Postglacial Recolonization of Continental Europe by the Pygmy Shrew (Sorex minutus) Inferred From Mitochondrial and Y Chromosomal DNA Sequences

2009 ◽  
pp. 217-236 ◽  
Author(s):  
Allan D. McDevitt ◽  
Glenn Yannic ◽  
Ramugondo V. Rambau ◽  
Thomas J. Hayden ◽  
Jeremy B. Searle
Keyword(s):  
Dna Sequences ◽  
Chromosomal Dna ◽  
Postglacial Recolonization ◽  
Sorex Minutus ◽  
Pygmy Shrew

scholarly journals Small-mammal assemblages inhabiting Sphagnum peat bogs in various regions of Poland

2012 ◽  
Vol 49 (2) ◽  
pp. 115-133
Author(s):  
Mateusz Ciechanowski ◽  
Jan Cichocki ◽  
Agnieszka Ważna ◽  
Barbara Piłacińska
Keyword(s):  
Small Mammal ◽  
Western Europe ◽  
Habitat Degradation ◽  
Myodes Glareolus ◽  
Peat Bogs ◽  
Trophic Conditions ◽  
Characteristic Features ◽  
Mammal Assemblages ◽  
Sorex Minutus ◽  
Pygmy Shrew

Abstract We studied species composition of assemblages of small mammals (rodents and shrews) inhabiting Polish 25 ombrotrophic mires and quaking bogs in several regions in order to reveal characteristic features of their quantitative structure and compare them between regions, internal zones of the bog habitats, and different levels of anthropogenic degradation. We reviewed also all published results of small-mammal trapping in such habitats. Mammals were captured in pitfalls, snap traps and live traps on 12 bogs of the Pomerania region, 4 bogs of the Orawa-Nowy Targ Basin (Kotlina Orawsko-Nowotarska), 3 bogs in the Świętokrzyskie Mts, and 6 bogs in Wielkopolska and the Lubusz Land. Additionally, we included materials collected from Barber traps (pitfalls) used during studies of epigeic invertebrates on 4 bogs. In total, 598 individuals of 12 species were collected. The number of pitfall captures per 100 trapnights was very low (7.0-7.8), suggesting low population density. Shrews predominated among mammals captured in pitfalls, and the assemblage structure appeared to be similar to impoverished forest fauna, slightly enriched with ubiquitous species from meadows and agroecosystems, with a very small percentage of typical wetland species (Neomys fodiens, Neomys anomalus, Microtus oeconomus). Rodents (mostly Myodes glareolus) predominated only in samples obtained by live and snap traps. Pygmy shrew Sorex minutus was the most numerous species at most sites, sometimes being the only small mammal in that habitat, especially in well-preserved, treeless parts of bogs, dominated by Sphagnum peatmoss. The dominance and high constancy of S. minutus appear to be a characteristic feature of small-mammal assemblages inhabiting ombrotrophic mires, at least in some regions of Central and Western Europe. Enrichment of the fauna with other species might be related to either improved trophic conditions (by contact with mineralized ground waters) or habitat degradation (by peat mining, drainage, and subsequent secondary succession).

scholarly journals Recombination hotspots as a point process

2005 ◽  
Vol 360 (1460) ◽  
pp. 1597-1603 ◽  
Author(s):  
Maria De Iorio ◽  
Eric de Silva ◽  
Michael P.H Stumpf
Keyword(s):  
Point Process ◽  
Dna Sequences ◽  
Recombination Rate ◽  
Population Genetic ◽  
Process Model ◽  
Chromosomal Dna ◽  
New Approach ◽  
Recombination Hotspots ◽  
Minimum Number ◽  
Fully Bayesian

The variation of the recombination rate along chromosomal DNA is one of the important determinants of the patterns of linkage disequilibrium. A number of inferential methods have been developed which estimate the recombination rate and its variation from population genetic data. The majority of these methods are based on modelling the genealogical process underlying a sample of DNA sequences and thus explicitly include a model of the demographic process. Here we propose a different inferential procedure based on a previously introduced framework where recombination is modelled as a point process along a DNA sequence. The approach infers regions containing putative hotspots based on the inferred minimum number of recombination events; it thus depends only indirectly on the underlying population demography. A Poisson point process model with local rates is then used to infer patterns of recombination rate estimation in a fully Bayesian framework. We illustrate this new approach by applying it to several population genetic datasets, including a region with an experimentally confirmed recombination hotspot.

scholarly journals Triple-Helical DNA in Drosophila Heterochromatin

Cells ◽  
2018 ◽  
Vol 7 (12) ◽  
pp. 227 ◽  
Author(s):  
Eduardo Gorab
Keyword(s):  
Nucleic Acids ◽  
Dna Sequences ◽  
Detection Methods ◽  
Triplex Dna ◽  
Thiazole Orange ◽  
Chromosomal Dna ◽  
Mitotic Chromosomes ◽  
Satellite Repeats

Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences. The satellite probe hybridized to AAGAG-containing regions omitting chromosomal DNA denaturation, as expected, for the intra-molecular triplex DNA formation model in which single-stranded DNA coexists with triplexes. In addition, Thiazole Orange, previously described as capable of reproducing results obtained by antibodies to triple-helical DNA, binds to AAGAG repeats in situ thus validating both detection methods. Unusual phenotype and nuclear structure exhibited by Drosophila correlate with the non-canonical conformation of tandem satellite arrays. From the approaches that lead to the identification of triple-helical DNA in chromosomes, facilities particularly provided by Thiazole Orange use may broaden the investigation on the occurrence of triplex DNA in eukaryotic genomes.

scholarly journals SirR, a Novel Iron-Dependent Repressor inStaphylococcus epidermidis

1998 ◽  
Vol 66 (9) ◽  
pp. 4123-4129 ◽  
Author(s):  
Philip J. Hill ◽  
Alan Cockayne ◽  
Patrick Landers ◽  
Julie A. Morrissey ◽  
Catriona M. Sims ◽  
...  
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Blot Analysis ◽  
Target Genes ◽  
Consensus Sequence ◽  
Dependent Manner ◽  
Chromosomal Dna ◽  
Iron Starvation ◽  
Mobility Shift ◽  
Western Blots

ABSTRACT In Staphylococcus epidermidis and Staphylococcus aureus, a number of cell wall- and cytoplasmic membrane-associated lipoproteins are induced in response to iron starvation. To gain insights into the molecular basis of iron-dependent gene regulation in the staphylococci, we sequenced the DNA upstream of the 3-kb S. epidermidis sitABC operon, which Northern blot analysis indicates is transcriptionally regulated by the growth medium iron content. We identified two DNA sequences which are homologous to elements of the Corynebacterium diphtheriae DtxR regulon, which controls, in response to iron stress, for example, production of diphtheria toxin, siderophore, and a heme oxygenase. Upstream of thesitABC operon and divergently transcribed lies a 645-bp open reading frame (ORF), which codes for a polypeptide of approximately 25 kDa with homology to the DtxR family of metal-dependent repressor proteins. This ORF has been designated SirR (staphylococcal iron regulator repressor). Within thesitABC promoter/operator region, we also located a region of dyad symmetry overlapping the transcriptional start ofsitABC which shows high homology to the DtxR operator consensus sequence, suggesting that this region, termed the Sir box, is the SirR-binding site. The SirR protein was overexpressed, purified, and used in DNA mobility shift assays; SirR retarded the migration of a synthetic oligonucleotide based on the Sir box in a metal (Fe2+ or Mn2+)-dependent manner, providing confirmatory evidence that this motif is the SirR-binding site. Furthermore, Southern blot analysis of staphylococcal chromosomal DNA with the synthetic Sir box as a probe confirmed that there are at least five Sir boxes in the S. epidermidis genome and at least three in the genome of S. aureus, suggesting that SirR controls the expression of multiple target genes. Using a monospecific polyclonal antibody raised against SirR to probe Western blots of whole-cell lysates of S. aureus, S. carnosus,S. epidermidis, S. hominis, S. cohnii, S. lugdunensis, and S. haemolyticus, we identified an approximately 25-kDa cross-reactive protein in each of the staphylococcal species examined. Taken together, these data suggest that SirR functions as a divalent metal cation-dependent transcriptional repressor which is widespread among the staphylococci.

scholarly journals Phylogeographical structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe

2020 ◽  
Vol 129 (4) ◽  
pp. 901-917 ◽  
Author(s):  
Rodrigo Vega ◽  
Allan D McDevitt ◽  
Joanna Stojak ◽  
Alina Mishta ◽  
Jan M Wójcik ◽  
...  
Keyword(s):  
Demographic History ◽  
Glacial Refugia ◽  
Intraspecific Diversity ◽  
Evolutionary Potential ◽  
Mountain Ranges ◽  
Early Diversification ◽  
Patterns And Processes ◽  
Sorex Minutus ◽  
Pygmy Shrew ◽  
The Last Glacial

Abstract Southern and northern glacial refugia are considered paradigms that explain the complex phylogeographical patterns and processes of European biota. Here, we provide a revisited statistical phylogeographical analysis of the pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae), examining its genetic diversity, genetic differentiation and demographic history in the Mediterranean peninsulas and in Western and Central Europe. The results showed support for genetically distinct and diverse phylogeographical groups consistent with southern and northern glacial refugia, as expected from previous studies. We also identified geographical barriers concordant with glaciated mountain ranges during the Last Glacial Maximum (LGM), early diversification events dated between the Late Pleistocene and Early Holocene for the main phylogeographical groups, and recent (post-LGM) patterns of demographic expansions. This study is the most comprehensive investigation of this species to date, and the results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.

scholarly journals Measurement of transcribed human X-chromosomal DNA sequences transferred to rodent cells by chromosome-mediated gene transfer.

1982 ◽  
Vol 2 (1) ◽  
pp. 52-65 ◽  
Author(s):  
O W McBride ◽  
A S Olsen ◽  
G S Aulakh ◽  
R S Athwal
Keyword(s):  
Dna Sequences ◽  
Genetic Information ◽  
Hybrid Cell ◽  
Single Copy ◽  
Nucleic Acid Hybridization ◽  
Chromosomal Dna ◽  
Metaphase Chromosomes ◽  
Transfer Event ◽  
Donor Chromosome ◽  
Labeled Probe

Transfer of genetic information can be effected by incubation of cultured eucaryotic cells with isolated metaphase chromosomes. In most cases, a resulting transformed cell contains only a fragment of a donor chromosome. The amount of transferred donor DNA has been quantified in 11 independent mouse A9 transformants by nucleic acid hybridization analysis. Each transformant had been selected for hprt (hypoxanthine phosphoribosyltransferase; EC 2.4.2.8) transfer and contained part of the human X chromosome. A labeled probe of transcribed human X-chromosomal DNA was prepared by hybridization of nick-translated unique-sequence human DNA with whole cellular RNA from a human-mouse hybrid cell line, A9/HRBC2-A, containing a single human chromosome., X. The amount of human X-chromosomal DNA in the transformants was quantitated by comparing the hybridization of this probe with transformant and A9/HRBC2-A DNAs. Two unstable transformants which had a microscopically detectable donor chromosome fragment contained 15% of the human X-chromosomal single-copy DNA. Four other unstable transformants contained 4 to 7% of human X-chromosomal DNA sequences. The transferred DNA was below the level of detection in three other unstable and in all three stable transformants. We conclude that the initial transfer event can introduce a substantial amount of genetic information but only smaller amounts of DNA are stably incorporated by integration.

Clarification of chromosomal abnormalities associated with sexual ambiguity by studies with Y-chromosomal DNA sequences

1988 ◽  
Vol 47 (3) ◽  
pp. 140-143 ◽  
Author(s):  
J.R.D. Stalvey ◽  
R.P. Erickson ◽  
M. Dasouki ◽  
T. Glover ◽  
M. Shokir
Keyword(s):  
Dna Sequences ◽  
Chromosomal Abnormalities ◽  
Chromosomal Dna ◽  
Sexual Ambiguity

scholarly journals Construction, replication, and chromatin structure of TRP1 RI circle, a multiple-copy synthetic plasmid derived from Saccharomyces cerevisiae chromosomal DNA.

1982 ◽  
Vol 2 (3) ◽  
pp. 221-232 ◽  
Author(s):  
V A Zakian ◽  
J F Scott
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Dna Sequences ◽  
Recombinant Dna ◽  
Suitable Model ◽  
Chromosomal Dna ◽  
Base Pairs ◽  
Autonomously Replicating Sequence ◽  
Cell Cycles ◽  
Initiation Of Replication

Transformation studies with Saccharomyces cerevisiae (bakers' yeast) have identified DNA sequences which permit extrachromosomal maintenance of recombinant DNA plasmids in transformed cells. It has been hypothesized that such sequences (called ARS for autonomously replicating sequence) serve as initiation sites for DNA replication in recombinant DNA plasmids and that they represent the normal sites for initiation of replication in yeast chromosomal DNA. We have constructed a novel plasmid called TRP1 R1 Circle which consists solely of 1,453 base pairs of yeast chromosomal DNA. TRP1 RI Circle contains both the TRP1 gene and a sequence called ARS1. This plasmid is found in 100 to 200 copies per cell and is relatively stable during both mitotic and meiotic cell cycles. Replication of TRP1 RI Circle requires the products of the same genes (CDC28, CDC4, CDC7, and CDC8) required for replication of chromosomaL DNA. Like chromosomal DNA, its replication does not occur in cells arrested in the B1 phase of the cell cycle by incubation with the yeast pheromone alpha-factor. In addition, TRP1 RI Circle DNA is organized into nucleosomes whose size and spacing are indistinguishable from that of bulk yeast chromatin. These results indicate that TRP1 RI Circle has the replicative and structural properties expected for an origin of replication from yeast chromosomal DNA. Thus, this plasmid is a suitable model for further studies of yeast DNA replication in both cells and cell-free extracts.

scholarly journals Long-Range Mapping of the Streptococcus agalactiae Phylogenetic Lineage Restriction Digest Pattern Type III-3 Reveals Clustering of Virulence Genes

2002 ◽  
Vol 70 (1) ◽  
pp. 134-139 ◽  
Author(s):  
John F. Bohnsack ◽  
April A. Whiting ◽  
Russell D. Bradford ◽  
Brenna K. Van Frank ◽  
Shinji Takahashi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Streptococcus Agalactiae ◽  
Virulence Genes ◽  
Physical Map ◽  
Group B Streptococcus ◽  
Subtractive Hybridization ◽  
Chromosomal Dna ◽  
Type Iii ◽  
Phylogenetic Lineage ◽  
Restriction Digest

ABSTRACT Human isolates of serotype III Streptococcus agalactiae (group B streptococcus [GBS]) can be divided into three separate phylogenetic lineages based on analysis of the restriction digest patterns (RDPs) of chromosomal DNA. Nine DNA sequences that are present in all isolates of the RDP III-3 phylogenetic lineage, but not in the other lineages, were identified by genomic subtractive hybridization. A complete physical map of a III-3 chromosome was constructed. Six of the nine III-3-specific sequences mapped to a 340-kb Sse8387I fragment which contains or is located close to known GBS virulence genes. One of the III-3-specific probes, AW-10, encodes part of GBSi1, a group II intron that is inserted at two sites within the GBS genome. The second chromosomal site for GBSi1 was isolated, sequenced, and mapped to a location near the locus responsible for hemolysin production. These findings suggest that the genetic variation that distinguishes the RDP type III-3 strains from other serotype III strains occurs largely within localized areas of the genome containing known or putative virulence genes.

scholarly journals Replication timing of DNA sequences associated with human centromeres and telomeres.

1990 ◽  
Vol 10 (12) ◽  
pp. 6348-6355 ◽  
Author(s):  
K G Ten Hagen ◽  
D M Gilbert ◽  
H F Willard ◽  
S N Cohen
Keyword(s):  
Dna Sequences ◽  
Cell Sorting ◽  
Replication Timing ◽  
S Phase ◽  
Alpha Satellite ◽  
Chromosomal Dna ◽  
Telomeric Sequences ◽  
Alpha Satellite Dna ◽  
Satellite Sequences ◽  
Satellite Repeats

The timing of replication of centromere-associated human alpha satellite DNA from chromosomes X, 17, and 7 as well as of human telomeric sequences was determined by using density-labeling methods and fluorescence-activated cell sorting. Alpha satellite sequences replicated late in S phase; however, the alpha satellite sequences of the three chromosomes studied replicated at slightly different times. Human telomeres were found to replicate throughout most of S phase. These results are consistent with a model in which multiple initiations of replication occur at a characteristic time within the alpha satellite repeats of a particular chromosome, while the replication timing of telomeric sequences is determined by either telomeric origins that can initiate at different times during S phase or by replication origins within the flanking chromosomal DNA sequences.

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