bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon limitation of soil respiration under winter snowpacks: potential feedbacks between growing season and winter carbon fluxes
Authors: Brooks Paul D. , McKnight Diane , Elder Kelly 
Published: February 2005

AbstractA reduction in the length of the snow‐covered season in response to a warming of high‐latitude and high‐elevation ecosystems may increase soil carbon availability both through increased litter fall following longer growing seasons and by allowing early winter soil frosts that lyse plant and microbial cells. To evaluate how an increase in labile carbon during winter may affect ecosystem carbon balance we investigated the relationship between carbon availability and winter CO2 fluxes at several locations in the Colorado Rockies. Landscape‐scale surveys of winter CO2 fluxes from sites with different soil carbon content indicated that winter CO2 fluxes were positively related to carbon availability and experimental additions of glucose to soil confirmed that CO2 fluxes from snow‐covered soil at temperatures between 0 and −3°C were carbon limited. Glucose added to snow‐covered soil increased CO2 fluxes by 52–160% relative to control sites within 24 h and remained 62–70% higher after 30 days. Concurrently a shift in the δ13C values of emitted CO2 toward the glucose value indicated preferential utilization of the added carbon confirming the presence of active heterotrophic respiration in soils at temperatures below 0°C. The sensitivity of these winter fluxes to substrate availability, coupled with predicted changes in winter snow cover, suggests that feedbacks between growing season carbon uptake and winter heterotrophic activity may have unforeseen consequences for carbon and nutrient cycling in northern forests. For example, published winter CO2 fluxes indicate that on average 50% of growing season carbon uptake currently is respired during the winter; changes in winter CO2 flux in response to climate change have the potential to reduce substantially the net carbon sink in these ecosystems.
Comparing soil organic carbon dynamics in plantation and secondary forest in wet tropics in Puerto Rico
Authors: Li Yiqing , Xu Ming , Zou Xiaoming , Shi Peijun , Zhang Yaoqi 
Published: February 2005

AbstractWe compared the soil carbon dynamics between a pine plantation and a secondary forest, both of which originated from the same farmland abandoned in 1976 with the same cropping history and soil conditions, in the wet tropics in Puerto Rico from July 1996 to June 1997. We found that the secondary forest accumulated the heavy‐fraction organic carbon (HF‐OC) measured by the density fractionation technique, more efficiently than the tree plantation did. Although there was no significant difference in total soil organic carbon (SOC) between the plantation (5.59±0.09 kg m−2) and the secondary forest (5.68±0.16 kg m−2), the proportion of HF‐OC carbon to the total SOC was significantly higher in the secondary forest (61%) than in the plantation (45%) (P<0.05). Forest floor mass and aboveground litterfall in the plantation were 168% and 22.8% greater than those in the secondary forest, respectively, while the decomposition rate of leaf litter in the plantation was 23.3% lower than that in the secondary forest. The annual mean soil respirations in the plantation and the secondary forest were 2.32±0.15 and 2.65±0.18 g C m−2 day−1, respectively, with a consistently higher rate in the secondary forest than in the plantation throughout the year. Microbial biomass measured by fumigation–incubation method demonstrated a strong seasonal variation in the secondary forest with 804 mg kg−1in the wet season and 460 mg kg−1in the dry season. However, the seasonal change of microbial biomass in the plantation was less significant. Our results suggested that secondary forests could stock more long‐term SOC than the plantations in the wet tropics because the naturally generated secondary forest accumulated more HF‐OC than the managed plantation.
Analyzing the ecosystem carbon and hydrologic characteristics of forested wetland using a biogeochemical process model
Authors: Cui Jianbo , Li Changsheng , Trettin Carl 
Published: February 2005

AbstractA comprehensive biogeochemical model, Wetland‐DNDC, was applied to analyze the carbon and hydrologic characteristics of forested wetland ecosystem at Minnesota (MN) and Florida (FL) sites. The model simulates the flows of carbon, energy, and water in forested wetlands. Modeled carbon dynamics depends on physiological plant factors, the size of plant pools, environmental factors, and the total amount and turnover rates of soil organic matter. The model realistically simulated water level fluctuation, forest production, carbon pools change, and CO2 and CH4 emission under natural variations in different environmental factors at two sites. Analyses were focused on parameters and inputs potentially cause the greatest uncertainty in calculated change in plant and soil C and water levels fluctuation and shows that it was important to obtain accurate input data for initial C content, climatic conditions, and allocation of net primary production to various forested wetland components. The magnitude of the forest responses was dependent not only on the rate of changes in environmental factors, but also on site‐specific conditions such as climate and soil. This paper explores the ability of using the biogeochemical process model Wetland‐DNDC to estimate the carbon and hydrologic dynamics of forested wetlands and shifts in these dynamics in response to changing environmental conditions.
Saprobic microfungi underLolium perenneandTrifolium repensat different fertilization intensities and elevated atmospheric CO2concentration
Authors: Řezáčová Veronika , Blum Herbert , Hršelová Hana , Gamper Hannes , Gryndler Milan 
Published: February 2005

AbstractAnthropogenic increases in atmospheric CO2concentration and the connected deposition of organic matter into the soil influence the occurrence of decomposers who regulate carbon release back into the atmosphere. The effects of increased concentration of atmospheric carbon dioxide, plant species cover quality and nitrogen (N) fertilization on the coenosis composition of soil saprobic microfungi were studied under field conditions (Swiss Free Air Carbon Dioxide Enrichment experiment). In total, 42 species of microfungi were detected in examined soil. The most significant response of soil mycoflora was induced by the species identity of plant cover. Higher N fertilization significantly suppressed the abundance of soil microfungi at ambient CO2. The effect of increased CO2on colony‐forming units was not significant when taken as an independent treatment; however, this factor interacted significantly with N availability. Some species, e.g. theClonostachys rosea, were proven associated with the plant cover components, in this particular case withTrifolium repens. Therefore, we suggest the identity of plant species constituting plant cover as the most important factors affecting soil microfungi in agroecosystems.
The contribution of MvfR to Pseudomonas aeruginosa pathogenesis and quorum sensing circuitry regulation: multiple quorum sensing‐regulated genes are modulated without affecting lasRI, rhlRI or the production of N‐acyl‐ l‐homoserine lactones
Authors: Déziel Eric , Gopalan Suresh , Tampakaki Anastasia P. , Lépine François , Padfield Katie E. , Saucier Maude , Xiao Gaoping , Rahme Laurence G. 
Published: February 2005

SummaryThe transcriptional regulator MvfR is required for full Pseudomonas aeruginosa virulence, the function of multiple quorum sensing (QS)‐regulated virulence factors and the synthesis of 4‐hydroxy‐2‐alkylquinolines (HAQs), including the Pseudomonas quinolone signal (PQS). Here we investigate the role of MvfR in the QS circuitry and P. aeruginosa pathogenesis. We demonstrate using a combination of biochemical and molecular approaches, including transcription profiling, that MvfR is involved in the regulation of multiple P. aeruginosa QS‐controlled genes without altering the expression of lasRI/rhlRI or the production of N‐acyl‐ l‐homoserine lactone (AHL) signals. Dissection of how mvfR is interwoven into the P. aeruginosa QS circuitry reveals that the MvfR system, through the essential contribution of PqsE, positively regulates a subset of genes dependant on both LasR and RhlR. Animal studies show that MvfR contributes to P. aeruginosa virulence by controlling the transcription of genes not under RhlR regulation, and that reduced virulence of a mvfR mutant is caused by the loss of pqsE expression and not only a deficiency in HAQs/PQS production. This study provides novel insights into the unique role of the MvfR system in AHL‐mediated QS and further supports its importance in P. aeruginosa pathogenesis.
The stress‐responsive chaperone α‐crystallin 2 is required for pathogenesis of Mycobacterium tuberculosis
Authors: Stewart Graham R. , Newton Sandra M. , Wilkinson Katalin A. , Humphreys Ian R. , Murphy Helen N. , Robertson Brian D. , Wilkinson Robert J. , Young Douglas B. 
Published: February 2005

Summary Mycobacterium tuberculosis has two members of the α‐crystallin (Acr) family of molecular chaperones. Expression of Acr1 is induced by exposure to hypoxia or nitric oxide and is associated with bacterial persistence in a non‐replicating state. Expression of Acr2 is induced by heat shock, oxidative stress, and uptake by macrophages. We have shown that Acr2 continues to be expressed at a high level during both acute and chronic infection in the mouse model, with an increased ratio of acr2:acr1 mRNA in the persistent phase. Deletion of the acr2 gene resulted in a decrease in the resistance of M. tuberculosis to oxidative stress but did not impair growth in mouse bone marrow macrophages. There was no difference in bacterial load in mice infected with an acr2 deletion mutant, but a marked alteration in disease progression was evident from reduced weight loss over a prolonged infection. This correlated with reduced recruitment of T‐cells and macrophages to the lungs of mice infected with the acr2 mutant and reduced immune‐related pathology. These findings demonstrate that both α‐crystallins contribute to persistent infection with M. tuberculosis and suggest that manipulation of acr expression can influence the host response to infection.
Transcription activation of a UV‐inducible Clostridium perfringens bacteriocin gene by a novel σ factor
Authors: Dupuy Bruno , Mani Nagraj , Katayama Seiichi , Sonenshein Abraham L. 
Published: February 2005

SummaryExpression of the plasmid‐encoded Clostridium perfringens gene for bacteriocin BCN5 was shown to depend in vivo and in vitro on the activity of UviA protein. UviA,  also  plasmid‐encoded,  proved  to  be an RNA polymerase σ factor and was also partly autoregulatory. The uviA gene has two promoters; one provided a UviA‐independent, basal level of gene expression while the stronger, UviA‐dependent promoter was only utilized after the cell experienced DNA damage. As a result, BCN5 synthesis is induced by treatment with UV light or mitomycin C. UviA is related to a special class of σ factors found to date only in Clostridium species and responsible for activating transcription of toxin genes in Clostridium difficile, Clostridium tetani, and Clostridium botulinum.
A potential novel mechanism for the insertion of a membrane protein revealed by a biochemical analysis of the Plasmodium falciparum cytoadherence molecule PfEMP‐1
Authors: Papakrivos Janni , Newbold Chris I. , Lingelbach Klaus 
Published: February 2005

Summary Plasmodium falciparum erythrocyte membrane protein‐1 (PfEMP‐1) is exposed on the surface of infected erythrocytes where it both acts as an important pathogenicity factor in malaria and undergoes antigenic variation as a means of immune evasion. Because the mammalian erythrocyte lacks a protein secretory machinery there has been much interest in elucidating the mechanism whereby this protein is transferred from its site of synthesis within the parasite to its final destination. Current opinion favours a mechanism whereby PfEMP‐1 becomes cotranslationally inserted into the endoplasmic reticulum of the parasite and is subsequently transported as an integral part of an erythrocyte cytoplasmic membrane system derived from the parasite. Here we show that the solubility characteristics of this protein during several stages of its transport pathway are inconsistent with this view. Instead we propose that the protein is synthesized as a peripheral membrane protein which only when it arrives at its final destination assumes a transmembrane topology. Even in this state, the extractability of the protein with urea suggest that it is anchored in the membrane by protein‐protein rather than by protein–lipid interaction.
Differing requirements for the Arabidopsis Rad51 paralogs in meiosis and DNA repair
Authors: Bleuyard Jean‐Yves , Gallego Maria E. , Savigny Florence , White Charles I. 
Published: February 2005

SummaryIn addition to the recombinase Rad51, vertebrates have five paralogs of Rad51, all members of the Rad51‐dependent recombination pathway. These paralogs form two complexes (Rad51C/Xrcc3 and Rad51B/C/D/Xrcc2), which play roles in somatic recombination, DNA repair and chromosome stability. However, little is known of their possible involvement in meiosis, due to the inviability of the corresponding knockout mice. We have recently reported that the Arabidopsis homolog of one of these Rad51 paralogs (AtXrcc3) is involved in DNA repair and meiotic recombination and present here Arabidopsis lines carrying mutations in three other Rad51 paralogs (AtRad51B, AtRad51C and AtXrcc2). Disruption of any one of these paralogs confers hypersensitivity to the DNA cross‐linking agent Mitomycin C, but not to γ‐irradiation. Moreover, the atrad51c‐1 mutant is the only one of these to show meiotic defects similar to those of the atxrcc3 mutant, and thus only the Rad51C/Xrcc3 complex is required to achieve meiosis. These results support conservation of functions of the Rad51 paralogs between vertebrates and plants and differing requirements for the Rad51 paralogs in meiosis and DNA repair.
Control of expression and autoregulation of AGL15, a member of the MADS‐box family
Authors: Zhu Cong , Perry Sharyn E. 
Published: February 2005

SummaryAGL15 is an Arabidopsis thaliana MADS‐domain regulatory factor that not only preferentially accumulates during embryogenesis but is also expressed at lower levels after the completion of germination. To better understand the control of expression of AGL15, a series of 5′ and internal deletions within the regulatory regions of AGL15 was generated. Regions important for the level of expression, including a region involved in expression in response to auxin, were identified. Additionally, AGL15 expression was found to respond to AGL15 accumulation amounts and to altered forms of AGL15. This feedback loop is at least in part due to direct regulation, as assessed by in vivo and in vitro binding of AGL15 to its own regulatory regions and by site‐directed mutagenesis studies.
Functional distribution and dynamics of Arabidopsis SR splicing factors in living plant cells
Authors: Tillemans Vinciane , Dispa Laurence , Remacle Claire , Collinge Mélanie , Motte Patrick 
Published: February 2005

SummarySerine/arginine‐rich (SR) proteins constitute an important class of splicing regulators in higher eukaryotes that share a modular structure consisting of one or two N‐terminal RNA recognition motif (RRM) domains and a C‐terminal RS‐rich domain. Herein, we have investigated the in vivo functional distribution of Arabidopsis SR factors. Agrobacterium‐mediated transient transformation revealed nuclear speckled distribution and the overall colocalization of fluorescent protein (FP)‐tagged SR factors in both tobacco and Arabidopsis cells. Their overall colocalization in larger nucleoplasmic domains was further observed after transcriptional and phosphorylation/dephosphorylation inhibition, indicating a close functional association between SR factors, independent of their phosphorylation state. Furthermore, we demonstrated in vivo the conserved role of the RS and RRM domains in the efficient targeting of Arabidopsis SR proteins to nuclear speckles by using a series of structural domain‐deleted mutants of atRSp31 and atRSZp22. We suggest additional roles of RS domain such as the shuttling of atRSZp22 between nucleoplasm and nucleolus through its phosphorylation level. The coexpression of deletion mutants with wild‐type SR proteins revealed potential complex associations between them. Fluorescence recovery after photobleaching demonstrated similar dynamic properties of SR factors in both tobacco transiently expressing cells and Arabidopsis transgenics. Cell cycle phase‐dependent organization of FP‐tagged SR proteins was observed in living tobacco BY‐2 cells. We showed that atRSp31 is degraded at metaphase by fluorescence quantification. SR proteins also localized within small foci at anaphase. These results demonstrate interesting related features as well as potentially important differences between plant and animal SR proteins.
Comparison of standard phenotypic assays with a PCR method to discriminate Candida albicans and C. dubliniensis
Authors: Mähnß B. , Stehr F. , Schäfer W. , Neuber K. 
Published: January 2005

SummaryIn 1995, Candida dubliniensis was described as a new species in the genus Candida. Its close relationship to C. albicans has proved problematic in the identification of C. dubliniensis in clinical specimens. The objective of this study was to determine if reproducible differentiation between both species can be obtained by phenotypic assays. Therefore, 100 strains from 86 patients with the ability to produce chlamydospores were examined with different methods including API ID 32 C, colour development on CHROMagar, chlamydospore formation on Staib agar, growth at different temperatures and germ tube formation at 39 °C. Additionally, polymerase chain reaction (PCR) was used as gold standard. Six of the investigated strains were C. dubliniensis. The results suggest that there is still no single phenotypic method satisfactory to distinguish between C. albicans and C. dubliniensis.
Chromoblastomycosis
Authors: Vijaya D. , Kumar B. H. 
Published: January 2005

SummaryA 70‐year‐old male agriculturist from a rural area presented with a history of a painless verrucous lesion over the medial aspect of the left leg for 1 year following abrasion by a branch of a coconut tree. KOH preparation of the skin biopsy showed evidence of fungal elements. Cladophilalospora sp. was isolated in culture. The case was diagnosed as chromoblastomycosis. As there was no response to itraconazole, complete surgical resection of the lesion was done. At follow‐up after 1 year there was clinical as well as mycological cure.
The pT1a and pT1b category subdivision in renal cell carcinoma: is it reflected by differences in tumour biology?
Authors: Langner Cord , Ratschek Manfred , Rehak Peter , Tsybrovskyy Oleksiy , Zigeuner Richard 
Published: January 2005

OBJECTIVETo assess systematically the possible differences in pathology between pT1a and pT1b renal cell carcinomas (RCCs), as the sixth edition of the Tumour‐Nodes‐Metastasis (TNM) system implemented a subdivision of category pT1 into pT1a (<4 cm) and pT1b (4–7 cm), based on clinical outcome analysis and the approach to therapy.PATIENTS AND METHODSConventional histopathology and immunohistochemical expression of several biomarkers were analysed in 66 patients with pT1a and 29 with pT1b RCCs, using a tissue microarray technique.RESULTSAfter 2 years of follow‐up, none of the 66 patients with pT1a and three of the 29 with pT1b tumours developed progressive disease. The tumour was grade 3 in four (6%) pT1a and 11 (38%) pT1b RCCs. Immunohistochemically, pT1a RCCs were characterized by strong expression of p27 (79%), bcl‐2 (67%), MUC1 (87%), insulin‐like growth factor (IGF)‐I (71%) and CD10 (88%), as well as moderate expression of IGF‐I receptor (43%) and low expression of epidermal growth factor receptor (EGFR, 20%). During progression to category pT1b, expression of p27 significantly decreased (54%) and EGFR expression increased (38%). Moreover, membranous staining patterns of MUC1 and CD10 changed from apical to circumferential in clear cell RCCs. p53 (pT1a 23%, pT1b 28%), E‐cadherin (10% and 17%), MIB‐1 (1.2% and 1.5%) and Skp2 (2% and none) expression seemed to be of minor importance.CONCLUSIONThis is the first study to show that the subdivision of category pT1 implemented in the latest issue of the TNM system is reflected by differences in conventional histopathology and expression of biomarkers.
A prospective evaluation of efficacy and compliance with a multistep treatment approach for erectile dysfunction in patients after non‐nerve sparing radical prostatectomy
Authors: Gontero Paolo , Fontana Francesco , Zitella Andrea , Montorsi Francesco , Frea Bruno 
Published: January 2005

Associate EditorMichael G. WyllieEditorial BoardIan Eardley, UKJean Fourcroy, USASidney Glina, BrazilJulia Heiman, USAChris McMahon, AustraliaBob Millar, UKAlvaro Morales, CanadaMichael Perelman, USAMarcel Waldinger, NetherlandsOBJECTIVETo assess the response rate to different erectile aids in a consecutive series of patients treated with non‐nerve sparing radical prostatectomy (NNSRP).PATIENTS AND METHODSNinety‐four potent men were counselled about the different treatment options to restore an assisted erection before they had NNSRP. They were invited to participate in a multiphase protocol involving the sequential use of different erectile aids which aimed at restoring erectile function after surgery. The first proposed treatment was oral apomorphine sublingual. Patients with a positive response to the 1‐item overall efficacy question and a minimum score of 3 in both question 3 and 4 of the International Index of Erectile Function were considered responders to oral pharmacotherapy. Treatment with sildenafil was then suggested to those not responding. If patients did not respond to oral pharmacotherapy a trial with a vacuum erectile device was offered; those not responding to this were then offered intracavernosal injection therapy with prostaglandin‐E alone as the first option, followed by a mixture of vasoactive agents if needed. In those in whom injections also failed, a penile implant was recommended. At the 1‐year follow‐up visit all patients were offered a second trial with oral therapy regardless of the treatment currently in use.RESULTSSeventy‐six patients entered the protocol; there was no response to apomorphine. Five of 59 (8%) patients responded to sildenafil when they first used it at a mean of 7 months after NNSRP, while there were three additional responders in 22 patients who tried it for a second time a year later. Of patients achieving at least a complete tumescence sufficient for vaginal penetration, 52% and 60% were considered responders to the vacuum device and intracavernosal injections, respectively. Overall, 44% of patients enrolled in the protocol chose to use an erectile aid for at‐home use. At the 1‐year follow‐up, only 20% of patients were still using an erectile aid, including two who had had a penile implant.CONCLUSIONSUp to 10% of patients may achieve a clinically significant erection with sildenafil after NNSRP, but 80% will not be using any erectile aid at 1 year after surgery. In the present study protocol the proposed erectile aids were largely inadequate for treating the permanent erectile dysfunction that follows NNSRP.