum-infected erythrocytes.

PLoS Pathog 2021 Jun 11;17(6):e1009659. Epub 2021 Jun 11.

Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America.

Sickle-trait hemoglobin protects against severe Plasmodium falciparum malaria. Severe malaria is governed in part by the expression of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) that are encoded by var genes, specifically those variants that bind Endothelial Protein C Receptor (EPCR). In this study, we investigate the effect of sickle-trait on parasite var gene expression and function in vitro and in field-collected parasites. Read More

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Morphological and Molecular Identification of Emerged Lophomonas blattarum Infection in Mazandaran Province, Northern Iran: First Registry-Based Study.

Acta Parasitol 2021 Jun 11. Epub 2021 Jun 11.

Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Lophomoniasis (INRCL), Mazandaran University of Medical Sciences, Farah-Abad Road, P.O Box: 48471- 91971, Sari, Iran.

Background: In the last decade, several cases of bronchopulmonary lophomoniasis (BPL) have been recorded. Little information is available about epidemiological aspects on Lophomonas infection among BPL patients. The present study was aimed to investigate the prevalence of Lophomonas spp. Read More

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Applied shotgun metagenomics approach for the genetic characterization of dengue viruses.

J Biotechnol 2019 15;306S:100009. Epub 2019 May 15.

University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands. Electronic address:

Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to detect and type DENV directly from clinical samples without targeted amplification. Read More

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