bluuebunny/crossref_metadata_2025 huggingface dataset:
Intravenous glycerol therapy should not be used in patients with unrecognized fructose‐1,6‐bisphosphatase deficiency
Authors: HASEGAWA YUKIHIRO , KIKAWA YOSHIHARU , MIYAMAOTO JUNKO , SUGIMOTO SHUJI , ADACHI MASANORI , OHURA TOSHIHIRO , MAYUMI MITSUFUMI
Published: May 2004

Abstract

Background
: In Asian countries, glycerol solution that contains fructose (5%) is often used for management of brain edema. However, glycerol and fructose may cause severe hypoglycemia and metabolic acidosis in patients with fructose‐1,6‐bisphosphatase (FBPase) deficiency, even under stable conditions. The aim of the present study was to determine whether glycerol solution was used for brain edema during acute metabolic decompensation of hypoglycemia and metabolic acidosis in patients with unrecognized FBPase deficiency in Japan and to examine a long‐term prognosis of the patients who had this kind of severe metabolic decompensation with or without glycerol therapy.

Methods
: A retrospective study of 20 children with FBPase deficiency was conducted, based on their medical records.

Results
: Six of the 20 children were given glycerol solution for the presence or possibility of brain edema during acute metabolic decompensation of hypoglycemia and metabolic acidosis; two of the six patients administered with glycerol were given dialysis. In four patients treated with glycerol alone without dialysis, two had no brain edema before glycerol administration but it developed later after the administration. These four patients treated with glycerol alone died or developed severe neurological complications. Fourteen patients who were not treated with glycerol solution had no brain edema and showed good prognosis.

Conclusion
: Glycerol solution, which contains fructose in Asian countries including Japan, should not be used as an osmotic agent for treatment of brain edema in patients who have hypoglycemia and retention‐type metabolic acidosis, until FBPase deficiency is ruled out by measuring blood concentration of lactate.
Analysis of the circumstances at the end of life in children with cancer: A single institution's experience in Japan
Authors: FUJII YUJI , WATANABE CHIEKO , OKADA SHUICHI , INOUE NORIKO , ENDOH AKIRA , YAJIMA SHUHEI , HONGO TERUAKI , OHZEKI TAKEHIKO , SUZUKI ERIKO
Published: May 2004

Abstract

Background
: With the aim of improving the quality of life of children with cancer, this study presents an analysis of one hospital's experience with terminal care.

Methods
: Between 1994 and 2000, 28 children died after treatment for cancer at Hamamatsu University Hospital. The circumstances of their deaths were analyzed through medical records and interviews with 8 sets of bereaved parents. We compared results of this analysis with our previous data collected from 1978 to 1993.

Results
: Of the 28 children, 11 had leukemia/lymphoma (LL group) and 17 had solid tumors (ST group). Six children (21.4%), all of whom were in the LL group, died of treatment‐related complications. Twenty children (71.4%) died during terminal care: three (27.3%) were in the LL group and 17 (100%) in the ST group. Eleven children (39.3%) received terminal care at home and eight (28.6%) of these died at home. The number of children who received terminal care and died at home had increased in comparison with the previous period. Among problems with terminal care identified by parents were the lack of opportunity for the child to continue with education and an inadequate support system after the child's death.

Conclusions
: Some advances in the quality of life of the children were recognized. However, these advances were extended to a greater percentage of children in the ST group than in the LL group. The psychosocial problems faced by children and their families are now changing for the better.
Analysis of the circumstances at the end of life in children with cancer: Symptoms, suffering and acceptance
Authors: HONGO TERUAKI , WATANABE CHIEKO , OKADA SHUICHI , INOUE NORIKO , YAJIMA SHUHEI , FUJII YUJI , OHZEKI TAKEHIKO
Published: May 2004

Abstract

Background
: In an effort to improve the quality of life of children with cancer, this study analyzes the signs and symptoms at the end of life in such children. It is hoped that these data will contribute to the development of appropriate programs to address the challenges faced by these children.

Procedure
: Between 1994 and 2000, 28 children died after treatment for cancer at Hamamatsu University Hospital, Japan. The circumstances, signs and symptoms at the end of life of these children were analyzed through their medical records.

Results
: Of the 28 children, the underlying diseases were leukemia/lymphoma (LL group; n=11), brain tumors (BT group; n=7), and other solid tumors (OST group; n=10). Records showed poor appetite (100%), dyspnea (82.1%), pain (75.0%), fatigue (71.4%), nausea/vomiting (57.1%), constipation (46.4%) and diarrhea (21.4%) among these children. Anxiety was reported in 53.6% of the entire group of 28 children; however, no child in the BT group manifested anxiety. However, disturbance of consciousness was reported in all children in the BT group, which was significantly greater than in the other groups. Awareness, fear or acceptance of the imminence of his/her own death as indicated by verbal expression was reported in nine children (32.1%).

Conclusions
: Using the data obtained in the present study, we describe situations faced in the terminal care of children. It is important to address the problems revealed by this analysis in order to achieve improvements in both the physical and psychological care of children with terminal cancer.
Prevention of antibiotic‐associated diarrhea in children by Clostridium butyricum MIYAIRI
Authors: SEKI HIROMI , SHIOHARA MASAAKI , MATSUMURA TADAO , MIYAGAWA NATSUKI , TANAKA MAMORU , KOMIYAMA ATSUSHI , KURATA SUSUMU
Published: May 2004

Abstract

Background
: Clostridium butyricum MIYAIRI (CBM) is a probiotic bacteria used for anti‐diarrheal medicine in Japan. The preventive effect of CBM was investigated for antibiotic‐associated diarrhea (AAD) in children.

Methods
: One hundred and ten children who suffered from upper respiratory tract infection or gastroenteritis were divided into three groups. Twenty‐seven of the patients received only antibiotics, 38 received CBM from the mid point of the antibiotic treatment and 45 concomitantly received CBM from the beginning of the antibiotic treatment. To examine the effects of CBM on AAD, the changes in intestinal flora were investigated.

Results
: Diarrhea was observed in 59% of the subjects who received only antibiotics, and total fecal anaerobes, especially Bifidobacterium, were remarkably decreased. In contrast, diarrhea in the subjects who received CBM from either the middle or the beginning of the antibiotic therapy was decreased to 5% and 9%, respectively. Concomitant administration of CBM increased anaerobes and prevented the decrease of Bifidobacterium in the subjects who received antibiotics.

Conclusion
: Clostridium butyricum MIYAIRI is effective for both the treatment and the prophylaxis of AAD in children, as it normalizes the intestinal flora disturbed by antibiotics.
A small-molecule approach to studying invasive mechanisms of
Toxoplasma gondii
Authors: Carey Kimberly L. , Westwood Nicholas J. , Mitchison Timothy J. , Ward Gary E.
Published: May 2004

Toxoplasma gondii
is the most common protozoan parasite of humans. Infection with
T. gondii
can lead to life-threatening disease as a result of repeated cycles of host cell invasion, parasite replication, and host cell lysis. Relatively little is known about the invasive mechanisms of
T. gondii
and related parasites within the Phylum Apicomplexa (including
Plasmodium
spp., the causative agents of malaria), due to difficulties associated with studying genes essential to invasion in haploid obligate intracellular organisms. To circumvent this problem, we have developed a high-throughput microscope-based assay, which we have used to screen a collection of 12,160 structurally diverse small molecules for inhibitors of
T. gondii
invasion. A total of 24 noncytotoxic invasion inhibitors were identified. Secondary assays demonstrated that different inhibitors perturb different aspects of invasion, including gliding motility, secretion of host cell adhesins from apical organelles (the micronemes), and extension of a unique tubulin-based structure at the anterior of the parasite (the conoid). Unexpectedly, the screen also identified six small molecules that dramatically enhance invasion, gliding motility, and microneme secretion. The small molecules identified here reveal a previously unrecognized complexity in the control of parasite motility and microneme secretion, and they constitute a set of useful probes for dissecting the invasive mechanisms of
T. gondii
and related parasites. Small-molecule-based approaches provide a powerful means to address experimentally challenging problems in host-pathogen interaction, while simultaneously identifying new potential targets for drug development.
Production of α-1,3-galactosyltransferase null pigs by means of nuclear transfer with fibroblasts bearing loss of heterozygosity mutations
Authors: Kolber-Simonds Donna , Lai Liangxue , Watt Steven R. , Denaro Maria , Arn Scott , Augenstein Monica L. , Betthauser Jeffery , Carter David B. , Greenstein Julia L. , Hao Yanhong , Im Gi-Sun , Liu Zhonghua , Mell Greg D. , Murphy Clifton N. , Park Kwang-Wook , Rieke August , Ryan David J. J. , Sachs David H. , Forsberg Erik J. , Prather Randall S. , Hawley Robert J.
Published: May 2004

Hyperacute rejection of porcine organs by old world primate recipients is mediated through preformed antibodies against galactosyl-α-1,3-galactose (Galα-1,3-Gal) epitopes expressed on the pig cell surface. Previously, we generated inbred miniature swine with a null allele of the α-1,3-galactosyltransferase locus (
GGTA1
) by nuclear transfer (NT) with gene-targeted fibroblasts. To expedite the generation of
GGTA1
null pigs, we selected spontaneous null mutant cells from fibroblast cultures of heterozygous animals for use in another round of NT. An unexpectedly high rate of spontaneous loss of
GGTA1
function was observed, with the vast majority of null cells resulting from loss of the WT allele. Healthy piglets, hemizygous and homozygous for the gene-targeted allele, were produced by NT by using fibroblasts that had undergone deletional and crossover/gene conversion events, respectively. Aside from loss of Galα-1,3-Gal epitopes, there were no obvious phenotypic differences between these null piglets and WT piglets from the same inbred lines. In fact, congenital abnormalities observed in the heterozygous NT animals did not reappear in the serially produced null animals.
Impaired spontaneous anthropomorphizing despite intact perception and social knowledge
Authors: Heberlein Andrea S. , Adolphs Ralph
Published: May 2004

Humans spontaneously imbue the world with social meaning: we see not only emotions and intentional behaviors in humans and other animals, but also anger in the movements of thunderstorms and willful sabotage in crashing computers. Converging evidence supports a role for the amygdala, a collection of nuclei in the temporal lobe, in processing emotionally and socially relevant information. Here, we report that a patient with bilateral amygdala damage described a film of animated shapes (normally seen as full of social content) in entirely asocial, geometric terms, despite otherwise normal visual perception. Control tasks showed that the impairment did not result from a global inability to describe social stimuli or a bias in language use, nor was a similar impairment observed in eight comparison subjects with damage to orbitofrontal cortex. This finding extends the role of the amygdala to the social attributions we make even to stimuli that are not explicitly social and, in so doing, suggests that the human capacity for anthropomorphizing draws on some of the same neural systems as do basic emotional responses.
Imaging single membrane fusion events mediated by SNARE proteins
Authors: Fix Marina , Melia Thomas J. , Jaiswal Jyoti K. , Rappoport Joshua Z. , You Daoqi , Söllner Thomas H. , Rothman James E. , Simon Sanford M.
Published: May 2004

Using total internal reflection fluorescence microscopy, we have developed an assay to monitor individual fusion events between proteoliposomes containing vesicle soluble
N
-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and a supported planar bilayer containing cognate target SNAREs. Approach, docking, and fusion of individual vesicles to the target membrane were quantified by delivery and subsequent lateral spread of fluorescent phospholipids from the vesicle membrane into the target bilayer. Fusion probability was increased by raising divalent cations (Ca
2+
and Mg
2+
). Fusion of individual vesicles initiated in <100 ms after the rise of Ca
2+
and membrane mixing was complete in 300 ms. Removal of the N
-
terminal H
abc
domain of syntaxin 1A increased fusion probability >30-fold compared to the full-length protein, but even in the absence of the H
abc
domain, vesicle fusion was still enhanced in response to Ca
2+
increase. Our observations establish that the SNARE core complex is sufficient to fuse two opposing membrane bilayers at a speed commensurate with most membrane fusion processes in cells. This real-time analysis of single vesicle fusion opens the door to mechanistic studies of how SNARE and accessory proteins regulate fusion processes
in vivo
.
Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome
Authors: Liang Gangning , Lin Joy C. Y. , Wei Vivian , Yoo Christine , Cheng Jonathan C. , Nguyen Carvell T. , Weisenberger Daniel J. , Egger Gerda , Takai Daiya , Gonzales Felicidad A. , Jones Peter A.
Published: May 2004

Almost 1-2% of the human genome is located within 500 bp of either side of a transcription initiation site, whereas a far larger proportion (≈25%) is potentially transcribable by elongating RNA polymerases. This observation raises the question of how the genome is packaged into chromatin to allow start sites to be recognized by the regulatory machinery at the same time as transcription initiation, but not elongation, is blocked in the 25% of intragenic DNA. We developed a chromatin scanning technique called ChAP, coupling the chromatin immunoprecipitation assay with arbitrarily primed PCR, which allows for the rapid and unbiased comparison of histone modification patterns within the eukaryotic nucleus. Methylated lysine 4 (K4) and acetylated K9/14 of histone H3 were both highly localized to the 5′ regions of transcriptionally active human genes but were greatly decreased downstream of the start sites. Our results suggest that the large transcribed regions of human genes are maintained in a deacetylated conformation in regions read by elongating polymerase. Common models depicting widespread histone acetylation and K4 methylation throughout the transcribed unit do not therefore apply to the majority of human genes.
The soluble ectodomain of herpes simplex virus gD contains a membrane-proximal pro-fusion domain and suffices to mediate virus entry
Authors: Cocchi Francesca , Fusco Daniela , Menotti Laura , Gianni Tatiana , Eisenberg Roselyn J. , Cohen Gary H. , Campadelli-Fiume Gabriella
Published: May 2004

Entry of herpes simplex virus (HSV) 1 into cells requires the interaction of HSV gD with herpesvirus entry mediator or nectin1 receptors, and fusion with cell membrane mediated by the fusion glycoproteins gB, gH, and gL. We report that the gD ectodomain in soluble form (amino acids 1-305) was sufficient to rescue the infectivity of a gD-null HSV mutant, indicating that gD does not need to be anchored to the virion envelope to mediate entry. Entry mediated by soluble gD required, in addition to the receptor-binding sites contained within residues 1-250, a discrete downstream portion (amino acids 261-305), located proximal to the transmembrane segment in full-length gD. We named it as profusion domain. The pro-fusion domain was required for entry mediated by virion-bound gD, because its substitution with the corresponding region of CD8 failed to complement the infectivity of gD
-/+
HSV. Furthermore, a receptor-negative gD (gD
Δ6-259
) inhibited virus infectivity when coexpressed with wild-type gD; i.e., it acted as a dominant-negative gD mutant. The pro-fusion domain is proline-rich, which is characteristic of regions involved in protein-protein interactions. P291L-P292A substitutions diminished the gD capacity to complement gD
-/+
HSV infectivity. We propose that gD forms a tripartite complex with its receptor and, by way of the proline-rich pro-fusion domain, with the fusion glycoproteins, or with one of them. The tripartite complex would serve to recruit/activate the fusion glycoproteins and bring them from a fusion-inactive to a fusion-active state, such that they execute fusion of the virion envelope with cell membrane.
In vivo
tracking of T cell development, ablation, and engraftment in transgenic zebrafish
Authors: Langenau David M. , Ferrando Adolfo A. , Traver David , Kutok Jeffery L. , Hezel John-Paul D. , Kanki John P. , Zon Leonard I. , Look A. Thomas , Trede Nikolaus S.
Published: May 2004

Transgenic zebrafish that express GFP under control of the T cell-specific tyrosine kinase (
lck
) promoter were used to analyze critical aspects of the immune system, including patterns of T cell development and T cell homing after transplant. GFP-labeled T cells could be ablated in larvae by either irradiation or dexamethasone added to the water, illustrating that T cells have evolutionarily conserved responses to chemical and radiation ablation. In transplant experiments, thymocytes from
lck-GFP
fish repopulated the thymus of irradiated wild-type fish only transiently, suggesting that the thymus contains only short-term thymic repopulating cells. By contrast, whole kidney marrow permanently reconstituted the T lymphoid compartment of irradiated wild-type fish, suggesting that long-term thymic repopulating cells reside in the kidney.
CD81 is an entry coreceptor for hepatitis C virus
Authors: Cormier Emmanuel G. , Tsamis Fay , Kajumo Francis , Durso Robert J. , Gardner Jason P. , Dragic Tatjana
Published: May 2004

Hepatitis C virus (HCV) envelope glycoproteins E1/E2 can pseudotype retroviral particles and efficiently mediate entry into target cells. Using this experimental system, we determined HCV tropism for different cell types. Only primary hepatocytes and one hepatoma cell line were susceptible to HCV pseudovirus entry, which could be inhibited by sera from HCV-infected individuals. Furthermore, expression of the putative HCV receptor CD81 on nonpermissive human hepatic but not murine cells enabled HCV pseudovirus entry. Importantly, inhibition of viral entry by an anti-CD81 mAb occurred at a step following HCV attachment to target cells. Our results indicate that CD81 functions as a post-attachment entry coreceptor and that other cellular factors act in concert with CD81 to mediate HCV binding and entry into hepatocytes.
A random-periods model for expression of cell-cycle genes
Authors: Liu Delong , Umbach David M. , Peddada Shyamal D. , Li Leping , Crockett Patrick W. , Weinberg Clarice R.
Published: May 2004

We propose a nonlinear regression model for quantitatively analyzing periodic gene expression in studies of experimentally synchronized cells. Our model accounts for the observed attenuation in cycle amplitude by a simple and biologically plausible mechanism. We represent the expression level for each gene as an average across a large number of cells. For a given cell-cycle gene, we model its expression in each cell in the culture as following the same sinusoidal function except that the period, which in any individual cell must be the same for all cell-cycle genes, varies randomly across cells. We model these random periods by using a lognormal distribution. The variability in period causes the measured amplitude of the cyclic expression trajectory to attenuate over time as cells fall increasingly out of synchrony. Gene-specific parameters include initial amplitude and phase angle. Applying the model to data from Whitfield
et al.
[Whitfield, M. L., Sherlock, G., Saldanha, A. J., Murray, J, I., Ball, C. A.,
et al.
(2002)
Mol. Biol. Cell
13, 1977-2000], we fit the trajectories of 18 well characterized phase-marker genes and find that the fit does not suffer when a common lognormal distribution is assumed for all 18 genes compared with a separate distribution for each. We then use the model to identify 337 periodically expressed transcripts, including the 18 phase-marker genes. The model permits estimation of and hypothesis testing about biologically meaningful parameters that characterize cycling genes.
Involvement of caspase-4 in endoplasmic reticulum stress-induced apoptosis and Aβ-induced cell death
Authors: Hitomi Junichi , Katayama Taiichi , Eguchi Yutaka , Kudo Takashi , Taniguchi Manabu , Koyama Yoshihisa , Manabe Takayuki , Yamagishi Satoru , Bando Yoshio , Imaizumi Kazunori , Tsujimoto Yoshihide , Tohyama Masaya
Published: May 2004

Recent studies have suggested that neuronal death in Alzheimer's disease or ischemia could arise from dysfunction of the endoplasmic reticulum (ER). Although caspase-12 has been implicated in ER stress-induced apoptosis and amyloid-β (Aβ)–induced apoptosis in rodents, it is controversial whether similar mechanisms operate in humans. We found that human caspase-4, a member of caspase-1 subfamily that includes caspase-12, is localized to the ER membrane, and is cleaved when cells are treated with ER stress-inducing reagents, but not with other apoptotic reagents. Cleavage of caspase-4 is not affected by overexpression of Bcl-2, which prevents signal transduction on the mitochondria, suggesting that caspase-4 is primarily activated in ER stress-induced apoptosis. Furthermore, a reduction of caspase-4 expression by small interfering RNA decreases ER stress-induced apoptosis in some cell lines, but not other ER stress-independent apoptosis. Caspase-4 is also cleaved by administration of Aβ, and Aβ-induced apoptosis is reduced by small interfering RNAs to caspase-4. Thus, caspase-4 can function as an ER stress-specific caspase in humans, and may be involved in pathogenesis of Alzheimer's disease.
Smad6/Smurf1 overexpression in cartilage delays chondrocyte hypertrophy and causes dwarfism with osteopenia
Authors: Horiki Mitsuru , Imamura Takeshi , Okamoto Mina , Hayashi Makoto , Murai Junko , Myoui Akira , Ochi Takahiro , Miyazono Kohei , Yoshikawa Hideki , Tsumaki Noriyuki
Published: May 2004

Biochemical experiments have shown that Smad6 and Smad ubiquitin regulatory factor 1 (Smurf1) block the signal transduction of bone morphogenetic proteins (BMPs). However, their in vivo functions are largely unknown. Here, we generated transgenic mice overexpressing Smad6 in chondrocytes. Smad6 transgenic mice showed postnatal dwarfism with osteopenia and inhibition of Smad1/5/8 phosphorylation in chondrocytes. Endochondral ossification during development in these mice was associated with almost normal chondrocyte proliferation, significantly delayed chondrocyte hypertrophy, and thin trabecular bone. The reduced population of hypertrophic chondrocytes after birth seemed to be related to impaired bone growth and formation. Organ culture of cartilage rudiments showed that chondrocyte hypertrophy induced by BMP2 was inhibited in cartilage prepared from Smad6 transgenic mice. We then generated transgenic mice overexpressing Smurf1 in chondrocytes. Abnormalities were undetectable in Smurf1 transgenic mice. Mating Smad6 and Smurf1 transgenic mice produced double-transgenic pups with more delayed endochondral ossification than Smad6 transgenic mice. These results provided evidence that Smurf1 supports Smad6 function in vivo.
Identification of the membrane receptor of a class XIV myosin in Toxoplasma gondii
Authors: Gaskins Elizabeth , Gilk Stacey , DeVore Nicolette , Mann Tara , Ward Gary , Beckers Con
Published: May 2004

Apicomplexan parasites exhibit a unique form of substrate-dependent motility, gliding motility, which is essential during their invasion of host cells and during their spread between host cells. This process is dependent on actin filaments and myosin that are both located between the plasma membrane and two underlying membranes of the inner membrane complex. We have identified a protein complex in the apicomplexan parasite Toxoplasma gondii that contains the class XIV myosin required for gliding motility, TgMyoA, its associated light chain, TgMLC1, and two novel proteins, TgGAP45 and TgGAP50. We have localized this complex to the inner membrane complex of Toxoplasma, where it is anchored in the membrane by TgGAP50, an integral membrane glycoprotein. Assembly of the protein complex is spatially controlled and occurs in two stages. These results provide the first molecular description of an integral membrane protein as a specific receptor for a myosin motor, and further our understanding of the motile apparatus underlying gliding motility in apicomplexan parasites.
Proximal, selective, and dynamic interactions between integrin αIIbβ3 and protein tyrosine kinases in living cells
Authors: de Virgilio Maddalena , Kiosses William B. , Shattil Sanford J.
Published: May 2004

Stable platelet aggregation, adhesion, and spreading during hemostasis are promoted by outside-in αIIbβ3 signals that feature rapid activation of c-Src and Syk, delayed activation of FAK, and cytoskeletal reorganization. To evaluate these αIIbβ3–tyrosine kinase interactions at nanometer proximity in living cells, we monitored bioluminescence resonance energy transfer between GFP and Renilla luciferase chimeras and bimolecular fluorescence complementation between YFP half-molecule chimeras. These techniques revealed that αIIbβ3 interacts with c-Src at the periphery of nonadherent CHO cells. After plating cells on fibrinogen, complexes of αIIbβ3–c-Src, αIIbβ3–Syk, and c-Src–Syk are observed in membrane ruffles and focal complexes, and the interactions involving Syk require Src activity. In contrast, FAK interacts with αIIbβ3 and c-Src, but not with Syk, in focal complexes and adhesions. All of these interactions require the integrin β3 cytoplasmic tail. Thus, αIIbβ3 interacts proximally, if not directly, with tyrosine kinases in a coordinated, selective, and dynamic manner during sequential phases of αIIbβ3 signaling to the actin cytoskeleton.
ERK activation promotes neuronal degeneration predominantly through plasma membrane damage and independently of caspase-3
Authors: Subramaniam Srinivasa , Zirrgiebel Ute , von Bohlen und Halbach Oliver , Strelau Jens , Laliberté Christine , Kaplan David R. , Unsicker Klaus
Published: May 2004

Our recent studies have shown that extracellular-regulated protein kinase (ERK) promotes cell death in cerebellar granule neurons (CGN) cultured in low potassium. Here we report that the “death” phenotypes of CGN after potassium withdrawal are heterogeneous, allowing the distinction between plasma membrane (PM)–, DNA-, and PM/DNA-damaged populations. These damaged neurons display nuclear condensation that precedes PM or DNA damage. Inhibition of ERK activation either by U0126 or by dominant-negative mitogen-activated protein kinase/ERK kinase (MEK) overexpression results in a dramatic reduction of PM damaged neurons and nuclear condensation. In contrast, overexpression of constitutively active MEK potentiates PM damage and nuclear condensation. ERK-promoted cellular damage is independent of caspase-3. Persistent active ERK translocates to the nucleus, whereas caspase-3 remains in the cytoplasm. Antioxidants that reduced ERK activation and PM damage showed no effect on caspase-3 activation or DNA damage. These data identify ERK as an important executor of neuronal damage involving a caspase-3–independent mechanism.
Degradative organelles containing mislocalized α- and β-synuclein proliferate in presenilin-1 null neurons
Authors: Wilson Christina A. , Murphy Diane D. , Giasson Benoit I. , Zhang Bin , Trojanowski John Q. , Lee Virginia M.-Y.
Published: May 2004

Presenilin-1 null mutation (PS1 −/−) in mice is associated with morphological alterations and defects in cleavage of transmembrane proteins. Here, we demonstrate that PS1 deficiency also leads to the formation of degradative vacuoles and to the aberrant translocation of presynaptic α- and β-synuclein proteins to these organelles in the perikarya of primary neurons, concomitant with significant increases in the levels of both synucleins. Stimulation of autophagy in control neurons produced a similar mislocalization of synucleins as genetic ablation of PS1. These effects were not the result of the loss of PS1 γ-secretase activity; however, dysregulation of calcium channels in PS1 −/− cells may be involved. Finally, colocalization of α-synuclein and degradative organelles was observed in brains from patients with the Lewy body variant of AD. Thus, aberrant accumulation of α- and β-synuclein in degradative organelles are novel features of PS1 −/− neurons, and similar events may promote the formation of α-synuclein inclusions associated with neurodegenerative diseases.
A Ubiquitous β-tubulin Disrupts Microtubule Assembly and Inhibits Cell Proliferation
Authors: Bhattacharya Rajat , Cabral Fernando
Published: May 2004

Vertebrate tubulin is encoded by a multigene family that produces distinct gene products, or isotypes, of both the α- and β-tubulin subunits. The isotype sequences are conserved across species supporting the hypothesis that different isotypes subserve different functions. To date, however, most studies have demonstrated that tubulin isotypes are freely interchangeable and coassemble into all classes of microtubules. We now report that, in contrast to other isotypes, overexpression of a mouse class V β-tubulin cDNA in mammalian cells produces a strong, dose-dependent disruption of microtubule organization, increased microtubule fragmentation, and a concomitant reduction in cellular microtubule polymer levels. These changes also disrupt mitotic spindle assembly and block cell proliferation. Consistent with diminished microtubule assembly, there is an increased tolerance for the microtubule stabilizing drug, paclitaxel, which is able to reverse many of the effects of class V β-tubulin overexpression. Moreover, transfected cells selected in paclitaxel exhibit increased expression of class V β-tubulin, indicating that this isotype is responsible for the drug resistance. The results show that class V β-tubulin is functionally distinct from other tubulin isotypes and imparts unique properties on the microtubules into which it incorporates.
Disturbed Cholesterol Traffic but Normal Proteolytic Function in LAMP-1/LAMP-2 Double-deficient Fibroblasts
Authors: Eskelinen Eeva-Liisa , Schmidt Christine Katrin , Neu Silja , Willenborg Marion , Fuertes Graciela , Salvador Natalia , Tanaka Yoshitaka , Lüllmann-Rauch Renate , Hartmann Dieter , Heeren Jörg , von Figura Kurt , Knecht Erwin , Saftig Paul
Published: May 2004

Mice double deficient in LAMP-1 and -2 were generated. The embryos died between embryonic days 14.5 and 16.5. An accumulation of autophagic vacuoles was detected in many tissues including endothelial cells and Schwann cells. Fibroblast cell lines derived from the double-deficient embryos accumulated autophagic vacuoles and the autophagy protein LC3II after amino acid starvation. Lysosomal vesicles were larger and more peripherally distributed and showed a lower specific density in Percoll gradients in double deficient when compared with control cells. Lysosomal enzyme activities, cathepsin D processing and mannose-6-phosphate receptor expression levels were not affected by the deficiency of both LAMPs. Surprisingly, LAMP-1 and -2 deficiencies did not affect long-lived protein degradation rates, including proteolysis due to chaperone-mediated autophagy. The LAMP-1/2 double-deficient cells and, to a lesser extent, LAMP-2 single-deficient cells showed an accumulation of unesterified cholesterol in endo/lysosomal, rab7, and NPC1 positive compartments as well as reduced amounts of lipid droplets. The cholesterol accumulation in LAMP-1/2 double-deficient cells could be rescued by overexpression of murine LAMP-2a, but not by LAMP-1, highlighting the more prominent role of LAMP-2. Taken together these findings indicate partially overlapping functions for LAMP-1 and -2 in lysosome biogenesis, autophagy, and cholesterol homeostasis.
HPID: The Human Protein Interaction Database
Authors: Han Kyungsook , Park Byungkyu , Kim Hyongguen , Hong Jinsun , Park Jong
Published: May 2004

Summary: The Human Protein Interaction Database (http://www.hpid.org) was designed (1) to provide human protein interaction information pre-computed from existing structural and experimental data, (2) to predict potential interactions between proteins submitted by users and (3) to provide a depository for new human protein interaction data from users. Two types of interaction are available from the pre-computed data: (1) interactions at the protein superfamily level and (2) those transferred from the interactions of yeast proteins. Interactions at the superfamily level were obtained by locating known structural interactions of the PDB in the SCOP domains and identifying homologs of the domains in the human proteins. Interactions transferred from yeast proteins were obtained by identifying homologs of the yeast proteins in the human proteins. For each human protein in the database and each query submitted by users, the protein superfamilies and yeast proteins assigned to the protein are shown, along with their interacting partners. We have also developed a set of web-based programs so that users can visualize and analyze protein interaction networks in order to explore the networks further.

Availability:  http://www.hpid.org

Supplementary information:  http://wilab.inha.ac.kr/HPID/Statistics.htm
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
Authors: Laval Guillaume , Excoffier Laurent
Published: May 2004

Summary: We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias.

Availability:  http://cmpg.unibe.ch/software/simcoal2/

Supplementary information:  http://cmpg.unibe.ch/software/simcoal2/
Identification of DNA regulatory motifs using Bayesian variable selection
Authors: Tadesse Mahlet G. , Vannucci Marina , Liò Pietro
Published: May 2004

Motivation: Understanding the mechanisms that determine gene expression regulation is an important and challenging problem. A common approach consists of identifying DNA-binding sites from a collection of co-regulated genes and their nearby non-coding DNA sequences. Here, we consider a regression model that linearly relates gene expression levels to a sequence matching score of nucleotide patterns. We use Bayesian models and stochastic search techniques to select transcription factor binding site candidates, as an alternative to stepwise regression procedures used by other investigators.

Results: We demonstrate through simulated data the improved performance of the Bayesian variable selection method compared to the stepwise procedure. We then analyze and discuss the results from experiments involving well-studied pathways of Saccharomyces cerevisiae and Schizosaccharomyces pombe. We identify regulatory motifs known to be related to the experimental conditions considered. Some of our selected motifs are also in agreement with recent findings by other researchers. In addition, our results include novel motifs that constitute promising sets for further assessment.

Availability: The Matlab code for implementing the Bayesian variable selection method may be obtained from the corresponding author.
Predicting allergenic proteins using wavelet transform
Authors: Li Kuo-Bin , Issac Praveen , Krishnan Arun
Published: May 2004

Motivation: With many transgenic proteins introduced today, the ability to predict their potential allergenicity has become an important issue. Previous studies were based on either sequence similarity or the protein motifs identified from known allergen databases. The similarity-based approaches, although being able to produce high recalls, usually have low prediction precisions. Previous motif-based approaches have been shown to be able to improve the precisions on cross-validation experiments. In this study, a system that combines the advantages of similarity-based and motif-based prediction is described.

Results: The new prediction system uses a clustering algorithm that groups the known allergenic proteins into clusters. Proteins within each cluster are assumed to carry one or more common motifs. After a multiple sequence alignment, proteins in each cluster go through a wavelet analysis program whereby conserved motifs will be identified. A hidden Markov model (HMM) profile will then be prepared for each identified motif. The allergens that do not appear to carry detectable allergen motifs will be saved in a small database. The allergenicity of an unknown protein may be predicted by comparing it against the HMM profiles, and, if no matching profiles are found, against the small allergen database by BLASTP. Over 70% of recall and over 90% of precision were observed using cross-validation experiments. Using the entire Swiss-Prot as the query, we predicted about 2000 potential allergens.

Availability: The software is available upon request from the authors.
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets
Authors: Lazzarato F. , Franceschinis G. , Botta M. , Cordero F. , Calogero R. A.
Published: May 2004

Summary: RRE allows the extraction of non-coding regions surrounding a coding sequence [i.e. gene upstream region, 5′-untranslated region (5′-UTR), introns, 3′-UTR, downstream region] from annotated genomic datasets available at NCBI.

Availability: RRE parser and web-based interface are accessible at http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html
Genome wide identification and classification of alternative splicing based on EST data
Authors: Gupta S. , Zink D. , Korn B. , Vingron M. , Haas S. A.
Published: May 2004

Motivation: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon–intron boundaries, gene structure and alternative splicing events. However, the alternative splicing events are obscured by a large number of putatively artificial exon boundaries arising due to genomic contamination or alignment errors. The current work describes a methodology to associate quality values to the predicted exon–intron boundaries. High quality exon–intron boundaries are used to predict constitutive and alternative splicing ranked by confidence values, aiming to facilitate large-scale analysis of alternative splicing and splicing in general.

Results: Applying the current methodology, constitutive splicing is observed in 33 270 EST clusters, out of which 45% are alternatively spliced. The classification derived from the computed confidence values for 17 of these splice events frequently correlate (15/17) with RT–PCR experiments performed for 40 different tissue samples. As an application of the confidence measure, an evaluation of distribution of alternative splicing revealed that majority of variants correspond to the coding regions of the genes. However, still a significant fraction maps to non-coding regions, thereby indicating a functional relevance of alternative splicing in untranslated regions.

Availability: The predicted alternative splice variants are visualized in the SpliceNest database at http://splicenest.molgen.mpg.de

Supplementary information: For supplementary data, please refer Bioinformatics Online.
Gene-Ontology-based clustering of gene expression data
Authors: Adryan Boris , Schuh Reinhard
Published: May 2004

Summary: The expected correlation between genetic co-regulation and affiliation to a common biological process is not necessarily the case when numerical cluster algorithms are applied to gene expression data. GO-Cluster uses the tree structure of the Gene Ontology database as a framework for numerical clustering, and thus allowing a simple visualization of gene expression data at various levels of the ontology tree.

Availability: The 32-bit Windows application is freely available at http://www.mpibpc.mpg.de/go-cluster/

Supplementary information: A comprehensive software manual, hints for troubleshooting and commented examples are available from the website.
Occupational immunologic contact urticaria from pine processionary caterpillar (Thaumetopoea pityocampa): experience in 30 cases
Authors: Vega Jesús , Vega Jose María , Moneo Ignacio , Armentia Alicia , Caballero Maria Luisa , Miranda Alberto
Published: May 2004

Cutaneous lesions caused by the pine processionary caterpillar Thaumetopoea pityocampa (TP) are frequent in pinewood areas. In the present study, 30 patients diagnosed with occupational immunologic urticaria from this caterpillar were included. Immediate hypersensitivity was demonstrated by performing prick and IgE‐immunoblotting tests. Workers were grouped according to their common tasks. Occupations at risk of exposure to TP were pine‐cone collectors/woodcutters (14), farmers/stockbreeders (8), other forestry personnel (4), construction workers (2), residential gardeners (1) and entomologists (1). Besides contact urticaria, angioedema (60%), papular lesions of several days of evolution (30%) and anaphylactic reactions (40%) were also detected. The most frequently detected molecular weight bands by immunoblot were 15 (70%), 17 (57%) and 13 kDa (50%). The appearance of isolated bands corresponds with the least serious cases. Only 8 subjects had bands higher than 33 kDa, which was present in the 3 most severe cases of anaphylactic reactions. By presenting these cases, we wish to offer the largest series reported so far of occupational immunologic contact urticaria caused by TP. We include the first cases described in certain occupations, some of them not directly related to forestry work. Pine‐cone or resin collectors, woodcutters, farmers and stockbreeders were the most frequently and severely affected workers.
Occupational skin diseases among dental nurses
Authors: Alanko Kristiina , Susitaival Päivikki , Jolanki Riitta , Kanerva Lasse
Published: May 2004

Out of 923 female dental nurses in the Helsinki district, 799 were interviewed using a computer‐assisted telephone interview. A structured questionnaire was used to inquire about skin, respiratory symptoms, atopy, work history and methods, and exposure at work. The 328 nurses, who reported work‐related dermatitis on their hands, forearms or face, were invited to an interview by an occupational physician; 245 nurses participated. 31 nurses had previously been diagnosed with an occupational skin disease (OSD). 133 nurses with a suspected OSD were selected for further clinical examinations with prick and patch testing. Among the 107 nurses examined, 22 new cases of OSD were diagnosed. There were altogether 29 cases of allergic contact dermatitis, 15 of contact urticaria, 12 of irritant contact dermatitis, and 1 case of onychomycosis. Rubber chemicals and natural rubber latex (NRL) in protective gloves, as well as dental‐restorative plastic materials [(meth)acrylates], were the most common causes of allergy. 42% of the OSD cases in the studied population had been missing from the statistics (Finnish Register of Occupational Diseases). Plastic gloves or NRL gloves with a low‐protein content are recommended for dental work. Skin exposure to (meth)acrylates should be avoided.
Changing patterns of contact allergy in chronic inflammatory ear disease
Authors: Millard T.P. , Orton D.I.
Published: May 2004

Chronic inflammatory ear disease comprises a wide range of conditions. Although contact allergy to topical medicaments is common in such conditions, the causes of these reactions have not been examined in a large series for over a decade. Our aim was to investigate the major sensitizers recorded in 179 patients over the last 17 years. Medicament contact allergic dermatitis was diagnosed in 45 patients (25%), of whom 34 (76%) demonstrated a relevant allergy to neomycin, 28 (62%) to framycetin, 11 (31%) to gentamicin, 8 (18%) to quinoline mix and 5 (11%) to caine mix. Of all neomycin‐allergic patients, 28 (76%) were also allergic to framycetin and 12 (43%) to gentamicin. Comparing the first 60 patients (1985–94) to the most recent 60 (1998–2002) identified a significant recent reduction in the number of patients allergic to neomycin (P = 0.002) and framycetin (P = 0.050), with a non‐significant reduction in the total number diagnosed as medicament‐allergic (P = 0.066). We have therefore demonstrated a high frequency of medicament contact allergy in chronic inflammatory ear disease, supporting the routine use of patch testing in these patients. We have also shown a significant recent reduction in the number of such patients with allergy to neomycin and framycetin.
State Income Tax Treatment of the Elderly
Authors: Edwards Barbara , Wallace Sally
Published: May 2004

The state and local tax treatment of the elderly varies significantly from state to state. In this article, we analyze the differences in effective tax rates for the state personal income tax for elderly versus non‐elderly taxpayers. We find that in a majority of states, the average effective tax rate facing the elderly is significantly lower than that of non‐elderly taxpayers. The consequences of this tax rate difference may impact long‐term state income tax revenues as the elderly population continues to grow.
Risk Aversion and the Pricing of Municipal Bonds
Authors: Kriz Kenneth A.
Published: May 2004

Risk aversion in the municipal bond market has been an assumption of most discussions regarding the municipal bond market, but has not been formally documented. The research in this article tests for the presence of risk aversion through comparing a risk‐neutral bond yield with the observed yields on municipal bonds. A significant level of risk aversion is found to exist in the municipal bond market.
Special and Differential Treatment of Developing Countries in the WTO: Moving Forward After Cancún
Authors: Hoekman Bernard , Michalopoulos Constantine , Winter L. Alan
Published: May 2004

The issue of special and differential treatment (SDT) for developing countries in the WTO has become a source of tension in North‐South trade relations. The absence of an effective SDT regime clearly contributed to the failure of the Cancún Ministerial meeting of the WTO. This paper argues for a new approach that puts the emphasis on efforts to improve the development relevance of WTO rules and create mechanisms which allow greater differentiation across WTO members in determining the applicability of WTO disciplines; complemented by non‐discriminatory liberalisation of trade in goods and services in which developing countries have an export interest. The former is key in allowing the WTO to expand its reach to new ‘behind the border’ policies; and the latter is important to establishing a development dimension in multilateral trade negotiations.