Biomolecular Function Discovery Division

Influenza passaging annotations: what they tell us and why we should listen

Published date : 30 Jun 2019

Influenza databases now contain over 100,000 worldwide sequence records for strains influenza A(H3N2) and A(H1N1). Although these data facilitate global research efforts and vaccine development practices, they also represent a stumbling block for researchers because of their confusing and heterogeneous annotation. Unclear passaging annotations are particularly concerning given the recent work highlighting the presence and risk of false adaptation signals introduced by cell passaging of viral isolates.

type
Journal Paper
journal
Virus Evolution, Vol. 5, Issue 1, Jan 2019, doi: 10.1093/ve/vez016
Impact Factor
5.408

Identification and in vivo Efficacy Assessment of Approved Orally Bioavailable Human Host Protein-Targeting Drugs With Broad Anti-influenza A Activity

Published date : 05 Jun 2019

The high genetic variability of influenza A viruses poses a continual challenge to seasonal and pandemic vaccine development, leaving antiviral drugs as the first line of defense against antigenically different strains or new subtypes. As resistance against drugs targeting viral proteins emerges rapidly, we assessed the antiviral activity of already approved drugs that target cellular proteins involved in the viral life cycle and were orally bioavailable. Out of 15 candidate compounds, four were able to inhibit infection by 10- to 100-fold without causing toxicity, in vitro.

type
Journal Paper
journal
Frontiers in Immunology, 5 June 2019, Vol. 10, Article 1097, doi: 10.3389/fimmu.2019.01097
Impact Factor
6.4

Hypocrisy Around Medical Patient Data: Issues of Access for Biomedical Research, Data Quality, Usefulness for the Purpose and Omics Data as Game Changer

Published date : 01 Jun 2019

Whether due to simplicity or hypocrisy, the question of access to patient data for biomedical research is widely seen in the public discourse only from the angle of patient privacy. At the same time, the desire to live and to live without disability is of much higher value to the patients. This goal can only be achieved by extracting research insight from patient data in addition to working on model organisms, something that is well understood by many patients.

type
Journal Paper
journal
Asian Bioethics Review, Jun 2019, Vol. 11, Issue 2, pg 189-207, doi: 10.1007/s41649-019-00085-3

Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723

Published date : 23 May 2019

BACKGROUND:
Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis.

type
Journal Paper
journal
BMC Genomics 2019, 20:374, doi: 10.1186/s12864-019-5762-6
Impact Factor
3.730

A novel method for the capture-based purification of whole viral native RNA genomes

Published date : 08 May 2019

Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for characterizing properties innate to RNA strands such as secondary structure, RNA-RNA interactions, and also for nanopore direct RNA sequencing involving the sequencing of native RNA strands. The latter strategy, ultracentrifugation, causes loss in genomic information due to its inability to retrieve unassembled viral RNA.

type
Journal
journal
AMB Express, 2019 Apr 8;9(1):45. doi: 10.1186/s13568-019-0772-y
Impact Factor
1.719

Effect of the additional cysteine 503 of vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F (AhpF) and the mechanism of AhpF and subunit C assembling

Published date : 30 Apr 2019

The vancomycin-resistant Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) is of paramount importance to restore redox homeostasis. Therefore, knowledge about this defense system is essential to understand its antibiotic-resistance and survival in hosts.

type
Journal Paper
journal
Free Radical Biology and Medicine, Vol. 138, July 2019, Pg 10-12, doi:10.1016/j.freeradbiomed.2019.04.036
Impact Factor
5.657

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