Mesenchymal Stromal Cells Derived from Human Embryonic Stem Cells, Fetal Limb and Bone Marrow Share a Common Phenotype but Are Transcriptionally and Biologically Different

Mesenchymal stromal cells (MSCs) can be obtained from several sources and the significant differences in their properties make it crucial to investigate the differentiation potential of MSCs from different sources to determine the optimal source of MSCs. We investigated if this biological heterogeneity in MSCs from different sources results in different mechanisms for their differentiation.

type: 
Journal Paper
journal: 
Stem Cell Discovery, 2017, 7, Pg 1-26, doi: 10.4236/scd.2017.71001
Url: 
http://file.scirp.org/Html/1-1080128_77869.htm
Date of acceptance: 
2017-01-20

Discovery of Rab1 binding sites using an ensemble of clustering methods

Targeting non-native-ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus.

type: 
Journal Paper
journal: 
PROTEINS: Structure, Function, and Bioinformatics, doi: 10.1002/prot.25254
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/prot.25254/abstract
Impact Factor: 
2.499
Date of acceptance: 
2017-01-19

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: a story of bad signal peptides and good ones that nevertheless do not make it

The IgA receptor, Fcar (CD89) consists of five sequence segments: two segments (S1, S2) forming the potential signal peptide, two extracellular EC domains that include the IgA binding site, and the transmembrane and cytoplasmic tail (TM/C) region. Numerous Fcar splice variants have been reported with various combinations of the sequence segments mentioned above. Here, we report a novel splice variant termed variant APD isolated from a healthy volunteer that lacks only the IgA-binding EC1 domain.

type: 
Journal Paper
journal: 
Cell Cycle 2016, doi: 10.1080/15384101.2017.1281480
Url: 
http://www.tandfonline.com/doi/full/10.1080/15384101.2017.1281480?scroll=top&needAccess=true
Impact Factor: 
3.952
Date of acceptance: 
2017-01-05

Fast and accurate de novo genome assembly from long uncorrected reads

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon.

type: 
Journal Paper
journal: 
Genome Research, 2017, doi: 10.1101/gr.214270.116
Url: 
http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116.abstract
Impact Factor: 
11.922
Date of acceptance: 
2017-01-17

Symmetrically Substituted Xanthone Amphiphiles Combat Gram- Positive Bacterial Resistance with Enhanced Membrane Selectivity

This is the first report of the design of a new series of symmetric xanthone derivatives that mimic antimicrobial peptides using a total synthesis approach. This novel design is advantageous because of its low cost, synthetic simplicity and versatility, and easy tuning of amphiphilicity by controlling the incorporated cationic and hydrophobic moieties. Two water-soluble optimized compounds, 6 and 18, showed potent activities against Gram-positive bacteria, including MRSA and VRE (MICs = 0.78–6.25 μg/mL) with a rapid bactericidal effect, low toxicity, and no emergence of drug resistance.

type: 
Journal Paper
journal: 
Journal of Medicinal Chemistry, 2017, 60 (4), pg: 1362–1378, doi: 10.1021/acs.jmedchem.6b01403
Url: 
http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b01403
Impact Factor: 
5.589
Date of acceptance: 
2016-06-24

Macrocyclized extended peptides: Inhibiting the substrate-recognition domain of tankyrase

We report a double-click macrocyclization approach for the constraint of peptide inhibitors in non-helical or extended conformations. Our targets are the tankyrase proteins (TNKS), poly(ADP-ribose) polymerases that regulate Wnt signaling by targeting Axin for degradation. TNKS are deregulated in many different cancer types, and inhibition of TNKS therefore represents an attractive therapeutic strategy. However, the clinical development of TNKS-specific PARP inhibitors is challenging due to off-target effects and cellular toxicity.

type: 
Journal Paper
journal: 
Journal of the American Chemical Society, doi: 10.1021/jacs.6b10234
Url: 
http://pubs.acs.org/doi/pdf/10.1021/jacs.6b10234
Impact Factor: 
13.038
Date of acceptance: 
2017-01-12

Editorial overview : Proteins: bridging theory and experiment

type: 
Journal Paper
journal: 
Current Opinion in Structural Biology, Vol. 42, Feb 2017,doi: 10.1016/j.sbi.2016.12.013
Url: 
http://www.sciencedirect.com/science/article/pii/S0959440X16302457
Impact Factor: 
6.7
Date of acceptance: 
2017-06-02

Editorial overview : Proteins: bridging theory and experiment

type: 
Journal Paper
journal: 
Current Opinion in Structural Biology, Vol. 42, Feb 2017,doi: 10.1016/j.sbi.2016.12.013
Url: 
http://www.sciencedirect.com/science/article/pii/S0959440X16302457
Impact Factor: 
6.7

Toward Understanding the Molecular Recognition of Albumin by p53-Activating Stapled Peptide ATSP-7041

Reactivation of tumor-suppressing activity of p53 protein by targeting its negative regulator MDM2/MDMX has been pursued as a potential anticancer strategy. A promising dual inhibitor of MDM2/MDMX that has been developed and is currently in clinical trials is the stapled peptide ATSP-7041. The activity of this molecule is reported to be modulated in the presence of serum. Albumin is the most abundant protein in serum and is known to bind reversibly to several molecules. To study this interaction, we develop a protocol combining molecular modeling, docking, and simulations.

type: 
Journal Paper
journal: 
The Journal of Physical Chemistry B, 2017, 121 (4), pg 657-670, doi : 10.1021/acs.jpcb.6b09900
Url: 
http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b09900
Impact Factor: 
2.883

Genome-wide analysis of mRNAs associated with mouse peroxisomes

Background: RNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required.

type: 
Journal Paper
journal: 
BMC Genomics 2016, 17 (Supp 13), 1028, doi: 10.1186/s12864-016-3330-x
Url: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259856/
Impact Factor: 
3.869
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