Repetitive DNA Regions Research Articles

Inferring short tandem repeat variation from paired-end short reads

The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method’s ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.

Telomere length in relation to incident chronic stress in the Bangladeshi-American: the experience from the Massachusetts United States of America

Meeting abstracts Telomere is a region of repetitive DNA located at the ends of eukaryotic chromosomes, which protect genetic material from degradation during cellular replication. Telomere length in individuals is highly variable, and studies have shown that shortened telomeres are associated with

Bidirectional transcription of trinucleotide repeats: Roles for excision repair

Genomic instability at repetitive DNA regions in cells of the nervous system leads to a number of neurodegenerative and neuromuscular diseases, including those with an expanded trinucleotide repeat (TNR) tract at or nearby an expressed gene. Expansion causes disease when a particular base sequence is repeated beyond the normal range, interfering with the expression or properties of a gene product. Disease severity and onset depend on the number of repeats. As the length of the repeat tract grows, so does the size of the successive expansions and the likelihood of another unstable event. In fragile X syndrome, for example, CGG repeat instability and pathogenesis are not typically observed below tracts of roughly 50 repeats, but occur frequently at or above 55 repeats, and are virtually certain above 100–300 repeats.Recent evidence points to bidirectional transcription as a new aspect of TNR instability and pathophysiology. Bidirectional transcription of TNR genes produces novel proteins and/or regulatory RNAs that influence both toxicity and epigenetic changes in TNR promoters. Bidirectional transcription of the TNR tract appears to influence aspects of its stability, gene processing, splicing, gene silencing, and chemical modification of DNAs. Paradoxically, however, some of the same effects are observed on both the expanded TNR gene and on its normal gene counterpart. In this review, we discuss the possible normal and abnormal effects of bidirectional transcription on trinucleotide repeat instability, the role of DNA repair in causing, preventing, or maintaining methylation, and chromatin environment of TNR genes.

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacerrDNAregion in fungi

The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.

Genome organization and the role of centromeres in evolution of the erythroleukaemia cell line HEL

The human erythroleukaemia (HEL) cell line has a highly rearranged genome. We matched whole chromosome analysis with cytogenomic microarray data to build a detailed description of these rearrangements. We used a combination of single nucleotide polymorphism array and multiple fluorescence in situ hybridization approaches, and compared our array data with publicly available data for different sublines of HEL. B allele frequencies revealed the fate of each homologue for most chromosomes. At least two instances of the breakage-fusion-bridge cycle appear to have facilitated amplification of oncogenes and deletion of tumour suppressor genes. Because our study included centromere identification, we found that some abnormal chromosomes had centromeres that did not match the identity of the rest of the chromosome. This study highlights the variety of complementary methods required to understand remodelling of the genome in cancer and uncover some of the mechanisms involved. We present evidence of centromere capture as a means of preserving broken chromosome segments. Testing for another highly repetitive DNA region, the nucleolus organizer region, helped identify the steps involved in chromosome 9 copy number aberrations. Increased use of techniques for identifying centromeres and other repetitive DNA regions will add to our understanding of genome remodelling and evolution. The pattern of chromosome 20 aberration in HEL supports an association of 20q11.21 amplification with erythroleukaemia (acute myeloid leukaemia subtype M6) in the context of 20q12 deletion. The differences between the karyotypes in different HEL sublines highlight the constantly evolving genomes of cultured cell lines.

117 Non-B DNA structure-induced genetic instability in mammalian cells

Repetitive regions of genomic DNA can adopt a number of different structures, e.g. Z-DNA and they are at risk for increased genetic instability and disease development [As reviewed in (Zhao, Bacolla, Wang, & Vasquez, 2010)]. We found Z-DNA structure is intrinsically mutagenic in cultured mammalian cells and in chromosomes of transgenic mice (Wang Carbajal, Vijg, DiGiovanni, & Vasquez, 2008). Our recent data showed CG14 repeats, a model Z-DNA-forming sequence, could stall DNA polymerase progress in mammalian COS-7 cells, while AT14 repeats that does not form Z-DNA conformation, did not affect replication. These data suggested a replication-dependent model of Z-DNA-induced mutagenesis in mammalian cells. In addition, we also found that Z-DNA caused mutation and DNA breakage in the absence of DNA replication, and the spectrum of mutation from unreplicated system tended to have more large deletions than replicated DNA, suggested a replicated-independent pathway of Z-DNA-induced genetic instability (Wang, Christensen, & Vasquez, 2004). Several DNA repair proteins were found to be involved in Z-DNA induced mutagenesis, but in different ways: adding XPA protein back in, otherwise, deficient XP12RO cells increased Z-DNA-induced mutation frequency by −50%, while expressing MSH2 protein in Hec59 cells reduced Z-DNA-induced mutation frequency by −25%. Interestingly, cytosine methylation in CpG repeats induced higher frequencies of deletions and rearrangements with a broader mutant size distribution than that found with unmethylated CpG repeats. We discovered that unusual structural features of the methylated CpG sequences precluded local nucleosome assembly leading to genetic instability. Thus, non-B DNA-induced mutation appears to be a very complex process where DNA replication, repair and epigenetic modification are all involved.

A Mutagenesis Method for the Addition and Deletion of Highly Repetitive DNA Regions: The Paradigm of EPIYA Motifs in the cagA Gene of Helicobacter pylori

CagA protein of Western origin Helicobacter pylori isolates contains at its carboxyl-terminal end repeating types of EPIYA motifs, depending on the surrounding sequence, which dictate hierarchic tyrosine phosphorylation. To produce, in an isogenic background, mutant strains expressing CagA protein with variable numbers of EPIYA-C terminal motifs, we have adopted a mutagenesis assay using a megaprimer approach. The H. pylori P12 reference strain containing two terminal EPIYA-C motifs was utilized. Initially, we cloned, full-length cagA gene, next to the Campylobacter jejuni kanamycin-resistance cassette, followed by the 1200-bp region located immediately after cagA gene (metacagA region). Then, we generated a megaprimer consisting of three consecutive copies of the EPIYA-C coding sequence of cagA gene, followed by the 140-bp region of the cagA genomic sequence present immediately after the second EPIYA-C repeat. We utilized these two products to perform a QuikChange mutagenesis assay and were able to obtain all desired combinations of EPIYA-C motifs, followed by Kan(r) cassette and metacagA region. These constructions were used to perform natural transformation of the P12 parental strain, by directional homologous recombination. We produced isogenic H. pylori strains that express CagA with variable number of EPIYA-C motifs (AB, ABC, ABCCC) and their phosphorylation-deficient counterparts. They exhibited similar growth characteristics to the parental strain, adhered equally well to gastric cells and successfully translocated CagA, following pilus induction. Our method can be used in other cases where highly repetitive sequences need to be reproduced.

Identification of G-Quadruplex Inducers Usinga Simple, Inexpensiveand Rapid High Throughput Assay, and TheirInhibition of Human Telomerase

Telomeres are protein and DNA complexes located atchromosome ends. Telomeric DNA is composed of a double stranded region of repetitive DNA followed by single-stranded 3' extension of aG-rich sequence. Single-stranded G-rich sequencescan fold into G-quadruplex structures,and molecules that stabilize G-quadruplexes are known to inhibit the enzyme telomerase and disrupt telomere maintenance. Because telomere maintenance is required for proliferation of cancer cells, G-quadruplex stabilizers have become attractive prospects for anticancer drug discovery.However, telomere-targeting G-quadruplex ligands have yet to enter the clinic owing in part to poor pharmacokinetics and target selectivity. Increasing the pharmacophore diversity of G-quadruplex and specifically telomeric-DNA targeting agents should assist in overcoming these shortcomings. In this work, we report the identification and validation ofligands that bind telomeric DNA and induce G-quadruplex formationusing the NCI Diversity Set I, providing validation of anextremely simple, rapid and high-throughput screen using FRET technology. Hits from the screen were validated by examining telomerase inhibition and G-quadruplex inductionusing CD spectroscopy and DNA polymerase stop assays. We show that two known DNA binding molecules, ellipticine derivativeNSC 176327 (apyridocarbazole) and NSC 305831 (an antiparasitic hetero-cyclediamidine referred to as furamidine and DB75),are selective induceG-quadruplex formation in the human telomeric sequence and bind telomeric DNA quadruplexes in the absence of stabilizing monovalent cations with molar ratios(molecule: DNA)of 4:1and 1.5:1, respectively.

Abstract A69: The association between chronic stress and telomere length in African American men.

Abstract The telomere is a region of repetitive DNA located at the ends of eukaryotic chromosomes, which protect genetic material from degradation during cellular replication. As a consequence of the inability of DNA polymerase to fully replicate the ends of the chromosome, the telomere progressively shortens as an organism ages. Telomere length in individuals is highly variable, and studies have shown that shortened telomeres are associated with poor prognoses in many diseases, including cancers and other diseases that disproportionately affect American-Americans. There is also strong evidence that environmental and behavioral factors can play an epigenetic role in telomere length homeostasis. Chronic stress is associated with shorter telomeres in women, but studies have not been explicitly done to assess the role of chronic stress in men or minorities. Though there is little evidence of a functional relationship between shortened telomeres and heightened disease states, it is clear that telomeres reflect the health of the individual. We hypothesize that telomere length can be used as a diagnostic indicator of health status, and that the average telomere length are shorter in African-American men due in part to higher levels of chronic stress. To test this hypothesis, we examined the telomere length of DNA from the peripheral blood mononuclear leukocytes of more than 40 African-American men and administered a stress survey to assess chronic stress levels. Preliminary analysis of the data indicates a potential negative association between stress and telomere length, though the results are not significant. We also observed a significant negative correlation between telomere length and body mass index. The results indicate that environmental factors can affect telomere length in African-American men, and that telomere length may be a useful health status indicator in this population. Citation Format: Samantha Simon, Wallace Sharif. The association between chronic stress and telomere length in African American men. [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr A69.

2 Lasers are not dangerous

We investigated a region of repetitive DNA located in intron 40 of the von Willebrand factor (vWF) gene (nucleotides [nt] 1639–2404; i.e., F8VWF). We identified 13 alleles and 33 genotypes in 49 unrelated Japanese individuals. The heterozygosity of the region was 0.897. Direct sequence analyses revealed five single-base substitutions, one tetranucleotide (TTAT) insertion, and seven short tandem repeats (STRs) in the intron; four of the STRs and one single-base substitution had been reported previously. The four new base substitutions we identified were 1849T>A, 2122C>T, 2180C>T, and 2192C>T. The novel TTAT tetranucleotide was inserted between nt 2057 and 2058. The three newly identified STRs were 1978(TATC)1–2, 2193(ATCT)5–13, and 2234(TGTA)5–7. The five single-base substitutions and the TTAT insertion were identified only with 3′ downstream of vWA allele 14.

The Williams-Beuren Syndrome—A Window into Genetic Variants Leading to the Development of Cardiovascular Disease

Williams-Beuren Syndrome (WBS) arises when there is a genomic microdeletion at human chromosome 7q11.23 (Mouse 5G2), resulting in various cardiovascular, developmental, metabolic, and mental disorders [1]. Cardiovascular complications from WBS are a frequent cause of death. The deleted region is predisposed to non-allelic homologous recombination (NAHR) due to the presence of repetitive DNA regions called segmental duplications. WBS can result in deletions of up to 1.83 Mb in a region containing roughly 28 genes that includes the gene ELN encoding the tissue structural protein elastin [2]. Many of the cardiovascular features of WBS can be partially explained by elastin defects. WBS individuals have a combined prevalence of cardiovascular disease of 84% that includes supraand sub-aortic stenosis (SVAS); aortic, pulmonary, and mitral valvular disease; aortic coarctation; hypertension; and, less commonly, myocardial infarction [2,3]. These defects have also been found in mouse models [4]. Elastin not only provides ‘‘elastic’’ support for vessels, it also serves as a negative regulator for smooth muscle cell proliferation. WBS patients are also at high risk for hypertension and Eln mice are hypertensive [1,4]. In 2006, Del Campo et al. recognized that hemizygosity of the NCF1 gene as a result of the largest recognized WBS microdeletion—about 1.83 Mb—decreases the risk for hypertension in WBS patients compared to those possessing the more common smaller deletion (1.55 Mb) not incorporating NCF1 (Figure 1, top) [5]. NCF1 codes for p47, a critical subunit in the assembly of NADPH oxidase (NOX); homozygous deficiency accounts for 20% of patients with chronic granulomatous disease, a disorder associated with repeated infections due to an inability to kill bacteria. p47 is a major effector of angiotensin II (AngII), as demonstrated by a lack of elevation in blood pressure of Ncf1 mice [6]. In this issue of PLoS Genetics, Campuzano and colleagues replicate the WBS cardiovascular phenotype in a WBS mouse model with and without a deletion of the Ncf1 gene [7]. Their study has broad implications for our understanding of hypertensionand reactive oxygen species (ROS)-related cardiovascular disease.

Molecular typing of colorectal cancer: applications in diagnosis and treatment

Molecular typing of colorectal cancer (CRC) is at an early stage of development with analysis of KRAS mutation status and DNA mismatch repair (MMR) deficiency representing the two major approaches currently in use for diagnosis and treatment-related purposes. RAS proteins act as molecular switches that regulate cellular processes including cell growth and survival. Activating KRAS mutations are found in 40–50% of colorectal adenomas and cancers. Detection of KRAS mutations guide the decision to use anti-EGFR antibody therapy, which is not effective in KRAS mutant cancers. MMR deficiency results in failure to repair replication-associated DNA errors, allowing persistence of mismatch mutations all over the genome, especially in regions of repetitive DNA known as microsatellites, giving rise to microsatellite instability (MSI). A high frequency of microsatellite instability (MSI-H) often with abnormal expression of MMR proteins is key to the diagnosis of Lynch Syndrome, but is also observed in ∼15% of sporadic CRC.

Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR

BackgroundGenotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required.ResultsIn order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals.ConclusionThis study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

Telomere length is age-dependent and reduced in monocytes of Alzheimer patients

Telomeres are regions of repetitive DNA at the end of eukaryotic chromosomes, which prevent chromosomal instability. Telomere shortening is linked to age-related disease including Alzheimer's disease (AD) and has been reported to be reduced in leukocytes of AD patients. The aim of the present study was to measure telomere length in monocytes of patients with AD or mild cognitive impairment (MCI) compared to healthy subjects. Our data show significant shorter telomere length in AD patients (6.6±0.2kb; p=0.05) compared to controls (7.3±0.2kb). Telomere length of MCI patients did not differ compared to healthy subjects (7.0±0.2kb). We observe a strong correlation between telomere length and age (p=0.01, r=−0.38), but no association between telomere length and Mini-Mental State Examination score. In conclusion, the telomere length is age-dependent in monocytes and decreased in AD patients, which could mean that the AD pathology may contribute to telomere length shortening. The high variability of telomere lengths in individuals suggests that it will not be useful as a general biomarker for AD. However, it could become a biomarker in personalized long-term monitoring of an individuals’ health.

Identification and Analysis of Papillomavirus E2 Protein Binding Sites in the Human Genome

Papillomavirus E2 protein is required for the replication and maintenance of viral genomes and transcriptional regulation of viral genes. E2 functions through sequence-specific binding to 12-bp DNA motifs-E2 binding sites (E2BS)-in the virus genome. Papillomaviruses are able to establish persistent infection in their host and have developed a long-term relationship with the host cell in order to guarantee the propagation of the virus. In this study, we have analyzed the occurrence and functionality of E2BSs in the human genome. Our computational analysis indicates that most E2BSs in the human genome are found in repetitive DNA regions and have G/C-rich spacer sequences. Using a chromatin immunoprecipitation approach, we show that human papillomavirus type 11 (HPV11) E2 interacts with a subset of cellular E2BSs located in active chromatin regions. Two E2 activities, sequence-specific DNA binding and interaction with cellular Brd4 protein, are important for E2 binding to consensus sites. E2 binding to cellular E2BSs has a moderate or no effect on cellular transcription. We suggest that the preference of HPV E2 proteins for E2BSs with A/T-rich spacers, which are present in the viral genomes and underrepresented in the human genome, ensures E2 binding to specific binding sites in the virus genome and may help to prevent extensive and possibly detrimental changes in cellular transcription in response to the viral protein.

Both Polymorphic Variable Number of Tandem Repeats and Autoimmune Regulator Modulate Differential Expression of Insulin in Human Thymic Epithelial Cells

OBJECTIVEPolymorphic INS-VNTR plays an important role in regulating insulin transcript expression in the human thymus that leads to either insulin autoimmunity or tolerance. The molecular mechanisms underlying the INS-VNTR haplotype-dependent insulin expression are still unclear. In this study, we determined the mechanistic components underlying the differential insulin gene expression in human thymic epithelial cells, which should have profound effects on the insulin autoimmune tolerance induction.RESEARCH DESIGN AND METHODSA repetitive DNA region designated as a variable number of tandem repeats (VNTR) is located upstream of the human insulin gene and correlates with the incidence of type 1 diabetes. We generated six class I and two class III VNTR constructs linked to the human insulin basal promoter or SV40 heterologous promoter/enhancer and demonstrated that AIRE protein modulates the insulin promoter activities differentially through binding to the VNTR region.RESULTSHere we show that in the presence of the autoimmune regulator (AIRE), the class III VNTR haplotype is responsible for an average of three-fold higher insulin expression than class I VNTR in thymic epithelial cells. In a protein-DNA pull-down experiment, AIRE protein is capable of binding to VNTR class I and III probes. Further, the transcriptional activation of the INS-VNTR by AIRE requires the insulin basal promoter. The VNTR sequence loses its activation activity when linked to a heterologous promoter and/or enhancer.CONCLUSIONSThese findings demonstrate a type 1 diabetes predisposition encoded by the INS-VNTR locus and a critical function played by AIRE, which constitute a dual control mechanisms regulating quantitative expression of insulin in human thymic epithelial cells.

DNA Pol λˈs Extraordinary Ability To Stabilize Misaligned DNA

DNA polymerases have the venerable task of maintaining genome stability during DNA replication and repair. Errors, nonetheless, occur with error propensities that are polymerase specific. For example, DNA polymerase λ (pol λ) generates single-base deletions through template-strand slippage within short repetitive DNA regions much more readily than does the closely related polymerase β (pol β). Here we present in silico evidence to help interpret pol λ's greater tendency for deletion errors than pol β by its more favorable protein/DNA electrostatic interactions immediately around the extrahelical nucleotide on the template strand. Our molecular dynamics and free energy analyses suggest that pol λ provides greater stabilization to misaligned DNA than aligned DNA. Our study of several pol λ mutants of Lys544 (Ala, Phe, Glu) probes the interactions between the extrahelical nucleotide and the adjacent Lys544 to show that the charge of the 544 residue controls stabilization of the DNA misalignment. In addition, we identify other thumb residues (Arg538, Lys521, Arg517, and Arg514) that play coordinating roles in stabilizing pol λ's interactions with misaligned DNA. Interestingly, their aggregate stabilization effect is more important than that of any one component residue, in contrast to aligned DNA systems, as we determined from mutations of these key residues and energetic analyses. No such comparable network of stabilizing misaligned DNA exists in pol β. Evolutionary needs for DNA repair on substrates with minimal base-pairing, such as those encountered by pol λ in the non-homologous end-joining pathway, may have been solved by a greater tolerance to deletion errors. Other base-flipping proteins share similar binding properties and motions for extrahelical nucleotides.

Abstract 1160: Whole genome amplification and high-throughput sequencing of formalin-fixed paraffin-embedded colorectal cancer

Abstract Formalin-fixed paraffin-embedded (FFPE) tumors represent a valuable resource for translational cancer genomic research. However, genetic analysis of the FFPE material is challenging, as archived tissues are often small biopsies and the fixation process damages DNA. In researching a solution to this, we have evaluated the performance of different whole genome amplification methods for obtaining DNA samples from archived tumors and their use as a template in high-throughput sequencing. Two whole genome amplification methods were applied using 20 μm sections of FFPE colorectal cancer tissue and normal human genome DNA samples. Genomic DNA was amplified using Multiple Displacement Amplification (MDA) method and a modified version of Degenerate Oligonucleotide PCR (DOP) assay. Non-amplified human genomic DNA was used as a reference when genomic coverage, linearity and uniformity of the amplified products were assessed. Paired-end sequencing libraries were prepared from the DOP amplified templates while the MDA samples underwent single read library preparation. Sequencing was performed using an Illumina Genome Analyzer II. 2.5 million 54-mer reads mapping to the human genome were generated for each sample. Whole genome amplification was shown to produce artifacts when compared to non-amplified genomic DNA sequences. The modified DOP method preferentially amplified non-repetitive sequences in the human genome. Using the MDA-based method, genomic sequence coverage was generally more even between regions of repetitive and non-repetitive DNA. However, spread of the sequence read counts was greater in the MDA method and MDA amplification offered less dynamic range to identify copy number aberrations. Using whole genome amplification methods with the FFPE colorectal tumor sample we were able to generate 130 Mb of genomic sequence data and identify DNA copy number gains in chromosomes 13 and 20q. Whole genome amplification and high-throughput sequencing can be used to generate sequence data from minute amounts of FFPE material and identify DNA copy number aberrations in the archived tumors. Nonetheless, whole genome amplification produces artifacts by introducing bias towards specific regions of the genome, generating artificial and random DNA fragment assemblies (MDA) and introducing universal primer sequence in the ends of the amplified DNA fragments (DOP). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1160.

Switching cell fate: the remarkable rise of induced pluripotent stem cells and lineage reprogramming technologies

Cell reprogramming, in which a differentiated cell is made to switch its fate, is an emerging field with revolutionary prospects in biotechnology and medicine. The recent discovery of induced pluripotency by means of in vitro reprogramming has made way for unprecedented approaches for regenerative medicine, understanding human disease and drug discovery. Moreover, recent studies on regeneration and repair by direct lineage reprogramming in vivo offer an attractive novel alternative to cell therapy. Although we continue to push the limits of current knowledge in the field of cell reprogramming, the mechanistic elements that underlie these processes remain largely elusive. This article reviews landmark developments in cell reprogramming, current knowledge, and technological developments now on the horizon with significant promise for biomedical applications.

Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco

BackgroundSinorhizobium meliloti and S. medicae are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (Medicago sativa L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of Sinorhizobium nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco.ResultsRsaI digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as S. meliloti and the rest as S. medicae. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM), water stress (-1.5 MPa), high temperature (40°C) and low pH (3.5), respectively. Sixty-seven isolates of S. meliloti and thirteen isolates of S. medicae that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn) and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline). The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the S. meliloti and S. medicae strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P < 0.01) genetic variation was distributed within regions (89%) than among regions (11%).ConclusionHigh degree of phenotypic and genotypic diversity is present in S. meliloti and S. medicae populations from marginal soils affected by salt and drought, in arid and semi-arid regions of Morocco. Some of the tolerant strains have a potential for exploitation in salt and drought affected areas for biological nitrogen fixation in alfalfa.