bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thiol peroxidase is critical for virulence and resistance to nitric oxide and peroxide in the fungal pathogen, Cryptococcus neoformans
Authors: Missall Tricia Ann , Pusateri Mary Ellen , Lodge Jennifer K. 
Published: December 2004

Summary Cryptococcus neoformans is a fungal pathogen most commonly causing meningitis in immunocompromised patients. Current therapies are inadequate, and novel antifungal targets are needed. We have identified by proteomics two thiol peroxidases that are differentially expressed at 37°C, the temperature of the mammalian host. Consistent with their antioxidant role, we show that the genes encoding these thiol‐specific antioxidants, TSA1 and TSA3, are transcriptionally induced when C. neoformans is exposed to hydrogen peroxide. Genome sequence analysis of C. neoformans revealed a third thiol peroxidase, TSA4. We constructed single, double and triple mutants of the thiol peroxidase genes through homologous recombination and analysed their function by comparing the growth of these mutants with that of the wild‐type strain. The tsa1Δ mutant shows sensitivity to hydrogen peroxide and t‐butylhydroperoxide, as well as significant growth retardation at 25°C and 38.5°C. The tsa1Δ mutant is also sensitive to NO, demonstrating a link between oxidative and nitrosative stress pathways. In two mouse models of cryptococcosis, the tsa1Δ mutant is significantly less virulent.
Genes in the accessory sec locus of Streptococcus gordonii have three functionally distinct effects on the expression of the platelet‐binding protein GspB
Authors: Takamatsu Daisuke , Bensing Barbara A. , Sullam Paul M. 
Published: December 2004

SummaryPlatelet binding by Streptococcus gordonii strain M99 is strongly correlated with the expression of the large surface glycoprotein GspB. A 14 kb chromosomal region downstream of gspB was previously shown to be required for the expression of this protein. The region encodes SecA2 and SecY2, which are components of an accessory secretion system dedicated specifically to the export of GspB. The region also includes three genes (gly, nss and gtf) that encode proteins likely to function in carbohydrate metabolism, and four genes (orf1–4) that encode proteins of unknown function. In this report, we have investigated the role of these genes in GspB expression. We found that disruption of orf1, orf2 or orf3 resulted in a loss of GspB export and the intracellular accumulation of GspB. As they are apparently essential components of the accessory secretion system, these genes were renamed asp1–3 (for accessory secretory protein). In gtf and orf4 mutants, gspB was transcribed, but no GspB was detected. These results suggest that Gtf and Orf4 are required for the translation or for the stability of GspB. In contrast, gly and nss mutants were able to express and export GspB. However, disruption of these genes appeared to affect the carbohydrate composition of this glycoprotein. As asp1–3, gtf and orf4, but not gly and nss, are conserved in the accessory sec loci of several staphylococcal and streptococcal species, these genes may also have crucial roles in the expression and export of GspB homologues in the other Gram‐positive bacteria.
Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR‐dependent Escherichia coli nir promoter
Authors: Browning Douglas F. , Cole Jeffrey A. , Busby Stephen J. W. 
Published: December 2004

SummaryExpression from the Escherichia coli nir promoter is co‐dependent on both the FNR protein (an anaerobically triggered transcription activator) and NarL or NarP proteins (transcription activators triggered by nitrite and nitrate). We found previously that FNR binds to a site centred at position − 41.5 at the nir promoter, but that FNR‐dependent activation is repressed by IHF binding to a site centred at position −88 (IHF I) and Fis binding to sites centred at positions −142 (Fis I) and +23 (Fis II). Here, we have studied the binding of purified IHF, Fis and FNR to the nir promoter in vitro. Our results show that the nir promoter contains a second IHF site at position −115 (IHF II) and a third Fis site at position −97 (Fis III), and that IHF, Fis and FNR can bind together to form multiprotein complexes. Surprisingly, IHF binding at the IHF II site increases FNR‐dependent activation by decreasing the repression mediated by IHF and Fis binding at the other sites. In previous work, we found that NarL or NarP activates the nir promoter by binding to a site centred at position −69.5 and counteracting the repressive effects of IHF and Fis. We now show that NarL can displace IHF bound at the IHF I site, but IHF is unable to displace bound NarL. We suggest that NarL interferes with IHF binding at the nir promoter by distorting the minor groove at its target site, and we argue that the resulting activation by NarL results from remodelling of the local nucleoprotein structure to facilitate FNR‐dependent transcription.
Sortases and pilin elements involved in pilus assembly of Corynebacterium diphtheriae
Authors: Ton‐That Hung , Marraffini Luciano A. , Schneewind Olaf 
Published: December 2004

Summary Corynebacterium diphtheriae SpaA pili are composed of three pilin subunits, SpaA, SpaB and SpaC. SpaA, the major pilin protein, is distributed uniformly along the pilus shaft, whereas SpaB is observed at regular intervals, and SpaC seems to be positioned at the pilus tip. Pilus assembly in C. diphtheriae requires the pilin motif and the C‐terminal sorting signal of SpaA, and is proposed to occur by a mechanism of ordered cross‐linking, whereby pilin‐specific sortase enzymes cleave precursor proteins at sorting signals and involve the side‐chain amino groups of pilin motif sequences to generate covalent linkages between pilin subunits. We show here that two elements of SpaA pilin precursor, the pilin motif and the sorting signal, are together sufficient to promote the polymerization of an otherwise secreted protein by a process requiring the function of the sortase A gene (srtA). Five other sortase genes are dispensable for SpaA pilus assembly. Further, the incorporation of SpaB into SpaA pili requires a glutamic acid residue within the E box motif of SpaA, a feature that is found to be conserved in other Gram‐positive pathogens that encode sortase and pilin subunit genes with sorting signals and pilin motifs. When the main fimbrial subunit of Actinomyces naeslundii type I fimbriae, FimA, is expressed in corynebacteria, C. diphtheriae strain NCTC13129 polymerized FimA to form short fibres. Although C. diphtheriae does not depend on other actinomycetal genes for FimA polymerization, this process involves the pilin motif and the sorting signal of FimA as well as corynebacterial sortase D (SrtD). Thus, pilus assembly in Gram‐positive bacteria seems to occur by a universal mechanism of ordered cross‐linking of precursor proteins, the multiple conserved features of which are recognized by designated sortase enzymes.
Differentiate to thrive: lessons from the Legionella pneumophila life cycle
Authors: Molofsky Ari B. , Swanson Michele S. 
Published: December 2004

SummaryWhen confronted by disparate environments, microbes routinely alter their physiology to tolerate or exploit local conditions. But some circumstances require more drastic remodelling of the bacterial cell, as sporulation by the Bacillus and Streptomyces species of soil bacteria vividly illustrates. Cellular differentiation is also crucial for pathogens, the challenge for which is to colonize one host, then be transmitted to the next. Using the Gram‐negative Legionella pneumophila as a model intracellular pathogen, we describe how biogenesis of the replication vacuole is determined by the developmental state of the bacterium. Subsequently, when replicating bacteria have exhausted the nutrient supply, the pathogens couple their conversion to stationary phase physiology with expression of traits that promote transmission to a new host. The cellular differentiation of L. pneumophila is co‐ordinated by a regulatory circuit that integrates several elements that are broadly conserved in the microbial world. The alarmone (p)ppGpp promotes transcription directed by the alternative sigma factors RpoS, FliA and, probably, RpoN, and also post‐transcriptional control mediated by a two‐component regulatory system, LetA/S (GacA/S), and an mRNA‐binding protein, CsrA (RsmA). By applying knowledge of microbial differentiation in combination with tools to screen the complete genomes of pathogens, experiments can be designed to identify two distinct classes of virulence traits: factors that promote replication and those dedicated to transmission.
A hyperstructure approach to mitochondria
Authors: Trinei Mirella , Vannier Jean‐Pierre , Beurton‐Aimar Marie , Norris Vic 
Published: December 2004

SummarySeveral questions in our understanding of mitochondria are unanswered. These include how the ratio of mitochondrial (mt)DNA to mitochondria is maintained, how the accumulation of defective, rapidly replicating mitochondrial DNA is avoided, how the ratio of mitochondria to cells is adjusted to fit cellular needs, and why any proteins are synthesized in mitochondria rather than simply imported. In bacteria, large hyperstructures or assemblies of proteins, mRNA, lipids and ions have been proposed to constitute a level of organization intermediate between macromolecules and whole cells. Here, we suggest how the concept of hyperstructures together with other concepts developed for bacteria such as transcriptional sensing and spontaneous segregation may provide answers to mitochondrial problems. In doing this, we show how the problem of the very existence of mtDNA brings its own solution.
Subtilisin‐like proteases of the malaria parasite
Authors: Withers‐Martinez Chrislaine , Jean Létitia , Blackman Michael J. 
Published: December 2004

SummaryProteases play critical roles in the life cycle of the malaria parasite, Plasmodium spp. Within the asexual erythrocytic cycle, responsible for the clinical manifestations of malaria, substantial interest has focused on the role of parasite serine proteases as a result of indications that they are involved in red blood cell invasion. Over the past 6 years, three Plasmodium genes encoding serine proteases of the subtilisin‐like clan, or subtilases, have been identified. All are expressed in the asexual blood stages and, in at least two cases, the gene products localize to secretory organelles of the invasive merozoite. They may have potential as novel drug targets. Here, we review progress in our understanding of the maturation, specificity, structure and function of these Plasmodium subtilases.
The evolution of phenotypic plasticity in spatially structured environments: implications of intraspecific competition, plasticity costs and environmental characteristics
Authors: Ernande B. , Dieckmann U. 
Published: December 2004

Abstract
We model the evolution of reaction norms focusing on three aspects: frequency-dependent selection arising from resource competition, maintenance and production costs of phenotypic plasticity, and three characteristics of environmental heterogeneity (frequency of environments, their intrinsic carrying capacity and the sensitivity to phenotypic maladaptation in these environments). We show that (i) reaction norms evolve so as to trade adaptation for acquiring resources against cost avoidance; (ii) maintenance costs cause reaction norms to better adapt to frequent rather than to infrequent environments, whereas production costs do not; and (iii) evolved reaction norms confer better adaptation to environments with low rather than with high intrinsic carrying capacity. The two previous findings contradict earlier theoretical results and originate from two previously unexplored features that are included in our model. First, production costs of phenotypic plasticity are only incurred when a given phenotype is actually produced. Therefore, they are proportional to the frequency of environments, and these frequencies thus affect the selection pressure to avoid costs just as much as the selection pressure to improve adaptation. This prevents the frequency of environments from affecting the evolving reaction norm. Secondly, our model describes the evolution of plasticity for a phenotype determining an individual's capability to acquire resources, and thus its realized carrying capacity. When individuals are distributed randomly across environments, they cannot avoid experiencing environments with intrinsically low carrying capacity. As selection pressures arising from the need to improve adaptation are stronger under such extreme conditions than under mild ones, better adaptation to environments with low rather than with high intrinsic carrying capacity results.
Uneven segregation of sporophytic self-incompatibility alleles inArabidopsis lyrata
Authors: Bechsgaard J. , Bataillon T. , Schierup M. H. 
Published: December 2004

AbstractSelf-incompatibility in Arabidopsis lyrata is sporophytically controlled by the multi-allelic S-locus. Self-incompatibility alleles (S-alleles) are under strong negative frequency dependent selection because pollen carrying common S-alleles have fewer mating opportunities. Population genetics theory predicts that deleterious alleles can accumulate if linked to the S-locus. This was tested by studying segregation of S-alleles in 11 large full sib families in A. lyrata. Significant segregation distortion leading to an up to fourfold difference in transmission rates was found in six families. Differences in transmission rates were not significantly different in reciprocal crosses and the distortions observed were compatible with selection acting at the gametic stage alone. The S-allele with the largest segregation advantage is also the most recessive, and is very common in natural populations concordant with its apparent segregation advantage. These results imply that frequencies of S-alleles in populations of A. lyrata cannot be predicted based on simple models of frequency-dependent selection alone.
Epistasis affecting litter size in mice
Authors: Peripato A. C. , De Brito R. A. , Matioli S. R. , Pletscher L. S. , Vaughn T. T. , Cheverud J. M. 
Published: December 2004

Abstract
Litter size is an important reproductive trait as it makes a major contribution to fitness. Generally, traits closely related to fitness show low heritability perhaps because of the corrosive effects of directional natural selection on the additive genetic variance. Nonetheless, low heritability does not imply, necessarily, a complete absence of genetic variation because genetic interactions (epistasis and dominance) contribute to variation in traits displaying strong heterosis in crosses, such as litter size. In our study, we investigated the genetic architecture of litter size in 166 females from an F2 intercross of the SM/J and LG/J inbred mouse strains. Litter size had a low heritability (h2 = 12%) and a low repeatability (r = 33%). Using interval-mapping methods, we located two quantitative trait loci (QTL) affecting litter size at locations D7Mit21 + 0 cM and D12Mit6 + 8 cM, on chromosomes 7 and 12 respectively. These QTL accounted for 12.6% of the variance in litter size. In a two-way genome-wide epistasis scan we found eight QTL interacting epistatically involving chromosomes 2, 4, 5, 11, 14, 15 and 18. Taken together, the QTL and their interactions explain nearly 49% (39.5% adjusted multiple r2) of the phenotypic variation for litter size in this cross, an increase of 36% over the direct effects of the QTL. This indicates the importance of epistasis as a component of the genetic architecture of litter size and fitness in our intercross population.
Human birthweight evolution across contrasting environments
Authors: Thomas F. , Teriokhin A. T. , Budilova E. V. , Brown S. P. , Renaud F. , Guegan J. F. 
Published: December 2004

Abstract
We explore from both theoretical and empirical perspectives the hypothesis that a significant part of the worldwide variability in human birthweight results from adaptive responses to local selective pressures. We first developed an agent-based model to simulate the process of evolutionary selection on life history strategy, and then we performed a comparative analysis across 89 countries worldwide. The model illustrates that optimal birthweight depends on which fitness-reducing risk locally predominates (somatic diseases, parasitic diseases or adverse environmental conditions). When fitness variations between individuals mainly result from somatic diseases (e.g. industrialized countries), or conversely from infectious and parasitic diseases (e.g. developing countries), selection is expected to favour individuals producing larger children. Conversely, when environmental risks increase in relative importance, selective pressures for producing children with high birthweight are reduced. The comparative analysis supports these theoretical expectations, in particular the finding that birthweight is higher than predicted in highly parasitized countries.
An analysis of genetic differentiation among assortatively mating Drosophila melanogaster in Zimbabwe
Authors: Kauer M. O. , Schlötterer C. 
Published: December 2004

Abstract
African Drosophila melanogaster populations, and those from Zimbabwe in particular, have attracted much interest recently. African flies differ genetically from ‘cosmopolitan‘ populations and were found to exhibit discriminative mating behaviour against individuals from ‘cosmopolitan’ populations. It has therefore been proposed that Zimbabwean and some other African populations are in an ‘incipient stage of speciation’. However, whether the mating behaviour is an effective barrier against gene flow from other populations, and whether intra-population genetic differentiation has already evolved in sympatry is not known. Here, we took a population-based approach to test whether the well-characterized mating type differences have resulted in a genome-wide differentiation at the population level. Using 122 polymorphic microsatellite loci mapping to the third chromosome, we demonstrate a significant genetic differentiation between Zimbabwean flies differing in their mating behaviour. We also provide evidence to suggest that this difference is unlikely to be attributable to population structure within Zimbabwe. However, the analysis of individual microsatellite loci did not indicate more loci differentiating these two groups than expected by chance. Our data suggest that the ‘Z’-‘M’ mating behaviour is strong enough to result in a small but significant genetic differentiation. Thus, future studies based on a larger population sample of flies characterized for their mating behaviour and using more markers are expected to provide more information on the genetic basis of the mating traits in the Zimbabwe flies.
Levels of inbreeding depression over seven generations of selfing in the androdioecious clam shrimp, Eulimnadia texana
Authors: Weeks S. C. 
Published: December 2004

Abstract
Androdioecy (mixtures of males and hermaphrodites) is a rare mating system in both plants and animals. Theory suggests that high levels of inbreeding depression can maintain males in androdioecious populations if hermaphrodites commonly self-fertilize. However, if inbreeding depression (δ) can be ‘purged’ from selfing populations, maintaining males is more difficult. In the androdioecious clam shrimp, Eulimnadia texana, δ is estimated to be as high as 0.7. Previous work suggests that this high level is maintained in the face of high levels of inbreeding due to an associative overdominance of fitness-related loci with the sex-determining locus. Such associative overdominance would make purging of inbreeding depression difficult to impossible. The current experiment was designed to determine if δ can be purged in these shrimp by tracking fitness across seven generations in selfing and outcrossing treatments. Evidence of purging was found in one of four populations, but the remaining populations demonstrated a consistent pattern of δ across generations. Although the experimental design allowed ample opportunity for purging, the majority of populations were unable to purge their genetic load. Therefore, δ in this species is likely due to associative overdominance caused by deleterious recessive alleles linked to the sex determining locus.
Glycopeptide resistant Staphylococcus
Authors: Witte W. 
Published: December 2004

SummaryInsensitivity of Staphylococcus aureus to glycopeptides became known at the end of the 1990s. To distinguish intermediate (VISA and GISA) and full resistance (vancomycin‐resistant Staphylococcus aureus, VRSA) is of both epidemiological and clinical importance. The VISA (GISA) phenotype is obviously selected by glycopeptide usage in individual patients and can be disseminated by clonal spread of particularly affected staphylococcal isolates, preferentially methicillin‐resistant S. aureus (MRSA). In the meantime emergence of VISA became known worldwide. VRSA evolve by acquisition of the vanA gene from enterococci, which are of significance as reservoir of resistance genes among gram‐positive bacterial pathogens. Until now three independent single cases of emergence of VRSA became known from the USA, in two of them an association with vanA containing Enterococcus spp. at the same site of the affected patients could be established. The frequency of VISA (GISA) among MRSA in Central Europe is still low (<0.1%); no VRSA have been detected until now.
Monitoring of Antimicrobial Resistance Among Food Animals: Principles and Limitations
Authors: Aarestrup F. M. 
Published: December 2004

SummaryLarge amounts of antimicrobial agents are in the production of food animals used for therapy and prophylactics of bacterial infections and in feed to promote growth. The use of antimicrobial agents causes problems in the therapy of infections through the selection for resistance among bacteria pathogenic for animals or humans. Current knowledge regarding the occurrence of antimicrobial resistance in food animals, the quantitative impact of the use of different antimicrobial agents on selection for resistance and the most appropriate treatment regimes to limit the development of resistance is incomplete. Programmes monitoring the occurrence and development of resistance are essential to determine the most important areas for intervention and to monitor the effects of interventions. When designing a monitoring programme it is important to decide on the purpose of the programme. Thus, there are major differences between programmes designed to detect changes in a national population, individual herds or groups of animals. In addition, programmes have to be designed differently according to whether the aim is to determine changes in resistance for all antimicrobial agents or only the antimicrobial agents considered most important in relation to treatment of humans. In 1995 a continuous surveillance for antimicrobial resistance among bacteria isolated from food animals was established in Denmark. Three categories of bacteria, indicator bacteria, zoonotic bacteria and animal pathogens are continuously isolated from broilers, cattle and pigs and tested for susceptibility to antimicrobial agents used for therapy and growth promotion by disc diffusion or minimal inhibitory concentration determinations. This programme will only detect changes on a national level. However, isolating the bacteria and testing for several antimicrobial agents will enable us to determine the effect of linkage of resistance. Since 1995 major differences in the consumption pattern of different antimicrobial agents have occurred in Denmark. The Danish monitoring programme has enabled us to determine the effect of these changes on the occurrence of resistance. The Danish monitoring is, however, not suited to determine changes on a herd level or to detect emergence of new types of resistance only occurring at a low level.