DNA diagnostics for reliable and universal identification of .

Reliable diagnostics are a major challenge for the detection and treatment of () infection. Currently at the forefront are non-invasive urea breath test (UBT) and stool antigen test (SAT). Polymerase chain reaction (PCR) is not endorsed due to nonspecific primers and the threat of false-positives.

WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas.

Many hereditary cancer syndromes are associated with an increased risk of small and large intestinal adenocarcinomas. However, conditions bearing a high risk to both adenocarcinomas and neuroendocrine tumors are yet to be described. We studied a family with 16 individuals in four generations affected by a wide spectrum of intestinal tumors, including hyperplastic polyps, adenomas, small intestinal neuroendocrine tumors, and colorectal and small intestinal adenocarcinomas.

Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization.

mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA.

Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease-Associated Colorectal Cancer.

Background & Aims: Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs.

Reliable and Sensitive Nested PCR for the Detection of in Sputum.

Chlamydia are Gram-negative, intracellular pathogens colonizing epithelial mucosa. They cause primarily atypical pneumonia and have recently been associated with chronic diseases. Diagnostics relies almost exclusively on serological methods; PCR tests are used rarely because in patients with positive ELISA, it is nearly impossible to identify chlamydial DNA.

Candidate Predisposition Variants in Kaposi Sarcoma as Detected by Whole-Genome Sequencing.

Familial clustering of classic Kaposi sarcoma (CKS) is rare with, approximately 100 families reported to date. We studied 2 consanguineous families, 1 Iranian and 1 Israeli, with multiple cases of adult CKS and without overt underlying immunodeficiency. We performed genome-wide linkage analysis and whole-genome sequencing to discover the putative genetic cause for predisposition.

Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival.

Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains poorly understood. Although retrotransposons are usually repressed, they become active in several human cancers, in particular those of the gastrointestinal tract. Here we characterize retrotransposon insertions in 202 colorectal tumor whole genomes and investigate their associations with molecular and clinical characteristics.

Contribution of allelic imbalance to colorectal cancer.

Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge.

The complete mitochondrial DNA sequence from Kazachstania sinensis reveals a general +1C frameshift mechanism in CTGY codons.

The complete mitochondrial DNA (mtDNA) sequence from Kazachstania sinensis was analysed and compared to mtDNA from related yeasts. It contained the same set of genes; however, it only contained 23 tRNAs, as the trnR2 gene was absent. Most of the 12 introns within cox1, cob and rnl genes were inserted in the same sites as in other yeasts; however, two introns in rnl were in unusual positions.

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing.

Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction.

The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'.

The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species.

Post-zygotic sterility and cytonuclear compatibility limits in S. cerevisiae xenomitochondrial cybrids.

Nucleo-mitochondrial interactions, particularly those determining the primary divergence of biological species, can be studied by means of xenomitochondrial cybrids, which are cells where the original mitochondria are substituted by their counterparts from related species. Saccharomyces cerevisiae cybrids are prepared simply by the mating of the ρ(0) strain with impaired karyogamy and germinating spores from other Saccharomyces species and fall into three categories. Cybrids with compatible mitochondrial DNA (mtDNA) from Saccharomyces paradoxus CBS 432 and Saccharomyces cariocanus CBS 7994 are metabolically and genetically similar to cybrids containing mtDNA from various S.

The reassignment of three 'lost' Taphrina species (Taphrina bullata, Taphrina insititiae and Taphrina rhizophora) supported by the divergence of nuclear and mitochondrial DNA.

The ascomycetous genus Taphrina Fries originally contained more than 90 phytopathogenic microscopic dimorphic ascomycetes causing specific infections in different vascular plants. Although species have mainly been identified historically according to their host and morphological and physiological traits, they can be studied and preserved in the form of yeasts arising from germinating ascospores. Due to low DNA sequence divergence and the lack of available strains, the number of accepted Taphrina species has currently been reduced to 28.

A complete sequence of Saccharomyces paradoxus mitochondrial genome that restores the respiration in S. cerevisiae.

We determined the complete sequence of 71 355-bp-long mitochondrial genome from Saccharomyces paradoxus entirely by direct sequencing of purified mitochondrial DNA (mtDNA). This mtDNA possesses the same features as its close relative Saccharomyces cerevisiae - A + T content 85.9%, set of genes coding for the three components of cytochrome oxidase, cytochrome b, three subunits of ATPase, both ribosomal subunits, gene for ribosomal protein, rnpB gene, tRNA package (24) and yeast genetic code.

Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis contains the NADH dehydrogenase subunit genes.

The progenitor of the Dekkera/Brettanomyces clade separated from the Saccharomyces/Kluyveromyces clade over 200 million years ago. However, within both clades, several lineages developed similar physiological traits. Both Saccharomyces cerevisiae and Dekkera bruxellensis are facultative anaerobes; in the presence of excess oxygen and sugars, they accumulate ethanol (Crabtree effect) and they both spontaneously generate respiratory-deficient mutants (petites).

Geotrichum bryndzae sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces.

Ten strains of an asexual arthroconidial yeast species were isolated from Bryndza, a traditional Slovak artisanal sheep cheese, which was manufactured from raw milk during a 4-month summer production period at two Slovakian sites (the northern RuZomberok and the central-southern Tisovec areas). Sequence comparison of the D1/D2 domains of the large-subunit rRNA gene revealed that this yeast represents a novel species of the genus Geotrichum, which contains anamorphs of the ascogenous genus Galactomyces, for which the name Geotrichum bryndzae sp. nov.

The diversity of eukaryotic microbiota in the traditional Slovak sheep cheese--bryndza.

We investigated the occurrence and diversity of yeasts and filamentous fungi in bryndza an artisanal Slovak soft spreadable cheese prepared from raw sheep milk or from a mixture of sheep and cow milk. Samples collected during four months of the summer production period from two locations (northern and southern parts of central Slovakia) contained 10(5)-10(7) (cfu) yeasts and about 10(2) (cfu) of mold per gram of wet weight. Further characterization by conventional taxonomy and sequence comparison of D1/D2 region from 26S rRNA gene revealed Mucor circinelloides v.

Transition of the ability to generate petites in the Saccharomyces/Kluyveromyces complex.

Petite-positivity - the ability to tolerate the loss of mtDNA - was examined after the treatment with ethidium bromide (EB) in over hundred isolates from the Saccharomyces/Kluyveromyces complex. The identity of petite mutants was confirmed by the loss of specific mtDNA DAPI staining patterns. Besides unequivocal petite-positive and petite-negative phenotypes, a few species exhibited temperature sensitive petite positive phenotype and petiteness of a few other species could be observed only at the elevated EB concentrations.

Fermentative lifestyle in yeasts belonging to the Saccharomyces complex.

The yeast Saccharomyces cerevisiae is characterized by its ability to: (a) degrade glucose or fructose to ethanol, even in the presence of oxygen (Crabtree effect); (b) grow in the absence of oxygen; and (c) generate respiratory-deficient mitochondrial mutants, so-called petites. How unique are these properties among yeasts in the Saccharomyces clade, and what is their origin? Recent progress in genome sequencing has elucidated the phylogenetic relationships among yeasts in the Saccharomyces complex, providing a framework for the understanding of the evolutionary history of several modern traits. In this study, we analyzed over 40 yeasts that reflect over 150 million years of evolutionary history for their ability to ferment, grow in the absence of oxygen, and generate petites.

The KlPGS1 gene encoding phosphatidylglycerolphosphate synthase in Kluyveromyces lactis is essential and assigned to chromosome I.

The phosphatidylglycerolphosphate synthase (CDP-diacylglycerol:sn-glycerol-3-phosphate 3-phosphatidyltransferase, EC 2.7.8.

The efficiency of functional mitochondrial replacement in Saccharomyces species has directional character.

Optimal interactions among nuclear and mitochondria-coded proteins are required to assemble functional complexes of mitochondrial oxidative phosphorylation. The communication between the nuclear and mitochondrial genomes has been studied by transplacement of mitochondria from related species into mutants devoid of mitochondrial DNA (rho0). Recently we have reported that the mitochondria transferred from Saccharomyces paradoxus restored partially the respiration in Saccharomyces cerevisiae rho0 mutants.

High-rate evolution of Saccharomyces sensu lato chromosomes.

Forty isolates belonging to the Saccharomyces sensu lato complex were analyzed for one nuclear and two mitochondrial sequences, and for their karyotypes. These data are useful for description and definition of yeast species based on the phylogenetic species concept. The deduced phylogenetic relationships among isolates based on the nuclear and mitochondrial sequences were usually similar, suggesting that horizontal transfer/introgression has not been frequent.

GC clusters and the stability of mitochondrial genomes of Saccharomyces cerevisiae and related yeats.

The occurrence of GC clusters in Saccharomyces spp. and related yeasts was examined to clarify their association with the stability of intact mitochondrial genome. Abundance of nonspecific or specific GC clusters in these species decreases with phylogenetic distance from S.