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Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach

FEBS Open Bio, EarlyView.
This study utilized a novel sampling method, ERAT (i.e. endoscopic retrograde appendicitis treatment)‐guided lumen aspiration, to obtain samples from the appendix, and shotgun metagenomic sequencing was performed for in situ characterization of the appendix microbiome in patients with acute appendicitis.
Huimin Ma, Mingfei Wang, Yanhu Feng, Wanqi Zhang, Wenbo Wang, Yanfeng Xie, Guixiang Kong, Jie Feng, Pengfei Wang, Qi Wang, Xiaojun Huang   +10 more
wiley   +1 more source

Transcriptional regulation of neuropeptide receptors underlies context‐dependent adaptation in Drosophila melanogaster

FEBS Open Bio, EarlyView.
Under environmental changes, the expression level of neuropeptide (NP) and neuropeptide receptor (NPR) genes changes to confer context‐dependent adaptation to the model organism Drosophila melanogaster. Through finding more regulatory elements in the NPR genes in comparison with their ligands (NPs), we found that NPR‐biased transcriptional regulation ...
SeungHeui Ryu, Yanan Wei, Zekun Wu, Tianmu Zhang, DoHoon Lee, Hadi Najafi, Woo Jae Kim   +6 more
wiley   +1 more source

A unified model for Duchenne muscular dystrophy gene involvement in cancer: context‐dependent tumour suppression and oncogenicity

FEBS Open Bio, EarlyView.
We propose a context‐dependent model where the Duchenne muscular dystrophy (DMD) gene acts as a tumour suppressor in aggressive tumours and as an oncogene in less aggressive ones. We propose this model as a unified framework to explain the opposing survival associations with DMD expression and to guide experimental exploration of the dual role of DMD ...
Lee Machado, Leanne Jones, Sonika Divakar, Michael Naidoo, Karen Anthony   +4 more
wiley   +1 more source

Diffusion‐based size determination of solute particles: a method adapted for postsynaptic proteins

FEBS Open Bio, EarlyView.
We present a diffusion‐based approach for measuring the size of macromolecules and their complexes, and demonstrate its use on postsynaptic proteins. The method requires fluorescein‐labelled protein samples, a microfluidic device that maintains laminar flow for said samples, a microscope recording the emitted fluorescent signals, and an analytic ...
András László Szabó, Eszter Nagy‐Kanta, Soma Varga, Edit Andrea Jáger, Csaba István Pongor, Mária Laki, András József Laki, Zoltán Gáspári   +7 more
wiley   +1 more source

Electrical pulse stimulation reflecting the episodic nature of real‐life exercise modulates metabolic and secretory profile of primary human myotubes

FEBS Open Bio, EarlyView.
Here, we introduced an intermittent electrical stimulation protocol mimicking the episodic nature of real‐life exercise in vitro by alternating low‐ and high‐frequency stimulation. In comparison with widely used continuous stimulation, it enhanced the rate of glucose and fatty acid oxidation, but not the myokine release.
Klára Gabrišová, Tímea Kurdiová, Daria Barkova, Natália Pálešová, Jana Babulicová, Silvia Tyčiaková, Marta Novotová, Mária Balážová, Miroslav Sabo, Václav Pustka, Jozef Ukropec, Barbara Ukropcová   +11 more
wiley   +1 more source

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Complexity of automated gene annotation

Biosystems, 2011
Integration of high-throughput data with functional annotation by graph-theoretic methods has been postulated as promising way to unravel the function of unannotated genes. Here, we first review the existing graph-theoretic approaches for automated gene function annotation and classify them into two categories with respect to their relation to two ...
Nikoloski, Zoran (Prof. Dr.), Grimbs, Sergio (Dr.), Klie, Sebastian, Selbig, Joachim   +3 more
openaire   +4 more sources

Methods for Gene Ontology Annotation [PDF]

, 2007
The Gene Ontology (GO) is an established dynamic and structured vocabulary that has been successfully used in gene and protein annotation. Designed by biologists to improve data integration, GO attempts to replace the multiple nomenclatures used by specialised and large biological knowledgebases.
Emily Dimmer, Tanya Z. Berardini, Daniel Barrell, Evelyn Camon   +3 more
openaire   +2 more sources

Visual annotation of the gene database

2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2009
The genes in NCBI databases are currently annotated with itemized text (Gene Reference Into Function, or GeneRIF). A previous work suggests that the visual presentation can be more effective when time and space are under heavy constraints. Here we report a novel annotation of the genome information using Web 2.0 technologies: GeneGIF (Gene Graphics ...
Xishu Wang, Hui Lu, Simon Lin, Jing Wen, Warren A. Kibbe   +4 more
openaire   +3 more sources

Gene Annotation: Prediction and Testing

Annual Review of Genomics and Human Genetics, 2003
Fifty years after the publication of DNA structure, the whole human genome sequence will be officially finished. This achievement marks the beginning of the task to catalogue every human gene and identify each of their function expression patterns. Currently, researchers estimate that there are about 30,000 human genes and approximately 70% of these ...
Jennifer L. Ashurst, John E. Collins
openaire   +3 more sources

Annotating Noncoding RNA Genes

Annual Review of Genomics and Human Genetics, 2007
Noncoding RNA genes produce a functional RNA product rather than a translated protein. More than 1500 homologs of known “classical” RNA genes can be annotated in the human genome sequence, and automatic homology-based methods predict up to 5000 related sequences.
openaire   +3 more sources