Functional characterization and biological properties of pectin from Parkia biglobosa pulp

Abstract Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.

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Functional Characterization of Sesquiterpene Synthase fromPolygonum minus

The Scientific World JOURNAL ◽

10.1155/2014/840592 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11 ◽

Cited By ~ 8

Author(s):

Su-Fang Ee ◽

Zeti-Azura Mohamed-Hussein ◽

Roohaida Othman ◽

Noor Azmi Shaharuddin ◽

Ismanizan Ismail ◽

...

Keyword(s):

Transgenic Plants ◽

Metal Binding ◽

Functional Characterization ◽

Biological Properties ◽

Mass Spectrometry Analysis ◽

Gas Chromatography Mass Spectrometry ◽

Sesquiterpene Synthase ◽

Conserved Motifs ◽

Spectrometry Analysis ◽

Metal Binding Domain

Polygonum minusis an aromatic plant, which contains high abundance of terpenoids, especially the sesquiterpenes C15H24. Sesquiterpenes were believed to contribute to the many useful biological properties in plants. This study aimed to functionally characterize a full length sesquiterpene synthase gene fromP. minus.P. minussesquiterpene synthase (PmSTS) has a complete open reading frame (ORF) of 1689 base pairs encoding a 562 amino acid protein. Similar to other sesquiterpene synthases, PmSTS has two large domains: the N-terminal domain and the C-terminal metal-binding domain. It also consists of three conserved motifs: the DDXXD, NSE/DTE, and RXR. A three-dimensional protein model for PmSTS built clearly distinguished the two main domains, where conserved motifs were highlighted. We also constructed a phylogenetic tree, which showed that PmSTS belongs to the angiosperm sesquiterpene synthase subfamily Tps-a. To examine the function ofPmSTS, we expressed this gene inArabidopsis thaliana. Two transgenic lines, designated asOE3andOE7, were further characterized, both molecularly and functionally. The transgenic plants demonstrated smaller basal rosette leaves, shorter and fewer flowering stems, and fewer seeds compared to wild type plants. Gas chromatography-mass spectrometry analysis of the transgenic plants showed that PmSTS was responsible for the production ofβ-sesquiphellandrene.

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Extracellular Vesicles from Plants: Current Knowledge and Open Questions

International Journal of Molecular Sciences ◽

10.3390/ijms22105366 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5366

Author(s):

Ornella Urzì ◽

Stefania Raimondo ◽

Riccardo Alessandro

Keyword(s):

Extracellular Vesicles ◽

Current Knowledge ◽

Functional Characterization ◽

Biological Properties ◽

Controversial Issues ◽

Animal Cells ◽

Natural Substances ◽

Open Questions ◽

Potential Use

The scientific interest in the beneficial properties of natural substances has been recognized for decades, as well as the growing attention in extracellular vesicles (EVs) released by different organisms, in particular from animal cells. However, there is increasing interest in the isolation and biological and functional characterization of these lipoproteic structures in the plant kingdom. Similar to animal vesicles, these plant-derived extracellular vesicles (PDEVs) exhibit a complex content of small RNAs, proteins, lipids, and other metabolites. This sophisticated composition enables PDEVs to be therapeutically attractive. In this review, we report and discuss current knowledge on PDEVs in terms of isolation, characterization of their content, biological properties, and potential use as drug delivery systems. In conclusion, we outline controversial issues on which the scientific community shall focus the attention shortly.

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Functional Characterization of Cardiac Actin Mutants Causing Hypertrophic (p.A295S) and Dilative Cardiomyopathy (p.R312H and p.E361G)

10.21203/rs.3.rs-159358/v1 ◽

2021 ◽

Author(s):

Constanze Erdmann ◽

Roua Hassoun ◽

Sebastian Schmitt ◽

Setsuko Fujita-Becker ◽

Antonina J. Mazur ◽

...

Keyword(s):

Mdck Cells ◽

Functional Characterization ◽

Biological Properties ◽

Cell System ◽

Neonatal Rat ◽

Actin Binding ◽

Rat Cardiomyocytes ◽

Dilative Cardiomyopathy ◽

Cardiac Actin ◽

Myosin S1

Abstract The human mutant cardiac α-actins p.A295S or p.R312H (plus p.R312K) and p.E361G correlated with hypertrophic or dilative cardiomyopathy, respectively, were expressed by using the baculovirus/Sf21 insect cell system. After purification their biochemical and cell biological properties were analysed and compared to wild type (wt) cardiac actin identically obtained or conventionally isolated from bovine hearts. DNase I inhibition and their polymerization behaviour indicated that all c-α-actins had maintained their native state. Cardiomyopathy type specific differences were observed except for the p.R312K mutant, which behaved like wt c-α-actin. The extent of myosin-S1 ATPase stimulation by the c-actin variants and its Ca2+-sensitivity after decoration with tropomyosin (cTm) and troponin complex (cTn) varied being highest for the HCM p.A295S and lower for both DCM mutants. Similar Ca2+-sensitivity differences were observed by recording the fluorescence increase of pyrene-cTm in the absence or presence of myosin-S1 and/or the actin-binding N-terminal fragment of cardiac myosin binding protein C (N-cMyBP-C). Transfection experiments showed the incorporation of the c-actin variants into existing cytoskeletal elements of non-muscle cells. Wt and p.A295S c-α-actin preferably incorporated into the microfilament system and p.R312H and p.E361G into the submembranous actin network of MDCK cells. Transduction of neonatal rat cardiomyocytes with adenoviral constructs coding for HA-tagged c-α-actins showed their incorporation into thin filaments of nascent sarcomeric structures at their plus ends (Z-lines) except the p.E361G mutant, which preferably incorporated at the minus ends. Our data indicate functional differences of the c-α-actins that may be causative for the different cardiomyopathy phenotypes.

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ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility

10.1101/2020.10.27.20220665 ◽

2020 ◽

Author(s):

Gita A Pathak ◽

Frank R Wendt ◽

Aranyak Goswami ◽

Flavio De Angelis ◽

Renato Polimanti ◽

...

Keyword(s):

Gene Network ◽

Functional Characterization ◽

Gene Interaction ◽

Biological Properties ◽

Angiotensin Converting Enzyme 2 ◽

Interaction Database ◽

Functional Consequences ◽

Multi Level ◽

Ace2 Gene

AbstractAngiotensin-converting enzyme-2 (ACE2) receptor has been identified as the key adhesion molecule for the transmission of the SARS-CoV-2. However, there is no evidence that human genetic variation in ACE2 is singularly responsible for COVID-19 susceptibility. Therefore, we performed a multi-level characterization of genes that interact with ACE2 (ACE2-gene network) for their over-represented biological properties in the context of COVID-19.The phenome-wide association of 51 genes including ACE2 with 4,756 traits categorized into 26 phenotype categories, showed enrichment of immunological, respiratory, environmental, skeletal, dermatological, and metabolic domains (p<4e-4). Transcriptomic regulation of ACE2-gene network was enriched for tissue-specificity in kidney, small intestine, and colon (p<4.7e-4). Leveraging the drug-gene interaction database we identified 47 drugs, including dexamethasone and spironolactone, among others.Considering genetic variants within ± 10 kb of ACE2-network genes we characterized functional consequences (among others) using miRNA binding-site targets. MiRNAs affected by ACE2-network variants revealed statistical over-representation of inflammation, aging, diabetes, and heart conditions. With respect to variants mapped to the ACE2-network, we observed COVID-19 related associations in RORA, SLC12A6 and SLC6A19 genes.Overall, functional characterization of ACE2-gene network highlights several potential mechanisms in COVID-19 susceptibility. The data can also be accessed at https://gpwhiz.github.io/ACE2Netlas/

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BRIEF DESCRIPTION OF THE BIOLOGICAL PROPERTIES OF CORONAVIRUS (COVID-19)

MODERN ISSUES OF MEDICINE AND MANAGEMENT ◽

10.52340/mid.2021.475 ◽

2021 ◽

Author(s):

David Aphkhazava ◽

Marina Pirtskhalava ◽

Malkhaz Vakhania ◽

Mariam Kobiashvili ◽

Tornike Mindiashvili ◽

...

Keyword(s):

Functional Characterization ◽

Scientific Research ◽

Biological Properties ◽

Research Data ◽

Infectious Process ◽

Treatment And Prevention

The article provides morphological and functional characterization of the new coronavirus (COVID-19) based on the latest scientific research data, study of biological properties, epidemiology and the course of the infectious process in humans, some issues of treatment and prevention.

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Isolation, functional characterization, and biological properties of MCh‐AMP1, a novel antifungal peptide from Matricaria chamomilla L.

Chemical Biology & Drug Design ◽

10.1111/cbdd.13500 ◽

2019 ◽

Vol 93 (5) ◽

pp. 949-959 ◽

Cited By ~ 6

Author(s):

Sima Sadat Seyedjavadi ◽

Soghra Khani ◽

Hadi Zare‐Zardini ◽

Raheleh Halabian ◽

Mehdi Goudarzi ◽

...

Keyword(s):

Functional Characterization ◽

Biological Properties ◽

Antifungal Peptide ◽

Matricaria Chamomilla

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ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility

Frontiers in Genetics ◽

10.3389/fgene.2021.698033 ◽

2021 ◽

Vol 12 ◽

Author(s):

Gita A. Pathak ◽

Frank R. Wendt ◽

Aranyak Goswami ◽

Dora Koller ◽

Flavio De Angelis ◽

...

Keyword(s):

Genetic Variation ◽

Gene Network ◽

Genome Wide Association Study ◽

Functional Characterization ◽

Gene Interaction ◽

Biological Properties ◽

Interaction Database ◽

Genome Wide ◽

Ace2 Gene

Angiotensin-converting enzyme-2 (ACE2) receptor has been identified as the key adhesion molecule for the transmission of the SARS-CoV-2. However, there is no evidence that human genetic variation in ACE2 is singularly responsible for COVID-19 susceptibility. Therefore, we performed an integrative multi-level characterization of genes that interact with ACE2 (ACE2-gene network) for their statistically enriched biological properties in the context of COVID-19. The phenome-wide association of 51 genes including ACE2 with 4,756 traits categorized into 26 phenotype categories, showed enrichment of immunological, respiratory, environmental, skeletal, dermatological, and metabolic domains (p < 4e-4). Transcriptomic regulation of ACE2-gene network was enriched for tissue-specificity in kidney, small intestine, and colon (p < 4.7e-4). Leveraging the drug-gene interaction database we identified 47 drugs, including dexamethasone and spironolactone, among others. Considering genetic variants within ± 10 kb of ACE2-network genes we identified miRNAs whose binding sites may be altered as a consequence of genetic variation. The identified miRNAs revealed statistical over-representation of inflammation, aging, diabetes, and heart conditions. The genetic variant associations in RORA, SLC12A6, and SLC6A19 genes were observed in genome-wide association study (GWAS) of COVID-19 susceptibility. We also report the GWAS-identified variant in 3p21.31 locus, serves as trans-QTL for RORA and RORC genes. Overall, functional characterization of ACE2-gene network highlights several potential mechanisms in COVID-19 susceptibility. The data can also be accessed at https://gpwhiz.github.io/ACE2Netlas/.

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A Novel Reconstitution Method for Inducing the Formation of Regular 2-Dimensional Arrays of Membrane Proteins and Lipids

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102845 ◽

1988 ◽

Vol 46 ◽

pp. 152-153 ◽

Cited By ~ 1

Author(s):

A. Engel ◽

A. Holzenburg ◽

K. Stauffer ◽

J. Rosenbusch ◽

U. Aebi

Keyword(s):

Membrane Proteins ◽

Flow Rate ◽

Lipid Membranes ◽

Functional Characterization ◽

Dimensional Structure ◽

Electron Crystallography ◽

Peltier Element ◽

Protein Ratio ◽

Precise Control ◽

3 Dimensional

Reconstitution of solubilized and purified membrane proteins in the presence of phospholipids into vesicles allows their functions to be studied by simple bulk measurements (e.g. diffusion of differently sized solutes) or by conductance measurements after transformation into planar membranes. On the other hand, reconstitution into regular protein-lipid arrays, usually forming at a specific lipid-to-protein ratio, provides the basis for determining the 3-dimensional structure of membrane proteins employing the tools of electron crystallography.To refine reconstitution conditions for reproducibly inducing formation of large and highly ordered protein-lipid membranes that are suitable for both electron crystallography and patch clamping experiments aimed at their functional characterization, we built a flow-dialysis device that allows precise control of temperature and flow-rate (Fig. 1). The flow rate is generated by a peristaltic pump and can be adjusted from 1 to 500 ml/h. The dialysis buffer is brought to a preselected temperature during its travel through a meandering path before it enters the dialysis reservoir. A Z-80 based computer controls a Peltier element allowing the temperature profile to be programmed as function of time.

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Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100127608 ◽

1987 ◽

Vol 45 ◽

pp. 633-635

Author(s):

David A. Agard ◽

Yasushi Hiraoka ◽

John W. Sedat

Keyword(s):

Dimensional Space ◽

Three Dimensional ◽

Developmental State ◽

Mitotic Cell ◽

Biological Properties ◽

Dimensional Structure ◽

Specific Gene ◽

Three Dimensional Structure ◽

Complementary Techniques ◽

Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

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