79,959 results match your criteria analyses sequences


Phylogenetic and topological analyses of the bovine interferon-induced transmembrane protein (IFITM3).

Acta Vet Hung 2021 Apr 15. Epub 2021 Apr 15.

1Korea Zoonosis Research Institute, Jeonbuk National University, 820-120 Hana-ro, Iksan, Jeonbuk 54531, Republic of Korea.

Interferon-induced transmembrane protein 3 (IFITM3) plays a pivotal role in antiviral capacity in several species. However, to date, investigations of the IFITM3 protein in cattle have been rare. According to recent studies, interspecific differences in the IFITM3 protein result in several unique features of the IFITM3 protein relative to primates and birds. Read More

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A Gamified, Social Media-Inspired, Web-Based Personalized Normative Feedback Alcohol Intervention for Lesbian, Bisexual, and Queer-Identified Women: Protocol for a Hybrid Trial.

JMIR Res Protoc 2021 Apr 16;10(4):e24647. Epub 2021 Apr 16.

HeadsUp Labs, Department of Psychology, Loyola Marymount University, Los Angeles, CA, United States.

Background: Sexual minority women are more likely to drink alcohol, engage in heavy drinking, and experience alcohol-related problems than heterosexual women. However, culturally tailored interventions for this population have been slow to emerge.

Objective: This type 1 effectiveness-implementation trial examines the feasibility and efficacy of a gamified, culturally tailored, personalized normative feedback (PNF) alcohol intervention for sexual minority women who psychologically identify as lesbian, bisexual, or queer (LBQ). Read More

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The topology of ventricle surfaces and its application in the analysis of hydrocephalic ventricles: a proof-of-concept study.

Neuroradiology 2021 Apr 15. Epub 2021 Apr 15.

Department of Neurosurgery, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore.

Purpose: The cerebral ventricles deform in a non-uniform fashion in response to increased CSF volume and/or pressure in hydrocephalic syndromes. Current research is focused on volumetric analyses, while topological analysis of ventricular surfaces remains understudied. We developed a method of quantitatively modeling the curvature of ventricular surfaces to analyze changes in ventricular surfaces in normal pressure hydrocephalus (NPH) and Alzheimer's disease (AD), using the left frontal horn as an example. Read More

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n. sp. (Rhabditida: Tylaphelenchinae) associated with bark of a beech tree ( Lipsky) from northern Iran.

J Nematol 2021 17;53. Epub 2021 Mar 17.

Department of Plant Protection, College of Agriculture and Natural resources, University of Tehran, Karaj, Iran.

n. sp., the sixth species of the newly established genus was isolated during a nematode survey associated with bark samples of beech tree in northern Iran, which differs from the other species by body size, stylet length, metacorpus structure, and tail characters of both genders. Read More

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Morphology, development stages, and phylogeny of the (Nematoda: Diplogastridae), a phoront of the bark beetle from the elm Huds. in Northwest Russia.

J Nematol 2021 11;53. Epub 2021 Mar 11.

Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA, 95832.

The nematode was found in galleries, adults, and larvae of , the vector of the Dutch elm disease, in St. Petersburg parks. This nematode co-occurred with , which is another phoretic partner of . Read More

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Integrative taxonomy, distribution, and host associations of and from southern Alberta, Canada.

J Nematol 2021 1;53. Epub 2021 Mar 1.

Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario, ceiA3, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain.

Two stunt nematode species, and , were recovered from the potato growing regions of southern Alberta, described and characterized based on integrative taxonomy. Morphometrics, distribution, and host associations of both species are discussed. The Canadian populations of both species displayed minor variations in morphometrical characteristics (viz. Read More

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A Vernalization Response in a Winter Safflower () Involves the Upregulation of Homologs of , , and .

Front Plant Sci 2021 30;12:639014. Epub 2021 Mar 30.

Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia.

Safflower () is a member of the Asteraceae family that is grown in temperate climates as an oil seed crop. Most commercially grown safflower varieties can be sown in late winter or early spring and flower rapidly in the absence of overwintering. There are winter-hardy safflower accessions that can be sown in autumn and survive over-wintering. Read More

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Computational identification of variables in neonatal vocalizations predictive for postpubertal social behaviors in a mouse model of 16p11.2 deletion.

Mol Psychiatry 2021 Apr 15. Epub 2021 Apr 15.

Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.

Autism spectrum disorder (ASD) is often signaled by atypical cries during infancy. Copy number variants (CNVs) provide genetically identifiable cases of ASD, but how early atypical cries predict a later onset of ASD among CNV carriers is not understood in humans. Genetic mouse models of CNVs have provided a reliable tool to experimentally isolate the impact of CNVs and identify early predictors for later abnormalities in behaviors relevant to ASD. Read More

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Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences.

Sci Rep 2021 Apr 15;11(1):8245. Epub 2021 Apr 15.

Institute for Parasitology and Tropical Veterinary Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.

Cyathostomins are important intestinal nematode parasites of equines and include 50 accepted species. Their taxonomy has been frequently revised and the presence of cryptic species suggested. Furthermore, usually molecular- and morphology-based phylogenetic analyses give divergent results. Read More

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All genera of Flaviviridae host a conserved Xrn1-resistant RNA motif.

RNA Biol 2021 Apr 16:1-9. Epub 2021 Apr 16.

Leiden Institute of Chemistry, Leiden University, RA, Leiden, The Netherlands.

After infection by flaviviruses like Zika and West Nile virus, eukaryotic hosts employ the well-conserved endoribonuclease Xrn1 to degrade the viral genomic RNA. Within the 3' untranslated regions, this enzyme encounters intricate Xrn1-resistant structures. This results in the accumulation of subgenomic flaviviral RNAs, an event that improves viral growth and aggravates viral pathogenicity. Read More

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First Report of Leaf Spot in Farfugium japonicum Caused by Alternaria alternata in China.

Plant Dis 2021 Apr 15. Epub 2021 Apr 15.

HUNAN AGRICULTURAL UNIVERSITY, PLANT DISEASE, ROOM S416, BUILDING 11, COLLEGE OF PLANT PROTECTION, HUNAN AGRICULTUTAL UNIVERSITY, 1 NONGDA ROAD, FURONG DISTRICT, CHANGSHA, HUNAN,CHINA, CHANGSHA, HUNAN, China, 410128;

Farfugium japonicum (L.) Kitam (with the common name leopard plant) is known as a garden and medical herb, and belongs to the family Asteraceae. In May 2019, a leaf spot disease was observed on the upper leaf surface of F. Read More

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Co-Circulation of 3 Dengue Virus Serotypes led to a Severe dengue outbreak in Xishuangbanna, a border area of China, Myanmar and Laos, 2019.

Int J Infect Dis 2021 Apr 12. Epub 2021 Apr 12.

Institute of Medical Biology, Chinese academy of Medical Sciences, and Peking Union Medical College, Kunming, PR China; Kunming Medical University, Kunming, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming, PR China. Electronic address:

Dengue fever has been included in the top ten global health threats announced by the World Health Organization (WHO) in early 2019. In some southern provinces of China, autochthonous outbreak have also been reported in the last decade. An unexpected large outbreak of dengue fever was reported in Xishuangbanna, a border area of China, Myanmar and Laos, in 2019. Read More

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Distinct community structures of soil nematodes from three ecologically different sites revealed by high-throughput amplicon sequencing of four 18S ribosomal RNA gene regions.

PLoS One 2021 15;16(4):e0249571. Epub 2021 Apr 15.

Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, Japan.

Quantitative taxonomic compositions of nematode communities help to assess soil environments due to their rich abundance and various feeding habitats. DNA metabarcoding by the 18S ribosomal RNA gene (SSU) regions were preferentially used for analyses of soil nematode communities, but the optimal regions for high-throughput amplicon sequencing have not previously been well investigated. In this work, we performed Illumina-based amplicon sequencing of four SSU regions (regions 1-4) to identify suitable regions for nematode metabarcoding using the taxonomic structures of nematodes from uncultivated field, copse, and cultivated house garden soils. Read More

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Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin.

PLoS Negl Trop Dis 2021 Apr 15;15(4):e0009327. Epub 2021 Apr 15.

Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.

Background: The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location.

Methodology/principal Findings: Here, we report the sequences of 59 SARS-CoV-2 samples from inhabitants of the Colombian Amazonas department. Read More

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Field-transcriptome analyses reveal developmental transitions during flowering in cassava (Manihot esculenta Crantz).

Plant Mol Biol 2021 Apr 15. Epub 2021 Apr 15.

Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.

Key Message: We characterized genes that function in the photoperiodic flowering pathway in cassava. Transcriptome analysis of field-grown plants revealed characteristic expression patterns of these genes, demonstrating that field-grown cassava experiences two distinct developmental transitions. Cassava is an important crop for both edible and industrial purposes. Read More

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Molecular characterization of Trichomonas gypaetinii isolated from the upper alimentary tract of Steller's sea eagles (Haliaeetus pelagicus) and white-tailed sea eagles (Haliaeetus albicilla) in Hokkaido, Japan.

Parasitol Res 2021 Apr 15. Epub 2021 Apr 15.

Laboratory of Veterinary Pathology, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido, 080-8555, Japan.

Recent phylogenetic and morphologic studies of Trichomonas spp. suggests that there are more than 3 species that infect the upper alimentary tract of wild birds, which include T. gallinae, T. Read More

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mi-IsoNet: systems-scale microRNA landscape reveals rampant isoform-mediated gain of target interaction diversity and signaling specificity.

Brief Bioinform 2021 Apr 14. Epub 2021 Apr 14.

Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.

MicroRNA (miRNA) is not a single sequence, but a series of multiple variants (also termed isomiRs) with sequence and expression heterogeneity. Whether and how these isoforms contribute to functional variation and complexity at the systems and network levels remain largely unknown. To explore this question systematically, we comprehensively analyzed the expression of small RNAs and their target sites to interrogate functional variations between novel isomiRs and their canonical miRNA sequences. Read More

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Phylogenetic estimates of SARS-CoV-2 introductions into Washington State.

medRxiv 2021 Apr 7. Epub 2021 Apr 7.

Background: The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington.

Methods: We conducted a phylogenetic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. Read More

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The complete chloroplast genome of (Ranunculaceae).

Mitochondrial DNA B Resour 2021 Mar 31;6(4):1319-1320. Epub 2021 Mar 31.

Tasly Pharmaceutical Group Co., Ltd, Tianjin, China.

The complete chloroplast genome of was determined in this study. The genome was 159,675 base pair (bp) in length, containing a large single-copy (LSC) region of 79,443 bp, a small single-copy region (SSC) of 18,100 bp and a pair of inverted repeats (IRs) of 31,066 bp. It contains 130 unique genes, including 86 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Read More

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Priority Intervention Targets Identified Using an In-Depth Sampling HIV Molecular Network in a Non-Subtype B Epidemics Area.

Front Cell Infect Microbiol 2021 29;11:642903. Epub 2021 Mar 29.

NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China.

Molecular network analysis based on the genetic similarity of HIV-1 is increasingly used to guide targeted interventions. Nevertheless, there is a lack of experience regarding molecular network inferences and targeted interventions in combination with epidemiological information in areas with diverse epidemic strains of HIV-1.We collected 2,173 sequences covering 84% of the total newly diagnosed HIV-1 infections in Shenyang city, Northeast China, between 2016 and 2018. Read More

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MRI T1 Contrast-Enhanced Signal Intensity Is a Prognostic Indicator of Imatinib Therapy in Desmoid-Type Fibromatosis.

Front Oncol 2021 15;11:615986. Epub 2021 Mar 15.

Department Radiology, Peking University Cancer Hospital, Beijing, China.

Objective: To investigate the efficiency of pre-therapy magnetic resonance imaging (MRI) features in predicting the prognosis of desmoid-type fibromatosis patients treated with imatinib.

Materials And Methods: A total of 38 desmoid-type fibromatosis patients treated with imatinib were collected in this retrospective study. The high signal intensity on pre-therapy MRI was evaluated on axial T2 and T1 contrast-enhanced sequences with fat suppression. Read More

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Characterization of the first vaginal genomes isolated in Brazil.

PeerJ 2021 10;9:e11079. Epub 2021 Mar 10.

Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.

Background: is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. Read More

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Elevation as a selective force on mitochondrial respiratory chain complexes of the lizards in the Tibetan plateau.

Curr Zool 2021 Apr 22;67(2):191-199. Epub 2020 Sep 22.

International Laboratory of Statistical and Computational Genomics, National Research University Higher School of Economics, Moscow, Russia.

Animals living in extremely high elevations have to adapt to low temperatures and low oxygen availability (hypoxia), but the underlying genetic mechanisms associated with these adaptations are still unclear. The mitochondrial respiratory chain can provide >95% of the ATP in animal cells, and its efficiency is influenced by temperature and oxygen availability. Therefore, the respiratory chain complexes (RCCs) could be important molecular targets for positive selection associated with respiratory adaptation in high-altitude environments. Read More

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Characterization of ZmCOLD1, novel GPCR-Type G Protein genes involved in cold stress from L. and the evolution analysis with those from other species.

Physiol Mol Biol Plants 2021 Mar 15;27(3):619-632. Epub 2021 Mar 15.

College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China.

Maize is one of the most vital staple crops worldwide. G proteins modulate plentiful signaling pathways, and G protein-coupled receptor-type G proteins (GPCRs) are highly conserved membrane proteins in plants. However, researches on maize G proteins and GPCRs are scarce. Read More

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Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences.

IMA Fungus 2021 Apr 15;12(1):10. Epub 2021 Apr 15.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

"Sanghuang" refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of "Sanghuang" in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. Read More

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Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level.

Mar Environ Res 2021 Mar 26;168:105315. Epub 2021 Mar 26.

Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain. Electronic address:

Vitellogenin (Vtg), a large multidomain protein precursor of egg-yolk proteins, is used as an endocrine disruption biomarker in fish, and in the last decades, its use has been extended to invertebrates like mollusks. However, it remains unclear whether invertebrate endocrine system produces Vtg in response to estrogens, like it occurs in oviparous vertebrates. In a previous study, no evidence of induction of Vtg expression at protein level was found in gonads of the marine mussel Mytilus galloprovincialis after exposure to the estrogenic chemical 17α-ethinylestradiol (EE2). Read More

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Statistical Learning and Prosodic Bootstrapping Differentially Affect Neural Synchronization during Speech Segmentation.

Neuroimage 2021 Apr 10:118051. Epub 2021 Apr 10.

Department of Cognition, Development and Educational Psychology, Campus Bellvitge, University of Barcelona, 5L'Hospitalet de Llobregat, 08097, Barcelona, Spain; Cognition and Brain Plasticity Group, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, 08097, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, ICREA, 08010, Barcelona, Spain. Electronic address:

Neural oscillations constitute an intrinsic property of functional brain organization that facilitates the tracking of linguistic units at multiple time scales through brain-to-stimulus alignment. This ubiquitous neural principle has been shown to facilitate speech segmentation and word learning based on statistical regularities. However, there is no common agreement yet on whether speech segmentation is mediated by a transition of neural synchronization from syllable to word rate, or whether the two time scales are concurrently tracked. Read More

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A large-scale snapshot of intratumor heterogeneity in human cancer.

Authors:
Young Seok Ju

Cancer Cell 2021 Apr;39(4):463-465

Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. Electronic address:

Using sophisticated statistical analyses on population-scale cancer whole-genome sequences, a new study published in Cell characterizes the genomic architecture of intratumor heterogeneity (ITH). It results in an unprecedented snapshot of subclones in about 30 cancer types, generating a wealth of insight into the underlying mutational events, processes, and their selection. Read More

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gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate.

Int J Syst Evol Microbiol 2021 Apr;71(4)

Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China.

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1-8 %, at pH 6.5-8 and at temperatures of 10-40 °C. Read More

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Prognostic value of intratumoral Fusobacterium nucleatum and association with immune-related gene expression in oral squamous cell carcinoma patients.

Sci Rep 2021 Apr 12;11(1):7870. Epub 2021 Apr 12.

Department of Genetics, Institut Curie, PSL Research University, Paris, France.

Changes in the oral microbiome, particularly Fusobacterium nucleatum, are associated with oral squamous cell carcinoma (OSCC). F. nucleatum has been reported to modulate local immunity in cancers. Read More

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