bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topology of the network integrating salicylate and jasmonate signal transduction derived from global expression phenotyping
Authors: Glazebrook Jane , Chen Wenqiong , Estes Bram , Chang Hur‐Song , Nawrath Christiane , Métraux Jean‐Pierre , Zhu Tong , Katagiri Fumiaki 
Published: December 2004

SummaryThe signal transduction network controlling plant responses to pathogens includes pathways requiring the signal molecules salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). The network topology was explored using global expression phenotyping of wild‐type and signaling‐defective mutant plants, including eds3, eds4, eds5, eds8, pad1, pad2, pad4, NahG, npr1, sid2, ein2, and coi1. Hierarchical clustering was used to define groups of mutations with similar effects on gene expression and groups of similarly regulated genes. Mutations affecting SA signaling formed two groups: one comprised of eds4, eds5, sid2, and npr1‐3 affecting only SA signaling; and the other comprised of pad2, eds3, npr1‐1, pad4, and NahG affecting SA signaling as well as another unknown process. Major differences between the expression patterns in NahG and the SA biosynthetic mutant sid2 suggest that NahG has pleiotropic effects beyond elimination of SA. A third group of mutants comprised of eds8, pad1, ein2, and coi1 affected ethylene and jasmonate signaling. Expression patterns of some genes revealed mutual inhibition between SA‐ and JA‐dependent signaling, while other genes required JA and ET signaling as well as the unknown signaling process for full expression. Global expression phenotype similarities among mutants suggested, and experiments confirmed, that EDS3 affects SA signaling while EDS8 and PAD1 affect JA signaling. This work allowed modeling of network topology, definition of co‐regulated genes, and placement of previously uncharacterized regulatory genes in the network.
ER quality control can lead to retrograde transport from the ER lumen to the cytosol and the nucleoplasm in plants
Authors: Brandizzi Federica , Hanton Sally , DaSilva Luis L. Pinto , Boevink Petra , Evans David , Oparka Karl , Denecke Jürgen , Hawes Chris 
Published: December 2004

SummaryQuality control in the secretory pathway is a fundamental step in preventing deleterious effects that may arise by the release of malfolded proteins into the cell or apoplast. Our aims were to visualise and analyse the disposal route followed by aberrant proteins within a plant cell in vivo using fluorescent protein technology. A green fluorescent protein (GFP) fusion was detected in the cytosol and the nucleoplasm in spite of the presence of an N‐terminal secretory signal peptide. In contrast to secreted GFP, the fusion protein was retained in the cells where it was degraded slowly, albeit at a rate much higher than that of the endoplasmic reticulum (ER)‐retained derivative GFP‐HDEL. The fusion protein could not be stabilised by inhibitors of transport or the cytosolic proteasome. However, the protein is a strong lumenal binding protein (BiP) ligand. Complete signal peptide processing even after long‐term expression in virus‐infected leaves rules out the possibility that the documented accumulation in the cytosol and nucleoplasm is because of the bypassing of the translocation pores. The data are consistent with the hypothesis that the fusion protein is disposed off from the ER via a retrograde translocation back to the cytosol. Moreover, accumulation in the nucleoplasm was shown to be microtubule dependent unlike the well‐documented diffusion of cytosolically expressed GFP into the nucleoplasm. The apparent active transport of the GFP fusion into the nucleoplasm may indicate an as yet undiscovered feature of the ER‐associated degradation (ERAD) pathway and explain the insensitivity to degradation by proteasome inhibitors.
Cyclopentenone isoprostanes induced by reactive oxygen species trigger defense gene activation and phytoalexin accumulation in plants
Authors: Thoma Ingeborg , Loeffler Christiane , Sinha Alok K. , Gupta Meetu , Krischke Markus , Steffan Bert , Roitsch Thomas , Mueller Martin J. 
Published: December 2004

SummaryLipid peroxidation may be initiated either by lipoxygenases or by reactive oxygen species (ROS). Enzymatic oxidation of α‐linolenate can result in the biosynthesis of cyclic oxylipins of the jasmonate type while free‐radical‐catalyzed oxidation of α‐linolenate may yield several classes of cyclic oxylipins termed phytoprostanes in vivo. Previously, we have shown that one of these classes, the E1‐phytoprostanes (PPE1), occurs ubiquitously in plants. In this work, it is shown that PPE1 are converted to novel cyclopentenone A1‐ and B1‐phytoprostanes (PPA1 and PPB1) in planta. Enhanced formation of PPE1, PPA1, and PPB1 is observed after peroxide stress in tobacco cell cultures as well as after infection of tomato plants with a necrotrophic fungus, Botrytis cinerea. PPA1 and PPB1 display powerful biologic activities including activation of mitogen‐activated protein kinase (MAPK) and induction of glutathione‐S‐transferase (GST), defense genes, and phytoalexins. Data collected so far infer that enhanced phytoprostane formation is a general consequence of oxidative stress in plants. We propose that phytoprostanes are components of an oxidant‐injury‐sensing, archaic signaling system that serves to induce several plant defense mechanisms.
ydk1‐D, an auxin‐responsive GH3 mutant that is involved in hypocotyl and root elongation
Authors: Takase Tomoyuki , Nakazawa Miki , Ishikawa Akie , Kawashima Mika , Ichikawa Takanari , Takahashi Naoki , Shimada Hiroaki , Manabe Katsushi , Matsui Minami 
Published: December 2004

SummaryTo study the GH3 gene family of Arabidopsis, we investigated a flanking sequence database of Arabidopsis activation‐tagged lines. We found a dwarf mutant, named yadokari 1‐D (ydk1‐D), that had a T‐DNA insertion proximal to a GH3 gene. ydk1‐D is dominant and has a short hypocotyl not only in light but also in darkness. Moreover, ydk1‐D has a short primary root, a reduced lateral root number, and reduced apical dominance. A GH3 gene, named YDK1, was upregulated in ydk1‐D, and YDK1 transgenic plants showed the ydk1‐D phenotype. YDK1 gene expression was induced by exogenously applied auxin and regulated by auxin‐response factor (ARF)7. In addition, YDK1 gene expression was downregulated by blue and far‐red (FR) lights. Strong promoter activity of YDK1 was observed in roots and flowers. These results suggest that YDK1 may function as a negative component in auxin signaling by regulating auxin activity.
Chromosome termini of the monocot plant Othocallis siberica are maintained by telomerase, which specifically synthesises vertebrate‐type telomere sequences
Authors: Weiss‐Schneeweiss Hanna , Riha Karel , Jang Chang Gee , Puizina Jasna , Scherthan Harry , Schweizer Dieter 
Published: December 2004

SummaryLack of Arabidopsis‐type T3AG3 telomere sequences has recently been reported for the majority of investigated taxa of the monocot order Asparagales. In order to investigate this phenomenon in more detail, we conducted extensive cytogenetic and molecular analyses of the telomeres in Othocallis siberica, a member of this order. Terminal restriction fragment analysis together with Bal31 exonuclease assay showed that chromosome termini in O. siberica are formed by long stretches (more than 10 kbp) of vertebrate‐type T2AG3 repeats. In addition, telomerase activity specifically synthesising (T2AG3)n sequence was detected in O. siberica protein extracts by telomerase repeat amplification protocol (TRAP). Fluorescence in situ hybridisation (FISH) revealed the presence of the vertebrate‐type T2AG3 telomere sequences at all chromosome termini and at a few additional regions of O. siberica chromosomes, whereas Arabidopsis‐type T3AG3 DNA and peptide nucleic acid (PNA) probes did not hybridise to chromosomes of Othocallis, except for polymorphic blocks in chromosomes 2 (interstitial) and 4 (terminal). These interstitial/terminal regions are apparently composed of large blocks of (T2AG3)n and (T3AG3)n DNA and represent a unique example of interspersion of two types of telomeric repeats within one genome. This may be a reflection of the recent evolutionary switch from Arabidopsis‐ to vertebrate‐type telomeric repeats in this plant group.
Cryopreservation of transformed and wild‐type Arabidopsis and tobacco cell suspension cultures
Authors: Menges Margit , Murray James A. H. 
Published: December 2004

SummaryWe have recently described Arabidopsis cell suspension cultures that can be effectively synchronised. Here, we describe procedures that allow clonal‐transformed cell suspension lines to be produced using Agrobacterium‐mediated transformation, and an optimised and straightforward procedure for the cryopreservation and recovery of both parental and transformed lines. Frozen cultures show 90% viability and rapid re‐growth after recovery. We show that the cryopreservation procedure is equally applicable to the frequently used tobacco bright yellow (BY)2 cell suspension culture, and that cell cycle synchronisation capacity of parental lines is maintained after both transformation and recovery from cryopreservation. The techniques require no specialised equipment, and are suitable for routine laboratory use, greatly facilitating the handling and maintenance of cell cultures and providing security against both contamination and cumulative somaclonal variation. Finally, the ability to store easily large numbers of transformed lines opens the possibility of using Arabidopsis cell suspension cultures for high‐throughput analysis.
Conservation of class C function of floral organ development during 300 million years of evolution from gymnosperms to angiosperms
Authors: Zhang Pingyu , Tan Hugh T. W. , Pwee Keng‐Hock , Kumar Prakash P. 
Published: December 2004

SummaryFlower development in angiosperms is regulated by the family of MADS‐box transcription factors. MADS‐box genes have also been reported from gymnosperms, another major group of seed plants. AGAMOUS (AG) is the class C MADS‐box floral organ identity gene controlling the stamen and carpel development in Arabidopsis. We report the characterization of an ortholog of the AG gene, named Cycas AGAMOUS (CyAG), from the primitive gymnosperm Cycas edentata. The expression pattern of CyAG in Cycas parallels that of AG in Arabidopsis. Additionally, the gene structure, including the number and location of the introns, is conserved in CyAG and other AG orthologs known. Most importantly, functional analysis shows that CyAG driven by the AG promoter can rescue the loss‐of‐function ag mutant of Arabidopsis. However, the ectopic expression of CyAG in ag mutant Arabidopsis cannot produce the carpeloid and stamenoid organs in the first and second whorls, although the stamen and carpel are rescued in the third and fourth whorls of the transformants. These observations show that the molecular mechanism of class C function controlling reproductive organ identity (stamen and carpel of angiosperms or microsporophyll and megasporophyll of gymnosperms) arose before the divergence of angiosperms and gymnosperms, and has been conserved during 300 million years of evolution thereafter.
Evaluation of efficacy of community‐based vs. institutional‐based direct observed short‐course treatment for the control of tuberculosis in Kilombero district, Tanzania
Authors: Lwilla Fred , Schellenberg David , Masanja Honorath , Acosta Camilo , Galindo Claudia , Aponte John , Egwaga Said , Njako Blasdus , Ascaso Carlos , Tanner Marcel , Alonso Pedro 
Published: December 2004

SummaryTuberculosis (TB) has reappeared as a serious public health problem. Non‐compliance to antituber‐culous drug treatment is cited as one of the major obstacles to the containment of the epidemic. Compliance may be optimized by Directly Observed Treatment (DOT) and short‐course treatment regimens. Since 1986, Tanzanian TB patients have received daily DOT at health facilities for the first 2 months of the treatment course. However, adherence and cure rates have been falling as the number of TB cases continues to increase and the burden on already stretched health facilities threatens to become unmanageable. We used an open cluster randomized controlled trial to compare community‐based DOT (CBDOT) using a short‐course drug regimen with institutional‐based DOT (IBDOT). A total of 522 (301 IBDOT and 221 CBDOT) patients with sputum‐positive TB were recruited. Overall, there was no significant difference in conversion and cure rates between the two strategies [M‐H pooled odds ratio (OR) 0.62; 95% confidence interval (CI) 0.23, 1.71 and OR = 1.58; 95% CI 0.32, 7.88, respectively] suggesting that CBDOT may be a viable alternative to IBDOT. CBDOT may be particularly useful in parts of the country where people live far from health facilities.
Intestinal parasitic infection and associated symptoms in children attending day care centres in Trujillo, Venezuela
Authors: Miller Steven A. , Rosario Carlos Luis , Rojas Elina , Scorza Jose Vicente 
Published: December 2004

Summaryobjectives  To examine the presence of intestinal protozoan and helminth infections and their association with clinical signs and symptoms in children in Trujillo, Venezuela.methods  Conventional microscopic methods (thick‐smear, saline and iodine solutions) were used to identify parasites in stool samples of 301 children attending day care centres. A subgroup of 45 children was evaluated clinically and parasitologically five times during a 1‐month period using conventional methods and the Kinyoun acid‐fast stain for Cryptosporidium identification.results  The point prevalence of protozoan infections was 21% for Giardia duodenalis, 1.0% for Entamoeba histolytica/dispar, 4% for Entamoeba coli, 16% for Blastocystis hominis, and 89% for Cryptosporidium parvum. Prevalence of helminth infection was 11% for Ascaris lumbricoides, 10% for Trichuris trichiura, 0.3% for Strongyloides stercoralis, and 1.3% for Hymenolepis nana. Over a 1‐month time frame, new infections were observed at a rate of 11% for G. duodenalis, 4% for E. histolytica/dispar, 7% for A. lumbricoides, 11% for T. trichiura, 0% for S. stercoralis, and 2% for H. nana. Intestinal symptoms (diarrhoea, vomiting, gas, stomach pain, and loss of appetite) were associated with presence of one or more of C. parvum or B. hominis organisms in stool samples.conclusions  Intestinal parasitic infections contribute significantly to the enteric disease burden experienced by this group of children. The organisms most strongly implicated by this study are common and difficult‐to‐treat protozoan pathogens.
A health facility based case–control study of effectiveness of insecticide treated nets: potential for selection bias due to pre‐treatment with chloroquine
Authors: Webster Jayne , Chandramohan Daniel , Freeman Tim , Greenwood Brian , Kamawal Amin Ullah , Rahim Fazle , Rowland Mark 
Published: December 2004

SummaryCase control studies offer an attractive way to assess the effectiveness of insecticide treated nets (ITN) under programme conditions but have the drawback of being susceptible to bias in the choice of controls. We evaluated the potential for pre‐treatment with chloroquine to result in misclassification of cases and controls and affect estimates of ITN effectiveness in case control studies in urban and rural clinics in Eastern Afghanistan. During the one‐month study, use of ITN showed no effect against malaria in the urban clinic (adjusted odds ratio OR 1.08; 95% CI 0.73–1.6) and the protective effect seen in the rural clinic was not significant (OR 0.62; 95% CI 0.2–2.4). Levels of pre‐treatment were high in both clinics: 24% in urban and 19% in rural clinic attenders. In the urban clinic attenders the level of pre‐treatment between bed net users and non‐users was not significantly different (OR 1.07, 95% CI 0.70–1.64); therefore the misclassification of cases as controls did not introduce any selection bias. Amongst rural clinic attenders, bed net users were less likely to pre‐treat with chloroquine than users (OR 0.33, 95% CI 0.14–0.77); this introduced a selection bias that resulted in an underestimation of the effectiveness of bed nets. Case control studies using health facility data are liable to selection bias especially in areas of high pre‐treatment rates with chloroquine. Generalisation of results over a wide geographic region, or between urban and rural settings, may not be appropriate.
Clinical efficacy of chloroquine in young children with uncomplicated falciparum malaria – a community‐based study in rural Burkina Faso
Authors: Müller Olaf , Traoré Corneille , Kouyaté Bocar 
Published: December 2004

SummaryWe report on a 14‐day study on the efficacy of chloroquine for treating uncomplicated falciparum malaria in young children of a malaria holoendemic area in rural Burkina Faso. In this community‐based study, the overall treatment failure rate was 12/120 (10%), with no differences between villages. This supports the evidence for a still sufficient efficacy of chloroquine in north‐western Burkina Faso.
Lot quality assurance sampling for screening communities hyperendemic for Schistosoma mansoni
Authors: Rabarijaona L. P. , Boisier P. , Ravaoalimalala V. E. , Jeanne I. , Roux J. F. , Jutand M. A. , Salamon R. 
Published: December 2004

SummaryLot quality assurance sampling (LQAS) was evaluated for rapid low cost identification of communities where Schistosoma mansoni infection was hyperendemic in southern Madagascar. In the study area, S. mansoni infection shows very focused and heterogeneous distribution requiring multifariousness of local surveys. One sampling plan was tested in the field with schoolchildren and several others were simulated in the laboratory. Randomization and stool specimen collection were performed by voluntary teachers under direct supervision of the study staff and no significant problem occurred. As expected from Receiver Operating Characteristic (ROC) curves, all sampling plans allowed correct identification of hyperendemic communities and of most of the hypoendemic ones. Frequent misclassifications occurred for communities with intermediate prevalence and the cheapest plans had very low specificity. The study confirmed that LQAS would be a valuable tool for large scale screening in a country with scarce financial and staff resources. Involving teachers, appeared to be quite feasible and should not lower the reliability of surveys. We recommend that the national schistosomiasis control programme systematically uses LQAS for identification of communities, provided that sample sizes are adapted to the specific epidemiological patterns of S. mansoni infection in the main regions.
Domiciliation process of Rhodnius stali (Hemiptera: Reduviidae) in Alto Beni, La Paz, Bolivia
Authors: Matias A. , De la Riva J. , Martinez E. , Torrez M. , Dujardin J. P. 
Published: December 2004

SummaryWe report a systematic collection of Triatominae inside houses and in the peridomestic environment of Alto Beni, department of La Paz, Bolivia. This area is free of Triatoma infestans and although we detected previously seropositivity for Trypanosoma cruzi, the Alto Beni region is not officially considered as endemic for Chagas disease. From 11 houses of five localities, we collected adults, nymphs and eggs of a Rhodnius species, which was confirmed by morphological and morphometric analysis as Rhodnius stali. This little‐known species has long been confused with R. pictipes, and was originally described from museum specimens labelled as R. pictipes. Our data show that R. stali is able to establish colonies in domestic and peridomestic habitats in Bolivia, and it is probably the vector responsible for Chagas disease seropositivity observed in the indigenous population of Alto Beni.
An evaluation of antiretroviral HIV/AIDS treatment in a Rio de Janeiro public clinic
Authors: Carmody Ellie R. , Diaz Theresa , Starling Paulo , Santos Ana Paula Rocha Beruth dos , Sacks Henry S. 
Published: December 2004

SummaryThe Brazilian public health system has implemented free, universal access to antiretroviral (ARV) therapy for HIV‐infected patients. To evaluate this system, we performed a pilot study to determine whether ARVs were prescribed according to Brazilian guidelines in place in 2000, and whether prescriptions were refilled in a timely manner. Year 2000 data were abstracted from all medical and pharmacy records of adult patients first registered for HIV/AIDS care in a Rio de Janeiro public clinic from January to June 2000 (n = 67). Results were analysed using frequency analyses, chi‐square tests and logistic regression. The patient sample was 41.8% female and had a mean age of 34.9 years. 54 (81%) had AIDS; total sample mean baseline CD4+/viral counts were 276 cells/mm3 and 237 517 copies per millilitre, respectively. Delays between clinic request and receipt of first CD4+/viral load results ranged from 25 to 107 (mean 66) and 33 to 139 (mean 86) days, respectively. Fifty‐nine patients (88.1%) were prescribed ARV treatment. Forty‐two regimens (71.2%) were highly active antiretroviral therapies; 17 (28.8%) were combination regimens with two nucleoside reverse transcriptase inhibitors. No combinations were prescribed that were contraindicated in Brazilian guidelines, however 33 patients (55.9%) were prescribed ARV drugs before one or both HIV status parameters (initial CD4+ level or viral load) were recorded. Fourteen patients prescribed ARVs (23.7%) lacked a supply of medication for >1 month during the year at least once. Of these patients, 11 had treatment lapses as a result of failure to pick up medications, and three lacked medication because of drug shortages. Medication lapses were associated with female sex, being hospitalized in 2000, and having more than two drugs in regimen, but were not associated with age, CD4+ level or use of ARVs before 2000. The results from this pilot study suggest conservative prescription of HAART, high practitioner adherence to guidelines, and some problems with refilling medications in a timely manner. Monitoring delays were identified as a structural limitation to optimal adherence to practice guidelines. Better access to monitoring‐laboratory facilities and greater drug availability would improve programme success.
Treatment failure of pyrimethamine‐sulphadoxine and induction of Plasmodium falciparum gametocytaemia in children in western Kenya
Authors: Bousema J. T. , Gouagna L. C. , Meutstege A. M. , Okech B. E. , Akim N. I. J. , Githure J. I. , Beier J. C. , Sauerwein R. W. 
Published: December 2004

SummarySub‐Saharan Africa faces increasing levels of resistance of Plasmodium falciparum parasites to the first‐line drug pyrimethamine‐sulphadoxine (SP). Successful treatment with SP is reported to induce gametocytes and drug resistance may further increase gametocytaemia after treatment. Treatment success, gametocyte prevalence and gametocyte density were determined in 224 asymptomatic children in western Kenya on day 7 after treatment with SP. Treatment failure (R2 or R3 resistance) was observed in 22% of the children. The relative risk to show gametocytes on day 7 after treatment in children with treatment failure was 4.1 (95% CI 1.4–11.6) times higher compared to children with a sensitive infection, after adjustment for age and trophozoite density at the start of treatment. In addition, the gametocyte density was also higher upon SP treatment failure. These findings are reason for concern, as the increased gametocyte prevalence and density after SP treatment failure may increase the spread of SP‐resistant strains in the population.