Linking multiple bonds between metal atoms: clusters, dimers of "dimers", and higher ordered assemblies.
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Defective structure of BN nanotubes: from single vacancies to dislocation lines.
A combination of electron microscopy and theoretical calculations provides new insights into the structure, electronics, and energetics of point defects and vacancy lines in BN single-wall nanotubes (SWNT). We show that the point defects forming under electron irradiation in the BN SWNTs are primarily divacancies. Due to the partially ionic character of the BN bonding, divacancies behave like an associated Schottky pair, with a dissociation energy of around 8 eV. Clustering of multiple vacancies is energetically favorable and leads to extended defects which locally change the nanotube diameter and chirality. Nevertheless these defects do not alter significantly the band gap energy, and all of them have electronic structure similar to that of BN divacancies. We thus conclude that under irradiation BN SWNT may have a very stable alteration of its electronic and optical properties.
Boron Compounds↗
Distribution of selected bacterial species on intraoral surfaces.
BACKGROUND/AIM: To examine the proportions of 40 bacterial species in samples from 8 oral soft tissue surfaces and saliva in systemically healthy adult subjects and to compare these microbiotas with those of supra- and subgingival plaque. METHODS: Microbial samples were taken from 8 oral soft tissue surfaces of 225 systemically healthy subjects using a "buccal brush". Saliva was taken by expectoration. Forty-four of these subjects provided additional supra- and subgingival plaque samples. Samples were individually evaluated for their content of 40 bacterial species using checkerboard DNA-DNA hybridization. The percentage of total DNA probe count was determined for each species, at each sample location and averaged across subjects. The significance of differences among the proportions of the 40 test species at different sample locations was sought in the 225 and 44 subjects separately using the Quade test and adjusted for multiple comparisons. Cluster analysis was performed using the proportions of the 40 species at the different sample locations using the minimum similarity coefficient and an average unweighted linkage sort. The proportions of each species were averaged across subjects in the resulting cluster groups and the significance of differences was tested using the t-test and ANOVA. RESULTS: Microbial profiles differed markedly among sample locations in the 225 subjects, with 34 of 40 species differing significantly. Proportions of Veillonella parvula and Prevotella melaninogenica were higher in saliva and on the lateral and dorsal surfaces of the tongue, while Streptococcus mitis and S. oralis were in significantly lower proportions in saliva and on the tongue dorsum. Cluster analysis resulted in the formation of 2 clusters with >85% similarity. Cluster 1 comprised saliva, lateral and dorsal tongue surfaces, while Cluster 2 comprised the remaining soft tissue locations. V. parvula, P. melaninogenica, Eikenella corrodens, Neisseria mucosa, Actinomyces odontolyticus, Fusobacterium periodonticum, F. nucleatum ss vincentii and Porphyromonas gingivalis were in significantly higher proportions in Cluster 1 and S. mitis, S. oralis and S. noxia were significantly higher in Cluster 2. These findings were confirmed using data from the 44 subjects providing plaque samples. The microbial profiles of supra- and subgingival plaque differed from the other sample locations, particularly in the increased proportions of the Actinomyces species. Species of different genera exhibited different proportions on the various intraoral surfaces, but even within the genus Streptococcus, there were differences in colonization patterns. S. oralis, S. mitis and S. constellatus colonized the soft tissues and saliva in higher proportions than the samples from the teeth, while the other 4 streptococcal species examined colonized the dental surfaces in proportions comparable to the soft tissue locations and saliva. CONCLUSIONS: Proportions of bacterial species differed markedly on different intraoral surfaces. The microbiota of saliva was most similar to that of the dorsal and lateral surfaces of the tongue. The microbiotas of the soft tissues resembled each other more than the microbiotas that colonized the teeth both above and below the gingival margin.
Adult↗
Mapping the interaction surface of linker histone H1(0) with the nucleosome of native chromatin in vivo.
H1 linker histones stabilize the nucleosome, limit nucleosome mobility and facilitate the condensation of metazoan chromatin. Here, we have combined systematic mutagenesis, measurement of in vivo binding by photobleaching microscopy, and structural modeling to determine the binding geometry of the globular domain of the H1(0) linker histone variant within the nucleosome in unperturbed, native chromatin in vivo. We demonstrate the existence of two distinct DNA-binding sites within the globular domain that are formed by spatial clustering of multiple residues. The globular domain is positioned via interaction of one binding site with the major groove near the nucleosome dyad. The second site interacts with linker DNA adjacent to the nucleosome core. Multiple residues bind cooperatively to form a highly specific chromatosome structure that provides a mechanism by which individual domains of linker histones interact to facilitate chromatin condensation.
Amino Acid Sequence↗
Lymph node micrometastasis and prognosis in patients with oesophageal squamous cell carcinoma.
BACKGROUND: The purpose of this study was to investigate whether the presence of lymph node micrometastasis in pathological lymph node-negative (pN0) oesophageal squamous cell carcinoma had prognostic value. METHODS: Some 1840 lymph nodes were obtained from 50 patients with pN0 oesophageal squamous cell carcinoma who underwent curative resection of the primary tumour with systematic lymphadenectomy. These lymph nodes were examined immunohistochemically with anticytokeratin antibody (AE1/AE3). Lymph node micrometastases newly detected by immunohistochemistry were classified as micrometastasis. Additionally, lymph node micrometastases were classified into three stages: stage 1, one individual AE1/AE3-positive cell; stage 2, multiple individual positive cells; stage 3, one or multiple positive clusters. RESULTS: Micrometastases were detected in 20 patients (40 per cent). A higher stage of micrometastasis was associated with greater pathological tumour (pT) size (P = 0.023). Recurrent tumours developed in nine patients. However, the frequency of recurrence was similar in patients with, or without, micrometastasis (five of 20 and four of 30 patients respectively; P = 0.25). Twenty-three of 30 patients without micrometastasis survived, whereas 15 of 20 patients with micrometastasis were still alive (5-year overall survival 75 and 78 percent respectively, P = 0.91). Twenty-six of 30 patients without micrometastasis had no recurrence, whereas 15 of 20 patients with micrometastasis had no recurrence (5-year relapse-free survival 86 and 73 per cent respectively, P = 0.37). There was no significant difference in prognosis with respect to the stages of micrometastasis. Multivariate analysis also showed that micrometastasis was not an independent prognostic factor (P = 0.73). CONCLUSION: Immunohistochemical detection of lymph node micrometastasis may be an indicator of lymphatic dissemination of tumour cells. However, the presence of micrometastasis had no impact on the prognosis of node-negative patients with oesophageal squamous cell carcinoma.
Aged↗
Chelicerate Hox genes and the homology of arthropod segments.
Genes of the homeotic complex (HOM-C) in insects and vertebrates are required for the specification of segments along the antero-posterior axis. Multiple paralogues of the Hox genes in the horseshoe crab Limulus poliphemus have been used as evidence for HOM-C duplications in the Chelicerata. We addressed this possibility through a limited PCR survey to sample the homeoboxes of two spider species, Steatoda triangulosa and Achaearanea tepidariorum. The survey did not provide evidence for multiple Hox clusters although we have found apparent duplicate copies of proboscipedia (pb) and Deformed (Dfd). In addition, we have cloned larger cDNA fragments of pb, zerknullt (zen/Hox3) and Dfd. These fragments allowed the determination of mRNA distribution by in situ hybridization. Our results are similar to the previously published expression patterns of Hox genes from another spider and an oribatid mite. Previous studies compared spider/mite Hox gene expression patterns with those of insects and argued for a pattern of segmental homology based on the assumption that the co-linear anterior boundaries of the Hox domains can be used as markers. To test this assumption we performed a comparative analysis of the expression patterns for UBX/ABD-A in chelicerates, myriapods, crustaceans, and insects. We conclude that the anterior boundary can be and is changed considerably during arthropod evolution and, therefore, Hox expression patterns should not be used as the sole criterion for identifying homology in different classes of arthropods.
Amino Acid Sequence↗
Tracking of serum lipids and lipoproteins from childhood to dyslipidemia in adults: the Bogalusa Heart Study.
Our data demonstrate that serum lipid and lipoprotein levels continue to track from childhood into young adulthood. The persistence and clustering of multiple CVD risk factors from childhood to adulthood and the impact of obesity in this regard point to the need for preventive measures aimed at developing healthy lifestyles early in life. Adverse levels of LDL-C in childhood persist over time, progress to adult dyslipidemias, and relate to obesity and hypertension as well. NCEP guidelines which classify CVD risk on the basis of LDL-C level, are helpful in targeting individuals at risk early in life.
Adolescent↗
Structure and promoter activity of the gene for the erythroid transcription factor GATA-1.
We have cloned the gene for the chicken erythroid transcription factor GATA-1 (formerly Eryf1, NF-E1, or GF-1). The gene is composed of six exons, two of which encode the two finger domains of the protein. Transcription of GATA-1 in chicken embryonic erythroid cells initiates from multiple sites clustered approximately 200 base pairs upstream from the start of protein-coding sequence. A number of sequence motifs for known DNA-binding proteins are found to be protected in DNase I-footprinting experiments by either erythroid or brain nuclear extracts or by both. Notably, a cluster of three GATA-1 sites is protected by the erythroid extract, as well as by purified GATA-1. We find that the upstream region of the gene functions as a powerful promoter when transfected into embryonic erythroid cells. In primary chicken embryo fibroblasts the promoter exhibits lower activity, which is increased when the cells are cotransfected with a second plasmid expressing the GATA-1 cDNA. The results suggest that GATA-1 protein plays an autoregulatory role in its own expression.
Animals↗
Unusual charge configurations in transcription factors of the basic RNA polymerase II initiation complex.
A systematic analysis of the primary sequences of the polymerase II initiation complex has revealed unusual charge features in the TFII family proteins. In particular, the proteins TFIIA alpha, TFIIE alpha, and TFIIF carry multiple charge clusters and hyper charge runs, sequence features occurring in < 4% of all (available) eukaryotic proteins. Possible implications for these charge structures are discussed in relation to the assembly and function of the polymerase II transcriptional complex.
Amino Acid Sequence↗
The chromosomal distribution of mouse odorant receptor genes.
Odorant receptors (ORs) on nasal olfactory sensory neurons are encoded by a large multigene family. Each member of the family is expressed in a small percentage of neurons that are confined to one of several spatial zones in the nose but are randomly distributed throughout that zone. This pattern of expression suggests that when the sensory neuron selects which OR gene to express it may be confined to a particular zonal gene set of several hundred OR genes but select from among the members of that set via a stochastic mechanism. Both locus-dependent and locus-independent models of OR gene choice have been proposed. To investigate the feasibility of these models, we determined the chromosomal locations of 21 OR genes expressed in four different spatial zones. We found that OR genes are clustered within multiple loci that are broadly distributed in the genome. These loci lie within paralogous chromosomal regions that appear to have arisen by duplications of large chromosomal domains followed by extensive gene duplication and divergence. Our studies show that OR genes expressed in the same zone map to numerous loci; moreover, a single locus can contain genes expressed in different zones. These findings raise the possibility that OR gene choice may be locus-independent or involve consecutive stochastic choices.
Animals↗
A 110-amino acid region within the A1-domain of coagulation factor VIII inhibits secretion from mammalian cells.
Factor VIII is the coagulation factor deficient in the X-chromosome-linked bleeding disorder hemophilia A. Factor VIII is homologous to blood coagulation factor V, both having a domain structure of A1-A2-B-A3-C1-C2. Previous transfection studies demonstrated that factor VIII is 10-fold less efficiently expressed than the homologous coagulation factor, factor V. The inefficient expression correlated with interaction of the factor VIII primary translation product with the protein chaperonin BiP in the lumen of the endoplasmic reticulum. In contrast, factor V was not detected in association with BiP and was secreted efficiently. To determine whether specific amino acid sequences within factor VIII inhibit secretion, we have studied the secretion of factor VIII deletion and factor VIII/factor V chimeric proteins upon transient transfection of COS-1 monkey cells. A chimeric factor VIII protein that contained the A1- and A2-domains of factor V was secreted with a similar efficiency as wild-type factor V, whereas the complementary chimera having the A1- and A2-domains of factor VIII was secreted with low efficiency, similar to wild-type factor VIII. These results suggested that sequences within the A1- and A2-domains were responsible for the low secretion efficiency of factor VIII. Secretion of A1-domain-deleted factor VIII was increased approximately 10-fold compared to wild-type factor VIII or A2-domain-deleted factor VIII. Expression of the factor VIII A1-domain alone did not yield secreted protein, whereas expression of the factor VIII A2-domain alone or the factor V A1-domain or A2-domain alone directed synthesis of secreted protein. Secretion of a hybrid in which the carboxyl-terminal 110 amino acids of the A1-domain were replaced by homologous sequences from the factor V A1-domain was also increased 10-fold compared to wild-type factor VIII, however, the secreted protein was not functional and the heavy and light chains were not associated. These results localize a 110-amino acid region within the A1-domain that inhibits factor VIII secretion. This region is clustered with multiple short peptide sequences that have potential to bind BiP.
Amino Acid Sequence↗
Transcription of the blk gene in human B lymphocytes is controlled by two promoters.
Genomic DNA containing the first exon and 5'-flanking region of the human protein tyrosine kinase, blk, was isolated. Sequence analysis identified a TG repeat element in this region with enhancer activity, but no TATA or CCAAT sequences were found. Two blk transcripts of 2.2 and 2.5 kilobases were identified in various B-cell lines by Northern blot analyses, and primer extension experiments demonstrated two clusters of multiple transcription start sites. Subsequent promoter analyses by transient transfection assays with a reporter gene identified two promoter elements in the human blk gene. Promoter P1 contains sequences that have been shown to regulate the expression of immunoglobulin genes and promoter P2 contains elements that are highly conserved in the promoter of major histocompatibility complex class II genes, as well as a B-cell-specific activator protein- (BSAP) binding site. Electrophoretic mobility shift assays demonstrated that the binding of a protein to the BSAP-binding site was correlated with the presence of the 2.5-kilobase blk transcript. These data suggest that the two human blk RNAs arise from the transcription of the blk gene by two distinct promoters and that these promoters may be subject to regulation by different trans-acting factors.
B-Lymphocytes↗
Identification of a novel bone morphogenetic protein-responsive gene that may function as a noncoding RNA.
Bone morphogenetic proteins (BMPs)/osteogenic proteins (OPs), members of the transforming growth factor-beta superfamily, have a wide variety of effects on many cell types including osteoblasts and chondroblasts, and play critical roles in embryonic development. BMPs transduce their effects through binding to two different types of serine/threonine kinase receptors, type I and type II. Signaling by these receptors is mediated by the recently identified Smad proteins. Despite the rapid progress in understanding of the signaling mechanism downstream of BMP receptors, the target genes of BMPs are poorly understood in mammals. Here we identified a novel gene, termed BMP/OP-responsive gene (BORG), in C2C12 mouse myoblast cell line which trans-differentiates into osteoblastic cells in response to BMPs. Expression of BORG was dramatically induced in C2C12 cells by the treatment with BMP-2 or OP-1 within 2 h and peaked at 12-24 h, whereas transforming growth factor-beta had a minimal effect. BMP-dependent expression of BORG was also detected in other cell types which are known to respond to BMPs, suggesting that BORG is a common target gene of BMPs. Cloning and sequence analysis of BORG cDNA and the genomic clones revealed that, unexpectedly, the transcript of BORG lacks any extensive open reading frames and contains a cluster of multiple interspersed repetitive sequences in its middle part. The unusual structural features suggested that BORG may function as a noncoding RNA, although it is spliced and polyadenylated as authentic protein-coding mRNAs. Together with the observation that transfection of antisense oligonucleotides of BORG partially inhibited BMP-induced differentiation in C2C12 cells, it is possible that a new class of RNA molecules may have certain roles in the differentiation process induced by BMPs.
Animals↗
Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase.
The synthesis of high affinity antibodies requires activation-induced cytidine deaminase (AID) to initiate somatic hypermutation and class-switch recombination. Here we investigate AID-catalyzed deamination of C --> U on single-stranded DNA and on actively transcribed closed circular double-stranded DNA. Mutations are initially favored at canonical WRC (W = A or T, R = A or G) somatic hypermutation hot spot motifs, but over time mutations at neighboring non-hot spot sites increase creating random clusters of mutated regions in a seemingly processive manner. N-terminal AID mutants R35E and R35E/R36D appear less processive and have altered mutational specificity compared with wild type AID. In contrast, a C-terminal deletion mutant defective in CSR in vivo closely resembles wild type AID. A mutational spectrum generated during transcription of closed circular double-stranded DNA indicates that wild type AID retains its specificity for WRC hot spot motifs within the confines of a moving transcription bubble while introducing clusters of multiple deaminations predominantly on the nontranscribed strand.
Amino Acid Motifs↗
Egr-1 induces the expression of its corepressor nab2 by activation of the nab2 promoter thereby establishing a negative feedback loop.
The transcription factor Egr-1 regulates the expression of numerous genes involved in differentiation, growth, and in response to environmental signals. Egr-1 activity is modulated in part through the binding of corepressors Nab1 and Nab2. Nab2 appears crucial for controlling Egr-1-mediated transactivation because it is a delayed early response gene, induced by the same stimuli that induce the immediate early gene Egr-1. To identify important elements regulating Nab2 expression, we cloned the human Nab2 gene and investigated the 5'-region. The TATA- and initiator-less Nab2 promoter, located from -679 to -74 bp, contains a total of 11 Egr binding sites, including a cluster of multiple overlapping Egr/Sp1 sites between -329 and -260 bp. This region is critical for basal promoter activity as well as for maximum induction by phorbol esters. Electromobility shifts show that Sp1 binds to this region in normal and stimulated cells, whereas stimulation induces binding of Egr-1. In addition Egr-1 activates the Nab2 promoter in a pattern similar to phorbol esters, suggesting that Egr-1 is a major inducer of protein kinase C-mediated Nab2 induction. Depletion of Egr-1 by each of two distinct Egr-1 short-interfering RNAs reduces Nab2 expression and inducibility, confirming that Egr-1 is an important regulator of Nab2 expression. Transfection experiments show that Egr-1-induced Nab2 promoter activity is itself repressed by Nab2. These results indicate that Egr-1 mediates the induction of its own repressor, thereby preventing a permanent transactivation of Egr-1 target genes and a damaging overreaction in response to environmental signals.
Base Sequence↗
Does living in an urban environment confer advantages for childhood nutritional status? Analysis of disparities in nutritional status by wealth and residence in Angola, Central African Republic and Senegal.
OBJECTIVE: The purpose of this paper is to examine the relationship between childhood undernutrition and poverty in urban and rural areas. DESIGN: Anthropometric and socio-economic data from Multiple Indicator Cluster Surveys in Angola-Secured Territory (Angola ST), Central African Republic and Senegal were used in this analysis. The population considered in this study is children 0-59 months, whose records include complete anthropometric data on height, weight, age, gender, socio-economic level and urban or rural area of residence. In addition to simple urban/rural comparisons, the population was stratified using a wealth index based on living conditions and asset ownership to compare the prevalence, mean Z-score and odds ratios for stunting and wasting. RESULTS: In all cases, when using a simple urban/rural comparison, the prevalence of stunting was significantly higher in rural areas. However, when the urban and rural populations were stratified using a measure of wealth, the differences in prevalence of stunting and underweight in urban and rural areas of Angola ST, Central African Republic and Senegal disappeared. Poor children in these urban areas were just as likely to be stunted or underweight as poor children living in rural areas. The odds ratio of stunting in the poorest compared with the richest quintile was 3.4, 3.2 and 1.5 in Angola ST, Senegal and Central African Republic, respectively. CONCLUSIONS: This paper demonstrates that simple urban/rural comparisons mask wide disparities in subgroups according to wealth. There is a strong relationship between poverty and chronic undernutrition in both urban and rural areas; this relationship does not change simply by living in an urban environment. However, urban and rural living conditions and lifestyles differ, and it is important to consider these differences when designing programmes and policies to address undernutrition.
Angola↗
The metabolic syndrome and cardiovascular disease.
The metabolic syndrome, which is very common in the general population, is defined by the clustering of several classic cardiovascular risk factors, such as type 2 diabetes, hypertension, high triglycerides and low high-density lipoprotein cholesterol (HDL). Central obesity and insulin resistance, which are the two underlying disorders of the syndrome, are further risk factors for cardiovascular disease. Moreover, a panel of novel (non-traditional) risk factors are ancillary features of the metabolic syndrome. They include biomarkers of chronic mild inflammation (e.g. C-reactive protein, CRP), increased oxidant stress (e.g. oxidized low density lipoprotein, LDL), thrombophilia (e.g. plasminogen activator inhibitor-1, PAI-1) and endothelial dysfunction (e.g. E-selectin). Therefore, subjects with the metabolic syndrome are potentially at high risk of developing atherosclerosis and clinical cardiovascular events.In recent years several longitudinal studies have confirmed that subjects with the metabolic syndrome present with atherosclerosis and suffer from myocardial infarction and stroke at rates higher than subjects without the syndrome. The risk of cardiovascular disease (CVD) is particularly high in women with the syndrome and in subjects with pre-existing diabetes, CVD and/or high CRP. However, an increased risk is already present in subjects with a cluster of multiple mild abnormalities. The risk related to the metabolic syndrome is definitely higher when subjects affected are compared to subjects free of any metabolic abnormality.
Cardiovascular Diseases↗
Quantitative architecture distinguishes prefrontal cortical systems in the rhesus monkey.
The prefrontal cortex encompasses a large and heterogeneous set of areas, whose borders have been variously mapped in different architectonic studies. Differences in cortical maps present a formidable problem in comparing data across studies and in constructing databanks on the connections and functional attributes of cortical areas. Here we used quantitative approaches to cortical mapping to investigate (i) if architectonic areas of the prefrontal cortex in adult rhesus monkeys have unique profiles and (ii) if groups of architectonic areas belonging to distinct cortical types, ranging from agranular to eulaminate, have similar features. In addition, we used multidimensional analyses to see if, and how, prefrontal areas form clusters when multiple features are considered simultaneously. We used quantitative unbiased sampling procedures to estimate the areal and laminar density of neurons, glia and neurons positive for the calcium binding proteins parvalbumin (PV), calbindin (CB) and calretinin (CR) among 21 prefrontal areas or subdivisions of areas. Neuronal density varied among the prefrontal cortices (range: 38 569 +/- 4078 to 58 708 +/- 2327 neurons/mm(3)); it was lowest in caudal orbitofrontal and medial areas (OPAll, OPro, 13, 24a, 32, M25) and highest in lateral prefrontal areas (subdivisions of areas 46 and 8). Neurons positive for PV were most prevalent in lateral prefrontal areas and least prevalent in caudal orbitofrontal and medial pre-frontal areas, whereas the opposite trend was noted for neurons that expressed CB. Neurons positive for CR did not show regional differences, and the density of glia showed small variations among prefrontal cortices. The differences among areas, along with differences in the thickness of individual areas and layers, were used to establish a quantitative profile for each area. The results showed that differences in the density of neurons, and the preponderance of neurons positive for PV and CB, were related to different architectonic types of areas found within the prefrontal cortex. Conventional as well as multiparameter statistical analyses distinguished at one extreme the agranular and dysgranular (limbic) cortices, which were characterized by prominent deep layers (V-VI), the lowest neuronal density, the highest ratio of glia/neurons, and the lowest density of PV and the highest for CB. At the other extreme, lateral eulaminate cortices were characterized by the highest density of neurons, a prominent granular layer IV, denser supragranular (II-III) than infragranular (V-VI) layers, and a balanced distribution of neurons positive for PV and CB. The results provide insights into potentially different rates of development or maturation of limbic and eulaminate prefrontal areas, and their differential vulnerability in neurological and psychiatric diseases. The quantitative methods used provide an objective approach to construct maps, address differences in nomenclature across studies, establish homologies in different species and provide a baseline to identify changes in pathologic conditions.
Animals↗