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.

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

Simple yet functional phosphate-loop proteins

Published date : 30 Nov 2018

Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein’s scaffold. Can motifs such as P-loops confer function in a simpler context?

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Journal Paper
journal
Proceedings of the National Academy of Sciences of the United States of America, PNAS, doi: 10.1073/pnas.1812400115
Impact Factor
9.504

Lipid accumulation facilitates mitotic slippage-induced adaptation to anti-mitotic drug treatment

Published date : 27 Nov 2018

Aberrant lipid accumulation is a hallmark of cancer known to contribute to its aggressiveness and malignancy. Emerging studies have demonstrated context-dependent changes in lipid metabolism during chemotherapy. However, there is little known regarding the mechanisms linking lipid metabolism to chemotherapy-induced cell fates. Here, we describe lipid accumulation in cells following antimitotic drug treatment. Cells arrested in mitosis, as well as cells that escaped mitotic arrest and underwent mitotic slippage, showed elevated cytoplasmic lipid droplets.

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Journal Paper
journal
Cell Death Discovery 4, Article no: 109. 2018, doi: 10.1038/s41420-018-0127-5

On the perturbation nature of allostery: sites, mutations, and signal modulation

Published date : 12 Nov 2018

Regardless of the diversity of systems, allosteic signalling is found to be always caused by perturbations. This recurring trait of allostery serves as a foundation for developing different experimental efforts and theoretical models for the studies of allosteric mechanisms. Among computational approaches considered here particular emphasis is given to the structure-based statistical mechanical model of allostery (SBSMMA), which allows one to study the causality and energetics of allosteric communication.

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Journal Paper
journal
Current Opinion in Structural Biology, Vol. 56, June 2019, Pg 18-27, doi: 10.1016/j.sbi.2018.10.008
Impact Factor
7.179

A dual substrate-accessing mechanism of a major facilitator superfamily protein facilitates lysophospholipid flipping across the cell membrane

Published date : 29 Oct 2018

Lysophospholipid transporter (LplT) is a member of the major facilitator superfamily (MFS) present in many Gram-negative bacteria. LplT catalyzes flipping of lysophospholipids (LPLs) across the bacterial inner membrane, playing an important role in bacterial membrane homeostasis. We previously reported that LplT promotes both uptake of exogenous LPLs and intramembranous LPL flipping across the bilayer.

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Journal Paper
journal
Journal of Biological Chemistry, 2018, October 29, doi: 10.1074/jbc.RA118.005548
Impact Factor
4.01

AlloMAPS: allosteric mutation analysis and polymorphism of signaling database

Published date : 26 Oct 2018

AlloMAPS database provides data on the causality and energetics of allosteric communication obtained with the structure-based statistical mechanical model of allostery (SBSMMA). The database contains data on allosteric signaling in three sets of proteins and protein chains: (i) 46 proteins with comprehensively annotated functional and allosteric sites; (ii) 1908 protein chains from PDBselect set of chains with low (<25%) sequence identity; (iii) 33 proteins with more than 50 known pathological SNPs in each molecule.

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Journal Paper
journal
Nucleic Acis Research, 2018, Oct 26, doi:10.1093/nar/gky1028
Impact Factor
11.561

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.

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

Commentary: Augmented Reality Scientific Phone Apps - making the APD AR Holistic Review app and using existing AR apps for scientific publications

Published date : 02 Oct 2018

The average scientific publication is not the most palatable of reading materials, especially to those not in the relevant disciplines. Yet, conveying scientific concepts easily is precisely what scientific publications are meant to do. Imagine what the use of video pictures/paintings as depicted in the Harry Potter movie series can do to make things easier! While the fantasy of moving photos/pictures does not exist physically in the real world, just as Santa Claus cannot travel the world today without being shot down by anti-missiles, there are some shadows of reality in this idea.

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Journal Paper
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Scientific Phone Apps and Mobile Devices (2018) 4:4, doi:10.30943/2018/28092018

Editorial : A New Home for "Scientific Phone Apps and Mobile Devices" Journal

Published date : 28 Sep 2018

The original intent of academic publication to disseminate information and findings to the community for scientific progress has taken different twists and turns particularly in the last few decades. With the Internet, there is now the option of E-publications, and more recently, open access publishing to make articles freely available to readers. No longer are the articles restricted to subscribing academics, but now also to the general public.

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Journal Paper
journal
Scientific Phone Apps and Mobile Devices (2018) 4:3, doi: 10.30943/2018/26042018

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.

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