bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ATP-Binding Cassette Transporter GhWBC1 from Elongating Cotton Fibers
Authors: Zhu Yong-Qing , Xu Ke-Xiang , Luo Bin , Wang Jia-Wei , Chen Xiao-Ya 
Published: October 2003

Abstract
We have isolated a cDNA (GhWBC1) from cotton (Gossypium hirsutum) that encodes an ATP-binding cassette transporter of the WBC (white/brown complex) subfamily. Members of this subfamily are half-sized transporters and are reported to mediate lipid and drug excretion in human (Homo sapiens). GhWBC1 is highly expressed in developing fiber cells, but transcripts were also detectable in other tissues except roots. The transcript level peaked in rapidly expanding fibers from 5 to 9 DPA and then decreased. The GhWBC1 expression was weak in fiber cells of an li (ligon-lintless) mutant, which is defective in fiber cell elongation. These data indicate that GhWBC1 gene expression correlates with cotton fiber elongation. Transient expression of enhanced green fluorescence protein-GhWBC1 fusion protein in onion (Allium cepa) epidermal cells revealed plasma membrane localization. The GhWBC1 cDNA driven by a constitutive 35S promoter was introduced into Arabidopsis. About 13% of the transformants produced short siliques (SSs), whereas others had normal siliques (long siliques [LSs]). In siliques of SS lines, most embryos were severely shriveled, and only several seeds per silique could be found at maturity. The transgene expression level was higher in SS lines than in LS lines. Expression of AtWBC11, the closest homolog of GhWBC1 in Arabidopsis, was not altered in either SS or LS transgenic plants examined. These data suggest that GhWBC1 interferes with substance translocation that is required for Arabidopsis seed and silique development. Characterization of Arabidopsis WBC members, particularly AtWBC11, will help to dissect the role of GhWBC1 in cotton fiber development and elongation.
Cold Induction of Arabidopsis CBF Genes Involves Multiple ICE (Inducer of CBF Expression) Promoter Elements and a Cold-Regulatory Circuit That Is Desensitized by Low Temperature
Authors: Zarka Daniel G. , Vogel Jonathan T. , Cook Daniel , Thomashow Michael F. 
Published: October 2003

Abstract
The Arabidopsis CBF1, 2, and 3 genes (also known as DREB1b, c, and a, respectively) encode transcriptional activators that have a central role in cold tolerance. CBF1-3 are rapidly induced upon exposing plants to low temperature, followed by expression of CBF-targeted genes, the CBF regulon, resulting in an increase in plant freezing tolerance. At present, little is known about the cold-sensing mechanism that controls CBF expression. Results presented here indicate that this mechanism does not require a cold shock to bring about the accumulation of CBF transcripts, but instead, absolute temperature is monitored with a greater degree of input, i.e. lower temperature, resulting in a greater output, i.e. higher levels of CBF transcripts. Temperature-shift experiments also indicate that the cold-sensing mechanism becomes desensitized to a given low temperature, such as 4°C, and that resensitization to that temperature requires between 8 and 24 h at warm temperature. Gene fusion experiments identified a 125-bp section of the CBF2 promoter that is sufficient to impart cold-responsive gene expression. Mutational analysis of this cold-responsive region identified two promoter segments that work in concert to impart robust cold-regulated gene expression. These sequences, designated ICEr1 and ICEr2 (induction of CBF expression region 1 or 2), were also shown to stimulate transcription in response to mechanical agitation and the protein synthesis inhibitor, cycloheximide.
Characterization of the Targeting Signal of the Arabidopsis 22-kD Integral Peroxisomal Membrane Protein
Authors: Murphy Mary A. , Phillipson Belinda A. , Baker Alison , Mullen Robert T. 
Published: October 2003

AbstractUsing a combination of in vivo and in vitro assays, we characterized the sorting pathway and molecular targeting signal for the Arabidopsis 22-kD peroxisome membrane protein (PMP22), an integral component of the membrane of all peroxisomes in the mature plant. We show that nascent PMP22 is sorted directly from the cytosol to peroxisomes and that it is inserted into the peroxisomal boundary membrane with its N- and C-termini facing the cytosol. This direct sorting of PMP22 to peroxisomes contrasts with the indirect sorting reported previously for cottonseed (Gossypium hirsutum) ascorbate peroxidase, an integral PMP that sorts to peroxisomes via a subdomain of the endoplasmic reticulum. Thus, at least two different sorting pathways for PMPs exist in plant cells. At least four distinct regions within the N-terminal one-half of PMP22, including a positively charged domain present in most peroxisomal integral membrane-destined proteins, functions in a cooperative manner in efficient peroxisomal targeting and insertion. In addition, targeting with high fidelity to peroxisomes requires all four membrane-spanning domains in PMP22. Together, these results illustrate that the PMP22 membrane peroxisomal targeting signal is complex and that different elements within the signal may be responsible for mediating unique aspects of PMP22 biogenesis, including maintaining the solubility before membrane insertion, targeting to peroxisomes, and ensuring proper assembly in the peroxisomal boundary membrane.
A Negative Regulatory Element Controls mRNA Abundance of the
Leishmania mexicana
Paraflagellar Rod Gene
PFR2
Authors: Mishra Krishna K. , Holzer Timothy R. , Moore Landon L. , LeBowitz Jonathan H. 
Published: October 2003

ABSTRACT

The
Leishmania mexicana
PFR2 locus encodes a component of the paraflagellar rod (PFR), a flagellar structure found only in the insect stage of the life cycle.
PFR2
mRNA levels are 10-fold lower in the mammalian stage than in the insect stage. Nuclear run-on experiments indicate that the change in
PFR2
mRNA abundance is achieved posttranscriptionally. Deletion and block substitution analysis of the entire 1,400-nucleotide 3′ untranslated region (UTR) of
PFR2C
led to the identification of a regulatory element contained within 10 nucleotides of the 3′ UTR, termed the PFR regulatory element (PRE), that is necessary for the 10-fold regulation of
PFR2
mRNA levels. Comparison of the half-lives of
PFR2
transcripts, identical except for the presence or absence of the PRE, revealed that the PRE acts by destabilizing the
PFR2
mRNA in amastigotes. The PRE was inserted into a construct which directs the constitutive expression of a chimeric
PFR2
transcript. Insertion of the PRE resulted in regulated expression of this transcript, demonstrating that the regulatory element is sufficient for promastigote-specific expression. Since the PRE is present in the 3′ UTR of all
L. mexicana
PFR genes examined so far, we propose that it serves a means of coordinating expression of PFR genes.
Recapitulation of the Sexual Cycle of the Primary Fungal Pathogen
Cryptococcus neoformans
var.
gattii
: Implications for an Outbreak on Vancouver Island, Canada
Authors: Fraser James A. , Subaran Ryan L. , Nichols Connie B. , Heitman Joseph 
Published: October 2003

ABSTRACT

Cryptococcus neoformans
is a human fungal pathogen that exists as three distinct varieties or sibling species: the predominantly opportunistic pathogens
C. neoformans
var.
neoformans
(serotype D) and
C. neoformans
var.
grubii
(serotype A) and the primary pathogen
C. neoformans
var.
gattii
(serotypes B and C). While serotypes A and D are cosmopolitan, serotypes B and C are typically restricted to tropical regions. However, serotype B isolates of
C. neoformans
var.
gattii
have recently caused an outbreak on Vancouver Island in Canada, highlighting the threat of this fungus and its capacity to infect immunocompetent individuals. Here we report a large-scale analysis of the mating abilities of serotype B and C isolates from diverse sources and identify unusual strains that mate robustly and are suitable for further genetic analysis. Unlike most isolates, which are of both the
a
and α mating types but are predominantly sterile, the majority of the Vancouver outbreak strains are exclusively of the α mating type and the majority are fertile. In an effort to enhance mating of these isolates, we identified and disrupted the
CRG1
gene encoding the GTPase-activating protein involved in attenuating pheromone response.
crg1
mutations dramatically increased mating efficiency and enabled mating with otherwise sterile isolates. Our studies provide a genetic and molecular foundation for further studies of this primary pathogen and reveal that the Vancouver Island outbreak may be attributable to a recent recombination event.
Developmentally Regulated Chromosome Fragmentation Linked to Imprecise Elimination of Repeated Sequences in Paramecia
Authors: Le Mouël Anne , Butler Alain , Caron François , Meyer Eric 
Published: October 2003

ABSTRACT

The chromosomes of ciliates are fragmented at reproducible sites during the development of the polyploid somatic macronucleus, but the mechanisms involved appear to be quite diverse in different species. In
Paramecium aurelia
, the process is imprecise and results in de novo telomere addition at locally heterogeneous positions. To search for possible determinants of chromosome fragmentation, we have studied an ∼21-kb fragmentation region from the germ line genome of
P. primaurelia
. The mapping and sequencing of alternative macronuclear versions of the region show that two distinct multicopy elements, a minisatellite and a degenerate transposon copy, are eliminated by an imprecise mechanism leading either to chromosome fragmentation and the formation of new telomeres or to the rejoining of flanking sequences. Heterogeneous internal deletions occur between short direct repeats containing TA dinucleotides. The complex rearrangement patterns produced vary slightly among genetically identical cell lines, show non-Mendelian inheritance during sexual reproduction, and can be experimentally modified by transformation of the maternal macronucleus with homologous sequences. These results suggest that chromosome fragmentation in
Paramecium
is the consequence of imprecise DNA elimination events that are distinct from the precise excision of single-copy internal eliminated sequences and that target multicopy germ line sequences by homology-dependent epigenetic mechanisms.
Termite Gut Symbiotic Archaezoa Are Becoming Living Metabolic Fossils
Authors: Li Li , Fröhlich Jürgen , Pfeiffer Peter , König Helmut 
Published: October 2003

ABSTRACT

Over the course of several million years, the eukaryotic gut symbionts of lower termites have become adapted to a cellulolytic environment. Up to now it has been believed that they produce nutriments using their own cellulolytic enzymes for the benefit of their termite host. However, we have now isolated two endoglucanases with similar apparent molecular masses of approximately 36 kDa from the not yet culturable symbiotic Archaezoa living in the hindgut of the most primitive Australian termite,
Mastotermes darwiniensis
. The N-terminal sequences of these cellulases exhibited significant homology to cellulases of termite origin, which belong to glycosyl hydrolase family 9. The corresponding genes were detected not in the mRNA pool of the flagellates but in the salivary glands of
M. darwiniensis
. This showed that cellulases isolated from the flagellate cells originated from the termite host. By use of a PCR-based approach, DNAs encoding cellulases belonging to glycosyl hydrolase family 45 were obtained from micromanipulated nuclei of the flagellates
Koruga bonita
and
Deltotrichonympha nana
. These results indicated that the intestinal flagellates of
M. darwiniensis
take up the termite's cellulases from gut contents.
K. bonita
and
D. nana
possess at least their own endoglucanase genes, which are still expressed, but without significant enzyme activity in the nutritive vacuole. These findings give the impression that the gut Archaezoa are heading toward a secondary loss of their own endoglucanases and that they use exclusively termite cellulases.
Biosynthesis of Glycosylphosphatidylinositol Is Essential to the Survival of the Protozoan Parasite
Toxoplasma gondii
Authors: Wichroski Michael J. , Ward Gary E. 
Published: October 2003

ABSTRACT

The
PIGA
gene from
Toxoplasma gondii
has been cloned and characterized. Like mammalian PIGA, the transmembrane and C-terminal domains are sufficient to direct localization to the parasite endoplasmic reticulum. A functional copy of
PIGA
is required for tachyzoite viability, demonstrating that glycosylphosphatidylinositol biosynthesis is an essential process in
T. gondii.
α-Pheromone-Induced “Shmooing” and Gene Regulation Require White-Opaque Switching during
Candida albicans
Mating
Authors: Lockhart Shawn R. , Zhao Rui , Daniels Karla J. , Soll David R. 
Published: October 2003

ABSTRACT

A 14-mer α-pheromone peptide of
Candida albicans
was chemically synthesized and used to analyze the role of white-opaque switching in the mating process. The α-pheromone peptide blocked cell multiplication and induced “shmooing” in
a/a
cells expressing the opaque-phase phenotype but not in
a/a
cells expressing the white-phase phenotype. The α-pheromone peptide induced these effects at 25°C but not at 37°C. An analysis of mating-associated gene expression revealed several categories of gene regulation, including (i)
MTL
-homozygous-specific, pheromone stimulated, switching-independent (
CAG1
and
STE4
); (ii) mating type-specific, pheromone-induced, switching-independent (
STE2
); and (iii) pheromone-induced, switching-dependent (
FIG1
,
KAR4
, and
HWP1
). An analysis of switching-regulated genes revealed an additional category of opaque-phase-specific genes that are downregulated by α-pheromone only in
a/a
cells (
OP4
,
SAP1
, and
SAP3
). These results demonstrate that α-pheromone causes shmooing, the initial step in the mating process, only in
a/a
cells expressing the opaque phenotype and only at temperatures below that in the human host. These results further demonstrate that although some mating-associated genes are stimulated by the α-pheromone peptide in both white- and opaque-phase cells, others are stimulated only in opaque-phase cells, revealing a category of gene regulation unique to
C. albicans
in which α-pheromone induction requires the white-opaque transition. These results demonstrate that in
C. albicans
, the mating process and associated gene regulation must be examined within the context of white-opaque switching.
Deficiency of mannose 6‐phosphate receptors and lysosomal storage: a morphometric analysis of hepatocytes of neonatal mice
Authors: Schellens Jacques P.M , Saftig Paul , Von Figura Kurt , Everts Vincent 
Published: October 2003

AbstractTransport of lysosomal enzymes is mediated by two mannose 6‐phosphate receptors: a cation dependent (CD‐MPR) and a cation independent receptor (CI‐MPR). In the present study the effect of MPR‐deficiency on the lysosomal system of neonatal mouse hepatocytes was studied by ultrastructural morphometric analyses.The volume density of the lysosomal system in hepatocytes of mice that lack both receptors was significantly increased in comparison with controls and with mice deficient for CI‐MPR only. This higher volume density was due to a nine‐fold increase of residual bodies. In CI‐MPR‐deficient mice the volume density of the lysosomal system was not different from controls and no increase of residual bodies was observed.It is concluded that in hepatocytes of MPR‐deficient neonatal mice lysosomal storage occurs when both MPRs are lacking, whereas deficiency of CI‐MPR only has no effect on the ultrastructure of the lysosomal system.
Neurokinin 1‐receptors and sensory neuropeptides in tendon insertions at the medial and lateral epicondyles of the humerus Studies on tennis elbow and medial epicondylalgia
Authors: Ljung Björn‐Ove , Alfredson Håkan , Forsgren Sture 
Published: October 2003

AbstractThere is no information on the sensory innervation at the flexor muscle origin at the medial epicondyle of the humerus and it is not known if substance P receptors (Neurokinin 1‐receptors, NK1‐R) are present in tendon insertions in general. In the present investigation, we have studied the muscle origin in patients suffering from medial epicondylalgia and tennis elbow. Immunohistochemistry and antibodies to substance P (SP) and CGRP as well as the general nerve marker PGP 9.5 were used. Specific immunoreactions were observed in nerve bundles and as free nerve fibers. The immunoreactive structures were partly seen in association with some of the blood vessels. The observations constitute a morphological correlate for the occurrence of nerve mediated effects in this region. By using immunohistochemistry and antibodies to NK1‐R, the distribution of this receptor was studied at the insertion of the proximal tendon of the extensor carpi radialis brevis muscle at the lateral epicondyle. Specific immunoreactions were seen as varicose fibers occurring as single fibers or grouped into bundles, indicating that SP has effects in the nerves in this region. The results give further evidence for a possible neurogenic involvement in the pathophysiology of tennis elbow and in medial epicondylalgia. © 2003 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Arabidopsis Genes Encoding Mitochondrial Type II NAD(P)H Dehydrogenases Have Different Evolutionary Origin and Show Distinct Responses to Light
Authors: Michalecka Agnieszka M. , Svensson Å. Staffan , Johansson Fredrik I. , Agius Stephanie C. , Johanson Urban , Brennicke Axel , Binder Stefan , Rasmusson Allan G. 
Published: October 2003

Abstract
In addition to proton-pumping complex I, plant mitochondria contain several type II NAD(P)H dehydrogenases in the electron transport chain. The extra enzymes allow the nonenergy-conserving electron transfer from cytoplasmic and matrix NAD(P)H to ubiquinone. We have investigated the type II NAD(P)H dehydrogenase gene families in Arabidopsis. This model plant contains two and four genes closely related to potato (Solanum tuberosum) genes nda1 and ndb1, respectively. A novel homolog, termed ndc1, with a lower but significant similarity to potato nda1 and ndb1, is also present. All genes are expressed in several organs of the plant. Among the nda genes, expression of nda1, but not nda2, is dependent on light and circadian regulation, suggesting separate roles in photosynthesis-associated and other respiratory NADH oxidation. Genes from all three gene families encode proteins exclusively targeted to mitochondria, as revealed by expression of green fluorescent fusion proteins and by western blotting of fractionated cells. Phylogenetic analysis indicates that ndc1 affiliates with cyanobacterial type II NADH dehydrogenase genes, suggesting that this gene entered the eukaryotic cell via the chloroplast progenitor. The ndc1 should then have been transferred to the nucleus and acquired a signal for mitochondrial targeting of the protein product. Although they are of different origin, the nda, ndb, and ndc genes carry an identical intron position.
Down-Regulating α-Galactosidase Enhances Freezing Tolerance in Transgenic Petunia
Authors: Pennycooke Joyce C. , Jones Michelle L. , Stushnoff Cecil 
Published: October 2003

Abstract
α-Galactosidase (α-Gal; EC 3.2.1.22) is involved in many aspects of plant metabolism, including hydrolysis of the α-1,6 linkage of raffinose oligosaccharides during deacclimation. To examine the relationship between endogenous sugars and freezing stress, the expression of α-Gal was modified in transgenic petunia (Petunia × hybrida cv Mitchell). The tomato (Lycopersicon esculentum) Lea-Gal gene under the control of the Figwort Mosaic Virus promoter was introduced into petunia in the sense and antisense orientations using Agrobacterium tumefaciens-mediated transformation. RNA gel blots confirmed that α-Gal transcripts were reduced in antisense lines compared with wild type, whereas sense plants had increased accumulation of α-Gal mRNAs. α-Gal activity followed a similar trend, with reduced activity in antisense lines and increased activity in all sense lines evaluated. Raffinose content of nonacclimated antisense plants increased 12- to 22-fold compared with wild type, and 22- to 53-fold after cold acclimation. Based upon electrolyte leakage tests, freezing tolerance of the antisense lines increased from –4°C for cold-acclimated wild-type plants to –8°C for the most tolerant antisense line. Down-regulating α-Gal in petunia results in an increase in freezing tolerance at the whole-plant level in nonacclimated and cold-acclimated plants, whereas overexpression of the α-Gal gene caused a decrease in endogenous raffinose and impaired freezing tolerance. These results suggest that engineering raffinose metabolism by transformation with α-Gal provides an additional method for improving the freezing tolerance of plants.
wCLUTO: A Web-Enabled Clustering Toolkit
Authors: Rasmussen Matthew D. , Deshpande Mukund S. , Karypis George , Johnson James , Crow John A. , Retzel Ernest F. 
Published: October 2003

Abstract
As structural and functional genomics efforts provide the biological community with ever-broadening sets of interrelated data, the need to explore such complex information for subtle relationships expands. We present wCLUTO, a Web-enabled version of the stand-alone application CLUTO, designed to apply clustering methods to genomic information. Its first application is focused on the clustering transcriptome data from microarrays. Data can be uploaded by the user into the clustering tool, a choice of several clustering methods can be made and configured, and data are presented to the user in a variety of visual formats, including a three-dimensional “mountain” view of the clusters. Parameters can be explored to rapidly examine a variety of clustering results, and the resulting clusters can be downloaded either for manipulation by other programs or to be saved in a format for publication.
The Subcellular Localization of Plant Protein Phosphatase 5 Isoforms Is Determined by Alternative Splicing
Authors: de la Fuente van Bentem Sergio , Vossen Jack H. , Vermeer Josephus E.M. , de Vroomen Marianne J. , Gadella Theodorus W.J. , Haring Michel A. , Cornelissen Ben J.C. 
Published: October 2003

AbstractProtein serine/threonine phosphatase 5 (PP5) plays an important role in signal transduction in animal cells, but in plants, knowledge about PP5 is scarce. Here, we describe the isolation of a full-length cDNA encoding tomato (Lycopersicon esculentum) PP5 (LePP5) and its expression in Escherichia coli. Biochemical characterization showed that recombinant LePP5 has a low intrinsic protein phosphatase activity. This activity was increased 6- to 10-fold by either removal of the N-terminal tetratricopeptide repeat domain or by addition of fatty acids, indicating that biochemical features specific for PP5 homologs from other species are conserved in tomato. The single-copy LePP5 gene was cloned and shown to encode two mRNA species that arise by alternative pre-mRNA splicing. Similarly, Arabidopsis was found to express two PP5 transcripts, suggesting that alternative splicing of PP5 pre-mRNA is not specific for tomato. Alternative splicing results in a larger transcript containing an additional exon encoding two putative transmembrane domains and, hence, in a larger PP5 isoform. Subcellular fractionation studies on tomato protein lysates indicated that the majority of the 55-kD LePP5 isoform is soluble, whereas the 62-kD isoform is an integral membrane protein. Production of yellow fluorescent protein-PP5 chimeras in plant cells indicated that the 55-kD isoform is localized in both the nucleus and the cytoplasm, whereas the 62-kD isoform is targeted to the endoplasmic reticulum, including the nuclear envelope. Our findings show that alternative splicing generates two LePP5 isoforms with a different subcellular localization.