SEARCH · PubMed Health

Results for “simple sequence repeat”

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.

At least 757 records · Page 42Linked to original sources

PubMed2006

In silico mining in expressed sequences of Neurospora crassa for identification and abundance of microsatellites.

In the present study, 3217 UniGene sequences of Neurospora crassa downloaded from the National Center for Biotechnology Information (NCBI) were mined for the identification of microsatellites or simple sequence repeats (SSRs). A total of 287 SSRs detected gives density of 1SSR/14.6 kb of 4187.86 kb sequences mined suggests that only 250 (7.8%) of sequences contained SSRs. Depending on the repeat units, the length of SSRs ranged from 14 to 17 bp for mono-, 14 to 48 bp for di-, 18 to 90 bp for tri-, 24 to 48 bp for tetra-, 30 for penta- and 42 to 48 bp for hexa-nucleotide repeats. Tri-nucleotide repeats were the most frequent repeat type (88.8%) followed by di-nucleotide repeats (5.9%). An attempt was also made with the help of bioinformatics approach to find out primer pairs for identified SSRs and primers were found only for 239 sequences. But, this part needs experimental validation. Annotation of SSRs containing sequences was also carried out.

Computational Biology↗

PubMed2005

Germline genomic instability in PCNA mutants of Drosophila: DNA fingerprinting and microsatellite analysis.

PCNA participates in multiple processes of DNA metabolism with an essential role in DNA replication and intervening in DNA repair. Temperature-sensitive PCNA mutants of Drosophila (mus209) are sensitive to mutagens, impair developmental processes and suppress positional-effect variegation. To investigate the role of proliferating cell nuclear antigen (PCNA) in germline genomic stability, independent mus209-defective and mus209-normal lines were established and maintained over six generations. A time course study was carried out and general genomic alterations were analyzed in the progeny by using arbitrarily primed PCR (AP-PCR) and microsatellite analysis. The AP-PCR analysis has shown that a dysfunctional PCNA leads to germline genomic instability, being the amount of genomic alterations transmitted to the progeny directly related to the number of mus209B1 mutant alleles. In addition, we have found that the frequency of genomic alterations tends to increase over successive generations. Surprisingly, the highest microsatellite instability was found in the heterozygous mus209-defective lines, suggesting a greater mutation rate in these individuals, in comparison with the homozygous mus209-defective lines. In conclusion, our results clearly indicate that PCNA is an important factor to maintain genomic stability in germinal cells, both in the overall genome and in simple repeated sequences. The implication of PCNA mutations in transgenerational genomic instability and related to cancer susceptibility is also discussed.

Animals↗

PubMed2006

Evidence for asexual genetic recombination in sunflower downy mildew, Plasmopara halstedii.

Field isolates and single sporangium lines of the biotrophic Oomycete Plasmopara halstedii, differing in host preference and fungicide sensitivity, were used simultaneously for infection of sunflower. Dual infections led to asexually formed zoosporangia which gave rise to a new phenotype combining the characteristics of the parental strains. The new phenotype showed the metalaxyl-tolerance of one parent and virulence behaviour characteristic of the other, thus being able to infect a specific and fungicide treated sunflower line that neither of the parental strains could infect alone. These characteristics were inherited over many generations and did not occur spontaneously when parental strains were propagated separately. DNA fingerprints with minisatellite and simple sequence repeat primers showed characteristic differences between the patterns of the parental strains and the new phenotype. PCR experiments with mixed parental DNA resulted in additive patterns, but did not show the amplification product specific for the new phenotype. Since sexual reproduction was excluded under the experimental conditions used, the results provide evidence for genetic recombination through parasexual events in dual infections of sunflower downy mildew.

Alanine↗

PubMed2006

Polyphasic classification of Alternaria isolated from hazelnut and walnut fruit in Europe.

Brown apical necrosis of English walnut and grey necrosis of hazelnut are destructive fruit diseases caused by a complex of opportunistic fungi including several small-spored catenulate Alternaria taxa. Thirty Alternaria isolates recovered from walnut and hazelnut fruit that were pathogenic on their respective host were compared along with type or representative isolates of A. alternata, A. tenuissima, A. arborescens, and A. infectoria using morphological and molecular criteria. Morphological examination using standardized procedures separated the walnut and hazelnut isolates into three morphological groups: the A. alternata group, the A. tenuissima group, and the A. arborescens group based upon common characteristics of the conidium and the sporulation apparatus. To evaluate genetic relationships among these groups, AFLP markers, inter simple sequence repeat (ISSR) markers, and histone gene sequence data were compared. Based upon AFLP data, the A. alternata and A. tenuissima groups comprised a single lineage, and the A. arborescens group comprised a separate lineage. ISSR data supported the grouping by AFLP data except for three isolates of the A. alternata group that clustered with the A. arborescens group. Base substitution of the H4 gene supported the discrimination of the A. arborescens group from the A. alternata and A. tenuissima groups. Tests of hypotheses based upon groupings derived from the various data sets supported the discrimination of the A. arborescens group but did not support the discrimination of the A. alternata group from the A. tenuissima group.

Alternaria↗

PubMed2004

Neuropeptide research discloses part of the secrets of Alzheimer's disease neuropathogenesis: state of the art 2004.

Molecular misreading, a process discovered in the late 1990s, entails the formation of aberrant transcripts due to the inaccurate conversion of genomic information, and results in an accumulation of aberrant proteins. The aberrant transcripts are formed as a result of a dinucleotide deletion (e.g. DeltaGA, DeltaGU) during or after transcription. Either the RNA polymerase starts to make mistakes (e.g. stuttering) in simple sequence repeats, such as GAGAG, or erroneous editing of transcripts occurs. If these aberrant transcripts are not detected and degraded efficiently, they can be translated from the deletion onwards into the +1 reading frame. The resulting proteins are therefore called +1 proteins. If functional domains are located downstream of the frameshift site, the result will be a protein with a potential loss or gain of function. It has been hypothesized that quality control mechanisms for both transcripts and proteins work less efficiently during aging, which is why +1 proteins may become manifest and contribute to age-related diseases in neuronal and non-neuronal cells.

Aging↗

PubMed2006

Genomic instability in the progression of sporadic nasopharyngeal carcinoma.

OBJECTIVE: Genomic instability reflecting the susceptibility of the genome to acquire multiple genetic alterations plays a major role in tumorigenesis and tumor progression. We evaluated the prognostic significance of the extent of genomic instability in nasopharyngeal carcinoma. STUDY DESIGN AND SETTING: Genomic instability was assessed by inter-simple sequence repeats polymerase chain reaction (inter-SSR PCR) in 38 patients with nasopharyngeal carcinoma. Characterization and verification of band alterations shared in different tumors were carried out by sequencing and nest PCR. RESULTS: 31 (81.6%) of 38 patients showed genomic alterations, and genomic instability index ranged from 0 to 16.2%. A gain-based genomic damage shared in 6 tumors was identified on chromosome 6q27, a new mutator phenotype in nasopharyngeal carcinoma. Significantly more genomic alteration was found in patients without 5-year survival than that with 5-year survival (P<0.05), suggesting that higher genomic instability predicts a poor prognosis in nasopharyngeal carcinoma. CONCLUSIONS AND SIGNIFICANCE: Our data suggests that genomic instability can be an early event marker in carcinogenesis of nasopharyngeal carcinoma. Also, aggravation of genomic alterations is a poor prognosis for cancer recovery.

Carcinoma↗

PubMed2005

Gene-particulate matter-health interactions.

Inter-individual variation in human responses to air pollutants suggests that some subpopulations are at increased risk to the detrimental effects of pollutant exposure. Extrinsic factors such as previous exposure and nutritional status may influence individual susceptibility. Intrinsic (host) factors that determine susceptibility include age, gender, and pre-existing disease (e.g., asthma), and it is becoming clear that genetic background also contributes to individual susceptibility. Environmental exposures to particulates and genetic factors associated with disease risk likely interact in a complex fashion that varies from one population and one individual to another. The relationships between genetic background and disease risk and severity are often evaluated through traditional family-based linkage studies and positional cloning techniques. However, case-control studies based on association of disease or disease subphenotypes with candidate genes have advantages over family pedigree studies for complex disease phenotypes. This is based in part on continued development of quantitative analysis and the discovery and availability of simple sequence repeats and single nucleotide polymorphisms. Linkage analyses with genetically standardized animal models also provide a useful tool to identify genetic determinants of responses to environmental pollutants. These approaches have identified significant susceptibility quantitative trait loci on mouse chromosomes 1, 6, 11, and 17. Physical mapping and comparative mapping between human and mouse genomes will yield candidate susceptibility genes that may be tested by association studies in human subjects. Human studies and mouse modeling will provide important insight to understanding genetic factors that contribute to differential susceptibility to air pollutants.

Air Pollutants↗

PubMed2005

Genic microsatellite markers in plants: features and applications.

Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.

Chromosome Mapping↗

PubMed2005

Environmentally caused dwarfism or a valid species--is Testudo weissingeri Bour, 1996 a distinct evolutionary lineage? New evidence from mitochondrial and nuclear genomic markers.

We examine the evolutionary relationships of the five traditionally recognized species of the western Palearctic tortoise genus Testudo (T. graeca, T. hermanni, T. horsfieldii, T. kleinmanni, and T. marginata) and the newly described dwarfed species T. weissingeri by using sequence data of the mitochondrial cytochrome b gene and nuclear genomic fingerprints with inter-simple sequence repeats (ISSR). Testudo weissingeri differs from T. marginata mainly by its smaller size and some color-pattern characteristics. T. weissingeri lives in the driest, poorest and hottest part of the distributional range of T. marginata. While both data sets demonstrated phylogenetic distinctness of the five traditionally recognized species of Testudo, some subspecies and even some local populations, we detected no differentiation between T. marginata and T. weissingeri. We conclude that T. weissingeri is not a distinct evolutionary unit. We suggest that its small size is the result of suboptimal environmental conditions with limited resources and synonymize it with T. marginata. T. marginata and T. kleinmanni form a clade that is supported both by our mtDNA and nuclear genomic data sets. According to mtDNA data, this clade is the sister taxon to the T. graeca complex. A sister group relationship of T. hermanni and ((T. marginata+T. kleinmanni)+T. graeca) is moderately to weakly supported by mtDNA data; T. horsfieldii is the sister taxon to a clade comprising all other Testudo species.

Animals↗

PubMed2006

Molecular evidence for adaptive radiation of Micromeria Benth. (Lamiaceae) on the Canary Islands as inferred from chloroplast and nuclear DNA sequences and ISSR fingerprint data.

The Canary Islands have been a focus for phylogeographic studies on the colonization and diversification of endemic angiosperm taxa. Based on phylogeographic patterns, both inter island colonization and adaptive radiation seem to be the driving forces for speciation in most taxa. Here, we investigated the diversification of Micromeria on the Canary Islands and Madeira at the inter- and infraspecific level using inter simple sequence repeat PCR (ISSR), the trnK-Intron and the trnT-trnL-spacer of the cpDNA and a low copy nuclear gene. The genus Micromeria (Lamiaceae, Mentheae) includes 16 species and 13 subspecies in Macaronesia. Most taxa are restricted endemics, or grow in similar ecological conditions on two islands. An exception is M. varia, a widespread species inhabits the lowland scrub on each island of the archipelago and could represent an ancestral taxon from which radiation started on the different islands. Our analyses support a split between the "eastern" islands Fuerteventura, Lanzarote and Gran Canaria and the "western" islands Tenerife, La Palma and El Hierro. The colonization of Madeira started from the western Islands, probably from Tenerife as indicated by the sequence data. We identified two lineages of Micromeria on Gomera but all other islands appear to be colonized by a single lineage, supporting adaptive radiation as the major evolutionary force for the diversification of Micromeria. We also discuss the possible role of gene flow between lineages of different Micromeria species on one island after multiple colonizations.

Adaptation, Biological↗

PubMed2006

Evolution of Piperales--matK gene and trnK intron sequence data reveal lineage specific resolution contrast.

Piperales represent the largest basal angiosperm order with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 2000 species), Peperomia (ca. 1500-1700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of six amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogeneity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia.

Base Sequence↗

PubMed1999

Genetic diversity in parthenogenetic triploid Paragonimus westermani.

Paragonimus westermani is a medically important foodborne trematode occurring throughout southeast Asia. We have used molecular techniques to test the hypothesis that the parthenogenetic triploid form of P. westermani has arisen only once. Sources of data for comparison were: (a) restriction fragment length polymorphisms (RFLPs) of ribosomal internal transcribed spacers (ITS); and (b) 'fingerprint' patterns observed when genomic digests were probed with simple sequence repeats (ATT)10 and (ATGT)7. In all cases there were distinct differences among triploid isolates from southwest Japan, northeast China and Korea. These findings are considered in the context of previous cytogenetic, allozyme, mitochondrial-RFLP and partial cytochrome c-oxidase subunit I (COI) sequence studies and indicate that triploid lineages may have arisen independently on more than one occasion. We favour this view. An alternative explanation is that the triploids did have a single origin, but that different clonal lineages have undergone subsequent mutations.

Animals↗

PubMed1998

Familial hyperinsulinism with apparent autosomal dominant inheritance: clinical and genetic differences from the autosomal recessive variant.

We describe three families with hypoglycemia caused by familial hyperinsulinism (HI) in whom vertical transmission of the disorder occurred, suggesting autosomal dominant (AD) inheritance. We therefore examined the relationship between the apparent AD disorder and the more common autosomal recessive (AR) form of HI, which has recently been linked to the sulfonylurea receptor on chromosome 11p15.1. The clinical features of the 11 patients with AD HI were milder than those seen in 14 patients with AR HI. Hypoglycemia was readily controlled with either diet alone or with diazoxide in 10 of 11 patients with AD HI but in none of those with the AR form. In one large pedigree, analysis of genomic DNA with polymorphic simple sequence repeat markers excluded linkage of AD HI to the SUR locus in a dominant manner. The possibility of linkage to the SUR locus could not be absolutely excluded in the two smaller pedigrees. None of the published mutations of the SUR gene identified in patients with AR HI were detected in the patients with the AD form. We conclude that the AD form of hyperinsulinism is phenotypically different from the AR variant. The identification of more families with this form of HI may make it possible to locate the responsible gene by the use of linkage analysis.

Adolescent↗

PubMed1997

Frequent alterations in gene expression in colon tumor cells of the microsatellite mutator phenotype.

Tumors of the microsatellite mutator phenotype (MMP) are characterized by the accumulation of many thousands of somatic mutations in tracts of simple repeated sequences or microsatellites. Using arbitrarily primed PCR fingerprinting of RNA (RAP-PCR), we have comparatively analyzed the overall gene expression patterns of several colorectal tumor cell lines with and without the MMP. A reproducible pattern of 30-40 main products was obtained for each fingerprint with a total of about 200 cell transcripts analyzed. Differences in RAP-PCR fingerprints were detected between these tumor cell lines. Some of these expression polymorphisms appeared to be specific for tumor cells of the MMP because they were present in two or more different MMP+ cell lines but absent in all MMP- cell lines analyzed. We also analyzed RNAs prepared from single cell clones isolated from these tumor cell lines. Reproducible differences in the fingerprints were detected between single cell clones from each of the cell lines analyzed. Examples of single cell clone-specific fingerprint differences from one of the MMP tumor cell lines were cloned and sequenced. Differential expression of some of these sequences was confirmed by Northern analysis using the cloned fragments as probes. Similar fingerprint alterations were also observed among single cell clones derived from single cell clones from mutator tumor cell lines, which appeared to exhibit higher clonal variation in gene expression compared with MMP- cells. The detection of inter- and intra-tumor alterations in gene expression by unbiased RAP-PCR show that these fluctuations occur with high frequency in tumor cells of the MMP. These results indicate that the profound genomic instability of tumor cells of the MMP is also reflected in a high incidence of alterations in their patterns of gene expression.

Blotting, Northern↗

PubMed2001

Analysis and interpretation of ligand-DNA binding isotherms.

Binding studies provide information of fundamental and central importance for the complete understanding of ligand-DNA interactions. Studies of ligand binding to long natural DNA samples, to synthetic deoxypolynucleotides of simple repeating sequence, and to oligonucleotides of defined sequence are all needed to begin to understand the interaction in detail. Binding studies provide entry into the thermodynamics of the DNA interactions, which in turn provides great insight into the molecular forces that drive the binding process. This chapter summarizes both model-dependent and -independent approaches for the analysis and interpretation of binding isotherms, and should serve as a concise guide for handling experimental data.

Animals↗

PubMed2005

ISSR techniques for evolutionary biology.

Inter-simple sequence repeat (ISSR) markers were originally devised for differentiating among closely related plant cultivars but have become extremely useful for studies of natural populations of plants, fungi, insects, and vertebrates. The markers are easily generated using minimal equipment and are hypervariable, yielding a large amount of data for a reasonable cost to the researcher. The methods for Miniprep DNA extraction and cleanup, polymerase chain reaction (PCR) amplification, optimization, data gathering and scoring, and data analyses are outlined.

DNA, Plant↗

PubMed2005

In situ hybridization of phytoplankton using fluorescently labeled rRNA probes.

Phytoplankton are one of the major components of ecosystem processes and play an important role in many biogeochemical cycles in the marine and freshwater environment. Despite their importance, many microalgae are poorly described and little is known of broad spatial and temporal scale trends in their abundance and distribution. Reasons for this are that microalgae are often small, lack distinct morphological features, and are unculturable, which make analyses difficult. It is now possible by using molecular biological techniques to advance our knowledge of aquatic biodiversity and to understand how biodiversity supports ecosystem structure, dynamics, and resilience. We present in this chapter a brief review of the progress that has been made in analyzing microalgae from populations to the species level. The described methods range from DNA fingerprinting techniques, such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs), and simple sequence repeats (SSRs), to microsatellites, which are used in population studies, to sequence analysis, which help to reconstruct the evolutionary history of organisms and to examine relationships at various taxonomic levels. Special emphasis is given to the application of molecular probes for the identification and characterization of microalgal taxa. The fast and secure identification of phytoplankton, especially of toxic species, is important from an ecological and economical point of view and whole-cell hybridization with specific fluorochrome-labeled probes followed by fluorescence microscopy or flow cytometry offers a fast method for this purpose. In this context, we present a detailed protocol for fluorescence in situ hybridization (FISH) of ribosomal RNA (rRNA) probes that can be applied to many algal cell types and discuss practical considerations of its use.

DNA Fingerprinting↗

PubMed2002

Two regions of deletion in 9p22- p24 in neuroblastoma are frequently observed in favorable tumors.

Neuroblastoma is a tumor of infancy that presents several chromosomal abnormalities. Nonrandom deletion of chromosome arm 9p has been identified in primary neuroblastoma suggesting the presence of a tumor suppressor gene located on this chromosome. In previous work, we showed that CDKN2A and CDKN2B genes, mapped at 9p21, were not deleted in neuroblastoma cells. In the present article, we refine the deleted region of 9p using polymerase chain reaction-based analysis of highly polymorphic simple sequence repeats and a two color fluorescence in situ hybridization technique on interphase nuclei. We analyzed 71 primary tumors of patients at the onset of the disease. We found loss of heterozygosity (LOH) in 16 of 71 (23%) cases; the frequency of LOH for 9p was higher (28%) in favorable stages 1, 2, and 4s than in unfavorable stages 3 and 4 (14%). Our results identify two regions of frequent allelic loss: the first at the locus D9S1849 and the second at the locus D9S157. These regions appear to be distant from CDKN2A and CDKN2B loci suggesting that other genes may be involved in 9p deletion. Finally, our data show that 9p deletion is more frequent in tumors of patients with a favorable prognosis, indicating that deleted genes may not be crucial for tumor progression.

Alleles↗