Conformational and intermolecular interactions of proteins in amyloidosis

A conception on amyloidosis as a key factor of neuronal death in neurodegenerative diseases is stated. Experimental evidence is presented that amyloidosis is caused by alterations in the activity of a number of enzymes as well as conformational changes in pathogenic proteins. Arguments for amyloidosis as the universal biological mechanism of specific elimination of neurons showing changed metabolic and physiological status of cell differentiation are adduced. The final pattern of cell death seems to differ cardinally from that in both apoptosis and necrosis.     

Ultrastructural changes in the cerebral cortex of an 100 1/2-year-old man

Age changes in fields 39 and 40 (after Broadman) have been studied in a 100 years and 6 months old man died from peritonitis resulted from the surgical intervention, performed in connection with strangulation of the hernia. In the medical history there were no ++neuro-physical signs. The material was taken in 1 h 15 min after clinical death had been stated. The results obtained have been compared with those studied in the brain of persons, who had not yet reached the age of 100 years and had not any signs of ++neuro-physical disturbances and died after urgent surgical interventions in the abdominal cavity. In this group of persons the material for investigation was taken in 15-30 min after clinical death had been stated. The technique for treatment the material, its preparation for electron-microscopical examination is identical. Immersion fixation has been applied. The material obtained from an old animal fixed by means of vital perfusion of 2.5% glutaraldehyde solution is also used. In the person of 100 years and 6 months old the changes do not practically differ from those obtained from persons of younger age, however, the time from the statement of clinical death up to obtaining the material essentially influences preservation of the synaptic apparatus components.     

Correlation of heredity and environmental factors in the etiology of Vilyui encephalomyelitis. I. Patient frequency in families]

Viljuisk encephalomyelitis (VE) is a severe neurologic disease characterized by slow progressive dementia', oligobradykinesia, low spastic paraparesis and speech disturbances. It develops in persons of 20-50 years old. VE occurs in a small region of middle Viljui, but for last years the focus has considerably expanded. Etiology of VE is still obscure. 194 families with VE patients were examined. The data obtained contradict the hypothesis of simple recessive inheritance of VE. The value of the heredity coefficient, calculated on the basis of the Falconer - Edwards model, is 22-29% for relatives of the first relation degree. It suggests the existence of individual hereditary determined susceptibility to VE. 14 secondary cases were observed in affected families among adopted relatives (adopted children, husbands and wives of patients) with a rate exceeding random possible frequency. These observations have been evaluated as an evidence of horizontal transmission of the disease from patients with chronic forms to healthy persons. Obligatory condition for the transmission consists in a long-term contact (as a rule, more than one year). According to all known characteristics VE should be refferred to slow infections.     

Carriers of ataxia-telangiectasia gene display additional protein fraction and changes in the environment of SH groups in erythrocyte membrane

Additional protein fraction migrating slower than spectrin has been detected in erythrocyte membranes from an ataxia-telangiectasia (A-T) patient and from his mother (A-T heterozygote). In erythrocyte membranes labelled with maleimide spin label changes in signal of the weakly immobilized spin label as related to that of strongly immobilized one (w/s) were noted. In comparison to age-matched control groups the values of w/s were lower in A-T heterozygotes (ten persons) and higher in A-T homozygotes (four persons). In control persons the values of w/s increased with age, whereas in families with A-T no significant differences in this parameter were noted between children and parents. The presence of additional protein fraction in erythrocytes membranes of A-T patient and A-T heterozygote indicates that these phenotypes can be differentiated from the healthy control persons for the first time on the basis of changes detected in the erythrocytes. This change in erythrocyte membrane may explain the decrease in the w/s parameter of electron spin resonance in A-T heterozygotes. On the other hand increased values of w/s in A-T patients may be caused by disease process.     

Family Rubella Study in Los Angeles

A prospective study was initiated before the expected rubella epidemics in 1964 and 1965 in Los Angeles. Seventy-six families were evaluated by means of rubella complement fixing (cf) antibodies. The cf test, which has notable limitations, was chosen as a serologic test because it was possible to secure repeated samples of sera from all members of the families if venipuncture could be avoided.Definite evidence of clinical or serological rubella occurred in 13 of 399 persons enrolled in 1964, an attack rate of 3.3 percent. Four persons had clinical rubella only, five had clinical disease with seroconversion and four had seroconversion only. The ratio of apparent to unapparent disease was nine to four.There were four key families, each of which had more than one individual with definite clinical or serological evidence of rubella, suggesting that clustering of rubella cases does occur in families having an index case. In these families three types of intra-family spread were demonstrated: (1) all affected members had clinical disease, (2) all those affected had only inapparent disease, and (3) both apparent and inapparent disease in the same family.     

Metagenomic analysis of novel lignocellulose-degrading enzymes from higher termite guts inhabiting microbes

A metagenomic fosmid library was constructed from genomic DNA isolated from the microbial community residing in hindguts of a wood-feeding higher termite (Microcerotermes sp.) collected in Thailand. The library was screened for clones expressing lignocellulolytic activities. Fourteen independent active clones (2 cellulases and 12 xylanases) were obtained by functional screening at pH 10.0. Analysis of shotgun-cloning and pyrosequencing data revealed six ORFs, which shared less than 59% identity and 73% similarity of their amino acid sequences with known cellulases and xylanases. Conserved domain analysis of these ORFs revealed a cellulase belonging to the glycoside hydrolase family 5, whereas the other five xylanases showed significant identity to diverse families including families 8, 10, and 11. Interestingly, one fosmid clone was isolated carrying three contiguous xylanase genes that may comprise a xylanosome operon. The enzymes with the highest activities at alkaline pH from the initial activity screening were characterized biochemically. These enzymes showed a broad range of enzyme activities from pH 5.0 to 10.0, with pH optimal of 8.0 retaining more than 70% of their respective activities at pH 9.0. The optimal temperatures of these enzymes ranged from 50 degrees C to 55 degrees C. This study provides evidence for the diversity and function of lignocellulose-degrading enzymes in the termite gut microbial community, which could be of potential use for industrial processes such as pulp biobleaching and denim biostoning.     

Evidence of a sex-dependent association between the MSX1 locus and nonsyndromic cleft lip with or without cleft palate in the Chilean population

Prior studies have implicated an involvement of the Msx1 homeobox gene in cleft palate in mice and its homolog in humans (called MSX1 in the HOX7 gene, located on chromosome 4). In this study we present evidence of a sex-dependent association between MSX1 and non-syndromic cleft lip/palate (NSCLP) in the Chilean population. The sample included 73 NSCLP cases, 37 from multiplex families (Mx), 36 from simplex families (Sx), and 87 controls. Polymerase chain reaction amplification of the MSX1 intragenic microsatellite (CA)n-sequence shows significant (p = 0.035) differences in the allele frequencies between NSCLP-Mx males and control males. These differences are mainly due to frequency differences in allele *2 (173 base pairs) among cases (21.9%) and controls (13.2%). When the NSCLP cases are subdivided by sex and positive family history (Mx versus Sx), the Mx males (27.8%) as well as the total NSCLP-Mx cases (25.7%) showed significantly higher frequencies of allele *2, compared to controls (11.4% and 13.2%, respectively). Analysis of the genotype data indicates that the relative risk for NSCLP is greater for persons carrying allele *2 (i.e., odds ratio [OR] larger than 1), reaching significance for all Mx cases (OR = 2.67; 95% confidence interval [CI], 1.10 to 6.52) and even more pronounced for Mx males (OR = 3.33; 95% CI, 1.08 to 10.32). Taken together, these findings support the hypothesis that the genetic variation at the MSX1 locus is a predisposing gene involved in sex-dependent susceptibility to clefting and that it also differentiates simplex from multiplex families.     

Mitochondrial DNA polymorphism in Finnish families with Leber's hereditary optic neuroretinopathy

Summary Leukocyte mitochondrial DNA (mtDNA) from 17 Finnish families iwth Leber's hereditary optic neuroretinopathy and 70 maternally unrelated controls as well as skeletal muscle mtDNA from four of the Leber families and three controls was analyzed with 30 restriction enzymes. By this means, over 10% of the nucleotides of mtDNA were screened. No major deletion or insertion was found in any of the mtDNAs studied. The restriction fragment patterns of mtDNA showed no evidence of mtDNA heteroplasmy (mixture of different mtDNA types) in either blood or muscle cells. In all, 24 mtDNA types were observed in the material. In the maternal lines of Leber families, 11 mtDNA types were found, indicating no recent common maternal ancestor for the Finnish Leber families. In spite of several previously unknown polymorphisms, no mutation of mtDNA could be found exclusively in families with Leber's disease. However, a couple of mutations leading to amino acid replacements of mitochondrially encoded proteins were observed in certain Leber families only. These mutations have occurred in genes coding for subunits of NADH dehydrogenase, suggesting that a defect of the respiratory chain complex I may cause Leber's disease.     

Linkage disequilibrium and modification of risk for Huntington disease.

The major limitation in performing predictive testing for Huntington disease (HD) is the unavailability of DNA from crucial family members. In our program approximately 20% (36/183) of persons have been excluded from predictive testing because of this reason. The major aim of this study was to examine whether data derived from linkage disequilibrium could modify risk analysis for persons at risk for HD. As a first step, we assessed whether the previously reported linkage disequilibrium between alleles recognized by probe pBS674E-D at locus D4S95 remained significant in a much larger data set. A total of 1,150 chromosomes from 622 individuals--200 affected and 422 unaffected--from 118 families were assessed. Significant haplotype association was detected with AccI and MboI RFLPs at the locus D4S95, with all the families (P = .00003), as well as for a subset from the United Kingdom (P = .0037). Data derived from linkage disequilibrium studies using D4S95 modifies the risk for HD, especially in persons of U.K. descent. Utilization of this approach for risk modification of HD awaits both validation of these data and additional information concerning ethnic-specific alleles at the D4S95 locus.     

Enzyme family classification by support vector machines

One approach for facilitating protein function prediction is to classify proteins into functional families. Recent studies on the classification of G-protein coupled receptors and other proteins suggest that a statistical learning method, Support vector machines (SVM), may be potentially useful for protein classification into functional families. In this work, SVM is applied and tested on the classification of enzymes into functional families defined by the Enzyme Nomenclature Committee of IUBMB. SVM classification system for each family is trained from representative enzymes of that family and seed proteins of Pfam curated protein families. The classification accuracy for enzymes from 46 families and for non-enzymes is in the range of 50.0% to 95.7% and 79.0% to 100% respectively. The corresponding Matthews correlation coefficient is in the range of 54.1% to 96.1%. Moreover, 80.3% of the 8,291 correctly classified enzymes are uniquely classified into a specific enzyme family by using a scoring function, indicating that SVM may have certain level of unique prediction capability. Testing results also suggest that SVM in some cases is capable of classification of distantly related enzymes and homologous enzymes of different functions. Effort is being made to use a more comprehensive set of enzymes as training sets and to incorporate multi-class SVM classification systems to further enhance the unique prediction accuracy. Our results suggest the potential of SVM for enzyme family classification and for facilitating protein function prediction. Our software is accessible at http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.     

Breast and ovarian cancer incidence in BRCA1-mutation carriers. Breast Cancer Linkage Consortium.

Dominant predisposition to early-onset breast cancer and/or ovarian cancer in many families is known to be the result of germ-line mutations in a gene on chromosome 17q, known as BRCA1. In this paper we use data from families with evidence of linkage to BRCA1 to estimate the age-specific risks of breast and ovarian cancer in BRCA1-mutation carriers and to examine the variation in risk between and within families. Under the assumption of no heterogeneity of risk between families, BRCA1 is estimated to confer a breast cancer risk of 54% by age 60 years (95% confidence interval [CI] 27%-71%) and an ovarian cancer risk of 30% by age 60 years (95% CI 8%-47%). Similar lifetime-risk estimates are obtained by examining the risks of contralateral breast cancer and of ovarian cancer, in breast cancer cases in linked families. However, there is significant evidence of heterogeneity of risk between families; a much better fit to the data is obtained by assuming two BRCA1 alleles, one conferring a breast cancer risk of 62% and an ovarian cancer risk of 11% by age 60 years, the other conferring a breast cancer risk of 39% and an ovarian cancer risk of 42%, with the first allele representing 71% of all mutations (95% CI 55%-87%). There is no evidence of clustering of breast and ovarian cancer cases within families.     

The intestinal microflora of persons subjected to a radiation lesion]

The content of large intestine has been studied in persons exposed to radiation injury in consequence of the accident at the Chernobyl Atomic Power Plant. It is stated that bifidobacteria (10(7)-10(10) cells in 1 g of feces) prevailed (as in healthy people), Bifidobacterium indicum being a dominating species. Amount of lactic-acid bacteria in 1 g of defecations of examined patients was within the range of 10(6)-10(9) cells and in certain persons it reached 10(10) cells (primarily fecal Enterococci). A considerable amount of patients with acute radiation sickness of the 3d degree had in their intestine 10(9)/g of lactic-acid bacteria, Lactobacillus casei and L. plantarum prevailing there. The frequency of yeast isolation from defecations of patients constituted 83%, while the number of cells in 1 g of feces--from 10 to 10(4). Yeast of the Candida genus, mainly Candida parapsilosis, prevailed. The species composition of isolated microorganisms has no substantial differences from microcenosis of healthy people. The content of intestine of persons suffered from radiation is characterized only by greater amount of lactic-acid bacteria and enterococci as compared with healthy adults.     

眼镜蛇咬伤患者早期肝肾功能、心肌酶的变化

目的观察眼镜蛇咬伤患者早期肝、肾功能及心肌酶的改变,以探讨其临床意义。方法对30例眼镜蛇咬伤患者入院时即抽取静脉血2.0 ml,分离血清,按常规方法行肝、肾功能及心肌酶的测定,并与健康体检者进行比较。结果与对照组比较,眼镜蛇咬伤患者早期肝功能及心肌酶指标显著升高(P0.05);肾功能检测结果差异无显著性(P0.05)。结论通过对眼镜蛇咬伤患者肝、肾功能及心肌酶的测定,了解患者肝脏、肾脏、心肌损害程度,对指导临床治疗具有一定意义。     

Changes of mitochondrial respiration,mitochondrial content and cell size after induction of apoptosis in leukemia cells

Mitochondrial damage with release of cytochrome c is implicated in cell death signalling pathways. To examine mitochondrial function in apoptotic cells, we applied high-resolution respirometry to human leukemia cells arrested in the G1- and S-phase by exposure to the glucocorticoid dexamethasone and nucleotide analogue gemcitabine. At 30% apoptosis, opposite effects were observed on respiratory capacity (71% and 131% of controls, respectively). These changes correlated with alterations in cell size, cytosolic, and mitochondrial marker enzymes. Mitochondrial ATP production and membrane potential were maintained in all treatments, as deduced from high respiratory uncoupling control ratios (UCR). Bcl-2 over-expression did not prevent apoptosis after gemcitabine-treatment, but protected dexamethasone-treated cells from apoptosis, without fully preventing the decline of respiration and cell size. These results, therefore, provide conclusive evidence that alterations in respiratory capacity and enzyme activities per cell are mainly caused by opposite changes in cell size, occurring upon cell cycle arrest triggered by dexamethasone and gemcitabine in the early phase of apoptosis.     

On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2

The Dnmt2 enzymes show strong amino acid sequence similarity with eukaryotic and prokaryotic DNA-(cytosine C5)-methyltransferases. Yet, Dnmt2 enzymes from several species were shown to methylate tRNA-Asp and had been proposed that eukaryotic DNA methyltransferases evolved from a Dnmt2-like tRNA methyltransferase ancestor [Goll et al., 2006, Science, 311, 395-8]. It was the aim of this study to investigate if this hypothesis could be supported by evidence from sequence alignments. We present phylogenetic analyses based on sequence alignments of the methyltransferase catalytic domains of more than 2300 eukaryotic and prokaryotic DNA-(cytosine C5)-methyltransferases and analyzed the distribution of DNA methyltransferases in eukaryotic species. The Dnmt2 homologues were reliably identified by an additional conserved CFT motif next to motif IX. All DNA methyltransferases and Dnmt2 enzymes were clearly separated from other RNA-(cytosine-C5)-methyltransferases. Our sequence alignments and phylogenetic analyses indicate that the last universal eukaryotic ancestor contained at least one member of the Dnmt1, Dnmt2 and Dnmt3 families of enzymes and additional RNA methyltransferases. The similarity of Dnmt2 enzymes with DNA methyltransferases and absence of similarity with RNA methyltransferases combined with their strong RNA methylation activity suggest that the ancestor of Dnmt2 was a DNA methyltransferase and an early Dnmt2 enzyme changed its substrate preference to tRNA. There is no phylogenetic evidence that Dnmt2 was the precursor of eukaryotic Dnmts. Most likely, the eukaryotic Dnmt1 and Dnmt3 families of DNA methyltransferases had an independent origin in the prokaryotic DNA methyltransferase sequence space.     

A multidetachable sulfamate linker successfully used in a solid-phase strategy to generate libraries of sulfamate and phenol derivatives

The sulfamates and phenols constitute two families of compounds with numerous interesting biological properties. Using the ability of a new multidetachable sulfamate linker to generate these two families of compounds from the same resin, we designed and synthesized libraries of estradiol derivatives, sulfamoylated or not. A C-16beta side chain was then judiciously diversified to target two key steroidogenic enzymes, the steroid sulfates and the type 1 17beta-HSD. Four libraries of sulfamate and phenol derivatives were easily obtained by solid-phase parallel synthesis in good crude overall yields (13-62%) and HPLC purities (85-96%). Such strategy using the new two-in-line sulfamate linker could be also extended to other therapeutic targets than steroidogenic enzymes, thus adding to its potential.     

Amino acid sequence alignment of bacterial and mammalian pancreatic serine proteases based on topological equivalences.

The three-dimensional structures of the bacterial serine proteases SGPA, SGPB, and alpha-lytic protease have been compared with those of the pancreatic enzymes alpha-chymotrypsin and elastase. This comparison shows that approximately 60% (55-64%) of the alpha-carbon atom positions of the bacterial serine proteases are topologically equivalent to the alpha-carbon atom positions of the pancreatic enzymes. The corresponding value for a comparison of the bacterial enzymes among themselves is approximately 84%. The results of these topological comparisons have been used to deduce an experimentally sound sequence alignment for these several enzymes. This alignment shows that there is extensive tertiary structural homology among the bacteria and pancreatic enzymes without significant primary sequence identity (less than 21%). The acquisition of a zymogen function by the pancreatic enzymes is accompanied by two major changes to the bacterial enzymes' architecture: an insertion of 9 residues to increase the length of the N-terminal loop, and one of 12 residues to a loop near the activation salt bridge. In addition, in these two enzyme families, the methionine loop (residues 164-182) adopts very different comformations which are associated with their altered substrate specificities.     

Fertility intentions: are the undecided more like those who want more or want no more children?

In fertility surveys often women (and sometimes men) are asked their fertility desires, i.e. whether they want a/nother birth or not. Some respond that they are undecided. This study examines whether these persons are more like those who say they want more births or like those who say they want no more births. Data on married men and women in 29 Demographic and Health Surveys with sample sizes ranging from 300 to 3000 are used. A logistic regression equation is estimated within each country for those with known desires and then used to classify each person who was undecided. In all sub-Saharan African countries (n=20) and for both sexes, 50% or more of the undecided persons are classified as wanting more children (with one exception of wives in Kenya). By contrast in all five Latin American countries for both sexes less than 50% of the undecided were classified in the 'want more' group (with an exception of husbands in the Dominican Republic). Generally, the undecided tend to be classified the same as the majority among those in the survey with stated desires.