Application Notes on APD Areametric App: Automated area quantification for both Android and iOS

Published date : 08 Feb 2019

Area measurements have a wide range of uses from the monitoring of skin features in healthcare, celestial bodies in astronomy, to determining furniture sizes in everyday indoor uses. Current measurement methods utilize some form of measuring tool and unless performed by skilled and trained professionals, human errors leading to inaccurate measurements can often arise. This is especially so for irregularly shaped objects with complex dimensions.

type
Journal Paper
journal
APD Trove 2019, Vol: 2;1, doi: 10.30943/2019/08022019

A Review of Apps for Programming: programming languages and making apps with apps

Published date : 26 Jan 2019

With the latest technologies enabling smartphones to work like mini computers, there are now numerous opportunities to use smartphones for the development of mobile apps. Given the multiple Operating Systems (OS) available, there is a significant demand for apps for the various platforms. To meet this demand, some apps exist to impart the necessary knowledge to make apps, while others make the programming of apps possible on these devices. Surveying both the Google Play and Apple App stores, there are a plethora of such programming apps, classified based on the various languages.

type
Journal Paper
journal
Scientific Phone Apps and Mobile Devices (2019) 5:1, doi:10.30943/2019/25012019

Kinetic and thermodynamic effects of phosphorylation on p53 binding to MDM2

Published date : 24 Jan 2019

p53 is frequently mutated in human cancers. Its levels are tightly regulated by the E3 ubiquitin ligase MDM2. The complex between MDM2 and p53 is largely formed by the interaction between the N-terminal domain of MDM2 and the N-terminal transactivation (TA) domain of p53 (residues 15-29). We investigated the kinetic and thermodynamic basis of the MDM2/p53 interaction by using wild-type and mutant variants of the TA domain. We focus on the effects of phosphorylation at positions Thr18 and Ser20 including their substitution with phosphomimetics.

type
Journal Paper
journal
Scientific Reports 9, Article no: 693 (2019). doi: 10.1038/s41598-018-36589-5
Impact Factor
4.122

Organic cation transporter 3 (Oct3) is a distinct catecholamines clearance route in adipocytes mediating the beiging of white adipose tissue

Published date : 17 Jan 2019

Beiging of white adipose tissue (WAT) is a particularly appealing target for therapeutics in the treatment of metabolic diseases through norepinephrine (NE)-mediated signaling pathways. Although previous studies report NE clearance mechanisms via SLC6A2 on sympathetic neurons or proinflammatory macrophages in adipose tissues (ATs), the low catecholamine clearance capacity of SLC6A2 may limit the cleaning efficiency.

type
Journal Paper
journal
PLOS Biology, January 17 2019, doi: 10.1371/journal.pbio.2006571
Impact Factor
9.163

Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket

Published date : 15 Jan 2019

The DNA binding domain (DBD) of the tumor suppressor p53 is the site of several oncogenic mutations. A subset of these mutations lowers the unfolding temperature of the DBD. Unfolding leads to the exposure of a hydrophobic β-strand and nucleates aggregation which results in pathologies through loss of function and dominant negative/gain of function effects.

type
Journal Paper
journal
Nuclei Acids Research, 2019, doi: 10.1093/nar/gky1314
Impact Factor
11.561

Perspective: The promises of a holistic view of proteins-impact on antibody engineering and drug discovery

Published date : 10 Jan 2019

The reductionist approach is prevalent in biomedical science. However, increasing evidence now shows that biological systems cannot be simply considered as the sum of its parts. With experimental, technological and computational advances, we can now do more than view parts in isolation, thus wepropose that an increasing holistic view (where a protein is investigated as much as a whole as possible) is now timely. To further advocate this, we review and discuss several studies and applications involving allostery,where distant protein regions can cross-talk to influence functionality.

type
Journal Paper
journal
Bioscience Reports, Jan 10, 2019, DOI: 10.1042/BSR20181958
Impact Factor
2.899

Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein

Published date : 07 Jan 2019

Stapled-peptides have emerged as an exciting class of molecules which can modulate protein–protein interactions. We have used a structure-guided approach to rationally develop a set of hydrocarbon stapled-peptides with high binding affinities and residence times against the oncogenic eukaryotic translation initiation factor 4E (eIF4E) protein. Crystal structures of these peptides in complex with eIF4E show that they form specific interactions with a region on the protein-binding interface of eIF4E which is distinct from the other well-established canonical interactions.

type
Journal Paper
journal
Chemical Science, 2019, doi: 10.1039/C8SC03759K
Impact Factor
9.063

Exploring chromatin hierarchical organization via Markov State Modelling

Published date : 31 Dec 2018

We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function.

type
Journal Paper
journal
PLoS Computational Biology, 2018 Dec 31;14(12), doi: 10.1371/journal.pcbi.100668
Impact Factor
3.955

Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway

Published date : 24 Dec 2018

Networks of biological molecules are key to cellular function, governing processes ranging from signal cascade propagation to metabolic pathway regulation. Genetic duplication processes give rise to sets of regulatory proteins that have evolved from a common ancestor, leading to interactomes whose dysregulation is often associated with disease. A better understanding of the determinants of specificity at 21 interfaces shared by functionally related proteins is crucial to the rational design of novel pharmacotherapeutic agents.

type
Journal Paper
journal
Journal of Chemical Inofrmation and Modeling, 2018 Dec 24. doi: 10.1021/acs.jcim.8b00765
Impact Factor
3.804

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