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PubMed2006

Mitochondrial phylogeography and genetic diversity of Tibetan gazelle (Procapra picticaudata): implications for conservation.

The Tibetan gazelle (Procapra picticaudata) is a threatened species and distributed on the Qinghai-Tibet Plateau of China (Qinghai Province, Tibet Autonomous Region and the adjacent Gansu Province, Sichuan Province, and Xinjiang Uigur Autonomous Region). Small peripheral populations of Tibetan gazelle were once found in northern Sikkim and Ladakh, but now these are close to extinction. To describe the evolutionary history and to assess the genetic diversity within this monotypic species and population structure among different geographic locations in China, we sequenced mitochondrial DNA from the control region (CR) and cytochrome (cyt) b gene for 46 individuals from 12 geographic localities in Qinghai, Tibet, Xinjiang, Gansu, and Sichuan. A total of 25 CR haplotypes and 16 cyt b haplotypes were identified from these gazelle samples. CR haplotype diversity (0.98+/-0.01) and nucleotide diversity (0.08+/-0.009) were both high. Phylogenetic trees indicate that the Tibetan gazelle in China can be divided into three main clades: Tibet, Sichuan (SCH) and Qinghai-Arjin Shan-Kekexili (QH-ARJ-KKXL). Analysis of molecular variance (AMOVA) and network analysis consistently support this geographic structure in both datasets. Significant differentiation between populations argues for the presence of management units (MUs). Such differentiation may reflect a geographic separation resulting from the uplift of the Qinghai-Tibet Plateau during the Late Pliocene and Pleistocene. Mismatch distribution analysis implies that Tibetan gazelle has undergone complex population changes. We suggest that the present population structure has resulted from habitat fragmentation during the recent glacial period on the Qinghai-Tibet Plateau and population expansion from glacial refugia after the glacial period. It is likely that the present populations of Tibetan gazelle exhibit a pattern reminiscent of several bottlenecks and expansions in the recent past.

Animals↗
PubMed1998

Mitochondrial control region polymorphism reveal high amount of gene flow in Fennoscandian willow tits (Parus montanus borealis).

We studied the genetic variability and differentiation of two Fennoscandian willow tit (Parus montanus borealis) populations located ca. 1000 km apart in Finland and Sweden by using the control region sequences of the mitochondrial DNA. Individual variation in the control region was extensive since all the 13 Finnish and the 12 Swedish individuals had unique haplotypes and the mean pairwise genetic distance resulted in 0.0052 (range 0.0008-0.0109). In the minimum spanning network connecting the genotypes, the two populations were completely intermingled. The mismatch distribution of the combined data set was very close to expected distribution of an expanding population. This result was supported by a significantly negative Tajima's D value. The sequence data indicate that (1) the long-term effective population size of the breeding willow tits has been large (122,000 and 110,000 females for the Finnish and the Swedish populations, respectively); and that (2) the gene exchange between distant localities is/has been extensive. Dispersal area for the Finnish females was estimated to be about 19,000-30,000 km2 and for the Swedish, 22,000-28,000 km2. Thus, the whole Fennoscandian population can be regarded as one panmictic unit, without any subdivisions to local demes. The amount of gene flow is remarkable because the willow tit has been considered a highly sedentary species. Provided that adult birds are site-tenacious, the gene flow must occur through juvenile summer dispersal, or irruptive autumn invasions, or both.

Animals↗
PubMed1999

Systematic relationships within the dasyurid marsupial tribe Sminthopsini--a multigene approach.

We report analyses of complete DNA sequences of the mitochondrial cytochrome b (1146 bp), 12S rRNA (974 bp), partial control region (371 bp) loci, and the nuclear protamine P1 (616 bp) gene from all but one species (Sminthopsis butleri) of the dasyurid marsupial tribe Sminthopsini, as well as several outgroups. Parsimony analyses of combined nuclear and mitochondrial data suggest that Antechinomys is sister to a clade consisting of Sminthopsis and Ningaui. Parsimony, maximum-likelihood, and mixed-model distance analyses consistently resolve several species groups within Sminthopsis. The Macroura group includes S. macroura, S. virginiae, S. douglasi, and S. bindi; S. butleri is also included here on the basis of partial 12S rRNA sequences. S. crassicaudata is resolved as sister to the Macroura clade. The Murina group includes S. murina, S. leucopus, S. gilberti, S. dolichura, and S. archeri. S. griseoventer and S. aitkeni are resolved as a clade, and there is moderate support for a group consisting of the genetically divergent species S. psammophila, S. hirtipes, S. youngsoni, and S. ooldea (possibly along with S. longicaudata and S. granulipes). Compositions of species groups are partially congruent with clades previously proposed on the basis of morphological data. Radiations within Sminthopsini appear to be coincident with major environmental changes since the mid-Miocene.

Animals↗
PubMed2006

Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations.

We improve the taxon sampling for avian phylogeny by analyzing 7 new mitochondrial genomes (a toucan, woodpecker, osprey, forest falcon, American kestrel, heron, and a pelican). This improves inference of the avian tree, and it supports 3 major conclusions. The first is that some birds (including a parrot, a toucan, and an osprey) exhibit a complete duplication of the control region (CR) meaning that there are at least 4 distinct gene orders within birds. However, it appears that there are regions of continued gene conversion between the duplicate CRs, resulting in duplications that can be stable for long evolutionary periods. Because of this stable duplicated state, gene order can eventually either revert to the original order or change to the new gene order. The existence of this stable duplicate state explains how an apparently unlikely event (finding the same novel gene order) can arise multiple times. Although rare genomic changes have theoretical advantages for tree reconstruction, they can be compromised if these apparently rare events have a stable intermediate state. Secondly, the toucan and woodpecker improve the resolution of the 6-way split within Neoaves that has been called an "explosive radiation." An explosive radiation implies that normal microevolutionary events are insufficient to explain the observed macroevolution. By showing the avian tree is, in principle, resolvable, we demonstrate that the radiation of birds is amenable to standard evolutionary analysis. Thirdly, and as expected from theory, additional taxa breaking up long branches stabilize the position of some problematic taxa (like the falcon). In addition, we report that within the birds of prey and allies, we did not find evidence pairing New World vultures with storks or accipitrids (hawks, eagles, and osprey) with Falconids.

Animals↗
PubMed2005

[Study on mitochondrial DNA genetic polymorphism of some yak breeds in China].

This study determined yak's complete sequence of mitochondrial DNA control region (D-loop) of 35 individuals in 5 yak breeds at the first time. The result showed that the length of D-loop in yak was 891 -895 bp. Content of nucleotide T, C, A, G were 28.5%, 25.3%, 32.5% and 13.7% respectively. There were 55 polymorphic sites (6.16% in total analyzed sites). The transition,transversion and insertion/deletion were found in this region.24 haplotypes was defined in this study, in which haplotype H4 and H6 were major haplotypes of Chinese yak. The distribution of all the haplotypes among the breeds was disequilibrium. The average diversity of haplotypes were 0.9697 +/-0.0180, indicating the abundance of haplotypes of yak's D-loop. The average nucleotide difference and the nucleotide diversity in Chinese yak breeds were 10.936% and 1.231% respectively. Nucleotide divergence and Kimura 2-parameter distance between yak breeds were 0.760% -2.155%, and 0.000-0.029 respectively. The results indicated that the genetic diversity of Chinese yak was very abundant. Analysis of molecular variance and network construction results indicated that there was significant divergence among Chinese yak breeds. The network construction indicated that Chinese yak had been divided into 2 types and had probably 2 maternal origins or 2 domesticated places.

Animals↗
PubMed2002

Phylogeny of Antarctic dragonfishes (Bathydraconidae, Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes.

Although Antarctic teleosts of the suborder Notothenioidei are well studied, the status of some families remains unclear because of limited taxonomic sampling and sometimes poor statistical support from molecular phylogenies. It is true for the Bathydraconidae, the sister-family of the famous haemoglobin-less icefishes, the Channichthyidae. The present study is aimed at clarifying bathydraconid phylogeny and the interrelationships of higher notothenioid families, taking nototheniids as the outgroup. For this purpose, about 300 positions in the mitochondrial control region, 750 positions in the cytochrome b, and a matrix of morphological characters were employed for separate and simultaneous phylogenetic analyses. We conclude that (1) molecular data strongly support the split of bathydraconids into three clades, here called the Bathydraconinae (Bathydraco, Prionodraco, Racovitzia), the Gymnodraconinae (Gymnodraco, Psilodraco, Acanthodraco), and the Cygnodraconinae (Cygnodraco, Gerlachea, Parachaenichthys). Interrelationships between these three and the Channichthyidae remain unclear. Molecular data support neither paraphyly nor monophyly of the bathydraconids, while morphology leads to the monophyly of the family based on the synapomorphic loss of the spinous dorsal fin; (2) The Channichthyidae, the Harpagiferidae, and the Artedidraconidae are monophyletic families; (3) the phylogeny of the haemoglobin-less channichthyids is completely resolved and congruent with the conclusions of based on anatomical characters; (4) The present molecular results as well as other molecular studies favour the hypothesis that harpagiferids are the sister-group of artedidraconids, though our morphological matrix puts harpagiferids as the sister-group of all other families on the basis of a single character. With regard to harpagiferid relationships, it is interesting to notice that, when analysed simultaneously, morphological characters are not automatically "swamped" within molecular ones: in the tree based on the simultaneous analysis of all available data, morphological characters impose their topology on molecules.

Animals↗
PubMed2002

Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies.

Complete mitochondrial DNA (mtDNA) control regions (CR) were sequenced and analysed in order to investigate wild sheep taxonomy and the origin of domestic sheep (Ovis aries). The dataset for phylogenetic analyses includes 63 unique CR sequences from wild sheep of the mouflon (O. musimon, O. orientalis), urial (O. vignei), argali (O. ammon) and bighorn (O. canadensis) groups, and from domestic sheep of Asia, Europe and New Zealand. Domestic sheep occurred in two clearly separated branches with mouflon (O. musimon) mixed into one of the domestic sheep clusters. Genetic distances and molecular datings based on O. canadensis CR and mtDNA protein-coding sequences provide strong evidence for domestications from two mouflon subspecies. Other wild sheep sequences are in two additional well-separated branches. Ovis ammon collium and O. ammon nigrimontana are joined with a specimen from the transkaspian Ust-Urt plateau currently named O. vignei arkal. Ovis ammon ammon, O. ammon darwini and O. vignei bochariensis represent a separate clade and the earliest divergence from the mouflon group. Therefore, O. musimon, O. vignei bochariensis and Ust-Urt sheep are not members of a 'moufloniform' or O. orientalis species, but belong to different clades. Furthermore, Ust-Urt sheep could be a hybrid population or an O. ammon subspecies closely related to O. ammon nigrimontana.

Animals↗
PubMed1998

The BPV-4 co-carcinogen quercetin induces cell cycle arrest and up-regulates transcription from the LCR of BPV-4.

Bracken fern is the environmental co-carcinogen of BPV-4 in the induction of neoplasias of the upper alimentary canal of cattle. The flavonoid quercetin is one of the most potent and best characterised mutagens present in the fern. We have shown that transfection with BPV-4 DNA and exposure to a single dose of quercetin leads to tumorigenic transformation of primary bovine cells. We now show that quercetin induces cell cycle arrest and up-regulates transcription from the BPV-4 long control region (LCR). This up-regulation is mediated by a 21 nucleotide-long cis-element in the LCR, designated QRE-1, which is located immediately downstream of the TATA box. Cellular proteins bind to QRE-1 and removal or substitution of QRE-1 lead to the abrogation of the response to quercetin. As expression of the viral oncogenes is controlled by the LCR, perturbation in this control and increased oncoprotein expression are likely to contribute to fully malignant cell transformation by overcoming the cell cycle arrest induced by quercetin, thus forcing damaged cells to proliferate.

Adaptor Protein Complex alpha Subunits↗
PubMed2002

Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps.

We used noninvasive methods to obtain genetic and demographic data on the wolf packs (Canis lupus), which are now recolonizing the Alps, a century after their eradication. DNA samples, extracted from presumed wolf scats collected in the western Italian Alps (Piemonte), were genotyped to determine species and sex by sequencing parts of the mitochondrial DNA (mtDNA) control-region and ZFX/ZFY genes. Individual genotypes were identified by multilocus microsatellite analyses using a multiple tubes polymerase chain reaction (PCR). The performance of the laboratory protocols was affected by the age of samples. The quality of excremental DNA extracts was higher in samples freshly collected on snow in winter than in samples that were older or collected during summer. Preliminary mtDNA screening of all samples allowed species identification and was a good predictor of further PCR performances. Wolf, and not prey, DNA targets were preferentially amplified. Allelic dropout occurred more frequently than false alleles, but the probability of false homozygote determinations was always < 0.001. A panel of six to nine microsatellites would allow identification of individual wolf genotypes, also whether related, with a probability of identity of < 0.015. Genealogical relationships among individuals could be determined reliably if the number of candidate parents was 6-8, and most of them had been sampled and correctly genotyped. Genetic data indicate that colonizing Alpine wolves originate exclusively from the Italian source population and retain a high proportion of its genetic diversity. Spatial and temporal locations of individual genotypes, and kinship analyses, suggest that two distinct packs of closely related wolves, plus some unrelated individuals, ranged in the study areas. This is in agreement with field observations.

Animals↗
PubMed2002

An exceptional case of historical outbreeding in African sable antelope populations.

Empirical investigations of intraspecific outbreeding and subsequent introgressive hybridization in natural populations are rare, particularly among conspecific populations of large mammals. Using mitochondrial DNA data [partial control region (496 basepairs - bp) and cytochrome b gene (343 bp) sequences analysed from 95 individuals representing 17 sampling locations scattered through the African miombo (Brachystegia) woodland ecosystem] and phylogeographical statistical procedures (gene genealogy, nested cladistic and admixture proportion analyses), we (i) give a detailed dissection of the geographical genetic structure of Hippotragus niger; (ii) infer the processes and events potentially involved in the population history; and (iii) trace extensive introgressive hybridization in the species. The present-day sable antelope population shows a tripartite pattern of genetic subdivision representing West Tanzanian, Kenya/East Tanzanian and Southern Africa locations. Nested clade analysis revealed that past allopatric fragmentation, caused probably by habitat discontinuities associated with the East African Rift Valley system, together with intermediary episodic long-distance colonization and restricted, recurrent gene flow have played an predominant role in shaping the extent of maternal genetic diversity (10.4%) and population structure. An extensive (average rate of admixture = 20.0%), but geographically circumscribed and unidirectional hybridization event in the past was inferred, resulting in an extreme (the highest discovered so far in mammals) intraspecific difference of 18.2% among morphologically monotypic sable antelopes from West Tanzania. The results are used to provide an evolutionary framework within which taxonomic implications and conservation decisions can be evaluated.

Africa South of the Sahara↗
PubMed2006

Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic.

In Europe, southern peninsulas served as refugia during cold periods in the Pleistocene, acting both as centres of origin of endemisms and as sources from which formerly glaciated areas were recolonized during interglacial periods. Previous studies have revealed that within the main refugial areas, intraspecific lineages often survived in allopatric refugia. We analysed two mitochondrial markers (nad4, control region, approximately 1.4 kb) in 103 individuals representing the entire distribution of Lissotriton boscai, a newt endemic to the western Iberian Peninsula. We inferred the evolutionary history of the species through phylogenetic, phylogeographic and historical demographic analyses. The results revealed unexpected, deep levels of geographically structured genetic variability. We identified two main evolutionary lineages, each containing three well-supported clades. The first historical split involved populations from central-southwestern coastal Portugal and the ancestor of all the remaining populations around 5.8 million years ago. Both lineages were subsequently fragmented into different population groups between 2.5 and 1.2 million years ago. According to nested clade analysis, at lower hierarchical levels the patterns suggest restricted gene flow with isolation by distance, whereas at higher levels the clades exhibit signatures of contiguous range expansion. Bayesian Skyline Plots show recent bottlenecks, followed by demographic expansions in all lineages. The significant genetic structure found is consistent with long-term survival of populations in allopatric refugia, supporting the 'refugia-within-refugia' scenario for southern European peninsulas. The comparison of our results with other co-distributed species highlights the generality of this hypothesis for the Iberian herpetofauna and suggests that Mediterranean refuges had more relevance for the composition and distribution of present biodiversity patterns than currently acknowledged. We briefly discuss the taxonomic and conservation implications of our results.

Animals↗
PubMed2002

Yin Yang 1, Oct1, and NFAT-4 form repeating, cyclosporin-sensitive regulatory modules within the murine CD21 intronic control region.

The murine complement receptor type 2 gene (Cr2/CD21) is expressed by murine B and follicular dendritic cells, but not murine T cells. We have previously shown that appropriate transcriptional control of the CD21 gene requires the CD21 promoter as well as intronic sequences. We have also demonstrated that altering chromatin structure by inhibiting histone deacetylases induces CD21 expression in murine T cells by increasing the accessibility of promoter and intronic regulatory elements. In this report, we identify seven distinct regulatory areas within the first intron of the murine CD21 gene that are conserved between mouse and human CD21 intronic sequences. EMSA competition and supershift analyses reveal the formation of multiple DNA-protein complexes at these sites that include Yin Yang 1, Oct1, and NFAT-4. NFAT-containing complexes were altered in B cells treated with the NFAT inhibitor cyclosporin A and correlated with a repression of CD21 gene transcription implicating NFAT transcriptional control. Functional data revealed that no single region conferred cell-specific reporter gene expression, but rather the entire CD21 regulatory element was required to confer cell-specific gene expression. Taken together, these data demonstrate the formation of repeating, overlapping regulatory modules, all of which are required to coordinately control the cell-specific expression of the murine CD21 gene. We propose a model in which Yin Yang 1 and Oct1 may recruit histone deacetylase to multiple sites in the CD21 intronic regulatory element in nonexpressing cells and NFAT either displaces this histone deacetylase or recruits a histone acetylase to allow the formation of a functional transcriptional complex in expressing cells.

Animals↗
PubMed2005

Juxtaposition of the HPFH2 enhancer is not sufficient to reactivate the gamma-globin gene in adult erythropoiesis.

Previous studies have suggested that juxtaposition of a downstream enhancer to the fetal gamma-globin gene results in reactivation of the gamma-gene in adult erythrocytes of individuals with hereditary persistence of fetal hemoglobin (HPFH). To test the hypothesis in a much stricter basis, we produced beta locus YAC transgenic mice carrying an exact beta locus replicate of a deletional HPFH mutation, HPFH 2. Although the gamma-globin gene was expressed in the HPFH 2/beta locus YAC (HPFH2/YAC) transgenic mice in the early stage of development, it was completely silenced in the adult mice. The failure of gamma-gene reactivation by the juxtaposed HPFH2 enhancer contradicts the results of previous studies. We speculate that the discrepant results reflect differences in the distance between the locus of region (LCR) and the gamma-globin gene characteristic of the plasmid, cosmid or YAC constructs used for production of transgenic mice. The difference in the phenotype of the HPFH2/YAC transgenic mice and the humans with HPFH2 mutation suggests that in addition to juxtaposition of HPFH enhancers, the upstream region that is absent in the beta-YAC construct might be involved in gamma-gene reactivation in HPFH individuals. The DNase I hypersensitive sites of the LCR were well formed and the chromatin histones were acetylated. A moderate level of pol II binding was detected in the LCR, despite the fact that no transcription occurred in the globin-genes of the adult HPFH2/YAC transgenic mice. The results suggest that formation of the LCR chromatin structure in erythroid cells is independent of globin-gene transcription in the locus.

Acetylation↗
PubMed2005

A boundary for histone acetylation allows distinct expression patterns of the Ad4BP/SF-1 and GCNF loci in adrenal cortex cells.

Ad4BP/SF-1 is a nuclear receptor whose expression is restricted to tissues involved in steroid hormone synthesis such as the adrenal cortex and gonads. Recent sequence data analysis has shown that the Ad4BP/SF-1 gene is located only 13kb downstream of the last exon of the neighboring GCNF gene that is expressed in some neurons and gonadal germ cells. Despite the close proximity of the two genes, regulatory elements from one do not interfere with the transcription of the neighboring gene, resulting in distinct expression patterns of Ad4BP/SF-1 and GCNF. This observation has led to the prediction that an insulator element must exist between the two loci to establish independent transcription units. We performed DNase I hypersensitivity assays on the adrenal cortex cell line, Y-1, to test for the existence of an insulator. Three hypersensitive sites were identified in the region spanning 2.1kb between the last exon of GCNF and the first exon of Ad4BP/SF-1. The most upstream site contains a binding site for CTCF, a known insulator protein, while the other sites are predicted to associate with the nuclear matrix. Chromatin immunoprecipitation analysis using anti-acetylated histone H3 and H4 antibodies showed a discontinuous pattern of histone H3 and H4 acetylation upstream of these sites. Our data suggest that the chromatin architecture specialized by CTCF and the nuclear matrix contribute to the distinct pattern of transcriptional regulation of these genes.

Acetylation↗
PubMed2006

Broadening of DNA replication origin usage during metazoan cell differentiation.

We have examined whether replication of the chicken beta-globin locus changes during differentiation of primary erythroid progenitors into erythrocytes. In undifferentiated progenitors, four principal initiation sites and a replication fork pausing region (RFP) were observed. Forty-eight hours after induction of differentiation, the principal sites were maintained, even in the activated beta(A)-globin gene, some minor sites were enhanced, three new sites appeared and the RFP disappeared. One of the activated origins showed increased histone H3 K9K14 diacetylation, but the others did not. These results demonstrate a broadening of DNA replication origin usage during differentiation of untransformed metazoan cells and indicate that histone H3 diacetylation, other histone modifications so far reported and transcription are not crucial determinants of origin selection in this system.

Acetylation↗
PubMed2005

Extensively high load of internal tumors determined by whole body MRI scanning in a patient with neurofibromatosis type 1 and a non-LCR-mediated 2-Mb deletion in 17q11.2.

Deletions in 17q11.2 affecting the NF1 gene and surrounding regions occur in 5% of patients with NF1. The two major types of NF1 deletions encompass 1.4-Mb and 1.2-Mb, respectively, and have breakpoints in the NF1 low-copy repeats or in the JJAZ gene and its pseudogene. Deletions larger than 1.4-Mb are rare, and only seven cases have been reported so far. Here, we describe a 26-year-old NF1 patient with an "atypical" NF1 deletion of 2-Mb. In contrast to the 1.4-Mb deletions, which preferentially occur by interchromosomal recombination during maternal meiosis, the deletion described here occurred intrachromosomally on the paternal chromosome. The centromeric deletion breakpoint lies in an L1-element located 1.3-Mb proximal to the NF1 gene. The telomeric deletion boundary is located in a single copy segment between an AT-rich segment and an AluSx-element in intron 15 of the JJAZ1 gene. Structural analysis implies that non-B DNA conformations at the breakpoints destabilized the duplex DNA and caused double-strand breaks. Although the breakpoints of this 2-Mb deletion are not recurrent, it is conspicuous that one breakpoint is located in the JJAZ1 gene. Paralogous recombination between the JJAZ1 gene and its pseudogene causes the recurrent 1.2 Mb deletions. The genomic architecture of the NF1 gene region, influenced by paralogous sequences such as the JJAZ1 gene and its pseudogene, seems also to stimulate the occurrence of non-recurrent deletions mediated by non-homologous end joining. Patient 442 described here suffers from a very high burden of subdermal neurofibromas. Magnetic resonance imaging of the whole body revealed numerous internal tumors, mainly plexiform neurofibromas and spinal tumors. This demonstrates the value of whole-body MRI scanning in determining the total tumor load, which is an important aspect in genotype/phenotype correlations with regard to large NF1 deletions.

Adult↗
PubMed2006

Genetic characterization of strains of Saccharomycescerevisiae responsible for 'refermentation' in Botrytis-affected wines.

AIMS: Saccharomyces cerevisiae is responsible for alcoholic fermentation of wines. However, some strains can also spoil sweet Botrytis-affected wines. Three 'refermentation' strains were isolated during maturation. Characterization of those strains in regards to their fingerprint, rDNA sequence and resistance to SO2, which constituted the main source of stress in Botrytis-affected wines, was carried out. METHODS AND RESULTS: Refermentation strains could be clearly discriminated by interdelta fingerprinting. However, they exhibited close relationships by karyotyping. A part of RDN1 locus sequence was examined by using PCR-RFLP and PCR-DGGE. The resistance of refermentation strains to SO2 was performed by using real time quantitative PCR focusing on SSU1 gene. CONCLUSIONS: Results suggested that refermentation strains were heterozygote in 26S rDNA and their ITS1-5.8S rDNA-ITS2 region sequence revealed relationships with 'flor' strains. As described in the literature for flor strain, two out of three refermentation strains constitutively developed a higher level of SSU1 expression than the reference strains, improving their putative tolerance to SO2. Therefore, refermentation strains of S. cerevisiae had developed many strategies to survive during maturing sweet wines. SIGNIFICANCE AND IMPACT OF THE STUDY: Singularities in rDNA sequence and SSU1 overexpression revealed a natural adaptation. Moreover, genomic relationship between flor and refermentation strains suggested that stress sources could induced selection of survivor strains.

Acetaldehyde↗
PubMed2003

Transcriptional activation of the enterocyte differentiation marker intestinal alkaline phosphatase is associated with changes in the acetylation state of histone H3 at a specific site within its promoter region in vitro.

Enterocyte differentiation is thought to occur through the transcriptional regulation of a small subset of specific genes. A recent growing body of evidence indicates that post-translational modifications of chromatin proteins (histones) play an important role in the control of gene transcription. Previous work has demonstrated that one such modification, histone acetylation, occurs in an in vitro model of enterocyte differentiation, butyrate-treated HT-29 cells. In the present work, we sought to determine if the epigenetic signal of histone acetylation occurs in an identifiable pattern in association with the transcriptional activation of the enterocyte differentiation marker gene intestinal alkaline phosphatase (IAP). HT-29 cells were maintained under standard culture conditions and differentiated with sodium butyrate. The chromatin immunoprecipitation (ChIP) assay was used to compare the acetylation state of histones associated with specific regions of the IAP promoter in the two cell populations (undifferentiated vs. differentiated). Chromatin was extracted from cells and cleaved by sonication or enzymatic digestion to obtain fragments of approximately 200 to 600 base-pairs, as confirmed by polymerase chain reaction using primers designed to amplify the IAP segments of interest. The ChIP assay selects DNA sequences that are associated with acetylated histones by immunoprecipitation. Unbound segments represent DNA sequences whose histones are not acetylated. After immunoprecipitation, sequences were detected by radiolabeled polymerase chain reaction, and the relative intensity of the bands was quantified by densitometry. The relative acetylation state of histones at specific sites was determined by comparing the ratios of bound/unbound segments. We determined that in a segment of the IAP promoter between -378 and -303 base-pairs upstream from the transcriptional start site, the acetylation state of histone H3 increased twofold in the differentiated, IAP expressing cells, whereas that of histone H4 remained essentially constant. Additionally, at a distant site, between -1378 and -1303 base-pairs, the acetylation state of H3 and H4 did not change appreciably between the undifferentiated and differentiated cells. We conclude that butyrate-induced differentiation is associated with specific and localized changes in the histone acetylation state within the IAP promoter. These changes within the endogenous IAP gene may underlie its transcriptional activation in the context of the enterocyte differentiation program.

Alkaline Phosphatase↗