SEARCH · PubMed Health

Results for “Copy Number Variations”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

1,691 records · Page 94Linked to original sources

PubMed2003

Apparent intrachromosomal exchange on the human Y chromosome explained by population history.

The human Y chromosome displays an unusual content of repetitive sequences. Y-chromosomal repeats are potential targets for intrachromosomal recombination, which is thought to be involved in a number of Y-associated defects, such as male infertility. Such rearrangements could potentially be investigated by the use of highly polymorphic DNA markers located within the repeat units, such as microsatellites. Here we analyse the two copies of the Y-chromosomal microsatellite DYS385, which we identified and localized to an approximately 190 kb duplicated and inverted fragment at Yq11.223. We found a highly significant correlation (r=0.853, P&<0.001) and a nonsignificant difference in a chi(2)-test (chi(2)=15.45, P>0.05) between the allele frequency distributions at both copies of the Y-STR in a German population sample (n=70). Such nearly identical allele frequency distribution between two copies of a duplicated highly polymorphic microsatellite cannot be explained by the independent mutational process that creates microsatellite alleles. Instead, this might be interpreted as evidence for a reciprocal intrachromosomal exchange process between the duplicated fragments. However, more detailed analyses using additional human populations as well as additional Y chromosome markers revealed that this phenomenon is highly population-specific and disappears completely when Y-STR diversity is analysed in association with two Y-SNP haplogroups. We found that the diversity of the two DYS385 loci (and other Y-STRs) is highly depending on the haplogroup background, and that equal proportions of both haplogroups in the German sample explains the nearly identical allele frequency distributions at the two DYS385 loci. Thus, we demonstrate here that allele frequency distributions at duplicate loci that are suggestive of intrachromosomal recombination can be explained solely by population history.

Chromosome Mapping↗

PubMed2026

RAS signaling in lung adenocarcinoma is defined by lineage context and DUSP4 loss.

BACKGROUNDThe molecular landscape of lung adenocarcinoma (LUAD) is often illustrated as a driver-oncogene pie chart, but identical mutations exhibit heterogeneous signaling shaped by comutations, transcriptional programs, and lineage context. We propose a lineage-integrated signaling framework using an EGFR mutation signature (mSig).METHODSWe defined EGFR mSig using differentially expressed genes in EGFR-mutant (EGFR-mt) LUADs. Semisupervised clustering and machine learning models were used to test reproducibility in different combinations of datasets. We analyzed molecular subtypes, lineage markers, co-occurring mutations, and EGFR copy number alterations in EGFR mSig-defined subtypes of LUAD.RESULTSEGFR mSig showed robust classification performance (area under receiver operating characteristic curve = 0.83-0.95; mean negative predictive value = 96.3%). Validated gene expression subtypes and lung lineage markers were closely aligned with EGFR mSig status. Most EGFR mSig+ tumors, including many without EGFR mutations, belonged to the bronchioid subtype. A subset of canonical RAS mutations were mSig+ and mirrored the EGFR mutation pattern. EGFR WT/mSig- tumors were enriched for nonbronchioid subtypes and had comutations in TP53 or RAS/RAF/RTKs. We highlight a parsimonious collection of coordinated mutations, including RAS, KEAP1, STK11, TP53, and CDKN2A, that taken together suggest coordination of tumor signaling previously suggested but now reproduced and expanded.CONCLUSIONA potentially novel EGFR mSig that captures the transcriptional footprint of EGFR activation revealed a subset of EGFR WT LUADs with mt-like features. mSig refines LUAD taxonomy beyond mutation-only pie-chart models by incorporating lineage and comutation context. Lineage-directed stratification with coalteration identifies clinically relevant groups across EGFR and RAS states and highlights treatment opportunities for patients currently considered oncogene-negative.FUNDINGNational Cancer Institute (NCI) U01CA272541, R01CA262296, U24CA264021, UG1CA233333, R01CA211939.

Humans↗

PubMed1994

Genomic organization of the canrep repetitive DNA in Brassica juncea.

Canrep is a heterogeneous, tandemly repeated, 176 bp nucleotide sequence that contains a single Hind III site and is present in high copy numbers in the genomes of many Brassica species. Complete clusters of repeats of this DNA were cloned from the nuclear DNA of Brassica juncea. Restriction-fragment dimers and higher multimers of the 176 bp sequence have arisen by mutations within the Hind III recognition sequence. Adjacent repeats from within the same cluster usually have different nucleotide sequences with features indicating that diversity is generated by a mechanism that causes site-specific base substitutions. While most of the units of canrep DNA are clustered in long arrays of tandem repeats, some are dispersed throughout the genome as isolated copies or in small clusters. Regardless of the size of the arrays, each cluster begins and ends with a variable-length, truncated repeat and is flanked by inverted copies of the sequence 5'-ATCTCAT3'-, which is not part of the basic sequence of the canrep family of DNAs. Furthermore, some clusters are located close to nucleotide sequences related to those of known plant transposons. Thus, canrep elements may be dispersed by transposition. There are two distinct subfamilies of canrep sequences in B. juncea, and one of these is closely related to one of the two subfamilies of this type of DNA from B. napus, indicating that it originated from B. campestris, the common diploid ancestor of both amphidiploid species. Neither the repetitive DNA nor nucleotide sequences flanking canrep clusters are transcribed in seedlings, suggesting that even small arrays of repeats are located in heterochromatic regions and might be involved in chromatin condensation and/or chromosome segregation.

Base Sequence↗

PubMed2002

Preferential expression of a mutant allele of the amplified MDR1 (ABCB1) gene in drug-resistant variants of a human sarcoma.

Activation of the MDR1 (ABCB1) gene is a common event conferring multidrug resistance (MDR) in human cancers. We investigated MDR1 activation in MDR variants of a human sarcoma line, some of which express a mutant MDR1, which facilitated the study of allelic gene expression. Structural alterations of MDR1, gene copy numbers, and allelic expression were analyzed by cytogenetic karyotyping, oligonucleotide hybridization, Southern blotting, polymerase chain reaction, and DNA heteroduplex assays. Both chromosome 7 alterations and several cytogenetic changes involving the 7q21 locus are associated with the development of MDR in these sarcoma cells. Multistep-selected cells and their revertants contain three- to six-fold MDR1 gene amplification compared with that of the drug-sensitive parental cell line MES-SA and single-step doxorubicin-selected mutants. MDR1 gene amplification precedes the emergence of a mutant allele in cells that were coselected with doxorubicin and a cyclosporin inhibitor of P-glycoprotein (P-gp). Allele-specific oligonucleotide hybridization showed that the endogenous mutant allele was present as a single copy, with multiple copies of the normal allele. Reselection of revertant cells with doxorubicin in either the presence or the absence of the P-gp inhibitor resulted in exclusive reexpression of the mutant MDR1 allele, regardless of the presence of multiple wild-type MDR1 alleles. These data provide new insights into how multiple alleles are regulated in the amplicon of drug-resistant cancer cells and indicate that increased expression of an amplified gene can result from selective transcription of a single mutant allele of the gene.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2006

Comparison of the epidermal growth factor receptor gene and protein in primary non-small-cell-lung cancer and metastatic sites: implications for treatment with EGFR-inhibitors.

BACKGROUND: Very recent studies have suggested that EGFR gene copy number and expression obtained by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) should be used to predict which lung cancer patients are expected to respond to anti-EGFR treatments. However, it is still not known whether EGFR expression differs in metastases compared to primary non-small cell lung cancer (NSCLC). PATIENTS AND METHODS: EGFR status was analysed by IHC and FISH on tumor samples of primary NSCLC and at least one distant metastatic lesion in 30 patients. RESULTS: Ten cases (33.3%) showed primary tumor/metastasis discordance by IHC analysis (n = 30): in seven cases, EGFR was expressed in the primary tumor but not in the metastasis, while three samples showed EGFR expression in the metastasis but not in the primary tumor (Pearson correlation coefficient = 0.331, P = 0.0074). By FISH (n = 26), seven (27%) cases were discordant: six cases showed a high-level of EGFR polysomy in the primary tumor but not in the metastasis and one case showed a high-level of EGFR polysomy in the metastasis but not in the primary sample (Pearson correlation coefficient = 0.52, P = 0.007). CONCLUSION: EGFR expression is not stable during metastatic progression in a significant proportion of NSCLC. These findings have to be considered in future prospective studies.

Adult↗

PubMed1994

Molecular characterization of the outer capsid spike protein (VP4) gene from human group C rotavirus.

A cDNA copy of the third genomic RNA segment of a noncultivatable human group C rotavirus (Bristol) was generated by single primer amplification. Human group C rotavirus genome segment 3 contains 2283 bp and encodes the VP4 gene with an open reading frame of 2232 nucleotides (744 amino acids) starting at nucleotide 21 and terminating at nucleotide 2251. PCR primers designed from the 5' and 3' terminal sequences of the C/Bristol VP4 gene were used to amplify the corresponding VP4 gene of a human group C rotavirus from Belém, Brazil. Nucleotide sequence comparisons of the Bristol and Belém VP4 genes revealed 45 differences of which only 6 were predicted to give amino acid changes. Alignment of the two human VP4 sequences with the prototype porcine group C/Cowden rotavirus VP4 showed only 71.2% nucleotide sequence identity. Protein sequence alignments showed that the human group C rotavirus VP4 sequences were 8 amino acids longer than the porcine VP4 sequence with an insertion of 6 amino acids, 252NSKLGD257 adjacent to the proposed proteolytic cleavage region (amino acids 231-250). The large overall number of differences between the human and porcine VP4 sequences strongly suggested that the porcine C/Cowden isolate may belong to a different group C rotavirus P "serotype." In contrast the very close similarity of the VP4 sequences of the UK and Brazilian group C rotaviruses support the hypothesis that these human isolates originate from a recent common ancestor.

Amino Acid Sequence↗

PubMed2003

Patterns of point mutations associated with antiretroviral drug treatment failure in CRF01_AE (subtype E) infection differ from subtype B infection.

An increasing number of HIV-1-infected patients living in developing countries now have access to antiretroviral drugs. Information regarding the drug-resistant mutations of non-B subtype HIV-1 remains limited, however. The authors cross-sectionally compared patterns of the drug-resistant point mutations in patients infected with either subtype B or CRF01_AE (subtype E) among patients who acquired HIV by sexual transmission in Japan. Protease sequence data were available from 216 patients with a detectable level of RNA copies in plasma. Based on phylogenetic analysis of the protease and the C2V3 regions, 162 subtype B and 45 CRF01_AE cases were identified; 82 subtype B and 24 CRF01_AE patients had a treatment failure with nucleoside reverse transcriptase inhibitors; and 69 subtype B and 19 CRF01_AE patients had a treatment failure with a protease inhibitor. Antiretroviral drug history was similar in subtype B-infected and CRF01_AE-infected patients. The mutations T69N and V75M in reverse transcriptase and L10F, K20I, L33I, and N88S in protease were seen more frequently in patients infected with CRF01_AE than in patients with subtype B. The mutations, D30N, A71V, and N88D were found exclusively in patients with subtype B. Most of the characteristic mutation patterns were associated with a history of receiving nelfinavir. The pattern of drug resistance mutations differs between the subtypes. Data derived from subtype B drug-resistant genotypes may not always be applicable to non-B subtypes.

Adult↗

PubMed2005

New insights into the nature and phylogeny of prasinophyte antenna proteins: Ostreococcus tauri, a case study.

The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b-binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c-like pigment (Mg-2,4-divinyl-phaeoporphyrin a5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI)- and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b-containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components.

Amino Acid Sequence↗

PubMed2003

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications.

BACKGROUND: Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. METHODS: In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. RESULTS: MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. CONCLUSIONS: The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved in a node like pattern, rather than according to a linear progression model. Due to their capacity to undergo rapid genetic changes MCF-7 cells could represent an interesting model for genetic evolution of breast tumors.

Breast Neoplasms↗

PubMed1996

Mutational analysis and properties of the msbA gene of Escherichia coli, coding for an essential ABC family transporter.

The htrB gene was discovered because its insertional inactivation interfered with Escherichia coli growth and viability at temperatures above 32.5 degrees C, as a result of accumulation of phospholipids. The msbA gene was originally discovered because when cloned on a low-copy-number plasmid vector it was able to suppress the temperature-sensitive growth phenotype of an htrB null mutant as well as the accumulation of phospholipids. The msbA gene product belongs to the superfamily of ABC transporters, a universally conserved family of proteins characterized by a highly conserved ATP-binding domain. The msbA gene is essential for bacterial viability at all temperatures. In order to understand the physiological role of the MsbA protein, we mutated the ATP-binding domain using random PCR mutagenesis. Six independent mutants were isolated and characterized. Four of these mutations resulted in single-amino-acid substitutions in non-conserved residues and were able to support cell growth at 30 degrees C but not at 43 degrees C. The remaining two mutations behaved as recessive lethals, and resulted in single-amino-acid substitutions in Walker motif B, one of the two highly conserved regions of the ATP-binding domain. Despite the fact that neither of these two mutant proteins can support E. coli growth, they both retained the ability to bind ATP in vitro. In addition, we present evidence to show that N-acetyl [3H]-glucosamine, a precursor of lipopolysaccharides, accumulates at the non-permissive temperature in the inner membrane of either htrB null or msbA conditional lethal strains. Translocation of the precursor to the outer membrane is restored by transformation with a plasmid containing the wild-type msbA gene. A possible role for MsbA as a translocator of lipopolysaccharides or its precursors is discussed.

ATP-Binding Cassette Transporters↗

PubMed2004

Evaluation of a wavelet-based computer-assisted detection system for identifying microcalcifications in digital full-field mammography.

PURPOSE: To evaluate a new wavelet-based computer-assisted detection (CAD) system for detecting and enhancing microcalcifications. MATERIAL AND METHODS: A total of 280 mammograms acquired by full-field digital mammography (Senographe 2000D; G.E. Medical Systems Milwaukee, Wisc., USA) were analyzed with and without a new wavelet-based CAD system for detecting and enhancing microcalcifications. The mammograms comprised roughly equal numbers of cases from each of the BIRADS (Breast Imaging, Reporting and Data System, according to the American College of Roentgenology) categories 1-5. Histologic confirmation was available for all of the 180 cases assigned BIRADS categories 3-5. Four readers interpreted all 280 images for suspicious microcalcifications using a scale of 1-5. The readers alternately assessed 5 images with and 5 without CAD. In a second reading immediately following the first, the readers had to reassess the 280 mammograms. The images that had already been interpreted without CAD were now presented with CAD and vice versa. The images were interpreted as soft copies on a diagnostic mammography workstation (Image Diagnost GmbH, Neufahrn/Munich, Germany). All images interpreted with CAD were presented with enhancement of microcalcifications by wavelet algorithms and prompting of microcalcifications. ROC (receiver operating characteristic) analyses were performed, and image interpretation time with and without CAD was measured. RESULTS: The overall time for interpretation required by all 4 readers together was 483 min with CAD compared to 580 min without CAD. ROC analysis revealed no significant advantage of CAD for the individual readers. Readers 3 (0.811/0.817) and 4 (0.799/0.843) had a slightly improved AUC (area under the curve) with CAD. Readers 1 and 2 had a slightly lower AUC with CAD (0.832 versus 0.861 and 0.818 versus 0.849). CONCLUSION: The CAD system significantly (P<0.05, t test) speeded up image interpretation with respect to the identification of microcalcifications, while the diagnostic quality remained almost identical under the study conditions.

Breast Diseases↗

PubMed1996

Severe head injury in the United Kingdom and Ireland: a survey of practice and implications for management.

OBJECTIVE: To study the current intensive care management of patients with severe head injury (defined as a Glasgow Coma Scale score of < or = 8) in neurosurgical referral centers in the United Kingdom (UK) and ireland. DATA COLLECTION: A questionnaire was sent to the directors of the 44 neurosurgical referral units identified from the UK Medical Directory. After 4 wks, a copy of the questionnaire was sent to all nonresponders, with a cover letter urging them to respond. The aim was to collect data regarding the characteristics of the intensive care units (ICU), sedation, monitoring modalities used, the treatment of intracranial hypertension, and general care of severely head-injured patients. DATA EXTRACTION: Forty completed questionnaires were returned. Only 35 (88%) centers provided care for the severely head-injured as defined in the questionnaire. Patients were managed in specialized neurosurgical ICUs in 66% of centers and in general ICUs in the remainder of the centers. The ICUs were coordinated by an anesthesiologist in 66% of instances and by a neurosurgeon in 23%. The mean number of beds per units was 7.9 (range 4 to 16), with 1:1 nurse/bed ratio and 5.5 nurses per bed (total number of nursing staff per bed) (range 2.75 to 8). Annual caseload varied between units with the majority of units (49%) receiving between 25 and 50 patients with severe head injury, 23% receiving between 50 and 100 patients with severe head injury, and 29% receiving > 100 patients with severe head injury. There was considerable variability in both the nature of monitoring and therapy between centers. Although blood and central venous pressures were invasively monitored in > 50% of the patients in 94% and 77% of the centers, respectively, intracranial pressure was only monitored routinely in 57% of the centers. Jugular venous bulb oximetry, transcranial Doppler ultrasonography, electroencephalography, and near-infrared spectroscopy were rarely used. Nearly all centers used propofol and midazolam for sedation, with morphine, fentanyl, and alfentanil as the main analgesics. Muscle relaxation was commonly used, with 40% of the centers employing it in 100% of their patients. Atracurium and vecuronium were the most commonly used agents. Only 68% of the centers had a protocol for the treatment of intracranial hypertension. Although hyperventilation to a Paco2 of 26 to 30 torr (3.5 to 4.0 kPa) was the norm in the majority of centers (56%), two centers aimed for Paco2 values < 26 torr (< 3.5 kPa). A quarter of the units did not aim for a cerebral perfusion pressure of > 60 mm Hg. Mild hypothermia was rarely used and 14% of the centers continued to use corticosteroids for the treatment of intracranial hypertension as a result of head trauma. CONCLUSION: We conclude that there are wide variations in the management of the severely head-injured patient in the UK and Ireland. Some of the therapies employed are not supported by available research findings. Rationalization (using rational management, i.e., based on good evidence) of the intensive care management of severe head injury with the development of widely accepted guidelines may result in an improvement in the quality of care of the head-injured patient.

Brain Injuries↗

PubMed1999

Expression of OVCA1, a candidate tumor suppressor, is reduced in tumors and inhibits growth of ovarian cancer cells.

Loss of all or part of one copy of chromosome 17p is very common in ovarian and breast tumors. OVCA1 is a candidate tumor suppressor gene mapping to a highly conserved region on chromosome 17p13.3 that shows frequent loss of heterozygosity in breast and ovarian carcinomas. Western blot analysis of extracts prepared from breast and ovarian carcinomas revealed reduced expression of OVCA1 compared with extracts from normal epithelial cells from these tissues. Subcellular localization studies indicate that OVCA1 is localized to punctate bodies scattered throughout the cell but is primarily clustered around the nucleus. Attempts to create cell lines that stably expressed OVCA1 from the cytomegalovirus promoter were generally unsuccessful in a variety of different cell lines. This reduction of colony formation was quantified in the ovarian cancer cell line A2780, where it was demonstrated that cells transfected with plasmids expressing OVCA1 had a 50-60% reduction in colony number as compared with appropriate controls, and only a few of these clones expressed OVCA1, albeit at low levels. The clones that expressed exogenous OVCA1 were found to have dramatically reduced rates of proliferation. Reduced growth rates correlated with an increased proportion of the cells in the G1 fraction of the cell cycle compared with the parental cell line and decreased levels of cyclin D1. The low levels of cyclin D1 appeared to be caused by an accelerated rate of cyclin D1 degradation. Overexpression of cyclin D1 was able to override OVCA1's suppression of clonal outgrowth. These results suggest that slight alterations in the level of OVCA1, such as would occur after reduction of chromosome 17p13.13 to hemizygosity, may result in cell cycle deregulation and promote tumorigenesis.

Amino Acid Substitution↗

PubMed1994

In vivo distribution and cytopathology of variants of human immunodeficiency virus type 1 showing restricted sequence variability in the V3 loop.

The distribution, cell tropism, and cytopathology in vivo of human immunodeficiency virus (HIV) was investigated in postmortem tissue samples from a series of HIV-infected individuals who died either of complications associated with AIDS or for unrelated reasons while they were asymptomatic. Proviral sequences were detected at a high copy number in lymphoid tissue of both presymptomatic patients and patients with AIDS, whereas significant infection of nonlymphoid tissue such as that from brains, spinal cords, and lungs were confined to those with AIDS. V3 loop sequences from both groups showed highly restricted sequence variability and a low overall positive charge of the encoded amino acid sequence compared with those of standard laboratory isolates of HIV type 1 (HIV-1). The low charge and the restriction in sequence variability were comparable to those observed with isolates showing a non-syncytium-inducing (NSI) and macrophage-tropic phenotype in vitro. All patients were either exclusively infected (six of seven cases) or predominantly infected (one case) with variants with a predicted NSI/macrophage-tropic phenotype, irrespective of the degree of disease progression. p24 antigen was detected by immunocytochemical staining of paraffin-fixed sections in the germinal centers within lymphoid tissue, although little or no antigen was found in areas of lymph node or spleen containing T lymphocytes from either presymptomatic patients or patients with AIDS. The predominant p24 antigen-expressing cells in the lungs and brains of the patients with AIDS were macrophages and microglia (in brains), frequently forming multinucleated giant cells (syncytia) even though the V3 loop sequences of these variants resembled those of NSI isolates in vitro. These studies indicate that lack of syncytium-forming ability in established T-cell lines does not necessarily predict syncytium-forming ability in primary target cells in vivo. Furthermore, variants of HIV with V3 sequences characteristic of NSI/macrophage-tropic isolates form the predominant population in a range of lymphoid and nonlymphoid tissues in vivo, even in patients with AIDS.

Acquired Immunodeficiency Syndrome↗

PubMed2006

Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis.

Gene duplication provides a window of opportunity for biological variants to persist under the protection of a co-expressed copy with similar or redundant function. Duplication catalyzes innovation (neofunctionalization), subfunction degeneration (subfunctionalization), and genetic buffering (redundancy), and the genetic survival of each paralog is triggered by mechanisms that add, compromise, or do not alter protein function. We tested the applicability of three types of mechanisms for promoting the retained expression of duplicated genes in 290 expressed paralogs of the tetraploid clawed frog, Xenopus laevis. Tests were based on explicit expectations concerning the ka/ks ratio, and the number and location of nonsynonymous substitutions after duplication. Functional constraints on the majority of paralogs are not significantly different from a singleton ortholog. However, we recover strong support that some of them have an asymmetric rate of nonsynonymous substitution: 6% match predictions of the neofunctionalization hypothesis in that (1) each paralog accumulated nonsynonymous substitutions at a significantly different rate and (2) the one that evolves faster has a higher ka/ks ratio than the other paralog and than a singleton ortholog. Fewer paralogs (3%) exhibit a complementary pattern of substitution at the protein level that is predicted by enhancement or degradation of different functional domains, and the remaining 13% have a higher average ka/ks ratio in both paralogs that is consistent with altered functional constraints, diversifying selection, or activity-reducing mutations after duplication. We estimate that these paralogs have been retained since they originated by genome duplication between 21 and 41 million years ago. Multiple mechanisms operate to promote the retained expression of duplicates in the same genome, in genes in the same functional class, over the same period of time following duplication, and sometimes in the same pair of paralogs. None of these paralogs are superfluous; degradation or enhancement of different protein subfunctions and neofunctionalization are plausible hypotheses for the retained expression of some of them. Evolution of most X. laevis paralogs, however, is consistent with retained expression via mechanisms that do not radically alter functional constraints, such as selection to preserve post-duplication stoichiometry or temporal, quantitative, or spatial subfunctionalization.

Amino Acid Substitution↗

PubMed2003

Molecular characterization and Austrian Caucasian population data of the multi-copy Y-chromosomal STR DYS464.

DYS464 is a multi-copy STR system with four positions on the Y-chromosome (DYS464a, b, c, and d) which was recently identified and characterized [Forensic Sci. Int. 130 (2002) 97]. The aims of our study were to perform a population study, to estimate the mutation rate and an extensive sequence analysis in order to confirm the nomenclature. Fourteen different alleles were found in an Austrian population sample with an allele length varying from 9 to 19 repeats. All alleles were cloned and sequenced. Alleles 9-19 showed the general repeat structure (CCTT)n...(CCTT)2...(CCTT)3...(CCTT)4...(CCTT)2...(CCTT)2. The nomenclature is based on the number of repeated units of the variable (CCTT)n-stretch only. In 13% of the samples intermediate alleles, namely 14.3A, 14.3B and 15.3 were detected. In these alleles the variable repeat block is interrupted by a CTT motif (14.3A: (CCTT)3CTT(CCTT)11; 14.3B and 15.3: (CCTT)7CTT(CCTT)7/8). A comparison with GenBank entries revealed the existence of a length variant due to a deletion of one cytosine in the 5' flanking region of the first repeat block. We designed an alternative forward primer to circumvent possible ambiguities in the allele designation. A total of 54 different genotypes were identified in 135 men corresponding to a discrimination capacity (DC) of 40% and a gene diversity (GD) of 0.97. These values are much higher than those of other Y-chromosomal short tandem repeats (Y-STRs). DYS464 has the same haplotype diversity (HD) as the combination of the five Y-STR loci with the lowest gene diversities of the Y-STR core set. On the other hand, a combination of the three most diverse loci (DYS464, DYS385 and DYS390) has the same capacity to distinguish between paternal lineages than the complete minimal haplotype (minHT) consisting of eight Y-STR loci. In our population sample the addition of DYS464 to the minHT increases the number of different haplotypes from 110 to 122. The mutation-rate estimate based on the 70 meioses analyzed amounts to 2.86 x 10(-2) (95% confidence interval 3.5 x 10(-3) to 9.95 x 10(-2)). This value is approximately 10 times higher than the average mutation-rate estimate for Y-STRs.

Alleles↗

PubMed2002

Fusion of vestibular and podokinesthetic information during self-turning towards instructed targets.

When observers step about their vertical axis ("active turning") without vision they dispose of essentially two sources of information that can tell them by how much they have turned: the vestibular cue which reflects head rotation in space and the "podokinesthetic" cue, a compound of leg proprioceptive afferents and efference copy signals which reflects the observer's motion relative to his support. We ask how these two cues are fused in the process leading to the perception of self-displacement during active turning. To this end we compared the performance of observers in three angular navigation tasks which differed with regard to the number and type of available motion cues: (1) Passive rotation, vestibular cue ( ves) only; observers are standing on a platform which is being rotated. (2) Treadmill stepping, podokinesthetic cue ( pod) only; observers step counter to the rotating platform so as to remain stable in space. (3) Active turning, ves and pod available; observers step around on the stationary platform. In all three tasks, angular velocity varied from trial to trial (15, 30, 60 degrees /s) but was constant during trials. Perception was probed by having the observers signal when they thought to have reached a previously instructed angular displacement, either in space or relative to the platform ("target"; range 60-1080 degrees ). Performance was quantified in terms of the targeting gain (displacement reached by the observer divided by target angle) and of the random error ( E(r)), which records an observer's deviation during single trials from his average performance. Confirming previous observations, E(r) was found to be significantly smaller during active turning than during passive turning, and we now complement these observations by showing that it is also significantly smaller than during treadmill stepping. This behaviour of E(r) is compatible with the idea that ves and pod be averaged during active turning. On the other hand, the observed characteristics of the targeting gain ( G(T)) support this idea only for the case of fast rotations (60 degrees /s); at lower velocities, the gain found during active turning was clearly not the average of the G(T) values recorded in the passive and the treadmill modes. We therefore also discuss alternative scenarios as to how ves and pod could interact, among these one based on the concept of a vestibular eigenmodel. A common denominator of these scenarios is that ves assumes the role of a prerequisite for an optimal use of pod during turning on a stationary support, without itself entering the calculation of displacement perception; this perception would be based exclusively on pod. Finally, it was a consistent observation that during passive rotations cognitive mechanisms fill in for the decaying vestibular signal in the context of the present navigation task, enabling observers to achieve large displacements surprisingly well although the duration of these movements exceeds by far the conventionally cited value of the central vestibular time constant (=20 s).

Adolescent↗