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Directional gene silencing induced by a complex subtelomeric satellite from Drosophila.

The telomeric regions in Drosophila cause transcriptional silencing of integrated transgenes. A complex satellite has recently been identified in the subterminal region of the left arm of chromosome 2 that is a good candidate for the source of the observed telomeric silencing, because genetically marked transposable elements that have inserted into this subtelomeric array show repression and variegation of the reporter gene. We asked whether this satellite can also cause transcriptional repression in ectopic chromosomal positions by placing it upstream of a mini-white reporter gene in P element constructs used for germ line transformation. The transgenes are shielded from external influences at the integration site using SU(HW) binding sites at either end. It was found that the satellite represses transcription of the reporter gene in an orientation dependent and an array length dependent manner. The satellite does not, however, induce variegation under the conditions used. The repressed transgenes do not respond to typical modifiers of centromeric position effect variegation, such as Su(var)2055, Su(var)2-11, Su(var)3-11, and Su(var)3-61, or to the addition of a Y chromosome. However, as with the original variegating telomeric insertion, suppression in the transgenes is relieved by Su(z)25, suggesting that suppression induced by the subtelomeric satellite retains aspects of telomeric silencing in ectopic positions.

ATP-Binding Cassette Transporters↗

Molecular mechanisms of epigenetics.

The main epigenetic mechanisms in regulation of gene expression are discussed. The definition of epigenetics and its specific mechanisms including DNA methylation and gene imprinting, modifications of nucleosomal histones associated with silencing or activation of gene transcription, RNA interference, chromosomal silencing, and the role of mobile elements are discussed.

Acetylation↗

Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms.

Abundant human interspersed repetitive DNA sequences of the form (dC-dA)n.(dG-dT)n have been shown to exhibit length polymorphisms. Examination of over 100 human (dC-dA)n.(dG-dT)n sequences revealed that the sequences differed from each other both in numbers of repeats and in repeat sequence type. Using a set of precise classification rules, the sequences were divided into three categories: perfect repeat sequences without interruptions in the runs of CA or GT dinucleotides (64% of total), imperfect repeat sequences with one or more interruptions in the run of repeats (25%), and compound repeat sequences with adjacent tandem simple repeats of a different sequence (11%). Informativeness of (dC-dA)n.(dG-dT)n markers in the perfect sequence category was found to increase with increasing average numbers of repeats. PIC values ranged from 0 at about 10 or fewer repeats to above 0.8 for sequences with about 24 or more repeats. (dC-dA)n.(dG-dT)n polymorphisms in the imperfect sequence category showed lower informativeness than expected on the basis of the total numbers of repeats. The longest run of uninterrupted CA or GT repeats was found to be the best predictor of informativeness of (dC-dA)n.(dG-dT)n polymorphisms regardless of the repeat sequence category.

Base Sequence↗

Heritable alteration in DNA methylation pattern occurred specifically at mobile elements in rice plants following hydrostatic pressurization.

Intrinsic DNA methylation pattern is an integral component of the epigenetic network in many eukaryotes. Exploring the extent to which DNA methylation patterns can be altered under a specific condition is important for elucidating the biological functions of this epigenetic modification. This is of added significance in plants wherein the newly acquired methylation patterns can be inherited through organismal generations. We report here that DNA methylation patterns of mobile elements but not of cellular genes were specifically altered in rice plants following hydrostatic pressurization. This was evidenced by methylation-sensitive gel-blot analysis, which showed that 10 out of 10 studied low-copy transposons and retrotransposons manifested methylation alteration in at least one of the 8 randomly chosen pressure-treated plants, whereas none of the 16 studied low-copy cellular genes showed any change. Both gel-blotting and genome-wide fingerprinting indicated that the methylation alteration in mobile elements was not accompanied by a general genetic instability. Progeny analysis indicated retention of the altered methylation patterns in most progeny plants, underscoring early occurrence of the alterations, and their faithful epigenetic inheritance.

Cytosine↗

AGG interspersion analysis of the FMR1 CGG repeats in mental retardation of unspecific cause.

OBJECTIVES: To study the AGG interspersion pattern in mentally retarded patients of unspecified cause. METHODS: FMR1 CGG substructure in 104 normal and 232 mentally retarded (MR) males was determined by CGG repeat and AGG interspersion analyses. Genomic DNA of the study subjects was obtained for PCR and Southern hybridization analyses. RESULTS: All study subjects had less than 53 CGG repeats and none had fragile X syndrome of mental retardation. There was a significant difference (P < 0.006) in the AGG interspersion pattern. MR males had (1) more variable internal substructures, (2) proportionally less 2 and 3 AGG but more 0 and 1 AGG, less (CGG)(9)AGG(CGG)(9)AGG(CGG)(9) but more (CGG)(9)AGG(CGG)(19) alleles and (3) a longer pure 3' CGG repeat. CONCLUSIONS: Our results suggest that the MR alleles have a lesser number of interspersed AGG and a longer pure 3' CGG repeat than the normal population. They are thus more prone to instability and expansion to long repeat lengths as in the fragile X syndrome of mental retardation.

Alleles↗

Centrosomes: Sfi1p and centrin unravel a structural riddle.

The discovery of Sfi1p as a novel binding partner for the Ca2+-binding protein centrin has provided new insight into the dynamic behavior of centrosomes. Sfi1 binds to multiple centrin molecules along a series of internal repeats, and the complex forms Ca2+-sensitive contractile fibers that function to reorient centrioles and alter centrosome structure.

Calcium↗

A modified automated high-throughput mycobacterial interspersed repetitive unit method for genotyping Mycobacterium tuberculosis.

A total of 502 isolates of Mycobacterium tuberculosis collected in Taiwan were genotyped using a modified and high-throughput typing system involving mycobacterial interspersed repetitive units. The Hunter-Gaston discriminatory index improved significantly to 0.972 with the modified 15-locus scheme, including ETR-A, ETR-B, and ETR-C, compared with 0.951 for the previously reported 12-locus design.

Bacterial Typing Techniques↗

Evaluation of multiple genetic markers for typing drug-resistant Mycobacterium tuberculosis strains from Poland.

In the present study, 77 drug-resistant Mycobacterium tuberculosis strains isolated in Poland in 2000 were characterized by the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and our novel method based on PCR amplification of DNA regions between IS6110 and 16-bp GC-rich frequent repeats (designated IS6110-Mtb1/Mtb2 PCR). The results were compared with previous data of the more commonly used methods, IS6110 restriction fragment length polymorphism (RFLP) and spoligotyping. The discriminatory power of IS6110-Mtb1/Mtb2 method was only slightly lower than that of IS6110 RFLP, whereas MIRU-VNTR typing was the least discriminative among the 4 methods used. Clustering of strains by using results of IS6110-Mtb1/Mtb2 PCR correlated well with RFLP-defined clusters, further confirming epidemiologic relationships among patients. These results indicate that the novel genotyping method could be an attractive alternative for other PCR-based typing procedures, such as spoligotyping and MIRU-VNTR typing. Also, it seems to be a valuable adjunct to the reference IS6110 RFLP method for studying the genetic diversity of drug-resistant M. tuberculosis strains in Poland.

Bacterial Typing Techniques↗

Enterobacterial repetitive intergenic consensus PCR is a useful tool for typing Mycobacterium chelonae and Mycobacterium abscessus isolates.

Outbreaks of rapidly growing mycobacterium (RGM) infections are increasingly being reported worldwide. Information about genetic relatedness of isolates obtained during outbreaks can provide opportunities for prompt intervention. Pulsed-field gel electrophoresis (PFGE) is expensive, time consuming, and labor intensive. Other than that, Mycobacterium abscessus isolates can suffer DNA degradation during electrophoresis. Polymerase chain reaction (PCR)-based methods are cheaper, faster, and easier to perform, but discriminatory power varies depending on the primer used. In this study, we tested the competence of enterobacterial repetitive intergenic consensus (ERIC) PCR in comparison with PFGE to distinguish unrelated isolates (24 Mycobacterium chelonae and 24 M. abscessus) obtained from human and/or environmental samples and to group 56 isolates from 6 outbreaks confirmed epidemiologically, caused by M. chelonae and M. abscessus after ophthalmologic refractive surgery and mesotherapy. Enterobacterial repetitive intergenic consensus PCR presented discriminatory power, calculated using Simpson's index of diversity, of 0.989 for M. abscessus and 0.975 for M. chelonae and grouped outbreak isolates in distinct groups showing epidemiologic concordance. Pulsed-field gel electrophoresis also grouped outbreak isolates and presented discriminatory power of 0.972 and 0.993 for M. abscessus and M. chelonae, respectively. DNA from 8 (22%) of 36 M. abscessus isolates analyzed showed degradation during electrophoresis. Compared with PFGE and epidemiologic information as the gold standard, ERIC PCR is a simple, high throughput, affordable, reproducible, and discriminatory molecular typing method for inference of genetic relatedness of RGMs of the M. chelonae-abscessus group.

Bacteriological Techniques↗

A review focusing on mechanisms and ecological risks of enrichment and propagation of antibiotic resistance genes and mobile genetic elements by microplastic biofilms.

Microplastics (MPs) are emerging ubiquitous pollutants in aquatic environment and have received extensive global attention. In addition to the traditional studies related to the toxicity of MPs and their carrier effects, their unique surface-induced biofilm formation also increases the ecotoxicity potential of MPs from multiple perspectives. In this review, the ecological risks of MPs biofilms were summarized and assessed in detail from several aspects, including the formation and factors affecting the development of MPs biofilms, the selective enrichment and propagation mechanisms of current pollution status of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in MPs biofilms, the dominant bacterial communities in MPs biofilms, as well as the potential risks of ARGs and MGEs transferring from MPs biofilms to aquatic organisms. On this basis, this paper also put forward the inadequacy and prospects of the current research and revealed that the MGEs-mediated ARG propagation on MPs under actual environmental conditions and the ecological risk of the transmission of ARGs and MGEs to aquatic organisms and human beings are hot spots for future research. Relevant research from the perspective of MPs biofilm should be carried out as soon as possible to provide support for the ecological pollution prevention and control of MPs.

Biofilms↗

Trypanosoma brucei s.l.: characterisation of stocks from Central Africa by PCR analysis of mobile genetic elements.

To better understand the epidemiology of sleeping sickness in the Central African sub-region, notably the heterogeneity of Human African Trypanosomiasis (HAT) foci, the mobile genetic element PCR (MGE-PCR) technique was used to genotype Trypanosoma brucei s.l. (T. brucei s.l.) isolates from this sub-region. Using a single primer REV B, which detects positional variation of the mobile genetic element RIME, via amplification of flanking regions, MGE-PCR revealed a micro genetic variability between Trypanosoma brucei gambiense (T. b. gambiense) isolates from Central Africa. The technique also revealed the presence of several T. b. gambiense genotypes and allowed the identification of minor and major ubiquitous genotypes in HAT foci. The presence of several T. b. gambiense genotypes in HAT foci may explain the persistence and the resurgence phenomena of the disease and also the epidemic and the endemic status of some Central African sleeping sickness foci. The MGE-PCR technique represents a simple, rapid, and specific method to differentiate Central African T. brucei s.l. isolates.

Africa, Central↗

Inference of human geographic origins using Alu insertion polymorphisms.

The inference of an individual's geographic ancestry or origin can be critical in narrowing the field of potential suspects in a criminal investigation. Most current technologies rely on single nucleotide polymorphism (SNP) genotypes to accomplish this task. However, SNPs can introduce homoplasy into an analysis since they can be identical-by-state. We introduce the use of insertion polymorphisms based on short interspersed elements (SINEs) as a potential alternative to SNPs. SINE polymorphisms are identical-by-descent, essentially homoplasy-free, and inexpensive to genotype using a variety of approaches. Herein, we present results of a blind study using 100 Alu insertion polymorphisms to infer the geographic ancestry of 18 unknown individuals from a variety of geographic locations. Using a Structure analysis of the Alu insertion polymorphism-based genotypes, we were able to correctly infer the geographic affiliation of all 18 unknown human individuals with high levels of confidence. This technique to infer the geographic affiliation of unknown human DNA samples will be a useful tool in forensic genomics.

Alu Elements↗

Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome.

Interspersed repeats are a major component of most eukaryotic genomes and have an impact on genome size and stability, but the repetitive element landscape of crocodilian genomes has not yet been fully investigated. In this report, we provide the first detailed characterization of an interspersed repeat element in any crocodilian genome. Chompy is a putative miniature inverted-repeat transposable element (MITE) family initially recovered from the genome of Alligator mississippiensis (American alligator) but also present in the genomes of Crocodylus moreletii (Morelet's crocodile) and Gavialis gangeticus (Indian gharial). The element has all of the hallmarks of MITEs including terminal inverted repeats, possible target site duplications, and a tendency to form secondary structures. We estimate the copy number in the alligator genome to be approximately 46,000 copies. As a result of their size and unique properties, Chompy elements may provide a useful source of genomic variation for crocodilian comparative genomics.

Alligators and Crocodiles↗

Molecular characterisation and mechanisms of resistance of multidrug-resistant human Salmonella enterica serovar Typhimurium isolated in Amiens (France).

Antimicrobial resistance patterns of Salmonella enterica serovar Typhimurium isolates obtained during the study period were examined. The molecular epidemiology and the mechanisms of resistance to ampicillin, chloramphenicol and tetracycline were investigated. Resistance to ampicillin increased from 59% between 1996 and 1999 to 62.5% in 2000 and to 66.6% in 2001. Of 51 S. Typhimurium isolates studied, 100% were resistant to ampicillin (minimum inhibitory concentration (MIC)>256 mg/L) and sulphonamide (MIC range, 128 to >256 mg/L). Ninety-eight percent of isolates were resistant to streptomycin (MIC range, 48-256 mg/L), 92.2% to tetracycline (MIC range, 32 to >256 mg/L), 88.2% to chloramphenicol (MIC>256 mg/L), 21.5% to sulphamethoxazole/trimethoprim (MIC>32 mg/L), 5.8% to amoxicillin/clavulanic acid (MIC, 32 mg/L) and 1.9% to cefalothin (MIC, 64mg/L). Six resistance phenotypes were found (a-f), with phenotypes a (47%) and b (27.5%) being predominant. Twenty-five (49%) of 51 isolates produced a single beta-lactamase, among which 48% produced PSE-1, 44% produced TEM-1 and 8% produced OXA-1. Among 26 of the 51 isolates, 10 produced PSE-1+OXA-1, 7 produced TEM-1+PSE-1+OXA-1, 6 produced TEM-1+PSE-1, and 3 produced TEM-1+OXA-1. Forty-eight (94.1%) of the 51 isolates had the plasmid-mediated resistance gene flo(ST) to chloramphenicol and tetracycline. Combining enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) and pulsed-field gel electrophoresis (PFGE), 16 distinct patterns were identified, among which patterns IA (35.3%) and IF (27.4%) were considered as epidemic patterns. The dendrogram obtained from S. Typhimurium pulsotypes allowed five clones (S1-S5) to be identified, with two prevalent clones comprising 47.8% (S2) and 27.3% (S4) of the isolates.

Ampicillin Resistance↗

The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.

The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.

Humans↗

The Horizontal Gene Pool: an ESF workshop summary.

The European Science Foundation (ESF) funds a limited number of exploratory workshops each year that enable scientists to meet and develop plans for a program of integrated research which would benefit from a coordinated European effort. In summer 2003, the Standing Committee for Life and Environmental Sciences (LESC) sponsored such a workshop called The Horizontal Gene Pool: The Functional Role of Mobile Genetic Information--How Bacteria Perceive, Sample, and Utilize Genetic Elements in evolution and Local Adaptation. The workshop took place at St. Catherine's College, Oxford, UK. Its purpose was to identify how recent advances in the application of genomics and microbial ecology can be harnessed to determine the genetic mechanisms that underpin the biological role of the horizontal gene pool. Scientific excellence at the workshop was contributed by senior scientists and young investigators from research institutes located in nine European countries.

Bacteria↗

Bap: a family of surface proteins involved in biofilm formation.

A group of surface proteins sharing several structural and functional features is emerging as an important element in the biofilm formation process of diverse bacterial species. The first member of this group of proteins was identified in a Staphylococcus aureus mastitis isolate and was named Bap (biofilm-associated protein). As common structural features, Bap-related proteins: (i) are present on the bacterial surface; (ii) show a high molecular weight; (iii) contain a core domain of tandem repeats; (iv) confer upon bacteria the capacity to form a biofilm; (v) play a relevant role in bacterial infectious processes; and (vi) can occasionally be contained in mobile elements. This review summarizes recent studies that have identified and assigned roles to Bap-related proteins in biofilm biology and virulence.

Bacteria↗