bluuebunny/crossref_metadata_2025_split huggingface dataset:
The tails of two geckos tell the story of dispersal in a fragmented landscape
Authors: DAVIES KENDI F. , MELBOURNE BRETT A. 
Published: July 2007

AbstractThe fragmentation of habitat is a major cause of biodiversity loss. However, while numerous studies have suggested that reducing the size of populations and isolating them on fragments leads ultimately to the extinction of a species (small isolated populations are extinction prone), the evidence has been rather conjectural. This is because dispersal is so difficult to measure and isolation difficult to confirm. In past studies, evidence that populations become small and isolated on fragments, leading to declines, has relied on spatial patterns of distribution and abundance. Thus, a species not trapped in the matrix in which fragments are embedded might be assumed isolated on fragments, and if low in abundance on fragments compared to continuous habitat is assumed to have declined on fragments due to this isolation. However, without accurately measuring the degree of isolation, it is difficult to distinguish the role of isolation from other important causes of population decline that are correlated with fragment and population size, such as habitat degradation. Developments in molecular techniques and statistical methods now make it possible to measure isolation. Refreshingly, in this issue Hoehn et al. analyse microsatellite DNA with a suite of statistical methods to show convincingly that a declining species of gecko suffers from greater isolation on habitat fragments than a contrasting gecko that is able to disperse between fragments and hence persist in the severely fragmented wheatbelt of Western Australia.
Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob)
Authors: LORENZEN ELINE D. , DE NEERGAARD RIKKE , ARCTANDER PETER , SIEGISMUND HANS R. 
Published: July 2007

AbstractMitochondrial DNA control region sequences and seven microsatellites were used to estimate the genetic structuring, evolutionary history and historic migration patterns of the kob antelope (Kobus kob). Ten populations were analysed, representing the three recognized K. kob subspecies: K. k. kob in west Africa, K. k. thomasi in Uganda and K. k. leucotis in Sudan and Ethiopia. Despite being classified as K. k. thomasi and being phenotypically identical to the kob in Queen Elizabeth National Park (NP), the Murchison Falls population in Uganda showed high genetic similarity with the phenotypically distinct K. k. leucotis populations in Sudan and Ethiopia. This was regardless of marker type. Pairwise comparisons and genetic distances between populations grouped Murchison with K. k. leucotis, as did the Bayesian analysis, which failed to find any genetic structuring within the group. We propose that the divergent phenotype and life‐history adaptations of K. k. leucotis reflect the isolation of kob populations in refugia in west and east Africa during the Pleistocene. Subsequent dispersal has led to secondary contact and hybridization in northern Uganda between lineages, which was supported by high levels of genetic diversity in Murchison. The reduced variability observed in Queen Elizabeth NP reflects a small founder population from west Africa and in part the decimation of Uganda's wildlife during the country's political turmoil in the 1970s. Due to similarities in phenotype and ecology, and the joint evolutionary history of their mtDNA sequences, the taxonomic status of K. k. kob and K. k. thomasi as separate subspecies is called into question.
Delimiting species boundaries and the conservation genetics of the endangered maritime ringlet butterfly (Coenonympha nipisiquitMcDunnough)
Authors: SEI MAKIRI , PORTER ADAM H. 
Published: July 2007

AbstractSpecies delimitation is a difficult problem that has implications across organismal biology, yet no single method has proved wholly satisfactory. We tested the utility of combining species‐delimitation methods based on phylogeny and gene flow statistics using two parapatric members of theCoenonympha tulliagroup as an example: the endangered maritime ringlet butterfly (Coenonympha nipisiquitMcDunnough) and the common inornate ringlet butterfly (Coenonympha inornataEdwards). We reconstructed the phylogeny of the nearcticC. tullia‐group taxa from mitochondrial DNA (mtDNA) sequences (cytochrome oxidase I and mitochondrial control region) to explore the ancestry of theC. nipisiquitlineage within the group. We investigated the extent of gene flow between the two taxa withF‐statistics using 587 nuclear amplified fragment length polymorphism markers, accounting for the effect of potential scoring ‘collisions’ where a marker may represent more than one DNA fragment. Combining species‐delimitation methods was especially effective because it uncovered both historical and recent evolutionary patterns. Phylogenetic analysis of mtDNA revealed the early divergence ofC. nipisiquitfrom otherC. tullia‐group taxa, including the morphologically similarC. inornata. F‐statistics and gene‐by‐gene introgression profiles demonstrated clear isolation between the two taxa and revealed strong population structure withinC. nipisiquit. C. nipisiquitis the first taxon in the nearcticC. tulliagroup showing strong evidence of genetic isolation. The methods we used are relatively inexpensive and can be widely used to delimit taxonomic boundaries near the species level, both generally and in particular for taxa that may be targets of conservation efforts.
Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability
Authors: STOCKMAN AMY K. , BOND JASON E. 
Published: July 2007

AbstractSpecies exhibiting morphological homogeneity and strong population structuring present challenging taxonomic problems: morphology‐based approaches infer few species, whereas genetic approaches often indicate more. Morphologically cryptic, yet genetically divergent species groups require alternative approaches to delimiting species that assess adaptive divergence and ecological interchangeability of lineages. We apply such an approach toPromyrmekiaphila, a small genus (three nominal taxa) of trapdoor spiders endemic to northern California to define cohesion species (lineages that are genetically exchangeable and ecologically interchangeable). Genetic exchangeability is evaluated using standard phylogeographical techniques (e.g. nested clade analysis); ecological interchangeability is assessed using two GIS‐based approaches. First, climatic values are extracted from layer data for each locality point and utilized in a principal components analysis followed by MANOVA. Second, niche‐based distribution models of genetically divergent lineages are created using a maximum‐entropy modelling approach; the amount of overlap among lineages is calculated and evaluated against a probability distribution of null overlap. Lineages that have significant amounts of predicted overlap are considered ecologically interchangeable. Based on a synthetic evaluation of ecological interchangeability, geographical concordance, and morphological differentiation, we conclude thatPromyrmekiaphilacomprises six cohesion species, five of which are cryptic (i.e. undetectable by conventional means).
Involvement of a periplasmic protein kinase in DNA strand break repair and homologous recombination in Escherichia coli
Authors: Khairnar Nivedita P. , Kamble Vidya A. , Mangoli Suhas H. , Apte Shree K. , Misra Hari S. 
Published: July 2007

SummaryThe involvement of signal transduction in the repair of radiation‐induced damage to DNA has been known in eukaryotes but remains understudied in bacteria. This article for the first time demonstrates a role for the periplasmic lipoprotein (YfgL) with protein kinase activity transducing a signal for DNA strand break repair in Escherichia coli. Purified YfgL protein showed physical as well as functional interaction with pyrroloquinoline‐quinone in solution and the protein kinase activity of YfgL was strongly stimulated in the presence of pyrroloquinoline‐quinone. Transgenic E. coli cells producing Deinococcus radiodurans pyrroloquinoline‐quinone synthase showed nearly four log cycle improvement in UVC dark survival and 10‐fold increases in gamma radiation resistance as compared with untransformed cells. Pyrroloquinoline‐quinone enhanced the UV resistance of E. coli through the YfgL protein and required the active recombination repair proteins. The yfgL mutant showed higher sensitivity to UVC, mitomycin C and gamma radiation as compared with wild‐type cells and showed a strong impairment in homologous DNA recombination. The mutant expressing an active YfgL in trans recovered the lost phenotypes to nearly wild‐type levels. The results strongly suggest that the periplasmic phosphoquinolipoprotein kinase YfgL plays an important role in radiation‐induced DNA strand break repair and homologous recombination in E. coli.
Mutation of a key residue in the type II secretion system ATPase uncouples ATP hydrolysis from protein translocation
Authors: Shiue Sheng‐Jie , Chien I‐Ling , Chan Nei‐Li , Leu Wei‐Ming , Hu Nien‐Tai 
Published: July 2007

SummaryMembrane‐associated ATPase constitutes an essential element common to all secretion machineries in Gram‐negative bacteria. How ATP hydrolysis by these ATPases is coupled to secretion process remains unclear. Here we identified R286 as a key residue in the type II secretion system (T2SS) ATPase XpsE of Xanthomonas campestris that plays a pivotal role in coupling ATP hydrolysis to protein translocation. Mutation of R286 to alanine made XpsE hydrolyse ATP at a rate five times that of the wild‐type XpsE. Yet the mutant XpsE(R286A) is non‐functional in protein secretion via T2SS. Detailed analyses indicated that the mutant XpsE(R286A) lost the ability co‐ordinating the N‐ and C‐domain of XpsE. Without significantly influencing XpsE binding affinity with ATP or its oligomerization, R286A mutation however, caused XpsE lose the ability to associate with the cytoplasmic membrane via XpsLN. As a consequence, ATP hydrolysis by XpsE was uncoupled from protein secretion. Because R286 is highly conserved among members of the secretion NTPase superfamily, we speculate that its equivalent in other homologues may also play a critical energy coupling role for T2SS, type IV pilus assembly and type IV secretion system.
The multiple roles of CRP at the complex acs promoter depend on activation region 2 and IHF
Authors: Sclavi Bianca , Beatty Christine M. , Thach David S. , Fredericks Christine E. , Buckle Malcolm , Wolfe Alan J. 
Published: July 2007

Summary acs encodes a high‐affinity enzyme that permits survival during carbon starvation. As befits a survival gene, its transcription is subject to complex regulation. Previously, we reported that cAMP receptor protein (CRP) activates acs transcription by binding tandem DNA sites located upstream of the major acsP2 promoter and that the nucleoid protein IHF (integration host factor) binds three specific sites located just upstream. In vivo, the sequence that includes these IHF sites exerts a positive effect on CRP‐dependent transcription, while a construct containing only the most proximal site exhibits reduced transcription compared with the full‐length promoter or with a construct lacking all three IHF sites. Here, we defined the minimal system required for this IHF‐dependent inhibition, showing it requires the promoter‐distal CRP site and an amino acid residue located within activation region 2 (AR2), a surface determinant of CRP that interacts with RNA polymerase (RNAP). Surprisingly, for a Class III promoter, disruption of AR2 caused significant changes in the activity and structure of both the full‐length promoter and the construct with the single proximal IHF site. We propose that AR2, together with IHF, mediates formation of a multi‐protein complex, in which RNAP is stabilized in an open complex that remains poised on the promoter ready to respond rapidly to environmental changes.
Signal integration in the galactose network of Escherichia coli
Authors: Semsey Szabolcs , Krishna Sandeep , Sneppen Kim , Adhya Sankar 
Published: July 2007

SummaryThe gal regulon of Escherichia coli contains genes involved in galactose transport and metabolism. Transcription of the gal regulon genes is regulated in different ways by two iso‐regulatory proteins, Gal repressor (GalR) and Gal isorepressor (GalS), which recognize the same binding sites in the absence of d‐galactose. DNA binding by both GalR and GalS is inhibited in the presence of d‐galactose. Many of the gal regulon genes are activated in the presence of the adenosine cyclic‐3′,5′‐monophosphate (cAMP)–cAMP receptor protein (CRP) complex. We studied transcriptional regulation of the gal regulon promoters simultaneously in a purified system and attempted to integrate the two small molecule signals, d‐galactose and cAMP, that modulate the isoregulators and CRP respectively, at each promoter, using Boolean logic. Results show that similarly organized promoters can have different input functions. We also found that in some cases the activity of the promoter and the cognate gene can be described by different logic gates. We combined the transcriptional network of the galactose regulon, obtained from our experiments, with literature data to construct an integrated map of the galactose network. Structural analysis of the network shows that at the interface of the genetic and metabolic network, feedback loops are by far the most common motif.
Multiple interactions among the competence proteins of Bacillus subtilis
Authors: Kramer Naomi , Hahn Jeanette , Dubnau David 
Published: July 2007

SummaryProteins required for transformation of Bacillus subtilis and other competent bacteria are associated with the membrane or reside in the cytosol. Previous work has shown that RecA, ComGA, ComFA and SsbB are directed to the cell poles in competent cells, and that the uptake of transforming DNA occurs preferentially at the poles. We show that ComGA, ComFA, DprA (Smf), SsbB (YwpH), RecA and YjbF (CoiA) are located at the cell poles, where they appear to colocalize. Using fluorescence resonance energy transfer, we have shown that these six competent (Com) proteins reside in close proximity to one another. This conclusion was supported by the effects of com gene knockouts on the stabilities of Com proteins. Data obtained from the com gene knockout studies, as well as information from other sources, extend the list of proteins in the transformation complex to include ComEC and ComEA. Because ComGA and ComFA are membrane‐associated, while DprA, SsbB, RecA and YjbF are soluble, a picture emerges of a large multiprotein polar complex, involving both cytosolic and membrane proteins. This complex mediates the binding and uptake of single‐stranded DNA, the protection of this DNA from cellular nucleases and its recombination with the recipient chromosome.
EfeUOB (YcdNOB) is a tripartite, acid‐induced and CpxAR‐regulated, low‐pH Fe2+ transporter that is cryptic in Escherichia coli K‐12 but functional in E. coli O157:H7
Authors: Cao Jieni , Woodhall Mark R. , Alvarez Javier , Cartron Michaël L. , Andrews Simon C. 
Published: July 2007

Summary Escherichia coli possesses iron transporters specific for either Fe2+ or Fe3+. Although Fe2+ is far more soluble than Fe3+, it rapidly oxidizes aerobically at pH ≥ 7. Thus, FeoAB, the major Fe2+ transporter of E. coli, operates anaerobically. However, Fe2+ remains stable aerobically under acidic conditions, although a low‐pH Fe2+ importer has not been previously identified. Here we show that ycdNOB (efeUOB) specifies the first such transporter. efeUOB is repressed at high pH by CpxAR, and is Fe2+–Fur repressed. EfeU is homologous to the high‐affinity iron permease, Ftr1p, of Saccharomyces cerevisiae and other fungi. EfeO is periplasmic with a cupredoxin N‐terminal domain; EfeB is also periplasmic and is haem peroxidase‐like. All three Efe proteins are required for Efe function. The efeU gene of E. coli K‐12 is cryptic due to a frameshift mutation – repair of the single‐base‐pair deletion generates a functional EfeUOB system. In contrast, the efeUOB operon of the enterohaemorrhagic strain, O157:H7, lacks any frameshift and is functional. A ‘wild‐type’ K‐12 strain bearing a functional EfeUOB displays a major growth advantage under aerobic, low‐pH, low‐iron conditions when a competing metal is provided. 55Fe transport assays confirm the ferrous iron specificity of EfeUOB.
Deletion of putative apoptosis factors leads to lifespan extension in the fungal ageing model Podospora anserina
Authors: Hamann Andrea , Brust Diana , Osiewacz Heinz D. 
Published: July 2007

Summary Podospora anserina is a filamentous fungus with a limited lifespan. After a strain‐specific period of growth, cultures turn to senescence and ultimately die. Here we provide evidence that the last step in the ageing of P. anserina is not accidental but programmed. In this study, PaAMID1, a homologue of a mammalian ‘AIF‐homologous mitochondrion‐associated inducer of death’, was analysed as a putative member of a caspase‐independent signalling pathway. In addition, two metacaspases, PaMCA1 and PaMCA2, were investigated. While deletion of PaAmid1 as well as of PaMca2 was found to result in a moderate lifespan extension (59% and 78%, respectively), a 148% increase in lifespan was observed after deletion of PaMca1. Measurement of arginine‐specific protease activity demonstrates a metacaspase‐dependent activity in senescent but not in juvenile cultures, pointing to an activation of these proteases in the senescent stage of the life cycle. Moreover, treatment of juvenile wild‐type cultures with hydrogen peroxide leads to a PaMCA1‐dependent activity. The presented data strongly suggest that death of senescent wild‐type cultures is triggered by an apoptotic programme induced by an age‐dependent increase of reactive oxygen species during ageing of cultures and is executed after metacaspase activation.
Stromal haze after combined riboflavin‐UVA corneal collagen cross‐linking in keratoconus: in vivo confocal microscopic evaluation
Authors: Mazzotta Cosimo , Balestrazzi Angelo , Baiocchi Stefano , Traversi Claudio , Caporossi Aldo 
Published: July 2007

AbstractThe technique of corneal collagen cross‐linking consists of photopolymerization of stromal fibres by the combined action of a photosensitizing substance (riboflavin or vitamin B2) and ultraviolet light from a solid state UVA source. Photopolymerization increases the rigidity of corneal collagen and its resistance to keratectasia. In this report we present two cases, studied through in vivo confocal microscopy, with stage III keratoconus that developed stromal haze after the cross‐linking treatment.
Conditions for young infants’ failure to perceive trajectory continuity
Authors: Bremner J. Gavin , Johnson Scott P. , Slater Alan , Mason Uschi , Cheshire Andrea , Spring Joanne 
Published: July 2007

Abstract When viewing an event in which an object moves behind an occluder on part of its trajectory, 4‐month‐old infants perceive the trajectory as continuous only when time or distance out of sight is short. Little is known, however, about the conditions under which young infants perceive trajectories to be discontinuous. In the present studies we focus first on infants’ perception of trajectories that change during a period of occlusion. Four‐month‐olds perceive discontinuity in trajectories that change in height or orientation while behind an occluder, and this is true even when a change in direction could be due to an invisible bouncing collision with a surface. Further experiments reveal that infants do not perceive diagonal linear trajectories as continuous across an occlusion unless the occluding and revealing edges are orthogonal to the path of movement. Implications for theories of perceptual and cognitive development are discussed.
Using cardinality to compare quantities: the role of social‐cognitive conflict in early numeracy
Authors: Muldoon Kevin P. , Lewis Charlie , Francis Brian 
Published: July 2007

AbstractA key question in early number development is how 4‐ and 5‐year‐olds learn the roles that counting and cardinal numbers play when comparing quantities. Children who wrongly used length to identify numerosity were assigned to five experimental groups and trained to judge whether a puppet – who sometimes miscounted – created equivalent sets. Over three training sessions, children who were asked to compare sets after they were counted learned to base their judgments on cardinal numbers when the puppet counted accurately by being given feedback. However, only the groups who were also asked to explain either their own or the experimenter's reasoning made progress in identifying the puppet's miscounts. This ability to recognize the importance of counting accuracy for quantitative comparisons predicted whether children would spontaneously count to compare sets on a post‐test. The importance of asking children to identify miscounts is discussed alongside the social factors that influence children's recognition of the relationship between procedural counting, cardinality and relative number.
Maturation of the long‐latency auditory ERP: step function changes at start and end of adolescence
Authors: Bishop Dorothy V.M. , Hardiman Mervyn , Uwer Ruth , Von Suchodoletz Waldemar 
Published: July 2007

Abstract The auditory event‐related potential (ERP) is obtained by averaging electrical impulses recorded from the scalp in response to repeated stimuli. Previous work has shown large differences between children, adolescents and adults in the late auditory ERP, raising the possibility that analysis of waveform shape might be useful as an index of brain maturity. We reanalysed auditory ERPs from samples previously described by Albrecht, von Suchodoletz and Uwer (2000) and Uwer, Albrecht and von Suchodoletz (2002), using the intraclass correlation (ICC) as a global measure of similarity of an individual's waveform to a grand average comparison waveform for each age band. Three developmental periods were clearly distinguished: 5 to 12 years, 13 to 16 years, and adulthood. However, within each of these periods, there was no evidence of any developmental progression with age.
An analysis of nucleotide and amino acid variability in the barcode region of cytochromecoxidase I (cox1) in fishes
Authors: WARD ROBERT D. , HOLMES BRONWYN H. 
Published: July 2007

AbstractThe 655 bp cytochromecoxidase subunit I barcode region of single specimens of 388 species of fishes (four Holocephali, 61 Elasmobranchii and 323 Actinopterygii) was examined. All but two (Urolophus cruciatusandUrolophus sufflavus) showed differentcox1nucleotide sequences (99.5% species discrimination); the two that could not be resolved are suspected to hybridize. Most of the power ofcox1nucleotide sequence analysis for species identification comes from the degenerate nature of the genetic code and the highly variable nature of the third codon position of amino acids. Variation at the third codon position is bimodally distributed, and the more variable mode is dominated by amino acids with four or six codons, while the less variable mode is dominated by amino acids with two codons. The ratio of nonsynonymous to synomymous changes is much less than one, indicating that this gene is subject to strong purifying selection. Consequently,cox1amino acid sequence diversity is much less than nucleotide sequence diversity and has very poor species resolution power. Fourteen of the 16 amino acid residues recognized as having important functions in the region ofcox1sequenced were completely conserved over all 388 species (and the bovinecox1sequence), with one fish species varying at one of these sites, and three fish at another site. No significant differences in amino acid conservation were observed between residues in helices, strands and turns. Patterns of nucleotide and amino acid variability were very similar between elasmobranchs and actinopterygians.