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Bioinformatics Research

09:46 EDT 19th August 2018 | BioPortfolio

Characterization of three strains of Capnocytophaga canis isolated from septic patients.

Capnocytophaga canimorsus and Capnocytophaga cynodegmi, both commensal bacteria in the oral cavity of dogs and cats, are zoonotic pathogens. In particular, C. canimorsus causes sepsis and fatal septic shock. Recently, a novel Capnocytophaga species, C. canis, was isolated from the oral cavity of healthy dogs. C. canis was reported to be oxidase-negative, thus considered to be avirulent in humans. ...

Biosynthesis of the Thiopeptins and Identification of an FH-Dependent Dehydropiperidine Reductase.

Thiopeptins are highly decorated thiopeptide antibiotics similar in structure to thiostrepton A and harbor two unusual features. All thiopeptins contain a thioamide, a rare moiety among natural products, and a subset of thiopeptins present with a piperidine in the core macrocycle rather than the more oxidated dehydropiperidine or pyridine rings typically observed in the thiopeptides. Here, we repo...

Susceptibility of antibody CDR residues to chemical modifications can be revealed prior to antibody humanization and aid in the lead selection process.

A critical part of the clinical development path for a therapeutic antibody involves evaluating the physical and chemical stability of candidate molecules throughout the manufacturing process. In particular, the risks of chemical liabilities which can impact antigen binding, such as deamidation, oxidation, and isomerization in the antibody CDR sequences, need to be controlled through formulation d...

Landau Level Diagram and the Continuous Rotational Symmetry Breaking in Trilayer Graphene.

The sequence of the zeroth Landau levels (LLs) between filling factors ν=-6 to 6 in ABA-stacked trilayer graphene (TLG) is unknown because it depends sensitively on the nonuniform charge distribution on the three layers of ABA-stacked TLG. Using the sensitivity of quantum Hall data on the electric field and magnetic field, in an ultraclean ABA-stacked TLG sample, we quantitatively estimate the no...

Pneumonia Outcome Measures Modified to Address Concerns about Coding-Related Biases.

Reply: Pneumonia Outcome Measures Modified to Address Concerns about Coding-Related Biases.

BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence.

Restriction enzymes are the bread and butter of Molecular Biology. Nonetheless, how restriction enzymes recognize and cleave their target is not always clear. When developing a method for the enzymatic production of oligonucleotides, we noticed that type II endonucleases BtsCI and BseGI, which recognize the sequence GGATGNN^, perform incomplete digestions of DNA hairpins, with the top strand nick ...

Defining the genetic components of callus formation: A GWAS approach.

A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this proc...

Insertion of a transposon-like sequence in the 5'-flanking region of the YUCCA gene causes the stony hard phenotype.

Melting-flesh peaches produce large amounts of ethylene, resulting in rapid fruit softening at the late-ripening stage. In contrast, stony hard peaches do not soften and produce little ethylene. The indole-3-acetic acid (IAA) level in stony hard peaches is low at the late-ripening stage, resulting in low ethylene production and inhibition of fruit softening. To elucidate the mechanism of low IAA c...

Sequencing Grade Tandem Mass Spectrometry for Top-Down Proteomics Using Hybrid Electron Capture Dissociation Methods in a Benchtop Orbitrap Mass Spectrometer.

Compared to traditional collision induced dissociation methods, electron capture dissociation (ECD) provides more comprehensive characterization of large peptides and proteins and preserves labile post-translational modifications. However, ECD experiments are generally restricted to the high magnetic fields of FTICR-MS that enable simultaneous trapping of large polycations and electrons. Here, we ...

Multiple Recurrent Cardiac Myxomas with Protein Kinase A regulatory Subunit 1α Gene Mutation.

Multiple recurrent cardiac myxomas are quite rare in clinical practice. A young male patient had four times of myxoma occurrence, with two times in the left atrium and two times in the left ventricle. He had no medical history of cardiovascular diseases, familial cardiac neoplasm, and endocrinopathy. He underwent surgical resection four times. Genetic analysis revealed a heterozygous base pair mut...

Mitochondrial genome of the yellow catfish Pelteobagrus fulvidraco and insights into Bagridae phylogenetics.

The mitochondrial genome (mitogenome) can provide important information for understanding phylogenetic analysis and thus molecular evolution. Herein, we amplified the complete mitogenome sequence of Pelteobagrus fulvidraco. The mitogenome was 16,526 bp in length and included 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and a non-coding control region (D-loop). B...

A novel familial truncating mutation in the filamin C gene associated with cardiac arrhythmias.

The authors report for the first time a novel mutation in the FLNC gene associated with cardiac arrhythmias in two half-siblings. The FLNC gene on chromosome 7q32 encodes filamin C, which stabilizes the actin network within the cardiomyocyte. The proband is an 8-year-old asymptomatic patient with frequent premature ventricular contractions noted on serial monitoring. Interestingly, the proband and...

Expression, purification and molecular characterization of a novel transcription factor KcCBF3 from Kandelia candel.

Kandelia candel, a major species of mangrove in the tropical and subtropical area, is susceptible to low temperature in winter. K. candel was introduced into Zhejiang Province (the northern margin of South China) several decades ago, and suffered from low temperature causing growth retardation, in server cases, even death. To explore the molecular mechanisms of cold acclimation in K. candel, a nov...

Bridging the gap by discerning SNPs in linkage disequilibrium and their role in breast cancer.

Breast Cancer is the most common cancer among women with several genes involved in disease susceptibility. As majority of genome-wide significant variants fall outside the coding region, it is likely that some of them alter specific gene functions. GWAS database was used to interpret the regulatory functions of these genetic variants. A total of 320 SNPs for breast cancer were selected via GWAS, w...

A review of opioid addiction genetics.

Opioid use disorder (OUD) affects millions of people worldwide and the risk of developing the disorder has a significant genetic component according to twin and family studies. Identification of the genetic variants underlying this inherited risk has focused on two different methods: candidate gene studies and genome-wide association studies (GWAS). The most studied candidate genes have included t...

An Analysis of the Frequency of Y-Chromosome Microdeletions and the Determination of a Threshold Sperm Concentration for Genetic testing in Infertilie Men.

To describe the prevalence of Y-chromosome microdeletions in a multi-ethnic urban population in London, UK. To also determine predictive factors and a clinical threshold for genetic testing in men with Y chromosome microdeletions.

Minimizing context-dependency of gene networks using artificial cells.

The functioning of synthetic gene circuits depends on their local chemical context defined by the types and concentrations of biomolecules in the surrounding milieu that influence gene transcription and translation. This chemical-context dependence of synthetic gene circuits arises from significant yet unknown crosstalk between engineered components, host cells, and environmental factors, and has ...

iRNA-2OM: A Sequence-Based Predictor for Identifying 2'-O-Methylation Sites in Homo sapiens.

2'-O-methylation plays an important biological role in gene expression. Owing to the explosive increase in genomic sequencing data, it is necessary to develop a method for quickly and efficiently identifying whether a sequence contains the 2'-O-methylation site. As an additional method to the experimental technique, a computational method may help to identify 2'-O-methylation sites. In this study,...

Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model.

The recently developed Hi-C technology enables a genome-wide view of chromosome spatial organizations, and has shed deep insights into genome structure and genome function. However, multiple sources of uncertainties make downstream data analysis and interpretation challenging. Specifically, statistical models for inferring three-dimensional (3D) chromosomal structure from Hi-C data are far from th...

Polarization independent fast BOTDA based on pump frequency modulation and cyclic coding.

We propose and experimentally demonstrate a scheme of polarization independent fast Brillouin optical time domain analysis (F-BOTDA) based on pump frequency modulation and cyclic coding. The Brillouin gain spectrum (BGS) is reconstructed by fast scanning frequency of the pump using an arbitrary waveform generator (AWG). To realize long range distributed dynamic strain sensing, polarization diversi...

Polarization division multiplexing pulse coding for eliminating the effect of polarization pulling in Golay-coded BOTDA fiber sensor.

An approach to eliminating the effect of polarization pulling in Golay-coded Brillouin optical time domain analysis (BOTDA) fiber sensor by employing polarization division multiplexing (PDM) pulse coding is presented. Three different schemes, including polarization switching, polarization scrambling, and PDM pulse coding are implemented and compared. Experimental results indicate that sensing stab...

AAV9-mediated telomerase activation does not accelerate tumorigenesis in the context of oncogenic K-Ras-induced lung cancer.

Short and dysfunctional telomeres are sufficient to induce a persistent DNA damage response at chromosome ends, which leads to the induction of senescence and/or apoptosis and to various age-related conditions, including a group of diseases known as "telomere syndromes", which are provoked by extremely short telomeres owing to germline mutations in telomere genes. This opens the possibility of usi...

Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia.

Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate sig...

Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica 'JinhuaiJ2'.

Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica 'JinhuaiJ2', the most widely planted variety ...

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