bluuebunny/crossref_metadata_2025 huggingface dataset:
The intellectual abilities of early‐treated individuals with pyridoxine‐nonresponsive homocystinuria due to cystathionine β‐synthase deficiency
Authors: Yap S. , Rushe H. , Howard P. M. , Naughten E. R.
Published: December 2002

The pathological sequelae of untreated homocystinuria due to cystathionine β‐synthase deficiency include ectopia lentis, osteoporosis, thromboembolic events and mental retardation. They occur at a significantly higher rate with poorer mental capabilities (mean IQ = 57) in the untreated pyridoxine‐nonresponsive individuals. The mental capabilities of 23 pyridoxine‐nonresponsive individuals with 339 patient‐years of treatment were assessed using age‐appropriate psychometric tests and were compared to those of 10 unaffected siblings (controls). Of the 23 individuals, 19 were diagnosed through newborn screening with early treatment, two were late‐detected and two were untreated at the time of assessment. Thirteen of the newborn, screened group who were compliant with treatment had no complications, while the remaining 6, who had poor compliance, developed complications. Good compliance was defined by a lifetime plasma free homocystine median < 11 μmol/L. The newborn screened, good compliance group (n = 13) with a mean age of 14.4 years (range 4.4–24.9) had mean full‐scale IQ (FIQ) of 105.8 (range 84–120), while the poorly compliant group (n = 6) with a mean age of 19.9 years (range 13.8–25.5) had a mean FIQ of 80.8 (range 40–103). The control group (n = 10) with mean age of 19.4 years (range 9.7–32.9) years had a mean FIQ of 102 (range 76–116). The two late‐detected patients aged 18.9 and 18.8 years had FIQ of 80 and 102, while the two untreated patients aged 22.4 and 11.7 years had FIQ of 52 and 53, respectively. There was no statistical evidence of significant differences between the compliant, early‐treated individuals and their unaffected siblings (controls) except for the FIQ, which was significantly higher than that of the unaffected siblings (p = 0.0397). These data, despite the relatively small numbers, suggest that early treatment with good biochemical control (lifetime plasma free homocystine median < 11 μmol/L) seems to prevent mental retardation.
Tetrahydrobiopterin‐responsive phenylalanine hydroxylase deficiency in Dutch neonates
Authors: Spaapen L. J. M. , Bakker J. A. , Velter C. , Loots W. , Rubio‐Gonzalbo M. E. , Forget P. P. , Dorland L. , De Koning T. J. , Poll‐The B. T. , Ploos Van Amstel H. K. , Bekhof J. , Blau N. , Duran M.
Published: December 2002

Four neonates with a positive phenylalanine screening test (Phe concentrations between 258 and 1250 μmol/L) were investigated further to differentiate between phenylalanine hydroxylase (PAH) deficiency and variant hyperphenylalaninaemia (HPA) forms. In patients 1 and 2 a tetrahydrobiopterin (BH4) load caused a significant decrease of the plasma Phe levels. A combined phenylalanine/BH4 loading test was performed in patients 2, 3 and 4. In the latter two patients, plasma Phe concentrations completely normalized within 8 h after the BH4 load (20 mg/kg). Basal urinary pterins were normal in all four patients. The activity of dihydropteridine reductase (DHPR) was normal in patients 1, 2 and 3 and 50% of control values in patient 4 (not in the range of DHPR‐deficient patients). In patient 3 a subsequent phenylalanine loading test with concomitant analysis of plasma biopterins revealed a normal increase of biopterin, excluding a BH4 biosynthesis defect. Pterins and neurotransmitter metabolites in CSF of patients 1, 3 and 4 were normal. DNA mutations detected in the PAH gene of patients 1–4 were A313T, and L367fsinsC; V190A and R243X; A300S and A403V; R241C and A403V. The results are suggestive for mutant PAH enzymes with decreased affinity for the cofactor BH4.
PTSD symptoms and partner abuse: Low income women at risk
Authors: Vogel Laura C. M. , Marshall Linda L.
Published: December 2002

Aspects of partner abuse (types, severity, chronicity, treatment of injury, fear, etc.) were addressed with low income community women, half of whom scored above the cutoff on the Crime Related PTSD scale. Using this cutoff, 47% of women who sustained moderate violence were high in CR‐PTSD symptoms. If their partner also raped them, the rate (63%) was similar to women who sustained severe violence (65%) or severe violence and rape (71%). No ethnic differences were found for rates or severity of CR‐PTSD symptoms. A MANCOVA by ethnicity (African Americans, Euro‐Americans, Mexican Americans) and CR‐PTSD symptoms (low vs. high) identified ethnic differences only on total sexual aggression and recent threats of violence. The high symptom group reported more abuse on all measures. Results from the CR‐PTSD and the general lack of ethnic differences support the notion that SES contributes more to women's vulnerability to abuse and stress symptoms than does ethnicity.
Posttraumatic stress disorder in rape victims: Autonomic habituation to auditory stimuli
Authors: Rothbaum Barbara Olasov , Kozak Michael J. , Foa Edna B. , Whitaker Daniel J.
Published: December 2002

Impaired capacity for physiological habituation may contribute to the persistence of PTSD. Habituation ofautonomic responses to auditory tones was examined in 43 women in three groups: 14 adult female rape survivors with chronic PTSD, 11 without PTSD, and a comparison group of 18 who had not been raped. There were no significant differences among the groups in baseline cardiac or electrodermal activity. The PTSD group showed significantly slower electrodermal habituation, as measured by trials to extinction and percentage of nonhabituators, than did the comparison groups. The present study found slower habituation of electrodermal responses for PTSD rape victims to neutral stimuli than for non‐PTSD victims and nonvictims.
Child sexual abuse, peer sexual abuse, and sexual assault in adulthood: A multi‐risk model of revictimization
Authors: Maker Azmaira Hamid , Kemmelmeier Markus , Peterson Christopher
Published: December 2002

This study explored the predictors and consequences of sexual assault occurring after the age of 16 years in a nonclinical sample of women. Child sexual abuse occurring before the age of 16 years was the only predictor of later sexual assault among comorbid risk factors. Peer sexual abuse, number of perpetrators, age at time of sexual abuse, and severity of sexual abuse did not increase the risk for later sexual assault. Adult sexual assault victims showed lower levels of mental health functioning than did survivors of child or peer sexual abuse. We discuss a specificity model of revictimization and the differential effects of child, peer, and adult sexual trauma on the developmental trajectory of sexual violence and psychosocial functioning.
Derivation of the Prior Distribution in Bayesian Analysis from the Principle of Statistical Equivalence
Authors: Lavenda B. H.
Published: December 2002

The distinction between uniform and logarithmic uniform prior distributions is made in terms of the principle of statistical equivalence, consisting of two statistically equivalent experiments, where the variable and parameter of the distribution exchange their roles. The two choices of the prior correspond to two terms in the drift of a diffusion process, and the condition for a stationary solution eliminates the choice of the uniform prior. Parameter randomization gives rise to a new distribution where the parameter of the original distribution is replaced by a ‘hitting point’ value of the variate.
Remaining problems in the management of patients with Gaucher disease
Authors: Erikson A.
Published: December 2002

The history of treatment of Gaucher disease started with splenectomy and continued with bone marrow transplantation, before the recent introduction of enzyme replacement therapy. Although the latter has revolutionized the prognosis of patients, many questions remain to be answered and clinical management problems resolved. These include how to monitor enzyme replacement to determine the optimal dosage, how to treat mild disease, whether intermittent treatment is an option, and the causes of the neurological signs and how to treat them. The pulmonary hypertension problem has also not been resolved, and we need to determine how to treat and monitor bone disease. In addition, the future role of substrate deprivation needs to be determined, and further research is required before gene therapy becomes a potential clinical option. The high cost of enzyme replacement treatment for Gaucher disease remains an important issue.
Renal disease in Fabry patients
Authors: Grünfeld J.‐P. , Lidove O. , Joly D. , Barbey F.
Published: December 2002

Renal dysfunction is a major complication in hemizygous males with Fabry disease. This often results in end‐stage renal failure (ESRF), requiring dialysis or transplantation, on average 10 years after the start of renal impairment. ESRF usually occurs between 40 and 50 years of age, but may occur much earlier. Although progression of renal disease can be rapid, it is variable and may depend on whether there is residual α‐galactosidase enzyme activity and on environmental or genetic factors. Significant renal disease is much less common in women carriers of the disease. However, renal changes do occur, which may progress to ESRF as in male patients.
Characterization of altered myocardial fatty acid metabolism in patients with inherited cardiomyopathy
Authors: Bergmann S. R. , Herrero P. , Sciacca R. , Hartman J. J. , Rubin P. J. , Hickey K. T. , Epstein S. , Kelly D. P.
Published: December 2002

Inherited defects in myocardial long‐chain fatty acid metabolism are increasingly recognized as a cause of cardiomyopathy and sudden death in children. To evaluate whether the phenotypic expression of these genetic diseases could be delineated using positron emission tomography (PET), 11 patients with inherited defects in fatty acid metabolism were evaluated and results were compared with those of 6 nonaffected siblings. Myocardial perfusion, myocardial oxygen consumption (MVO2), and long‐chain fatty acid metabolism were determined noninvasively with PET using quantitative mathematical models. There were no differences in haemodynamics, perfusion, MVO2 or plasma substrate levels between groups. Patients with defects in enzymes of fatty acid β‐oxidation (acyl‐CoA dehydrogenase and 3‐hydroxyacyl‐CoA dehydrogenase deficiencies) n = 5 had diminished myocardial palmitate oxidation compared with healthy siblings (3.2 ± 3.0 vs 13.0 ± 5.6 nmol/g per min, p < 0.03) and a decrease in the percentage of MVO2 accounted for by palmitate (2% ± 3% vs 9% ± 5%), p > 0.04). In these patients, extracted palmitate was shunted into a slow‐turnover compartment (predominantly reflecting esterification to triglycerides) with expansion of palmitate in that pool (185 ± 246 compared with 27 ± 67 nmol/g in healthy siblings, p < 0.02). In contrast, myocardium of patients with carnitine deficiency (n = 6 (all on oral carnitine therapy) had normal palmitate extraction but expansion of the interstitial/cytosolic fatty acid pool (617 ± 399 vs 261 ± 73 nmol/g in healthy siblings, p < 0.04), suggesting different mechanisms for handling upstream fatty acyl intermediates. Thus, PET can be used to noninvasively assess abnormal myocardial handling of fatty acids in patients with inherited defects of metabolism. This approach should be useful in the assessment of altered myocardial fatty acid metabolism associated with cardiomyopathy as well as for evaluating the efficacy of therapeutic interventions in affected patients.
Prospects in the Treatment of Rare Diseases 2nd International Conference Trieste, Italy, 23–26 May 2001
Authors: Bembi Bruno
Published: December 2002

ABSTRACTS OF PRESENTED PAPERS

POSTER ABSTRACTS
The relationship of sleep quality and posttraumatic stress to potential sleep disorders in sexual assault survivors with nightmares, insomnia, and PTSD
Authors: Krakow Barry , Germain Anne , Warner Teddy D. , Schrader Ron , Koss Mary , Hollifield Michael , Tandberg Dan , Melendrez Dominic , Johnston Lisa
Published: December 2002

Sleep quality and posttraumatic stress disorder (PTSD) were examined in 151 sexual assault survivors, 77% of whom had previously reported symptoms of sleep‐disordered breathing (SDB) or sleep movement disorders (SMD) or both. Participants completed the Pittsburgh Sleep Quality Index (PSQI) and the Posttraumatic Stress Scale (PSS). High PSQI scores reflected extremely poor sleep quality and correlated with PSS scores. PSQI scores were greater in participants with potential SDB or SMD or both. PSQI or PSS scores coupled with body‐mass index and use of antidepressants or anxiolytics predicted potential sleep disorders. The relationship between sleep and posttraumatic stress appears to be more complex than can be explained by the current PTSD paradigm; and, sleep breathing and sleep movement disorders may be associated with this complexity.
Relationships among alcohol use, hyperarousal, and marital abuse and violence in Vietnam veterans
Authors: Savarese Vincent W. , Suvak Michael K. , King Lynda A. , King Daniel W.
Published: December 2002

Alcohol use (frequency and quantity) and the hyperarousal feature of PTSD were examined in relation to male‐perpetrated marital abuse and violence using data from 376 couples who participated in the National Vietnam Veterans Readjustment Study. Veteran's self‐reported hyperarousal was significantly associated with partner's report of physical violence and psychological abuse toward her. Differential relationships were found between veteran's self‐reported drinking frequency and drinking quantity and the outcomes; of the two components, only the average quantity consumed per occasion was independently related to husband‐to‐wife violence. Moreover, a complex interaction emerged between hyperarousal and the two dimensions of alcohol consumption in predicting violence, with the relationship between hyperarousal and violence varying as a function of both drinking frequency and drinking quantity.
The childhood trauma questionnaire in a community sample: Psychometric properties and normative data
Authors: Scher Christine D. , Stein Murray B. , Asmundson Gordon J. G. , McCreary Donald R. , Forde David R.
Published: December 2002

Interpretation of research on the prevalence and sequelae of childhood trauma has been hindered by the use of assessment instruments with unknown psychometric properties. Thus, we examined the psychometric properties of a new childhood trauma measure, the Childhood Trauma Questionnaire (CTQ). The CTQ has demonstrated strong psychometric properties in clinical samples; limited information exists on its psychometric properties in community samples. Therefore, we explored the factor structure and reliability of the CTQ in a community sample and calculated normative data. Consistent with previous literature, a 5‐factor model best described the CTQ, with a hierarchical model also providing excellent fit. Additionally, the CTQ demonstrated acceptable internal consistency. Overall, our findings suggest that the CTQ is appropriate for use in a community sample.
Psychophysiological reactivity in female sexual abuse survivors
Authors: McDonagh‐Coyle Annmarie , McHugo Gregory J. , Friedman Matthew J. , Schnurr Paula P. , Zayfert Claudia , Descamps Monica
Published: December 2002

This study examined psychophysiological reactivity in 37 female childhood sexual abuse (CSA) survivors. After assessment of posttraumatic stress disorder (PTSD), psychiatric comorbidity, and trauma history, we conducted a psychophysiological assessment of forehead muscle tension, electrodermal activity, and heart rate during a mental arithmetic task and 4 script‐driven imagery tasks (neutral, consensual sex, pleasant, and trauma). PTSD symptom severity correlated positively with psychophysiologic changes and negative emotions during the trauma imagery task. During mental arithmetic, PTSD symptom severity correlated negatively with autonomic changes and positively with negative emotions. These results extend earlier PTSD research showing trauma‐specific increased psychophysiological reactivity related to CSA in women with PTSD. They further suggest a negative association between PTSD severity and autonomic reactions to mental arithmetic.
Alternative Oxidase and Uncoupling Protein: Thermogenesis Versus Cell Energy Balance
Authors: Jarmuszkiewicz Wieslawa , Sluse-Goffart Claudine M. , Vercesi Anibal E. , Sluse Francis E.
Published: December 2002

The physiological role of an alternative oxidase and an uncoupling protein in plant and protists is discussed in terms of thermogenesis and energy metabolism balance in the cell. It is concluded that thermogenesis is restricted not only by a lower-limit size but also by a kinetically-limited stimulation of the mitochondrial respiratory chain.
Mechanism of Thyroid-Hormone Regulated Expression of the SERCA Genes in Skeletal Muscle: Implications for Thermogenesis
Authors: Simonides Walter S. , Thelen Marc H. M. , van der Linden C. Gerard , Muller Alice , van Hardeveld Cornelis
Published: December 2002

Thyroid hormone increases the Ca2+-ATPase activity of the sarcoplasmic reticulum (SR) in skeletal muscle, thereby increasing the energy-turnover associated with Ca2+-cycling during contraction and rest. The fast-muscle isoform of the Ca2+-ATPase (SERCA1) and the slow-muscle isoform (SERCA2a), are encoded by two genes that are transcriptionally regulated by T3. The SERCA1 isoform can be expressed to considerably higher levels than the SERCA2a isoform. The stimulation of transcription of the SERCA1 gene by T3 is mediated by two thyroid hormone response elements, located in the promoter of this gene. The intracellular [Ca2+] can modulate the effect of T3. The increase in SR Ca2+-ATPase activity seen when T3-levels rise above normal, results from the induction of SERCA1 expression in slow muscle fibers. Concomitant high levels of Ca2+-ATPase activity are associated with down-regulation of SERCA2a expression in these fibers. The observed T3-dependent increase in SERCA1 expression and associated Ca2+-ATPase activity will increase the overall metabolic rate of the organism significantly under normal conditions, because of the high average level of contractile activity of slow fibers. Given the rise in serum T3-levels during prolonged cold exposure, these data suggest that fiber-specific stimulation of SERCA1 expression contributes to the thermogenic response in non-shivering thermogenesis. This mechanism may be particularly relevant in larger mammals, which have a relatively high percentage of slow fibers in skeletal muscle, and which need to rely on tissues other than brown fat for the generation of extra heat.
Liver Cancer Detection System Based on the Analysis of Digitized Color Images of Tissue Samples Obtained Using Needle Biopsy
Authors: Sammouda Mohamed , Sammouda Rachid , Niki Noboru , Mukai Kiyoshi
Published: December 2002

In this article, the authors propose a method for automatic diagnosis of liver cancer based on analysis of digitized color images of liver tissue obtained by needle biopsy. The approach is a combination of an unsupervised segmentation algorithm, using a modified artificial Hopfield neural network (HNN), and an analysis algorithm based on image quantization. The segmentation algorithm is superior to HNN in the sense that it converges to a nearby global minimum rather than a local one in a prespecified time. Furthermore, as the segmentation of color images does not only depend on the segmentation algorithm but also on the color space representation, and in order to choose the best segmentation result, segmentation was performed with HNN and using components of the raw image with respect to each of the RGB, HLS, and HSV color spaces. Then, the segmented image was labeled based on chromaticity features and histogram analysis of the RGB color space components of the raw image. The image regions were then classified into normal and cancerous using diagnostic rules formulated based on those used by experienced pathologists in the clinic. The proposed method provides quantitative satisfactory results in diagnosing a liver pathological image set of 17 cases.
Information Visualization for Advanced Vehicle Displays
Authors: Marcus Aaron
Published: December 2002

Almost all vehicles soon will acquire advanced user interfaces with specialized information visualization. This revolution poses significant human factors issues, but also new challenges of appeal, cultural orientation, and branding. This article describes considerations beyond traditional human factors and shows conceptual visual prototypes that explore new approaches to vehicle information displays.
DEViD: A Media Design and Software Ergonomics Integrating Visualization for Document Retrieval
Authors: Eibl Maximilian
Published: December 2002

Human Computer Interaction (HCI) and Media Design are two separated schools that have few common goals in the area of designing user interfaces. Whereas HCI places the accent on the most effective operation, media design emphasizes the aesthetic aspect. Thus, the design of a user interface offers a choice between the effective ugliness of ergonomics and the hard-to-use elegance of media design. One example of the successful integration of both schools is the DEViD (media design and software ergonomics integrating visualization for document retrieval systems) visualization described in this article. DEViD supports users in searching databases and integrates Boolean retrieval as well as probabilistic ranking and vague retrieval within one single interface. DEViD was created through cooperation between HCI and media design. Participants in this cooperation were the Social Science Information Center, Bonn (Germany), the University of Koblenz (Germany) and the School of Design, Offenbach (Germany).
Genes for the cytoskeletal protein tubulin in the bacterial genus
Prosthecobacter
Authors: Jenkins Cheryl , Samudrala Ram , Anderson Iain , Hedlund Brian P. , Petroni Giulio , Michailova Natasha , Pinel Nicolas , Overbeek Ross , Rosati Giovanna , Staley James T.
Published: December 2002

Tubulins, the protein constituents of the microtubule cytoskeleton, are present in all known eukaryotes but have never been found in the Bacteria or Archaea. Here we report the presence of two tubulin-like genes [bacterial tubulin a (
btuba
) and bacterial tubulin b (
btubb
)] in bacteria of the genus
Prosthecobacter
(Division Verrucomicrobia). In this study, we investigated the organization and expression of these genes and conducted a comparative analysis of the bacterial and eukaryotic protein sequences, focusing on their phylogeny and 3D structures. The
btuba
and
btubb
genes are arranged as adjacent loci within the genome along with a kinesin light chain gene homolog. RT-PCR experiments indicate that these three genes are cotranscribed, and a probable promoter was identified upstream of
btuba
. On the basis of comparative modeling data, we predict that the
Prosthecobacter
tubulins are monomeric, unlike eukaryotic α and β tubulins, which form dimers and are therefore unlikely to form microtubule-like structures. Phylogenetic analyses indicate that the
Prosthecobacter
tubulins are quite divergent and do not support recent horizontal transfer of the genes from a eukaryote. The discovery of genes for tubulin in a bacterial genus may offer new insights into the evolution of the cytoskeleton.
Stomatocyte–discocyte–echinocyte sequence of the human red blood cell: Evidence for the bilayer– couple hypothesis from membrane mechanics
Authors: Lim H. W. Gerald , Wortis Michael , Mukhopadhyay Ranjan
Published: December 2002

Red-cell shape is encoded in the mechanical properties of the membrane. The plasma membrane contributes bending rigidity; the protein-based membrane skeleton contributes stretch and shear elasticity. When both effects are included, membrane mechanics can reproduce in detail the full stomatocyte–discocyte–echinocyte sequence by variation of a single parameter related to the bilayer couple originally introduced by Sheetz and Singer [Sheetz, M. P. & Singer, S. J. (1974)
Proc. Natl. Acad. Sci. USA
71, 4457–4461].
Low intracellular zinc induces oxidative DNA damage, disrupts p53, NFκB, and AP1 DNA binding, and affects DNA repair in a rat glioma cell line
Authors: Ho Emily , Ames Bruce N.
Published: December 2002

Approximately 10% of the U.S. population ingests <50% of the current recommended daily allowance for zinc. We investigate the effect of zinc deficiency on DNA damage, expression of DNA-repair enzymes, and downstream signaling events in a cell-culture model. Low zinc inhibited cell growth of rat glioma C6 cells and increased oxidative stress. Low intracellular zinc increased DNA single-strand breaks (comet assay). Zinc-deficient C6 cells also exhibited an increase in the expression of the zinc-containing DNA-repair proteins p53 and apurinic endonuclease (APE). Repletion with zinc restored cell growth and reversed DNA damage. APE is a multifunctional protein that not only repairs DNA but also controls DNA-binding activity of many transcription factors that may be involved in cancer progression. The ability of the transcription factors p53, nuclear factor κB, and activator protein 1 (AP1) to bind to consensus DNA sequences was decreased markedly with zinc deficiency, as assayed by electrophoretic mobility-shift assays. Thus, low intracellular zinc status causes oxidative DNA damage and induces DNA-repair protein expression, but binding of p53 and important downstream signals leading to proper DNA repair are lost without zinc.
Mechanism of regulation of phosphate dissociation from actomyosin-ADP-Pi by thin filament proteins
Authors: Heeley David H. , Belknap Betty , White Howard D.
Published: December 2002

Regulation by calcium and myosin-S1 of the acceleration of the rate of phosphate release from myosin-ADP-inorganic phosphate (M-ADP-Pi) by the thin filament actin-tropomyosin (Tm)-troponin (Tn), was measured directly by using double mixing stopped-flow experiments with fluorescent phosphate binding protein. At low calcium and without rigor myosin-S1, saturating concentrations of thin filaments accelerate the rate of phosphate dissociation from M-ADP-Pi 8-fold, from 0.08 to 0.64 s
−1
. If either myosin-S1 or calcium is bound to the thin filaments, phosphate release is a biphasic process in which the fast phase is the dissociation of Pi from actoTmTnM-ADP-Pi and the slow phase is limited by the hydrolysis of actoTmTnM-ATP to actoTmTnM-ADP-Pi. The maximum accelerations of the fast components by saturating thin filaments (relative to M-ADP-Pi alone) are: ≈200-fold, 16 s
−1
(calcium only); ≈400-fold, 30 s
−1
(EGTA and rigor S1); and ≈1,000-fold, 75 s
−1
(calcium and rigor S1). The maximum rate of phosphate dissociation attained with S1 and calcium bound to the thin filament is the same as for unregulated actin. Regulation of the rate of phosphate dissociation by calcium and myosin-S1 is partially explained by the model of Geeves [McKillop, D. F. and Geeves, M. A. (1993)
Biophys. J.
65, 693–701], in which calcium and rigor S1 perturb the equilibria among three states of the thin filament (blocked, closed, and open). However, a quantitative description of the regulatory mechanism requires acceleration by calcium of an additional step of the mechanism, either phosphate dissociation or a preceding conformational change.
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic
Escherichia coli
Authors: Welch R. A. , Burland V. , Plunkett G. , Redford P. , Roesch P. , Rasko D. , Buckles E. L. , Liou S.-R. , Boutin A. , Hackett J. , Stroud D. , Mayhew G. F. , Rose D. J. , Zhou S. , Schwartz D. C. , Perna N. T. , Mobley H. L. T. , Donnenberg M. S. , Blattner F. R.
Published: December 2002

We present the complete genome sequence of uropathogenic
Escherichia coli
, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic
E. coli
EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic
E. coli
. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic
E. coli
strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic
E. coli
arose independently from multiple clonal lineages. The different
E. coli
pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.
Spin-dependent mechanism for diatomic ligand binding to heme
Authors: Franzen Stefan
Published: December 2002

The nature of diatomic ligand recombination in heme proteins is elucidated by using a Landau–Zener model for the electronic coupling in the recombination rate constant. The model is developed by means of explicit potential energy surfaces calculated by using density functional theory (DFT). The interaction of all possible spin states of the three common diatomic ligands, CO, NO, and O
2
, and high-spin heme iron is compared. The electronic coupling, rebinding barrier, and Landau–Zener force terms can be obtained and used to demonstrate significant differences among the ligands. In particular the intermediate spin states of NO (
S
= 3/2) and O
2
(
S
= 1) are shown to be bound states. Rapid recombination occurs from these bound states in agreement with experimental data. The slower phases of O
2
recombination can be explained by the presence of two higher spin states,
S
= 2 and
S
= 3, which have a small and relatively large barrier to ligand recombination, respectively. By contrast, the intermediate spin state for CO is not a bound state, and the only recombination pathway for CO involves direct recombination from the
S
= 2 state. This process is significantly slower according to the Landau–Zener model. Quantitative estimates of the parameters used in the rate constants provide a complete description that explains rebinding rates that range from femtoseconds to milliseconds at ambient temperature.
Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril
Authors: Jaroniec Christopher P. , MacPhee Cait E. , Astrof Nathan S. , Dobson Christopher M. , Griffin Robert G.
Published: December 2002

The molecular conformation of peptide fragment 105–115 of transthyretin, TTR(105–115), previously shown to form amyloid fibrils
in vitro
, has been determined by magic-angle spinning solid-state NMR spectroscopy.
13
C and
15
N linewidth measurements indicate that TTR(105–115) forms a highly ordered structure with each amino acid in a unique environment. 2D
13
C-
13
C and
15
N-
13
C-
13
C chemical shift correlation experiments, performed on three fibril samples uniformly
13
C,
15
N-labeled in consecutive stretches of 4 aa, allowed the complete sequence-specific backbone and side-chain
13
C and
15
N resonance assignments to be obtained for residues 105–114. Analysis of the
15
N,
13
CO,
13
C
α
, and
13
C
β
chemical shifts allowed quantitative predictions to be made for the backbone torsion angles φ and ψ. Furthermore, four backbone
13
C–
15
N distances were determined in two selectively
13
C,
15
N-labeled fibril samples by using rotational-echo double-resonance NMR. The results show that TTR(105–115) adopts an extended β-strand conformation that is similar to that found in the native protein except for substantial differences in the vicinity of the proline residue.
More antibody with less antigen: Can immunogenicity of attenuated live virus vaccines be improved?
Authors: Bukreyev Alexander , Skiadopoulos Mario H. , McAuliffe Josephine , Murphy Brian R. , Collins Peter L. , Schmidt Alexander C.
Published: December 2002

New or improved vaccines against viruses such as influenza, parainfluenza types 1–3, measles, dengue, and respiratory syncytial virus would prevent an enormous burden of morbidity and mortality. Vaccines or vaccine candidates exist against these viral diseases, but all could potentially be improved if the immunogenicity of the vaccine could be enhanced. We found that the immunogenicity in primates of a live-attenuated vaccine candidate for parainfluenza virus type 3, an enveloped RNA virus that is an important etiologic agent of pediatric respiratory tract disease, could be enhanced by expression of granulocyte–macrophage colony-stimulating factor (GM-CSF) from an extra gene inserted into the genome of a cDNA-derived virus. Expression of GM-CSF by the live attenuated recombinant virus did not
per se
affect the level of pulmonary viral replication in rhesus monkeys after topical administration, which was 40-fold lower than that of WT parainfluenza virus type 3. Despite that, the expressed extra gene augmented the virus-specific serum antibody response to a level that was (
i
) 3- to 6-fold higher than that induced by the same virus with an unrelated RNA insert of equal length and (
ii
) equal to the response induced by nonattenuated WT virus. In addition, topical immunization with the attenuated virus expressing GM-CSF induced a greater number of virus-specific IFN-γ-secreting T lymphocytes in the peripheral blood of monkeys than did immunization with the control virus bearing an unrelated RNA insert. These findings show that the immunogenicity of a live-attenuated vaccine virus in primates can be enhanced without increasing the level of virus replication. Thus, it might be possible to develop live-attenuated vaccines that are as immunogenic as parental WT virus or, possibly, even more so.
Alternate pathways involving Sgs1/Top3, Mus81/ Mms4, and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication
Authors: Fabre Francis , Chan Allan , Heyer Wolf-Dietrich , Gangloff Serge
Published: December 2002

Toxic recombination events are detected in vegetative
Saccharomyces cerevisiae
cells through negative growth interactions between certain combinations of mutations. For example, mutations affecting both the Srs2 and Sgs1 helicases result in extremely poor growth, a phenotype suppressed by mutations in genes that govern early stages of recombination. Here, we identify a similar interaction involving double mutations affecting Sgs1 or Top3 and Mus81 or Mms4. We also find that the primary DNA structures that initiate these toxic recombination events cannot be double-strand breaks and thus are likely to be single-stranded DNA. We interpret our results in the context of the idea that replication stalling leaves single-stranded DNA, which can then be processed by two competing mechanisms: recombination and nonrecombination gap-filling. Functions involved in preventing toxic recombination would either avoid replicative defects or act on recombination intermediates. Our results suggest that Srs2 channels recombination intermediates back into the gap-filling route, whereas Sgs1/Top3 and Mus81/Mms4 are involved in recombination and/or in replication to allow replication restart.
A unique molecular chaperone Cosmc required for activity of the mammalian core 1 β3-galactosyltransferase
Authors: Ju Tongzhong , Cummings Richard D.
Published: December 2002

Human core 1 β3-galactosyltransferase (C1β3Gal-T) generates the core 1 O-glycan Galβ1-3GalNAcα1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in animal glycoproteins. We report here that C1β3Gal-T activity requires expression of a molecular chaperone designated Cosmc (core 1 β3-Gal-T-specificmolecularchaperone). The humanCosmcgene is X-linked (Xq23), and its cDNA predicts a 318-aa transmembrane protein (≈36.4 kDa) with type II membrane topology. The human lymphoblastoid T cell line Jurkat, which lacks C1β3Gal-T activity and expresses the Tn antigen GalNAcα1-Ser/Thr, contains a normal gene and mRNA encoding C1β3Gal-T, but contains a mutatedCosmcwith a deletion introducing a premature stop codon. Expression of Cosmc cDNA in Jurkat cells restored C1β3Gal-T activity and T antigen expression. Without Cosmc, the C1β3Gal-T is targeted to proteasomes. Expression of active C1β3Gal-T in Hi-5 insect cells requires coexpression of Cosmc. Overexpression of active C1β3Gal-T in mammalian cell lines also requires coexpression of Cosmc, indicating that endogenous Cosmc may be limiting. A small portion of C1β3Gal-T copurifies with Cosmc from cell extracts, demonstrating physical association of the proteins. These results indicate that Cosmc acts as a specific molecular chaperone in assisting the folding/stability of C1β3Gal-T. The identification of Cosmc, a uniquely specific molecular chaperone required for a glycosyltransferase expression in mammalian cells, may shed light on the molecular basis of acquired human diseases involving altered O-glycosylation, such as IgA nephropathy, Tn syndrome, Henoch-Schönlein purpura, and malignant transformation, all of which are associated with a deficiency of C1β3Gal-T activity.
Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA
Authors: Mori Tetsuya , Saveliev Sergei V. , Xu Yao , Stafford Walter F. , Cox Michael M. , Inman Ross B. , Johnson Carl H.
Published: December 2002

KaiC from
Synechococcus elongatus
PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in the circadian clock mechanism that regulates global changes in gene expression patterns.
Reversal of DNA alkylation damage by two human dioxygenases
Authors: Duncan Tod , Trewick Sarah C. , Koivisto Pertti , Bates Paul A. , Lindahl Tomas , Sedgwick Barbara
Published: December 2002

The
Escherichia coli
AlkB protein protects against the cytotoxicity of methylating agents by repair of the DNA lesions 1-methyladenine and 3-methylcytosine, which are generated in single-stranded stretches of DNA. AlkB is an α-ketoglutarate- and Fe(II)-dependent dioxygenase that oxidizes the relevant methyl groups and releases them as formaldehyde. Here, we identify two human AlkB homologs, ABH2 and ABH3, by sequence and fold similarity, functional assays, and complementation of the
E. coli alkB
mutant phenotype. The levels of their mRNAs do not appear to correlate with cell proliferation but tissue distributions are different. Both enzymes remove 1-methyladenine and 3-methylcytosine from methylated polynucleotides in an α-ketoglutarate-dependent reaction, and act by direct damage reversal with the regeneration of the unsubstituted bases. AlkB, ABH2, and ABH3 can also repair 1-ethyladenine residues in DNA with the release of acetaldehyde.
An epigenetic mouse model for molecular and behavioral neuropathologies related to schizophrenia vulnerability
Authors: Tremolizzo L. , Carboni G. , Ruzicka W. B. , Mitchell C. P. , Sugaya I. , Tueting P. , Sharma R. , Grayson D. R. , Costa E. , Guidotti A.
Published: December 2002

Reelin and glutamic acid decarboxylase (GAD)
67
expressed by cortical γ-aminobutyric acid-ergic interneurons are down-regulated in schizophrenia. Because epidemiological studies of schizophrenia fail to support candidate gene haploinsufficiency of Mendelian origin, we hypothesize that epigenetic mechanisms (i.e., cytosine hypermethylation of CpG islands present in the promoter of these genes) may be responsible for this down-regulation. Protracted
l
-methionine (6.6 mmol/kg for 15 days, twice a day) treatment in mice elicited in brain an increase of
S
-adenosyl-homocysteine, the processing product of the methyl donor
S
-adenosyl-methionine, and a marked decrease of reelin and GAD
67
mRNAs in both WT and heterozygous
reeler
mice. This effect of
l
-methionine was associated with an increase in the number of methylated cytosines in the CpG island of the reelin promoter region. This effect was not observed for GAD
65
or neuronal-specific enolase and was not replicated by glycine doses 2-fold greater than those of
l
-methionine. Prepulse inhibition of startle declined at a faster rate as the prepulse/startle interval increased in mice receiving
l
-methionine. Valproic acid (2 mmol/kg for 15 days, twice a day) reverted
l
-methionine-induced down-regulation of reelin and GAD
67
in both WT and heterozygous
reeler
mice, suggesting an epigenetic action through the inhibition of histone deacetylases. The same dose of valproate increased acetylation of histone H3 in mouse brain nearly 4-fold. This epigenetic mouse model may be useful in evaluating drug efficacy on schizophrenia vulnerability. Hence the inhibition of histone deacetylases could represent a pharmacological intervention mitigating epigenetically induced vulnerability to schizophrenia in individuals at risk.
The structure of
Escherichia coli
BtuF and binding to its cognate ATP binding cassette transporter
Authors: Borths Elizabeth L. , Locher Kaspar P. , Lee Allen T. , Rees Douglas C.
Published: December 2002

Bacterial binding protein-dependent ATP binding cassette (ABC) transporters facilitate uptake of essential nutrients. The crystal structure of
Escherichia coli
BtuF, the protein that binds vitamin B
12
and delivers it to the periplasmic surface of the ABC transporter BtuCD, reveals a bi-lobed fold resembling that of the ferrichrome binding protein FhuD. B
12
is bound in the “base-on” conformation in a deep cleft formed at the interface between the two lobes of BtuF. A stable complex between BtuF and BtuCD (with the stoichiometry BtuC
2
D
2
F) is demonstrated to form
in vitro
and was modeled using the individual crystal structures. Two surface glutamates from BtuF may interact with arginine residues on the periplasmic surface of the BtuCD transporter. These glutamate and arginine residues are conserved among binding proteins and ABC transporters mediating iron and B
12
uptake, suggesting that they may have a role in docking and the transmission of conformational changes.
A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR
Authors: Petkova Aneta T. , Ishii Yoshitaka , Balbach John J. , Antzutkin Oleg N. , Leapman Richard D. , Delaglio Frank , Tycko Robert
Published: December 2002

We present a structural model for amyloid fibrils formed by the 40-residue β-amyloid peptide associated with Alzheimer's disease (Aβ
1–40
), based on a set of experimental constraints from solid state NMR spectroscopy. The model additionally incorporates the cross-β structural motif established by x-ray fiber diffraction and satisfies constraints on Aβ
1–40
fibril dimensions and mass-per-length determined from electron microscopy. Approximately the first 10 residues of Aβ
1–40
are structurally disordered in the fibrils. Residues 12–24 and 30–40 adopt β-strand conformations and form parallel β-sheets through intermolecular hydrogen bonding. Residues 25–29 contain a bend of the peptide backbone that brings the two β-sheets in contact through sidechain-sidechain interactions. A single cross-β unit is then a double-layered β-sheet structure with a hydrophobic core and one hydrophobic face. The only charged sidechains in the core are those of D23 and K28, which form salt bridges. Fibrils with minimum mass-per-length and diameter consist of two cross-β units with their hydrophobic faces juxtaposed.
Longitudinal pattern of basilar membrane vibration in the sensitive cochlea
Authors: Ren Tianying
Published: December 2002

In the normal mammalian ear, sound vibrates the eardrum, causing the tiny bones of the middle ear to vibrate, transferring the vibration to the inner ear fluids. The vibration propagates from the base of the cochlea to its apex along the cochlear partition. As essential as this concept is to the theory of hearing, the waveform of cochlear partition vibration has yet to be measured
in vivo
. Here I report a “snapshot” (the instantaneous waveform of cochlear partition vibration) measured in the basal turn of the sensitive gerbil cochlea using a scanning laser interferometer. For 16-kHz tones, the phase delay is up to 6π radians over the observed cochlear length (<1,000 μm), and instantaneous waveforms show sound propagation along the cochlear partition, supporting the existence of the cochlear traveling wave. The detectable basilar membrane response to a low-level 16-kHz tone occurs over a very restricted (≈600 μm) range. The observed vibration shows compressive nonlinear growth, a shorter wavelength, and a slower propagation velocity along the cochlear length than previously reported. Data obtained at different frequencies show the relationship between the longitudinal pattern and frequency tuning, demonstrating that the observed localized traveling wave in this study is indeed the spatial representation of the sharp tuning observed in the frequency domain.
Alternate surfaces of transcriptional coregulator GRIP1 function in different glucocorticoid receptor activation and repression contexts
Authors: Rogatsky Inez , Luecke Hans F. , Leitman Dale C. , Yamamoto Keith R.
Published: December 2002

Members of the mammalian p160 family, such as GRIP1, are known as glucocorticoid receptor (GR) coactivators; at certain glucocorticoid response elements (GREs), however, GRIP1 acts as a GR corepressor. We characterized functional interactions of GR and GRIP1 in a repression complex where GR tethers to DNA-bound activator protein-1 (AP-1), as at the human collagenase-3 gene, and tested whether the identified interactions were similar or different at other response elements. At the AP-1 tethering GRE, we mapped the GRIP1 corepressor activity to a domain distinct from the two known GRIP1 activation domains; it exhibited intrinsic GR-independent repression potential when recruited to DNA via Gal4 DNA-binding domain. Interestingly, neither the domain nor the activity was detected in the other two p160 family members, SRC1 and RAC3. The same GRIP1 corepression domain was required for GR-mediated repression at the nuclear factor-κB (NF-κB) tethering GRE of the human IL-8 gene. In contrast, at the osteocalcin gene GRE, where GR represses transcription by binding to a DNA site overlapping the TATA box, both GRIP1 and SRC1 corepressed, and the GRIP1-specific repression domain was dispensable. Thus, in a single cell type, GR and GRIP1 conferred one mode of activation and two modes of repression by selectively engaging distinct surfaces of GRIP1 in a response element-specific manner.