29,604 results match your criteria clade clade

Direct and indirect effects of fenoxycarb on freshwater systems dominated by Neocaridina palmata (Decapoda: Atyidae) and macrophyte Ceratophyllum demersum.

Ecotoxicol Environ Saf 2021 May 12;219:112304. Epub 2021 May 12.

Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, PR China.

Few studies have been conducted with regard to the effects of insecticides on population dynamics of shrimps and associated groups such as macrophytes, phytoplankton, microorganisms etc. In the present study, effects of a single application of fenoxycarb were tested using indoor freshwater systems dominated by Neocaridina palmata and Ceratophyllum demersum (Dicotyledons: Ceratophyllales). The no observed effect concentration (NOEC) and lowest observed effect concentration (LOEC) for the N. Read More

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Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage.

Clin Microbiol Infect 2021 May 12. Epub 2021 May 12.

IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France. Electronic address:

Objectives: Our surveillance of the SARS-CoV-2 genomic epidemiology led us to detect several variants since summer 2020. We report the recent spread of a new SARS-CoV-2 spike 501Y variant.

Methods: SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analyzed using Nextclade and an in-house Python script and compared using BLASTn to the GISAID database. Read More

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Outbreak of equine pythiosis in a southeastern region of Brazil: environmental isolation and phylogeny.

Transbound Emerg Dis 2021 May 15. Epub 2021 May 15.

UNESP Univ Estadual Paulista, School of Veterinary Medicine and Animal Science, Brazil.

Pythiosis is a disease caused by the oomycete Pythium insidiosum, mainly reported in equines, dogs, and humans and directly transmitted through contaminant zoospores in aquatic environments. We report the first outbreak of equine pythiosis in five equines. Wound samples were submitted for diagnostic testing including mycological culture and nested PCR. Read More

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Retrospective whole-genome comparison of Salmonella enterica serovar Enteritidis from foodborne outbreaks in Southern Brazil.

Braz J Microbiol 2021 May 14. Epub 2021 May 14.

Lutheran University of Brazil, 8001, Canoas, Rio Grande Do Sul, 92425-020, Brazil.

Salmonella enterica serovar Enteritidis is frequently isolated from animal-source foods associated with human salmonellosis outbreaks. This serovar was spread to animal (mainly poultry) farms worldwide in the 1980s, and it is still detected in foods produced in many countries, including Brazil. The present study reports a retrospective genome-wide comparison of S. Read More

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The Longest Infectious Virus Shedding in a Child Infected With the G614 Strain of SARS-CoV-2.

Pediatr Infect Dis J 2021 May 7. Epub 2021 May 7.

From the Division of Infectious Disease, Department of Pediatrics, Medical School of Ege University, Izmir, Turkey Department of Virology, Faculty of Veterinary Medicine, Ankara, Turkey.

COVID-19 spread globally and caused over 97 million cases with more than 2 million deaths. There is still ongoing discussion on the duration of infectious interval SARS-CoV-2 infection. Symptomatic children had longer virus shedding and there are some reports of prolonged infectious virus shedding in adults particularly patients having an immunocompromised status. Read More

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Neutralization diversity of HIV-1 Indian subtype C envelopes obtained from cross sectional and followed up individuals against broadly neutralizing monoclonal antibodies having distinct gp120 specificities.

Retrovirology 2021 May 14;18(1):12. Epub 2021 May 14.

HIV Vaccine Translational Research Laboratory, Translational Health Sciences & Technology Institute, Faridabad, Haryana, India.

Background: The potential use of the broadly neutralizing monoclonal antibodies (bnAbs) towards prophylaxis and treatment to HIV-1 is currently being explored. While a number of promising bnAbs have been discovered and a few of them have progressed towards clinical development, their extent of neutralization coverage with respect to global HIV-1 variants given the existence of genetically distinct subtypes and recombinants circulating globally is not clearly known. In the present study, we examined the variation in the neutralization susceptibility of pseudoviruses expressing 71 full length primary HIV-1 subtype C envs obtained from limited cross-sectional individuals over different time points against four bnAbs that target gp120 with distinct specificities: VRC01, CAP256-VRC26. Read More

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Molecular phylogeny, classification, biogeography and diversification patterns of a diverse group of moths (Geometridae: Boarmiini).

Mol Phylogenet Evol 2021 May 11:107198. Epub 2021 May 11.

Department of Biology, Lund University, Sweden. Electronic address:

Understanding how and why some groups have become more species-rich than others, and how past biogeography may have shaped their current distribution, are questions that evolutionary biologists have long attempted to answer. We investigated diversification patterns and historical biogeography of a hyperdiverse lineage of Lepidoptera, the geometrid moths, by studying its most species-rich tribe Boarmiini, which comprises ca. 200 genera and ca. Read More

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Striking developmental convergence in angiosperm endoparasites.

Am J Bot 2021 May 14. Epub 2021 May 14.

Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.

Premise: A subset of parasitic plants bear extremely reduced features and grow nearly entirely within their hosts. Until recently, most of these endoparasites were thought to represent a single clade united by their reduced morphology. Current phylogenetic understanding contradicts this assumption and indicates these plants represent distantly related clades, thus offering an opportunity to examine convergence among plants with this life history. Read More

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A molecular analysis of microalgae from around the globe to revise Raphidonema (trebouxiophyceae, chlorophyta).

J Phycol 2021 May 14. Epub 2021 May 14.

Department of Molecular Biology and Biochemistry, South Sciences Building room 8166, 8888 University Drive Burnaby, B.C, V5A 1S6, Canada.

We isolated five microalgal strains from alpine snow near Vancouver Canada, which display morphological features suggestive of the genera Koliella and Raphidonema. Due to variations in cell size and shape we could not make a clear delimitation based on morphology. We proceeded to a molecular analysis and included 22 strains from the CCCryo culture collection, previously identified as members of four closely related genera: Raphidonema, Koliella, Stichococcus, and Pseudochlorella. Read More

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Genetic assessment of BoLA-DRB3 polymorphisms by comparing Bangladesh, Ethiopian, and Korean cattle.

J Anim Sci Technol 2021 Mar 31;63(2):248-261. Epub 2021 Mar 31.

Ethiopian Biotechnology Institute, Addis Ababa 5954, Ethiopia.

Attributable to their major function in pathogen recognition, the use of bovine leukocyte antigens (BoLA) as disease markers in immunological traits in cattle is well established. However, limited report exists on polymorphism of the BoLA gene in zebu cattle breeds by high resolution typing methods. Thus, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n = 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red Chittagong zebu (n = 14). Read More

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A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other "protorosaurs", and its implications for the early evolution of stem archosaurs.

PeerJ 2021 3;9:e11143. Epub 2021 May 3.

University of Zurich, Palaeontological Institute and Museum, Zurich, Switzerland.

The historical clade "Protorosauria" represents an important group of archosauromorph reptiles that had a wide geographic distribution between the Late Permian and Late Triassic. "Protorosaurs" are characterized by their long necks, which are epitomized in the genus and in . Recent phylogenetic analyses have indicated that "Protorosauria" is a polyphyletic clade, but the exact relationships of the various "protorosaur" taxa within the archosauromorph lineage is currently uncertain. Read More

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Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020.

Sci Rep 2021 May 13;11(1):10203. Epub 2021 May 13.

Department of Medical Research, Ministry of Health and Sports, 5, Ziwaka Road, Dagon, Yangon, 11191, Republic of the Union of Myanmar.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. Read More

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IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome.

BMC Bioinformatics 2021 May 13;22(1):247. Epub 2021 May 13.

Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, 410210, India.

Background: Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SARS-CoV-2 sequence data generated at an unprecedented rate.

Results: We present an updated version of the SARS-CoV-2 analysis module of our automated computational pipeline, Infectious Pathogen Detector (IPD) 2. Read More

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Biogeographic origins of southern African Silene (Caryophyllaceae).

Mol Phylogenet Evol 2021 May 10:107199. Epub 2021 May 10.

Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs Gata 22 B, 413 19 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.

Silene (Caryophyllaceae) is distributed predominantly in the northern Hemisphere, where it is most diverse around the Mediterranean Basin. The genus is also well represented in North Africa, extending into tropical, sub-Saharan and southern Africa. Eight native species are recognized in southern Africa, taxonomically placed in two sections: Elisanthe and Silene s. Read More

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Description of sp. nov., a phytopathogenic actinobacterium isolated from barley seeds, causing leaf brown spot and decline.

Int J Syst Evol Microbiol 2021 May;71(5)

Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, Charlottetown, PE C1A 5T1, Canada.

is a Gram-stain-positive bacterium with eight subspecies, five of which have been redefined as different species on the basis of their genome sequence data. On the basis of the results of phylogenetic analysis of gene sequences, strains of members of the genus isolated from barley have been grouped in a separate clade from other species and subspecies of the genus . In this study, the biochemical, physiological, fatty acids and genetic characteristics of strains DM1 and DM3, which represented the barley isolates, were examined. Read More

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First Report of Causing Leaf Spot of Tartary Buckwheat () in China.

Plant Dis 2021 May 13. Epub 2021 May 13.

School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, China, China.

Buckwheat (Fagopyrum tataricum) is recognized as a healthy food with abundant nutrients and high levels of rutin. In April and May of 2020, an unknown tartary buckwheat leaf spot distinct from Nigrospora leaf spot (Shen et al. 2020) was observed in Xiangxiang, Hunan, China (27°49'54″N, 112°span style="font-family:'Times New Roman'; color:#0000ff">18'48″E. Read More

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Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie.

Genetics 2021 May 13. Epub 2021 May 13.

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21211, USA.

The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Read More

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Evidence of the American was introduced along with its host in Europe: Molecular and histological data.

Int J Parasitol Parasites Wildl 2021 Aug 15;15:51-57. Epub 2021 Apr 15.

Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary.

The American pumpkinseed , was introduced to Europe more than one hundred years ago. Currently it is a common fish in European freshwaters but relatively few specific parasites infect this fish in this new habitat. In Europe only a single species, seems to represent the American myxosporean fauna of centrarchid fishes. Read More

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Planktonic associations between medusae (classes Scyphozoa and Hydrozoa) and epifaunal crustaceans.

PeerJ 2021 23;9:e11281. Epub 2021 Apr 23.

Department of Marine Biology, Texas A&M University - Galveston, Galveston, Texas, United States.

Jellyfish are known to carry various epibionts, including many of the subphylum Crustacea. However, the associations between gelatinous zooplankton and other invertebrates have been chronically overlooked. Crustacea, a massive clade of economically, ecologically, and culturally important species, includes many taxa that utilize gelatinous zooplankton for food, transport, and protection as both adults and juveniles. Read More

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The Structural Difference of Isobaric -Glycans of Two Microalgae Samples Reveals Taxonomic Distance.

Front Plant Sci 2021 26;12:643249. Epub 2021 Apr 26.

Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.

Microalgae of the clade are extensively investigated as an environmentally friendly source of renewable biofuels and high-value nutrients. In addition, essentially unprocessed serves as wholesome food additive. A recent study on 80 commercial preparations revealed an unexpected variety of protein-linked -glycan patterns with unprecedented structural features, such as the occurrence of arabinose. Read More

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Mitogenome and phylogenetic analysis of typhlocybine leafhoppers (Hemiptera: Cicadellidae).

Sci Rep 2021 May 12;11(1):10053. Epub 2021 May 12.

School of Karst Science, State Key Laboratory Cultivation Base for Guizhou Karst Mountain Ecology Environment of China, Guizhou Normal University, Guiyang, 550001, Guizhou, China.

Mitogenomes have been widely used to estimate phylogenetic relationships among insects and provide data useful for augmenting traditional morphological characters in delimiting species. Here, complete mitogenome sequences of two closely related typhlocybine leafhoppers, Cassianeura cassiae (Ahmed, 1970) and C. bimaculata Dworakowska, 1984, were obtained and found to be 15,423 bp and 14,597 bp in length, respectively. Read More

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Evolution of Old World Equus and origin of the zebra-ass clade.

Sci Rep 2021 May 12;11(1):10156. Epub 2021 May 12.

Laboratory of Evolutionary Biology, Department of Anatomy, College of Medicine, 520 W St. N.W, Washington, DC, 20059, USA.

Evolution of the genus Equus has been a matter of long debate with a multitude of hypotheses. Currently, there is no consensus on either the taxonomic content nor phylogeny of Equus. Some hypotheses segregate Equus species into three genera, Plesippus, Allohippus and Equus. Read More

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Varicella Outbreak in Children from Silvassa, Dadra and Nagar Haveli, India.

Indian Pediatr 2021 May;58(5):483-484

State Health Society, IDSP, National Health Mission, Shri VBCH Campus, Silvassa, India.

Study describes epidemiological and laboratory findings of the fever with skin-rash cases (n=247) reported from Dadra and Nagar Haveli during 2018-19. For laboratory diagnosis, 33 sera and 5 blister swabs were obtained from 36 suspected cases. Varicella-zoster-virus DNA PCR and IgM EIA confirmed 33 cases and sequencing revealed circulation of clade-1 viruses. Read More

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A derivative of the D5 monoclonal antibody that targets the gp41 N-heptad repeat of HIV-1 with broad tier-2 neutralizing activity.

J Virol 2021 May 12. Epub 2021 May 12.

Stanford ChEM-H, Stanford University, Stanford, California, USA

HIV-1 infection is initiated by the viral glycoprotein Env, which, after interaction with cellular coreceptors, adopts a transient conformation known as the pre-hairpin intermediate (PHI). The N-heptad repeat (NHR) is a highly conserved region of gp41 exposed in the PHI; it is the target of the FDA-approved drug enfuvirtide and of neutralizing monoclonal antibodies (mAbs). However, to date these mAbs have only been weakly effective against tier-1 HIV-1 strains, which are most sensitive to neutralizing antibodies. Read More

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Complete genomes derived by directly sequencing freshwater bloom populations emphasize the significance of the genus level ADA clade within the Nostocales.

Harmful Algae 2021 Mar 10;103:102005. Epub 2021 Mar 10.

Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR 97331, USA.

The genome sequences of 16 Nostocales cyanobacteria have been determined. Most of them are complete or near-complete genome sequences derived by long-read metagenome sequencing of recent harmful algal blooms (HABs) in freshwater lakes without the potential bias of culture isolation. The genomes are all members of the recently recognized ADA clade (Driscoll et al. Read More

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Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae).

Syst Biol 2021 May 12. Epub 2021 May 12.

Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA.

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. Read More

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Genomic Analysis of Antibiotic-Resistant and -Susceptible Isolated from Bovine Sources in Maputo, Mozambique.

Foodborne Pathog Dis 2021 May 11. Epub 2021 May 11.

Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, USA.

This study reports a genomic analysis of isolates recovered from 25 bovine fecal composite samples collected from four different production units in Maputo city and around Maputo Province, Mozambique. The genomes were analyzed to determine the presence of antibiotic resistance genes (ARGs), genetic relatedness, and virulence factors known to cause diseases in humans. Whole-genome sequencing was conducted on 28 isolates using an Illumina NextSeq 500 sequencing platform. Read More

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(Urticaceae), a new species from limestone karst in Guangxi, China.

PeerJ 2021 19;9:e11148. Epub 2021 Apr 19.

Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China.

L.F. Fu, A. Read More

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Alternation between taxonomically divergent hosts is not the major determinant of flavivirus evolution.

Virus Evol 2021 Jan 21;7(1):veab040. Epub 2021 Apr 21.

Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy.

Flaviviruses display diverse epidemiological and ecological features. Tick-borne and mosquito-borne flaviviruses (TBFV and MBFV, respectively) are important human pathogens that alternate replication in invertebrate vectors and vertebrate hosts. The genus also includes insect-specific viruses (ISFVs) and viruses with unknown invertebrate hosts. Read More

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January 2021