scholarly journals AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential

2019 ◽  
Vol 47 (W1) ◽  
pp. W276-W282 ◽  
Author(s):  
Mohammad Alanjary ◽  
Katharina Steinke ◽  
Nadine Ziemert
Keyword(s):  
Natural Product ◽  
Phylogenetic Analyses ◽  
Species Trees ◽  
Web Interfaces ◽  
As Species ◽  
Wide Range ◽  
High Sequence Conservation ◽  
Reference Genomes ◽  
Automate Selection ◽  
Selection Of

Abstract Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid ‘one-click’ pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.

Gerricola queenslandensis n. g., n. sp., a new monorchiid trematode from the eastern Australian coast and its life cycle partially elucidated

2021 ◽  
Vol 95 ◽  
Author(s):  
N.Q.-X. Wee ◽  
S.C. Cutmore ◽  
T.H. Cribb
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Lack Of Information ◽  
Terminal Organ ◽  
As Species ◽  
Wide Range ◽  
Generic Position

Abstract Of over 250 species of Monorchiidae Odhner, 1911, just four are known from gerreid fishes. Here, we report adult specimens of a new species infecting Gerres oyena (Forsskål) and Gerres subfasciatus Cuvier from off Heron Island and North Stradbroke Island, Queensland, Australia. The species is morphologically most similar to the concept of Lasiotocus Looss, 1907, which currently comprises eight species, in the possession of an unspined genital atrium, bipartite terminal organ, round oral sucker and unlobed ovary. However, phylogenetic analyses of the 28S ribosomal DNA gene region shows the species to be distantly related to the two sequenced species of Lasiotocus – Lasiotocus mulli (Stossich, 1883) Odhner, 1911 and Lasiotocus trachinoti Overstreet & Brown, 1970 – and that it clearly requires a distinct genus; thus, we propose Gerricola queenslandensis n. g., n. sp. Morphologically, G. queenslandensis n. g., n. sp. differs significantly from L. mulli and L. trachinoti only in the possession of distinctly longer caeca, which terminate in the post-testicular region, and in the absence of a distinct gap in the terminal organ spines. The remaining species of Lasiotocus possess caeca that also terminate in the post-testicular region, which might warrant their transfer to Gerricola n. g. However, doubt about their monophyly due to a combination of significant morphological variation, a lack of information on some features and infection of a wide range of hosts, lead us to retain these taxa as species of Lasiotocus until molecular sequence data are available to better inform their phylogenetic and taxonomic positions. Sporocysts and cercariae of G. queenslandensis n. g., n. sp. were found in a lucinid bivalve, Codakia paytenorum (Iredale), from Heron Island. Sexual adult and intramolluscan stages were genetically matched with the ITS2 ribosomal DNA and cox1 mitochondrial DNA regions. This is the second record of the Lucinidae as a first intermediate host for the Monorchiidae. Additionally, we report sporocysts and cercariae of another monorchiid infection in a tellinid bivalve, Jactellina clathrata (Deshayes), from Heron Island. Molecular sequence data for this species do not match any sequenced species and phylogenetic analyses do not suggest any generic position.

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

2020 ◽  
Vol 7 (2) ◽  
pp. 34-41
Author(s):  
VLADIMIR NIKONOV ◽  
◽  
ANTON ZOBOV ◽  
Keyword(s):  
Mathematical Expectation ◽  
Point Of View ◽  
Small Range ◽  
Computational Point ◽  
Wide Range ◽  
Bijective Function ◽  
The Difference ◽  
Element Base ◽  
Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

Synthesis, Characterization and Antiproliferative Activity Assessment of a Novel 1H-5-mercapto-1,2,4 Triazole Derivative

2017 ◽  
Vol 68 (4) ◽  
pp. 745-747 ◽  
Author(s):  
Marius Mioc ◽  
Sorin Avram ◽  
Vasile Bercean ◽  
Mihaela Balan Porcarasu ◽  
Codruta Soica ◽  
...  
Keyword(s):  
Antiproliferative Activity ◽  
Biological Activities ◽  
Cancer Cell Line ◽  
Vascular Endothelial ◽  
Triazole Derivative ◽  
Activity Assessment ◽  
Wide Range ◽  
Specific Receptors ◽  
Endothelial Growth Factor ◽  
Selection Of

Angiogenesis plays an important function in tumor proliferation, one of the main angiogenic promoters being the vascular endothelial growth factor (VEGF) which activates specific receptors, particularly VEGFR-2. Thus, VEGFR-2 has become an essential therapeutic target in the development of new antitumor drugs. 1,2,4-triazoles show a wide range of biological activities, including antitumor effect, which was documented by numerous reports. In the current study the selection of 5-mercapto-1,2,4-triazole structure (1H-3-styryl-5-benzylidenehydrazino-carbonyl-methylsulfanil-1,2,4-triazole, Tz3a.7) was conducted based on molecular docking that emphasized it as suitable ligand for VEGFR-2 and EGFR1 receptors. Compound Tz3a.7 was synthesized and physicochemically and biologically evaluated thus revealing a moderate antiproliferative activity against breast cancer cell line MDA-MB-231.

Effect of Contact Ratio on Spur Gear Dynamic Load With No Tooth Profile Modifications

1996 ◽  
Vol 118 (3) ◽  
pp. 439-443 ◽  
Author(s):  
Chuen-Huei Liou ◽  
Hsiang Hsi Lin ◽  
F. B. Oswald ◽  
D. P. Townsend
Keyword(s):  
Dynamic Load ◽  
Spur Gear ◽  
Tooth Size ◽  
Contact Ratio ◽  
Gear Dynamics ◽  
Wide Range ◽  
Gear Contact ◽  
Center Distance ◽  
Selection Of ◽  
Better Than

This paper presents a computer simulation showing how the gear contact ratio affects the dynamic load on a spur gear transmission. The contact ratio can be affected by the tooth addendum, the pressure angle, the tooth size (diametral pitch), and the center distance. The analysis presented in this paper was performed by using the NASA gear dynamics code DANST. In the analysis, the contact ratio was varied over the range 1.20 to 2.40 by changing the length of the tooth addendum. In order to simplify the analysis, other parameters related to contact ratio were held constant. The contact ratio was found to have a significant influence on gear dynamics. Over a wide range of operating speeds, a contact ratio close to 2.0 minimized dynamic load. For low-contact-ratio gears (contact ratio less than two), increasing the contact ratio reduced gear dynamic load. For high-contact-ratio gears (contact ratio equal to or greater than 2.0), the selection of contact ratio should take into consideration the intended operating speeds. In general, high-contact-ratio gears minimized dynamic load better than low-contact-ratio gears.

scholarly journals A Virtual Telescope for the Open University Science Foundation Course

1998 ◽  
Vol 162 ◽  
pp. 100-105
Author(s):  
Andrew J. Norton ◽  
Mark H. Jones
Keyword(s):  
Social Science ◽  
Open University ◽  
Distance Teaching ◽  
The Arts ◽  
Wide Range ◽  
University Science ◽  
First Time ◽  
Degree Level ◽  
Selection Of

The Open University is the UK's foremost distance teaching university. For over twenty five years we have been presenting courses to students spanning a wide range of degree level and vocational subjects. Since we have no pre-requisites for entry, a major component of our course profile is a selection of foundation courses comprising one each in the Arts, Social Science, Mathematics, Technology and Science faculties. The Science Faculty's foundation course is currently undergoing a substantial revision. The new course, entitled “S103: Discovering Science”, will be presented to students for the first time in 1998.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

scholarly journals BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space

2021 ◽  
Vol 22 (15) ◽  
pp. 7773
Author(s):  
Neann Mathai ◽  
Conrad Stork ◽  
Johannes Kirchmair
Keyword(s):  
Large Scale ◽  
Computational Approach ◽  
Large Sets ◽  
Compound Libraries ◽  
Wide Range ◽  
Protein Space ◽  
High Chance ◽  
Large Scale Screening ◽  
Early Drug ◽  
Selection Of

Experimental screening of large sets of compounds against macromolecular targets is a key strategy to identify novel bioactivities. However, large-scale screening requires substantial experimental resources and is time-consuming and challenging. Therefore, small to medium-sized compound libraries with a high chance of producing genuine hits on an arbitrary protein of interest would be of great value to fields related to early drug discovery, in particular biochemical and cell research. Here, we present a computational approach that incorporates drug-likeness, predicted bioactivities, biological space coverage, and target novelty, to generate optimized compound libraries with maximized chances of producing genuine hits for a wide range of proteins. The computational approach evaluates drug-likeness with a set of established rules, predicts bioactivities with a validated, similarity-based approach, and optimizes the composition of small sets of compounds towards maximum target coverage and novelty. We found that, in comparison to the random selection of compounds for a library, our approach generates substantially improved compound sets. Quantified as the “fitness” of compound libraries, the calculated improvements ranged from +60% (for a library of 15,000 compounds) to +184% (for a library of 1000 compounds). The best of the optimized compound libraries prepared in this work are available for download as a dataset bundle (“BonMOLière”).

scholarly journals What Do Meditators Do When They Meditate? Proposing a Novel Basis for Future Meditation Research

Mindfulness ◽  
2021 ◽  
Author(s):  
Karin Matko ◽  
Ulrich Ott ◽  
Peter Sedlmeier
Keyword(s):  
Qualitative Study ◽  
Quantitative Study ◽  
Literature Search ◽  
Comprehensive Overview ◽  
Contemplative Practices ◽  
Comprehensive List ◽  
Scientific Investigations ◽  
Wide Range ◽  
Vast Range ◽  
Selection Of

Abstract Objectives Meditation is an umbrella term for a vast range of contemplative practices. Former proposals have struggled to do justice to this variety. To our knowledge, there is to date no comprehensive overview of meditation techniques spanning all major traditions. The present studies aimed at providing such a comprehensive list of meditation techniques. Methods In a qualitative study, we compiled a collection of 309 meditation techniques through a literature search and interviews with 20 expert meditators. Then, we reduced this collection to 50 basic meditation techniques. In a second, quantitative study, 635 experienced meditators from a wide range of meditative backgrounds indicated how much experience they had with each of these 50 meditation techniques. Results Meditators’ responses indicated that our choice of techniques had been adequate and only two techniques had to be added. Our additional statistical and cluster analyses illustrated preferences for specific techniques across and within diverse traditions as well as sets of techniques commonly practiced together. Body-centered techniques stood out in being of exceptional importance to all meditators. Conclusions In conclusion, we found an amazing variety of meditation techniques, which considerably surpasses previous collections. Our selection of basic meditation techniques might be of value for future scientific investigations and we encourage researchers to use this set.

scholarly journals Hospital-Based Donor Recruitment and Predonation Serologic Testing for COVID-19 Convalescent Plasma

2021 ◽  
Author(s):  
Joanna Balcerek ◽  
Evelin Trejo ◽  
Kendall Levine ◽  
Paul Couey ◽  
Zoe V Kornberg ◽  
...  
Keyword(s):  
Blood Donation ◽  
High Titer ◽  
Igg Antibodies ◽  
Serologic Testing ◽  
Wide Range ◽  
The Us ◽  
Polymerase Chain ◽  
Igg Level ◽  
Donor Recruitment ◽  
Selection Of

Abstract Objectives Serologic testing for antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in potential donors of coronavirus disease 2019 (COVID-19) convalescent plasma (CCP) may not be performed until after blood donation. A hospital-based recruitment program for CCP may be an efficient way to identify potential donors prospectively Methods Patients who recovered from known or suspected COVID-19 were identified and recruited through medical record searches and public appeals in March and April 2020. Participants were screened with a modified donor history questionnaire and, if eligible, were asked for consent and tested for SARS-CoV-2 antibodies (IgG and IgM). Participants positive for SARS-CoV-2 IgG were referred for CCP collection. Results Of 179 patients screened, 128 completed serologic testing and 89 were referred for CCP donation. IgG antibodies to SARS-CoV-2 were detected in 23 of 51 participants with suspected COVID-19 and 66 of 77 participants with self-reported COVID-19 confirmed by polymerase chain reaction (PCR). The anti–SARS-CoV-2 IgG level met the US Food and Drug Administration criteria for “high-titer” CCP in 39% of participants confirmed by PCR, as measured by the Ortho VITROS IgG assay. A wide range of SARS-CoV-2 IgG levels were observed. Conclusions A hospital-based CCP donor recruitment program can prospectively identify potential CCP donors. Variability in SARS-CoV-2 IgG levels has implications for the selection of CCP units for transfusion.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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