bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transgenic Leishmania and the immune response to infection
Authors: BEATTIE L. , EVANS K. J. , KAYE P. M. , SMITH D. F. 
Published: February 2008

SUMMARY Genetic manipulation of single‐celled organisms such as the Leishmania parasite enables in depth analysis of the consequences of genotypic change on biological function. In probing the immune responses to infection, use of transgenic Leishmania has the potential to unravel both the contribution of the parasite to the infection process and the cellular interactions and mechanisms that characterize the innate and adaptive immune responses of the host. Here, we briefly review recent technical advances in parasite genetics and explore how these methods are being used to investigate parasite virulence factors, elucidate immune regulatory mechanisms and contribute to the development of novel therapeutics for the leishmaniases. Recent developments in imaging technology, such as bioluminescence and intravital imaging, combined with parasite transfection with fluorescent or enzyme‐encoding marker genes, provides a rich opportunity for novel assessment of intimate, real‐time host–parasite interactions at a previously unexplored level. Further advances in transgenic technology, such as the introduction of robust inducible gene cassettes for expression in intracellular parasite stages or the development of RNA interference methods for down‐regulation of parasite gene expression in the host, will further advance our ability to probe host–parasite interactions and unravel disease‐promoting mechanisms in the leishmaniases.
Chilling induces a decrease in pyrophosphate‐dependent H+‐accumulation associated with a ΔpHvac‐stat in mung bean, a chill‐sensitive plant
Authors: KAWAMURA YUKIO 
Published: February 2008

ABSTRACTChilling leads to cytoplasmic acidification in chill‐sensitive plants. A possible explanation for this observation is that a ΔpH‐stat between the cytosol and vacuole (ΔpHvac‐stat) is perturbed by chilling. To understand the nature of this ΔpHvac‐stat, the effect of temperature, between 20 and 0 °C, on pyrophosphate (PPi)‐ or ATP‐dependent acidification of vacuolar vesicles, isolated from mung bean hypocotyls, was determined. Over the temperature range investigated, the H+‐influx mediated by PPase was balanced with the H+‐efflux, which was PPi‐dependently suppressed, and consequently a constant pH in vesicles (pHin) of ca. 5 was maintained against temperature changes. However, the ΔpHin driven by ATP decreased as the temperature dropped. Thus, the PPi‐dependent H+‐accumulation may function as an essential factor to form a ΔpHvac‐stat against temperature changes. Next, to study the chilling sensitivity of PPi‐dependent H+‐accumulation, vacuolar vesicles were isolated from control seedlings or from seedlings chilled at 0 °C for 1 d. Chilling treatment resulted in a decrease in the H+‐accumulation rate and in the steady‐state ΔpHin formed by PPi, the causes of which were enhanced by PPi‐dependent H+‐efflux and reduced by H+‐influx driven by PPase. Together, the results suggest that the decrease of PPi‐dependent H+‐accumulation associated with the ΔpHvac‐stat could result in cytoplasmic acidification.
The role of cytokinins in responses to water deficit in tobacco plants over‐expressing trans‐zeatin O‐glucosyltransferase gene under 35S or SAG12 promoters
Authors: HAVLOVÁ MARIE , DOBREV PETRE I. , MOTYKA VÁCLAV , ŠTORCHOVÁ HELENA , LIBUS JIŘÍ , DOBRÁ JANA , MALBECK JIŘÍ , GAUDINOVÁ ALENA , VANKOVÁ RADOMIRA 
Published: February 2008

ABSTRACTThe impact of water deficit progression on cytokinin (CK), auxin and abscisic acid (ABA) levels was followed in upper, middle and lower leaves and roots of Nicotiana tabacum L. cv. Wisconsin 38 plants [wild type (WT)]. ABA content was strongly increased during drought stress, especially in upper leaves. In plants with a uniformly elevated total CK content, expressing constitutively the trans‐zeatin O‐glucosyltransferase gene (35S::ZOG1), a delay in the increase of ABA was observed; later on, ABA levels were comparable with those of WT.As drought progressed, the bioactive CK content in leaves gradually decreased, being maintained longer in the upper leaves of all tested genotypes. Under severe stress (11 d dehydration), a large stimulation of cytokinin oxidase/dehydrogenase (CKX) activity was monitored in lower leaves, which correlated well with the decrease in bioactive CK levels. This suggests that a gradient of bioactive CKs in favour of upper leaves is established during drought stress, which might be beneficial for the preferential protection of these leaves.During drought, significant accumulation of CKs occurred in roots, partially because of decreased CKX activity. Simultaneously, auxin increased in roots and lower leaves. This indicates that both CKs and auxin play a role in root response to severe drought, which involves the stimulation of primary root growth and branching inhibition.
Characterization of growth‐phase‐specific responses to cold in Arabidopsis thaliana suspension‐cultured cells
Authors: SASAKI YUTAKA , TAKAHASHI KAZUE , OONO YOKO , SEKI MOTOAKI , YOSHIDA RIICHIRO , SHINOZAKI KAZUO , UEMURA MATSUO 
Published: February 2008

ABSTRACTTo understand complex responses of plant cells to low temperatures, suspension‐cultured cells of Arabidopsis thaliana (line T87) were characterized during cold treatment. Freezing tolerance of cells collected at the lag or log phase was quite different: an increase in freezing tolerance during cold treatment was only detectable with cells at the lag phase. Although there were little differences in the osmolality of cells at the two growth phases, sugar content increased during cold treatment only in lag phase cells. Abscisic acid (ABA) content was greater at the lag phase than at the log phase throughout the cold treatment, and increased only in lag phase cells. Interestingly, ABA treatment resulted in an increase in freezing tolerance only in lag phase cells. Expression of cold‐responsive genes such as DREB1A/CBF3, COR15a and RD29A occurred in cells at the two growth phases; however, the extent of the induction of COR15a and RD29A was somewhat greater in cells at the lag phase than at the log phase. Microarray analysis revealed that cold‐regulated genes (COR genes) were categorized into three groups: up‐ or down‐regulated consistently during cold treatment, transiently after 1 d and later after 2 d of cold treatment. Among genes that were up‐regulated throughout or transiently after 1 d of cold treatment only in lag phase cells, functions in upstream of signal transduction such as kinase and transcription factor were often deduced. These results collectively suggest that these genes seem to be associated with induction of freezing tolerance by cold treatment in cells at the lag phase.
Metabolomic and proteomic changes in the xylem sap of maize under drought
Authors: ALVAREZ SOPHIE , MARSH ELLEN L. , SCHROEDER STEVE G. , SCHACHTMAN DANIEL P. 
Published: February 2008

ABSTRACTPlants produce compounds in roots that are transported to shoots via the xylem sap. Some of these compounds are vital for signalling and adaptation to environmental stress such as drought. In this study, we screened the xylem sap using mass spectrometry to quantify the changes in new and previously identified sap constituents under extended drought. We detected and quantified the changes in the concentration of 31 compounds present in the xylem sap under progressively increasing drought stress. We found changes in the hormones abscisic acid (ABA) and cytokinin, and the presence of high concentrations of the aromatic cytokinin 6‐benzylaminopurine (BAP). Several phenylpropanoid compounds (coumaric, caffeic and ferulic acids) were found in xylem sap. The concentrations of some of these phenylpropanoid compounds changed under drought. In parallel, an analysis of the xylem sap proteome was conducted. We found a higher abundance of cationic peroxidases, which with the increase in phenylpropanoids may lead to a reduction in lignin biosynthesis in the xylem vessels and could induce cell wall stiffening. The application of new methodologies provides insights into the range of compounds in sap and how alterations in composition may lead to changes in development and signalling during adaptation to drought.
Comparing model predictions and experimental data for the response of stomatal conductance and guard cell turgor to manipulations of cuticular conductance, leaf‐to‐air vapour pressure difference and temperature: feedback mechanisms are able to account for all observations
Authors: EAMUS DEREK , TAYLOR DANIEL T. , MACINNIS‐NG CATRIONA M. O. , SHANAHAN STEVE , DE SILVA LIONEL 
Published: February 2008

ABSTRACTStomata respond to increasing leaf‐to‐air vapour pressure difference (LAVPD) (D) by closing. The mechanism by which this occurs is debated. A role for feedback and peristomatal transpiration has been proposed. In this paper, we apply a recent mechanistic model of stomatal behaviour, and compare model and experimental data for the influence of increasing D on stomatal conductance.We manipulated cuticular conductance (gc) by three independent methods. First, we increased gc by using a solvent mixture applied to both leaf surfaces prior to determining stomatal responses to D; second, we increased gc by increasing leaf temperature at constant D; and third, we coated a small area of leaf with a light oil to decrease gc. In all three experiments, experimental data and model outputs showed very close agreement.We conclude, from the close agreement between model and experimental data and the fact that manipulations of gc, and hence cuticular transpiration, influenced gs in ways consistent with a feedback mechanism, that feedback is central in determining stomatal responses to D.
Short‐term responses of leaf growth rate to water deficit scale up to whole‐plant and crop levels: an integrated modelling approach in maize
Authors: CHENU KARINE , CHAPMAN SCOTT C. , HAMMER GRAEME L. , MCLEAN GREG , SALAH HALIM BEN HAJ , TARDIEU FRANÇOIS 
Published: February 2008

ABSTRACTPhysiological and genetic studies of leaf growth often focus on short‐term responses, leaving a gap to whole‐plant models that predict biomass accumulation, transpiration and yield at crop scale. To bridge this gap, we developed a model that combines an existing model of leaf 6 expansion in response to short‐term environmental variations with a model coordinating the development of all leaves of a plant. The latter was based on: (1) rates of leaf initiation, appearance and end of elongation measured in field experiments; and (2) the hypothesis of an independence of the growth between leaves. The resulting whole‐plant leaf model was integrated into the generic crop model APSIM which provided dynamic feedback of environmental conditions to the leaf model and allowed simulation of crop growth at canopy level. The model was tested in 12 field situations with contrasting temperature, evaporative demand and soil water status. In observed and simulated data, high evaporative demand reduced leaf area at the whole‐plant level, and short water deficits affected only leaves developing during the stress, either visible or still hidden in the whorl. The model adequately simulated whole‐plant profiles of leaf area with a single set of parameters that applied to the same hybrid in all experiments. It was also suitable to predict biomass accumulation and yield of a similar hybrid grown in different conditions. This model extends to field conditions existing knowledge of the environmental controls of leaf elongation, and can be used to simulate how their genetic controls flow through to yield.
Human B Cells and Macrophages Cooperate in T‐cell‐independent Type 2 Response
Authors: Mättö M. , Raunio A.‐R. , Postila V. , Huttunen K. , Hirvonen M.‐R. , Pelkonen J. 
Published: February 2008

AbstractWe have analysed separately the role of B‐cell receptor (BCR) stimulation and the soluble second signal in the T‐cell‐independent type 2 (TI‐2) B‐cell response. We were able to show that human B cells and macrophages (Mφ) could function together in TI‐type microbial response. Interestingly, BCR cross‐linking of peripheral blood (PB) B cells enhanced IgG production induced by Mφ‐derived growth factors whereas interleukin (IL)‐12 + IL‐18 had milder effect on IgG production. We demonstrated that B‐cell‐derived soluble mediators primed lipopolysaccharide (LPS)‐stimulated Mφ for tumour necrosis factor‐α (TNF‐α) and IL‐6 production significantly better than IFN‐γ, confirming the role of B cells in the activation of Mφ. We could show that human PB B cells were active cytokine producers and could be induced to produce interferon (IFN)‐γ mRNA in the presence of known Mφ cytokines, like IL‐12 and IL‐18. BCR stimulation also stabilized and enhanced the IFN‐γ mRNA production induced by IL‐12 and IL‐18. In addition, our novel finding was that a known Mφ cytokine, IL‐10, induced the expression of IFN‐γ mRNA from human B‐cell line (HF28R0) cells. In summary, we propose a model for the active role of B cells in the induction of the inflammatory response during TI antigen challenge in close collaboration with Mφ.
Susceptibility of Human Monocyte‐macrophages to Chlamydia pneumoniae Infection In Vitro is Highly Variable and Associated with levels of Soluble CD14 and C. pneumoniae IgA and Human HSP‐IgG Antibodies in Serum
Authors: Poikonen K. , Lajunen T. , Silvennoinen‐Kassinen S. , Paldanius M. , Leinonen M. , Saikku P. 
Published: February 2008

Abstract Chlamydia pneumoniae, an intracellular microbe, causes respiratory infections and may participate in the development of atherosclerosis. It is able to survive and multiply in macrophages. The susceptibility of monocyte‐macrophages from healthy individuals to C. pneumoniae infection in vitro was studied. Intracellular growth of C. pneumoniae, as an indicator of susceptibility to infection, was compared to serum levels of C‐reactive protein, soluble CD14 (sCD14), human heat shock protein (HSP)‐IgG, human HSP‐IgA, C. pneumoniae IgG and IgA antibodies. The production of C. pneumoniae in infected macrophages was highly variable, ranging from 0 to 638 chlamydial genomes per human genome. Chlamydia pneumoniae production associated positively with serum C. pneumoniae IgA (titre: ≥10) and hHSP‐IgG and negatively with sCD14 concentration. The association between sCD14 concentration, C. pneumoniae IgA and human HSP‐IgG antibodies and C. pneumoniae production was statistically significant only among males. Age and gender did not correlate with the production. We hypothesize that persons whose macrophages cannot restrict the growth of C. pneumoniae are more prone to chronic infection by this agent.
CD4+ T Cells Transfer Resistance Against Citrobacter rodentium‐Induced Infectious Colitis by Induction of Th 1 Immunity
Authors: Spahn T. W. , Ross M. , Von Eiff C. , Maaser C. , Spieker T. , Kannengiesser K. , Domschke W. , Kucharzik T. 
Published: February 2008

Abstract Citrobacter rodentium induces an acute, self‐limited colitis in mice which is histologically associated with crypt hyperplasia. The infection serves as a model for human infectious colitis induced by enteropathogenic Escherichia coli. We investigated if Balb/c mice, which had spontaneously cleared C. rodentium infection, were protected against re‐infection and if resistance against intestinal infection can be systemically transferred using spleen cells. The course of infection was monitored by faecal excretion. Spleen cells, splenic CD3+ and CD4+ cells were transferred from resistant mice to non‐infected recipients prior to infection. Cytokine secretion, serum and faecal antibody titres and histological disease severity were assessed. Balb/c mice were resistant against re‐infection. The course of infection was shorter in mice receiving primed spleen cells, CD3+ and CD4+ cells. Transfer of CD4+ T cells from resistant mice induced γ‐interferon, interleukin (IL)‐2 and IL‐17 secretion and suppressed IL‐10 secretion. Anti‐Citrobacter serum IgG1 and IgG2a enzyme‐linked immunosorbent assay OD levels were increased. Faecal IgA secretion was increased while serum IgA was suppressed in recipients of CD4+ cells. Large bowel histology showed protection from colitis in recipients of primed cells as indicated by normal colonic epithelium. In Balb/c mice, C. rodentium infection is followed by resistance, which can be transferred by CD4+ cells. Transfer of protection is associated with IL‐17 secretion, enhanced serum IgG and faecal IgA secretion. This is the first study to demonstrate the mechanisms by which systemic resistance from previously C. rodentium‐infected mice can be transferred to non‐infected animals.
Antigen Analysis of Mycobacterium tuberculosis H37Rv Culture Filtrate Proteins
Authors: Målen H. , Søfteland T. , Wiker H. G. 
Published: February 2008

AbstractCulture filtrates of Mycobacterium tuberculosis H37Rv highly enriched with secreted proteins were used to identify antigens recognized by a serum pool from tuberculosis patients. Two different approaches were used to separate the culture filtrate protein mixture: (i) proteins were fractionated according to their hydrophobicity using an HPLC‐C18 chromatography column followed by separation based on their molecular mass by SDS‐PAGE and subsequent immunoblotting or (ii) proteins were separated by two‐dimensional gel electrophoresis, based on their isoelectric point and their molecular mass. Twenty serologically reactive proteins were ultimately identified by both methods, including four novel antigens. Further, to estimate the immunogenicity of the identified culture filtrate proteins, the relative antibody quantities were measured using Image master software. Our results show that the antibodies against proteins belonging to the antigen 85 complex were the most abundant in the serum of patients with active tuberculosis. The most immunogenic proteins in terms of high antibody‐to‐protein‐ratio were Rv3881c and three lipoproteins Rv0934 (the 38 kDa antigen), Rv0932c (pstS2), and Rv3006 (LppZ). Rv3881c is located in the region of difference 1 (RD1) which is deleted from Mycobacterium bovis BCG, and is therefore a particularly promising candidate for development of serodiagnostic assays to detect active tuberculosis. The proteins from the M. tuberculosis H37Rv culture filtrate are strong candidates to be evaluated for improvement of the serodiagnostic tests of tuberculosis.
Absence of In vitro Responses to Type II Collagen by Splenocytes from Arthritic BALB/c Mice is Possibly Caused by Intrinsic CD25+ Regulatory Cells
Authors: Bäckström F. , Dahlgren U. 
Published: February 2008

AbstractCollagen‐induced arthritis‐resistant BALB/c mice develop arthritis if a foreign protein is added to an emulsion of type II collagen (CII) and adjuvant. The IgG autoantibody activity to CII is increased, whereas no CII autoreactive T cells in vitro can be recorded. In this study, we have explored whether CD25+ cells inhibit T‐cell autoreactivity to CII. We also followed the IgG anti‐CII autoantibody activity and the IL‐6 level in serum during the development of arthritis. BALB/c mice were coimmunized with bovine CII (BCII) and keyhole limpet haemocyanin (KLH) in complete Freund’s adjuvant and boostered 3 weeks later. Control animals were immunized with either BCII or KLH. Sera were collected prior to and during the development of arthritis and examined for IgG anti‐CII antibody activity and IL‐6 content. When all BCII–KLH immunized mice had developed arthritis, splenocytes were prepared, with and without CD25+ cells, and tested for BCII reactivity in vitro. The serum IgG, IgG1 and IgG2a anti‐CII antibody activities and the IL‐6 level were significantly higher in BCII–KLH immunized mice than in BCII‐immunized animals that failed to develop arthritis. The BCII‐specific IL‐2 secretion in vitro was significantly increased in CD25‐depleted splenocyte cultures prepared from arthritic BCII–KLH‐immunized mice. Development of arthritis in BALB/c mice induced by coimmunization with BCII/KLH results in increased levels of circulating IL‐6 and IgG autoantibodies to CII. The arthritogenic BCII–KLH immunization potentiates BCII‐specific IL‐2 secretion by CD25‐depleted splenocytes, but CD25+ cells hamper the outcome of their action, at least in vitro.
Complex variations in sediment transport at three large river bifurcations during discharge waves in the river Rhine
Authors: FRINGS ROY M. , KLEINHANS MAARTEN G. 
Published: February 2008

AbstractRiver bifurcations strongly control the distribution of water and sediment over a river system. A good understanding of this distribution process is crucial for river management. In this paper, an extensive data set from three large bifurcations in the Dutch Rhine is presented, containing data on bed‐load transport, suspended bed sediment transport, dune development and hydrodynamics. The data show complex variations in sediment transport during discharge waves. The objective of this paper is to examine and explain these measured variations in sediment transport. It is found that bend sorting upstream of the bifurcations leads to supply limitation, particularly in the downstream branch that originates in the outer bend of the main channel. Tidal water level variations lead to cyclical variations in the sediment distribution over the downstream branches. Lags in dune development cause complex hysteresis patterns in flow parameters and sediment transport. All bifurcations show evidence of sediment waves, which probably are intrinsic bifurcation phenomena. The complex transport processes at the three bifurcations cause distinct discontinuities in the downstream fining trend of the river. Differences among the studied river bifurcations are mainly due to differences in sediment mobility (Shields value). Because the variations in sediment transport are complex and poorly correlated with the flow discharge, prediction of the sediment distribution with existing relationships for one‐dimensional models is problematic.
How to usefully compare homologous plant genes and chromosomes as DNA sequences
Authors: Lyons Eric , Freeling Michael 
Published: February 2008

SummaryThere are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non‐coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.