bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlates of survival rates for 10 African ungulate populations: density, rainfall and predation
Authors: OWEN‐SMITH NORMAN , MASON DARRYL R. , OGUTU JOSEPH O. 
Published: July 2005

Summary

Through reconciling census totals with population structure, annual survival rates were estimated for the juvenile, yearling and adult stages of 10 ungulate species over 14 years or longer in South Africa's Kruger National Park. During this period four species maintained high abundance levels, while six species declined progressively in abundance.
Multiple regression models fitted to these estimates indicated that juvenile survival was sensitive to annual variability in rainfall for most of these species, especially in the dry season component, but with no density feedback apparent. Rainfall components affected adult survival in several of the declining species, while negative density dependence in adult survival was evident for three of the four species that maintained high abundance. A negative effect of past prey availability, indexing putative changes in predator abundance, on adult survival was more strongly supported statistically among the declining species than the lagged effect of prior rainfall, potentially affecting herbaceous vegetation cover and composition.
The high sensitivity of juvenile survival to environmental variability among these ungulate species was consistent with the general pattern identified for large mammalian herbivores, although the absence of any survival response counteracting the density declines was surprising. The susceptibility of adult survival to environmental influences for the declining species appeared unusual and probably reflected an interaction between nutritional shortfalls and a numerical increase in lions, preying largely upon the adult segment of these species. The ungulate species that persisted at high abundance seemed resistant to effects of rainfall on food resources and evidently drove the changes in predator abundance. The sharp density effect on adult survival among these species could indicate prey switching by lions following changes in their relative availability.
Findings extend past generalizations about the demographic processes underlying the population dynamics of large mammalian herbivores and reveal how the survival rates of particular population segments respond differently to environmental influences. Demographic patterns help reveal the interplay of changing resource supplies, predation pressure and population abundance on population changes.
Decomposing the variation in population growth into contributions from multiple demographic rates
Authors: COULSON TIM , GAILLARD JEAN‐MICHEL , FESTA‐BIANCHET MARCO 
Published: July 2005

Summary

The decomposition of variation in population growth into the relative contributions from different demographic rates has multiple uses in population, conservation and evolutionary biology. Recent research has favoured methods based on matrix models termed ‘life‐table‐response experiments’ or more generally ‘the retrospective matrix method’, which provide an approximation of a complete demographic decomposition. The performance of the approximation has not been assessed.
We compare the performance of the retrospective matrix method to a complete decomposition for two bighorn sheep populations and one red deer population.
Different demographic rates make markedly different contributions to variation in growth rate between populations, because each population is subject to different types of environmental variation.
The most influential demographic rates identified from decomposing observed variation in population growth are often not those showing the highest elasticity. Consequently, those demographic rates most strongly associated with deterministic population growth are not necessarily strongly associated with temporal variation in population growth.
The retrospective matrix method provides a good approximation of the demographic rate associated most strongly with variation in population growth. However, failure to incorporate the contribution of covariation between demographic rates when decomposing variation in population growth can lead to spurious conclusions.
The NusA:RNA polymerase ratio is increased at sites of rRNA synthesis in Bacillus subtilis
Authors: Davies Karen M. , Dedman Amy J. , van Horck Stephanie , Lewis Peter J. 
Published: July 2005

SummaryBacterial RNA polymerases (RNAPs) are capable of producing full‐length transcripts in the absence of additional factors using in vitro assays. However, in vivo RNAP can become stalled during the elongation phase of transcription due to the presence of various sequence motifs. Subsequently, a host of elongation factors are required to modulate the activity of RNAP. NusA, the most intensively studied elongation factor, plays a role in increasing RNAP pausing and termination. Conversely, it is also important in transcription of rRNA where it functions as an anti‐termination factor, helping to ensure only full‐length transcripts are produced. Here we show that NusA is closely associated with RNAP within the bacterial nucleoid and that it is preferentially recruited to sites of rRNA synthesis. In vivo and in vitro analyses indicate this results in a change in stoichiometry of NusA:RNAP from 1:1 to approximately 2:1 at the subcellular sites of rRNA synthesis. A model is presented showing how the ratio of NusA:RNAP could affect the activity of the elongation complex so that it functions as an anti‐terminator complex during rRNA synthesis.
Where asymmetry in gene expression originates
Authors: Barák Imrich , Wilkinson Anthony J. 
Published: July 2005

SummaryA general problem in developmental biology concerns the process by which cells of one type divide to give dissimilar daughter cells. Even though these daughter cells may be genetically identical, they can differ morphologically and physiologically and have different fates. As one of the simplest differentiation processes, Bacillus subtilis sporulation represents an excellent model system for studying cell differentiation. Several decades of study of this process have provided insight into cell cycle regulation and development. This review summarizes important advances in our understanding of asymmetric gene expression during spore formation with an emphasis on developmental stages that lead to asymmetric septum formation and especially to activation of the first compartment‐specific sigma factor –σF.
The phage‐shock‐protein response
Authors: Darwin Andrew J. 
Published: July 2005

SummaryThe phage‐shock‐protein (Psp) system responds to extracytoplasmic stress that may reduce the energy status of the cell. It is conserved in many different bacteria and has been linked to several important phenotypes. Escherichia coli psp mutants have defects in maintenance of the proton‐motive force, protein export by the sec and tat pathways, survival in stationary phase at alkaline pH, and biofilm formation. Yersinia enterocolitica psp mutants cannot grow when the secretin component of a type III secretion system is mislocalized, and have a severe virulence defect in animals. A Salmonella enterica psp mutation exacerbates some phenotypes of an rpoE null mutant and the psp genes of S. enterica and Shigella flexneri are highly induced during macrophage infection. PspA, the most abundant of the Psp proteins, is required for most of the phenotypes associated with the Psp system. Therefore, PspA is probably an effector that may play a role in maintaining cytoplasmic membrane integrity and/or the proton‐motive force. However, PspA is not required for the ability to tolerate secretin mislocalization, which suggests an important physiological role for other Psp proteins. This article summarizes our current understanding of the Psp system: inducing signals, the underlying signal transduction mechanisms, the physiological roles it may play, and a genomic analysis of its conservation.
C‐di‐GMP: the dawning of a novel bacterial signalling system
Authors: Römling Ute , Gomelsky Mark , Galperin Michael Y. 
Published: July 2005

SummaryBis‐(3′‐5′)‐cyclic dimeric guanosine monophosphate (c‐di‐GMP) has come to the limelight as a result of the recent advances in microbial genomics and increased interest in multicellular microbial behaviour. Known for more than 15 years as an activator of cellulose synthase in Gluconacetobacter xylinus, c‐di‐GMP is emerging as a novel global second messenger in bacteria. The GGDEF and EAL domain proteins involved in c‐di‐GMP synthesis and degradation, respectively, are (almost) ubiquitous in bacterial genomes. These proteins affect cell differentiation and multicellular behaviour as well as interactions between the microorganisms and their eukaryotic hosts and other phenotypes. While the role of GGDEF and EAL domain proteins in bacterial physiology and behaviour has gained appreciation, and significant progress has been achieved in understanding the enzymology of c‐di‐GMP turnover, many questions regarding c‐di‐GMP‐dependent signalling remain unanswered. Among these, the key questions are the identity of targets of c‐di‐GMP action and mechanisms of c‐di‐GMP‐dependent regulation. This review discusses phylogenetic distribution of the c‐di‐GMP signalling pathway in bacteria, recent developments in biochemical and structural characterization of proteins involved in its metabolism, and biological processes affected by c‐di‐GMP. The accumulated data clearly indicate that a novel ubiquitous signalling system in bacteria has been discovered.
SpeB–Spi: a novel protease–inhibitor pair fromStreptococcus pyogenes
Authors: Kagawa Todd F. , O'Toole Paul W. , Cooney Jakki C. 
Published: July 2005

SummaryThis study presents evidence for a novel protease–protease inhibitor couple, SpeB–Spi, in the human pathogenStreptococcus pyogenes. The gene for the inhibitor Spi is located directly downstream of the gene for the streptococcal cysteine protease SpeB. Spi is 37% identical and 70% similar to the sequence of the SpeB propeptide, suggesting that Spi and the SpeB propeptide might bind to SpeB in an analogous manner. Secondary structure predictions and molecular modelling suggested that Spi would adopt a structure similar to the SpeB propeptide. Thespigene was co‐transcribed withspeBon the 1.7 knt and 2.2 knt transcripts previously identified forspeB. The Spi protein was purified by SpeB‐affinity chromatography from theS. pyogenescytoplasm. Recombinant Spi was produced and purified, and shown to bind to SpeB and to inhibit its protease activity. Although a similar genetic arrangement of protease and inhibitor is present in staphylococci, this is the first example of an inhibitor molecule that is a structural homologue of the cognate propeptide, and which is genetically linked to the protease gene. Thus, this represents a novel system whereby bacteria may control the intracellular activity of their proteases.
Bacillus anthracis CapD, belonging to the γ‐glutamyltranspeptidase family, is required for the covalent anchoring of capsule to peptidoglycan
Authors: Candela Thomas , Fouet Agnès 
Published: July 2005

SummarySeveral examples of bacterial surface‐structure anchoring have been described, but they do not include polyglutamate capsule. Bacillus anthracis capsule, which is composed only of poly‐γ‐ d‐glutamate, is one of the two major virulence factors of the bacterium. We analysed its anchoring. We report that the polyglutamate is anchored directly to the peptidoglycan and that the bond is covalent. We constructed a capD mutant strain, capD being the fourth gene of the capsule biosynthetic operon. The mutant bacilli are surrounded by polyglutamate material that is not covalently anchored. Thus, CapD is required for the covalent anchoring of polyglutamate to the peptidoglycan. Sequence similarities suggest that CapD is a γ‐glutamyltranspeptidase. Furthermore, CapD is cleaved at the γ‐glutamyltranspeptidase consensus cleavage site, and the two subunits remain associated, as necessary for γ‐glutamyltranspeptidase activity. Other Gram‐positive γ‐glutamyltranspeptidases are secreted, but CapD is located at the Bacillus surface, associated both with the membrane and the peptidoglycan. Polyglutamate is hydrolysed by CapD indicating that it is a CapD substrate. We suggest that CapD catalyses the capsule anchoring reaction. Interestingly, the CapD– strain is far less virulent than the parental strain.
DNA polymerase I acts in translesion synthesis mediated by the Y‐polymerases in Bacillus subtilis
Authors: Duigou Stéphane , Ehrlich S. Dusko , Noirot Philippe , Noirot‐Gros Marie‐Françoise 
Published: July 2005

SummaryTranslesion synthesis (TLS) across damaged DNA bases is most often carried out by the ubiquitous error‐prone DNA polymerases of the Y‐family. Bacillus subtilis encodes two Y‐polymerases, Pol Y1 and Pol Y2, that mediate TLS resulting in spontaneous and ultraviolet light (UV)‐induced mutagenesis respectively. Here we show that TLS is a bipartite dual polymerase process in B. subtilis, involving not only the Y‐polymerases but also the A‐family polymerase, DNA polymerase I (Pol I). Both the spontaneous and the UV‐induced mutagenesis are abolished in Pol I mutants affected solely in the polymerase catalytic site. Physical interactions between Pol I and either of the Pol Y polymerases, as well as formation of a ternary complex between Pol Y1, Pol I and the β‐clamp, were detected by yeast two‐ and three‐hybrid assays, supporting the model of a functional coupling between the A‐ and Y‐family polymerases in TLS. We suggest that the Pol Y carries the synthesis across the lesion, and Pol I takes over to extend the synthesis until the functional replisome resumes replication. This key role of Pol I in TLS uncovers a new function of the A‐family DNA polymerases.
MsmR, a specific positive regulator of the Streptococcus pyogenes FCT pathogenicity region and cytolysin‐mediated translocation system genes
Authors: Nakata Masanobu , Podbielski Andreas , Kreikemeyer Bernd 
Published: July 2005

SummaryAs a prerequisite for colonization or causing local infections, Streptococcus pyogenes (group A streptococci, GAS) need to specifically adhere to eukaryotic cell surfaces. Predominantly responsible adhesin genes are contained in a genotype‐specific pattern within the FCT region of the GAS genome. In this study, MsmR, belonging to AraC/XylS type transcriptional regulators, was identified in the FCT region as a positive regulator of the major fibronectin‐binding adhesin protein F2 in a serotype M49 strain. Compared with the wild‐type strain, the msmR mutant showed reduced binding to immobilized fibronectin and decreased adherence to and internalization into human pharyngeal epithelial cells. These results suggested that altered levels of fibronectin‐binding proteins in the mutant affect eukaryotic cell attachment and internalization. Complete transcriptome and reporter fusion assay data revealed that MsmR positively regulates FCT region genes including Nra and cytolysin‐mediated translocation system genes. Consistent with the genetic data, the mutant showed attenuated streptolysin O activity and eukaryotic cell cytotoxity. Direct binding of recombinant MsmR to nga, nra/cpa and prtF2 promoter regions was confirmed by EMSA assays. As prior analysis demonstrated the Nra regulator negatively affects gene expression from the FCT region, MsmR and Nra appear to adversely control crucial virulence factor expression in GAS and thus contribute to a fine‐tuned balance between local destructive process and metastatic spreading of the bacteria.
HilD, HilC and RtsA constitute a feed forward loop that controls expression of the SPI1 type three secretion system regulator hilA in Salmonella enterica serovar Typhimurium
Authors: Ellermeier Craig D. , Ellermeier Jeremy R. , Slauch James M. 
Published: July 2005

Summary Salmonella enterica serovar Typhimurium invades intestinal epithelial cells using a type three secretion system (TTSS) encoded on Salmonella Pathogenicity Island 1 (SPI1). The SPI1 TTSS injects effector proteins into the cytosol of host cells where they promote actin rearrangement and engulfment of the bacteria. We previously identified RtsA, an AraC‐like protein similar to the known HilC and HilD regulatory proteins. Like HilC and HilD, RtsA activates expression of SPI1 genes by binding upstream of the master regulatory gene hilA to induce its expression. HilA activates the SPI1 TTSS structural genes. Here we present evidence that hilA expression, and hence the SPI1 TTSS, is controlled by a feedforward regulatory loop. We demonstrate that HilC, HilD and RtsA are each capable of independently inducing expression of the hilC, hilD and rtsA genes, and that each can independently activate hilA. Using competition assays in vivo, we show that each of the hilA regulators contribute to SPI1 induction in the intestine. Of the three, HilD has a predominant role, but apparently does not act alone either in vivo or in vitro to sufficiently activate SPI1. The two‐component regulatory systems, SirA/BarA and OmpR/EnvZ, function through HilD, thus inducing hilC, rtsA and hilA. However, the two‐component systems are not responsible for environmental regulation of SPI1. Rather, we show that ‘SPI1 inducing conditions’ cause independent activation of the rtsA, hilC and hilD genes in the absence of known regulators. Our model of SPI1 regulation provides a framework for future studies aimed at understanding this complicated regulatory network.
Post‐Flowering Photoperiod Effects on Reproductive Development and Agronomic Traits of Long‐Day and Short‐Day Crops
Authors: Han T. , Wu C. , Mentreddy R. S. , Zhao J. , Xu X. , Gai J. 
Published: July 2005

AbstractPre‐flowering photoperiod effects on floral initiation, flowering time and yield components of various crops have been well studied, but the post‐flowering photoperiod effects on major field crops are not clearly understood. A controlled environment study was carried out using six long‐day (LD) crops, flax, sugar beet, broad bean, triticale, wheat, and rapeseed, and seven short‐day (SD) crops including Adzuki bean, potato, rice, peanut, mungbean, cotton and corn with a major objective of evaluating the post‐flowering photoperiod effects on their reproductive development and yield components. There were significant inter‐ and intra‐specific differences in their response to post‐flowering photoperiod treatments. The effects of short days on LD crops were similar to LD effects on SD crops. The post‐flowering duration was prolonged by short photoperiod in LD crops and long photoperiod in SD crops. There was, however, significant genotypic variation within a species for such effects. The post‐flowering LD treatment caused abscission of flowers and pods and the resumption of vegetative growth in Adzuki bean. The post‐flowering LD treatment also delayed the shoot senescence of one of the two potato varieties and decreased the number of tubers per plant in both varieties. The LD treatment delayed maturation of rice and mungbean, and decreased seed yield and 100‐seed weight of peanut, although the shoot senescence of peanut was not apparently affected. Rapeseed, wheat, cotton and corn genotypes in this study did not show any sensitivity to post‐flowering photoperiod. In triticale (an LD crop) exposure to short photoperiod post‐flowering increased the number of spikes per plant perhaps due to a greater assimilate accumulation over a longer duration. The results from the current study as well as those from our previous experiments suggest that post‐flowering photoperiod responses do exist in diverse field crops, and that there are strong genotypic differences in sensitivity and magnitude of response to post‐flowering photoperiod. Photoperiod after flowering substantially regulates the source/sink relationship, and promotes partitioning and accumulation of assimilates to storage organs of crops when it favours the reproductive development of crops.
Barley Autotoxicity as Influenced by Varietal and Seasonal Variation
Authors: Oueslati O. , Ben‐Hammouda M. , Ghorbal M. H. , Guezzah M. , Kremer R. J. 
Published: July 2005

AbstractBarley (Hordeum vulgare L.) is widely cultivated in the semi‐arid region of Tunisia for grain production and grazing, which often occurs during the same season. We previously demonstrated autotoxic effects of barley among varieties. The present study was conducted to test the effects of barley variety and seasonal variation on the expression of autotoxicity by barley. Four barley varieties were grown in a field experiment over three growing seasons (1999–2000, 2000–01, 2001–02). In the laboratory, germination and seedling growth bioassays were used to assess autotoxicity potential of field‐harvested barley. Barley autotoxicity was fully expressed based on inhibition of radicle growth detected in seedling bioassays. Stems were often the most allelopathic plant component. Allelopathic activity of the barley varieties differed across growing seasons suggesting the influence of a seasonal effect due to the extent of water deficit during the dry season and monthly rainfall variability. The results suggest that when planning to integrate barley within cropping sequences, barley producers should carefully select appropriate barley varieties to minimize autotoxicity, which can be more severe under drought conditions.
Effects of Seed Treatment and Foliar Fungicides on Helminthosporium Leaf Blight and on Performance of Wheat in Warmer Growing Conditions
Authors: Sharma‐Poudyal D. , Duveiller E. , Sharma R. C. 
Published: July 2005

AbstractAs the wheat (Triticum aestivum L.) cultivars of south Asia are susceptible to Helminthosporium leaf blight (HLB) caused by Cochliobolus sativus and Pyrenophora tritici‐repentis, chemical control through seed treatment and foliar fungicides could increase yields. A field study was conducted in 2002 and 2003 to determine the effect of seed treatment and foliar fungicides on disease and performance of wheat. Presown seed infection by the pathogen was determined in a laboratory test. Seed was treated with Vitavax® 200B, Bavistin® and Simonis carbendazim in 2002, and Areestin® instead of Simonis carbendazim in 2003. One and two foliar sprays with Opus®, Allegro®, Horizon® and Tilt® were tested, along with a control treatment. Cochliobolus sativus was isolated from 8 and 34% presown seeds in 2002 and 2003, respectively, and no P. tritici‐repentis was found. Seed treatments were not equally effective: Vitavax® 200B increased germination by up to 43% in both years and reduced seedling infection by C. sativus in 2003. The foliar fungicides reduced HLB severity and increased grain yield. Compared with the control, the highest reduction in area under disease progress curve (AUDPC) was 53% in 2002 and 63% in 2003. The highest increase in grain yield over the control due to fungicide spray was 38% in 2002 and 83% in 2003. Grain infection in 2002 (39%) and 2003 (70%) in the control plot was reduced to 16 and 24%, respectively, thanks to the application of foliar fungicides. Two fungicide sprays in most cases did not reduce the AUDPC and grain infection and increased grain yield any more than did one spray. The results show that seed treatment was not effective in reducing HLB severity and increasing grain yield, but foliar fungicide spray was. The cost–benefit analysis shows that one spray could be cost‐effective for all four fungicides when a susceptible cultivar is planted under high HLB severity.