bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography of endemic ermine (Mustela erminea) in southeast Alaska
Authors: Fleming Melissa A. , Cook Joseph A. 
Published: March 2003

AbstractThe North Pacific Coast (NPC) of North America is a region of high mammalian endemism, possibly due to its highly fragmented landscape and complex glacial history. For example, four island and one mainland subspecies of ermine,Mustela erminea, have been described as endemic to southeast Alaska alone. To better understand the role of past climatic change in generating diversity in the region, we examined DNA sequence variation in the mitochondrial cytochrome b gene of 210 ermine from across North America, with an emphasis on Alaska and British Columbia. We found three distinct (1.5–3.6% uncorrected ‘p’) lineages of ermine, all of which occur in southeast Alaska. One lineage includes a southeast Alaska endemic and specimens from Alaska (outside of southeast) and Eurasia. A second lineage includes two southeast Alaskan endemics and ermine from western Canada and the coterminous United States. The close relationships of these purported endemics to ermine outside of southeast Alaska suggest that they colonized the region from Beringian and southern glacial refugia, respectively, following deglaciation of the NPC. The third lineage appears restricted to the Prince of Wales Island complex in southeast Alaska (two subspecies) and Graham Island (Haida Gwaii), British Columbia. This restricted distribution suggests that these populations may be derived from relicts that persisted in a coastal refugium during the Wisconsin glaciation. Studies of nuclear genes and adaptive morphological evolution are necessary to further explore discrepancies between the geographical pattern of differentiation based on mtDNA and the existing subspecific taxonomy based on morphology.
Comparative phylogeography of sympatric sister species, Clevelandia ios and Eucyclogobius newberryi (Teleostei, Gobiidae), across the California Transition Zone
Authors: Dawson M. N , Louie K. D. , Barlow M. , Jacobs D. K. , Swift C. C. 
Published: March 2003

AbstractIt is paradigmatic in marine species that greater dispersal ability often, but not always, results in greater gene flow and less population structure. Some of the exceptions may be attributable to studies confounded by comparison of species with dissimilar evolutionary histories, i.e. co‐occurring species that are not closely related or species that are closely related but allopatric. Investigation of sympatric sister species, in contrast, should allow differences in phylogeographic structure to be attributed reliably to recently derived differences in dispersal ability. Here, using mitochondrial DNA control region sequence, we first confirm that Clevelandia ios and Eucyclogobius newberryi are sympatric sister taxa, then demonstrate considerably shallower phylogeographic structure in C. ios than in E. newberryi. This shallower phylogeographic structure is consistent with the higher dispersal ability of C. ios, which most likely results from the interaction of habitat and life‐history differences between the species. We suggest that the paradigm will be investigated most rigorously by similar studies of other sympatric sister species, appended by thorough ecological studies, and by extending this sister‐taxon approach to comparative phylogeographic studies of monophyletic clades of sympatric species.
Recent introduction of the dominant tunicate,Pyura praeputialis(Urochordata, Pyuridae) to Antofagasta, Chile
Authors: Castilla J. C. , Collins A. G. , Meyer C. P. , Guiñez R. , Lindberg D. R. 
Published: March 2003

AbstractThe large sessile tunicatePyura stolonifera(Pleurogona: Stolibranchiata: Pyuridae), has been regarded as a complex taxon with disjointed distributions, including Australia (Pyura stolonifera praeputialis), South Africa (Pyura stolonifera stolonifera) and South America (Chile, Antofagasta:Pyurasp., the ‘piure de Antofagasta’), and has been cited under at least five taxonomic combinations. The ‘piure de Antofagasta’ is a competitively dominant species in rocky intertidal habitats and shows a limited geographical range (60–70 km) exclusively inside the Bay of Antofagasta. Using cytochrome oxidase I (COI) mitochondrial sequence data fromPyuraspecimens of the three taxa we tested whether the Chilean taxon represents: (i) a Gondwana relict; (ii) a more recently divergent species; or (iii) a recently introduced species. The results suggest that the Chilean taxon is a recent introduction to Chile from Australian populations and thatPyura stolonifera praeputialis, from Australia, and the ‘piure de Antofagasta’ are geographical populations of a single species:Pyura praeputialis; whereas the South African taxon represents a second species:Pyura stolonifera.
Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)
Authors: Williams Barry L. , Brawn Jeffrey D. , Paige Ken N. 
Published: March 2003

AbstractDetection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.
The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins
Authors: Yang Chien‐Chin , Huang Chih‐Hung , Li Chien‐Yi , Tsay Yeou‐Guang , Lee Sheng‐Chung , Chen Carton W. 
Published: March 2003

SummaryThe chromosomes of the soil bacteria Streptomyces, unlike those of most other bacteria, are linear DNA molecules. Their telomeres contain long‐terminal inverted repeats and covalently bound terminal proteins (TPs). These bacteria also harbour linear plasmids that share the same structural features. In this study, we demonstrated that the TP was covalently bound to the 5′ ends as proposed previously. A linear plasmid with chromosomal telomeres was constructed and used to purify the TPs of the Strep‐tomyces coelicolor A3(2) chromosome. A 20 kDa protein and its 10 kDa degradation product were isolated and their sequences determined by mass spectrometry. The coding sequence (tpgC) was about 100 kb from the right end of the chromosome. Two tpg homologues were identified by sequencing the 50 kb linear plasmid SLP2 of Streptomyces lividans: tpgSLP2 at 6 kb from the left end and a putative tpg pseudogene at 8 kb from the right. The latter was in a terminal repeat shared by the right end of SLP2 and both ends of the S. lividans chromosome. The lack of the typical Streptomyces codon preference in this open reading frame suggests that it is a pseudogene. The close physical linkage between the tpg genes and their cognate telomeres would favour their co‐segregation and co‐evolution. All the Tpg polypeptides are similar in length (184–185 amino acids) and sequences, which include a putative helix domain that is homologous to part of the DNA‐binding ‘thumb’ domain of HIV reverse transcriptase, and a putative amphiphilic beta‐sheet that may be involved in the observed self‐aggregation of the TP and/or the proposed membrane binding.
Control of the AcrAB multidrug efflux pump by quorum‐sensing regulator SdiA
Authors: Rahmati Sonia , Yang Shirley , Davidson Amy L. , Zechiedrich E. Lynn 
Published: March 2003

SummarySdiA is an Escherichia coli protein that regulates cell division in a cell
density‐dependent, or quorum‐sensing, manner. We report that SdiA also controls multidrug
resistance by positively regulating the multidrug resistance pump AcrAB. Overproduction
of SdiA confers multidrug resistance and increased levels of AcrAB. Conversely, sdiA null mutants are hypersensitive to drugs and have decreased levels of AcrB protein. Our findings provide a link between quorum sensing and multidrug efflux. Combined with previously published reports, our data support a model in which a role of drug efflux pumps is to mediate cell–cell communication in response to cell density. Xenobiotics expelled by pumps may resemble the communication molecules that they normally efflux.
Phage P4 origin‐binding domain structure reveals a mechanism for regulation of DNA‐binding activity by homo‐ and heterodimerization of winged helix proteins
Authors: Yeo Hye‐Jeong , Ziegelin Günter , Korolev Sergey , Calendar Richard , Lanka Erich , Waksman Gabriel 
Published: March 2003

SummaryThe origin‐binding domain of the gpα protein of phage P4 (P4‐OBD) mediates

origin recognition and regulation of gpα activity by the protein Cnr.

We have determined the crystal structure of P4‐OBD at 2.95 Å resolution. The

structure of P4‐OBD is that of a dimer with pseudo twofold symmetry. Each subunit

has a winged helix topology with a unique structure among initiator proteins. The

only structural homologue of the P4‐OBD subunit is the DNA‐binding domain of the

eukaryotic transcriptional activator Rfx1. Based on this structural alignment, a

model for origin recognition by the P4‐OBD dimer is suggested. P4‐OBD mutations that

interfere with Cnr binding locate to the dimer interface, indicating that Cnr acts

by disrupting the gpα dimer. P4‐OBD dimerization is mediated by helices

α1 and α3 in both subunits, a mode of winged helix protein dimerization that is reminiscent of that of the eukaryotic transcription factors E2F and DP. This, in turn, suggests that Cnr is also a winged helix protein, a possibility that is supported by previously unreported sequence homologies between Cnr and Rfx1 and homology modelling. Hence, in a mechanism that appears to be conserved from phage to man, the DNA‐binding activity of winged helix proteins can be regulated by other winged helix proteins via the versatile use of the winged helix motif as a homo‐ or heterodimerization scaffold.
The fle1 gene encoding a C2H2 zinc finger protein co‐ordinates male and female sexual differentiation in Podospora anserina
Authors: Coppin Evelyne 
Published: March 2003

SummaryThe flexuosa (fle1‐1) mutant, isolated in Podospora anserina,

displays vegetative defects and two antagonistic sexual phenotypes: it produces several

1000‐fold fewer microconidia (male gametes) than the wild‐type strain and, conversely,

more abundant protoperithecia (female organs). Cloning and sequencing of the fle1

gene and of cDNA identified an open reading frame encoding a 382‐amino‐acid polypeptide

with two C2H2 zinc finger motifs. The predicted FLE1 protein shares 46% identity

with the FlbC protein of Aspergillus nidulans and 68% identity

with a putative protein identified by a search in the Neurospora crassa database.

The nuclear localization of FLE1 was demonstrated by fusion with the green fluorescent

protein. Sequencing of the fle1‐1 mutant allele revealed a frameshift mutation

upstream of the zinc finger domain. The fle1‐1 mutant was a null mutant, as

targeted disruption of fle1 sequence led to the same pleiotropic phenotype.

When fle1 was overexpressed by introduction of a transgenic copy of the native

fle1 gene or a fusion with a strong promoter, formation of protoperithecia

was impaired, leading to partial or complete female sterility. We propose that fle1 acts as a repressor of female sexual differentiation in order to maintain the balance between male and female sexual pathways.
The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants
Authors: Oliver Antonio , Baquero Fernando , Blázquez Jesús 
Published: March 2003

SummaryWe have recently described the presence of a high proportion of Pseudomonas

aeruginosa isolates (20%) with an increased mutation frequency (mutators)

in the lungs of cystic fibrosis (CF) patients. In four out of 11 independent P.

aeruginosa strains, the high mutation frequency was found to be complemented

with the wild‐type mutS gene from P. aeruginosa PAO1. Here, we report

the cloning and sequencing of two additional P. aeruginosa mismatch repair

genes and the characterization, by complementation of deficient strains, of these

two putative P. aeruginosa mismatch repair genes (mutL and uvrD).

We also describe the alterations in the mutS, mutL and uvrD

genes responsible for the mutator phenotype of hypermutable P. aeruginosa

strains isolated from CF patients. Seven out of the 11 mutator strains were found

to be defective in the MMR system (four mutS, two mutL and one uvrD).

In four cases (three mutS and one mutL), the genes contained frameshift

mutations. The fourth mutS strain showed a 3.3 kb insertion after the 10th

nucleotide of the mutS gene, and a 54 nucleotide deletion between two eight

nucleotide direct repeats. This deletion, involving domain II of MutS, was found

to be the main one responsible for mutS inactivation. The second mutL

strain presented a K310M mutation, equivalent to K307 in Escherichia coli

MutL, a residue known to be essential for its ATPase activity. Finally, the uvrD

strain had three amino acid substitutions within the conserved ATP binding site of

the deduced UvrD polypeptide, showing defective mismatch repair activity. Interestingly,

cells carrying this mutant allele exhibited a fully active UvrABC‐mediated excision

repair. The results shown here indicate that the putative P. aeruginosa mutS,

mutL and uvrD genes are mutator genes and that their alteration results in a mutator phenotype.
Sin recombinase fromStaphylococcus aureus: synaptic complex architecture and transposon targeting
Authors: Rowland Sally‐J. , Stark W. Marshall , Boocock Martin R. 
Published: March 2003

SummaryThe Sin recombinase fromStaphylococcus aureusbuilds a distinctive DNA‐protein synaptic complex to regulate strand exchange. Sin binds at two sites within an 86 basepair (bp) recombination site,resH. We propose that inverted motifs at the crossover site, and tandem motifs at the regulatory site, are recognized by structurally disparate Sin dimers. An essential architectural protein, Hbsu, binds at a discrete central site inresH. Positions of Hbsu‐induced DNA deformation coincide with natural targets for Tn552integration. Remarkably, Sin has the same topological selectivity as Tn3and γδ resolvases. Our model for the recombination synapse has at its core an assembly of four Sin dimers; Hbsu plays an architectural role that is taken by two resolvase dimers in models of the Tn3/γδ synapse.
Overexpression of White Collar‐1 (WC‐1) activates circadian clock‐associated genes, but is not sufficient to induce most light‐regulated gene expression in Neurospora crassa
Authors: Lewis Z. A. , Correa A. , Schwerdtfeger C. , Link K. L. , Xie X. , Gomer R. H. , Thomas T. , Ebbole D. J. , Bell‐Pedersen D. 
Published: March 2003

SummaryMany processes in fungi are regulated by light, but the molecular mechanisms are not well understood. The White Collar‐1 (WC‐1) protein is required for all known blue‐light responses in Neurospora crassa. In response to light, WC‐1 levels increase, and the protein is transiently phosphorylated. To test the hypothesis that the increase in WC‐1 levels after light treatment is sufficient to activate light‐regulated gene expression, we used microarrays to identify genes that respond to light treatment. We then overexpressed WC‐1 in dark‐grown tissue and used the microarrays to identify genes regulated by an increase in WC‐1 levels. We found that 3% of the genes were responsive to light, whereas 7% of the genes were responsive to WC‐1 overexpression in the dark. However, only four out of 22 light‐induced genes were also induced by WC‐1 overexpression, demonstrating that changes in the levels of WC‐1 are not sufficient to activate all light‐responsive genes. The WC proteins are also required for circadian rhythms in dark‐grown cultures and for light entrainment of the circadian clock, and WC‐1 protein levels show a circadian rhythm in the dark. We found that representative samples of the mRNAs induced by over‐expression of WC‐1 show circadian fluctuations in their levels. These data suggest that WC‐1 can mediate both light and circadian responses, with an increase in WC‐1 levels affecting circadian clock‐responsive gene regulation and other features of WC‐1, possibly its phosphorylation, affecting light‐responsive gene regulation.
Sequence‐specific interaction of nascent antiterminator RNA with the zinc‐finger motif of Escherichia coli RNA polymerase
Authors: Sen Ranjan , King Rodney A. , Mzhavia Nino , Madsen Peter L. , Weisberg Robert A. 
Published: March 2003

SummaryThe N‐terminal Zn‐finger motif of the β′ subunit of RNA polymerase contains two pairs of invariant cysteines flanking a moderately well‐conserved segment of 13 amino acids that is rich in basic residues. Previous work showed that replacement of certain Zn‐finger residues prevented transcription antitermination in response to phage HK022 put sites. Nascent put RNA binds to and modifies transcribing polymerase, so that it becomes resistant to termination. To characterize the Zn finger further, we replaced each of the basic residues with alanine and determined the effects of the substitutions on termination, antitermination and cell viability. All the mutants were defective in put‐mediated antitermination. The severity of the defect depended on the mutant and on the sequence of the upstream stem–loop of put RNA. Some, but not all, mutants distinguished between put variants that differed in this region. This suggests that the Zn‐finger motif interacts directly and specifically with put RNA. All the mutants in the basic residues complemented a temperature‐sensitive β′ mutant for cell growth at a non‐permissive temperature, and those mutant enzymes that were tested transcribed and terminated normally in vitro on a template that lacked a put site.
Positive role of peptidoglycan breaks in lactococcal biofilm formation
Authors: Mercier Carine , Durrieu Christele , Briandet Romain , Domakova Elena , Tremblay Josselyne , Buist Girbe , Kulakauskas Saulius 
Published: March 2003

SummaryBacterial attachment to solid matrices depends on adhesive molecules present on the cell surface. Here we establish a positive correlation between peptidoglycan (PG) breaks, rather than particular molecules, and biofilm‐forming capacity in the Gram‐positive bacterium Lactococcus lactis. The L. lactis acmA strain, which is defective in PG hydrolase, adhered less efficiently than the wild‐type (wt) strain to different solid surfaces and was unable to form biofilms. These phenotypes were abolished by addition of lysozyme, a PG hydrolytic enzyme. Thus, the presence of PG breaks introduced by PG hydrolase, and not the AcmA protein itself, appears to be responsible for biofilm formation. Two different genetic screens confirmed the importance of PG breaks in L. lactis biofilm formation. Using the chain‐forming ability of the acmA strain as a phenotypic indicator of PG integrity, we selected for insertional mutants generating short chains. Five independent mutants were all mapped to ponA, which encodes the PG synthesis enzyme PBP1A. Double acmA ponA mutants displayed increased adhesion and biofilm‐forming capacity. Direct selection for strains with increased biofilm‐forming capacity resulted in the isolation of another five mutations in ponA. Based on these results, we conclude that PG breaks are important for both adhesion and biofilm formation in L. lactis.
Antifungal activity in Saccharomyces cerevisiae is modulated by calcium signalling
Authors: Edlind Thomas , Smith Lamar , Henry Karl , Katiyar Santosh , Nickels Joseph 
Published: March 2003

SummaryThe most important group of antifungals is the azoles (e.g. miconazole), which act by inhibiting lanosterol demethylase in the sterol biosynthesis pathway. Azole activity can be modulated through structural changes in lanosterol demethylase, altered expression of its gene ERG11, alterations in other sterol biosynthesis enzymes or altered expression of multidrug transporters. We present evidence that azole activity versus Saccharomyces cerevisiae is also modulated by Ca2+‐regulated signalling. (i) Azole activity was reduced by the addition of Ca2+. Conversely, azole activity was enhanced by the addition of Ca2+ chelator EGTA. (ii) Three structurally distinct inhibitors (fluphenazine, calmidazolium and a W‐7 analogue) of the Ca2+‐binding regulatory protein cal‐modulin enhanced azole activity. (iii) Two structurally distinct inhibitors (cyclosporin and FK506) of the Ca2+‐calmodulin‐regulated phosphatase calcineurin enhanced azole activity. (iv) Strains in which the Ca2+ binding sites of calmodulin were eliminated and strains in which the calcineurin subunit genes were disrupted demonstrated enhanced azole sensitivity; conversely, a mutant with constitutively activated calcineurin phosphatase demonstrated decreased azole sensitivity. (v) CRZ1/TCN1 encodes a transcription factor regulated by calcineurin phosphatase; its disruption enhanced azole sensitivity, whereas its overexpression decreased azole sensitivity. All the above treatments had comparable effects on the activity of terbinafine, an inhibitor of squalene epoxidase within the sterol biosynthesis pathway, but had little or no effect on the activity of drugs with unrelated targets. (vi) Treatment of S. cerevisiae with azole or terbinafine resulted in transcriptional upregulation of genes FKS2 and PMR1 known to be Ca2+ regulated. A model to explain the role of Ca2+‐regulated signalling in azole/terbinafine tolerance is proposed.