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At least 883 records · Page 49Linked to original sources
PubMed2004

Genetic variation in a compound short tandem repeat/Alu haplotype system at the SB19.3 locus: properties and interpretation.

The genetic variation at a compound nonrecombining haplotype system, consisting of the previously reported SB19.3 Alu insertion polymorphism and a newly identified adjacent short tandem repeat (STR), was studied in population samples from Portugal and São Tomé (Gulf of Guinea, West Africa). Age estimates based on the linked microsatellite variation suggest that the Alu insertion occurred about 190,000 years ago. In accordance with the global patterns of distribution of human genetic variation, the highest haplotype diversity was found in the African sample. This excess in African diversity was due to both a substantial reduction in heterozygosity at the Alu polymorphism and a lower STR variability associated with the predominant Alu insertion allele in the Portuguese sample. The high level of interpopulation differentiation observed at the Alu locus (F(ST) = 0.43) was interpreted under alternative selective and demographic scenarios. The need for compatibility between patterns of variation at the STR and Alu loci could be used to restrict the range of selection coefficients in selection-driven genetic hitchhiking frameworks and to favor demographic scenarios dominated by larger pre-expansion African population sizes. Taken together, the data show that the SB19.3 Alu-STR system is an informative marker that can be included in more extended batteries of compound haplotypes used in human evolutionary studies.

Africa, Western↗
PubMed2004

Intra- and intercontinental molecular variability of an Alu insertion in the 3' untranslated region of the LDLR gene.

One-hundred three individuals from two Mongolian, two Siberian, and ten native American populations were studied in relation to a 340-bp sequence from an Alu insertion located in the 3' untranslated region of the LDLR gene. Seven haplotypes have been determined, and haplotype B1 was the most common, accounting for about half the sequences found. In general, diversity values are quite high, about 2.5 times higher than those found in other autosomal Alu sequences. Almost all (93%) of the variability occurs at the intrapopulation level, but the greatest among-group differentiation (6-8%) was found when we grouped in a single population all Native Americans plus Siberian Eskimos and Chukchi and compared them with Mongolians. This result is compatible with earlier mtDNA and Y-chromosome suggestions of a single origin for the first colonizers of the American continent. With this nuclear locus it was not possible to broadly distinguish between Central and South American natives. No evidence of selection or marked demographic changes was obtained with these data.

3' Untranslated Regions↗
PubMed2004

A novel tetrameric short tandem repeat located in the 3' flanking region of the human ABO-secretor gene (FUT2) and association between FUT2 and FUT2/01 loci.

We found a novel polymorphic short tandem repeat (FUT2/01), 3.8 kb downstream of the coding region of FUT2. Seventeen length and 33 sequence variants were identified in 300 individuals representing three major human populations. Africans (Xhosa) and Europeans were characterized by high microvariation, and Japanese were characterized by a simple repeat structure. All exhibited high haplotype diversity.

ABO Blood-Group System↗
PubMed2005

Polymorphic Alu insertions and genetic diversity among African populations.

Thorough assessment of modern genetic diversity and interpopulation affinities within the African continent is essential for understanding the processes that have been at work during the course of worldwide human evolution. Regardless of whether autosomal, Y-chromosome, or mtDNA markers are used, allele- or haplotype-frequency data from African populations are necessary in setting the framework for the construction of global population phylogenies. In the present study we analyze genetic differentiation and population structure in a data set of nine African populations using 12 polymorphic Alu insertions (PAls). Furthermore, to place our findings within a global context, we also examined an equal number of non-African groups. Frequency data from 456 individuals presented for the first time in this work plus additional data obtained from the literature indicate an overall pattern of higher intrapopulation diversity in sub-Saharan populations than in northern Africa, a prominent differentiation between these two locations, an appreciably high degree of transcontinental admixture in Egypt, and significant discontinuity between Morocco and the Iberian peninsula. Moreover, the topologies of our phylogenetic analyses suggest that out of the studied sub-Saharan groups, the southern Bantu population of Sotho/ Tswana presents the highest level of antiquity, perhaps as a result of ancestral or acquired Khoisan genetic signals. Close affinities of eastern sub-Saharan populations with Egypt in the phylogenetic trees may indicate the existence of gene flow along the Nile River.

Africa South of the Sahara↗
PubMed2003

Telomerase accelerates osteogenesis of bone marrow stromal stem cells by upregulation of CBFA1, osterix, and osteocalcin.

Telomerase activity can prevent telomere shortening and replicative senescence in human somatic cells. We and others have previously demonstrated that forced expression of telomerase in human bone marrow stromal stem cells (BMSSCs) was able to extend their life-span and enhance their bone-forming capability, without inducing malignant transformation. In this study, we determined that telomerase was able to accelerate calcium accumulation of human BMSSCs under osteogenic inductive conditions. Similarly, xenogeneic transplantation of telomerase-expressing BMSSCs (BMSSC-Ts) yielded ectopic bone formation at 2 weeks post-transplantation, 2-4 weeks earlier than typically seen with BMSSCs transfected with empty vector (BMSSC-Cs). Low-density DNA array analysis revealed that telomerase activity increases the expression of G1 regulating genes including cyclin D3, cyclin E1, E2F-4, and DP2, associated with hyperphosphorylation of retinoblastoma (pRb), leading to the extended proliferative capacity of BMSSC-Ts. Importantly, BMSSC-T transplants showed a higher number of human osteogenic cells at 8 weeks post transplantation compared with the BMSSC-C transplants, coupled with a significantly increased osteogenic capacity. One possible mechanism leading to accelerated osteogenesis by BMSSC-Ts may be attributed, at least in part, to the upregulation of the important osteogenic genes such as CBFA1, osterix, and osteocalcin in vitro. Taken together, these findings show that telomerase can accelerate cell cycle progression from G1-to-S phase and enhance osteogenic differentiation of BMSSCs, because of the upregulation of CBFA1, osterix, and osteocalcin.

Alu Elements↗
PubMed2005

Quantification of HFV-integrated DNA in human cells by Alu-LTR real-time PCR.

Integration is described as a key step in viral replication of all retroviruses. A sensitive and quantitative measure of an integrated molecule is a good way to examine the importance of the integration step and to evaluate efficiency of retroviral vectors for gene transfer or anti-integrase drugs. Here, we report a sensitive and quantitative real-time polymerase chain reaction (PCR) technique to measure integrated viral DNA in human cells during a foamy virus (HFV) infection. This technique is based on two steps of PCR. The first round amplifies Alu-LTR (long terminal repeat) sequences resulting from viral integration. The second round of PCR is performed to quantify these events of integration. Quantification is monitored by the comparison of the amplification curve of the sample against a standard scale constituted of viral DNA from chronically infected cells. Sensitivity of this technique allows us to detect as few as 25 copies of HFV-integrated DNA in 50,000 cells.

Alu Elements↗
PubMed1999

New insights into signal recognition and elongation arrest activities of the signal recognition particle.

The signal recognition particle (SRP), a ubiquitous cytoplasmic ribonucleoprotein particle, plays an essential role in promoting co-translational translocation of proteins into the endoplasmic reticulum. Here, we summarise recent progress made in the understanding of two essential SRP functions: the signal recognition function, which ensures the specificity, and the elongation arrest function, which increases the efficiency of translocation. Our discussion is based on functional data as well as on atomic structure information, both of which also support the notion that SRP is a very ancient particle closely related to ribosomes. Based on the significant increase of knowledge that has been accumulating on the structure of elongation factors and on their interactions with the ribosome, we speculate about a possible mechanism of the elongation arrest function.

Alu Elements↗
PubMed2004

TaqMan-based quantification of invasive cells in the chick embryo metastasis assay.

The chick embryonic metastasis (CEM) assay is a fast in vivo method to investigate the invasive properties of tumor cells. Until now, most quantification methods were semiquantitative and time-consuming. Here we describe a rapid quantification method using TaqMan technology to quantify the invaded tumor cells in the chorioallantoic membrane of fertilized eggs. This method is based on specific detection of human ALU sequences. Moreover, it provides high sensitivity over a wide linearity range.

Alu Elements↗
PubMed1990

Cytoskeletal messenger RNA stability in human neocortex: studies in normal aging and in Alzheimer's disease.

Total RNA was extracted from human brain temporal and parietotemporal neocortical grey matter with postmortem intervals (PMI) of up to 13.5 hours. The integrity and rank abundance of heterogeneous nuclear RNA (HnRNA) and messenger RNA (mRNA) were analyzed by Northern gel dot blot hybridization with specific cloned probes of neurobiological interest: the RNA messages for four cytoskeletal components including glial fibrillary acidic protein (GFAP), alpha-tubulin, beta-actin and the human neurofilament light chain (HNF-L) genomic sequence, the Alu repetitive element, the scrapie prion PrP DNA probe and the chromatin condensing agent linker histone H1(0) genomic probe. Our observations indicate that for the cytoskeletal RNA messages studied here: (1) short postmortem intervals (of up to 4.5 hours) had only small effects upon RNA quality in these neocortices, (2) GFAP and HNF-L transcripts were represented at relatively high levels in the cerebral neocortex and (3) each RNA species in normal human brain had both unique and characteristic intracellular levels of abundance and decay kinetics. In the pathological condition, Alzheimer's disease (AD), cells of the temporal and parietotemporal neocortices of afflicted brains showed selective reductions in cytoskeletal RNA pool size which are not attributable to RNA transcript stability.

Adult↗
PubMed2001

Molecular cloning and sequence analysis of a human untranslated Alu-containing RNA.

A cDNA, designated LNX1, has been identified by subtractive hybridization on the basis that it is expressed in normal human prostate but not in LNCaP cells. Sequence analysis revealed that it contained two Alu repetitive sequences but no long open reading frame. Hence, it belongs to a class of untranslated Alu-containing RNAs. LNX1 is expressed in most tissues. It is encoded by a single copy gene, which is localized on human chromosome 14.

Alu Elements↗
PubMed1992

Sequencing and analysis of genomic fragments from the NF1 locus.

The sequence of five non-contiguous genomic fragments encompassing 14.4 kilobases from the NF1 locus have been determined by fluorescence-based automated DNA sequence analysis. These fragments included one kilobase of the NF1 coding region, which resulted in the identification of the intron/exon boundaries of five exons. Based on these sequences, five new NF1 exon-PCR assays have been developed, that could be useful for detecting new NF1 mutations. The genomic sequences were analyzed for the presence of Alu repetitive elements and their classification is described. This analysis may provide some insight into the characterization of genetic rearrangements resulting in disruption of the NF1 gene.

Base Sequence↗
PubMed2000

Extranodal marginal zone B-cell lymphoma genotyping by Alu-polymerase chain reaction.

DNA amplification by polymerase chain reaction (PCR) with primers designed on the widely distributed Alu sequences allows the production of specific inter-Alu DNA-fingerprints. Amplification of tumour and matched normal DNA can show differences due to genetic alterations within the tumour genome. We applied this approach to study low-grade extranodal marginal zone B-cell lymphoma (of MALT type). After digestion with restriction enzymes, DNA samples were separately amplified by PCR with three different Alu-primers. A comparison between the fingerprint pattern from lymphoma and normal samples was made. Inter-Alu bands differing between the two samples were excised from the gel, cloned and sequenced. Nine cases of low-grade MALT-lymphomas have been analysed, giving seventeen different bands between tumour and normal. DNA sequence analysis showed identities for three of them with sequences available at the GenBank. The methodology of Alu-PCR to detect DNA-based abnormalities, in addition or combination with RNA-based methods, is a powerful tool to identify candidate regions frequently altered in tumours. With the increased available genomic sequences through the Human Genome Project, there will be an increasing probability of picking up perfect homologies with these sequences using cloned differential Alu-PCR bands in BLAST searches through genome databases.

Alu Elements↗
PubMed2003

The whole structure of the human nonfunctional L-gulono-gamma-lactone oxidase gene--the gene responsible for scurvy--and the evolution of repetitive sequences thereon.

L-Gulono-gamma-lactone oxidase (GULO), which catalyzes the last step of ascorbic acid biosynthesis, is missing in humans. The whole structure of the human gene homologue for this enzyme was disclosed by a computer-assisted search. Only five exons, as compared to 12 exons constituting the functional rat GULO gene, remain in the human genome. A comparison of these exons with those of their functional counterparts in rat showed that there are two single nucleotide deletions, one triple nucleotide deletion, and one single nucleotide insertion in the human sequence. When compared in terms of codons, the human sequence has a deletion of a single amino acid, two stop codons, and two aberrant codons missing one nucleotide besides many amino acid substitutions. A comparison of the remaining human exon sequences with the corresponding sequences of the guinea pig nonfunctional GULO gene revealed that the same substitutions from rats to both species occurred at a large number of nucleotide positions. From analyses of the molecular evolution of Alu sequences in the human GULO gene homologue, it is thought that two Alu sequences were inserted in the vicinity of a presumed position of lost exon 11 during the same period as GULO lost its function. It is predicted that six LINE-1 sequences located in and near the gene homologue were inserted not during that period.

Alu Elements↗
PubMed2003

Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

Tissue plasminogen activator (t-PA) and plasminogen activator inhibitor type 1 (PAI-1) may be involved in the pathogenesis of peptic ulcers through suppression of fibrinolysis. This study was designed to investigate associations of t-PA and PAI-1 genes with clinical features of the patients with bleeding gastric ulcers. Eighty-four patients with peptic ulcers and 100 controls were studied between January 1998 and April 2000. We used polymerase chain reaction and endonuclease digestion to genotype for 4G/5G polymorphism in the promoter region of the PAI-1 gene and the Alurepeat insertion/deletion (I/D) polymorphism in intron h of the t-PA gene. Various clinical features, including lesion site, bleeding event, recurrence of ulcer, and rebleeding, were assessed using a multiple logistic regression model. The genotype distributions of both the t-PA and PAI-1 genes did not differ between the patient and control groups. The occurrence of the I/D or D/D genotype of t-PA was significantly higher in cases of duodenal ulcer (adjusted OR=4.39, 95% CI=1.12-17.21). When a dominant effect (i.e., 4G/4G or 4G/5G versus 5G/5G) of the 4G allele was assumed, the PAI-1 4G/4G genotype was independently associated with rebleeding after hemostasis (adjusted OR=5.07, 95% CI=1.03-24.87). Our data suggest that t-PA gene polymorphism is associated with duodenal ulcers, and that the PAI-1 gene may be a risk factor leading to recurrent bleeding after initial hemostasis.

Adult↗