bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa
Authors: CHEN GANG , HARE MATTHEW P. 
Published: February 2008

AbstractThe recent discovery of cryptic species in marine holoplankton, organisms that ‘drift’ in oceanic currents throughout their life cycle, contrasts with their potential for long‐distance passive dispersal and presumably high gene flow. These observations suggest that holoplankton species are adapting to surprisingly small‐scale oceanographic features and imply either limited dispersal or strong selection gradients. Acartia tonsa is a widespread and numerically dominant estuarine copepod containing deep mitochondrial lineages within and among populations along the northwestern Atlantic coast. In this study, we intensively investigated A. tonsa populations in Chesapeake Bay with the goals of testing species status for the deep lineages and testing for their association with environmental features over space and time. Phylogenetic analyses of DNA sequences from mitochondrial cytochrome c oxidase I (mtCOI) and the nuclear ribosomal internal transcribed spacer (nITS) resolved two concordant monophyletic clades. Deep divergence between the two clades (13.7% uncorrected sequence divergence for mtCOI and 32.2% for nITS) and genealogical concordance within sympatric populations strongly suggest that the two clades represent reproductively isolated cryptic species. Based on restriction fragment length polymorphisms of mtCOI, representatives from the two clades were found consistently associated with contrasting salinity regimes (oligohaline vs. meso‐polyhaline) with an overlap between 2 and 12 PSU in samples from 1995 to 2005. Finding these patterns in one of the best‐known estuarine copepods reinforces the conclusion that marine biodiversity is underestimated, not only in terms of species numbers, but also with respect to niche partitioning and the potential importance of ecological divergence in marine holoplankton.
How many species are in the genus Batrachuperus? A phylogeographical analysis of the stream salamanders (family Hynobiidae) from southwestern China
Authors: FU JINZHONG , ZENG XIAOMAO 
Published: February 2008

AbstractPhylogeographical analysis of DNA sequence data has been routinely used to test species boundaries using the monophyly criterion; however, a complementary criterion, reproductive isolation, is often ignored. We used a combination of phylogenetic and population genetic approaches to determine species boundaries among stream salamanders in the genus Batrachuperus. First, cytochrome b sequence data from 174 Batrachuperus individuals, sampled from 78 populations, were used to reconstruct historical relationships within the genus. Second, allozyme data for 14 presumptive nuclear loci, from 463 individuals sampled from 60 populations, were collected and analysed to assess population similarity or disparity, as well as potential reproductive isolation. The DNA sequence data grouped all populations into seven major monophyletic groups, and the allozyme data provided evidence for reproductive isolation among four of the seven groups, thereby supporting the species status of these groups. The allozyme data suggested that two of the other groups share the same gene pool, and therefore belong to a single species. Finally, the allozyme data revealed two reproductively isolated units within the seventh group, which we suggest represents a case of ‘budding speciation’ based on the DNA gene tree. In total, seven species of the genus Batrachuperus were defined, two of which were previously unknown. The phylogeographical analysis also revealed that vicariance events might have dominated the evolutionary history of this group, but the speciation events might precede the formation of the existing mountain topology. This study demonstrates the importance of including frequency data from multiple nuclear gene loci in determining species boundaries.
High paternal diversity in the self‐incompatible herbArabidopsis halleridespite clonal reproduction and spatially restricted pollen dispersal
Authors: LLAURENS V. , CASTRIC V. , AUSTERLITZ F. , VEKEMANS X. 
Published: February 2008

AbstractThe number of sires fertilizing a given dam is a key parameter of the mating system in species with spatially restricted offspring dispersal, since genetic relatedness among maternal sibs determines the intensity of sib competition. In flowering plants, the extent of multiple paternity is determined by factors such as floral biology, properties of the pollen vector, selfing rate, spatial organization of the population, and genetic compatibility between neighbours. To assess the extent of multiple paternity and identify ecological factors involved, we performed a detailed study of mating patterns in a small population of a self‐incompatible clonal herb,Arabidopsis halleri. We mapped and genotyped 364 individuals and 256 of their offspring at 12 microsatellite loci and jointly analysed the level of multiple paternity, pollen and seed dispersal, and spatial genetic structure. We found very low levels of correlated paternity among sibs (Pfull‐sib = 3.8%) indicating high multiple paternity. Our estimate of the outcrossing rate was 98.7%, suggesting functional self‐incompatibility. The pollen dispersal distribution was significantly restricted (mean effective pollen dispersal distance: 4.42 m) but long‐distance successful pollination occurred and immigrating pollen was at most 10% of all pollination events. Patterns of genetic structure indicated little extent of clonal reproduction, and a low but significant spatial genetic structure typical for a self‐incompatible species. Overall, in spite of restricted pollen dispersal, the multiple paternity in this self‐incompatible species was very high, a result that we interpret as a consequence of high plant density and high pollinator service in this population.
Identifying the source of species invasions: sampling intensity vs. genetic diversity
Authors: MUIRHEAD JIM R. , GRAY DEREK K. , KELLY DAVID W. , ELLIS SANDRA M. , HEATH DANIEL D. , MACISAAC HUGH J. 
Published: February 2008

AbstractPopulation geneticists and community ecologists have long recognized the importance of sampling design for uncovering patterns of diversity within and among populations and in communities. Invasion ecologists increasingly have utilized phylogeographical patterns of mitochondrial or chloroplast DNA sequence variation to link introduced populations with putative source populations. However, many studies have ignored lessons from population genetics and community ecology and are vulnerable to sampling errors owing to insufficient field collections. A review of published invasion studies that utilized mitochondrial or chloroplast DNA markers reveals that insufficient sampling could strongly influence results and interpretations. Sixty per cent of studies sampled an average of less than six individuals per source population, vs. only 45% for introduced populations. Typically, far fewer introduced than source populations were surveyed, although they were sampled more intensively. Simulations based on published data forming a comprehensive mtDNA haplotype data set highlight and quantify the impact of the number of individuals surveyed per source population and number of putative source populations surveyed for accurate assignment of introduced individuals. Errors associated with sampling a low number of individuals are most acute when rare source haplotypes are dominant or fixed in the introduced population. Accuracy of assignment of introduced individuals is also directly related to the number of source populations surveyed and to the degree of genetic differentiation among them (FST). Incorrect interpretations resulting from sampling errors can be avoided if sampling design is considered before field collections are made.
Intracellular mobility of plasmid DNA is limited by the ParA family of partitioning systems
Authors: Derman Alan I. , Lim‐Fong Grace , Pogliano Joe 
Published: February 2008

SummaryThe highly conserved ParA family of partitioning systems is responsible for positioning DNA and protein complexes in bacteria. In Escherichia coli, plasmids that rely upon these systems are positioned at mid‐cell and are repositioned at the quarter‐cell positions after replication. How they remain fixed at these positions throughout the cell cycle is unknown. We use fluorescence recovery after photobleaching and time‐lapse microscopy to measure plasmid mobility in living E. coli cells. We find that a minimalized version of plasmid RK2 that lacks its Par system is highly mobile, that the intact RK2 plasmid is relatively immobile, and that the addition of a Par system to the minimalized RK2 plasmid limits its mobility to that of the intact RK2. Mobility is thus the default state, and Par systems are required not only to position plasmids, but also to hold them at these positions. The intervention of Par systems is required continuously throughout the cell cycle to restrict plasmid movement that would, if unrestricted, subvert the segregation process. Our results reveal an important function for Par systems in plasmid DNA segregation that is likely to be conserved in bacteria.
A polymerase III‐like reinitiation mechanism is operating in regulation of histone expression in archaea
Authors: Spitalny Patrizia , Thomm Michael 
Published: February 2008

SummaryAn archaeal histone gene from the hyperthermophile Pyrococcus furiosus containing four consecutive putative oligo‐dT terminator sequences was used as a model system to investigate termination signals and the mechanism of termination in vitro. The archaeal RNA polymerase terminated with high efficiency at the first terminator at 90°C when it contained five to six T residues, at 80°C readthrough was significantly increased. A putative hairpin structure upstream of the first terminator had no effect on termination efficiency. Template competition experiments starting with RNA polymerase molecules engaged in ternary complexes revealed recycling of RNA polymerase from the terminator to the promoter of the same template. This facilitated reinitiation was dependent upon the presence of a terminator sequence suggesting that pausing at the terminator is required for recycling as in the RNA polymerase III system. Replacement of the sequences immediately downstream of the oligo‐dT terminator by an AT‐rich segment improved termination efficiency. Both AT‐rich and GC‐rich downstream sequences seemed to impair the facilitated reinitiation pathway. Our data suggest that recycling is dependent on a subtle interplay of pausing of RNA polymerase at the terminator and RNA polymerase translocation beyond the oligo‐dT termination signal that is dramatically affected by downstream sequences.
Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi
Authors: Hülter Nils , Wackernagel Wilfried 
Published: February 2008

SummaryAcquisition of foreign DNA by horizontal gene transfer is seen as a major source of genetic diversity in prokaryotes. However, strongly divergent DNA is not genomically integrated by homologous recombination and would depend on illegitimate recombination (IR) events which are rare. We show that, by two mechanisms, during natural transformation of Acinetobacter baylyi two IR events can integrate DNA segments. One mechanism is double illegitimate recombination (DIR) acting in the absence of any homology (frequency: 7 × 10−13 per cell). It occurs about 1010‐fold less frequent than homologous transformation. The other mechanism is homology‐facilitated double illegitimate recombination (HFDIR) being about 440‐fold more frequent (3 × 10−10 per cell) than DIR. HFDIR depends on a homologous sequence located between the IR sites and on recA+. In HFDIR two IR events act on the same donor DNA molecule as shown by the joint inheritance of molecular DNA tags. While the IR events in HFDIR occurred at microhomologies, in DIR microhomologies were not used. The HFDIR phenomenon indicates that a temporal recA‐dependent association of donor DNA at a homology in recipient DNA may facilitate two IR events on the 5′ and 3′ heterologous parts of the transforming DNA molecule.
Regulatory interplay between pap operons in uropathogenic Escherichia coli
Authors: Totsika Makrina , Beatson Scott A. , Holden Nicola , Gally David L. 
Published: February 2008

SummaryPathogenic bacteria have a large repertoire of surface organelles involved in adherence, motility and protein export, but how individual bacteria co‐ordinate surface organelle expression to prevent interference and excessive immune stimulation is unclear. Phase variation is a mechanism by which expression of surface factors is limited to a fraction of the bacterial population; however, the presence of multiple homologous surface structures controlled by related mechanisms and regulators antagonizes the independent expression achieved by phase variation. To investigate whether other mechanisms have evolved to sort out the bacterial cell surface, we examined regulatory cross‐talk between multiple phase‐variable pyelonephritis‐associated pili (pap) operons in Escherichia coli isolates associated with urinary tract infections. Allelic variation identified in the regulatory regions and regulators acts synergistically to limit coexpression of homologous fimbrial operons. In particular, there is evidence that papI is under positive selection and PapI variants displayed differences in their capacity to activate related pap operons. Alleles of the high‐affinity binding site for PapB were shown to contain a variable number of (T/A)3 repeats occurring every 9 bp that altered the sensitivity of pap operon activation. Taken together with other examples of surface organelle cross‐talk, we illustrate how this regulation could promote sequential expression.
Requirements for translation re‐initiation in Escherichia coli: roles of initiator tRNA and initiation factors IF2 and IF3
Authors: Yoo Jae‐Ho , RajBhandary Uttam L. 
Published: February 2008

SummaryDespite its importance in post‐transcriptional regulation of polycistronic operons in Escherichia coli, little is known about the mechanism of translation re‐initiation, which occurs when the same ribosome used to translate an upstream open reading frame (ORF) also translates a downstream ORF. To investigate translation re‐initiation in Escherichia coli, we constructed a di‐cistronic reporter in which a firefly luciferase gene was linked to a chloramphenicol acetyltransferase gene using a segment of the translationally coupled geneV–geneVII intercistronic region from M13 phage. With this reporter and mutant initiator tRNAs, we show that two of the unique properties of E. coli initiator tRNA – formylation of the amino acid attached to the tRNA and binding of the tRNA to the ribosomal P‐site – are as important for re‐initiation as for de novo initiation. Overexpression of IF2 or increasing the affinity of mutant initiator tRNA for IF2 enhanced re‐initiation efficiency, suggesting that IF2 is required for efficient re‐initiation. In contrast, overexpression of IF3 led to a marked decrease in re‐initiation efficiency, suggesting that a 30S ribosome and not a 70S ribosome is used for translation re‐initiation. Strikingly, overexpression of IF3 also blocked E. coli from acting as a host for propagation of M13 phage.
The Gα subunit BCG1, the phospholipase C (BcPLC1) and the calcineurin phosphatase co‐ordinately regulate gene expression in the grey mould fungusBotrytis cinerea
Authors: Schumacher Julia , Viaud Muriel , Simon Adeline , Tudzynski Bettina 
Published: February 2008

SummaryThe Gα subunit BCG1 is essential for pathogenicity of the grey mould fungusBotrytis cinerea. Several processes such as the transition from primary infection to secondary invasive growth and the production of the phytotoxin botrydial are regulated by BCG1 via a cAMP‐independent pathway. Our recent finding that the botrydial biosynthesis genes belong to the group of Ca2+/calcineurin‐dependent genes suggested for the first time a connection between this Gα subunit and the calcineurin signalling pathway. To investigate whether this co‐regulation of genes by BCG1 and calcineurin is a common feature, a cDNA macroarray approach was used to compare the gene expression pattern of the wild‐type and the Δbcg1mutant, non‐treated or treated with the calcineurin inhibitor cyclosporin A. We identified three sets of genes whose expression was regulated either by both BCG1 and calcineurin, or only by one of them. Among the BCG1/calcineurin‐co‐regulated genes, we found a new gene cluster coding for a yet unknown polyketide secondary metabolite. Furthermore, we show for the first time in a phytopathogenic fungus that the phospholipase C (BcPLC1) is a component of the BCG1‐ and calcineurin‐dependent signalling pathway as several BCG1‐ and calcineurin‐dependent genes were downregulated inbcplc1knock‐down mutants.
ABC‐type amino acid uptake transporters Bgt and N‐II of Anabaena sp. strain PCC 7120 share an ATPase subunit and are expressed in vegetative cells and heterocysts
Authors: Pernil Rafael , Picossi Silvia , Mariscal Vicente , Herrero Antonia , Flores Enrique 
Published: February 2008

Summary Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can fix N2 in differentiated cells called heterocysts. Anabaena open reading frames alr4167 and alr3187 encode, respectively, an ATPase subunit, BgtA, and a composite protein bearing periplasmic substrate‐binding and transmembrane domains, BgtB, of an ABC‐type high‐affinity basic amino acid uptake transporter (Bgt). Open reading frame alr4167 is clustered with open reading frames alr4164, alr4165 and alr4166 that encode a periplasmic substrate‐binding protein, NatF, and transmembrane proteins NatG and NatH respectively. The NatF, NatG, NatH and BgtA proteins constitute an ABC‐type uptake transporter for acidic and neutral polar amino acids (N‐II). The Bgt and N‐II transport systems thus share the ATPase subunit, BgtA. These transporters together with the previously characterized ABC‐type uptake transporter for proline and hydrophobic amino acids (N‐I) account for more than 98% of the amino acid transport activity exhibited by Anabaena sp. strain PCC 7120. In contrast to N‐I that is expressed only in vegetative cells, the Bgt and N‐II systems are present in both vegetative cells and heterocysts. Whereas Bgt is dispensable for diazotrophic growth, N‐II appears to contribute together with N‐I to the diazotrophic physiology of this cyanobacterium.
Mitochondrial fatty acid synthesis is required for normal mitochondrial morphology and function in Trypanosoma brucei
Authors: Guler Jennifer L. , Kriegova Eva , Smith Terry K. , Lukeš Julius , Englund Paul T. 
Published: February 2008

Summary Trypanosoma brucei use microsomal elongases for de novo synthesis of most of its fatty acids. In addition, this parasite utilizes an essential mitochondrial type II synthase for production of octanoate (a lipoic acid precursor) as well as longer fatty acids such as palmitate. Evidence from other organisms suggests that mitochondrially synthesized fatty acids are required for efficient respiration but the exact relationship remains unclear. In procyclic form trypanosomes, we also found that RNAi depletion of the mitochondrial acyl carrier protein, an important component of the fatty acid synthesis machinery, significantly reduces cytochrome‐mediated respiration. This reduction was explained by RNAi‐mediated inhibition of respiratory complexes II, III and IV, but not complex I. Other effects of RNAi, such as changes in mitochondrial morphology and alterations in membrane potential, raised the possibility of a change in mitochondrial membrane composition. Using mass spectrometry, we observed a decrease in total and mitochondrial phosphatidylinositol and mitochondrial phosphatidylethanolamine. Thus, we conclude that the mitochondrial synthase produces fatty acids needed for maintaining local phospholipid levels that are required for activity of respiratory complexes and preservation of mitochondrial morphology and function.
Compensatory role for Rad52 during recombinational repair in Ustilago maydis
Authors: Kojic Milorad , Mao Ninghui , Zhou Qingwen , Lisby Michael , Holloman William K. 
Published: February 2008

SummaryA single Rad52‐related protein is evident by blast analysis of the Ustilago maydis genome database. Mutants created by disruption of the structural gene exhibited few discernible defects in resistance to UV, ionizing radiation, chemical alkylating or cross‐linking agents. No deficiency was noted in spontaneous mutator activity, allelic recombination or meiosis. GFP‐Rad51 foci were formed in rad52 cells following DNA damage, but were initially less intense than normal suggesting a possible role for Rad52 in formation of the Rad51 nucleoprotein filament. A search for interacting genes that confer a synthetic fitness phenotype with rad52 after DNA damage by UV irradiation identified the genes for Mph1, Ercc1 and the Rad51 paralogue Rec2. Testing known mutants in recombinational repair revealed an additional interaction with the BRCA2 orthologue Brh2. Suppression of the rec2 mutant's UV sensitivity by overexpressing Brh2 was found to be dependent on Rad52. The results suggest that Rad52 serves in an overlapping, compensatory role with both Rec2 and Brh2 to promote and maintain formation of the Rad51 nucleoprotein filament.
How the early sporulation sigma factor σF delays the switch to late development in Bacillus subtilis
Authors: Karmazyn‐Campelli Céline , Rhayat Lamya , Carballido‐López Rut , Duperrier Sandra , Frandsen Niels , Stragier Patrick 
Published: February 2008

SummarySporulation in Bacillus subtilis is a primitive differentiation process involving two cell types, the forespore and the mother cell. Each cell implements two successive transcription programmes controlled by specific sigma factors. We report that activity of σG, the late forespore sigma factor, is kept in check by Gin, the product of csfB, a gene controlled by σF, the early forespore sigma factor. Gin abolishes σG transcriptional activity when σG is artificially synthesized during growth, but has no effect on σF. Gin interacts strongly with σG but not with σF in a yeast two‐hybrid experiment. The absence of Gin allows σG to be active during sporulation independently of the mother‐cell development to which it is normally coupled. Premature σG activity leads to the formation of slow‐germinating spores, and complete deregulation of σG synthesis is lethal when combined with gin inactivation. Gin allows σF to delay the switch to the late forespore transcription programme by preventing σG to take over before the cell has reached a critical stage of development. A similar strategy, following a completely unrelated route, is used by the mother cell.
Mid-infrared imaging of 18 planetary nebulae using the Spitzer Space Telescope
Authors: Phillips J. P. , Ramos-Larios G. 
Published: February 2008

Abstract
We present 3.6-, 4.5-, 5.8- and 8.0-μm photometric mapping of 18 galactic planetary nebulae, based on observations taken with the Spitzer Space Telescope. These are shown to have morphologies which are sometimes quite different from those observed in the visible, with much of the emission arising outside the ionized shells. There is also evidence for a change in nebular sizes between the differing photometric bands. An analysis of mid-infrared (MIR) colours suggests that many nebulae have dust/polycyclic aromatic hydrocarbon (PAH) emission components, and it seems likely that longer wave MIR fluxes (in particular) are associated with PAH emission features. Such features are likely to be associated, in addition, with photodissociative regimes, where shock fragmentation of dust may lead to the replenishment of smaller PAH grains.
Finally, we note that the source Ap 2–1 possesses a particularly interesting structure, and may represent a case in which the nebular shell is ploughing through an enveloping H ii region. Similarly, it appears that central emission in M 2–48 may arise from a warm and dusty collimating disc.