From clinical specimens to human cancer preclinical models—a journey the NCI-cell line database—25 years later

The intramural the National Cancer Institute (NCI) and more recently the University of Texas Southwestern Medical Center with many different collaborators comprised a complex, multi-disciplinary team that collaborated to generated large, comprehensively annotated, cell-line related research resources which includes associated clinical, and molecular characterization data. This material has been shared in an anonymized fashion to accelerate progress in overcoming lung cancer, the leading cause of cancer death across the world. However, this cell line collection also includes a range of other cancers derived from patient-donated specimens that have been remarkably valuable for other types of cancer and disease research. A comprehensive analysis conducted by the NCI Center for Research Strategy of the 278 cell lines reported in the original Journal of Cellular Biochemistry Supplement, documents that these cell lines and related products have since been used in more than 14 000 grants, and 33 207 published scientific reports. This has resulted in over 1.2 million citations using at least one cell line. Many publications involve the use of more than one cell line, to understand the value of the resource collectively rather than individually; this method has resulted in 2.9 million citations. In addition, these cell lines have been linked to 422 clinical trials and cited by 4700 patents through publications. For lung cancer alone, the cell lines have been used in the research cited in the development of over 70 National Comprehensive Cancer Network clinical guidelines. Finally, it must be underscored again, that patient altruism enabled the availability of this invaluable research resource.     

Trophic ecology and metabolism of two species of nonnative freshwater stingray (Chondrichthyes: Potamotrygonidae)

The stingrays Potamotrygon amandae and Potamotrygon falkneri are nonnative species established in the Upper Paraná basin. Although they are widely distributed, few studies on their diets or respective metabolic responses exist. Therefore, the aim was to evaluate the dietary composition, trophic niche breadth and lipid/protein concentrations in muscle and hepatic tissues of these two species, as well as the interrelationships between them. The individuals were collected in two areas on the Upper Paraná River. The stomachs and samples of muscle and liver tissues were taken for analysis. A broad dietary spectrum was observed for both species, along with differences in dietary composition, with a higher consumption of detritus by P. amandae and Baetidae by P. falkneri. No differences were observed in the trophic niche breadth. Regarding the metabolic variables, differences were only found in the hepatic protein, with a higher content observed in P. falkneri. A significant positive correlation was observed between items of animal origin and detritus with muscle protein for this species. This shows that such feeding habits, which are characteristic of a generalist, influenced the metabolism of the species and possibly contributed to the successful adjustment of the species to new habitats in the Upper Paraná River.

     

On the Importance of Amino Acid Sequence and Spatial Proximity of Interacting Residues for Protein Folding

Abstract

Membrane proteins can be classified among the following five types: (1) type I membrane protein. (2) type II membrane protein. (3) multipass transmembrane proteins. (4) lipid chain- anchored membrane proteins, and (5) GPI-anchored membrane proteins. T. Kohonen's self-organization model which is a typical neural network is applied for predicting the type of a given membrane protein based on its amino acid composition. As a result, the high rates of self-consistency (94.80%) and cross-validation (77.76%), and stronger fault-tolerant ability were obtained.     

Intermolecular interactions between DNA and methamphetamine,amphetamine, ecstasy and their major metabolites

In this work, we carried out a theoretical investigation regarding amphetamine-type stimulants, which can cause central nervous system degeneration, interacting with human DNA. These include amphetamine, methamphetamine, 3,4-Methylenedioxymethamphetamine (also known as ecstasy), as well as their main metabolites. The studies were performed through molecular docking and molecular dynamics simulations, where molecular interactions of the receptor–ligand systems, along with their physical–chemical energies, were reported. Our results show that 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine (ecstasy) present considerable reactivity with the receptor (DNA), suggesting that these molecules may cause damage due to human-DNA. These results were indicated by free Gibbs change of bind (ΔG_bind) values referring to intermolecular interactions between the drugs and the minor grooves of DNA, which were predominant for all simulations. In addition, it was observed that 3,4-Dihydroxymethamphetamine (ΔG_bind = ?13.15 kcal/mol) presented greater spontaneity in establishing interactions with DNA in comparison to 3,4-Methylenedioxymethamphetamine (ΔG_bind = ?8.61 kcal/mol). Thus, according with the calculations performed our results suggest that the 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine have greater probability to provide damage to human DNA fragments.     

146 Amyloid fibril polymorphism probed by advanced vibrational spectroscopy

Amyloid fibrils are associated with many neurodegenerative diseases. All known amyloids including pathogenic and nonpathogenic forms display functional and structural heterogeneity (polymorphism) which determines the level of their toxicity. Despite a significant biological and biomedical importance, the nature of the amyloid fibril polymorphism remains elusive. We utilized for the first time three most advanced vibrational techniques to probe the core, the surface, and supramolecular chirality of fibril polymorphs. A new type of folding, aggregation phenomenon, spontaneous refolding from one polymorph to another, was discovered (Kurouski, Lauro et al., 2010). Hydrogen–deuterium exchange deep UV resonance Raman spectroscopy (Oladepo, Xiong et al., 2012) combined with advanced statistical analysis (Shashilov & Lednev, 2010) allowed for structural characterization of the highly ordered cross-β core of amyloid fibrils. We reported several examples showing significant variations in the core structure for fibril polymorphs. Amyloid fibrils are generally composed of several protofibrils and may adopt variable morphologies, such as twisted ribbons or flat-like sheets. We discovered the existence of another level of amyloid polymorphism, namely, that associated with fibril supramolecular chirality. Two chiral polymorphs of insulin, which can be controllably grown by means of small pH variations, exhibit opposite signs of vibrational circular dichroism (VCD) spectra (Kurouski, Dukor et al. 2012). VCD supramolecular chirality is correlated not only by the apparent fibril handedness but also by the sense of supramolecular chirality from a deeper level of chiral organization at the protofilament level of fibril structure. A small pH change initiates spontaneous transformation of insulin fibrils from one polymorph to another. As a result, fibril supramolecular chirality overturns both accompanying morphological and structural changes (Kurouski, Dukor et al. 2012). No conventional methods could probe the fibril surface despite its significant role in the biological activity. We utilized tip-enhanced Raman spectroscopy (TERS) to characterize the surface structure of an individual fibril due to a high depth and lateral spatial resolution of the method in the nanometer range (Kurouski, Deckert-Gaudig et al. 2012). It was found that the surface is strongly heterogeneous and consists of clusters with various protein conformations and amino acid composition.     

The biostratigraphic and palaeoenvironmental significance of Lower Cambrian (Botomian) trilobites from the Ak-Kaya section of the Altai Mountains (southern Siberia,Russia)

The presence of one of the oldest records of polycystine Radiolaria in the Lower Cambrian sedimentary sequence of the Ak-Kaya section (Gorny Altai) requires a biostratigraphic dating. The trilobites found recently a few tens of meters below the radiolarian-bearing level belong to Calodiscus resimus Repina, Serrodiscus fossuliferus Repina and Alacephalus aff. contortus Repina; they suggest that this part of the Shashkunar Formation can be correlated with the lower part of the Botomian stage. The absence of eyes in the two former species suggests a mode of life buried in the fine pelagic sediments. Indications of the presence of a strongly developed musculature on the third species point to a palaeoenvironment characterized by a relatively high hydrodynamic regime.     

Hepatic retinoid stores are required for normal liver regeneration

Preliminary studies of liver regeneration induced by partial hepatectomy (PHE) identified a substantial depletion of hepatic retinoid stores, by greater than 70%, in regenerating livers of wild-type C57Bl/6J mice. To understand this, we compared responses of wild-type and lecithin:retinol acyltransferase (Lrat)-deficient mice, which totally lack hepatic retinoid stores, to PHE. The Lrat-deficient livers showed delayed regeneration in the first 24 h after PHE. At 12 h after PHE, we observed significantly less mRNA expression for growth factors and cytokines implicated in regulating the priming phase of liver regeneration, specifically for Hgf and Tgfα, but not Tgfβ. Compared with wild-type mice, the changes in mRNA levels for p21 and cyclins E1, B1, and A2 mRNAs and for hepatocellular BrdU incorporation and mitoses were delayed (i.e., shifted to later times) in regenerating Lrat^−/− livers. Concentrations of all-trans-retinoic acid were significantly lower in the livers of Lrat^−/− mice following PHE, and this was accompanied by diminished expression of known retinoid-responsive genes. At later times after PHE, the rate of liver weight restoration for Lrat^−/− mice was parallel to that of wild-type mice, although additional biochemical differences were observed. Thus, hepatic retinoid stores are required for maintaining expression of signaling molecules that regulate cell proliferation and differentiation immediately after hepatic injury, accounting for the delayed restoration of liver mass in Lrat^−/− mice.