scholarly journals Postsynaptic α-Neurotoxin Gene of the Spitting Cobra, Naja naja sputatrix: Structure, Organization, and Phylogenetic Analysis

1999 ◽  
Vol 9 (3) ◽  
pp. 259-266
Author(s):  
Fatemeh Afifiyan ◽  
Arunmoziarasi Armugam ◽  
Chee Hong Tan ◽  
Ponnampalam Gopalakrishnakone ◽  
Kandiah Jeyaseelan
Keyword(s):  
Dna Sequences ◽  
Dna Amplification ◽  
Complete Characterization ◽  
Long Distance ◽  
Ancestral Gene ◽  
Naja Naja ◽  
Link Type ◽  
Transcription Sites ◽  
Ccaat Box

The venom of the spitting cobra, Naja naja sputatrixcontains highly potent α-neurotoxins (NTXs) in addition to phospholipase A2 (PLA2) and cardiotoxin (CTX). In this study, we report the complete characterization of three genes that are responsible for the synthesis of three isoforms of α-NTX in the venom of a single spitting cobra. DNA amplification by long-distance polymerase chain reaction (LD-PCR) and genome walking have provided information on the gene structure including their promoter and 5′ and 3′ UTRs. Each NTX isoform is ∼4 kb in size and contains three exons and two introns. The sequence homology among these isoforms was found to be 99%. Two possible transcription sites were identified by primer extension analysis and they corresponded to the adenine (A) nucleotide at positions +1 and −45. The promoter also contains two TATA boxes and a CCAAT box. Putative binding sites for transcriptional factors AP-2 and GATA are also present. The high percentage of similarity observed among the NTX gene isoforms of N. n. sputatrix as well as with the α-NTX and κ-NTX genes from other land snakes suggests that the NTX gene has probably evolved from a common ancestral gene.[The genomic DNA sequences reported in this paper have been submitted to GenBank databases under accession nos. AF096999 to AF097001.]

scholarly journals A novel PCR-clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Emilie Lefèvre ◽  
Courtney M Gardner ◽  
Claudia K Gunsch
Keyword(s):  
Mitochondrial Dna ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Rrna Gene ◽  
Plant Host ◽  
Plant Chloroplast

ABSTRACT Due to the sequence homology between the bacterial 16S rRNA gene and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR-clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.

scholarly journals AmpliconDesign – An interactive web server for the design of high-throughput targeted DNA methylation assays

2020 ◽  
Author(s):  
Maximilian Schönung ◽  
Jana Hess ◽  
Pascal Bawidamann ◽  
Sina Stäble ◽  
Joschka Hey ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Quality Control ◽  
High Throughput ◽  
Dna Sequences ◽  
Web Server ◽  
Dna Amplification ◽  
Pcr Primers ◽  
Primer Design ◽  
Link Type ◽  
Targeted Analysis

ABSTRACTTargeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed AmpliconDesign, a webserver providing a scalable and user-friendly platform for the design and analysis of targeted DNA methylation studies based on BT-DNA, e.g. deep amplicon bisulfite sequencing (ampBS-seq), EpiTYPER MassArray, or pyrosequencing. Core functionality of the web server includes high-throughput primer design and binding site validation based on in silico bisulfite-converted DNA sequences, prediction of fragmentation patterns for EpiTYPER MassArray, an interactive quality control as well as a streamlined analysis workflow for ampBS-seq.Availability and ImplementationThe AmpliconDesign webserver is freely available online at: https://amplicondesign.dkfz.de/. AmpliconDesign has been implemented using the R Shiny framework (Chang et al., 2018). The source code is publicly available under the GNU General Public License v3.0 (https://github.com/MaxSchoenung/AmpliconDesign).ContactDaniel B. Lipka ([email protected]) & Maximilian Schönung ([email protected])

scholarly journals Characterization of Clustered MHC-Linked Olfactory Receptor Genes in Human and Mouse

2001 ◽  
Vol 11 (4) ◽  
pp. 519-530 ◽  
Author(s):  
Ruth M. Younger ◽  
Claire Amadou ◽  
Graeme Bethel ◽  
Anke Ehlers ◽  
Kirsten Fischer Lindahl ◽  
...  
Keyword(s):  
Olfactory Receptor ◽  
Mate Selection ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Long Distance ◽  
Functional Studies ◽  
Link Type ◽  
Genomic Environment ◽  
Human And Mouse

Olfactory receptor (OR) loci frequently cluster and are present on most human chromosomes. They are members of the seven transmembrane receptor (7-TM) superfamily and, as such, are part of one of the largest mammalian multigene families, with an estimated copy number of up to 1000 ORs per haploid genome. As their name implies, ORs are known to be involved in the perception of odors and possibly also in other, nonolfaction-related, functions. Here, we report the characterization of ORs that are part of the MHC-linked OR clusters in human and mouse (partial sequence only). These clusters are of particular interest because of their possible involvement in olfaction-driven mate selection. In total, we describe 50 novel OR loci (36 human, 14 murine), making the human MHC-linked cluster the largest sequenced OR cluster in any organism so far. Comparative and phylogenetic analyses confirm the cluster to be MHC-linked but divergent in both species and allow the identification of at least one ortholog that will be useful for future regulatory and functional studies. Quantitative feature analysis shows clear evidence of duplications of blocks of OR genes and reveals the entire cluster to have a genomic environment that is very different from its neighboring regions. Based on in silico transcript analysis, we also present evidence of extensive long-distance splicing in the 5′-untranslated regions and, for the first time, of alternative splicing within the single coding exon of ORs. Taken together with our previous finding that ORs are also polymorphic, the presented data indicate that the expression, function, and evolution of these interesting genes might be more complex than previously thought.[The sequence data described in this paper have been submitted to the EMBL nucleotide data library under accession nos.Z84475, Z98744, Z98745, AL021807, AL021808, AL022723, AL022727,AL031893, AL035402, AL035542, AL050328, AL050339, AL078630, AL096770,AL121944, AL133160, and AL133267.]

scholarly journals Priors for Genotyping Polyploids

2019 ◽  
Author(s):  
David Gerard ◽  
Luís Felipe Ventorim Ferrão
Keyword(s):  
Empirical Bayes ◽  
A Priori ◽  
Real Data ◽  
R Package ◽  
Complete Characterization ◽  
Genotype Distribution ◽  
Link Type ◽  
Systematic Biases ◽  
Technical Artifacts

AbstractMotivationEmpirical Bayes techniques to genotype polyploid organisms usually either (i) assume technical artifacts are known a priori or (ii) estimate technical artifacts simultaneously with the prior genotype distribution. Case (i) is unappealing as it places the onus on the researcher to estimate these artifacts, or to ensure that there are no systematic biases in the data. However, as we demonstrate with a few empirical examples, case (ii) makes choosing the class of prior genotype distributions extremely important. Choosing a class that is either too flexible or too restrictive results in poor genotyping performance.ResultsWe propose two classes of prior genotype distributions that are of intermediate levels of flexibility: the class of proportional normal distributions and the class of unimodal distributions. We provide a complete characterization of and optimization details for the class of unimodal distributions. We demonstrate, using both simulated and real data, that using these classes results in superior genotyping performance.Availability and ImplementationGenotyping methods that use these priors are implemented in the updog R package available on the Comprehensive R Archive Network: https://cran.r-project.org/package=updog. All code needed to reproduce the results of this paper is available on GitHub: https://github.com/dcgerard/[email protected]

Experimental Characterization of Mechanical Behavior of Cord-Rubber Composites

1982 ◽  
Vol 10 (1) ◽  
pp. 37-54 ◽  
Author(s):  
M. Kumar ◽  
C. W. Bert
Keyword(s):  
Response Characteristic ◽  
Cord Compression ◽  
Complete Characterization ◽  
Strain Response ◽  
Strain Gages ◽  
Experimental Characterization ◽  
Rubber Composites ◽  
Stress Strain ◽  
Strain Data

Abstract Unidirectional cord-rubber specimens in the form of tensile coupons and sandwich beams were used. Using specimens with the cords oriented at 0°, 45°, and 90° to the loading direction and appropriate data reduction, we were able to obtain complete characterization for the in-plane stress-strain response of single-ply, unidirectional cord-rubber composites. All strains were measured by means of liquid mercury strain gages, for which the nonlinear strain response characteristic was obtained by calibration. Stress-strain data were obtained for the cases of both cord tension and cord compression. Materials investigated were aramid-rubber, polyester-rubber, and steel-rubber.

Characterization of CMOS Structures (0.6 µm process) Submitted to HBM and COM ESD Stress Tests

1997 ◽  
Author(s):  
G. Meneghesso ◽  
E. Zanoni ◽  
P. Colombo ◽  
M. Brambilla ◽  
R. Annunziata ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electrostatic Discharge ◽  
Stress Test ◽  
Complete Characterization ◽  
Stress Tests ◽  
Test Procedures ◽  
Emission Microscopy ◽  
Fast Rise ◽  
Scanning Electron

Abstract In this work, we present new results concerning electrostatic discharge (ESD) robustness of 0.6 μm CMOS structures. Devices have been tested according to both HBM and socketed CDM (sCDM) ESD test procedures. Test structures have been submitted to a complete characterization consisting in: 1) measurement of the tum-on time of the protection structures submitted to pulses with very fast rise times; 2) ESD stress test with the HBM and sCDM models; 3) failure analysis based on emission microscopy (EMMI) and Scanning Electron Microscopy (SEM).

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

scholarly journals Complete characterization of spin chains with two Ising symmetries

2019 ◽  
Vol 125 (1) ◽  
pp. 10008 ◽  
Author(s):  
Bat-el Friedman ◽  
Atanu Rajak ◽  
Emanuele G. Dalla Torre
Keyword(s):  
Complete Characterization ◽  
Spin Chains

scholarly journals On the star forest polytope for trees and cycles

2019 ◽  
Vol 53 (5) ◽  
pp. 1763-1773
Author(s):  
Meziane Aider ◽  
Lamia Aoudia ◽  
Mourad Baïou ◽  
A. Ridha Mahjoub ◽  
Viet Hung Nguyen
Keyword(s):  
Undirected Graph ◽  
Dominating Set ◽  
Discrete Math ◽  
Complete Characterization ◽  
Facial Structure ◽  
Maximum Weight ◽  
Single Node ◽  
End Node ◽  
Vertex Disjoint

Let G = (V, E) be an undirected graph where the edges in E have non-negative weights. A star in G is either a single node of G or a subgraph of G where all the edges share one common end-node. A star forest is a collection of vertex-disjoint stars in G. The weight of a star forest is the sum of the weights of its edges. This paper deals with the problem of finding a Maximum Weight Spanning Star Forest (MWSFP) in G. This problem is NP-hard but can be solved in polynomial time when G is a cactus [Nguyen, Discrete Math. Algorithms App. 7 (2015) 1550018]. In this paper, we present a polyhedral investigation of the MWSFP. More precisely, we study the facial structure of the star forest polytope, denoted by SFP(G), which is the convex hull of the incidence vectors of the star forests of G. First, we prove several basic properties of SFP(G) and propose an integer programming formulation for MWSFP. Then, we give a class of facet-defining inequalities, called M-tree inequalities, for SFP(G). We show that for the case when G is a tree, the M-tree and the nonnegativity inequalities give a complete characterization of SFP(G). Finally, based on the description of the dominating set polytope on cycles given by Bouchakour et al. [Eur. J. Combin. 29 (2008) 652–661], we give a complete linear description of SFP(G) when G is a cycle.

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