Biomolecular Function Discovery Division

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

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

Supervised Segmentation of Un-annotated Retinal Fundus Images by Synthesis

Published date : 24 Jul 2018

We focus on the practical challenge of segmenting new retinal fundus images that are dissimilar to existing well-annotated datasets. It is addressed in this paper by a supervised learning pipeline, with its core being the construction of a synthetic fundus image dataset using the proposed R-sGAN technique. The resulting synthetic images are realistic-looking in terms of the query images, while maintaining the annotated vessel structures from the existing dataset. This helps to bridge the mismatch between the query images and the existing well-annotated dataset.

type
Journal Paper
journal
IEEE Transactions on Medical Imaging, 2018 Jul 24. doi: 10.1109/TMI.2018.2854886
Impact Factor
6.131

Synthesizing retinal and neuronal images with generative adversarial nets

Published date : 04 Jul 2018

This paper aims at synthesizing multiple realistic-looking retinal (or neuronal) images from an unseen tubular structured annotation that contains the binary vessel (or neuronal) morphology. The generated phantoms are expected to preserve the same tubular structure, and resemble the visual appearance of the training images. Inspired by the recent progresses in generative adversarial nets (GANs) as well as image style transfer, our approach enjoys several advantages.

type
Journal Paper
journal
Medical Image Analysis, 2018 Jul 4;49:14-26. doi: 10.1016/j.media.2018.07.001
Impact Factor
5.356

Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors and status of novel antivirals

Published date : 03 Jul 2018

A total of 13672 viruses, collected by World Health Organization recognised National Influenza Centres between May 2016 and May 2017, were assessed for neuraminidase inhibitor susceptibility by four WHO Collaborating Centres for Reference and Research on Influenza and one WHO Collaborating Centre for the Surveillance Epidemiology and Control of Influenza. The 50% inhibitory concentration (IC50) was determined for oseltamivir and zanamivir for all viruses, and for peramivir and laninamivir in a subset (n = 8457).

type
Journal Paper
journal
Antiviral Research 2018 Jul 3;157:38-46. doi: 10.1016/j.antiviral.2018.07.001
Impact Factor
4.307

Exome sequencing and rare variant analysis reveals multiple filaggrin mutations in Bangladeshi atopic eczema families and additional risk genes

Published date : 30 May 2018

Atopic eczema (AE) is a heterogeneous chronic inflammatory skin condition that affects approximately 15–20% of children worldwide (Nutten, 2015). The prevalence varies widely among different countries, between rural and urban areas within a single country, and particular Asian skin types are more sensitive to urban environments (Ben-Gashir et al., 2004; Krutmann et al., 2014; Nutten, 2015; Odhiambo et al., 2009).

type
Journal Paper
journal
Journal of Investigative Dermatology, May 2018, doi: 10.1016/j.jid.2018.05.013
Impact Factor
6.448