16,629 results match your criteria states phylogenetic

An efficient vector-based CRISPR/Cas9 system in an Oreochromis mossambicus cell line using endogenous promoters.

Sci Rep 2021 Apr 12;11(1):7854. Epub 2021 Apr 12.

Biochemical Evolution Laboratory, Department of Animal Science, University of California, Davis, CA, 95616, USA.

CRISPR/Cas9 gene editing is effective in manipulating genetic loci in mammalian cell cultures and whole fish but efficient platforms applicable to fish cell lines are currently limited. Our initial attempts to employ this technology in fish cell lines using heterologous promoters or a ribonucleoprotein approach failed to indicate genomic alteration at targeted sites in a tilapia brain cell line (OmB). For potential use in a DNA vector approach, endogenous tilapia beta Actin (OmBAct), EF1 alpha (OmEF1a), and U6 (TU6) promoters were isolated. Read More

View Article and Full-Text PDF

Structure-based phylogeny identifies Avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice.

J Clin Invest 2021 Apr 12. Epub 2021 Apr 12.

Department of Ophthalmology, Stanford University, Palo Alto, United States of America.

Drugs targeting host proteins can act prophylactically to reduce viral burden early in disease and limit morbidity, even with antivirals and vaccination. Transmembrane serine protease 2 (TMPRSS2) is a human protease required for SARS-CoV-2 viral entry and may represent such a target. We hypothesized that drugs selected from proteins related by their tertiary structure, rather than their primary structure, were likely to interact with TMPRSS2. Read More

View Article and Full-Text PDF

Abiotic Environment Predicts Micro- but Not Macroevolutionary Patterns of Flower Color in Monkeyflowers (Phrymaceae).

Front Plant Sci 2021 25;12:636133. Epub 2021 Mar 25.

California Botanic Garden, Claremont, CA, United States.

Anthocyanin pigments are responsible for many of the vivid pink, purple, red, and blue flower colors across angiosperms and frequently vary within and between closely related species. While anthocyanins are well known to influence pollinator attraction, they are also associated with tolerance to abiotic stressors such as extreme temperatures, reduced precipitation, and ultraviolet radiation. Using a comparative approach, we tested whether abiotic variables predict floral anthocyanin in monkeyflowers (Phrymaceae) across western North America. Read More

View Article and Full-Text PDF

Venomous Snakes Reveal Ecological and Phylogenetic Factors Influencing Variation in Gut and Oral Microbiomes.

Front Microbiol 2021 26;12:657754. Epub 2021 Mar 26.

Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, United States.

The gastrointestinal tract (GIT) of vertebrates contains a series of organs beginning with the mouth and ending with the anus or cloacal opening. Each organ represents a unique environment for resident microorganisms. Due to their simple digestive anatomy, snakes are good models for studying microbiome variation along the GIT. Read More

View Article and Full-Text PDF

Association of Loneliness and Wisdom With Gut Microbial Diversity and Composition: An Exploratory Study.

Front Psychiatry 2021 25;12:648475. Epub 2021 Mar 25.

Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States.

Loneliness and wisdom have opposite effects on health and well-being. Loneliness is a serious public health problem associated with increased morbidity and mortality. Wisdom is associated with better health and well-being. Read More

View Article and Full-Text PDF

Enhanced anaerobic digestion of waste-activated sludge via bioaugmentation strategy-Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis through hydrolytic enzymes and possible linkage to system performance.

Bioresour Technol 2021 Mar 31;332:125014. Epub 2021 Mar 31.

School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea. Electronic address:

In this study, anaerobic digestion of waste-activated sludge was bioaugmented with hydrolytic bacteria, Bacteroidetes uniformis (Bacteroidetes, B) and Clostridium sp. (Firmicutes, F) at various dosages. Bioaugmentation resulted in enhanced methane conversion of waste-activated sludge. Read More

View Article and Full-Text PDF

Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil.

Infect Genet Evol 2021 Apr 8:104854. Epub 2021 Apr 8.

Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil. Electronic address:

The HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. Read More

View Article and Full-Text PDF

Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses.

Syst Biol 2021 Apr 10. Epub 2021 Apr 10.

Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.

Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. Read More

View Article and Full-Text PDF

First detection of porcine respirovirus 1 in Germany and the Netherlands.

Transbound Emerg Dis 2021 Apr 9. Epub 2021 Apr 9.

University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.

Porcine respirovirus 1, also referred to as porcine parainfluenza virus 1 (PPIV-1), was first detected in deceased pigs from Hong Kong in 2013. It has since then been found in the USA, Chile, and most recently in Hungary. Information on the pathogenicity and global spread is sparse. Read More

View Article and Full-Text PDF

Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST.

Curr Protoc 2021 Apr;1(4):e98

Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium.

Advances in sequencing technologies have tremendously reduced the time and costs associated with sequence generation, making genomic data an important asset for routine public health practices. Within this context, phylogenetic and phylogeographic inference has become a popular method to study disease transmission. In a Bayesian context, these approaches have the benefit of accommodating phylogenetic uncertainty, and popular implementations provide the possibility to parameterize the transition rates between locations as a function of epidemiological and ecological data to reconstruct spatial spread while simultaneously identifying the main factors impacting the spatial spread dynamics. Read More

View Article and Full-Text PDF

First Report of Wilt of European hornbeam (Carpinus betulus L.) Caused by in China.

Plant Dis 2021 Apr 9. Epub 2021 Apr 9.

Nanjing Forestry University, 74584, College of Forestry, No.159, Longpan Road, Xuanwu District, Nanjing, China, 210037.

European hornbeam (Carpinus betulus L.) has been used as an important ornamental species for urban landscaping since the Italian Renaissance (Rocchi et al. 2010). Read More

View Article and Full-Text PDF

First Report of Grammothele lineata Causing Stem Rot of Areca catechu in Hainan Province, China.

Plant Dis 2021 Apr 8. Epub 2021 Apr 8.

Haikou, China;

Areca catechu L. (areca) belongs to the Arecaceae family, which is composed of 181 genera and 2,600 species (Christenhusz and Byng 2016), is cultivated extensively in Southern and Southeastern Asia (Peng et al. 2015). Read More

View Article and Full-Text PDF

Intraspecific variation in phenotypic and phylogenetic features among isolates from Wisconsin, USA.

J Nematol 2020 24;52. Epub 2020 Nov 24.

Department of Plant Pathology, University of Wisconsin-Madison, 484 Russell Laboratories, 1630 Linden Dr., Madison, WI, 53706.

is a common and important agricultural pest in Wisconsin, a USA state with a diverse agriculture. We compared populations from around the state to each other and to data published for populations around the world to gain insight on the variability of features important for identification of this cosmopolitan species. Thirteen isolates from samples collected in soybean fields in ten Wisconsin counties were established in monoxenic cultures. Read More

View Article and Full-Text PDF
November 2020

ITS secondary structure reconstruction to resolve taxonomy and phylogeny of the L. genus.

PeerJ 2021 23;9:e10889. Epub 2021 Mar 23.

Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany.

The taxonomy and phylogeny of the L. genus remain unresolved and are very difficult to assess due to several factors, especially because of frequent hybridization among different species. In the current study, we used nucleotide sequences of two internal transcribed spacer regions (ITS1 and ITS2), which are commonly used as phylogenetic markers. Read More

View Article and Full-Text PDF

Molecular Evolution of Human Norovirus GII.2 Clusters.

Front Microbiol 2021 22;12:655567. Epub 2021 Mar 22.

MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom.

Background: The human norovirus GII.2 outbreak during the 2016-2017 winter season was of unprecedented scale and geographic distribution.

Methods: We analyzed 519 complete gene sequences of the human norovirus GII. Read More

View Article and Full-Text PDF

The structure, function and evolution of a complete human chromosome 8.

Nature 2021 Apr 7. Epub 2021 Apr 7.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

The complete assembly of each human chromosome is essential for understanding human biology and evolution. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2. Read More

View Article and Full-Text PDF

Cooperative care and the evolution of the prelinguistic vocal learning.

Dev Psychobiol 2021 Apr 7. Epub 2021 Apr 7.

Department of Psychology, Princeton University, Princeton, NJ, USA.

The development of the earliest vocalizations of human infants is influenced by social feedback from caregivers. As these vocalizations change, they increasingly elicit such feedback. This pattern of development is in stark contrast to that of our close phylogenetic relatives, Old World monkeys and apes, who produce mature-sounding vocalizations at birth. Read More

View Article and Full-Text PDF

Research Methodology to Define the Introduction of the SARS-CoV-2 B.1.429 Variant in Hawaii.

Res Sq 2021 Apr 1. Epub 2021 Apr 1.

Here, we present a methodology to define the origin of SARS-CoV-2 variants as exemplified by defining the introduction of the B.1.429 variant in Hawaii. Read More

View Article and Full-Text PDF

Distinguishing -gene-containing IncF plasmids from epidemiologically related and unrelated Enterobacteriaceae based on short- and long-read sequence data.

Antimicrob Agents Chemother 2021 Apr 5. Epub 2021 Apr 5.

Department of Infection Control, Amphia Hospital, Breda, the Netherlands.

Background: Limited information is available on whether -containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated -containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated -containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids.

Method: Epidemiologically related isolates, were short- and long-read whole genome sequenced. Read More

View Article and Full-Text PDF