bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Copper-Inducible Promoter for Use in Ectopic Expression in the Fungal Pathogen
Histoplasma capsulatum
Authors: Gebhart Dana , Bahrami Adam K. , Sil Anita 
Published: June 2006

ABSTRACT

Despite the existence of a number of genetic tools to study the fungal pathogen
Histoplasma capsulatum
, strategies for conditional gene expression have not been developed. We used microarray analysis to identify genes that are transcriptionally induced or repressed by the addition of copper sulfate (CuSO
4
) to
H. capsulatum
yeast cultures. One of these genes,
CRP1
, encodes a putative copper efflux pump that is significantly induced in the presence of CuSO
4
. The upstream regulatory region of
CRP1
was sufficient to drive copper-regulated expression of two reporter genes,
lacZ
and the gene encoding green fluorescent protein. Microarray experiments were performed to determine a copper concentration that triggers accumulation of the
CRP1
transcript without significant perturbation of global gene expression. These studies show that the
CRP1
upstream regulatory region can be used for ectopic expression of heterologous genes in
H. capsulatum
. Furthermore, they demonstrate the strategic use of microarrays to identify conditional promoters that confer induction in the absence of large-scale shifts in gene expression.
Investigation of the Mechanism of Meiotic DNA Cleavage by
VMA1
-Derived Endonuclease Uncovers a Meiotic Alteration in Chromatin Structure around the Target Site
Authors: Fukuda Tomoyuki , Ohta Kunihiro , Ohya Yoshikazu 
Published: June 2006

ABSTRACT

VMA1
-derived endonuclease (VDE), a homing endonuclease in
Saccharomyces cerevisiae
, is encoded by the mobile intein-coding sequence within the nuclear
VMA1
gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the
VMA1
gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of
VMA1
intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the
VMA1
locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation.
PneumocystisMelanins Confer Enhanced Organism Viability
Authors: Icenhour Crystal R. , Kottom Theodore J. , Limper Andrew H. 
Published: June 2006

ABSTRACTPneumocystiscontinues to represent an important opportunistic fungal pathogen of those with compromised immunity. Thus, it is crucial to identify factors that affect its viability and pathogenicity. We previously reported the first identification of melanins inPneumocystis. In the present study, we sought to further characterize these components and define the function for these melanins. Melanins extracted fromPneumocystisand melanizedPneumocystiscells were analyzed by electron spin resonance spectroscopy, revealing spectra consistent with melanins from other fungi. Immunofluorescence assays using anti-melanin monoclonal antibodies showed that melanins are widely present acrossPneumocystishost species, including mouse-, ferret-, and human-derivedPneumocystisorganisms, as well asPneumocystis cariniiderived from rat. Using immunoelectron microscopy, melanins were found to localize to the cell wall and cytoplasm ofP. cariniicysts, as well as to intracystic bodies within mature cysts. Next, the role of melanins on the maintenance ofPneumocystisviability was determined by using quantitative reverse transcription-PCR measurement of the heat shock protein mRNA under adverse environmental conditions. Using a new method to promote the melanization ofPneumocystis, we observed that strongly melanizedPneumocystisretained viability to a greater degree when exposed to UV irradiation or desiccation compared to less-pigmented organisms. These studies support our previous identification ofPneumocystismelanins across the genus, further characterize thesePneumocystiscomponents, and demonstrate that melanins protectPneumocystisfrom environmental stressors.
Lipid Raft-Based Membrane Compartmentation of a Plant Transport Protein Expressed in
Saccharomyces cerevisiae
Authors: Grossmann Guido , Opekarova Miroslava , Novakova Linda , Stolz Jürgen , Tanner Widmar 
Published: June 2006

ABSTRACT

The hexose-proton symporter HUP1 shows a spotty distribution in the plasma membrane of the green alga
Chlorella kessleri. Chlorella
cannot be transformed so far. To study the membrane localization of the HUP1 protein in detail, the symporter was fused to green fluorescent protein (GFP) and heterologously expressed in
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
. In these organisms, the HUP1 protein has previously been shown to be fully active. The GFP fusion protein was exclusively targeted to the plasma membranes of both types of fungal cells. In
S. cerevisiae
, it was distributed nonhomogenously and concentrated in spots resembling the patchy appearance observed previously for endogenous H
+
symporters. It is documented that the
Chlorella
protein colocalizes with yeast proteins that are concentrated in 300-nm raft-based membrane compartments. On the other hand, it is completely excluded from the raft compartment housing the yeast H
+
/ATPase. As judged by their solubilities in Triton X-100, the HUP1 protein extracted from
Chlorella
and the GFP fusion protein extracted from
S. cerevisiae
are detergent-resistant raft proteins.
S. cerevisiae
mutants lacking the typical raft lipids ergosterol and sphingolipids showed a homogenous distribution of HUP1-GFP within the plasma membrane. In an ergosterol synthesis (
erg6
) mutant, the rate of glucose uptake was reduced to less than one-third that of corresponding wild-type cells. In
S. pombe
, the sterol-rich plasma membrane domains can be stained in vivo with filipin.
Chlorella
HUP1-GFP accumulated exactly in these domains. Altogether, it is demonstrated here that a plant membrane protein has the property of being concentrated in specific raft-based membrane compartments and that the information for its raft association is retained between even distantly related organisms.
Molecular and Biochemical Analysis of Periplastidial Starch Metabolism in the Cryptophyte
Guillardia theta
Authors: Haferkamp Ilka , Deschamps Philippe , Ast Michelle , Jeblick Wolfgang , Maier Uwe , Ball Steven , Neuhaus H. Ekkehard 
Published: June 2006

ABSTRACT

Starch in synchronously grown
Guillardia theta
cells accumulates throughout the light phase, followed by a linear degradation during the night. In contrast to the case for other unicellular algae such as
Chlamydomonas reinhardtii
, no starch turnover occurred in this organism under continuous light. The gene encoding granule-bound starch synthase (
GBSS1
), the enzyme responsible for amylose synthesis, displays a diurnal expression cycle. The pattern consisted of a maximal transcript abundance around the middle of the light phase and a very low level during the night. This diurnal regulation of
GBSS1
transcript abundance was demonstrated to be independent of the circadian clock but tightly light regulated. A similar yet opposite type of regulation pattern was found for two α-amylase isoforms and for one of the two plastidic triose phosphate transporter genes investigated. In these cases, however, the transcript abundance peaked in the night phase. The second plastidic triose phosphate transporter gene had the
GBSS1
mRNA abundance pattern. Quantification of the GBSS1 activity revealed that not only gene expression but also total enzyme activity exhibited a maximum in the middle of the light phase. To gain a first insight into the transport processes involved in starch biosynthesis in cryptophytes, we demonstrated the presence of both plastidic triose phosphate transporter and plastidic ATP/ADP transporter activities in proteoliposomes harboring either total membranes or plastid envelope membranes from
G. theta
. These molecular and biochemical data are discussed with respect to the environmental conditions experienced by
G. theta
and with respect to the unique subcellular location of starch in cryptophytes.
Cytogenetic analysis of myxoid liposarcoma and myxofibrosarcoma by array-based comparative genomic hybridisation
Authors: Ohguri T , Hisaoka M , Kawauchi S , Sasaki K , Aoki T , Kanemitsu S , Matsuyama A , Korogi Y , Hashimoto H 
Published: June 2006

Aim:To investigate overall chromosomal alterations using array-based comparative genomic hybridisation (CGH) of myxoid liposarcomas (MLSs) and myxofibrosarcomas (MFSs).Materials and methods:Genomic DNA extracted from fresh-frozen tumour tissues was labelled with fluorochromes and then hybridised on to an array consisting of 1440 bacterial artificial chromosome clones representing regions throughout the entire human genome important in cytogenetics and oncology.Results:DNA copy number aberrations (CNAs) were found in all the 8 MFSs, but no alterations were found in 7 (70%) of 10 MLSs. In MFSs, the most frequent CNAs were gains at 7p21.1–p22.1 and 12q15–q21.1 and a loss at 13q14.3–q34. The second most frequent CNAs were gains at 7q33–q35, 9q22.31–q22.33, 12p13.32–pter, 17q22–q23, Xp11.2 and Xq12 and losses at 10p13–p14, 10q25, 11p11–p14, 11q23.3–q25, 20p11–p12 and 21q22.13–q22.2, which were detected in 38% of the MFSs examined. In MLSs, only a few CNAs were found in two sarcomas with gains at 8p21.2–p23.3, 8q11.22–q12.2 and 8q23.1–q24.3, and in one with gains at 5p13.2–p14.3 and 5q11.2–5q35.2 and a loss at 21q22.2–qter.Conclusions:MFS has more frequent and diverse CNAs than MLS, which reinforces the hypothesis that MFS is genetically different from MLS. Out-array CGH analysis may also provide several entry points for the identification of candidate genes associated with oncogenesis and progression in MFS.
Receptor-activated Smad localisation in Bleomycin-induced pulmonary fibrosis
Authors: Higashiyama Hiroyuki , Yoshimoto Daisuke , Okamoto Yuji , Kikkawa Hideo , Asano Satoshi , Kinoshita Mine 
Published: June 2006

Background:Recent advances in fibrosis biology have identified transforming growth factor (TGF)-β type I receptor-mediated activation of Smads as playing a central part in the development of fibrosis. However, to date, there have been few studies that examined the localisation and distribution of receptor-activated Smads protein (R-Smads: Smad2 and 3) during the fibrosis progression.Aims:To histopathologically assess the time-course change of the localisation and distribution of the Smads protein in pulmonary fibrosis.Methods:Pulmonary fibrosis was induced by intranasal injection of bleomycin (0.3 U/mouse). Lungs were isolated 2, 5, 7, 9 and 14 days after bleomycin treatment. Histological changes in the lungs were evaluated by haematoxylin-eosin stain or Masson’s trichrome stain, and scored. TGF-β1, Smad3 and phosphorylated Smad2 localisations in lung tissues were determined by immunohistochemistry.Results:The bleomycin treatment led to considerable pulmonary fibrotic changes accompanied by marked increase in TGF-β1 expression in infiltrating macrophages. With the progression in fibrosis (day 7–14), marked increases in Smad3-positive and pSmad2-positive cells were observed. There were intense Smad3-positive and pSmad2-positive signals localised to the nuclei of the infiltrating macrophages and to type II epithelial cells, and less intense signals in fibroblasts and hyperplastic alveolar/bronchiolar epithelial cells.Conclusions:The time-course data of TGF-β1 and R-Smads indicate that progressive enhancement of TGF-β1 signalling via R-Smad is activated in the process of fibrosis progression.
Postglacial colonization and population genetic relationships in thePinus contortacomplex
Authors: Fazekas Aron J. , Yeh Francis C. 
Published: June 2006

To explore the evolutionary relationships among the subspecies of lodgepole pine ( Pinus contorta Dougl. ex Loud.) and the possible existence of a northern glacial refugium for Pinus contorta Dougl. ex Loud. subsp. latifolia Engelm. and a coastal refugium for Pinus contorta Dougl. ex Loud. subsp. contorta , 31 populations were analyzed using RAPD markers to determine whether a pattern of isolation by distance exists. A total of 52 markers from 10 primers were scored. A significant pattern of isolation by distance was detected when all 31 populations were analyzed together and for the 19 populations of subsp. latifolia. A phylogenetic tree constructed from all 31 populations does not show an unambiguous division of the subspecies of P. contorta into distinct clades. Our results provide no support for the separation of lodgepole pine into various subspecies and show that the subspecies of lodgepole pine have not been sufficiently isolated from one another for a large amount of genetic divergence to occur between them. For subsp. latifolia, the pattern of isolation by distance is consistent with the hypothesis of a single refugium south of the glacial maximum with population expansion following glacial retreat. The amount of genetic distance and the pattern of differentiation in populations of subsp. contorta suggest a more complex history associated with fluctuation in ocean levels and glacial margins.
Rhizosphere-competent isolates of streptomycete and non-streptomycete actinomycetes capable of producing cell-wall-degrading enzymes to controlPythium aphanidermatumdamping-off disease of cucumber
Authors: El-Tarabily Khaled A. 
Published: June 2006

Fifty-eight streptomycete and 35 non-streptomycete actinomycetes were isolated from cucumber rhizosphere soil. These isolates were screened for the production of cell-wall-degrading enzymes using mycelial ( Pythium aphanidermatum (Edson) Fitzp.) fragment agar. Eighteen promising isolates were screened for their competence as root colonizers. Eight isolates showing exceptional rhizosphere competence significantly inhibited, in vitro, P. aphanidermatum, the causal agent of postemergence damping-off of cucumber ( Cucumis sativus L.) seedlings. The four most inhibitory isolates ( Actinoplanes philippinensis Couch, Microbispora rosea Nonomura and Ohara, Micromonospora chalcea (Foulerton) Ørskov, and Streptomyces griseoloalbus (Kudrina) Pridham et al.) produced in vitro β-1,3-, β-1,4-, and β-1,6-glucanases and caused lysis of P. aphanidermatum hyphae. None of these produced volatile inhibitors or siderophores. Only S. griseoloalbus produced diffusible inhibitory metabolites, whilst A. philippinensis and Micromonospora chalcea parasitized the oospores of P. aphanidermatum. These four isolates were subsequently tested in the greenhouse, individually or as a mixture, for their ability to suppress damping-off of cucumber seedlings in soil with or without cellulose amendment. The treatment, which included all four isolates in soil amended with cellulose, was significantly superior to all other treatments in suppressing damping-off and was nearly as good as the metalaxyl treatment. Results show that there is a potential to use a mixture of antagonistic rhizosphere-competent actinomycetes along with cellulose amendment rather than fungicides for the field management of this disease. This is the first study that has involved the screening of rhizosphere-competent non-streptomycete actinomycetes capable of producing cell-wall-degrading enzymes, for the management of Pythium diseases.
Genetic variation of Populus tremuloides in ecophysiological responses to CO2 elevation
Authors: Liu Ning , Dang Qing-Lai , Parker William H. 
Published: June 2006

To investigate the genetic variation of trembling aspen ( Populus tremuloides Michx.) in ecophysiological responses to [CO2] elevation, 1-year-old seedlings of four provenances (three families per provenance) from northwestern Ontario were exposed to three [CO2] levels in the greenhouse: ambient (360 ppm), 1.5 × ambient (540 ppm), and 2 × ambient (720 ppm). Biomass and foliage gas exchange were examined after 60 d of treatment. [CO2] elevation significantly increased the rate of net CO2 assimilation and photosynthetic water use efficiency. The stimulation was generally greater in the 540 ppm [CO2] than in 720 ppm [CO2]. The 720 ppm [CO2] resulted in a 10% photosynthetic down-regulation, but no down-regulation was detected in the 540 ppm CO2 treatment. The 540 ppm [CO2] (but not the 720 ppm) treatment significantly decreased stomatal conductance and transpiration rate in the provenances from the Great Lakes – St. Lawrence Region but not in those from the Boreal Region. The intercellular to ambient CO2 concentration ratio (Ci/Ca) was significantly higher under 720 ppm [CO2] than under the other two [CO2]. The CO2 elevations generally increased the total and root biomass, and the stimulation was greater in the 540 ppm [CO2] than in the 720 ppm [CO2] treatment. The two provenances from the Great Lakes – St. Lawrence region generally had greater biomasses than those from the boreal region, while there were no significant differences between them in the physiological variables. However, we did not find any significant differences between provenances in the responses of biomass to [CO2] treatments.
Phylogenetic relationships within Cicuta (Apiaceae tribe Oenantheae) inferred from nuclear rDNA ITS and cpDNA sequence data
Authors: Lee Chang-Shook , Downie Stephen R. 
Published: June 2006

The genus Cicuta (Apiaceae tribe Oenantheae Dumort.) is the most virulently poisonous group of flowering plants native to the north temperate zone. A recent treatment recognized four species ( C. bulbifera L., C. douglasii (DC.) J.M. Coult. & Rose, C. maculata L., and C. virosa L.), with C. maculata divided into four varieties. We present results of phylogenetic analyses of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) locus and the region bounded by the chloroplast genes psbI and trnK 5′ exon to determine taxonomic limits and relationships among these taxa, and to assess the taxonomic status of C. douglasii, a polyploid thought to be derived from C. maculata and C. virosa. Cicuta bulbifera and C. virosa are each resolved as monophyletic, the latter is a sister group to all other species. Discordance between the ITS- and plastid-derived phylogenies and lack of resolution in the ITS trees preclude unequivocal hypotheses of relationship; all trees do suggest, however, that the allotetraploid C. douglasii is polyphyletic and possibly polytopic, with all examined accessions but one nested within C. maculata. This single outstanding accession is from California and, pending further study, might warrant recognition as a distinct species. The diploid C. bulbifera may also be of hybrid origin, as revealed by significant discordance between data sets. Within C. maculata, only the western North American var. angustifolia Hook. is resolved in the ITS trees. In the cpDNA trees, C. maculata var. angustifolia comprises a strongly supported clade with C. maculata var. bolanderi (S. Watson) G.A. Mulligan and C. douglasii, both of primarily western North American distribution. The eastern North American taxa, C. maculata vars. maculata and victorinii (Fernald) B. Boivin, also comprise a clade, sister group to C. bulbifera.
Neither 'Primitives' nor 'Others,' but Somehow Not Quite Like 'Us': The Fortunes of Psychic Unity and Essentialism in Chinese Studies
Authors: Brown Miranda 
Published: June 2006

AbstractThis paper re-evaluates a persistent but controversial claim in studies of China—to wit, that Chinese thought exhibited a different logical structure than that found in Europe. By situating what is now largely regarded as a Sinological problem within the broader context of the debate between Edward B. Tylor (1832-1917) and Lucien Lévy-Bruhl (1857-1939) about primitive thought, it argues that this line of inquiry about cultural difference, as exemplified by the work of its earliest exponents, Marcel Granet (1884-1940), Joseph Needham (1900-1995), and Angus Charles Graham (1919-1991), is still significant. The significance of these works lies not so much in their specific arguments about China as in the general approach they suggest for explaining cultural difference, an approach that can steer clear of the dangers in evolutionary and essentializing approaches to the study of human mentality. Dans cet article j'examine de nouveau une prétension persistante mais controversée dans les études de la Chine—c'est à dire, que la pensée chinoise fait preuve d'une différente structure logique que celle trouvée en Europe. En situant ce qui est principalement regardé comme un problème sinologique dans le contexte plus large d'un débat entre Edward B. Tylor (1832-1917) et Lucien Lévy-Bruhl (1857-1939) sur la pensée primitive, j'affirme la signifiance actuelle de cette approche de la différence culturelle, telle que représentée par les écrits de ses premiers partisans, Marcel Granet (1884-1940), Joseph Needham (1900-1995) et Angus Charles Graham (1919-1991). La signifiance de ces ouvrages dérive moins de leurs arguments spécifiques sur la Chine, que de leur approche générale de l'explication de la différence culturelle, une approche qui peut éviter les dangers des approches évolutionnaires et réductionnistes de l'étude des mentalités humaines.
Lying on the Edge of the Burning Ground: Rethinking Tinais
Authors: Devadevan Manu 
Published: June 2006

AbstractThis paper seeks to interrogate the prevailing paradigm in the historiography of early Tamil Nad, which treats tinais as constituting the geographic basis for early economic practices. On the one hand the case of Kodumanal excavations is juxtaposed as an archaeological instance vis-à-vis tinais. On the other, it is argued through a close reading of Sangam texts that tinais were aesthetic structures employed in the configuration of space in Sangam mythopoeic imagination. It is also argued that the form and content of the tinai-based aesthetics reveals the crisis of a milieu in transition towards early statedom. Cet article cherche à interroger le paradigme régnant en historiographie du Tamoul tôt Nad, ce qui traite des tinais en tant que constitution de la base géographique pour des pratiques économiques tôt. D'une part la caisse d'excavations de Kodumanal est juxtaposée comme exemple archéologique vis-à-vis des tinais. De l'autre, on lui discute par une lecture étroite des textes de Sangam que les tinais étaient les structures esthétiques utilisées dans la configuration de l'espace dans l'imagination mythopoeic de Sangam. On lui discute également que la forme et le contenu de l'esthétique tinai-basée indique la crise d'un milieu dans la transition vers le statedom tôt.