bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term interactions between Mediterranean climate, vegetation and fire regime at Lago di Massaciuccoli (Tuscany, Italy)
Authors: COLOMBAROLI DANIELE , MARCHETTO ALDO , TINNER WILLY 
Published: June 2007

Summary

A Holocene sedimentary sequence from a coastal lake in the Mediterranean area (Lago di Massaciuccoli, Tuscany, Italy, 0 m a.s.l.) was sampled for pollen and microscopic charcoal analyses. Contiguous 1‐cm samples represent an estimated time interval of c. 13 years, thus providing a high‐resolution sequence from 6100 to 5400 cal. years bp.
Just before 6000 cal. years bp, sub‐Mediterranean and Mediterranean forests were present together with fir (Abies alba), a submontane species that is today absent at low altitudes in the Mediterranean. A sharp vegetational change occurred after 6000 cal. years bp involving a drastic decline of Abies alba around the site.
Time‐series analyses suggest that increased fire activity at this time caused a strong decline in Abies alba, a highly fire‐sensitive species. During 100 years of higher fire incidence, diverse (predominantly evergreen) forest communities were converted to low‐diversity fire‐prone shrub communities.
Cross‐correlations reveal that fire during the mid‐Holocene hindered the expansion of holm oak (Quercus ilex), the most common tree species today in Mediterranean environments. While the factors that triggered the Holocene expansion of this species in the Mediterranean area are unclear, our results do not support the hypothesis that fire was key for holm oak expansion.
Diatom analyses of the same sediment core provide an independent palaeoenvironmental proxy for palaeoclimatic reconstruction. A change in the eutrophy and salinity of the lake occurred just before 6000 cal. years bp, suggesting that a climatic shift towards aridity may have triggered the observed change in hydrology and possibly also in fire regime.
Over the millennia fire has decisively contributed to the establishment of the present fire‐adapted vegetation type (macchia). Native fire‐sensitive species were displaced or repressed, and arboreal vegetation became less diverse. Combined ecological and palaeoecological data may help to assess possible future scenarios of biosphere responses to global change. Our results imply that the forecasted global warming and fire increase may trigger irrecoverable biodiversity losses and shifts in vegetational composition within a few decades or centuries at most. In particular, fire and drought‐sensitive vegetation types, such as the relict forests of Abies alba in the Apennines, seem particularly threatened by large‐scale displacement.
Ecosystem engineering facilitates invasions by exotic plants in high‐Andean ecosystems
Authors: BADANO ERNESTO I. , VILLARROEL ELISA , BUSTAMANTE RAMIRO O. , MARQUET PABLO A. , CAVIERES LOHENGRIN A. 
Published: June 2007

Summary

Ecosystem engineers are organisms that change abiotic conditions in ways that affect the performance and distribution of other species, including exotics. Several mechanisms have been proposed for the successful establishment of exotic plants in natural communities, but the positive effects that native engineer species may have on the distribution and performance of exotic plants remain unknown.
In this study, we propose that amelioration of extreme abiotic conditions by ecosystem engineers can make stressful habitats invadable by exotic plant species, with larger positive effects on the performance of exotic plants as environmental harshness increases. We tested this hypothesis by assessing the effects of a high‐Andean ecosystem engineer, the cushion plant Azorella monantha, which is known to create habitat patches where environmental conditions are less extreme than in the surrounding habitats, on the distribution and the performance of two exotic plant species, field chickweed (Cerastium arvense) and common dandelion (Taraxacum officinale), along a an elevation gradient in the Andes of central Chile.
We measured and compared the abundance, biomass and survival of both exotic species within and outside cushion habitat patches at three elevations (3200 m, 3400 m and 3600 m), and evaluated whether the effects of A. monantha varied across elevations.
The results indicated that cushion plants positively impact the performance of both exotics, and have greater facilitative effects at higher elevations. Indeed, at the higher elevation site, C. arvense was only detected within A. monantha patches, suggesting that cushions may expand the distribution range of exotics. These results suggest that ecosystem engineering by native species could promote biological invasions in harsh environments, leading to higher abundances of invaders than those expected in the absence of engineers.
Given the conspicuousness of ecosystem engineering in nature, we suggest that exotic species eradication programmes might be less successful by not taking into account the facilitative effects of native engineer species on invaders. Further, we suggest that the recent proposals to use engineer species in ecosystem restoration should be aware of their potential role in promoting invasions.
Links between arterial and venous disease
Authors: Prandoni P. 
Published: June 2007

Abstract.An increasing body of evidence suggests the likelihood of a link between arterial and venous disease. According to the results of recent studies, atherosclerosis and venous thromboembolism (VTE) share common risk factors, including age, obesity, diabetes mellitus and metabolic syndrome. Atherosclerosis has the potential to promote the development of thrombotic disorders in the venous system. Another scenario assumes that the two clinical conditions are simultaneously triggered by biological stimuli responsible for activating coagulation and inflammatory pathways in both the arterial and the venous system. Several recent studies have consistently shown that patients with VTE of unknown origin are at a higher risk of cardiovascular diseases, including atherosclerotic complications, than patients with secondary VTE and matched control individuals. Future studies are needed to clarify the nature of this association, to assess its extent and to evaluate its implications for clinical practice.
Inhibition of HIV‐1 entry by antibodies: potential viral and cellular targets
Authors: Phogat S. , Wyatt R. T. , Karlsson Hedestam G. B. 
Published: June 2007

Abstract.Vaccine‐induced antibodies that interfere with viral entry are the protective correlate of most existing prophylactic vaccines. However, for highly variable viruses such as HIV‐1, the ability to elicit broadly neutralizing antibody responses through vaccination has proven to be extremely difficult. The major targets for HIV‐1 neutralizing antibodies are the viral envelope glycoprotein trimers on the surface of the virus that mediate receptor binding and entry. HIV‐1 has evolved many mechanisms on the surface of envelope glycoproteins to evade antibody‐mediated neutralization, including the masking of conserved regions by glycan, quaternary protein interactions and the presence of immunodominant variable elements. The primary challenge in the development of an HIV‐1 vaccine that elicits broadly neutralizing antibodies therefore lies in the design of suitable envelope glycoprotein immunogens that circumvent these barriers. Here, we describe neutralizing determinants on the viral envelope glycoproteins that are defined by their function in receptor binding or by rare neutralizing antibodies isolated from HIV‐infected individuals. We also describe the nonvariable cellular receptors involved in the HIV‐1 entry process, or other cellular proteins, and ongoing studies to determine if antibodies against these proteins have efficacy as therapeutic reagents or, in some cases, as vaccine targets to interfere with HIV‐1 entry.
Gene encoding a deubiquitinating enzyme is mutated in artesunate‐ and chloroquine‐resistant rodent malaria parasites§
Authors: Hunt Paul , Afonso Ana , Creasey Alison , Culleton Richard , Sidhu Amar Bir Singh , Logan John , Valderramos Stephanie G. , McNae Iain , Cheesman Sandra , Rosario Virgilio do , Carter Richard , Fidock David A. , Cravo Pedro 
Published: June 2007

SummaryArtemisinin‐ and artesunate‐resistant Plasmodium chabaudi mutants, AS‐ART and AS‐ATN, were previously selected from chloroquine‐resistant clones AS‐30CQ and AS‐15CQ respectively. Now, a genetic cross between AS‐ART and the artemisinin‐sensitive clone AJ has been analysed by Linkage Group Selection. A genetic linkage group on chromosome 2 was selected under artemisinin treatment. Within this locus, we identified two different mutations in a gene encoding a deubiquitinating enzyme. A distinct mutation occurred in each of the clones AS‐30CQ and AS‐ATN, relative to their respective progenitors in the AS lineage. The mutations occurred independently in different clones under drug selection with chloroquine (high concentration) or artesunate. Each mutation maps to a critical residue in a homologous human deubiquitinating protein structure. Although one mutation could theoretically account for the resistance of AS‐ATN to artemisinin derivates, the other cannot account solely for the resistance of AS‐ART, relative to the responses of its sensitive progenitor AS‐30CQ. Two lines of Plasmodium falciparum with decreased susceptibility to artemisinin were also selected. Their drug‐response phenotype was not genetically stable. No mutations in the UBP‐1 gene encoding the P. falciparum orthologue of the deubiquitinating enzyme were observed. The possible significance of these mutations in parasite responses to chloroquine or artemisinin is discussed.
SaPI operon I is required for SaPI packaging and is controlled by LexA
Authors: Úbeda Carles , Maiques Elisa , Tormo MaÁngeles , Campoy Susana , Lasa Íñigo , Barbé Jordi , Novick Richard P. , Penadés José R. 
Published: June 2007

SummaryTransfer of Staphylococcus aureus pathogenicity islands (SaPIs) is directly controlled by the cellular repressor LexA. We have found that transcription of the SaPIbov1 operon I is repressed by LexA and is therefore SOS‐induced. Two copies of the LexA binding site consensus (Cheo box) are present in the 5′ region of this operon, at the same location in all of 15 different SaPIs analysed. Both of these boxes bind LexA protein. Furthermore, replacement of the chromosomal lexA with a non‐cleavable mutant LexA (G94E) greatly diminished expression of SaPIbov1 operon I and differentially reduced the production of SaPI transducing particles in comparison with the production of plaque‐forming particles. In concordance with this finding, deletion of operon I blocked the formation of SaPI transducing particles but had no effect on replication of the island. Operon I contains a gene encoding a homologue of the phage terminase small subunit plus two other genes that direct the assembly of the small sized SaPIbov1 capsids. Interestingly, mutations affecting the latter two genes were not defective in SaPI transfer, but rather encapsidated the island in full‐sized phage heads, which would have to contain a multimeric SaPI genome.
Critical roles for the digestive vacuole plasmepsins of Plasmodium falciparum in vacuolar function
Authors: Bonilla J. Alfredo , Bonilla Tonya D. , Yowell Charles A. , Fujioka Hisashi , Dame John B. 
Published: June 2007

SummaryKnockout mutants of Plasmodium falciparum lacking pfpm1, pfpm2 and pfhap (triple‐PM KO), and mutants lacking all four digestive vacuole (DV) plasmepsins (pfpm4, pfpm1, pfpm2 and pfhap; quadruple‐PM KO), were prepared by double cross‐over integration effecting chromosomal deletions of up to 14.6 kb. The triple‐PM KO was similar to the parental line (3D7) in growth rate, morphology and sensitivity to proteinase inhibitors. The quadruple‐PM KO showed a significantly slower rate of growth in standard medium, which manifested as delayed schizont maturation accompanied by reduced formation of haemozoin. In amino acid‐limited medium, the reduction in growth rate of the quadruple‐PM KO was pronounced. The sensitivity of both the triple‐ and quadruple‐PM KOs to six different HIV aspartic proteinase inhibitors was comparable to that of 3D7, thus establishing that the DV plasmepsins were not the primary targets of the antimalarial activity of these clinically important compounds. Electron microscopic analysis revealed the presence of multilamellar bodies resembling ceroid in the DV of the quadruple‐PM KO, and intermediates of the autophagic pathway accumulated as determined by Western blot analysis. Thus, the DV plasmepsins, although not essential, contribute significantly to the fitness of the parasite and are required for efficient degradation of endosomal vesicles delivered to the DV.
Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration
Authors: Alvarez‐Ortega Carolina , Harwood Caroline S. 
Published: June 2007

Summary Pseudomonas aeruginosa in the lungs of cystic fibrosis patients grows to high densities in mucopurulent material that is depleted in oxygen. Some have concluded that growth in these circumstances is dependent on anaerobic nitrate respiration. Here we present data in favour of the alternative hypothesis that microaerobic respiration is the predominant mode of P. aeruginosa growth in the cystic fibrosis lung. We found that P. aeruginosa strain PAO1 and a mucoid derivative of strain PAO1 each grew at dissolved oxygen concentrations of less than 3 μM. This is lower than the concentration of oxygen that has been measured in hypoxic cystic fibrosis mucous. A transcriptome analysis comparing cells grown under aerobic conditions (185 μM dissolved oxygen) with cells grown with 20 μM or 3 μM dissolved oxygen, or anaerobically with nitrate, revealed that overlapping sets of genes are expressed depending on oxygen availability. This suggests that P. aeruginosa responds to changes in oxygen concentration along a continuum rather than having a discrete low oxygen regulon. Any one of three high affinity terminal oxidases that P. aeruginosa encodes supported microaerobic growth. A triple mutant lacking all three of these oxidases failed to grow at low oxygen and formed abnormal biofilms.
A proline iminopeptidase gene upregulated in planta by a LuxR homologue is essential for pathogenicity of Xanthomonas campestris pv. campestris
Authors: Zhang Lili , Jia Yantao , Wang Li , Fang Rongxiang 
Published: June 2007

SummaryExpression of bacterial genes is often regulated by complex mechanisms, some of which involve host cues. Analysis of the Xanthomonas campestris pv. campestris (Xcc) genome sequence revealed the presence of an xccR/pip locus. The upstream gene xccR is a luxR homologue, while pip codes for a proline iminopeptidase. A lux box‐like element, named luxXc box, locates in the pip promoter region. In this work, we show that disruption of either xccR or pip resulted in significantly attenuated virulence of Xcc. Under medium culture conditions, the pip expression was significantly enhanced by overexpression of XccR and the luxXc box is necessary for this enhancement. We further show that expression of a pip promoter–gusA fusion either inserted in the bacterial chromosome or resided in a plasmid was markedly induced when the bacteria grew in planta. Disruption of either xccR or the luxXc box abolished the in planta induction, while disruption of pip enhanced the induction. Taken together, these data demonstrate that pip is indispensable for Xcc virulence and suggest a model for Xcc–host interaction in which the pathogen senses some host factor(s) to activate XccR that subsequently interacts with the luxXc box to induce the expression of pip for facilitating Xcc infection.
Temporal separation of distinct differentiation pathways by a dual specificity Rap‐Phr system in Bacillus subtilis
Authors: Smits Wiep Klaas , Bongiorni Cristina , Veening Jan‐Willem , Hamoen Leendert W. , Kuipers Oscar P. , Perego Marta 
Published: June 2007

SummaryIn bacterial differentiation, mechanisms have evolved to limit cells to a single developmental pathway. The establishment of genetic competence in Bacillus subtilis is controlled by a complex regulatory circuit that is highly interconnected with the developmental pathway for spore formation, and the two pathways appear to be mutually exclusive. Here we show by in vitro and in vivo analyses that a member of the Rap family of proteins, RapH, is activated directly by the late competence transcription factor ComK, and is capable of inhibiting both competence and sporulation. Importantly, RapH is the first member of the Rap family that demonstrates dual specificity, by dephosphorylating the Spo0F∼P response regulator and inhibiting the DNA‐binding activity of ComA. The protein thus acts at the stage where competence is well initiated, and prevents initiation of sporulation in competent cells as well as contributing to the escape from the competent state. A deletion of rapH induces both differentiation pathways and interferes with their temporal separation. Together, these results indicate that RapH is an integral part of a multifactorial regulatory circuit affecting the cell's decision between distinct developmental pathways.
DNA and origin region segregation are not affected by the transition from rod to sphere after inhibition of Escherichia coli MreB by A22
Authors: Karczmarek Aneta , Baselga Rocío Martínez‐Arteaga , Alexeeva Svetlana , Hansen Flemming G. , Vicente Miguel , Nanninga Nanne , Den Blaauwen Tanneke 
Published: June 2007

SummaryThe bacterial actin homologue MreB forms a helix underneath the cytoplasmic membrane and was shown to be essential in the morphogenesis of the rod‐shaped cells. Additionally, MreB was implicated to be involved in DNA segregation. However, in our hands the mreBCD deletion strain (PA340‐678) grew without apparent DNA segregation defect, suggesting that the reported chromosome segregation inhibition could be caused by a temporarily effect of MreB inhibition or depletion. To assess the involvement of MreB in DNA segregation during the transition from rod to sphere, we compared the effect of A22 and the PBP2 inhibitor mecillinam on the percentage of cells with segregated nucleoids and the number of oriC foci in wild‐type Escherichia coli cells. Cells became spherical in the same time window during both treatments and we could not detect any difference in the chromosome or oriC segregation between these two treatments. Additionally, flow cytometric analyses showed that A22 and mecillinam treatment gave essentially the same chromosome segregation pattern. We conclude that MreB is not directly involved in DNA segregation of E. coli.
Extracellular respiration
Authors: Gralnick Jeffrey A. , Newman Dianne K. 
Published: June 2007

SummaryAlthough it has long been known that microbes can generate energy using diverse strategies, only recently has it become clear that a growing number involve electron transfer to or from extracellular substrates. The best‐known example of what we will term ‘extracellular respiration’ is electron transfer between microbes and minerals, such as iron and manganese (hydr)oxides. This makes sense, given that these minerals are sparingly soluble. What is perhaps surprising, however, is that a number of substrates that might typically be classified as ‘soluble’ are also respired at the cell surface. There are several reasons why this might be the case: the substrate, in its ecological context, might be associated with a solid surface and thus effectively insoluble; the substrate, while soluble, might simply be too large to transport inside the cell; or the substrate, while benign in one redox state, might become toxic after it is metabolized. In this review, we discuss various examples of extracellular respiration, paying particular attention to what is known about the molecular mechanisms underlying these processes. As will become clear, much remains to be learned about the biochemistry, cell biology and regulation of extracellular respiration, making it a rich field of study for molecular microbiologists.
The essential YycFG two‐component system controls cell wall metabolism in Bacillus subtilis
Authors: Bisicchia Paola , Noone David , Lioliou Efthimia , Howell Alistair , Quigley Sarah , Jensen Thomas , Jarmer Hanne , Devine Kevin M. 
Published: June 2007

SummaryAdaptation of bacteria to the prevailing environmental and nutritional conditions is often mediated by two‐component signal transduction systems (TCS). The Bacillus subtilis YycFG TCS has attracted special attention as it is essential for viability and its regulon is poorly defined. Here we show that YycFG is a regulator of cell wall metabolism. We have identified five new members of the YycFG regulon: YycF activates expression of yvcE, lytE and ydjM and represses expression of yoeB and yjeA. YvcE(CwlO) and LytE encode endopeptidase‐type autolysins that participate in peptidoglycan synthesis and turnover respectively. We show that a yvcE lytE double mutant strain is not viable and that cells lacking LytE and depleted for YvcE exhibit defects in lateral cell wall synthesis and cell elongation. YjeA encodes a peptidoglycan deacetylase that modifies peptidoglycan thereby altering its susceptibility to lysozyme digestion and YdjM is also predicted to have a role in cell wall metabolism. A genetic analysis shows that YycFG essentiality is polygenic in nature, being a manifestation of disrupted cell wall metabolism caused by aberrant expression of a number of YycFG regulon genes.
Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c‐type cytochromes
Authors: Shi Liang , Squier Thomas C. , Zachara John M. , Fredrickson James K. 
Published: June 2007

SummaryDissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram‐negative bacteria Shewanella oneidensis MR‐1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c‐type cytochromes (c‐Cyts). In S. oneidensis MR‐1, multihaem c‐Cyts CymA and MtrA are believed to transfer electrons from the inner membrane quinone/quinol pool through the periplasm to the outer membrane. The type II secretion system of S. oneidensis MR‐1 has been implicated in the reduction of metal (hydr)oxides, most likely by translocating decahaem c‐Cyts MtrC and OmcA across outer membrane to the surface of bacterial cells where they form a protein complex. The extracellular MtrC and OmcA can directly reduce solid metal (hydr)oxides. Likewise, outer membrane multihaem c‐Cyts OmcE and OmcS of G. sulfurreducens are suggested to transfer electrons from outer membrane to type IV pili that are hypothesized to relay the electrons to solid metal (hydr)oxides. Thus, multihaem c‐Cyts play critical roles in S. oneidensis MR‐1‐ and G. sulfurreducens‐mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope.