bluuebunny/crossref_metadata_2025 huggingface dataset:
Dichotomous responses of inter and postprandial hyperglycaemia to short‐term calorie restriction in patients with type 2 diabetes
Authors: Colette C. , Ginet C. , Boegner C. , Benichou M. , Pham T. C. , Cristol J. P. , Monnier L.
Published: April 2005

Background  In type 2 diabetes the effects of short‐term calorie restrictions on glycaemia are usually judged on fasting plasma glucose. As fasting duration rarely exceeds 2–3 h, we determined the effects of calorie restriction over different daytime periods using a continuous glucose monitoring system (CGMS) in noninsulin‐using patients with type 2 diabetes.

Design  Fourteen poorly controlled (mean HbA1c = 9·3%) overweight or obese patients (mean body mass index = 30·1 ± 0·7 kg m−2) with type 2 diabetes were investigated twice with a CGMS, at baseline and at the end of a 18‐day calorie‐restricted diet (1490 kcal day−1). Areas under curves (AUCs) of 24‐h glucose monitoring were measured and divided into postprandial and interprandial AUCs according to meal times.

Results  Areas under curves of 24‐h glucose monitoring were significantly decreased after dieting: –37%, P = 0·0047. Both post and interprandial AUCs were significantly diminished (−26%, P = 0·0186 and −48%, P = 0·0037, respectively), but changes in interprandial AUCs were more marked than changes in postprandial AUCs (P = 0·0060). Nycthemeral peaks of glucose were observed at mid‐morning times and were not significantly different before (242 ± 15 mg dL−1) and after dieting (227 ± 16 mg dL−1).

Conclusions  Short‐term calorie restriction in overweight or obese patients with type 2 diabetes resulted in dichotomous responses between interprandial and postprandial glycaemic excursions. The resistance of mid‐morning glucose peaking to calorie restriction should result in additional dietary or pharmacological measures at breakfast.
Tamm‐Horsfall protein: a multilayered defence molecule against urinary tract infection
Authors: Säemann M. D. , Weichhart T. , Hörl W. H. , Zlabinger G. J.
Published: April 2005

Urinary tract infection (UTI) is the most common nonepidemic bacterial infection in humans, representing a constant danger for the host. Both innate and adaptive components of the immune system as well as stromal cells including bladder epithelium are involved in the prevention and clearance of UTI. However, the particular properties of the urogenital tract, which does not comprise typical physical barriers like a mucus or ciliated epithelium, necessitate soluble mediators with potent immunomodulatory capabilities. One candidate molecule capable of both mediating direct antimicrobial activity and alerting immune cells is the evolutionary conserved Tamm‐Horsfall protein (THP). Tamm‐Horsfall protein is exclusively produced by the kidney in the distal loop of Henle; however, its definite physiological function remains elusive. Mounting evidence indicates that beyond a mere direct antimicrobial activity, THP exerts potent immunoregulatory activity. Furthermore, the genetic ablation of the THP gene leads to severe infection and lethal pyelonephritis in an experimental model of UTI. Recent data are provided demonstrating that THP links the innate immune response with specific THP‐directed cell‐mediated immunity. In light of these novel findings we discuss the particular role of THP as a specialized defence molecule. We propose an integrated model of protective mechanisms against UTI where THP acts by two principle nonmutually exclusive mechanisms involving the capture of potentially dangerous microbes and the ability of this peculiar glycoprotein to induce robust protective immune responses against uropathogenic bacteria.
Pathogenesis, detection and treatment of Achilles tendon xanthomas
Authors: Tsouli S. G. , Kiortsis D. N. , Argyropoulou M. I. , Mikhailidis D. P. , Elisaf M. S.
Published: April 2005

Tendon xanthomatosis often accompanies familial hypercholesterolaemia, but it can also occur in other pathologic states. Achilles tendons are the most common sites of tendon xanthomas. Low‐density lipoprotein (LDL) derived from the circulation accumulates into tendons. The next steps leading to the formation of Achilles tendon xanthomas (ATX) are the transformation of LDL into oxidized LDL (oxLDL) and the active uptake of oxLDL by macrophages within the tendons. Although physical examination may reveal Achilles tendon xanthomas (ATX), there are several imaging methods for their detection. It is worth mentioning that ultrasonography is the method of choice in everyday clinical practice. Although several treatments for Achilles tendon xanthomas (ATX) have been proposed (LDL apheresis, statins, etc.), they target mostly in the treatment of the basic metabolic disorder of lipid metabolism, which is the main cause of these lesions. In this review we describe the formation, detection, differential diagnosis and treatment of ATX as well as the relationship between tendon xanthomas and atheroma.
Effects of simvastatin on blood lipids, vitamin E, coenzyme Q10 levels and left ventricular function in humans
Authors: Colquhoun D. M. , Jackson R. , Walters M. , Hicks B. J. , Goldsmith J. , Young P. , Strakosch C. , Kostner K. M.
Published: April 2005

Background  As statin therapy has been reported to reduce antioxidants such as vitamin E and coenzyme Q10 and there are indications that this reduction may cause impairment of left ventricular function (LVF), we studied the influence of simvastatin on LVF and serum vitamin E and coenzyme Q10 levels in humans.

Material and methods  We assessed the effect of simvastatin on left ventricular function and coenzyme Q10 levels in 21 (11 male, 10 female) hypercholesterolaemic subjects (mean age = 56 years) with normal LVF, over a period of 6 months. Subjects were re‐tested after a 1‐month wash‐out period (7 months). Echocardiography was performed on all subjects before commencement of simvastatin (20 mg day−1), and at 1, 3, 6 and 7 months after initiation of treatment. Fasting blood samples were also collected at these intervals to assess lipids, apoproteins, vitamin E and coenzyme Q10.

Results  Serum lipids showed the expected reductions. Plasma vitamin E and coenzyme Q10 levels were reduced by 17 ± 4% (P < 0·01) and 12 ± 4% (P < 0·03) at 6 months. However, the coenzyme Q10/LDL‐cholesterol ratio and vitamin E/LDL‐cholesterol ratio increased significantly. Left ventricular ejection fraction (EF) decreased transiently after 1 month, while no significant change was observed at 3 and 6 months. Other markers of left ventricular function did not change significantly at any time point.

Conclusion  Despite reduced plasma vitamin E and coenzyme Q10, 20 mg of simvastatin therapy is associated with a significantly increased coenzyme Q10/LDL‐cholesterol ratio and vitamin E/LDL‐cholesterol ratio. Simvastatin treatment is not associated with impairment in left ventricular systolic or diastolic function in hypercholesterolaemic subjects after 6 months of treatment.
Increased glomerular and extracellular malondialdehyde levels in patients and rats with focal segmental glomerulosclerosis
Authors: Kuo H.‐T. , Kuo M.‐C. , Chiu Y.‐W. , Chang J.‐M. , Guh J.‐Y. , Chen H.‐C.
Published: April 2005

Background  Evidence suggests an increase in oxidative stress in patients with chronic kidney disease, as glomerulosclerosis is the prerequisite for chronic kidney disease; whether the oxidative stress already exists early on is not known.

Materials and methods  In this study we measured the plasma and urinary levels of malondialdehyde (MDA), the end product of lipid peroxidation, and assessed the immunoreactivity of MDA and superoxide dismutase (SOD) in glomeruli of patients and rats with primary focal segmental glomerulosclerosis (FSGS), and compared our findings with those of minimal change disease (MCD) and normal controls (NC).

Results  Our results showed that plasma MDA level was significantly increased in patients with FSGS compared with both patients with MCD and normal controls. The urinary MDA level was also significantly increased and was significantly correlated with plasma MDA level in patients with FSGS. The immunostaining for glomerular MDA and SOD was significantly higher in the patients with FSGS than in either the patients with MCD or NC, and was also significantly higher in rats with puromycin aminonucleoside (PAN)‐induced FSGS than in rats with MCD. Glomerular MDA level was significantly correlated with the degree of glomerulosclerosis in the patients with FSGS.

Conclusions  Our data suggest that oxidative stress occurs early on before the onset of renal failure, and may play an important role in the pathogenesis of glomerulosclerosis.
Carbon fluxes, nitrogen cycling, and soil microbial communities in adjacent urban, native and agricultural ecosystems
Authors: Kaye J. P. , McCulley R. L. , Burke I. C.
Published: April 2005

Urban ecosystems are expanding globally, and assessing the ecological consequences of urbanization is critical to understanding the biology of local and global change related to land use. We measured carbon (C) fluxes, nitrogen (N) cycling, and soil microbial community structure in a replicated (n=3) field experiment comparing urban lawns to corn, wheat–fallow, and unmanaged shortgrass steppe ecosystems in northern Colorado. The urban and corn sites were irrigated and fertilized. Wheat and shortgrass steppe sites were not fertilized or irrigated. Aboveground net primary productivity (ANPP) in urban ecosystems (383±11 C m−2 yr−1) was four to five times greater than wheat or shortgrass steppe but significantly less than corn (537±44 C m−2 yr−1). Soil respiration (2777±273 g C m−2 yr−1) and total belowground C allocation (2602±269 g C m−2 yr−1) in urban ecosystems were both 2.5 to five times greater than any other land‐use type. We estimate that for a large (1578 km2) portion of Larimer County, Colorado, urban lawns occupying 6.4% of the land area account for up to 30% of regional ANPP and 24% of regional soil respiration from land‐use types that we sampled. The rate of N cycling from urban lawn mower clippings to the soil surface was comparable with the rate of N export in harvested corn (both ∼12–15 g N m−2 yr−1). A one‐time measurement of microbial community structure via phospholipid fatty acid analysis suggested that land‐use type had a large impact on microbial biomass and a small impact on the relative abundance of broad taxonomic groups of microorganisms. Our data are consistent with several other studies suggesting that urbanization of arid and semiarid ecosystems leads to enhanced C cycling rates that alter regional C budgets.
Carbon exchange of grazed pasture on a drained peat soil
Authors: Nieveen Joost P. , Campbell David I. , Schipper Louis A. , Blair Ian J.
Published: April 2005

Land‐use changes have contributed to increased atmospheric CO2 concentrations. Conversion from natural peatlands to agricultural land has led to widespread subsidence of the peat surface caused by soil compaction and mineralization. To study the net ecosystem exchange of carbon (C) and the contribution of respiration to peat subsidence, eddy covariance measurements were made over pasture on a well‐developed, drained peat soil from 22 May 2002 to 21 May 2003. The depth to the water table fluctuated between 0.02 m in winter 2002 to 0.75 m during late summer and early autumn 2003. Peat soil moisture content varied between 0.6 and 0.7 m3 m−3 until the water table dropped below 0.5 m, when moisture content reached 0.38 m3 m−3. Neither depth to water table nor soil moisture was found to have an effect on the rate of night‐time respiration (ranging from 0.4–8.0 μmol CO2 m−2 s−1 in winter and summer, respectively). Most of the variance in night‐time respiration was explained by changes in the 0.1 m soil temperature (r2=0.93). The highest values for daytime net ecosystem exchange were measured in September 2002, with a maximum of −17.2 μmol CO2 m−2 s−1. Grazing events and soil moisture deficiencies during a short period in summer reduced net CO2 exchange. To establish an annual C balance for this ecosystem, non‐linear regression was used to model missing data. Annually integrated (CO2) C exchange for this peat–pasture ecosystem was 45±500 kg C ha−1 yr−1. After including other C exchanges (methane emissions from cows and production of milk), the net annual C loss was 1061±500 kg C ha−1 yr−1.
Canopy‐scale δ13C of photosynthetic and respiratory CO2 fluxes: observations in forest biomes across the United States
Authors: Lai C.‐T. , Ehleringer J. R. , Schauer A. J. , Tans P. P. , Hollinger D. Y. , Paw U K. T. , Munger J. W. , Wofsy S. C.
Published: April 2005

The δ13C values of atmospheric carbon dioxide (CO2) can be used to partition global patterns of CO2 source/sink relationships among terrestrial and oceanic ecosystems using the inversion technique. This approach is very sensitive to estimates of photosynthetic 13C discrimination by terrestrial vegetation (ΔA), and depends on δ13C values of respired CO2 fluxes (δ13CR). Here we show that by combining two independent data streams – the stable isotope ratios of atmospheric CO2 and eddy‐covariance CO2 flux measurements – canopy scale estimates of ΔA can be successfully derived in terrestrial ecosystems. We also present the first weekly dataset of seasonal variations in δ13CR from dominant forest ecosystems in the United States between 2001 and 2003. Our observations indicate considerable summer‐time variation in the weekly value of δ13CR within coniferous forests (4.0‰ and 5.4‰ at Wind River Canopy Crane Research Facility and Howland Forest, respectively, between May and September). The monthly mean values of δ13CR showed a smaller range (2–3‰), which appeared to significantly correlate with soil water availability. Values of δ13CR were less variable during the growing season at the deciduous forest (Harvard Forest). We suggest that the negative correlation between δ13CR and soil moisture content observed in the two coniferous forests should represent a general ecosystem response to the changes in the distribution of water resources because of climate change. Shifts in δ13CR and ΔA could be of sufficient magnitude globally to impact partitioning calculations of CO2 sinks between oceanic and terrestrial compartments.
Site‐level evaluation of satellite‐based global terrestrial gross primary production and net primary production monitoring
Authors: Turner David P. , Ritts William D. , Cohen Warren B. , Maeirsperger Thomas K. , Gower Stith T. , Kirschbaum Al A. , Running Steve W. , Zhao Maosheng , Wofsy Steven C. , Dunn Allison L. , Law Beverly E. , Campbell John L. , Oechel Walter C. , Kwon Hyo Jung , Meyers Tilden P. , Small Eric E. , Kurc Shirley A. , Gamon John A.
Published: April 2005

Operational monitoring of global terrestrial gross primary production (GPP) and net primary production (NPP) is now underway using imagery from the satellite‐borne Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. Evaluation of MODIS GPP and NPP products will require site‐level studies across a range of biomes, with close attention to numerous scaling issues that must be addressed to link ground measurements to the satellite‐based carbon flux estimates. Here, we report results of a study aimed at evaluating MODIS NPP/GPP products at six sites varying widely in climate, land use, and vegetation physiognomy. Comparisons were made for twenty‐five 1 km2 cells at each site, with 8‐day averages for GPP and an annual value for NPP. The validation data layers were made with a combination of ground measurements, relatively high resolution satellite data (Landsat Enhanced Thematic Mapper Plus at ∼30 m resolution), and process‐based modeling. There was strong seasonality in the MODIS GPP at all sites, and mean NPP ranged from 80 g C m−2 yr−1 at an arctic tundra site to 550 g C m−2 yr−1 at a temperate deciduous forest site. There was not a consistent over‐ or underprediction of NPP across sites relative to the validation estimates. The closest agreements in NPP and GPP were at the temperate deciduous forest, arctic tundra, and boreal forest sites. There was moderate underestimation in the MODIS products at the agricultural field site, and strong overestimation at the desert grassland and at the dry coniferous forest sites. Analyses of specific inputs to the MODIS NPP/GPP algorithm – notably the fraction of photosynthetically active radiation absorbed by the vegetation canopy, the maximum light use efficiency (LUE), and the climate data – revealed the causes of the over‐ and underestimates. Suggestions for algorithm improvement include selectively altering values for maximum LUE (based on observations at eddy covariance flux towers) and parameters regulating autotrophic respiration.
Designing a programming‐based approach for modelling scientific phenomena
Authors: Simpson Gordon , Hoyles Celia , Noss Richard
Published: April 2005

Abstract
We describe an iteratively designed sequence of activities involving the modelling of one‐dimensional collisions between moving objects based on programming in ToonTalk. Students aged 13–14 years in two settings (London and Cyprus) investigated a number of collision situations, classified into six classes based on the relative velocities and masses of the colliding objects. We describe iterations of the system in which students engaged in a repeating cycle of activity for each collision class: prediction of object behaviour from given collision conditions, observation of a relevant video clip, building a model to represent the phenomena, testing, validating and refining their model, and publishing it – together with comments – on our web‐based collaboration system, WebReports. Students were encouraged to consider the limitations of their current model, with the aim that they would eventually appreciate the benefit of constructing a general model that would work for all collision classes, rather than a different model for each class. We describe how our intention to engage students with the underlying concepts of conservation, closed systems and system states was instantiated in the activity design, and how the modelling activities afforded an alternative representational framework to traditional algebraic description.
Constitutive expression of yeast phospholipid biosynthetic genes by variants of Ino2 activator defective for interaction with Opi1 repressor
Authors: Heyken Willm‐Thomas , Repenning Antje , Kumme Jacqueline , Schüller Hans‐Joachim
Published: April 2005

Regulated expression of structural genes involved in yeast phospholipid biosynthesis is mediated by inositol/choline‐responsive element (ICRE) upstream motifs, bound by the heterodimeric activator complex Ino2 + Ino4. Gene repression occurs in the presence of sufficient inositol and choline, requiring an intact Opi1 repressor which binds to Ino2. For a better understanding of interactions among regulators, we mapped an 18 aa repressor interaction domain (RID, aa 118–135) within Ino2 necessary and sufficient for binding by Opi1. By alanine scanning mutagenesis of the entire RID we were able to identify nine residues critical for Opi1‐dependent repression of Ino2 function. Consequently, the corresponding dominant Ino2 variants conferred constitutive expression of an ICRE‐dependent reporter gene and were no longer inhibited even by overproduction of Opi1. Interestingly, Ino2 RID partially overlaps with transcriptional activation domain TAD2. As certain mutations exclusively affect repression while others affect both repression and activation, both functions of Ino2 can be functionally uncoupled. Correspondingly, we mapped the RID–binding activator interaction domain (AID, aa 321–380) at the C‐terminus of Opi1 and introduced missense mutations at selected positions. An Opi1 variant simultaneously mutated at three highly conserved positions showed complete loss of repressor function, confirming RID–AID interaction as the crucial step of regulated expression of ICRE‐dependent genes.
Promoter architecture and response to a positive regulator of archaeal transcription
Authors: Ouhammouch Mohamed , Langham Geoffrey E. , Hausner Winfried , Simpson Anjana J. , El‐Sayed Najib M.A. , Geiduschek E. Peter
Published: April 2005

The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial‐type effectors, especially activators, regulate a eukaryote‐like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a ‘one‐site’ minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.
SspA is required for acid resistance in stationary phase by downregulation of H‐NS in Escherichia coli
Authors: Hansen Anne‐Marie , Qiu Yu , Yeh Norman , Blattner Frederick R. , Durfee Tim , Jin Ding Jun
Published: April 2005

The stringent starvation protein A (SspA) is a RNA polymerase‐associated protein and is required for transcriptional activation of bacteriophage P1 late promoters. However, the role of SspA in gene expression in Escherichia coli is essentially unknown. In this work, we show that SspA is essential for cell survival during acid‐induced stress. Apparently, SspA inhibits stationary‐phase accumulation of H‐NS, a global regulator which functions mostly as a repressor, thereby derepressing multiple stress defence systems including those for acid stress and nutrient starvation. Consequently, the gene expression pattern of the H‐NS regulon  is  altered  in  the  sspA mutant,  leading  to acid‐sensitive and hypermotile phenotypes. Thus, our study indicates that SspA is a global regulator, which acts upstream of H‐NS, and thereby plays an important role in the stress response of E. coli during stationary phase. In addition, our results indicate that the expression of the H‐NS regulon is sensitive to small changes in the cellular level of H‐NS, enabling the cell to response rapidly to environment cues. As SspA and H‐NS are highly conserved among Gram‐negative bacteria, of which many are pathogenic, the global role of SspA in the stress response and pathogenesis is discussed.
Cholesterol binding by the bacterial type III translocon is essential for virulence effector delivery into mammalian cells
Authors: Hayward Richard D. , Cain Robert J. , McGhie Emma J. , Phillips Neil , Garner Matthew J. , Koronakis Vassilis
Published: April 2005

A ubiquitous early step in infection of man and animals by enteric bacterial pathogens like Salmonella, Shigella and enteropathogenic Escherichia coli (EPEC) is the translocation of virulence effector proteins into mammalian cells via specialized type III secretion systems (TTSSs). Translocated effectors subvert the host cytoskeleton and stimulate signalling to promote bacterial internalization or survival. Target cell plasma membrane cholesterol is central to pathogen–host cross‐talk, but the precise nature of its critical contribution remains unknown. Using in vitro cholesterol‐binding assays, we demonstrate that Salmonella (SipB) and Shigella (IpaB) TTSS translocon components bind cholesterol with high affinity. Direct visualization of cell‐associated fluorescently labelled SipB and parallel immunogold transmission electron microscopy revealed that cholesterol levels limit both the amount and distribution of plasma membrane‐integrated translocon. Correspondingly, cholesterol depletion blocked effector translocation into cultured mammalian cells by not only the related Salmonella and Shigella TTSSs, but also the more divergent EPEC system. The data reveal that cholesterol‐dependent association of the bacterial TTSS translocon with the target cell plasma membrane is essential for translocon activation and effector delivery into mammalian cells.
Association of beta2 toxin production with Clostridium perfringens type A human gastrointestinal disease isolates carrying a plasmid enterotoxin gene
Authors: Fisher Derek J. , Miyamoto Kazuaki , Harrison Benjamin , Akimoto Shigero , Sarker Mahfuzur R. , McClane Bruce A.
Published: April 2005

Clostridium perfringens type A isolates carrying an enterotoxin (cpe) gene are an important cause of human gastrointestinal diseases, including food poisoning, antibiotic‐associated diarrhoea (AAD) and sporadic diarrhoea (SD). Using polymerase chain reaction (PCR), the current study determined that the cpb2 gene encoding the recently discovered beta2 toxin is present in <15% of food poisoning isolates, which typically carry a chromosomal cpe gene. However, >75% of AAD/SD isolates, which usually carry a plasmid cpe gene, tested cpb2+ by PCR. Western blot analysis demonstrated that >97% of those cpb2+/cpe+ AAD/SD isolates can produce CPB2. Additional PCR analyses, sequencing studies and pulsed field gel electrophoresis experiments determined that AAD/SD isolates carry cpb2 and cpe on the same plasmid when IS1151 sequences are present downstream of cpe, but cpb2 and cpe are located on different plasmids in AAD/SD isolates where IS1470‐like sequences are present downstream of cpe. Those analyses also demonstrated that two different CPB2 variants (named CPB2h1 or CPB2h2) can be produced by AAD/SD isolates, dependent on whether IS1470‐like or IS1151 sequences are present downstream of their cpe gene. CPB2h1 is ∼10‐fold more cytotoxic for CaCo‐2 cells than is CPB2h2. Collectively, these results suggest that CPB2 could be an accessory toxin in C. perfringens enterotoxin (CPE)‐associated AAD/SD.
Broad analysis reveals a consistent pattern of var gene transcription in Plasmodium falciparum repeatedly selected for a defined adhesion phenotype
Authors: Duffy Michael F. , Byrne Timothy J. , Elliott Salenna R. , Wilson Danny W. , Rogerson Stephen J. , Beeson James G. , Noviyanti Rintis , Brown Graham V.
Published: April 2005

Transcription of the majority of the members of the Plasmodium falciparum var multigene family were analysed in two isolates by a quantitative approach. Both of these isolates had been repeatedly selected for adhesion to chondroitin sulphate A (CSA) and one had also been selected for adhesion to hyaluronic acid (HA). These adhesion phenotypes are expressed by many parasites isolated from placentae and are associated with malaria disease in pregnancy. Increased transcription of the var gene var2csa, or its homologue IT4 var4, was associated with the CSA and HA adhesion phenotypes in all parasites suggesting that it was the dominant, if not the only, var gene that encoded adhesion to CSA in these allogeneic isolates. Some var genes were consistently transcribed at higher levels than others regardless of expressed adhesion phenotypes suggesting a transcriptional hierarchy. Unspliced or partial transcripts were detected for most var genes tested. These atypical var gene transcripts may have implications for the regulation of var gene transcription.
The alternative sigma factor σE is required for resistance of Salmonella enterica serovar Typhimurium to anti‐microbial peptides
Authors: Crouch Marie‐Laure , Becker Lynne A. , Bang Iel‐Soo , Tanabe Hiroki , Ouellette Andre J. , Fang Ferric C.
Published: April 2005

The enteric pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) encounters a variety of anti‐microbial peptides during the course of infection. We report here that the extracytoplasmic sigma factor σE (RpoE) is required for Salmonella resistance to killing by the bactericidal/permeability‐increasing protein (BPI)‐derived peptide P2 and the murine α‐defensin cryptdin‐4 (Crp4). Moreover, σE‐deficient S. Typhimurium is attenuated for virulence after oral infection of immunocompromised gp91phox–/– mice that lack a functional NADPH phagocyte oxidase, suggesting that σE plays an important role in resistance to non‐oxidative mucosal host defences such as anti‐microbial peptides. Although both P2 and Crp4 target the cell envelope, bacterial killing by these peptides appears to occur by distinct mechanisms. Formate enhances bacterial resistance to P2, as previously demonstrated, but not to Crp4. Both σE and cytoplasmic membrane‐associated formate dehydrogenase are required for the protective effect of formate against P2. In contrast to P2, Crp4 does not inhibit bacterial respiration at lethal concentrations. However, both peptides induce expression of rpoE, suggesting that they trigger a common mechanism for sensing extracytoplasmic stress.
The initial step of glycerolipid metabolism in Leishmania major promastigotes involves a single glycerol‐3‐phosphate acyltransferase enzyme important for the synthesis of triacylglycerol but not essential for virulence
Authors: Zufferey Rachel , Mamoun Choukri Ben
Published: April 2005

The synthesis of the major phospholipids, including those that play an essential role in Leishmania virulence, initiates with the acylation of glycerol‐3‐phosphate and dihydroxyacetonephosphate at the sn‐1 position by glycerol‐3‐phosphate and dihydroxyacetonephosphate acyltransferases respectively. In this study, we show that Leishmania major promastigotes express a single glycerol‐3‐phosphate acyltransferase activity important for triacylglycerol synthesis but not essential for virulence. The encoding gene, LmGAT, expressed in yeast results in full complementation of the lethality of a mutant, gat1Δgat2Δ, lacking glycerol‐3‐phosphate activity. Biochemical analyses revealed that LmGAT is a low‐affinity glycerol‐3‐phosphate acyltransferase and exhibits higher specific activity with unsaturated long fatty acyl‐CoA donors. A L. major null mutant, Δlmgat/Δlmgat, was created and a thorough analysis of its lipid composition was performed. Deletion of LmGAT resulted in a complete loss of Leishmania glycerol‐3‐phosphate acyltransferase activity and a major reduction in triacylglycerol synthesis. Consistent with the specificity of LmGAT for glycerol‐3‐phosphate but not dihydroxyacetonephosphate, Δlmgat/Δlmgat mutant expressed normal levels of the ether‐lipid derivatives and virulence factors, lipophosphoglycan and GPI‐anchored proteins, gp63, and its virulence was not affected in mice.
Alternative sigma factor interactions in Salmonella: σE and σH promote antioxidant defences by enhancing σS levels
Authors: Bang Iel‐Soo , Frye Jonathan G. , McClelland Michael , Velayudhan Jyoti , Fang Ferric C.
Published: April 2005

Hierarchical interactions between alternative sigma factors control sequential gene expression in Gram‐positive bacteria, whereas alternative sigma factors in Gram‐negative bacteria are generally regarded to direct expression of discrete gene subsets. In Salmonella enterica serovar Typhimurium (S. Typhimurium), σE responds to extracytoplasmic stress, whereas σH responds to heat shock and σS is induced during nutrient limitation. Deficiency of σE, σH or σS increases S. Typhimurium susceptibility to oxidative stress, but an analysis of double and triple mutants suggested that antioxidant actions of σE and σH might be dependent on σS. Transcriptional profiling of mutant Salmonella lacking σE revealed reduced expression of genes dependent on σH and σS in addition to σE. Further investigation demonstrated that σE augments σS levels during stationary phase via enhanced expression of σH and the RNA‐binding protein Hfq, leading to increased expression of σS‐dependent genes and enhanced resistance to oxidative stress. Maximal expression of the σS‐regulated gene katE required σE in Salmonella‐infected macrophages as well as stationary‐phase cultures. Interactions between alternative sigma factors permit the integration of diverse stress signals to produce coordinated genetic responses.
Budding yeast PDS5 plays an important role in meiosis and is required for sister chromatid cohesion
Authors: Zhang Zhaojie , Ren Qun , Yang Hui , Conrad Michael N. , Guacci Vincent , Kateneva Anna , Dresser Michael E.
Published: April 2005

Budding yeast PDS5 is an essential gene in mitosis and is required for chromosome condensation and sister chromatid cohesion. Here we report that PDS also is required in meiosis. Pds5p localizes on chromosomes at all stages during meiotic cycle, except anaphase I. PDS5 plays an important role at first meiotic prophase. Failure in function of PDS5 causes premature separation of chromosomes. The loading of Pds5p onto chromosome requires the function of REC8, but the association of Rec8p with chromosome is independent of PDS5. Mutant analysis and live cell imaging indicate that PDS5 play a role in meiosis II as well.
Antibiotic‐induced SOS response promotes horizontal dissemination of pathogenicity island‐encoded virulence factors in staphylococci
Authors: Úbeda Carles , Maiques Elisa , Knecht Erwin , Lasa Íñigo , Novick Richard P. , Penadés José R.
Published: April 2005

Although mobile genetic elements have a crucial role in spreading pathogenicity‐determining genes among bacterial populations, environmental and genetic factors involved in the horizontal transfer of these genes are largely unknown. Here we show that SaPIbov1, a Staphylococcus aureus pathogenicity island that belongs to the growing family of these elements that are found in many strains, is induced to excise and replicate after SOS induction of at least three different temperate phages, 80α, φ11 and φ147, and is then packaged into phage‐like particles and transferred at high frequency. SOS induction by commonly used fluoroquinolone antibiotics, such as ciprofloxacin, also results in replication and high‐frequency transfer of this element, as well as of SaPI1, the prototypical island of S. aureus, suggesting that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors. Although the strains containing these prophages do not normally contain SaPIs, we have found that RF122‐1, the original SaPIbov1‐containing clinical isolate, contains a putative second pathogenicity island that is replicated after SOS induction, by antibiotic treatment, of the prophage(s) present in the strain. Although SaPIbov1 is not induced to replicate after SOS induction in this strain, it is transferred by the antibiotic‐activated phages. We conclude that SOS induction by therapeutic agents can promote the spread of staphylococcal virulence genes.
Bistability in the Bacillus subtilis K‐state (competence) system requires a positive feedback loop
Authors: Maamar Hédia , Dubnau David
Published: April 2005

High expression of the transcriptional activator ComK occurs in 10–20% of the cells in stationary phase cultures of Bacillus subtilis strain 168. ComK drives the expression of more than 100 genes constituting the semidormant K‐state, distinct from sporulation and vegetative growth. Among the genes so activated are those that permit competence for genetic transformation. We have addressed the origin of bistability in expression of ComK. We show that bistability requires positive autoregulation at the promoter of comK, but not a potential toggle switch, in which ComK represses the promoter of rok and Rok represses the promoter of comK. We further address the source of the noise that results in the stochastic selection of cells that will express comK. A revised model for the regulation of comK expression is proposed that partially explains bistability.
Diversity within cyanobacterial mat communities in variable salinity meltwater ponds of McMurdo Ice Shelf, Antarctica
Authors: Jungblut Anne‐Dorothee , Hawes Ian , Mountfort Doug , Hitzfeld Bettina , Dietrich Daniel R. , Burns Brendan P. , Neilan Brett A.
Published: April 2005

This study investigated the diversity of cyanobacterial mat communities of three meltwater ponds – Fresh, Orange and Salt Ponds, south of Bratina Island, McMurdo Ice Shelf, Antarctica. A combined morphological and genetic approach using clone libraries was used to investigate the influence of salinity on cyanobacterial diversity within these ecosystems without prior cultivation or isolation of cyanobacteria. We were able to identify 22 phylotypes belonging to Phormidium sp., Oscillatoria sp. and Lyngbya sp. In addition, we identified Antarctic Nostoc sp., Nodularia sp. and Anabaena sp. from the clone libraries. Fresh (17 phylotypes) and Orange (nine phylotypes) Ponds showed a similar diversity in contrast to that of the hypersaline Salt Pond (five phylotypes), where the diversity within cyanobacterial mats was reduced. Using the comparison of identified phylotypes with existing Antarctic sequence data, it was possible to gain further insight into the different levels of distribution of phylotypes identified in the investigated cyanobacterial mat communities of McMurdo Ice Shelf.
Flux and turnover of fixed carbon in soil microbial biomass of limed and unlimed plots of an upland grassland ecosystem
Authors: Rangel‐Castro J. Ignacio , Prosser Jim I. , Ostle Nick , Scrimgeour Charlie M. , Killham Ken , Meharg Andy A.
Published: April 2005

The influence of liming on rhizosphere microbial biomass C and incorporation of root exudates was studied in the field by in situ pulse labelling of temperate grassland vegetation with 13CO2 for a 3‐day period. In plots that had been limed (CaCO3 amended) annually for 3 years, incorporation into shoots and roots was, respectively, greater and lower than in unlimed plots. Analysis of chloroform‐labile C demonstrated lower levels of 13C incorporation into microbial biomass in limed soils compared to unlimed soils. The turnover of the recently assimilated 13C compounds was faster in microbial biomass from limed than that from unlimed soils, suggesting that liming increases incorporation by microbial communities of root exudates. An exponential decay model of 13C in total microbial biomass in limed soils indicated that the half‐life of the tracer within this carbon pool was 4.7 days. Results are presented and discussed in relation to the absolute values of 13C fixed and allocated within the plant–soil system.
Three‐dimensional virtual worlds and distance learning: two case studies of Active Worlds as a medium for distance education
Authors: Dickey Michele D.
Published: April 2005

Online three‐dimensional (3D) virtual worlds are emerging technologies that offer unique learning opportunities for traditional and distributed education. One of the more popular 3D virtual worlds, Active Worlds, is currently being used as a medium for synchronous and asynchronous distance learning. This investigation presents two exploratory case studies of different, but exemplary educational activities using Active Worlds for formal and informal education. The focus of each case study is to investigate how Active Worlds is being used for distance learning and to determine the type of learning experiences afforded  by  this  3D  virtual  environment.  Whilst  more  research  is  necessary to explore fully the potential of 3D virtual worlds for learning, this initial investigation illustrates how Active Worlds affords opportunities for experiential learning and situated learning within a collaboration learning environment.
Managing content in e‐learning environments
Authors: Mwanza Daisy , Engeström Yrjö
Published: April 2005

The use of e‐learning environments to support teaching and learning has had great impact on the way content is developed and managed. In most cases, both teachers and students have had to re‐adapt the way they prepare, access and engage with educational matter. The adjustment in human mechanisms for organising and interacting with educational content has become necessary due to the re‐mediation of established practices through the introduction of software‐based techniques to structure content, for example, using metadata. Whilst metadata standards provide effective guidelines for organising content in web‐based e‐learning environments, technology‐based approaches to managing educational resources do not fully address social‐cultural and pedagogical aspects of users in the context in which teaching and learning takes place. In this regard, the effectiveness of using metadata to structure the discovery and access to educational content should be considered in relation to the extent by which metadata descriptors are associated with established socio‐cultural and pedagogical practices. Towards this end, we reflect on potential contributions of social‐cultural and learning theories to the task of managing content in e‐learning environments. The paper presents an activity‐centred approach to abstracting contextually and pedagogically enriched metadata descriptions of educational content and interactions with learning objects.
Evolution of a laptop university: a case study
Authors: McVay Gloria J. , Snyder Kimberlee D. , Graetz Kenneth A.
Published: April 2005

Technology is integral to carrying out many types of business transactions and has become entwined in the very fabric of everyday life. In the educational environment—particularly higher education—technology is underutilised as a pedagogical tool and in many cases remains largely untapped. Winona State University and its laptop programme learned some valuable lessons from the marriage between the application of the Seven Principles of Good Practice in Undergraduate Education and technology. The transformation into a leading laptop university was neither smooth nor easy, but it is a successful case about principle‐centred technological change and improved student learning outcomes.
Ring fenced research: the case of computer‐assisted learning in health sciences
Authors: Jacobs Gabriel , Ip Barry
Published: April 2005

Interdisciplinary research is being promoted in many quarters as the way forward, but “research islands” still persist. Taking computer‐assisted learning (CAL) within health sciences as a case in point, this paper describes a detailed study of the references to source material within papers published in general medical, specific nursing and general information and communications technology journals as pointing to papers published either in the same category of journal or journals of other categories. The results show that research within this area exhibits a disquieting inbred approach. Furthermore, there is clear evidence of a tendency amongst the papers examined to cite research published in journals with broadly the same impact factors as the journal in which the papers themselves are published. A discussion of the value of journal impact factors, which are a crude but useful index of the quality of journal, and their possible effect on the future of research in CAL within health sciences is embedded in the paper.
Issues in the adoption of broadband‐enabled learning
Authors: Murphy Elizabeth
Published: April 2005

This paper presents one case of broadband‐enabled learning (BEL) involving geo‐culturally and organisationally diverse collaboration using music as the vehicle. Findings from five evaluations over a 15‐month period were considered in relation to issues of relative advantage, compatibility, complexity, trialability, and observability. Advantages included access to mentors, peers, and experts; support for cross‐cultural and linguistic collaboration, interaction, and exchanges; promotion of a more open classroom; and exposure to alternative and new experiences. Compatibility with existing practices was evident, however, cross‐cultural interaction presented difficulties as did synchronous communication across time zones and between institutions. BEL technologies are complex, however, users can develop a capacity to use the tools if provided with adequate support. Trialability is dependent on access to a high‐speed connection and equipment, multiple partners, development of technical expertise, and support. Use of videoconferencing and choice of subject area can enhance observability.
A knowledge management technology architecture for educational research organisations: Scaffolding research projects and workflow processing
Authors: Muthukumar  , Hedberg John G.
Published: April 2005

There is growing recognition that the economic climate of the world is shifting towards a knowledge‐based economy where knowledge will be cherished as the most prized asset. In this regard, technology can be leveraged as a useful tool in effectually managing the knowledge capital of an organisation. Although several research studies have advanced knowledge management frameworks catering to the requirements of organisations specialising in diverse fields of expertise, no comprehensive knowledge‐management architecture has been found that is technology mediated and orientated towards the emergent needs of an educational research organisation. In this paper, we review a knowledge management technology approach modeled as a web portal that was developed to create a repository and to facilitate shared resources in a research organisation. This technology‐based framework encapsulates the knowledge management processes that capture and augment the explicit knowledge resources of the research organisation. The framework also supports social networks that enable the sharing and encoding of tacit knowledge by facilitating online exchanges and feedback.
Implementation and evaluation of computer‐aided Mandarin phonemes training system for hearing‐impaired students
Authors: Yang Hui‐Jen , Lay Yun‐Long
Published: April 2005

A computer‐aided Mandarin phonemes training (CAMPT) system was developed and evaluated for training hearing‐impaired students in their pronunciation of Mandarin phonemes. Deaf or hearing‐impaired people have difficulty hearing their own voice, hence most of them cannot learn how to speak. Phonemes are the basis for learning to read and speak in Mandarin. Thus, the main purpose of this study is to use voice‐recognition techniques to develop a Mandarin phoneme training system for the self‐training of hearing‐impaired people. The system analyses the spoken Mandarin phoneme of a hearing‐impaired person, compares it with the phonemes database, and shows the results on the computer monitor. Our CAMPT system helps hearing‐impaired people pronounce Mandarin phonemes, and the system automatically gives the learner a percentage score for each phoneme. In other words, learners can receive instant feedback from the system. Experiments conducted among high school students diagnosed with hearing impairment revealed that our system can help students learn the Mandarin phonemes with a neural net recognition algorithm for different users. After five months, most learners can pronounce 95% of the phonemes correctly.