Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells

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Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane protein domains. II. Optimization of hydrophobic contacts in transmembrane hairpin structures of Na+, K+-ATPase

A method of packing of transmembrane hairpin helices in proteins is described. The procedure is based on the optimization of hydrophobic contacts calculated using the three-dimensional (3D) molecular hydrophobicity potential technique. To verify the validity of the computational scheme, we calculated relative orientations of membrane-spanning peptides in pairs L2–L3, M2–M3, and M4–M5 from L- and M-subunits of the photoreaction center ofRhodopseudomonas viridis and compared the predicted structures with those derived from atomic coordinates. The results of computer modeling agree with the X-ray data. We applied the approach proposed to study possible interhelical interactions in transmembrane hairpin structures of Na⁺, K⁺-ATPase.     

Can carbon emissions from tropical deforestation drop by 50% in 5 years?

Halving carbon emissions from tropical deforestation by 2020 could help bring the international community closer to the agreed goal of <2 degree increase in global average temperature change and is consistent with a target set last year by the governments, corporations, indigenous peoples' organizations and non‐governmental organizations that signed the New York Declaration on Forests (NYDF). We assemble and refine a robust dataset to establish a 2001–2013 benchmark for average annual carbon emissions from gross tropical deforestation at 2.270 Gt CO₂ yr^?1. Brazil did not sign the NYDF, yet from 2001 to 2013, Brazil ranks first for both carbon emissions from gross tropical deforestation and reductions in those emissions – its share of the total declined from a peak of 69% in 2003 to a low of 20% in 2012. Indonesia, an NYDF signatory, is the second highest emitter, peaking in 2012 at 0.362 Gt CO₂ yr^?1 before declining to 0.205 Gt CO₂ yr^?1 in 2013. The other 14 NYDF tropical country signatories were responsible for a combined average of 0.317 Gt CO₂ yr^?1, while the other 86 tropical country non‐signatories were responsible for a combined average of 0.688 Gt CO₂ yr^?1. We outline two scenarios for achieving the 50% emission reduction target by 2020, both emphasizing the critical role of Brazil and the need to reverse the trends of increasing carbon emissions from gross tropical deforestation in many other tropical countries that, from 2001 to 2013, have largely offset Brazil's reductions. Achieving the target will therefore be challenging, even though it is in the self‐interest of the international community. Conserving rather than cutting down tropical forests requires shifting economic development away from a dependence on natural resource depletion toward recognition of the dependence of human societies on the natural capital that tropical forests represent and the goods and services they provide.     

Exome‐based proteogenomics of HEK‐293 human cell line: Coding genomic variants identified at the level of shotgun proteome

Genomic and proteomic data were integrated into the proteogenomic workflow to identify coding genomic variants of Human Embryonic Kidney 293 (HEK‐293) cell line at the proteome level. Shotgun proteome data published by Geiger et al. (2012), Chick et al. (2015), and obtained in this work for HEK‐293 were searched against the customized genomic database generated using exome data published by Lin et al. (2014). Overall, 112 unique variants were identified at the proteome level out of ～1200 coding variants annotated in the exome. Seven identified variants were shared between all the three considered proteomic datasets, and 27 variants were found in any two datasets. Some of the found variants belonged to widely known genomic polymorphisms originated from the germline, while the others were more likely resulting from somatic mutations. At least, eight of the proteins bearing amino acid variants were annotated as cancer‐related ones, including p53 tumor suppressor. In all the considered shotgun datasets, the variant peptides were at the ratio of 1:2.5 less likely being identified than the wild‐type ones compared with the corresponding theoretical peptides. This can be explained by the presence of the so‐called “passenger” mutations in the genes, which were never expressed in HEK‐293 cells. All MS data have been deposited in the ProteomeXchange with the dataset identifier PXD002613 ( http://proteomecentral.proteomexchange.org/dataset/PXD002613 ).     

Effect of lentivirus-mediated shRNA inactivation of HK1, HK2, and HK3 genes in colorectal cancer and melanoma cells

Background

The switch from oxidative phosphorylation to glycolysis in proliferating cancer cells, even under aerobic conditions, has been shown first in 1926 by Otto Warburg. Today this phenomenon is known as the “Warburg effect” and recognized as a hallmark of cancer. The metabolic shift to glycolysis is associated with the alterations in signaling pathways involved in energy metabolism, including glucose uptake and fermentation, and regulation of mitochondrial functions. Hexokinases (HKs), which catalyze the first step of glycolysis, have been identified to play a role in tumorigenesis of human colorectal cancer (CRC) and melanoma. However, the mechanism of action of HKs in the promotion of tumor growth remains unclear.

Results

The purpose of the present study was to investigate the effect of silencing of hexokinase genes (HK1, HK2, and HK3) in colorectal cancer (HT-29, SW 480, HCT-15, RKO, and HCT 116) and melanoma (MDA-MB-435S and SK-MEL-28) cell lines using short hairpin RNA (shRNA) lentiviral vectors. shRNA lentiviral plasmid vectors pLSLP-HK1, pLSLP-HK2, and pLSLP-HK3 were constructed and then transfected separately or co-transfected into the cells. HK2 inactivation was associated with increased expression of HK1 in colorectal cancer cell lines pointing to the compensation effect. Simultaneous attenuation of HK1 and HK2 levels led to decreased cell viability. Co-transfection with shRNA vectors against HK1, HK2, and HK3 mRNAs resulted in a rapid cell death via apoptosis.

Conclusions

We have demonstrated that simultaneous inactivation of HK1 and HK2 was sufficient to decrease proliferation and viability of melanoma and colorectal cancer cells. Our results suggest that HK1 and HK2 could be the key therapeutic targets for reducing aerobic glycolysis in examined cancers.