bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatially interactive simulation of climate change, harvesting, wind, and tree species migration and projected changes to forest composition and biomass in northern Wisconsin, USA
Authors: Scheller Robert M. , Mladenoff David J. 
Published: February 2005

AbstractIn the coming century, forecast climate changes caused by increasing greenhouse gases may produce dramatic shifts in tree species distributions and the rates at which individual tree species sequester carbon or release carbon back to the atmosphere. The species composition and carbon storage capacity of northern Wisconsin (USA) forests are expected to change significantly as a result. Projected temperature changes are relatively large (up to a 5.8°C increase in mean annual temperature) and these forests encompass a broad ecotone that may be particularly sensitive to climate change. Our objective was to estimate the combined effects of climate change, common disturbances, and species migrations on regional forests using spatially interactive simulations. Multiple scenarios were simulated for 200 years to estimate aboveground live biomass and tree species composition. We used a spatially interactive forest landscape model (LANDIS‐II) that includes individual tree species, biomass accumulation and decomposition, windthrow, harvesting, and seed dispersal. We used data from two global circulation models, the Hadley Climate Centre (version 2) and the Canadian Climate Center (version 1) to generate transient growth and decomposition parameters for 23 species. The two climate change scenarios were compared with a control scenario of continuing current climate conditions. The results demonstrate how important spatially interactive processes will affect the aboveground live biomass and species composition of northern Wisconsin forests. Forest composition, including species richness, is strongly affected by harvesting, windthrow, and climate change, although five northern species (Abies balsamea,Betula papyrifera,Picea glauca,Pinus banksiana,P. resinosa) are lost in both climate scenarios regardless of disturbance scenario. Changes in aboveground live biomass over time are nonlinear and vary among ecoregions. Aboveground live biomass will be significantly reduced because of species dispersal and migration limitations. The expected shift towards southern oaks and hickory is delayed because of seed dispersal limitations.
Indole induces the expression of multidrug exporter genes in Escherichia coli
Authors: Hirakawa Hidetada , Inazumi Yoshihiko , Masaki Takeshi , Hirata Takahiro , Yamaguchi Akihito 
Published: February 2005

SummaryOur comprehensive expression cloning studies previously revealed that 20 intrinsic xenobiotic exporter systems are encoded in the Escherichia coli chromosome, but most of them are not expressed under normal conditions. In this study, we investigated the compounds that induce the expression of these xenobiotic exporter genes, and found that indole induces a variety of xenobiotic exporter genes including acrD, acrE, cusB, emrK, mdtA, mdtE and yceL. Indole treatment of E. coli cells confers rhodamine 6G and SDS resistance through the induction of mdtEF and acrD gene expression respectively. The induction of mdtE by indole is independent of the EvgSA two‐component signal transduction system that regulates the mdtE gene, but mediated by GadX. On the other hand, the induction of acrD and mdtA was mediated by BaeSR and CpxAR, two‐component systems. Interestingly, CpxAR system‐mediated induction required intrinsic baeSR genes, whereas BaeSR‐mediated induction was observed in the cpxAR gene‐deletion mutant. BaeR and CpxR directly bound to different sequences of the acrD and mdtA promoter regions. These observations indicate that BaeR is a primary regulator, and CpxR enhances the effect of BaeR.
Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re‐initiation of DNA replication
Authors: Bruand Claude , Velten Marion , McGovern Stephen , Marsin Stéphanie , Sérèna Céline , Ehrlich S. Dusko , Polard Patrice 
Published: February 2005

SummaryInitiation and re‐initiation of chromosomal DNA replication in bacteria rely on divergent multiprotein assemblies, which direct the functional delivery of the replicative helicase on single‐stranded DNA (ssDNA) at specific sites. These two processes are triggered either at the single chromosomal origin oriC or at arrested forks by the conserved DnaA and PriA proteins respectively. In Bacillus subtilis, these two pathways further require the three essential proteins DnaB, DnaD and DnaI, restrictively encoded in Gram positive bacteria of low GC content. We have recently shown that DnaI and DnaB act as a pair of loaders of the DnaC replicative helicase. The role of DnaD appeared more enigmatic. It was previously shown to interact with DnaA and to display weak ssDNA binding activity. Here, we report that purified DnaD can interact physically with PriA and with DnaB. We show that the lethality of the temperature‐sensitive dnaD23 mutant can be suppressed by different DnaB point mutants, which were found to be identical to the suppressors of priA null mutants. The DnaD23 protein displays lower ssDNA binding activity than DnaD. Conversely, the DnaB75 protein, the main dnaD23 suppressor, has gained affinity for ssDNA. Finally, we observed that this interplay between DnaD and DnaB is crucial for their concerted interaction with SSB‐coated ssDNA, which is the expected substrate for the loading of the replicative helicase in vivo. Altogether, these results highlight the need for both DnaD and DnaB to interact individually and together with ssDNA during the early stages of initiation and re‐initiation of chromosomal DNA replication. They also point at a main structural role of DnaD in the multiprotein assemblies built during these two essential processes.
Use of the Rhodopseudomonas palustris genome sequence to identify a single amino acid that contributes to the activity of a coenzyme A ligase with chlorinated substrates
Authors: Samanta Sudip K. , Harwood Caroline S. 
Published: February 2005

Summary Rhodopseudomonas palustris strain RCB100 degrades 3‐chlorobenzoate (3‐CBA) anaerobically. We purified from this strain a coenzyme A ligase that is active with 3‐CBA and determined its N‐terminal amino acid sequence to be identical to that of a cyclohexanecarboxylate‐CoA ligase encoded by aliA from the R. palustris strain (CGA009) that has been sequenced. Strain CGA009 differs from strain RCB100 in that it does not use 3‐CBA as a sole carbon source. The aliA gene from the 3‐CBA degrading strain differed by a single nucleotide from the aliA gene from strain CGA009, causing the substitution of a serine for a threonine at position 208. Both AliA enzymes, purified as His‐tagged fusion proteins, had comparable activities with cyclohexanecarboxylate. However, AliA from the 3‐CBA degrading strain was 10‐fold more active with 3‐CBA (kcat/Km of 4.3 × 104 M−1 s−1) than the enzyme from the sequenced strain (kcat/Km 0.32 × 104 M−1 s−1). The CGA009 enzyme was not sufficiently active with 3‐CBA to complement an RCB100 aliA mutant for growth on this compound. Here, whole genome sequence information enabled us to identify a single nucleotide among 5.4 million nucleotides that contributes to the substrate preference of a coenzyme A ligase.
Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase‐binding protein
Authors: Gralla Jay D. 
Published: February 2005

SummaryRibosomal RNA transcription can limit the rate of Escherichia coli growth and is subject to complex regulation. Somehow, the cell is able to sense the general nutritional environment and adjust rRNA transcription so that an appropriate number of ribosomes is produced. This review discusses the current state of affairs, including recent information about the involvement of two nucleotide regulators, two architectural protein regulators, one new co‐regulator and stalled ribosomes.
Regulated degradation of chromosome replication proteins DnaA and CtrA in Caulobacter crescentus
Authors: Gorbatyuk Boris , Marczynski Gregory T. 
Published: February 2005

SummaryDnaA protein binds bacterial replication origins and it initiates chromosome replication. The Caulobacter crescentus DnaA also initiates chromosome replication and the C. crescentus response regulator CtrA represses chromosome replication. CtrA proteolysis by ClpXP helps restrict chromosome replication to the dividing cell type. We report that C. crescentus DnaA protein is also selectively targeted for proteolysis but DnaA proteolysis uses a different mechanism. DnaA protein is unstable during both growth and stationary phases. During growth phase, DnaA proteolysis ensures that primarily newly made DnaA protein is present at the start of each replication period. Upon entry into stationary phase, DnaA protein is completely removed while CtrA protein is retained. Cell cycle arrest by sudden carbon or nitrogen starvation is sufficient to increase DnaA proteolysis, and relieving starvation rapidly stabilizes DnaA protein. This starvation‐induced proteolysis completely removes DnaA protein even while DnaA synthesis continues. Apparently, C. crescentus relies on proteolysis to adjust DnaA in response to such rapid nutritional changes. Depleting the C. crescentus ClpP protease significantly stabilizes DnaA. However, a dominant‐negative clpX allele that blocks CtrA degradation, even when combined with a clpA null allele, did not decrease DnaA degradation. We suggest that either a novel chaperone presents DnaA to ClpP or that ClpX is used with exceptional efficiency so that when ClpX activity is limiting for CtrA degradation it is not limiting for DnaA degradation. This unexpected and finely tuned proteolysis system may be an important adaptation for a developmental bacterium that is often challenged by nutrient‐poor environments.
The acidocalcisome Ca2+‐ATPase (TgA1) of Toxoplasma gondii is required for polyphosphate storage, intracellular calcium homeostasis and virulence
Authors: Luo Shuhong , Ruiz Felix A. , Moreno Silvia N. J. 
Published: February 2005

SummaryA large proportion of intracellular Ca2+ in Toxoplasma gondii tachyzoites is stored within acidocalcisomes. These organelles are characterized by their acidic nature and high calcium and polyphosphate (polyP) content. The activity of a Ca2+/H+‐ATPase named TgA1 may be important for the accumulation of Ca2+ in these organelles. This enzyme belongs to a group of plasma membrane Ca2+‐ATPase (PMCA) that lack a calmodulin‐binding domain and have vacuolar localization. To investigate the role of this enzyme, we have generated T. gondii mutants deficient in TgA1 through gene disruption. Proliferation of these mutants decreased dramatically because of deficient cell invasion. In addition, these cells had reduced virulence in a mouse model. Biochemical analysis revealed that the cell polyP content was drastically reduced, and the basal calcium levels were increased and unstable. Microneme secretion under the conditions of stimulation by ionophores was altered. Complementation of null mutants with TgA1 restored most functions. In summary, these results establish a link between TgA1, calcium homeostasis, polyP storage and virulence.
Building a bacterial orisome: emergence of new regulatory features for replication origin unwinding
Authors: Leonard Alan C. , Grimwade Julia E. 
Published: February 2005

SummaryTriggering new rounds of chromosomal DNA replication during the bacterial cell cycle is exquisitely regulated, ensuring both proper timing and one round per cycle stringency. A critical first step is stable unwinding of oriC, the chromosomal replication origin, by multiprotein orisome complexes comprising the AAA+ initiator DnaA and modulator proteins that bend DNA. Recently identified oriC–DnaA interactions in Escherichia coli raise important questions regarding the molecular mechanisms that regulate origin unwinding in bacteria. We describe staged binding of E. coli origin recognition proteins and suggest an unwinding switch based on interactions between DnaA‐ATP and specialized oriC sites that must be filled during orisome assembly. By focusing multiple regulatory pathways on only a few key oriC DNA–protein interactions, this model includes an efficient way to control unwinding followed by orisome inactivation during the cell cycle. Future studies will determine whether this regulatory scheme is correct and whether it is generally applicable to other bacterial types.
pfmdr1 mutations associated with chloroquine resistance incur a fitness cost in Plasmodium falciparum
Authors: Hayward Rhys , Saliba Kevin J. , Kirk Kiaran 
Published: February 2005

SummaryEfforts to control malaria worldwide have been hindered by the development and expansion of parasite populations resistant to many first‐line antimalarial compounds. Two of the best‐characterized determinants of drug resistance in the human malaria parasite Plasmodium falciparum are pfmdr1 and pfcrt, although the mechanisms by which resistance is mediated by these genes is still not clear. In order to determine whether mutations in pfmdr1 associated with chloroquine resistance affect the capacity of the parasite to persist when drug pressure is removed, we conducted competition experiments between P. falciparum strains in which the endogenous pfmdr1 locus was modified by allelic exchange. In the absence of selective pressure, the component of chloroquine resistance attributable to mutations at codons 1034, 1042 and 1246 in the pfmdr1 gene also gave rise to a substantial fitness cost in the intraerythrocytic asexual stage of the parasite. The loss of fitness incurred by these mutations was calculated to be 25% with respect to an otherwise genetically identical strain in which wild‐type polymorphisms had been substituted at these three codons. At least part of the fitness loss may be attributed to a diminished merozoite viability. These in vitro results support recent in vivo observations that in several countries where chloroquine use has been suspended because of widespread resistance, sensitive strains are re‐emerging.
The Yak1p kinase controls expression of adhesins and biofilm formation in Candida glabrata in a Sir4p‐dependent pathway
Authors: Iraqui Ismail , Garcia‐Sanchez Susana , Aubert Sylvie , Dromer Françoise , Ghigo Jean‐Marc , D’Enfert Christophe , Janbon Guilhem 
Published: February 2005

SummaryBiofilm is the predominant type of microbial development in natural environments, and potentially represents a major form of resistance or source of recurrence during host infection. Although a large number of studies have focussed on the genetics of bacterial biofilm formation, very little is known about the genes involved in this type of growth in fungi. A genetic screen for Candida glabrata Biofilm mutants was performed using a 96‐well plate model of biofilm formation. Study of the isolated mutant strains allowed the identification of four genes involved in biofilm formation (RIF1, SIR4, EPA6 and YAK1). Epa6p is a newly identified adhesin required for biofilm formation in this pathogenic yeast. EPA6 and its close paralogue EPA7 are located in subtelomeric regions and their transcription is regulated by Sir4p and Rif1p, two proteins involved in subtelomeric silencing. Biofilm growth conditions induce the transcription of EPA6 and EPA7: this is dependent on the presence of an intact subtelomeric silencing machinery and is independent of the Mpk1p signalling pathway. Finally, the kinase Yak1p is required for expression of both adhesin genes and acts through a subtelomeric silencing machinery‐dependent pathway.
Nuclear fusion occurs during mating in Candida albicans and is dependent on the KAR3 gene
Authors: Bennett Richard J. , Miller Mathew G. , Chua Penelope R. , Maxon Mary E. , Johnson Alexander D. 
Published: February 2005

SummaryIt is now well established that mating can occur between diploid a and α cells of Candida albicans. There is, however, controversy over when, and with what efficiency, nuclear fusion follows cell fusion to create stable tetraploid a/α cells. In this study, we have analysed the mating process between C. albicans strains using both cytological and genetic approaches. Using strains derived from SC5314, we used a number of techniques, including time‐lapse microscopy, to demonstrate that efficient nuclear fusion occurs in the zygote before formation of the first daughter cell. Consistent with these observations, zygotes micromanipulated from mating mixes gave rise to mononuclear tetraploid cells, even when no selection for successful mating was applied to them. Mating between different clinical isolates of C. albicans revealed that while all isolates could undergo nuclear fusion, the efficiency of nuclear fusion varied in different crosses. We also show that nuclear fusion in C. albicans requires the Kar3 microtubule motor protein. Deletion of the CaKAR3 gene from both mating partners had little or no effect on zygote formation but reduced the formation of stable tetraploids more than 600‐fold, as determined by quantitative mating assays. These findings demonstrate that nuclear fusion is an active process that can occur in C. albicans at high frequency to produce stable, mononucleate mating products.
A polymorphic motif in the small subunit of ADP‐glucose pyrophosphorylase modulates interactions between the small and large subunits
Authors: Cross Joanna M. , Clancy Maureen , Shaw Janine R. , Boehlein Susan K. , Greene Thomas W. , Schmidt Robert R. , Okita Thomas W. , Curtis Hannah L. 
Published: February 2005

SummaryThe heterotetrameric, allosterically regulated enzyme, adenosine‐5′‐diphosphoglucose pyrophosphorylase (AGPase) catalyzes the rate‐limiting step in starch synthesis. Despite vast differences in allosteric properties and a long evolutionary separation, heterotetramers of potato small subunit and maize large subunit have activity comparable to either parent in an Escherichia coli expression system. In contrast, co‐expression of maize small subunit with the potato large subunit produces little activity as judged by in vivo activity stain. To pinpoint the region responsible for differential activity, we expressed chimeric maize/potato small subunits in E. coli. This identified a 55‐amino acid motif of the potato small subunit that is critical for glycogen production when expressed with the potato large subunit. Potato and maize small subunit sequences differ at five amino acids in this motif. Replacement experiments revealed that at least four amino acids of maize origin were required to reduce staining. An AGPase composed of a chimeric potato small subunit containing the 55‐amino acid maize motif with the potato large subunit exhibited substantially less affinity for the substrates, glucose‐1‐phosphate and ATP and an increased Ka for the activator, 3‐phosphoglyceric acid. Placement of the potato motif into the maize small subunit restored glycogen synthesis with the potato large subunit. Hence, a small polymorphic motif within the small subunit influences both catalytic and allosteric properties by modulating subunit interactions.
Overexpression of a petunia zinc‐finger gene alters cytokinin metabolism and plant forms
Authors: Nakagawa Hitoshi , Jiang Chang‐Jie , Sakakibara Hitoshi , Kojima Mikiko , Honda Ichiro , Ajisaka Hidetoshi , Nishijima Takaaki , Koshioka Masaji , Homma Tamaki , Mander Lewis N. , Takatsuji Hiroshi 
Published: February 2005

SummaryShoot branching and plant height are among the key factors that define the overall architecture of plants. We found that overexpression of a cDNA for a zinc‐finger protein of petunia, designated Lateral shoot‐Inducing Factor (LIF), in transgenic petunia plants resulted in a dramatic increase in lateral shoots and reduced plant height. LIF overexpression also caused a decrease in the number of cells in the stem, leaf, and flower, accompanied by enlargement of cells. trans‐Zeatin was decreased while N6‐(Δ2‐isopentenyl)adenine was increased in the leaves of LIF‐overexpressed petunia. Most of the riboside, ribotide, and glucoside forms were also increased. Expression analysis using a LIF::GUS fusion gene and RT‐PCR suggested that LIF is specifically expressed around the bases of axillary buds and weakly in basal part of flowers in wild‐type petunia. GFP‐LIF‐GUS fusion proteins were translocated into the nucleus when transiently expressed in onion epidermal cells. LIF overexpression resulted in enhanced branching also in tobacco and Arabidopsis, indicating the conservation of the response to LIF overexpression among dicotyledonous plants. On the basis of these results we discuss about possible functions of LIF.
Genetic variation in epigenetic inheritance of ribosomal RNA gene methylation in Arabidopsis
Authors: Riddle Nicole C. , Richards Eric J. 
Published: February 2005

SummaryWe investigated the fidelity of epigenetic inheritance in crosses between three accessions of the flowering plant Arabidopsis thaliana (Canary Islands, Cape Verde Islands, and Columbia). Specifically, we examined the cytosine methylation content of the ribosomal RNA genes at the two nucleolus organizer regions (NOR2 and NOR4) in F1 and F2 hybrid individuals derived from reciprocal crosses between the high NOR methylation strain, Columbia, and the two other accessions, both of which have less NOR methylation. In crosses between the Columbia and Cape Verde Islands strains, the cytosine methylation content segregated as an additive Mendelian trait: the high NOR methylation state was tightly associated with the inheritance of the two Columbia‐derived NOR loci. First‐generation hybrid individuals between the Canary Islands and Columbia strains also showed a cytosine methylation content at the NORs intermediate between the parental values, consistent with the epigenetic inheritance of parental methylation patterns. Interestingly, mapping data from F2 individuals derived from a Canary Islands × Columbia cross revealed that NOR2 accounted for nearly all of the NOR methylation variation segregating in the population. NOR4 retains a significant effect on total NOR methylation content only through a complex epistatic interaction with NOR2. Our results indicate that the inheritance of differential cytosine methylation states at NOR loci can be modified by their genetic context, opening up the possibility of genetic dissection of epigenetic inheritance.