Biomolecular Function Discovery Division

Proteomic and bioinformatic analyses for the identification of proteins with low allergenic potential for hazard assessment

Published date : 23 Mar 2019

Use of botanicals and natural substances in consumer products has increased in recent years. Such extracts can contain protein that may theoretically represent a potential risk of IgE-mediated allergy. No method has yet been generally accepted or validated for assessment of the allergenic potential of proteins. For development of suitable methods datasets of allergenic and non-allergenic (or low allergenic) proteins are required that can serve, respectively, as positive and negative controls. However, data are unavailable on proteins that lack or have low allergenic potential.

type
Journal Paper
journal
Toxicological Sciences, 2019 Mar 23. pii: kfz078. doi: 10.1093/toxsci/kfz078.
Impact Factor
4.081

Sterol regulatory element binding protein 1 couples mechanical cues and lipid metabolism

Published date : 22 Mar 2019

Sterol regulatory element binding proteins (SREBPs) are a family of transcription factors that regulate lipid biosynthesis and adipogenesis by controlling the expression of several enzymes required for cholesterol, fatty acid, triacylglycerol and phospholipid synthesis. In vertebrates, SREBP activation is mainly controlled by a complex and well-characterized feedback mechanism mediated by cholesterol, a crucial bio-product of the SREBP-activated mevalonate pathway.

type
Journal Paper
journal
Nature Communications, 2019 Mar 22;10(1):1326. doi: 10.1038/s41467-019-09152-7
Impact Factor
12.353

Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)

Published date : 11 Mar 2019

Sub-species nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI) H5Nx viruses. These nomenclature systems rely on absolute genetic distance thresholds to define the maximum genetic divergence tolerated between viruses designated as closely related.

type
Journal Paper
journal
Molecular Biology and Evolution, 2019 Mar 11. pii: msz053. doi: 10.1093/molbev/msz053
Impact Factor
10.217

AllerCatPro - Prediction of protein allergenicity potential from the protein sequence

Published date : 18 Jan 2019

MOTIVATION:
Due to the risk of inducing an immediate type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens.

type
Journal Paper
journal
Bioinformatics. 2019 Jan 18. doi: 10.1093/bioinformatics/btz029
Impact Factor
5.481

Individual immune selection pressure has limited impact on seasonal influenza virus evolution

Published date : 06 Dec 2018

Seasonal influenza viruses are subjected to strong selection as seen by the sequential replacement of existing viral populations on the emergence of new antigenic variants. However, the process of within-host de novo mutant generation and evolutionary selection that underlies these antigenic sweeps is poorly understood. Here, we investigate mutational patterns between evolutionarily closely related human seasonal influenza viruses using host age as a proxy for immune experience.

type
Journal Paper
journal
Nature Ecology & Evolution, 2018, doi: 10.1038/s41559-018-0741-x

The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine

Published date : 27 Nov 2018

Background
Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts.

type
Journal Paper
journal
Open Forum Infectious Diseases, Vol. 5, issue 12, 1 Dec 2018, doi: 10.1093/ofid/ofy318
Impact Factor
3.240

Influenza Vaccine-Induced Antibody Responses Are Not Impaired by Frailty in the Community-Dwelling Elderly With Natural Influenza Exposure

Published date : 24 Oct 2018

Background: Elderly adults over 65 years of age are recommended to receive seasonal influenza vaccination as they are at a higher risk of infection and its complications than the younger community. The elderly are often stratified according to frailty status where frail individuals are more susceptible to adverse health outcomes than their non-frail counterparts, however, it is not known whether immunity induced by influenza vaccination is impaired in the frail elderly.

type
Journal Paper
journal
Frontiers in Immunology, 24 Oct 2018, Vol. 9, Article 265, doi: 10.3389/fimmu.2018.02465
Impact Factor
5.511

Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

Published date : 28 Sep 2018

The mentioning of gene names in the body of the scientific literature 1901-2017 and their fractional counting was used as a proxy to assess the level of biological function discovery. We define a literature score of one as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. We find that less than 5000 human genes have each at least 100 FPEs in the available literature corpus.

type
Journal Paper
journal
Proteomics 2018, Sep 28, doi: 10.1002/pmic.201800093
Impact Factor
3.532

Molecular mechanism of the Escherichia coli AhpC in the function of a chaperone under heat-shock conditions

Published date : 20 Sep 2018

Peroxiredoxins (Prxs) are ubiquitous antioxidants utilizing a reactive cysteine for peroxide reduction and acting as a molecular chaperone under various stress conditions. Besides other stimulating factors, oxidative- and heat stress conditions trigger their ATP-independent chaperoning function. So far, many studies were intended to reveal the chaperoning mechanisms of the so-called sensitive Prxs of eukaryotes, which are susceptible to inactivation by over-oxidation of its reactive cysteine during H2O2 reduction.

type
Journal Paper
journal
Scientific Reports 8, No. 14151, 2018, doi: 10.1038/s41598-018-32527-7
Impact Factor
4.122

Integrated Multimodal Evaluation of Genotoxicity in ZFN-Modified Primary Human Cells

Published date : 29 Aug 2018

Iatrogenic adverse events in clinical trials of retroviral vector-mediated gene-corrected cells have prioritized the urgent need for more comprehensive and stringent assessment of potentially genotoxic off-target alterations and the biosafety of cells intended for therapeutic applications. Genome editing tools such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 nuclease systems are being investigated as safer and efficient alternatives for site-directed genome modification.

type
Book/Book Chapter
journal
Methods in Molecular Biology: Zinc Finger Proteins, 2018;1867:141-164. doi: 10.1007/978-1-4939-8799-3_11