Sequence analysis of the novel HLA-B35 (B*3576) allele in an African individual

A novel human leucocyte antigen (HLA)-B35 (HLA-B*3576) allele has been described in an African individual by polymerase chain reaction sequence-based typing. This new allele contains six nucleotide substitutions and is homologous to B*3501 with the exception of residues 66-74 resulting in five amino acid mutations.

Bulk and surface oxygen vacancy formation and diffusion in single crystals, ultrathin films, and metal grown oxide structures

The neutral oxygen vacancy (OV) energy formation for bulk, subsurface sites at different depths from the surface and various surface sites has been estimated for single crystals, unsupported ultrathin films of MgO, CaO, and BaO, and MgO ultrathin films supported on Ag(001). From the calculated energy barriers for diffusion through the surface and from the surface to the bulk it is found that diffusion is a hindered event, especially for MgO. Nevertheless, diffusion from the terrace to step edges is largely favored while diffusion through terrace sites is less likely and surface to bulk has a very low probability. It is argued that this explains recent scanning tunneling microscopy images for MgO thin films supported on Ag(001) showing OV populating preferentially the step edge sites.

First principles analysis of the stability and diffusion of oxygen vacancies in metal oxides

Oxygen vacancies in metal oxides are known to determine their chemistry and physics. The properties of neutral oxygen vacancies in metal oxides of increasing complexity (MgO, CaO, alpha-Al2O3, and ZnO) have been studied using density functional theory. Vacancy formation energies, vacancy-vacancy interaction, and the barriers for vacancy migration are determined and rationalized in terms of the ionicity, the Madelung potential, and lattice relaxation. It is found that the Madelung potential controls the oxygen vacancy properties of highly ionic oxides whereas a more complex picture arises for covalent ZnO.

Classical West “syndrome” phenotype with a subtelomeric 4p trisomy

We report a girl with mild mental retardation with onset of infantile spasms at age of 9 months. Treatment with a short course of adrenocorticotropic hormone (ACTH) was successful. Initially, a diagnosis of idiopathic West syndrome, with good neurological outcome and disappearance of epilepsy after treatment, was made. Conventional karyotype was normal. Reinvestigations were done at age 8 years, because of a new pregnancy. Karyotyping of both parents was done because of mild dysmorphic features in the proband, and to eliminate other causes than early age epilepsy as the etiology of her mental retardation. Parental karyotypes showed a balanced paternal translocation (4p;17q) resulting in partial 4p trisomy, without significant 17q monosomy in the proband. Chromosomal abnormalities usually lead to a severe West syndrome with poor prognosis of neurological outcome (persistent severe epilepsy, mental retardation, and behavioral disturbances). The presence of an undetected cytogenetic anomaly in our proband with transient hypsarythmia is unusual and led us to propose systematic telomeric screening in apparently "idiopathic" West syndrome patients with mild mental retardation and subtle dysmorphic features.

Bonding of gold nanoclusters to oxygen vacancies on rutile TiO2(110)

Through an interplay between scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, we show that bridging oxygen vacancies are the active nucleation sites for Au clusters on the rutile TiO2(110) surface. We find that a direct correlation exists between a decrease in density of vacancies and the amount of Au deposited. From the DFT calculations we find that the oxygen vacancy is indeed the strongest Au binding site. We show both experimentally and theoretically that a single oxygen vacancy can bind 3 Au atoms on average. In view of the presented results, a new growth model for the TiO2(110) system involving vacancy-cluster complex diffusion is presented.

Are immunoglobulin E levels associated with early wheezing? A prospective study in Brazilian infants

The relationship between wheezing or asthma and serum immunoglobulin (Ig)E levels in early life is unclear. The aim of this study was to follow-up the IgE immune response in infants that did, or did not, develop recurrent wheezing during their first year of life. One-hundred and two randomised term neonates were included, in which IgE levels were quantified in cord blood samples, at 3, 6, 9 and 12 months of age. Specific IgE levels for food and inhalant allergens and the skin-prick test for inhalant allergens were also assessed at 6 and 12 months. During clinical follow-up, 32 (31%) infants presented with two or more wheezing episodes, while 70 (69%) had no wheezing. Total IgE levels were significantly higher up to 12 months in wheezing infants when compared to nonwheezing group. At 12 months, the specific IgE levels to cow's milk, egg white and mites were higher in infants with recurrent wheezing. There was no influence of family history for atopy on IgE levels. The skin-prick tests were positive in 14% and 23% in wheezing infants at 6 and 12 months, respectively. These results indicate an early allergic sensitisation in wheezing infants, suggesting an altered immunoregulatory T-cell role in immunoglobulin E production.

Dipole localization of human induced focal afterdischarge seizure in simultaneous magnetoencephalography and electrocorticography

Localizations were compared for the same human seizure between simultaneously measured MEG and iEEG, which were both co-registered to MRI. The whole-cortex neuromagnetometer localized a dipole in a sphere phantom, co-registered to the MEG sensor array, with an error of 1.4 mm. A focal afterdischarge seizure was induced in a patient with partial epilepsy, by stimulation at a subdural electrocorticography (ECoG) electrode with a known location, which was co-registered to the MRI and to the MEG sensor array. The simultaneous MEG and ECoG during the 30-second seizure was measured and analyzed using the single, moving dipole model, which is the localization model used clinically. The dipole localizations from simultaneous whole cortex 68-channel MEG and 64-channel ECoG were then compared for the repetitive spiking at six different times during the seizure. There were two main regions of MEG and ECoG activity. The locations of these regions were confirmed by determining the location clusters of 8,000 dipoles on ECoG at consecutive time points during the seizure. The mean distances between the stimulated electrode location versus the dipole location of the MEG and versus the dipole location of the ECoG were each about one (1) centimeter. The mean distance between the dipole locations of the MEG versus the dipole locations of the ECoG was about 2 cm. These errors were compared to errors of MEG and ECoG reported previously for phantoms and for somatosensory evoked responses (SER) in patients. Comparing the findings from the present study to those from prior studies, there appeared to be the expected stepwise increase in mean localization error progressing from the phantom, to the SER, to the seizure.

Oxygen vacancies as active sites for water dissociation on rutile TiO(2)(110)

Through an interplay between scanning tunneling microscopy experiments and density functional theory calculations, we determine unambiguously the active surface site responsible for the dissociation of water molecules adsorbed on rutile TiO(2)(110). Oxygen vacancies in the surface layer are shown to dissociate H(2)O through the transfer of one proton to a nearby oxygen atom, forming two hydroxyl groups for every vacancy. The amount of water dissociation is limited by the density of oxygen vacancies present on the clean surface exclusively. The dissociation process sets in as soon as molecular water is able to diffuse to the active site.

Asian-american variants of human papillomavirus type 16 have extensive mutations in the E2 gene and are highly amplified in cervical carcinomas

Human-papillomavirus (HPV)-E2 protein is involved in gene-expression regulation and replication of HPV genome. Disruption of the E2 gene during viral integration has been proposed as a mechanism of tumoral progression, since the expression of E6/E7 viral oncogenes is allowed. However, retention of E1/E2 genes and high viral amplification are frequently found in HPV16-positive carcinomas of some populations. In this study, we investigated whether retention of E1/E2 and viral amplification are associated with particular HPV16 E2 variants in cervical carcinomas. HPV16 detection, E1/E2 integrity and viral amplification were explored by Southern blot in 123 cervical carcinomas. HPV16 variants were identified by Southern blot and by sequencing E6, L1/MY and E2 regions. Of 46 HPV16-positive tumors, 34 were positive for E1/E2 and 14 of them showed a variant restriction pattern by mutations in E2. All 14 were Asian-American (AA) variants and, of 11 sub-classified, 6 were AA-a and 5 AA-c. Two E1/E2-negative tumors also contained the AA-c variant, while the remaining HPV16-positive tumors contained only European variants. The E2 gene of AA variants showed 24 mutations, 19 identical in both sub-classes. The 24 mutations were distributed throughout the entire gene and 19 result in 18 amino-acid changes. The AA variants were associated with E1/E2-positive carcinomas with more than 50 viral copies/cell (p = 0.035). The association of Asian-American E2 variants with retention of E1/E2 suggests that E2 variation may be an alternative mechanism de-regulating the expression of viral oncogenes.

Full window stereo

Visualisation is the bioinformaticist's most important tool for the study of macromolecules, and being able to see molecules in stereo is a crucial aspect. Stereo vision is based on the principle that each eye is presented with the best possible image of what it would have seen if the object was really there in 3D. The simplest approach to stereo vision is to display the right eye picture on the right half of the screen and the left eye picture on the left half while using a mirror system to ensure that each eye sees what it is supposed to see. More expensive workstations use hardware to alternately display the left and right eye pictures while synchronously blocking the transparency in the right or left lens of the special glasses worn by the user. We present here some simple software that uses inexpensive hardware, originally designed for the computer game industry, to make full screen stereo available on Linux-based PCs. The quality of the stereo vision is similar to the top-of-the-line graphics workstations that are capable of quad-buffering. This stereo option has been incorporated in the XII based version of WHAT IF (Vriend, G. J. Mol. Graphics 1990, 8, 52-56), but the stereo source code is freely available and can easily be incorporated in other visualization packages.

Illegal drug-using trends among students in a Spanish university in the last decade (1984-1994)

A sample of 2,086 university students in Valladolid (Spain) were surveyed in 1994 to assess their current use of illicit drugs. That information was used as a baseline to show the trends in the last decade in order to compare two other studies carried out on a similar target population in 1984 and 1990. Of those surveyed, 28.3% had taken some illicit drug within their lifetime, 16.7% in the previous year, and 7.2% in the previous month. Cannabis was the most common illicit drug used in the three levels among these students. 14.2 is the average starting age at which inhalants are used and 19.3 for opiates. 49.8% were opposed to any drug legalization. More than a quarter of the students (28.7%) could be considered as a mental disorder case-finding as measured by Golberg's General Health Questionnaire (GHQ), which was much more relevant among illicit drug users than among nonusers. A decrease in illegal drug use frequency among university students has been observed in the last 10 years.

Hematopoietic damage prior to PBSCT and its influence on hematopoietic recovery

BACKGROUND AND OBJECTIVE

Patients with malignancies receive chemotherapy to induce tumor remission which could damage hematopoiesis and adversely influence hematopoietic reconstitution after transplantation. In the present study we used a long-term culture (LTBMC) system and clonogenic assays to evaluate the marrow damage in patients selected to receive peripheral blood stem cell transplantation (PBSCT).

DESIGN AND METHODS

Thirty-five patients - 20 with breast cancer (BC), 9 with non-Hodgkin's lymphoma (NHL) and 6 with Hodgkin's disease (HD) - were included. Bone marrow aspiration was performed one day prior to the initiation of the conditioning therapy. CFU-GM were cultured in methylcellulose with PHA-LCM. Delta assays of plastic adherent progenitor cells (PD) were performed according to Gordon's method. LTBMC were established for 5 weeks.

RESULTS

There were fewer CFU-GM from all patient groups than from normal BM (p<0.05). In contrast, the number of immature progenitor cells (PD) was not decreased. The total number of CFU-GM produced by LTBMC patients was significantly reduced (p<0.05). The adherent layer from patients was often qualitatively different. In order to know whether the hematopoietic damage could affect hematopoietic reconstitution, we correlated culture data with time taken to reach peripheral cell counts. A negative correlation (r= - 0.71) was found between percentage of stromal layer and time taken to reach 20x10(9) platelets/L (tplat= 20x3-0.08% stromal layer).

INTERPRETATION AND CONCLUSIONS

We can conclude that prior to PBSCT, hematopoietic function is impaired at both the level of committed progenitor cells and that of BM stroma. This damage could influence platelet recovery.

SSB, encoding a ribosome-associated chaperone, is coordinately regulated with ribosomal protein genes

Genes encoding ribosomal proteins and other components of the translational apparatus are coregulated to efficiently adjust the protein synthetic capacity of the cell. Ssb, a Saccharomyces cerevisiae Hsp70 cytosolic molecular chaperone, is associated with the ribosome-nascent chain complex. To determine whether this chaperone is coregulated with ribosomal proteins, we studied the mRNA regulation of SSB under several environmental conditions. Ssb and the ribosomal protein rpL5 mRNAs were up-regulated upon carbon upshift and down-regulated upon amino acid limitation, unlike the mRNA of another cytosolic Hsp70, Ssa. Ribosomal protein and Ssb mRNAs, like many mRNAs, are down-regulated upon a rapid temperature upshift. The mRNA reduction of several ribosomal protein genes and Ssb was delayed by the presence of an allele, EXA3-1, of the gene encoding the heat shock factor (HSF). However, upon a heat shock the EXA3-1 mutation did not significantly alter the reduction in the mRNA levels of two genes encoding proteins unrelated to the translational apparatus. Analysis of gene fusions indicated that the transcribed region, but not the promoter of SSB, is sufficient for this HSF-dependent regulation. Our studies suggest that Ssb is regulated like a core component of the ribosome and that HSF is required for proper regulation of SSB and ribosomal mRNA after a temperature upshift.

Haematopoietic damage persists 1 year after autologous peripheral blood stem cell transplantation

In the present study we have used cell culture assays in order to assess the damage in the haematopoietic system 1 year after peripheral blood stem cell transplantation (PBSCT), and to establish at what level, haematopoietic progenitor cells (HPC) or stroma, this damage occurs. Thirty-one patients, nine breast cancer (BC), 17 non-Hodgkin lymphoma (NHL) and five Hodgkin disease (HD), who had received autologous PBSCT were included. Forty-eight normal subjects who had given informed consent were used as controls. Results were also compared with a matched group of patients (25 cases) prior to PBSCT. Progenitor cells were analysed using CFU-GM and plastic adherent delta (Pdelta) assays. Long-term bone marrow cultures (LTBMC) in one and two stages were established. One year after transplant both the number of committed progenitor cells and the CFU-GM production in LTBMC were significantly reduced in the three groups of patients when compared with controls (P < 0.05 or P < 0.01). Two-stage LTBMC experiments showed that the impairment in CFU-GM production was due to damage in both patients' stroma and haematopoietic progenitor cells (HPC). All patients, except those with HD, showed a decreased stromal layer confluence (P < 0.05), with significant differences in cell composition as compared to normal bone marrow (P = 0.001). When all these variables were compared with pretransplant results, we observed that stroma formation was significantly lower after PBSCT (P < 0.05), while the number of progenitor cells analysed by the Pdelta assay was significantly increased (P < 0.05). We can conclude that even 1 year after PBSCT, both the committed HPC and BM stroma remain damaged.

Rapid selection in modified BHK-21 cells of a foot-and-mouth disease virus variant showing alterations in cell tropism

With persistent foot-and-mouth disease virus (FMDV) in BHK-21 cells, there is coevolution of the cells and the resident virus; the virulence of the virus for the parental BHK-21 cells is gradually increased, and the cells become partially resistant to FMDV. Here we report that variants of FMDV C3Arg/85 were selected in a single infection of partially resistant BHK-21 cells (termed BHK-Rb cells). Indirect immunofluorescence showed that the BHK-Rb cell population was heterogeneous with regard to susceptibility to C3Arg/85 infection. Infection of BHK-Rb cells with C3Arg/85 resulted in an early phase of partial cytopathology which was followed at 6 to 10 days postinfection by the shedding of mutant FMDVs, termed C3-Rb. The selected C3-Rb variants showed increased virulence for BHK-21 cells, were able to overcome the resistance of modified BHK-21 cells to infection, and had acquired the ability to bind heparin and to infect wild-type Chinese hamster ovary (CHO) cells. A comparison of the genomic sequences of the parental and modified viruses revealed only two amino acid differences, located at the surface of the particle, at the fivefold axis of the viral capsid (Asp-9-->Ala in VP3 and either Gly-110-->Arg or His-108-->Arg in VP1). The same phenotypic and genotypic modifications occurred in a highly reproducible manner; they were seen in a number of independent infections of BHK-Rb cells with viral preparation C3Arg/85 or with clones derived from it. Neither amino acid substitutions in other structural or nonstructural proteins nor nucleotide substitutions in regulatory regions were found. These results prove that infection of partially permissive cells can promote the rapid selection of virus variants that show alterations in cell tropism and are highly virulent for the same cells.

Reduced mitochondrial DNA transcription in senescent rat heart

We studied the effect of senescence on mitochondrial DNA (mtDNA) transcription with an in organello system using intact isolated rat heart mitochondria. A comparison of the electrophoretic patterns of mtDNA transcription products in young, adult and senescent rats showed an age-related reduction in newly-synthesized mitochondrial RNAs that reflects a decrease in the synthesis rate. These results correlate with the enzyme activities of the oxidative phosphorylation complexes I and IV, that are partially encoded by the mitochondrial genome. In addition, an age-related increase in the protein carbonyl content of the mitochondrial membranes was observed in senescent mitochondria suggesting an accumulation of mitochondrial oxidative damage. This reduction in the mtDNA transcriptional rate in the heart of senescent animals suggests that this could be one of the molecular bases underlying senescence of the myocardium.

Homology modeling, model and software evaluation: three related resources

MOTIVATION

Homology modeling is rapidly becoming the method of choice for obtaining three-dimensional coordinates for proteins because genome projects produce sequences at a much higher rate than NMR and X-ray laboratories can solve the three-dimensional structures. The quality of protein models will not be immediately clear to novices and support with the evaluation seems to be needed. Expert users are sometimes interested in evaluating the quality of modeling programs rather than the quality of the models themselves.

RESULTS

Three servers have been made available to the scientific community: a homology modeling server, a model quality evaluation server and a server that evaluates models built of proteins for which the structure is already known, thereby implicitly evaluating the quality of the modeling program.

AVAILABILITY

The modeling-related servers and several structure analysis servers are freely available at http://swift.embl-heidelberg.de/servers/

CONTACT

gert.vriend@embl-heidelberg.de

Providing care in an infectious disease clinic. Why students volunteer

This qualitative study explores the motivations of dental students who volunteered as care providers for patients identified as carriers of infectious diseases. The study involved 12 students, seven 4th year and five 3rd year students who worked 1-2.5 days per week in an infectious disease clinic in a dental school in the northeastern United States. 4 faculty members who also volunteered their time in the clinic supervised the students. Personal interviews were conducted with each student to determine their reasons for volunteering and to explore the perceived significance of their experiences in the clinic. Internal validity was established through group interviews wherein responses during the personal interviews were discussed with the students. All 12 students were interested in Oral Medicine and all 4th year students had completed a course on HIV-AIDS for their selective requirement. Students expressed willingness to care for patients who are medically compromised in anticipation of an increase of this type of patients in their future practice. Previous exposure to a family member or friend or patients (non-dental) who were terminally ill or to patients with HIV was another common reason. All 12 students preferred to work in the infectious disease clinic more than in other school clinics. They felt that there was more faculty-student interaction and a more stimulating learning atmosphere that the faculty created. The students felt that the patients treated in the clinic were more appreciative. Students also claim they experienced more team spirit among their fellow students and staff and that the clinic atmosphere was more relaxed and less competitive. Students got the most satisfaction from helping patients who were perceived to have had problems in accessing care prior to their visit to the clinic. Results of the study show that the students volunteered to treat patients who are known to have infectious diseases such as HIV/AIDS because they find personal and academic satisfaction from working in a clinic which provides care to individuals with specific medical needs.

Social anxiety among adolescents: linkages with peer relations and friendships

This study examined the utility of modifying the Social Anxiety Scale for Children-Revised (SASC-R) for use with adolescents, and examined associations between adolescents' social anxiety (SA) and their peer relations, friendships, and social functioning. Boys (n = 101) and girls (n = 149) in the 10th through 12th grades completed the Social Anxiety Scale for Adolescents (SAS-A) and measures of social support, perceived competence, and number and quality of their best friendships. Factor analysis of the SAS-A confirmed a three-factor structure: Fear of Negative Evaluation, Social Avoidance and Distress in General, and Social Avoidance Specific to New Situations or Unfamiliar Peers. Girls reported more SA than boys, and SA was more strongly linked to girls' social functioning than boys'. Specifically, adolescents with higher levels of SA reported poorer social functioning (less support from classmates, less social acceptance), and girls with higher levels of SA reported fewer friendships, and less intimacy, companionship, and support in their close friendships. These findings extend work on the SASC-R to adolescents, and suggest the importance of SA for understanding the social functioning and close friendships of adolescents, especially girls.

The value of cell cultures for the diagnosis of mixed myelodysplastic/myeloproliferative disorders

BACKGROUND AND OBJECTIVE

Myelodysplastic syndromes (MDS) are a group of disorders characterized by dyshematopolesis in bone marrow (BM) and peripheral blood (PB) cytopenias. In recent years particular attention has been paid to myeloproliferative disorders with dysplastic features or myelodysplastic syndromes that evolve into a myeloproliferative disorder. The present study was designed to analyze patients with MDS but with a normal or increased colony forming capacity, in order to see whether or not cell cultures could contribute to the diagnosis of intermediate MDS-MPD conditions.

DESIGN AND METHODS

A total of 80 patients diagnosed as having MDS were included in the study. CFU-GM assay was performed by plating 1 x 10(5) mononuclear cells/mL in IMDM and 0.9% methyl-cellulose containing 10% PHA-LCM. In all cases cultures were run in parallel without PHA-LCM to assess autonomous growth. Cultures were incubated at 37 degrees C in a fully humidified atmosphere with 5% CO2 and scored at day 14. Cytogenetic analysis was performed according to standard procedures. Short-term cultures of 24 and/or 48 hours were used.

RESULTS

Twenty-two patients out of the 80 MDS cases included in the study showed a normal or increased cell growth pattern. Among these 22 patients, eight were diagnosed as suffering from chronic myelomonocytic leukemia (CMML) according to the FAB criteria and were excluded from the present analysis. The remaining 14 cases, which constitute the body of this study, displayed an increased number of clusters and/or colonies, with an altered cluster/colony ratio (anomalous growth) in 10 cases. Autonomous colony formation was present in five of these 14 cases and autonomous cluster growth was seen in all but three of them. In addition, one patient showed endogenous BFU-E growth. Morphological diagnoses were then revised due to this aberrant colony growth pattern: based on actual criteria, 3 patients could have been considered as having a-CML (atypical chronic myeloid leukemia). Another 6 cases evolved to a more proliferative disorder: 5 to CMML, and one to a-CML. Interestingly, in 3 of these 6 patients the evolution took place concomitantly with an infectious episode. In one additional patient the platelet count increased up to 1000 x 10(9)/L and required treatment with hydroxyurea.

INTERPRETATION AND CONCLUSIONS

Our results show that intermediate MDS-MPD cases are relatively common and that in vitro characteristics, i.e. high clonogenic capacity with a high cluster/colony ratio and scanty autonomous growth, in patients showing myelodysplastic features could contribute to an early diagnosis in these cases. It is possible that in some cases an infectious episode, through higher cytokine secretion, contributes to the development of these disorders.