Quantitative microscopy uncovers ploidy changes during mitosis of live Drosophila maternal-haploid embryos and their effect on nuclear size

Time-lapse microscopy is a powerful tool to investigate cellular and developmental dynamics. In Drosophila melanogaster, it can be used to study division cycles in embryogenesis. To obtain quantitative information from 3D time-lapse data and track proliferating nuclei from the syncytial stage until gastrulation, we developed an image analysis pipeline consisting of nuclear segmentation, tracking, annotation and quantification. Image analysis of maternal-haploid (mh) embryos revealed that a fraction of haploid syncytial nuclei fused to give rise to nuclei of higher ploidy (2n, 3n, 4n).

type: 
Journal Paper
journal: 
Biology Open 2017 6: 390-401; doi: 10.1242/bio.022079
Url: 
http://bio.biologists.org/content/6/3/390
Impact Factor: 
2.135
Date of acceptance: 
2017-01-11

APD SpectBT: Arduino-based mobile vis-Spectrophotometer

Quantification of samples is an integral step in numerous biological and chemical experiments. Spectrophotometers are often used together with colorimetric assays that react with the compound of interest in the samples. However, spectrophotometers are often costly, bulky and immobile. To increase the convenience and ease the process of spectrophotometry, the APD SpectBT was developed using the Arduino-based platform to create a smartphone dependent mobile spectrophotometer.

type: 
Journal Paper
journal: 
Nature Methods Application Notes 2017

Early spatiotemporal-specific changes in intermediate signals are predictive of cytotoxic sensitivity to TNFα and co-treatments

Signaling pathways can generate different cellular responses to the same cytotoxic agents. Current quantitative models for predicting these differential responses are usually based on large numbers of intracellular gene products or signals at different levels of signaling cascades. Here, we report a study to predict cellular sensitivity to tumor necrosis factor alpha (TNFα) using high-throughput cellular imaging and machine-learning methods.

type: 
Journal Paper
journal: 
Scientific Reports 7, Article 43541 (2017), doi:10.1038/srep43541
Url: 
http://www.nature.com/articles/srep43541
Impact Factor: 
5.228
Date of acceptance: 
2017-01-27

Essential role of the flexible linker on the conformational equilibrium of bacterial peroxiredoxin reductase for effective regeneration of peroxiredoxin

Reactive oxygen species (ROS) can damage DNA, proteins, and lipids, so cells have antioxidant systems that regulate ROS. In many bacteria, a dedicated peroxiredoxin reductase, alkyl hydroperoxide reductase subunit F (AhpF), catalyzes the rapid reduction of the redox-active disulfide center of the antioxidant protein peroxiredoxin (AhpC) to detoxify ROS such as hydrogen peroxide, organic hydroperoxide, and peroxynitrite. AhpF is a flexible multi-domain protein that enables a series of electron transfers among the redox centers by accepting reducing equivalents from NADH.

type: 
Journal Paper
journal: 
The Journal of Biological Chemistry, 7 Mar 2017, doi : 10.1074/jbc.M117.775858
Url: 
http://www.jbc.org/content/early/2017/03/07/jbc.M117.775858
Impact Factor: 
4.258
Date of acceptance: 
2017-03-07

Hierarchical Assembly of Tough Bioelastomeric Egg Capsules is Mediated by a Bundling Protein

Marine snail egg capsules are shock-absorbing bioelastomers made from precursor "egg case proteins" (ECPs) that initially lack long-range order. During capsule formation, these proteins self-assemble into coiled-coil filaments that subsequently align into microscopic layers, a multiscale process which is crucial to the capsules' shock-absorbing properties.

type: 
Journal Paper
journal: 
Biomacromolecules, 2017, 18 (3), pg 931-942, doi: 10.1021/acs.biomac.6b01810
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28196415
Impact Factor: 
5.583
Date of acceptance: 
2017-03-16

Membrane Active Antimicrobial Peptides: Translating Mechanistic Insights to Design

Antimicrobial peptides (AMPs) are promising next generation antibiotics that hold great potential for combating bacterial resistance. AMPs can be both bacteriostatic and bactericidal, induce rapid killing and display a lower propensity to develop resistance than do conventional antibiotics. Despite significant progress in the past 30 years, no peptide antibiotic has reached the clinic yet. Poor understanding of the action mechanisms and lack of rational design principles have been the two major obstacles that have slowed progress.

type: 
Journal Paper
journal: 
Frontiers in Neuroscience, Feb 2017, Vol. 11, Article 73, doi: 10.3389/fnins.2017.00073
Url: 
http://journal.frontiersin.org/article/10.3389/fnins.2017.00073/full
Impact Factor: 
3.398
Date of acceptance: 
2017-01-31

Stabilization of Peptides against Proteolysis through Disulfide-Bridged Conjugation with Synthetic Aromatics

Peptides have been promising molecular scaffolds for the development of potential therapeutics with high affinity and specificity to biomacromolecules. However, their inherent proteolytic instability significantly hampers their biological applications. Strategies that can stabilize peptides against proteolytic digestion on the basis of noncovalent interactions—without extensive manipulation of the sequence or use of unnatural residues—are greatly desired.

type: 
Journal Paper
journal: 
Organic & Biomolecular Chemistry, 2017, Issue 15, Pg 1921-1929, doi: 10.1039/C6OB02786E
Url: 
http://pubs.rsc.org/en/content/articlelanding/2017/ob/c6ob02786e#!divAbstract
Impact Factor: 
3.559
Date of acceptance: 
2017-02-01

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

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
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