bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structures of RsbQ, a stress‐response regulator in Bacillus subtilis
Authors: Kaneko Tomonori , Tanaka Nobuo , Kumasaka Takashi 
Published: January 2005

AbstractGrowth‐limiting stresses in bacteria induce the general stress response to protect the cells against future stresses. Energy stress caused by starvation conditions in Bacillus subtilis is transmitted to the σB transcription factor by stress‐response regulators. RsbP, a positive regulator, is a phosphatase containing a PAS (Per‐ARNT‐Sim) domain and requires catalytic function of a putative α/β hydrolase, RsbQ, to be activated. These two proteins have been found to interact with each other. We determined the crystal structures of RsbQ in native and inhibitor‐bound forms to investigate why RsbP requires RsbQ. These structures confirm that RsbQ belongs to the α/β hydrolase superfamily. Since the catalytic triad is buried inside the molecule due to the closed conformation, the active site is constructed as a hydrophobic cavity that is nearly isolated from the solvent. This suggests that RsbQ has specificity for a hydrophobic small compound rather than a macromolecule such as RsbP. Moreover, structural comparison with other α/β hydrolases demonstrates that a unique loop region of RsbQ is a likely candidate for the interaction site with RsbP, and the interaction might be responsible for product release by operating the hydrophobic gate equipped between the cavity and the solvent. Our results support the possibility that RsbQ provides a cofactor molecule for the mature functionality of RsbP.
Myristoyl moiety of HIV Nef is involved in regulation of the interaction with calmodulin in vivo
Authors: Matsubara Mamoru , Jing Tao , Kawamura Kumi , Shimojo Naoshi , Titani Koiti , Hashimoto Keiichiro , Hayashi Nobuhiro 
Published: January 2005

AbstractHuman immunodeficiency virus Nef is a myristoylated protein expressed early in infection by HIV. In addition to the well known down‐regulation of the cell surface receptors CD4 and MHCI, Nef is able to alter T‐cell signaling pathways. The ability to alter the cellular signaling pathways suggests that Nef can associate with signaling proteins. In the present report, we show that Nef can interact with calmodulin, the major intracellular receptor for calcium. Coimmunoprecipitation analyses with lysates from the NIH3T3 cell line constitutively expressing the native HIV‐1 Nef protein revealed the presence of a stable Nef‐calmodulin complex. When lysates from NIH3T3 cells were incubated with calmodulin‐agarose beads in the presence of CaCl2 or EGTA, calcium ion drastically enhanced the interaction between Nef and calmodulin, suggesting that the binding is under the influence of Ca2+ signaling. Glutathione S‐transferase‐Nef fusion protein bound directly to calmodulin with high affinity. Using synthetic peptides based on the N‐terminal sequence of Nef, we determined that within a 20‐amino‐acid N‐terminal basic domain was sufficient for calmodulin binding. Furthermore, the myristoylated peptide bound to calmodulin with higher affinity than nonmyris‐toylated form. Thus, the N‐terminal myristoylation domain of Nef plays an important role in interacting with calmodulin. This domain is highly conserved in several HIV‐1 Nef variants and resembles the N‐terminal domain of NAP‐22/CAP23, a myristoylated calmodulin‐binder. These results for the interaction between HIV Nef and calmodulin in the cells suggested that the Nef might interfere with intracellular Ca2+ signaling through calmodulin‐mediated interactions in infected cells.
Comparative study of otolith organs between two species of upside‐down swimming catfish Synodontis nigriventris showing converse swimming postures
Authors: Ohnishi Ken , Ogawa Yoichi , Takahashi Akihisa , Yamashita Masayuki , Ohnishi Takeo 
Published: January 2005

AbstractTo clarify whether the unique postural control of the upside‐down swimming catfish (Synodontis nigriventris, family Mochokidae) is related to the histological characteristics of the otolith organs, we performed light microscopic observation of the utricle, the saccule and the lagena. The histological aspects of the otolith organs were compared between S. nigriventris and Synodontis multipunctatus, which belong to the same genus. S. multipunctatus usually shows upside‐up swimming posture except for feeding behaviour near water surface. As controls, we additionally used a miniature catfish, Corydoras paleatus and goldfish, Carassius auratus, which shows upside‐up swimming posture. We concluded that the structural aspects of the otolith organs did not cause the unique postural control of S. nigriventris. Light microscopic observation clarified the following aspects: (1) The utricle of S. nigriventris was located at the anterior region of the otocyst and under the semicircular canals, and the saccule and the lagena were located at the posteroventral region of the otocyst like those of S. multipunctatus and the other two fishes. (2) The hair cells of the utricle were arranged on the horizontal plane of the fishes with a variation in cell size at the ventral and ventrolateral sites in S. nigriventris, S. multipunctatus and the other two fishes. (3) The hair cells of the saccule and lagena of S. nigriventris, S. multipunctatus and C. auratus presented perpendicular to the horizontal plane of the fish. (4) Region‐specific differences in the size and shape of the hair cells of S. nigriventris were observed along the three‐dimensional axes of the otolith organs like those of S. multipunctatus and the other two fishes. It is unlikely that the unique postural control of upside‐down catfish is related to the localization of the utricle, the saccule and the lagena and the distribution of the different types of hair cell of the otolith organs. Furthermore, the distribution of the hair cells suggests that the otolith organs in S. nigriventris can detect three‐dimensional postural changes like the organs of other fishes showing generally observed upside‐up swimming posture.
The use of patient diaries in an intensive care unit
Authors: Combe Denise 
Published: January 2005

Summary• Many patients experience posttraumatic stress disorder following a stay in intensive care; this can be due to a lack of recall of their stay• Retrospective patient diaries (n = 8) with follow‐up have been used to try and help patients’ recovery but have been found to be impersonal• Prospective diaries (n = 35) were implemented and trialled with follow‐up at 2, 6 and 12 months postdischarge• Patients’ and relatives’ initial feedback regarding diaries is extremely positive. Benefits included better understanding of the events of the critical illness, helping with more realistic goal setting during the recovery period, improving communication within families through discussion of the diary and providing a source of comfort for the bereaved• More formal audit of these diaries is required and is currently being undertaken
Relevance of post‐methionine homocysteine and lipoprotein (a) in evaluating the cardiovascular risk in young CAD patients
Authors: Marcucci R. , Brunelli T. , Fedi S. , Pepe G. , Giusti B. , Gori A. M. , Prisco D. , Falai M. , Margheri M. , Abbate R. , Gensini G. F. 
Published: January 2005

AbstractBackground  Aims of our study were to evaluate the prevalence of high lipoprotein (a) [Lp(a)] and homocysteine levels – both in the fasting state (FHcy) and post‐methionine (PMHcy) – in young coronary artery disease (CAD) patients, and to investigate the role of genetic and environmental factors for hyperhomocysteinaemia.Materials and methods  We studied 140 patients with angiographically documented CAD (24 women ≤ 55 years and 116 men ≤ 50 years) and 140 healthy subjects as controls.Results  Both FHcy [13·2 (5·4–45·8) vs. 9·0 (5·1–24) µmol L−1); P < 0·0001] and PMHcy [(39·4 (9·0–66·4) vs. 25·2 (16·4–33·9); P < 0·0001] were significantly higher in patients than in controls. Lp(a) levels were significantly higher in patients than in controls (200 (3–1486) mg L−1 vs. 97 (10–412) mg L−1; P < 0·0001). At the multivariate analysis, adjusted for the classical cardiovascular risk factors and creatinine levels, the OR (95% CI) for CAD at young age significantly increased in the fourth quartile of the distribution of FHcy, PMHcy and Lp(a) levels [FHcy: 14·9 (4·1–58), P < 0·0001; PMHcy: 19·2 (4·0–86·3); P < 0·0001; Lp(a): 19·6 (4·7–78·6): < 0·0001]. Vitamin deficiencies were detected in 28/140 (20%) patients. The prevalence of the homozygous C677T (+/+) methylenetetrahydrofolatereductase genotype was higher, but not significantly different, in patients (22·8%) than in controls (18·6%). The allele frequency of the 844ins68 insertion variant in the cystathionine beta‐synthase gene was 0·08 in the control group and 0·06 in the patient group.Conclusions  Results of the present study indicate the usefulness of including fasting and post‐methionine Hcy, and Lp(a) determination in the diagnostic panels of young CAD patients, in order to obtain a better assessment of their cardiovascular risk profile.
Identification of fatty acid oxidation disorder patients with lowered acyl‐CoA thioesterase activity in human skin fibroblasts
Authors: Hunt M. C. , Ruiter J. , Mooyer P. , Van Roermond C. W. T. , Ofman R. , Ijlst L. , Wanders R. J. A. 
Published: January 2005

AbstractBackground  Acyl‐CoA thioesterases are enzymes that hydrolyze acyl‐CoAs to the free fatty acid and coenzyme A (CoASH). These enzymes have been identified in several cellular compartments and are thought to regulate intracellular levels of acyl‐CoAs, free fatty acids and CoASH. However, to date no patients deficient in acyl‐CoA thioesterases have been identified.Design  Acyl‐CoA thioesterase activity was measured in human skin fibroblasts. Western‐blot analysis was used to determine Type‐II acyl‐CoA thioesterase protein levels in patients.Results  Acyl‐CoA thioesterase activity was found in human fibroblasts with all saturated acyl‐CoAs from C4‐CoA to C18‐CoA, with highest activity detected with lauroyl‐CoA and myristoyl‐CoA (C12‐CoA and C14‐CoA). An antibody that recognizes the major isoforms of Type‐II acyl‐CoA thioesterases precipitated the majority of acyl‐CoA thioesterase activity in fibroblasts, showing that the main thioesterase activity detected in fibroblasts is catalyzed by Type‐II thioesterases. Measurement of acyl‐CoA thioesterase activity from fibroblasts of 34 patients with putative fatty acid oxidation disorders resulted in the identification of three patients with lowered Type‐II acyl‐CoA thioesterase activity in fibroblasts. These patients also had lowered expression of Type‐II acyl‐CoA thioesterase protein in fibroblasts as judged by Western‐blot analysis. However, mutation analysis failed to identify any mutation in the coding sequences for the mitochondrial acyl‐CoA thioesterase II (MTE‐II) or the cytosolic acyl‐CoA thioesterase II (CTE‐II).Conclusions  We have described three patients with lowered Type‐II acyl‐CoA thioesterase protein and activity in human skin fibroblasts, which is the first description of patients with a putative defect in acyl‐CoA thioesterases.
Admixed sexual and facultatively asexual aphid lineages at mating sites
Authors: HALKETT F. , PLANTEGENEST M. , PRUNIER‐LETERME N. , MIEUZET L. , DELMOTTE F. , SIMON J. C. 
Published: January 2005

AbstractCyclically parthenogenetic organisms may have facultative asexual counterparts. Such organisms, including aphids, are therefore interesting models for the study of ecological and genetic interactions between lineages differing in reproductive mode. Earlier studies on aphids have revealed major differences in the genetic outcomes of populations that are possibly resulting mostly either from sexual or from asexual reproduction. Besides, notable gene flow between sexual and asexual derivatives has been suspected, which could lead to the emergence of new asexual lineages. The present study examines the interplay between these lineages and is based on analyses of population structure of individuals that may contribute to the pool of sexual reproductive forms in the host alternating aphidRhopalosiphum padi. Using a Bayesian assignment method, we first show that the sexual forms ofR. padion mating sites encompass two genetically distinct clusters of individuals in the western part of France. The first cluster included unique genotypes of sexual lineages, while the second cluster included facultatively asexual lineages in numerous copies, the reproductive mode of the two clusters being confirmed by reference clones. Sexual reproductive forms produced by sexual and facultatively asexual lineages are thus admixed at mating sites which gives a large opportunity for the two clusters to mate with each other. Nevertheless, this study also highlights, as previously demonstrated, that the two clusters retained high genetic differentiation. Possible explanations for the inferred limited genetic exchanges are advanced in the discussion, but further dedicated investigations are required to solve this paradox.
Evaluating mixed samples as a source of error in non‐invasive genetic studies using microsatellites
Authors: ROON DAVID A. , THOMAS MIRANDA E. , KENDALL KATHERINE C. , WAITS LISETTE P. 
Published: January 2005

AbstractThe use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error‐checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.
Genetic monitoring of wild and repatriated populations of endangered razorback sucker (Xyrauchen texanus, Catostomidae, Teleostei) in Lake Mohave, Arizona‐Nevada
Authors: DOWLING T. E. , MARSH P. C. , KELSEN A. T. , A. TIBBETS C. 
Published: January 2005

AbstractThe Native Fishes Work Group, formed in 1991, developed and implemented a protocol to enhance the dwindling razorback sucker population in Lake Mohave, Arizona‐Nevada. This large, genetically diverse population is severely reduced in size as a result of recruitment failure associated with predation on larvae. To circumvent this problem, wild larvae are captured, reared in protective custody until they are large enough to escape predation, and then released back into the lake. We present results of a monitoring program designed to assess the effectiveness of the sampling design in transmitting the high genetic diversity found in wild adults. Variation in a fragment from the mitochondrial DNA gene cytochrome b was examined by analysis of single‐stranded polymorphisms and direct sequencing. Samples were characterized from three life history stages. Characterization of wild adults verified previous results that identified considerable diversity and provided baseline data. Samples of larvae from several temporal collections from throughout the spawning season and four geographical areas were characterized for 7 years (1997–2003) to assess the transmission of genetic variation from wild adults to larvae. Several analyses identified significant differences among temporal collections, resulting from sampling errors associated with finite number of females spawning at a given time and place. Comparisons among areas and years failed to identify significant variation, indicating that pooled collections for each year possess the same levels and patterns of genetic variation. Examination of repatriates representing 11 years (1992–2002) also failed to identify significant differences among cohorts; however, some sample sizes were small and the amova may lack sufficient power to detect differences. Contrasts of wild adults, larvae, and repatriates identified statistically significant differences among collections within these three groups; however, levels of variation are small and not biologically meaningful. More importantly, this analysis failed to detect significant differences among adults, larvae, and repatriates indicating that the program has been achieving its goal of transmitting variation from adults through the larvae and into the repatriate population. The reproductive capability of repatriates has not been examined, so it is unknown if the program will maintain genetic variation found in the original adult population. This will be most easily achieved by periodic monitoring of genetic variation in larval samples. If levels of variation become reduced in repatriates, levels and patterns of diversity in larvae are also expected to become reduced, and deviations in estimates of genetic diversity may become larger and more frequent. If this is the case, intervention may be necessary to ensure that certain individuals are not over‐represented in the repatriate population.
The relation between the absolute level of parenting and differential parental treatment with adolescent siblings’ adjustment
Authors: Tamrouti‐Makkink Ilse D. , Dubas Judith Semon , Gerris Jan R.M. , van Aken Marcel A.G. 
Published: January 2005

Background:  The present study extends existing studies on the role of differential parental treatment in explaining individual differences in adolescent problem behaviors above the absolute level of parenting and clarifies the function of gender of the child, birth rank and gender constellation of the sibling dyads.Method:  The absolute level of parenting practices and differential treatment were examined in a sample of 288 Dutch families consisting of two parents and two adolescents. Parents reported on adolescent internalizing and externalizing problem behavior and adolescents reported on parental warmth and coercive control.Results:  Parenting dimensions were related to problem behavior for same‐ and mixed‐gender sibling pairs, with coercive control as the strongest predictor. No direct association was found between differential parental treatment and child outcomes above the absolute levels of parenting in same‐gender sibling pairs. However, differential maternal and paternal control was related to internalizing behavior of girls and differential paternal warmth was linked to externalizing behavior of the older siblings in mixed‐gender sibling pairs.Conclusion:  Differential parental treatment is uniquely associated with child problem behavior above the absolute level of parenting for girls and early‐born children in mixed‐gender sibling pairs. Any examination of the effects of differential treatment should not be undertaken without considering the gender and birth rank of the sibling pairs.
Perceived support in sibling relationships and adolescent adjustment
Authors: Branje Susan J.T. , van Lieshout Cornelis F.M. , van Aken Marcel A.G. , Haselager Gerbert J.T. 
Published: January 2005

Background:  Siblings may support each other, but also reveal fierce rivalry and mutual aggression. Supportive sibling relationships have been linked to the development of psychosocial competence of children. In the present longitudinal study, we will focus on the development of perceived support in sibling dyads and on the influence of sibling support and sibling problem behavior on psychosocial adjustment in adolescence.Method:  In a three‐wave longitudinal sample of 285 Dutch families with two adolescent children (11‐ to 15‐year‐olds), these two siblings judged the support perceived from each other. In addition, they themselves and their parents judged their internalizing and externalizing problem behaviors. The relation of sibling support and sibling problem behavior with internalizing and externalizing problem behaviors was examined while controlling for support from parents and friends and, over time, controlling for the autoregressive effects of problem behavior.Results:  Support perceived from a sibling is mostly negatively related to externalizing problems; sibling problem behavior is strongly related to internalizing problems. Differential developmental trajectories of adolescents’ adjustment are associated with siblings’ support and problem behavior.Conclusion:  The results indicate that adolescents’ relationships with both older and younger siblings are characterized by modeling processes.
Persistence of Animal and Human Glycopeptide-Resistant Enterococci on Two Norwegian Poultry Farms Formerly Exposed to Avoparcin Is Associated with a Widespread Plasmid-Mediated
vanA
Element within a Polyclonal
Enterococcus faecium
Population
Authors: Johnsen P. J. , Østerhus J. I. , Sletvold H. , Sørum M. , Kruse H. , Nielsen K. , Simonsen G. S. , Sundsfjord A. 
Published: January 2005

ABSTRACT

The evolutionary processes responsible for the long-term persistence of glycopeptide-resistant
Enterococcus faecium
(GREF) in nonselective environments were addressed by genetic analyses of
E. faecium
populations in animals and humans on two Norwegian poultry farms that were previously exposed to avoparcin. A total of 222 fecal GREF (
n
= 136) and glycopeptide-susceptible (
n
= 86)
E. faecium
(GSEF) isolates were obtained from farmers and poultry on three separate occasions in 1998 and 1999. Pulsed-field gel electrophoresis (PFGE) and plasmid DNA analyses discerned 22 GREF and 32 GSEF PFGE types within shifting polyclonal animal and human
E. faecium
populations and indicated the presence of transferable plasmid-mediated
vanA
resistance, respectively. Examples of dominant, persistent GREF PFGE types supported the notion that environmentally well-adapted GREF types may counteract the reversal of resistance. PFGE analyses, sequencing of the
purK
housekeeping gene, and partial typing of
vanA
-containing Tn
1546
suggested a common animal and human reservoir of glycopeptide resistance. Inverse PCR amplification and sequence analyses targeting the right end of the Tn
1546
-plasmid junction fragment strongly indicated the presence of a common single Tn
1546
-plasmid-mediated element in 20 of 22 GREF PFGE types. This observation was further strengthened by
vanY-vanZ
hybridization analyses of plasmid DNAs as well as the finding of a physical linkage between Tn
1546
and a putative postsegregation killing system for seven GREF PFGE types. In conclusion, our observations suggest that the molecular unit of persistence of glycopeptide resistance is a common mobile plasmid-mediated
vanA
-containing element within a polyclonal GREF population that changes over time. In addition, we propose that “plasmid addiction systems” may contribute to the persistence of GREF in nonselective environments.