Minisatellite Sequences Research Articles

Assessment of genotyping markers in the molecular characterization of a population of clinical isolates of Fusarium in Colombia.

:Introduction:Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for humans and animals. Prevalence of clinical fusariosis and lack of effective treatments have increased the interest in the precise diagnosis, which implies a molecular characterization of Fusarium populations.Objective: We compared different genotyping markers in their assessment of the genetic variability and molecular identification of clinical isolates of Fusarium.Materials and methods: We evaluated the performance of the fingerprinting produced by two random primers: M13, which amplifies a minisatellite sequence, and (GACA)4, which corresponds to a simple repetitive DNA sequence. Using the Flunter Gaston Discriminatory Index (HGDI), an analysis of molecular variance (AMOVA), and a Mantel test, the resolution of these markers was compared to the reference sequencing-based and PCR genotyping methods.Results: The highest HGDI value was associated with the M13 marker followed by (GACA)4. AMOVA and the Mantel tests supported a strong correlation between the M13 classification and the reference method given by the partial sequencing of the transcription elongation factor 1-alpha (TEF1-α) and rDNA 28S.Conclusion: The strong correlation between the M13 classification and the sequencing- based reference together with its higher resolution demonstrates its adequacy for the characterization of Fusarium populations.

Polymorphisms in the human PRDM9 gene may lead to meiotic arrest and azoospermia

PRDM9 is responsible for directing the location of programmed double strand breaks and subsequent crossover events between homologous chromosomes during meiosis in human gametes. Prdm9 is also essential for meiosis and fertility in mice, with PRDM9 knockout males displaying complete azoospermia. PRDM9 contains a rapidly evolving DNA binding zinc finger array that is coded by a ∼84 nucleotide repeating unit mini-satellite sequence. The human A-type allele, which accounts for ∼90% of the alleles in the human population, contains 13 repeating units. We sought to develop a s strategy to effectively genotype this mini-satellite with PacBio sequencing and to determine whether PRDM9 variation, including mini-satellite length polymorphisms, is associated with infertility in the human male. Observational study. Using a normospermic human control, a two-step polymerase chain reaction (PCR) protocol was established to successfully amplify the PRDM9 zinc finger array mini-satellite and sequence it using both Sanger and PacBio next generation sequencing, which has the advantage of circular consensus sequencing and long reads. We next amplified PRDM9 from the genomic DNA of 48 azoospermic men and 5 controls. The samples were visually analyzed with gel electrophoresis, and potential mutant alleles that had an atypical band appearance were compared to the wild type. PacBio sequencing results from the normospermic control were found to be an identical match to the known human A allele, confirming our ability to effectively genotype the mini-satellite array in a single PacBio run. Gel electrophoresis of PCR amplified PRDM9 alleles from azoospermic men identified 6 potential mutant variants of distinct mini-satellite lengths differing from the A-allele. We have developed a protocol to effectively genotype the human PRDM9 zinc finger array mini-satellite to evaluate a potential etiology of azoospermia in the infertile human male. We found 6 potential PRDM9 alleles differing from the known A-allele in a small (n=48) azoospermia cohort. Current/ongoing research includes applying our PacBio sequencing protocol to genotype all 48 azoospermic men in comparison to a control group and evaluate if there is an association between PRDM9 mini-satellite repeat length, polymorphisms, or de novo mutations and azoospermia.

Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a comprehensive sequence analysis. The physical distribution of Ta-3A1 in chromosomes 3A, 5A, 5B, 5D, and 7A of wheat was confirmed by nondenaturing fluorescence in situ hybridization (ND-FISH) after labeling the oligonucleotide probe. The analysis of monomer variants indicated that rapid sequence amplification of Ta-3A1 occurred first on chromosomes of linkage group 5, then groups 3 and 7. Comparative ND-FISH analysis suggested that rapid changes occurred in copy number and chromosomal locations of Ta-3A1 among the different species in the tribe Triticeae, which may have been associated with chromosomal rearrangements during speciation and polyploidization. The labeling and subsequent use of Ta-3A1 by ND-FISH may assist in the precise identification and documentation of novel wheat germplasm engineered by chromosome manipulation.

Molecular markers used in forensic genetics.

Forensic genetics is a field that has become subject to increasing interest in recent years. Both the technology and the markers used for forensic purposes have changed since the 1980s. The minisatellite sequences used in the famous Pitchfork case introduced genetics to the forensic sciences. Minisatellite sequences have now been replaced by more sensitive microsatellite markers, which have become the basis for the creation of genetic profile databases. Modern molecular methods also exploit single nucleotide polymorphisms, which are often the only way to identify degraded DNA samples. The same type of variation is taken into consideration in attempting to establish the ethnicity of a perpetrator and to determine phenotypic traits such as the eye or hair colour of the individual who is the source of the genetic material. This paper contains a review of the techniques and molecular markers used in human and animal forensic genetics, and also presents the potential trends in forensic genetics such as phenotyping.

Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction

BackgroundIn our previous study, Citrobacter werkmanii BF-6 was isolated from an industrial spoilage sample and demonstrated an excellent ability to form biofilms, which could be affected by various environmental factors. However, the genome sequence of this organism has not been reported so far.ResultsWe report the complete genome sequence of C. werkmanii BF-6 together with the description of the genome features and its annotation. The size of the complete chromosome is 4,929,789 bp with an average coverage of 137×. The chromosome exhibits an average G + C content of 52.0%, and encodes 4570 protein coding genes, 84 tRNA genes, 25 rRNA operons, 3 microsatellite sequences and 34 minisatellite sequences. A previously unknown circular plasmid designated as pCW001 was also found with a length of 212,549 bp and a G + C content of 48.2%. 73.5%, 75.6% and 92.6% of the protein coding genes could be assigned to GO Ontology, KEGG Pathway, and COG (Clusters of Orthologous Groups) categories respectively. C. werkmanii BF-6 and C. werkmanii NRBC 105721 exhibited the closest evolutionary relationships based on 16S ribosomal RNA and core-pan genome assay. Furthermore, C. werkmanii BF-6 exhibits typical bacterial biofilm formation and development. In the RT-PCR experiments, we found that a great number of biofilm related genes, such as bsmA, bssR, bssS, hmsP, tabA, csgA, csgB, csgC, csgD, csgE, and csgG, were involved in C. werkmanii BF-6 biofilm formation.ConclusionsThis is the first complete genome of C. werkmanii. Our work highlights the potential genetic mechanisms involved in biofilm formation and paves a way for further application of C. werkmanii in biofilms research.

Telomeric localization of the Arabidopsis-type heptamer repeat, (TTTAGGG)n , at the chromosome ends in Saccharina japonica (Phaeophyta).

Telomeres generally consist of short repeats of minisatellite DNA sequences and are useful in chromosome identification and karyotype analysis. To date, telomeres have not been characterized in the economically important brown seaweed Saccharina japonica, thus its full cytogenetic research and genetic breeding potential has not been realized. Herein, the tentative sequence of telomeres in S.japonica was identified by PCR amplification with primers designed based on the Arabidopsis-type telomere sequence (TTTAGGG)n , which was chosen out of three possible telomeric repeat DNA sequences typically present in plants and algae. After PCR optimization and cloning, sequence analysis of the amplified products from S.japonica genomic DNA showed that they were composed of repeat units, (TTTAGGG)n , in which the repeat number ranged from 15 to 63 (n=46). This type of repeat sequence was verified by a Southern blot assay with the Arabidopsis-type telomere sequence as a probe. The digestion of S.japonica genomic DNA with the exonuclease Bal31 illustrated that the target sequence corresponding to the Arabidopsis-type telomere sequence was susceptible to Bal31 digestion, suggesting that the repeat sequence was likely located at the outermost ends of the kelp chromosomes. Fluorescence insitu hybridizations with the aforementioned probe provided the initial cytogenetic evidence that the hybridization signals were principally localized at both ends of S.japonica chromosomes. This study indicates that the telomeric repeat of the kelp chromosomes is (TTTAGGG)n which differs from the previously reported (TTAGGG)n sequence in Ectocarpus siliculosus through genome sequencing, thereby suggesting distinct telomeres in brown seaweeds.

A polymorphic minisatellite region of BORIS regulates gene expression and its rare variants correlate with lung cancer susceptibility.

Aberrant expression of BORIS/CTCFL (Brother of the Regulator of Imprinted Sites/CTCF-like protein) is reported in different malignancies. In this study, we characterized the entire promoter region of BORIS/CTCFL, including the CpG islands, to assess the relationship between BORIS expression and lung cancer. To simplify the construction of luciferase reporter cassettes with various-sized portions of the upstream region, genomic copies of BORIS were isolated using TAR cloning technology. We analyzed three promoter blocks: the GATA/CCAAT box, the CpG islands and the minisatellite region BORIS-MS2. Polymorphic minisatellite sequences were isolated from genomic DNA prepared from the blood of controls and cases. Of the three promoter blocks, the GATA/CCAAT box was determined to be a critical element of the core promoter, while the CpG islands and the BORIS-MS2 minisatellite region were found to act as regulators. Interestingly, the polymorphic minisatellite region BORIS-MS2 was identified as a negative regulator that repressed the expression levels of luciferase reporter cassettes less effectively in cancer cells compared with normal cells. We also examined the association between the size of BORIS-MS2 and lung cancer in a case–control study with 590 controls and 206 lung cancer cases. Rare alleles of BORIS-MS2 were associated with a statistically significantly increased risk of lung cancer (odds ratio, 2.04; 95% confidence interval, 1.02–4.08; and P=0.039). To conclude, our data provide information on the organization of the BORIS promoter region and gene regulation in normal and cancer cells. In addition, we propose that specific alleles of the BORIS-MS2 region could be used to identify the risk for lung cancer.

The molecular polymorphism evaluation in Salix sp. Romanian accessions – preliminary results

Salix is an important energetic genus, but  most of the genotypes are closely related genetically, due to frequent natural hybridisation in nature. Therefore it is of great interest to study its genetic background. In this work a collection of progenitors (Romanian accessions) collected from different locations were investigated to determine their genetic fingerprint in order to be used in future breeding programs. To evaluate the genetic diversity two types of molecular markers were used, namely ISSR (Inter Simple Sequence Repeats) and  DAMD (Direct amplification of minisatellite-region). In the first step 15 ISSR and 5 DAMD markers were analysed to choose those markers that give the best amplification. It was pointed out that all of the primers had complex fingerprints, but those  which generated the most definite patterns were A13 and UBC 818 (ISSR) and 1-URP6R and 4- 14C2 (DAMD).These primers were used to analyze seven different Salix L. samples collected from different locations. It was revealed that a high polymorphism was identified both between different accesions of a species and between species. The high degree of polymorphism for both  minisatellite and microsatellite sequences, emphasized the necessity of increasing markers number to be possible to perform a statistical analysis and to determine the genetic similarities.

Cryptococcus neoformans isolates from Yaoundé human immunodeficiency virus-infected patients exhibited intra-individual genetic diversity and variation in antifungal susceptibility profiles between isolates from the same patient.

Cryptococcal meningitis is a dreadful opportunistic fungal infection amongst human immunodeficiency virus (HIV)-infected patients. One complication in the management of the disease is the possible infection of a patient by two or more different strains of Cryptococcus neoformans. This study investigated the intra-individual genetic diversity and antifungal susceptibility of C. neoformans isolates from Yaoundé (Cameroon) HIV-infected patients with cryptococcal meningitis. Twenty-five clinical isolates were obtained during a prospective study. Five colonies were randomly collected from each initial sample. The 150 isolates obtained (125 colonies and 25 initial samples) were submitted to serotyping by multiplex PCR. Genotyping analyses were achieved using RFLP, and minisatellite- and microsatellite-length polymorphism. The antifungal susceptibility testing was carried out using a Sensititre YeastOne kit. Seven antifungals were tested: itraconazole, fluconazole, amphotericin B, ketoconazole, 5-fluorocytosine, posaconazole and voriconazole. The 150 isolates were identified as C. neoformans serotype A and genotype VNI. The microsatellite and minisatellite sequence analyses generated 15 genotypes. Six out of 25 (24 %) patients were found to be infected by two different genotypes. Antifungal susceptibility showed several profiles: posaconazole (0.015-0.25 µg ml-1), amphotericin B (0.06-1 µg ml-1), fluconazole (0.5-16 µg ml-1), itraconazole (0.008-0.12 µg ml-1), ketoconazole (0.008-0.12 µg ml-1), 5-fluorocytosine (0.25-16 µg ml-1) and voriconazole (0.008-0.12 µg ml-1). It was noted that isolates from the same patient might present different susceptibility profiles to an antifungal drug with differences of more than four dilutions. The results achieved highlighted the possible presence of isolates with different genotypes in a patient with dissimilar antifungal susceptibility profiles during a single episode of cryptococcal meningitis.

Clonal in vitro multiplication of grey mangrove and assessment of genetic fidelity using single primer amplification reaction (SPAR) methods

An efficient protocol for clonal multiplication of an important mangrove, Avicennia marina, was developed through in vitro culture of nodal segments obtained from a mature plant. The nodal explant induced multiple shoots when cultured on the Murashige and Skoog (MS) basal medium supplemented with varying concentrations and combinations of 6-benzyladenine (BA) and α-naphthalene acetic acid. The highest response in terms of per cent regeneration (73%), average number of shoots/explant (3.25 ± 0.25) and maximum shoot length (5.2 ± 0.27 cm) was obtained on the MS medium supplemented with BA 5.0 μmol/L + NAA 1.0 μmol/L + 3 g/L activated charcoal after 8 weeks of culturing. The regenerated shoots were rooted well in the MS medium supplemented with 1.0 μmol/L indole-3-butyric acid with an average of 2.9 ± 0.24 roots per microshoot. The rooted plantlets were successfully transferred to pots containing normal garden soil with 70% survival rate. The genetic stability of the regenerated plants was evaluated using single primer amplification reaction (SPAR) methods viz., random amplified polymorphic DNA, directed amplification of minisatellite DNA and intersimple sequence repeat polymorphism. The SPAR analysis revealed monomorphic banding patterns in all in vitro regenerated plantlets of A. marina and similar with that of the mother tree confirming their genetic uniformity and clonal fidelity.

Molecular and clinical analyses of 16q24.1 duplications involving FOXF1 identify an evolutionarily unstable large minisatellite.

BackgroundPoint mutations or genomic deletions of FOXF1 result in a lethal developmental lung disease Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. However, the clinical consequences of the constitutively increased dosage of FOXF1 are unknown.MethodsCopy-number variations and their parental origin were identified using a combination of array CGH, long-range PCR, DNA sequencing, and microsatellite analyses. Minisatellite sequences across different species were compared using a gready clustering algorithm and genome-wide analysis of the distribution of minisatellite sequences was performed using R statistical software.ResultsWe report four unrelated families with 16q24.1 duplications encompassing entire FOXF1. In a 4-year-old boy with speech delay and a café-au-lait macule, we identified an ~15 kb 16q24.1 duplication inherited from the reportedly healthy father, in addition to a de novo ~1.09 Mb mosaic 17q11.2 NF1 deletion. In a 13-year-old patient with autism and mood disorder, we found an ~0.3 Mb duplication harboring FOXF1 and an ~0.5 Mb 16q23.3 duplication, both inherited from the father with bipolar disorder. In a 47-year old patient with pyloric stenosis, mesenterium commune, and aplasia of the appendix, we identified an ~0.4 Mb duplication in 16q24.1 encompassing 16 genes including FOXF1. The patient transmitted the duplication to her daughter, who presented with similar symptoms. In a fourth patient with speech and motor delay, and borderline intellectual disability, we identified an ~1.7 Mb FOXF1 duplication adjacent to a large minisatellite. This duplication has a complex structure and arose de novo on the maternal chromosome, likely as a result of a DNA replication error initiated by the adjacent large tandem repeat. Using bioinformatic and array CGH analyses of the minisatellite, we found a large variation of its size in several different species and individuals, demonstrating both its evolutionarily instability and population polymorphism.ConclusionsOur data indicate that constitutional duplication of FOXF1 in humans is not associated with any pediatric lung abnormalities. We propose that patients with gut malrotation, pyloric or duodenal stenosis, and gall bladder agenesis should be tested for FOXF1 alterations. We suggest that instability of minisatellites greater than 1 kb can lead to structural variation due to DNA replication errors.Electronic supplementary materialThe online version of this article (doi:10.1186/s12881-014-0128-z) contains supplementary material, which is available to authorized users.

Kallikreins are involved in an miRNA network that contributes to prostate cancer progression.

MicroRNAs (miRNAs) are short RNA nucleotides that negatively regulate their target genes. They are differentially expressed in prostate cancer. Kallikreins are genes that encode serine proteases and are dysregulated in cancer. We elucidated a miRNA-kallikrein network that can be involved in prostate cancer progression. Target prediction identified 23 miRNAs that are dysregulated between high and low risk biochemical failure and are predicted to target five kallikreins linked to prostate cancer; KLK2, KLK3, KLK4, KLK14 and KLK15. We also identified 14 miRNAs that are differentially expressed between Gleason grades and are predicted to target these kallikreins. This demonstrates that kallikreins are downstream effectors through which miRNAs influence tumor progression. We show, through in-silico and experimental analysis, that miR-378/422a and its gene targets PIK3CG, GRB2, AKT3, KLK4 and KLK14 form an integrated circuit in prostate cancer. Our analysis shows that a minisatellite sequence in the kallikrein locus consists of a number of microsatellite repeats that represent predicted miRNA response elements. A number of kallikrein and non-kallikrein prostate cancer-related genes share these microsatellite repeats. We validated some of these interactions in prostate cancer cell lines. Finally, we provide preliminary evidence on the presence of a miRNA-mediated cross-talk between kallikreins, including a kallikrein pseudogene.

Conservation of intronic minisatellite polymorphisms in the SCK1/SHC2 gene of Hominidae

The neuronally expressed Shc adaptor homolog SCK1/SHC2 gene contains an unusually high number of minisatellites. In humans, twelve different minisatellite sequences are located in introns of SCK1/SHC2 and ten of them are highly polymorphic. Here we used primers developed for humans to screen ten intronic loci of SCK1/SHC2 in chimpanzee and gorilla, and undertook a comprehensive analysis of the genomic sequence to address the evolutionary events driving these variable repeats. All ten loci amplified in chimpanzee and gorilla contained hypervariable and low-variability minisatellites. The human polymorphic locus TR1 was monomorphic in chimpanzee and gorilla, but we detected polymorphic alleles in these apes for the human monomorphic TR7 locus. When we examined the repeat size among these hominoids, there was no consistent variation by length from humans to great apes. In spite of the inconsistent evolutionary dynamics in repeat length variation, exon 16 was highly conserved between humans and great apes. These results suggest that non-coding intronic minisatellites do not show a consistent evolutionary paradigm but evolved with different patterns among each minisatellite locus. These findings provide important insight for minisatellite conservation during hominoid evolution.

Characterization of Structure, Divergence and Regulation Patterns of Plant Promoters

Plant promoters have attracted increasing attention because of their irreplaceable role in modulating the spatio-temporal expression of genes interacting with transcription factors (TFs). Despite their importance, the basic characteristics of plant promoters are not well understood. In order to determine sequence diversity within promoter regions, evolutionary divergence of promoters between plant species, and the general structural characteristics of promoter sequences, we downloaded and analyzed 3922 plant promoter sequences from a wide range of plant species. The average plant promoter GC content was lower in dicotyledons than in monocotyledons, which might suggest different evolutionary pressures for promoter sequences between the two clades. Approximately 3.3% of plant promoters harbored minisatellite sequences, and 15.4% of plant promoters harbored microsatellite sequences (also called simple sequence repeats). Very few transposable elements were detected within the plant promoters. The most common transcription factor binding site (TFBS) motif was AGAGAGAGA, followed by TTAGGGTTT and then GCCGCC. Transcribed gene regions with promoters containing the corresponding TFBSs were predicted to be most commonly involved in metabolic processes, biological regulation, and stimulus response in plants. These results reveal some basic structural characteristics of plant promoters and clarify the evolutionary forces shaping plant promoters. This data might facilitate cloning of plant promoter sequences and aid in our understanding of gene spatio-temporal expression patterns in plants.

Comparison of Botrytis cinerea populations isolated from two open-field cultivated host plants

The necrotrophic fungus Botrytis cinerea is reported to infect more than 220 host plants worldwide. In phylogenetical–taxonomical terms, the pathogen is considered a complex of two cryptic species, group I and group II. We sampled populations of B. cinerea on sympatric strawberry and raspberry cultivars in the North-East of Hungary for three years during flowering and the harvest period. Four hundred and ninety group II B. cinerea isolates were analyzed for the current study. Three different data sets were generated: (i) PCR-RFLP patterns of the ADP-ATP translocase and nitrate reductase genes, (ii) MSB1 minisatellite sequence data, and (iii) the fragment sizes of five microsatellite loci. The structures of the different populations were similar as indicated by Nei's gene diversity and haplotype diversity. The F statistics (Fst, Gst), and the gene flow indicated ongoing differentiation within sympatric populations. The population genetic parameters were influenced by polymorphisms within the three data sets as assessed using Bayesian algorithms. Data Mining analysis pointed towards the five microsatellite loci as the most defining markers to study differentiation in the 490 isolates. The results suggest the occurrence of host-specific, sympatric divergence of generalist phytoparasites in perennial hosts.

Development of a Multilocus Sequence Typing Tool for High-Resolution Genotyping of Enterocytozoon bieneusi

Thus far, genotyping of Enterocytozoon bieneusi has been based solely on DNA sequence analysis of the internal transcribed spacer (ITS) of the rRNA gene. Both host-adapted and zoonotic (human-pathogenic) genotypes of E. bieneusi have been identified. In this study, we searched for microsatellite and minisatellite sequences in the whole-genome sequence database of E. bieneusi isolate H348. Seven potential targets (MS1 to MS7) were identified. Testing of the seven targets by PCR using two human-pathogenic E. bieneusi genotypes (A and Peru10) led to the selection of four targets (MS1, MS3, MS4, and MS7). Further analysis of the four loci with an additional 24 specimens of both host-adapted and zoonotic E. bieneusi genotypes indicated that most host-adapted genotypes were not amplified by PCR targeting these loci. In contrast, 10 or 11 of the 13 specimens of the zoonotic genotypes were amplified by PCR at each locus. Altogether, 12, 8, 7, and 11 genotypes of were identified at MS1, MS3, MS4, and MS7, respectively. Phylogenetic analysis of the nucleotide sequences obtained produced a genetic relationship that was similar to the one at the ITS locus, with the formation of a large group of zoonotic genotypes that included most E. bieneusi genotypes in humans. Thus, a multilocus sequence typing tool was developed for high-resolution genotyping of E. bieneusi. Data obtained in the study should also have implications for understanding the taxonomy of Enterocytozoon spp., the public health significance of E. bieneusi in animals, and the sources of human E. bieneusi infections.

Development of a Multilocus Sequence Tool for Typing Cryptosporidium muris and Cryptosporidium andersoni

Although widely used for the characterization of the transmission of intestinal Cryptosporidium spp., genotyping tools are not available for C. muris and C. andersoni, two of the most common gastric Cryptosporidium spp. infecting mammals. In this study, we screened the C. muris whole-genome sequencing data for microsatellite and minisatellite sequences. Among the 13 potential loci (6 microsatellite and 7 minisatellite loci) evaluated by PCR and DNA sequencing, 4 were eventually chosen. DNA sequence analyses of 27 C. muris and 17 C. andersoni DNA preparations showed the presence of 5 to 10 subtypes of C. muris and 1 to 4 subtypes of C. andersoni at each locus. Altogether, 11 C. muris and 7 C. andersoni multilocus sequence typing (MLST) subtypes were detected among the 16 C. muris and 12 C. andersoni specimens successfully sequenced at all four loci. In all analyses, the C. muris isolate (TS03) that originated from an East African mole rat differed significantly from other C. muris isolates, approaching the extent of genetic differences between C. muris and C. andersoni. Thus, an MLST technique was developed for the high-resolution typing of C. muris and C. andersoni. It should be useful for the characterization of the population genetics and transmission of gastric Cryptosporidium spp.

Single Molecule FRET Characterization of DNA G-Quadruplexes Formed In The Promoter of Human MEF2D and TNNI3 Genes

DNA G-quadruplexes are enriched near the transcription start site (TSS) of the human genes and have been suggested to be involved in gene transcription and translation. Informations about G-quadruplex conformation and dynamics is crucial to our understanding of the roles of quadruplex in gene regulation as well as to the development of novel therapeutic agents that interact with the quadruplex therefore modulate gene expression. Single molecule fluorescence resonance energy transfer (smFRET) can resolve conformational heterogeneity and dynamic fluctuations in nucleic acids, providing unique insights into the biophysics of quadruplex. We have recently elucidated the conformational heterogeneity and dynamics of the quadruplexes formed in the promoter of human c-myc and c-kit genes by smFRET. Here we present single molecule analysis of DNA quadruplex elements found in the TSS of the promoter of the MEF2D, a member of MEF2 (myocyte enhancer factor-2) family of transcription factors which regulate the response of heart to cardiac stress signals, and also in the chromosome 19 specific minisatellite sequences in the promoter of human cardiac troponin I (TNNI3), a gene encodes constituent protein of the troponin complex on the thin filament of cardiac muscle.

A new set of molecular markers for the genotyping of Babesia bovis isolates

Babesia bovis is a tick-borne apicomplexan pathogen that remains an important constraint for the development of cattle industries worldwide. The existence of different strains and subpopulations has long been described in this hemoparasite. However, few molecular markers have been reported for strain genotyping and characterization. Minisatellite sequences show high levels of variation and therefore provide excellent tools for both the genotyping and population genetic analysis. In this work we report a set of five molecular markers containing minisatellites that showed a variable degree of polymorphism in several American strains. We have used a bioinformatics approach to search for marker sequences contained in open reading frames. Five genes were chosen and primers were designed in conserved regions flanking the repeat region. Two of the genes were the previously described Bv80/Bb-1 and TRAP. The other three genes were named p200, Antigen 3 and Desmoyokin. Amplification by PCR, sequencing and comparative analysis of 11 strains from Argentina, Brazil, Uruguay, Mexico and USA determined that the tandem repeats varied in number and sequence among the isolates. Genome analysis of the five markers revealed that they were single copy and distributed across the four B. bovis chromosomes. When the new markers were analyzed in an experimental infection, absolute sequence conservation was found, indicating the stability of these markers during the course of infection. These markers were also stable during three syringe passages through calves. The application of this panel of molecular markers could provide new molecular tools for the genotyping of B. bovis isolates and analysis of changes in parasite populations following vaccination.

Detection and Identification of Brenneria nigrifluens, the Causal Agent of the Shallow Bark Canker of Walnut by, PCR Amplification

AbstractA 1 kb DNA band from strains of Brenneria nigrifluens, as shown by amplification of their genomic DNA by polymerase chain reaction (PCR) using minisatellite primer designed on the minisatellite sequence of the M13 phage, was isolated, cloned and sequenced. Specific oligonucleotides (F1–C3) were selected into this 1 kb DNA sequence and used in a PCR assay to detect and identify strains of B. nigrifluens. Several strains of B. nigrifluens were assessed with F1–C3 primers producing a specific band of approximately 250 bp pairs in length. This target was successfully amplified from purified genomic DNA, from bacterial culture and directly from infected walnut bark tissue. No amplification was obtained when the PCR assay was performed on other plant‐pathogenic species from the following genera Brenneria, Erwinia, Agrobacterium, Pseudomonas, Ralstonia, Pectobacterium, Xanthomonas and from walnut‐associated bacteria, indicating the specificity of these primers. The PCR assay with the primers described here provides a rapid, specific and sensitive diagnostic method for B. nigrifluens and a useful tool for epidemiological studies.