Response of brain amino acid metabolism to ketosis

Our objective was to study brain amino acid metabolism in response to ketosis. The underlying hypothesis is that ketosis is associated with a fundamental change of brain amino acid handling and that this alteration is a factor in the anti-epileptic effect of the ketogenic diet. Specifically, we hypothesize that brain converts ketone bodies to acetyl-CoA and that this results in increased flux through the citrate synthetase reaction. As a result, oxaloacetate is consumed and is less available to the aspartate aminotransferase reaction; therefore, less glutamate is converted to aspartate and relatively more glutamate becomes available to the glutamine synthetase and glutamate decarboxylase reactions. We found in a mouse model of ketosis that the concentration of forebrain aspartate was diminished but the concentration of acetyl-CoA was increased. Studies of the incorporation of 13C into glutamate and glutamine with either [1-(13)C]glucose or [2-(13)C]acetate as precursor showed that ketotic brain metabolized relatively less glucose and relatively more acetate. When the ketotic mice were administered both acetate and a nitrogen donor, such as alanine or leucine, they manifested an increased forebrain concentration of glutamine and GABA. These findings supported the hypothesis that in ketosis there is greater production of acetyl-CoA and a consequent alteration in the equilibrium of the aspartate aminotransferase reaction that results in diminished aspartate production and potentially enhanced synthesis of glutamine and GABA.     

Effect of DMSO on the dielectric properties of canine kidney tissue

The dielectric permittivity and conductivity of canine kidney tissue samples were measured at R_f frequencies between ?20 °C and +20 °C. Some of the kidneys had been perfused with DMSO (10%) in canine plasma, others with physiological saline alone. The DMSO greatly increases the conductivity of frozen tissue above that of tissue not treated with this cryoprotectant. Apparently, the chief reason for nonuniform heating of a partially frozen organ in a microwave field is the great change in tissue conductivity as it thaws. We suggest that the effect on the conductivity of tissue should be considered in the choice of a cryoprotectant for tissues which are to be thawed by microwave or radiofrequency irradiation.     

Electrophoretic properties of hypoxanthine-guanine phosphoribosyl transferase in erythrocytes of subjects with Lesch-Nyhan syndrome

Hypoxanthine-guanine phosphoribosyl transferase (HGPRT; E.C. 2.4.2.8) has been studied in erythrocytes of patients with Lesch-Nyhan syndrome by polyacrylamide gel electrophoresis. The location of this enzyme in gel was determined by radiochemical assay. Inosine monophosphate (the reaction product of HGPRT with radioactive hypoxanthine and 5-phosphorylribose-1-pyrophosphate) was precipitated in the gel at the site of its formation with lanthanum chloride. The zone containing radioactive inosine monophosphate was located by continuous monitoring of mechanically fractionated gels in a scintillation spectrometer. The sensitivity of this method has permitted the detection of the very low HGPRT activity in the electropherograms of hemolysates of patients with Lesch-Nyhan syndrome. Among six patients, four had a mutant enzyme which migrated 15% faster than the normal; the other two had a mutant enzyme with about 12% faster migration. These mutants were designated HGPRT-LN and HGPRT-LN slow, respectively. These observations indicate that the mutant gene on the X chromosome codes for a protein of altered structure.Aided by U.S. Public Health Service grants Nos. HD 04608 and HD 03015 from the National Institute of Child Health and Human Development and GM 17702 from the National Institute of General Medical Sciences, National Institutes of Health.Presented in part at the 1971 meeting of the Western Society for Pediatric Research, Carmel, California.     

Starch radicals. Part II: Cereals-native starch complexes

Several varieties of flours were subjected to thermolysis up to 400 °C. The thermal characteristics of 13 flours were similar for all flours except soy. The weight loss of these flours up to 400 °C ranged from 65 to 97%. Although flours began to decompose at lower temperatures than did corresponding starches, there was less radical decomposition in flours than in starches as proved by Electron Paramagnetic Resonance absorption (EPR) spectra. The order of heat resistance to the radical decomposition for starches and flours paralleled one another, however, flours generated radicals at temperatures approximately 20 °C higher than in corresponding starches. The data showed that cereals did not form free radicals before carbonization and thus they could be safely processed in the temperature intervals generally used in baking, roasting, and frying.     

Assessment of protein assembly prediction in CASP13

We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions, we observe that ignoring the oligomeric state of the targets hinders modeling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modeling. Homology modeling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches where subunits are modeled in the context of the assemblies they form.     

B cells drive early T cell autoimmunity in vivo prior to dendritic cell-mediated autoantigen presentation

Both B cells and dendritic cells (DCs) have been implicated as autoantigen-presenting cells in the activation of self-reactive T cells. However, most self-proteins are ubiquitously and/or developmentally expressed, making it difficult to determine the source and the exposure of autoantigens to APCs in a controlled manner. In this study, we have used an Ig transgenic mouse model to examine the mechanisms by which B cells and other APCs acquire and present lupus autoantigens in vivo. Targeting a lupus autoantigen, the small nuclear ribonucleoprotein particle D protein, to the BCR activates autoreactive T cells in the periphery. Our in vivo studies demonstrate that autoantigen-specific B cells, when present in the repertoire, are the first subset of APCs to capture and present self-proteins for activating T cells. Thereafter, DCs acquire self-Ag and become effective APCs for stimulating the same subsets of autoreactive T cells. This mechanism provides one explanation of how early steps in autoimmunity can focus responses, via BCR, at a small group of self-proteins among the total milieu of intracellular self-proteins. Subsequently, DCs and other professional APCs may then amplify and perpetuate the autoimmune T cell response.     

A short survey on protein blocks

Protein structures are classically described in terms of secondary structures. Even if the regular secondary structures have relevant physical meaning, their recognition from atomic coordinates has some important limitations such as uncertainties in the assignment of boundaries of helical and β-strand regions. Further, on an average about 50% of all residues are assigned to an irregular state, i.e., the coil. Thus different research teams have focused on abstracting conformation of protein backbone in the localized short stretches. Using different geometric measures, local stretches in protein structures are clustered in a chosen number of states. A prototype representative of the local structures in each cluster is generally defined. These libraries of local structures prototypes are named as "structural alphabets". We have developed a structural alphabet, named Protein Blocks, not only to approximate the protein structure, but also to predict them from sequence. Since its development, we and other teams have explored numerous new research fields using this structural alphabet. We review here some of the most interesting applications.     

Exploring the link between germline and somatic genetic alterations in breast carcinogenesis

Recent genome-wide association studies (GWASs) have identified candidate genes contributing to cancer risk through low-penetrance mutations. Many of these genes were unexpected and, intriguingly, included well-known players in carcinogenesis at the somatic level. To assess the hypothesis of a germline-somatic link in carcinogenesis, we evaluated the distribution of somatic gene labels within the ordered results of a breast cancer risk GWAS. This analysis suggested frequent influence on risk of genetic variation in loci encoding for “driver kinases” (i.e., kinases encoded by genes that showed higher somatic mutation rates than expected by chance and, therefore, whose deregulation may contribute to cancer development and/or progression). Assessment of these predictions using a population-based case-control study in Poland replicated the association for rs3732568 in EPHB1 (odds ratio (OR) = 0.79; 95% confidence interval (CI): 0.63–0.98; P_trend = 0.031). Analyses by early age at diagnosis and by estrogen receptor α (ERα) tumor status indicated potential associations for rs6852678 in CDKL2 (OR = 0.32, 95% CI: 0.10–1.00; P_recessive = 0.044) and rs10878640 in DYRK2 (OR = 2.39, 95% CI: 1.32–4.30; P_dominant = 0.003), and for rs12765929, rs9836340, rs4707795 in BMPR1A, EPHA3 and EPHA7, respectively (ERα tumor status P_interaction<0.05). The identification of three novel candidates as EPH receptor genes might indicate a link between perturbed compartmentalization of early neoplastic lesions and breast cancer risk and progression. Together, these data may lay the foundations for replication in additional populations and could potentially increase our knowledge of the underlying molecular mechanisms of breast carcinogenesis.