Number Of Tandem Repeat Sequences Research Articles

A Guide to Molecular Characterization of Genotype II African Swine Fever Virus: Essential and Alternative Genome Markers.

African swine fever is a contagious viral disease that has been spreading through Europe and Asia since its initial report from Georgia in 2007. Due to the large genome size of the causative agent, the African swine fever virus (ASFV), the molecular epidemiology, and virus evolution are analyzed by employing different markers. Most of these markers originate from single nucleotide polymorphisms or disparities in the copy number of tandem repeat sequences observed during the comparisons of full genome sequences produced from ASFVs isolated during different outbreaks. Therefore, consistent complete genome sequencing and comparative analysis of the sequence data are important to add innovative genomic markers that contribute to the delineation of ASFV phylogeny and molecular epidemiology during active circulation in the field. In this study, the molecular markers currently employed to assess the genotype II ASFVs circulating in Europe and Asia have been outlined. The application of each of these markers to differentiate between ASFVs from related outbreaks is described to implement a guideline to their suitability for analyzing new outbreaks. These markers do not signify the complete repertoire of genomic differences between ASFVs, but will be beneficial when analyzing the first outbreaks in a new region or a large number of samples. Furthermore, new markers must be determined via complete genome sequence analyses for enabling in-depth insights into the molecular epidemiology of ASFV.

Complete genome analysis of African swine fever virus isolated from domestic pigs during the first ASF outbreaks in India

African swine fever (ASF), considered as the most dreadful swine disease due to its very high mortality, emerged in India in 2020. The complete genome analysis of ASF viruses isolated during the first outbreaks in India showed a few unique non-synonymous mutations in MGF 369-11L, MGF 505-4R, K205R and B263R genes. Frame shifts in the protein coding sequences were observed in DP60R, ASFV-G_ACD 00190, MGF 110-10-L-MGF110-14L fusion, MGF 360-14L and I267L genes of Indian ASF viruses as compared to ASFV/Georgia/2007. Complete genome based phylogenetic analysis of p72-genotype-II viruses showed the clustering of Indian isolates with ASFV/Wuhan/2019 in a separate clade. Phylogenetic analysis of concatenated sequences of 14 open reading frames (ORF) having single nucleotide polymorphisms (SNP) showed distinct grouping of Indian ASFVs with other Asian ASFVs. This is the first complete genome characterization of ASF viruses isolated from domestic pigs in India. The results indicate that number of Tandem Repeat Sequence (TRS) in the intergenic region between I73R and I329L genes, and the 14 ORFs with SNP reported in this study could be the genetic determinants to differentiate the closely related p72-genotype II viruses circulating in Asia.

Genome-wide identification of U-box genes and protein ubiquitination under PEG-induced drought stress in potato.

Protein ubiquitination is one of the most important posttranslational modifications in eukaryotic cells, and it is involved in a variety of biological processes, including abiotic stress response. The ubiquitination modification is highly specific, which depends on the accurate recognition of substrate proteins by ubiquitin ligase. Plant U-box (PUB) proteins are a class of ubiquitin ligases, multiple members of which have shown to participate in water-deficit stress in Arabidopsis and rice. U-box gene family and large-scale profiling of the ubiquitome in potato has not been reported to date, although it is one of the most important food crops. The identified 66 U-box genes from the potato genome database were unevenly distributed on 10 chromosomes. These StPUBs have a large number of tandem repeat sequences. Analysis of gene expression characteristics revealed that many StPUBs responded to abiotic stress. Three hundred and fourteen lys modification sites were identified under PEG-induced drought stress, which were distributed on 200 proteins, with 25 differential ubiquitination modification sites, most of which were up-regulated. The ubiquitination modification in potato protein was enhanced under PEG-induced drought stress, and U-box ubiquitin ligase was involved. This study provides an overall strategy and rich data set to clarify the effects of ubiquitination on potatoes under PEG-induced drought stress and the ubiquitination modification involved in potato U-box genes in response to PEG-induced drought stress.

Termination of Replication and Mechanisms of Heteroplasmy in Sturgeon Mitochondrial DNA

The control region of mitochondrial DNA (mtDNA) in sturgeon contains one to seven tandem nucleotide repeats 78-83 bp in size. Some sturgeon species are homoplasmic by the D-loop size (Acipenser nudiventris, A. oxyrinchus, A. sturio), some are mildly heteroplasmic (A. fulvescens, Huso huso) and some are markedly heteroplasmic (A. brevirostrum, A. medirostris, A. mikadoi, A. naccarii, and A. transmontanus). This work presents a comparison of the D-loop sequences associated with the termination of mtDNA replication in fish and the conservative sequences determining the termination of replication (TAS) in these organisms. It is proposed that the D-loop heteroplasmy in sturgeon may be associated with variation in the number of tandem repeat sequences, which can form stable spatial structures during mtDNA replication. In most sturgeon species with pronounced heteroplasmy, the energy levels required for the folding of tandem repeats containing variable number of repeated units differ minimally.

GENETIC MARKERS: COMPARATIVE CLASSIFICATION OF MOLECULAR MARKERS

With the creation of the molecular markers allowing to carry out analysis of genotypes on the level initial genetic information – DNA, onset one of the most multifarious and one of the most large in number class of markers at the present day. It is concerned with that each separate nucleic acid sequence is unique on its structure. Set of molecular and genetic methods, named as DNA-fingerprinting, most wide used in modern investigations for solving different problems in different biological areas. In this connection, necessity in comparative classification of modern molecular and genetic markers is actual. Based on published literature material it shown data on different classifications of molecular markers. Determined definition of term “marker” in genetics and breeding. Gave the characters and distinctive features of genetic markers. It given the definition what is “good” genetic marker as well as kinds, categories, variations and types on heredity of molecular markers. Manifested by means of molecular markers polymorphisms can classified on polymorphism of sequence itself (including nucleotide substitution and insertion-deletion) and polymorphism the number of tandem repeat sequences in repeated regions. Moreover, molecular markers can classify on two variations: anonymous, for which nucleotide acid sequence unknown and for manifestation of the molecular marker its detection not necessary (for example, RAPD, AFLP, RFLP), and announce (or determined), for which nucleic acid sequence is known or can be detect during analysis (for example, SNP, CAPS, STS). However, in independence on using of molecular markers the choice of method of investigation will be depend on investigated plant species as well. The next influence of molecular and genetic methods on genetics and practical breeding of plants will be depend on results, which will be obtain, in particular, on revealing the possibility or not possibility of genotyping of individual on single genetic marker as wel as on economic price of obtain informative data.

Genome Sequence of Corynebacterium pseudotuberculosis Strain KM01, Isolated from the Abscess of a Goat in Kunming, China.

ABSTRACTCaseous lymphadenitis (CLA) is an acute, pyogenic, and contagious disease of goat that imposes considerable economic losses for farmers, and it is caused by Corynebacterium pseudotuberculosis. Herein, we introduce the genome sequencing of C. pseudotuberculosis strain KM01, isolated from an abscess of a Saanen goat from Kunming, China. The genome contains 2,198 genes, the total length of the genes was 2,337,666 bp, and the GC content was 52.18%. The number of tandem repeat sequences was 44, the total length of the tandem repeat sequences was 1,970 bp (0.0772% of the genome), the number of minisatellite DNAs was 36, and there were 48 tRNAs and 12 rRNAs.

Genetic variations among white spot syndrome virus (WSSV) isolates from shrimp farms in Gujarat, north-west coast of India

The present paper documents the molecular diagnosis and genotyping of white spot syndrome virus (WSSV) isolates collected from different shrimp farms of Gujarat, north-west coast of India. Preliminary diagnosis was done using singletube PCR and genotyping of isolates by analysis of variable number tandem repeat sequence (VNTRS) in minisatellites viz., ORF 94, ORF 125, ORF 75 and ORF 75 flank. Out of the 79 samples analysed, 32 (33.80%) were positive with low (54.17%), medium (8.33%) and high (37.50%) severity of infection. Genotyping, using ORF 94 revealed that repeat units (RUs) 4 and 11 were the most frequent ones (32%) while ORF 125 showed 5 different repeat types of which RU 5 was the most common (45.83%). Two genotypes were observed for ORF 75, one showed multiple repeats of two 45 bp, followed by a 57 bp, whereas the other showed two repeats that included 5 and 4 repeats of 45 bp. Sequence analysis of the 54 bp variable sequence of ORF 94 RU type 4 revealed single-nucleotide polymorphism (SNP) at 47th base. Based on the results from ORF94, dominance of RU types 11or 4 were recorded for the first time in India and one sample showed 2 bands of different sizes indicating the prevalence of two different genotypes infecting the same pond at a given time. Further, no correlation could be observed between the virus genotype and the severity of the mortality in the outbreaks. The results suggest the widespread occurrence of WSSV in the region and circulation of distinct virus genotypes.

Influence of thymidylate synthase expression on survival in patients with colorectal cancer

Background: Thymidylate synthase (TS) plays a critical role in nucleotide metabolism and is an important target for 5-fluorouracil (5-FU), the standard chemotherapeutic drug for treatment of colorectal cancer (CRC). Aims and Methods: The present study aimed to evaluate TS variable number tandem repeat sequences (VNTR) polymorphism by polymerase chain reaction and TS protein expression by immunohistochemistry and its association with clinicopathological parameters in untreated CRC patients (n = 100). Further, the prognostic and predictive role of TS has been evaluated. Results: For TS VNTR polymorphism, the observed frequencies of 2R/2R, 2R/3R, and 3R/3R genotypes were 22%, 51%, and 27%, respectively. When immunohistochemical localization was studied, cytoplasmic staining for TS was observed in 70% of patients. A significant inverse correlation was noted between TS protein expression and tumor, node, metastasis staging (P = 0.027), Dukes' staging (P = 0.039), and lymph node status (P = 0.012) of CRC patients. However, there was no significant correlation between TS VNTR polymorphism and TS protein expression. On survival analysis, a significantly shorter overall survival (OS) was seen in CRC patients with negative protein expression (P = 0.031). Moreover, the subgroup of CRC patients treated only with surgery also showed a trend of poor OS in patients with negative TS protein expression (P = 0.058). However, neither TS polymorphism nor its protein expression was able to predict relapse-free survival. Conclusion: Negative TS protein expression may be related to unfavorable clinical outcome in CRC patients. However, further studies in a larger set of patients are necessary to better assess TS as a prognostic and predictive marker for 5-FU response in CRC patients.

Endemic and epidemic Acinetobacter baumannii clones: a twelve-year study in a tertiary care hospital.

BackgroundNosocomial outbreaks of multidrug-resistant Acinetobacter baumannii are of worldwide concern. Using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and multiple locus variable number tandem repeat sequence (VNTR) analysis (MLVA), the present work examines the genetic diversity of the endemic and epidemic A. baumannii clones isolated in a single hospital over a twelve-year period.ResultsPFGE analysis of 405 A. baumannii-calcoaceticus complex isolates detected 15 A. baumannii endemic/epidemic PFGE types (EE1 to EE15) that grouped into five clusters: EE1-EE8, EE9, EE10, EE11 and EE12-EE15. The MLST sequence type (ST) distributions were: international clone II (ST-2) 60%, international clone III (ST-3) 26.7%, ST-15 6.7%, and ST-80 6.7%. MLVA-8Orsay returned 17 allelic profiles. The large (L) VNTR marker profiles were fully concordant with the detected STs, and concordant with 14 up to 15 PFGE types. Imipenem resistance was detected in five PFGE types; the prevalence of the blaOXA-58-like and blaOXA-40-like genes was 60% and 40% respectively.ConclusionsPFGE proved to be a vital tool for analysis of the temporal and spatial distribution of the clones. MLST and the VNTR L-markers grouped the isolates into clonal clusters. The wide diversity of MLVA small (S)-markers, however, did not permit clustering. The present results demonstrate the persistence of several endemic PFGE types in the hospital, the involvement of some of them in outbreaks, and the inter hospital transmission of extensively drug-resistant ST-15 and ST-80.

Strain discrimination of Yersinia pestis using a SERS-based electrochemically driven melting curve analysis of variable number tandem repeat sequences.

Strain discrimination within genetically highly similar bacteria is critical for epidemiological studies and forensic applications. An electrochemically driven melting curve analysis monitored by SERS has been utilised to reliably discriminate strains of the bacterial pathogen Yersinia pestis, the causative agent of plague. DNA amplicons containing Variable Number Tandem Repeats (VNTRs) were generated from three strains of Y. pestis: CO92, Harbin 35 and Kim. These amplicons contained a 10 base pair VNTR repeated 6, 5, and 4 times in CO92, Harbin 35 and Kim respectively. The assay also included a blocker oligonucleotide comprising 3 repeats of the 10-mer VNTR sequence. The use of the blocker reduced the effective length of the target sequence available to bind to the surface bound probe and significantly improved the sensitivity of the discrimination. The results were consistent during three replicates that were carried out on different days, using different batches of PCR product and different SERS sphere segment void (SSV) substrate. This methodology which combines low cost, speed and sensitivity is a promising alternative to the time consuming current electrophoretic methods.

Distinct roles for Toll and autophagy pathways in double-stranded RNA toxicity in a Drosophila model of expanded repeat neurodegenerative diseases

Dominantly inherited expanded repeat neurodegenerative diseases are caused by the expansion of variable copy number tandem repeat sequences in otherwise unrelated genes. Some repeats encode polyglutamine that is thought to be toxic; however, other repeats do not encode polyglutamine indicating either multiple pathogenic pathways or an alternative common toxic agent. As these diseases share numerous clinical features and expanded repeat RNA is a common intermediary, RNA-based pathogenesis has been proposed, based on its toxicity in animal models. In Drosophila, double-stranded (rCAG.rCUG∼100) RNA toxicity is Dicer dependent and generates single-stranded (rCAG)7, an entity also detected in affected Huntington's Disease (HD) brains. We demonstrate that Drosophila rCAG.rCUG∼100 RNA toxicity perturbs several pathways including innate immunity, consistent with the observation in HD that immune activation precedes neuronal toxicity. Our results show that Drosophila rCAG.rCUG∼100 RNA toxicity is dependent upon Toll signaling and sensitive to autophagy, further implicating innate immune activation. In exhibiting molecular and cellular hallmarks of HD, double-stranded RNA-mediated activation of innate immunity is, therefore, a candidate pathway for this group of human genetic diseases.

Synthesis of homogeneous MUC1 oligomers via a bi-directional ligation strategy

The efficient synthesis of homogeneous MUC1 peptide oligomers using sequential ligation reactions in the N-to-C and C-to-N directions is reported. The bi-directional ligation strategy makes use of thioester formation via N → S acyl shift chemistry in combination with peptide ligation reactions and was used to prepare a library of peptide oligomers ranging in molecular mass from 3.8-9.4 kDa, comprised of between 2 and 5 repeats of the MUC1 variable number tandem repeat sequence.

Characterization of α2,3- and α2,6-sialyltransferases from Helicobacter acinonychis

Genome sequence data were used to clone and express two sialyltransferase enzymes of the GT-42 family from Helicobacter acinonychis ATCC 51104, a gastric disease isolate from Cheetahs. The deposited genome sequence for these genes contains a large number of tandem repeat sequences in each of them: HAC1267 (RQKELE)(15) and HAC1268 (EEKLLEFKNI)(13). We obtained two clones with different numbers of repeat sequences for the HAC1267 gene homolog and a single clone for the HAC1268 gene homolog. Both genes could be expressed in Escherichia coli and sialyltransferase activity was measured using synthetic acceptor substrates containing a variety of terminal sugars. Both enzymes were shown to have a preference for N-acetyllactosamine, and they each made a product with a different linkage to the terminal galactose. HAC1267 is a mono-functional α2,3-sialyltransferase, whereas HAC1268 is a mono-functional α2,6-sialyltransferase and is the first member of GT-42 to show α2,6-sialyltransferase activity.

Variable number of tandem repeat sequences act as regulatory elements in Mycobacterium tuberculosis

VNTR (variable number of tandem repeats) has been used extensively for Mycobacterium tuberculosis strain discrimination. In contrast, their biological roles have been rarely investigated. We, herewith, studied whether two VNTR could promote expression of a downstream reporter gene, gfp. The VNTR loci, VNTR0960c and VNTR4052, reside upstream of the translational start sites of Rv0861c (helicase gene, ercc3) and Rv3610c (ftsH), respectively. Both are highly polymorphic among clinical strains of M. tuberculosis. DNA fragments containing various numbers of the repeat units were amplified and inserted upstream of the gfp gene and transformed into M. smegmatis mc(2)155 and M. tuberculosis H37Ra. The levels of fluorescence were determined by microplate fluorometry and flow cytometry. It was found that VNTR0960c could promote the expression of gfp while VNTR4052 alone could not. However, VNTR4052 was needed for complementing the promoter activity of the downstream sequence. The effects were discernible in M. tuberculosis, even though only the incomplete copy of the repeat was present. The addition of a complete copy of the repeat augmented the promoter activity. The presence of more copies of the repeat had minimal effects or even decreased the expressions. Significance of the effects on the cellular metabolisms of M. tuberculosis warrants further studies.

Thymidylate synthetase allelic imbalance in clear cell renal carcinoma

To investigate the allelic status of the thymidylate synthetase (TYMS) gene, located at chromosome band 18p11.32, in renal cell carcinoma (RCC). TYMS is a key target of the 5-fluorouracil (5-FU)-based class of drugs, frequently considered in combination therapies in advanced RCC. TYMS variants, such as the TYMS polymorphic 5'-untranslated region variable number tandem repeat sequence (VNTR), are under investigation to guide 5-FU treatment. Yet, no information is available with regard to changes in TYMS allele frequencies in RCC malignances. Blood and matched tumor samples were collected from 41 histological proven clear cell RCC affected patients (30 males, 11 females.). TYMS VNTR genotype was first determined in blood to identify heterozygotes employing PCR techniques. To evaluate for allelic imbalance, fragment analysis was performed both in blood and matched tumor DNA of the heterozygote patients. Microsatellite analysis, employing the markers D18S59 and D18S476 mapping, respectively, at the TYMS locus (18p11.32) and 1.5 Mb downstream of the TYMS gene sequence (18p11.31), was performed to confirm TYMS allelic imbalance in tumors. Germ-line TYMS VNTR distribution was: 2R/2R (19.5%), TYMS 2R/3R (36.6%) and TYMS 3R/3R (43.9%). Allelic imbalance for the TYMS tandem repeat region was detected in 26.6% of the heterozygote patients. Microsatellite analysis confirmed the allelic imbalance detected by TYMS VNTR analysis and revealed that the overall frequence of allelic imbalance of chromosome band 18p11.32 was 35%, while the overall allelic imbalance of chromosome band 18p11.31 was 28%. By focusing on the TYMS polymorphic variants in renal cancer, we here provide evidence, to our knowledge, for the first time showing loss of 18p11.32 and 18p11.31 in renal cell carcinomas. As allelic imbalances involving TYMS locus may be an important variable affecting 5-FU responsiveness, this study may contribute to explain different responses of advanced RCC in combined chemotherapeutic regimens incorporating fluoropyridines.

Thymidylate synthase gene polymorphosms and lung cancer susceptibility

22168 Background: Lung cancer is the most common type of cancer in Europe and non-small cell lung cancer (NSCLC) accounts for 75%-85% of all histological. The thymidylate synthase (TS) enzyme plays a key role in de novo DNA synthesis, essential for DNA replication and repair, thus it is important in cell proliferation and it is a target for several chemotherapy agents. The TS gene is highly polymorphic in Humans. Three polymorphisms of major relevance in the expression of TS levels were described, namely, on the 5’UTR, a variable number tandem repeat sequence with 28bp (where the most frequent have two and/or three repeats - 2R and/or 3R alleles, respectively) and a single nucleotide polymorphism (SNP) G>C in the 2nd sequence of the 3R allele; in the 3’UTR a deletion/insertion (del/ins) of 6bp. The main goal of this work was to study the influence of TS polymorphisms in the susceptibility to develop NSCLC using a case-control study. Methods: DNA was extracted from peripheral blood leukocytes of 213 patients from the North region of Portugal, admitted in Portuguese Oncology Institute of Oporto, diagnosed with NSCLC. TS genotypes were detected by PCR-RFLP techniques. The control group consisted of 510 individuals with no known oncological disease. Results: According to the results individuals carrying the 3R allele faces a higher risk for developing NSCLC when compared to homozygous 2R (OR=1.57; 95% CI [1.03–2.39]; P=0.034). However, concerning SNP G>C and del/ins polymorphisms, no statistically significant differences were found. Following the hypothesis that the G to C substitution can modulate the effect of TS 3R variant, we analyzed the association between the influence of the del/ins polymorphism and 3RC and 3RG genotype and, when combined analysis for the three polymorphisms were carried out, no statistically significant differences were found for the SNP G>C genotype distribution, where homozygous 3R/3R individuals that carry the ins allele showed no different probability risk to develop NSCLC when carrying the 3G allele, relatively to homozygous 3C/3C. Conclusions: Since the presence of 3R allele appears to be associated with an increased risk for develop NSCLC the pre-establishment of an individual molecular profile could help to predict differential susceptibility to develop this neoplasia. No significant financial relationships to disclose.

Endothelial Nitric Oxide Synthase Gene: Prospects for Treatment of Heart Disease

Nitric oxide functions as a signaling molecule with a well-established role in vascular homeostasis. It is synthesized from the oxidation of L-arginine by the enzyme, endothelial nitric oxide synthase (eNOS). The eNOS gene has a number of polymorphic sites, including SNPs, dinucleotide repeats and variable number tandem repeat sequences, and the opportunity exists to investigate polymorphic functional correlates as well as disease-specific associations, especially in cardiovascular disease, including coronary artery disease, and its most severe consequence, myocardial infarction. A number of clinical and functional correlative studies involving eNOS polymorphisms have been reported and are presented. The promise and complexity of pharmacogenetics is illustrated using eNOS as an example because of its relationship with cardiovascular biology and pathology. In this review, we will discuss the impact of nitric oxide, eNOS, genetic regulation, clinical investigation and, ultimately, prospects for treatment of heart disease.

Serotonin Transporter Gene Polymorphism and BPSD in Mild Alzheimer's Disease

The purpose of the present study was to confirm an association of functional polymorphism within the serotonin transporter (5-HTT) gene with Alzheimer's disease (AD) and behavioral and psychological symptoms of dementia (BPSD) in mild AD. Apolipoprotein E (ApoE) gene polymorphism and 2 types of functional polymorphism in the 5-HTT gene, 5-HTT-linked polymorphic region (5-HTTLPR) and a 5-HTT variable number of tandem repeats sequence (5-HTTVNTR) were analyzed longitudinally in outpatients with mild AD to find out whether there was a relation between any such polymorphisms and the occurrence of BPSD. No significant differences in genotype distribution or allele frequencies were identified for 5-HTTLPR or 5-HTTVNTR between AD patients and age- and sex-matched non-demented controls regardless of ApoE epsilon4 allele. No significant differences were noted in 5-HTTLPR genotype or allele distributions between AD patients with or without BPSD. However, significant associations were observed between presence of 5-HTTVNTR allele 10 and BPSD or aggressiveness. This difference was independent of the presence of the ApoE epsilon4 allele. As a result, 5-HTT polymorphisms are unlikely to play any substantial role in susceptibility to AD. Conversely, 5-HTTVNTR influences the risk of developing BPSD or aggressiveness and genetic variations in the 5-HTT gene may be involved in the development of symptomatology for mild AD.

Prognostic Role of Thymidylate Synthase Polymorphisms in Gastric Cancer Patients Treated with Surgery and Adjuvant Chemotherapy

To investigate the prognostic role of thymidylate synthase (TS) polymorphisms in gastric cancer patients treated with radical surgery and fluorouracil-based adjuvant chemotherapy. Ninety gastric cancer cases were identified among 187 patients previously enrolled in prospective case-control studies for disease susceptibility. Patients were genotyped for a G/C nucleotide change within a triple 28 bp variable number of tandem repeat sequence in the TS 5'-untranslated region (5'-UTR) and a 6 bp deletion in the TS 3'-untranslated region (3'-UTR). According to available functional data, patients with 5'-UTR 2R/2R, 2R/3C, 3C/3C genotypes were classified as low TS producers (5'-UTRlow) and patients with 5'-UTR 3G/3G, 3G/3C, 2R/3G genotypes as high TS producers (5'UTRhigh). Patients with 3'-UTR del6/del6 and del6/ins6 genotypes were classified as low TS producers (3'-UTRlow) and patients with 3'-UTR ins6/ins6 genotype as high TS producers (3'-UTRhigh). The prognostic analysis was based on 5'-UTR/3'-UTR combined genotypes. Ten patients (11%) were 5'-UTRhigh/3'-UTRhigh, 36 patients were 5'-UTRhigh/3'-UTRlow, 19 patients were 5'-UTRlow/3'-UTRhigh, and 25 patients were 5'-UTRlow/3'-UTRlow. 5'-UTRlow/3'-UTRlow patients showed the best outcome and the threshold of statistical significance was achieved in the comparison of disease-free survival and overall survival with 5'-UTRhigh/3'-UTRlow patients and 5'-UTRhigh/3'-UTRhigh patients. The presence of at least one high TS expression genotype showed independent adverse prognostic role in multivariate analysis. The prognostic role of TS polymorphisms in gastric cancer deserves further investigation because the adverse effect of high TS expression genotypes may be a relevant information to improve adjuvant chemotherapeutic strategies.

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis

Human DNA consists of a large number of tandem repeat sequences. Such sequences are usually called satellites, with the primary example being the centromeric alpha-satellite DNA. The basic repeat unit of the alpha-satellite DNA is a 171 bp monomer. Arbitrary monomer pairs usually have considerable sequence divergence (20-40%). However, with the exception of peripheral alpha-satellite DNA, monomers can be grouped into blocks of k-monomers (4 < or = k < or = 20) between which the divergence rate is much smaller (e.g., 5%). Perhaps the simplest and best understood mechanism for tandem repeat array evolution is unequal crossover. Although it is possible that alpha-satellite sequences developed as a result of subsequent unequal crossovers only, no formal computational framework seems to have been developed to verify this possibility. In this paper, we develop such a framework and report on experiments which imply that pericentromeric alpha-satellite segments (which are devoid of higher order structure) are evolutionarily distinct from the higher order repeat segments. It is likely that the higher order repeats developed independently in distinct regions of the genome and were carried into their current locations through an unknown mechanism of transposition.