bluuebunny/crossref_metadata_2025 huggingface dataset:
Complex genetic interactions underlying expression differences between
Drosophila
races: Analysis of chromosome substitutions
Authors: Wang Hurng-Yi , Fu Yonggui , McPeek Mary Sara , Lu Xuemei , Nuzhdin Sergey , Xu Anlong , Lu Jian , Wu Mao-Lien , Wu Chung-I
Published: April 2008

Regulation of gene expression is usually separated into
cis
and
trans
components. The separation may become artificial if much of the variation in expression is under multigenic and epistatic (e.g.,
cis
-by-
trans
) control. There is hence a need to quantify the relative contribution of
cis
,
trans
, and
cis
-by-
trans
effects on expression divergence at different levels of evolution. To do so across the whole genome, we analyzed the full set of chromosome-substitution lines between the two behavioral races of
Drosophila melanogaster
. Our observations: (
i
) Only ≈3% of the genes with an expression difference are purely
cis
regulated. In fact, relatively few genes are governed by simple genetics because nearly 80% of expression differences are controlled by at least two chromosomes. (
ii
) For 14% of the genes,
cis
regulation does play a role but usually in conjunction with
trans
regulation. This joint action of
cis
and
trans
effects, either additive or epistatic, is referred to as inclusive
cis
effect. (
iii
) The percentage of genes with inclusive
cis
effect increases to 32% among genes that are strongly differentiated between the two races. (
iv
) We observed a nonrandom distribution of
trans
-acting factors, with a substantial deficit on the second chromosome. Between
Drosophila
racial groups,
trans
regulation of expression difference is extensive, and
cis
regulation often evolves in conjunction with
trans
effects.
The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy
Authors: Kötting Carsten , Kallenbach Angela , Suveyzdis Yan , Wittinghofer Alfred , Gerwert Klaus
Published: April 2008

Members of the Ras superfamily of small G proteins play key roles in signal transduction pathways, which they control by GTP hydrolysis. They are regulated by GTPase activating proteins (GAPs). Mutations that prevent hydrolysis cause severe diseases including cancer. A highly conserved “arginine finger” of GAP is a key residue. Here, we monitor the GTPase reaction of the Ras·RasGAP complex at high temporal and spatial resolution by time-resolved FTIR spectroscopy at 260 K. After triggering the reaction, we observe as the first step a movement of the switch-I region of Ras from the nonsignaling “off” to the signaling “on” state with a rate of 3 s
−1
. The next step is the movement of the “arginine finger” into the active site of Ras with a rate of
k
2
= 0.8 s
−1
. Once the arginine points into the binding pocket, cleavage of GTP is fast and the protein-bound P
i
intermediate forms. The switch-I reversal to the “off” state, the release of P
i
, and the movement of arginine back into an aqueous environment is observed simultaneously with
k
3
= 0.1 s
−1
, the rate-limiting step. Arrhenius plots for the partial reactions show that the activation energy for the cleavage reaction is lowered by favorable positive activation entropy. This seems to indicate that protein-bound structured water molecules are pushed by the “arginine finger” movement out of the binding pocket into the bulk water. The proposed mechanism shows how the high activation barrier for phosphoryl transfer can be reduced by splitting into partial reactions separated by a P
i
-intermediate.
The cyclic AMP effector Epac integrates pro- and anti-fibrotic signals
Authors: Yokoyama Utako , Patel Hemal H. , Lai N. Chin , Aroonsakool Nakon , Roth David M. , Insel Paul A.
Published: April 2008

Scar formation occurs during the late stages of the inflammatory response but, when excessive, produces fibrosis that can lead to functional and structural damage of tissues. Here, we show that the profibrogenic agonist, transforming growth factor β1, transcriptionally decreases expression of Exchange protein activated by cAMP 1 (Epac1) in fibroblasts/fibroblast-like cells from multiple tissues (i.e., cardiac, lung, and skin fibroblasts and hepatic stellate cells). Overexpression of Epac1 inhibits transforming growth factor β1-induced collagen synthesis, indicating that a decrease of Epac1 expression appears to be necessary for the fibrogenic phenotype, an idea supported by evidence that Epac1 expression in cardiac fibroblasts is inhibited after myocardial infarction. Epac and protein kinase A, a second mediator of cAMP action, have opposite effects on migration but both inhibit synthesis of collagen and DNA by fibroblasts. Epac is preferentially activated by low concentrations of cAMP and stimulates migration via the small G protein Rap1 but inhibits collagen synthesis in a Rap1-independent manner. The regulation of Epac expression and activation thus appear to be critical for the integration of pro- and anti-fibrotic signals and for the regulation of fibroblast function.
Listening to the voice of living life with aphasia: Anne's story
Authors: Barrow Rozanne
Published: April 2008

Background: Listening to how people talk about the consequences of acquired aphasia helps one gain insight into how people construe disability and communication disability in particular. It has been found that some of these construals can be more of a disabling barrier in re‐engaging with life than the communication impairment itself.

Aims: To explore and identify the role that narratives of disability (i.e. the ‘inner stories we live by’) play in how Anne, a woman with aphasia, and those close to her, make sense of stroke and aphasia.

Methods & Procedures: Qualitative analyses of in‐depth interviews, of notes from participant observation, and of artefactual material were used to get access to these insider perspectives of both Anne and some of her conversation partners.

Outcomes & Results: The data revealed that Anne created, was surrounded by, and immersed in an intricate and elusive tapestry of narratives of disability that contributed to her experience of living life with aphasia. Narratives of ‘limited competence’ and ‘disability as less than whole’ emerged as strong voices that stemmed from cultural and societal views about disability. In response to this Anne and other participants sought refuge in the ‘grand’ narrative of Modern Medicine with its focus on restitution, in order to make sense of their situation and to chart a way forward. As a result her life revolved around activities that would ‘make her better’.

Conclusions: Prevailing cultural narratives of disability played a key role in how Anne and those close to her made sense of aphasia and so shaped how she lived her life. The implications of this for working practice are discussed.
Essential Role of Cyclin-G–associated Kinase (Auxilin-2) in Developing and Mature Mice
Authors: Lee Dong-won , Zhao Xiaohong , Yim Yang-In , Eisenberg Evan , Greene Lois E.
Published: April 2008

Hsc70 with its cochaperone, either auxilin or GAK, not only uncoats clathrin-coated vesicles but also acts as a chaperone during clathrin-mediated endocytosis. However, because synaptojanin is also involved in uncoating, it is not clear whether GAK is an essential gene. To answer this question, GAK conditional knockout mice were generated and then mated to mice expressing Cre recombinase under the control of the nestin, albumin, or keratin-14 promoters, all of which turn on during embryonic development. Deletion of GAK from brain, liver, or skin dramatically altered the histology of these tissues, causing the mice to die shortly after birth. Furthermore, by expressing a tamoxifen-inducible promoter to express Cre recombinase we showed that deletion of GAK caused lethality in adult mice. Mouse embryonic fibroblasts in which the GAK was disrupted showed a lack of clathrin-coated pits and a complete block in clathrin-mediated endocytosis. We conclude that GAK deletion blocks development and causes lethality in adult animals by disrupting clathrin-mediated endocytosis.
OnD-CRF: predicting order and disorder in proteins conditional random fields
Authors: Wang Lixiao , Sauer Uwe H.
Published: April 2008

Motivation: Order and Disorder prediction using Conditional Random Fields (OnD-CRF) is a new method for accurately predicting the transition between structured and mobile or disordered regions in proteins. OnD-CRF applies CRFs relying on features which are generated from the amino acids sequence and from secondary structure prediction. Benchmarking results based on CASP7 targets, and evaluation with respect to several CASP criteria, rank the OnD-CRF model highest among the fully automatic server group.

Availability:  http://babel.ucmp.umu.se/ond-crf/

Contact:  Uwe.Sauer@ucmp.umu.se
Government Control, Transaction Costs and Commitment Between the Hong Kong and Shanghai Banking Corporation (HSBC) and the Chinese Government
Authors: Lu Qing
Published: April 2008

We use the tools of transaction cost politics (TCP) developed from transaction cost economics and economic analysis, to analyze the business relationship building between the Hongkong and Shanghai Banking Corporation (HSBC), the largest and most successful foreign bank in China, and the Chinese government between 1949 and 1978. We demonstrate the value of the TCP-based approach to evaluating the specialized governance structure of commitment built on mutual dependency. In particular, we identify several transaction attributes that give rise to hazards: transaction uncertainty, the role of the government in the economy, and the strength of the supporting coalition. Our analysis also confirms that commitment built on the mutual dependency between the international company and the local authorities and between the international company's home country authorities and the local authorities did reduce the company's transaction costs by guarding against the local authorities' opportunism.
The Efficacy of Multilevel Surgery of the Upper Airway in Adults With Obstructive Sleep Apnea/Hypopnea Syndrome
Authors: Lin Hsin‐Ching , Friedman Michael , Chang Hsueh‐Wen , Gurpinar Berk
Published: April 2008

Objective: Many patients with obstructive sleep apnea/hypopnea syndrome (OSAHS) are incapable of using continuous positive airway pressure. These patients therefore turn to surgical options as a salvage treatment. Early studies and reviews focused on the efficacy of uvulopalatopharyngoplasty, a single‐level procedure for the treatment of OSAHS. Since OSAHS is usually caused by multilevel obstructions, the true focus on efficacy should be on multilevel surgical intervention. The purpose of this paper is to provide an overview of the literature on multilevel surgery for OSAHS patients.

Study Design: Systematic review of the literature and meta‐analysis focusing on subjective and objective outcomes of patients with OSAHS treated with multilevel surgery of the upper airway.

Methods: We searched PubMed, the Cochrane database, and MEDLINE bibliographic databases up to March 31, 2007, for studies dealing with multilevel surgical modification of the upper airway for the treatment of OSAHS. Additional studies were identified from their reference lists. Articles were included only if the surgical intervention involved at least two of the frequently involved anatomic sites: nose, oropharynx, and hypopharynx.

Results: After applying specific inclusion criteria, 49 multilevel surgery articles (58 groups) were identified. There were 1,978 patients included in the study. The mean minimal follow‐up time was 7.3 months (range, 1 to 100 months). A meta‐analysis was performed to redefine the success rate to be consistent with the commonly agreed upon criteria, namely “a reduction in the apnea/ hypopnea index (AHI) of 50% or more and an AHI of less than 20.” “Success” implies an improved condition and is not meant to imply cure. The recalculated success rate was 66.4%. The overall complication rate was 14.6%. The evidence‐base medicine (EBM) level of these 49 studies revealed that only one study was EBM level 1, two papers were EBM level 3, and the other 46 papers were ranked as level 4 evidence.

Conclusions: Multilevel surgery for OSAHS is obviously associated with improved outcomes, although this benefit is supported largely by level 4 evidence. Future research should focus on prospective and controlled studies.
Outcome of Adenoidectomy Versus Adenoidectomy With Maxillary Sinus Wash for Chronic Rhinosinusitis in Children
Authors: Ramadan Hassan H. , Cost Jamey L.
Published: April 2008

Objectives: To compare postoperative outcomes of adenoidectomy versus adenoidectomy with maxillary sinus wash as surgical treatment of chronic rhinosinusitis (CRS) in children.

Study Design: A retrospective review of prospectively collected data.

Methods: Children who failed to respond to medical therapy for CRS and had an adenoidectomy alone (A) or an adenoidectomy with a maxillary sinus wash (wash/A) were reviewed. Outcome was assessed at least 12 months postoperatively.

Results: Sixty children who satisfied the inclusion criteria were reviewed. Thirty‐two of the children had a sinus wash at the time of adenoidectomy. The age range was 3 to 13 years (mean, 6.3 years) and the mean computed tomography (CT) score was 6.1. The two surgical groups were comparable with regard to age, sex, presence of allergies, asthma, and smoking in the household. Twenty‐eight (87.5%) of the 32 patients who underwent wash/A showed improvement of their symptoms after 12 months follow‐up compared with 17 (60.7%) of 28 patients who underwent A (P = .017). Multivariable analysis using logistic regression analysis with age, sex, asthma, allergy, and CT score as covariables showed that the success of wash/A compared with adenoidectomy was higher (93% to 60%) for children with a high CT score compared to those with a lower CT score (P = .011). None of the other variables showed statistical significance.

Conclusions: Children with more severe sinus disease as evidenced by a high CT score had a higher success rate if a maxillary sinus wash was performed at the time of adenoidectomy. Children with a low CT score did not have that benefit.
Sleep Medicine for Surgeons
Authors: Davidson Terence M.
Published: April 2008

Sleep medicine is an important component of current head and neck surgery practices. Furthermore, obstructive sleep apnea is an anatomic disease of the upper respiratory tract, a region of anatomy best known to head and neck surgeons. If head and neck surgeons choose to participate in the surgical treatment of sleep apnea, they must develop expertise in the evaluation and home sleep testing aspects of sleep apnea. Because positive airway pressure remains the front line treatment, they must also develop expertise in the prescription of positive airway pressure therapy.
Effect of Blood and Mucus on Tympanostomy Tube Biofilm Formation
Authors: Malaty John , Antonelli Patrick J.
Published: April 2008

Objectives/Hypothesis: Tympanostomy tube (TT) biofilm formation may lead to refractory otorrhea and occlusion. The aim of this study was to determine whether TT biofilm formation may be promoted by mucus or blood exposure.

Study Design: In vitro, controlled.

Methods: Fluoroplastic TTs were exposed to blood, mucoid effusion, or saline. Half were allowed to dry. TTs were cultured with Pseudomonas aeruginosa. After 4 days, gentamicin was added to kill planktonic bacteria. Biofilm formation was assessed by quantitative bacterial counts and scanning electron microscopy.

Results: Mucus pretreatment (dry and wet) did not increase biofilm formation. Both dry and wet blood exposure increased biofilm formation by bacterial counts (P < .0001). Biofilm formation was demonstrated by electron microscopy in all groups.

Conclusions:
P. aeruginosa biofilm formation on fluoroplastic TTs is enhanced by blood exposure. Care should be taken to minimize bleeding with TT placement to reduce the risk of biofilm formation.
Mating system and
avpr1a
promoter variation in primates
Authors: Rosso Lia , Keller Laurent , Kaessmann Henrik , Hammond Robert L
Published: April 2008

It has been suggested that primate mating and social behaviours may be influenced by variation in promoter region repetitive DNA of the vasopressin receptor 1a gene (
avpr1a
). We show that male mating behaviour does not covary in a simple way with promoter repetitive DNA in 12 Old World primates. We found that one microsatellite (−553 bp upstream) was present in all species, irrespective of their behaviour. By contrast, two microsatellites (−3956 and −3625 bp upstream) were present only in some species, yet this variation did not correlate with behaviour. These findings agree with a recent comparative analysis of voles and show that the variation in repetitive DNA in the
avpr1a
promoter region does not generally explain variation in male mating behaviour. Phylogenetic analysis revealed a GAGTA motif that has been independently deleted three times and involved in another larger deletion. Importantly, the presence/absence of this GAGTA motif leads to changes in predicted transcription factor-binding sites. Given the repeated loss of this motif, we speculate that it might be of functional relevance. We suggest that such non-repetitive variation, either in indels or in sequence variation, are likely to be important in explaining interspecific variation in
avpr1a
expression.
Protein robustness promotes evolutionary innovations on large evolutionary time-scales
Authors: Ferrada Evandro , Wagner Andreas
Published: April 2008

Recent laboratory experiments suggest that a molecule's ability to evolve neutrally is important for its ability to generate evolutionary innovations. In contrast to laboratory experiments, life unfolds on time-scales of billions of years. Here, we ask whether a molecule's ability to evolve neutrally—a measure of its robustness—facilitates evolutionary innovation also on these large time-scales. To this end, we use protein designability, the number of sequences that can adopt a given protein structure, as an estimate of the structure's ability to evolve neutrally. Based on two complementary measures of functional diversity—catalytic diversity and molecular functional diversity in gene ontology—we show that more robust proteins have a greater capacity to produce functional innovations. Significant associations among structural designability, folding rate and intrinsic disorder also exist, underlining the complex relationship of the structural factors that affect protein evolution.
Feeding, fecundity and lifespan in femaleDrosophila melanogaster
Authors: Barnes Andrew I , Wigby Stuart , Boone James M , Partridge Linda , Chapman Tracey
Published: April 2008

Male seminal fluid proteins induce a profound remodelling of behavioural, physiological and gene signalling pathways in females of many taxa, and typically cause elevated egg production and decreased sexual receptivity. InDrosophila melanogaster, these effects can be mediated by an ejaculate ‘sex peptide’ (SP), which, in addition, contributes significantly to the cost of mating in females. Recent research has revealed that SP can stimulate female post-copulatory feeding, raising the possibility that the widespread female cost of mating could be due to over-feeding. In this study, we usedD. melanogasteras a model to test this hypothesis. We first show that elevated post-mating feeding is dependent upon egg production and does not occur in sterileovoD1mutant females. This conclusion was also supported by the increase in feeding of virgin females whose egg production was experimentally elevated. We then demonstrated that sterileovoD1and fertile females experienced identical survival costs of mating, related to their frequency of mating and not to female feeding rate or to egg production. We conclude that female mating costs are not the result of over-feeding, but may be due to other, potentially more direct, effects of ejaculate molecules.
Heart rate modulation in bystanding geese watching social and non-social events
Authors: Wascher Claudia A.F , Scheiber Isabella B.R , Kotrschal Kurt
Published: April 2008

Simply observing other individuals interacting has been shown to affect subsequent behaviour and also hormones in ‘bystander’ individuals. However, immediate physiological responses of an observer have been hardly investigated. Here we present results on individuals' heart rate (HR) responses during various situations, which occur regularly in a flock of greylag geese (Anser anser, e.g. agonistic encounters, vehicles passing by). We recorded simultaneously HR and behaviour of 21 semi-tame free-roaming geese, equipped with fully implanted transmitters. We considered 304 social and 81 non-social events during which the focal individuals did not respond behaviourally. Independent of the spatial distance to the event, these HR responses were significantly greater in social contexts (e.g. departing or landing geese, agonistic interactions) than in non-social situations (e.g. vehicles passing by, thunder). Focal individuals showed a significantly higher maximum HR as well as a greater HR increase in response to agonistic interactions, in which the pair partner or a family member was involved, as compared with a non-affiliated goose. Also, HR was significantly higher when the bystander watched non-affiliated geese interacting, which were higher ranking than the focal. We conclude that these differences are due to different relevance of the recorded events for the focal individual, depending on the individuals involved in the observed interaction.
Host manipulation by parasites in the world of dead-end predators: adaptation to enhance transmission?
Authors: Seppälä Otto , Valtonen E. Tellervo , Benesh Daniel P
Published: April 2008

Trophically transmitted parasites often alter their intermediate host's phenotype, thereby predisposing the hosts to increased predation. This is generally considered a parasite strategy evolved to enhance transmission to the next hosts. However, the adaptive value of host manipulation is not clear as it may be associated with costs, such as increased susceptibility to predators that are unsuitable next hosts for the parasites. We examined the ratio between the benefits and costs of host manipulation for transmission success ofAcanthocephalus lucii(Acanthocephala), a parasite that alters the hiding behaviour and pigmentation of its isopod hosts. We experimentally compared the susceptibility of infected and uninfected isopods to predation by perch (Perca fluvialis; definitive host of the parasite) and dragonfly larvae (dead end). We found that the parasite predisposed the isopods to predation by both predators. However, the increased predation vulnerability of the infected isopods was higher towards perch. This suggests that, despite the costs due to non-host predation, host manipulation may still be advantageous for the parasite.
Simian homologues of human herpesvirus 8
Authors: Damania Blossom , Desrosiers Ronald C.
Published: April 2008

γ–Herpesviruses can be found in most primates including Old World an New World monkeys. The γ–
herpesvirinae
are grouped into two classes: lymphocryptoviruses (γ
1
) and rhadinoviruses (γ
2
). The lymphocryptoviruses include Epstein–Barr virus, lymphocryptovirus of rhesus monkeys, and
Herpesvirus papio
of baboons. Rhadinoviruses that infect New World monkeys include
Herpesvirus saimiri
, whose natural host is the squirrel monkey, and
Herpesvirus ateles
, which infects spider monkeys. Rhadinoviruses that infect hominoids and Old World monkeys include Kaposi's sarcoma–associated herpesvirus, also known as HHV–8, and rhesus monkey rhadinovirus.
Biology and disease associations of Epstein–Barr virus
Authors: Crawford Dorothy H.
Published: April 2008

Epstein–Barr virus (EBV) is a human herpesvirus which infects almost all of the world's population subclinically during childhood and thereafter remains in the body for life. The virus colonizes antibody–producing (B) cells, which, as relatively long–lived resting cells, are an ideal site for long–term residence. Here EBV evades recognition and destruction by cytotoxic T cells. EBV is passed to naive hosts in saliva, but how the virus gains access to this route of transmission is not entirely clear. EBV carries a set of latent genes that, when expressed in resting B cells, induce cell proliferation and thereby increase the chances of successful virus colonization of the B–cell system during primary infection and the establishment of persistence. However, if this cell proliferation is not controlled, or if it is accompanied by additional genetic events within the infected cell, it can lead to malignancy. Thus EBV acts as a step in the evolution of an ever–increasing list of malignancies which are broadly of lymphoid or epithelial cell origin. In some of these, such as B–lymphoproliferative disease in the immunocompromised host, the role of the virus is central and well defined; in others, such as Burkitt's lymphoma, essential cofactors have been identified which act in concert with EBV in the evolution of the malignant clone. However, in several diseases in which the presence of EBV has more recently been discovered, the role of the virus is unclear. This review describes recent views on the EBV life cycle and its interlinks with normal B–cell biology, and discusses how this interrelationship may be upset and result in EBV–associated disease.
The amygdala and ventromedial prefrontal cortex: functional contributions and dysfunction in psychopathy
Authors: Blair R.J.R
Published: April 2008

The current paper examines the functional contributions of the amygdala and ventromedial prefrontal cortex (vmPFC) and the evidence that the functioning of these systems is compromised in individuals with psychopathy. The amygdala is critical for the formation of stimulus–reinforcement associations, both punishment and reward based, and the processing of emotional expressions. vmPFC is critical for the representation of reinforcement expectancies and, owing to this, decision making. Neuropsychological and neuroimaging data from individuals with psychopathy are examined. It is concluded that these critical functions of the amygdala and vmPFC, and their interaction, are compromised in individuals with the disorder. It is argued that these impairments lead to the development of psychopathy.
Identification of dermatophytes by sequence analysis of the rRNA gene internal transcribed spacer regions
Authors: Li Hsin Chieh , Bouchara Jean-Philippe , Hsu Mark Ming-Long , Barton Richard , Su Shuli , Chang Tsung Chain
Published: April 2008

Identification of dermatophytes using the traditional method is sometimes problematic because of atypical microscopic or macroscopic morphology. The aim of this study was to evaluate the feasibility of using sequencing of the ribosomal internal transcribed spacer (ITS)1 and ITS2 regions for identification of 17 dermatophyte species. The ITS regions of 188 strains (62 reference strains and 126 clinical isolates) were amplified by PCR and sequenced. Species identification was made by sequence comparison with an in-house database comprising ITS sequences of type or neotype strains or by blast searches for homologous sequences in public databases. Strains producing discrepant results between conventional methods and ITS sequence analysis were analysed further by sequencing the D1–D2 domain of the large-subunit rRNA gene for species clarification. The identification rates by ITS1 and ITS2 sequencing were higher than 97 %. Based on reference sequences of type or neotype strains, it was noted that most strains of Trichophyton mentagrophytes were misidentifications of Trichophyton interdigitale. In addition, barcode sequences were present in species of the Microsporum canis complex and Trichophyton rubrum complex. These barcode sequences are useful for species delineation when the results of ITS sequencing are ambiguous. In conclusion, ITS sequencing provides a very accurate and useful method for the identification of dermatophytes.
Cervical spondylodiscitis with spinal epidural abscess caused by Aggregatibacter aphrophilus
Authors: Pasqualini Leonella , Mencacci Antonella , Scarponi Anna Maria , Leli Christian , Fabbriciani Gianluigi , Callarelli Laura , Schillaci Giuseppe , Bistoni Francesco , Mannarino Elmo
Published: April 2008

Spondylodiscitis caused by Aggregatibacter aphrophilus, formerly known as Haemophilus paraphrophilus, is an unusual condition and can be very difficult to diagnose. We report a case of cervical spondylodiscitis complicated by spinal epidural abscess in a 63-year-old woman, without underlying predisposing conditions. The source of infection was identified as a periodontal infection. The patient was successfully treated with systemic antibiotics.
Severe course of rat bite-associated Weil's disease in a patient diagnosed with a new Leptospira-specific real-time quantitative LUX-PCR
Authors: Roczek Alexandra , Forster Christian , Raschel Heribert , Hörmansdorfer Stefan , Bogner Karl-Heinz , Hafner-Marx Angela , Lepper Hans , Dobler Gerhard , Büttner Mathias , Sing Andreas
Published: April 2008

Leptospirosis is a zoonotic disease with global distribution, caused by spirochaetes of the genus Leptospira. Transmission of Leptospira interrogans serovar Icterohaemorrhagiae, the causative agent of Weil's disease, to humans usually results from exposure to the urine of infected, but mostly asymptomatic, rodents, either by direct contact or indirectly through contaminated soil or water. Although regarded as a re-emerging infectious disease, human leptospirosis is probably underdiagnosed due to its often unspecific clinical appearance and difficulties in culturing leptospires. Therefore, more rapid and specific diagnostic procedures are needed. Here we describe a novel real-time quantitative PCR system developed for the accurate and fast diagnosis of pathogenic Leptospira spp. Its usefulness in the management of a patient with rat bite-associated multiorgan failure is demonstrated.
First report of vaginal infection caused by Enterococcus raffinosus
Authors: Savini Vincenzo , Manna Assunta , D'Antonio Francesco , Talia Marzia , Catavitello Chiara , Balbinot Andrea , Febbo Fabio , Carlino Daniela , Fioritoni Francesca , Di Bonaventura Giovanni , D'Antonio Domenico
Published: April 2008

The authors have reported the first case of vaginal infection caused by Enterococcus raffinosus. The latter is a rarely identified species, but some of the infections described in the literature should direct some attention to this, often opportunistic pathogen, and its emerging multidrug resistance.
Cl–π interactions in protein–ligand complexes
Authors: Imai Yumi N. , Inoue Yoshihisa , Nakanishi Isao , Kitaura Kazuo
Published: April 2008

During systematic analysis of nonbonded contacts in protein–ligand complexes derived from crystal structures in the Protein Data Bank, Cl–π interactions have been found, not only in the well‐documented serine proteases but also, to a lesser extent, in other proteins. From geometric analysis of such Cl–π interactions in the crystal structures, two distinct geometries were found: the “edge‐on” approach of a Cl atom to a ring atom or C–C bond and the “face‐on” approach toward the ring centroid with an average interatomic distance of 3.6 Å. High‐level ab initio calculations using benzene–chlorohydrocarbon model systems elucidated that the calculated Cl–π interaction energy is −2.01 kcal/mol, and the dispersion force is the major source of attraction. We also discussed the geometric flexibility in Cl–π interactions and a relationship between the intensity of the π density in an aromatic ring and the interaction position of the Cl atom.
Predicting protein folding rates from geometric contact and amino acid sequence
Authors: Ouyang Zheng , Liang Jie
Published: April 2008

Protein folding speeds are known to vary over more than eight orders of magnitude. Plaxco, Simons, and Baker (see References) first showed a correlation of folding speed with the topology of the native protein. That and subsequent studies showed, if the native structure of a protein is known, its folding speed can be predicted reasonably well through a correlation with the “localness” of the contacts in the protein. In the present work, we develop a related measure, the geometric contact number, N α, which is the number of nonlocal contacts that are well‐packed, by a Voronoi criterion. We find, first, that in 80 proteins, the largest such database of proteins yet studied, N α is a consistently excellent predictor of folding speeds of both two‐state fast folders and more complex multistate folders. Second, we show that folding rates can also be predicted from amino acid sequences directly, without the need to know the native topology or other structural properties.
Structures, basins, and energies: A deconstruction of the Protein Coil Library
Authors: Perskie Lauren L. , Street Timothy O. , Rose George D.
Published: April 2008

Globular proteins adopt complex folds, composed of organized assemblies of α‐helix and β‐sheet together with irregular regions that interconnect these scaffold elements. Here, we seek to parse the irregular regions into their structural constituents and to rationalize their formative energetics. Toward this end, we dissected the Protein Coil Library, a structural database of protein segments that are neither α‐helix nor β‐strand, extracted from high‐resolution protein structures. The backbone dihedral angles of residues from coil library segments are distributed indiscriminately across the φ,ψ map, but when contoured, seven distinct basins emerge clearly. The structures and energetics associated with the two least‐studied basins are the primary focus of this article. Specifically, the structural motifs associated with these basins were characterized in detail and then assessed in simple simulations designed to capture their energetic determinants. It is found that conformational constraints imposed by excluded volume and hydrogen bonding are sufficient to reproduce the observed ϕ,ψ distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with α‐helices, strands of β‐sheet, canonical β‐turns, and polyproline II conformers comprise ∼90% of all protein structure.
Molecular determinants of the aggregation behavior of α‐ and β‐synuclein
Authors: Rivers Robert C. , Kumita Janet R. , Tartaglia Gian Gaetano , Dedmon Matthew M. , Pawar Amol , Vendruscolo Michele , Dobson Christopher M. , Christodoulou John
Published: April 2008

α‐ and β‐synuclein are closely related proteins, the first of which is associated with deposits formed in neurodegenerative conditions such as Parkinson's disease while the second appears to have no relationship to any such disorders. The aggregation behavior of α‐ and β‐synuclein as well as a series of chimeric variants were compared by exploring the structural transitions that occur in the presence of a widely used lipid mimetic, sodium dodecyl sulfate (SDS). We found that the aggregation rates of all these protein variants are significantly enhanced by low concentrations of SDS. In particular, we inserted the 11‐residue sequence of mainly hydrophobic residues from the non‐amyloid‐β‐component (NAC) region of α‐synuclein into β‐synuclein and show that the fibril formation rate of this chimeric protein is only weakly altered from that of β‐synuclein. These intrinsic propensities to aggregate are rationalized to a very high degree of accuracy by analysis of the sequences in terms of their associated physicochemical properties. The results begin to reveal that the differences in behavior are primarily associated with a delicate balance between the positions of a range of charged and hydrophobic residues rather than the commonly assumed presence or absence of the highly aggregation‐prone region of the NAC region of α‐synuclein. This conclusion provides new insights into the role of α‐synuclein in disease and into the factors that regulate the balance between solubility and aggregation of a natively unfolded protein.
The PIP2 binding mode of the C2 domains of rabphilin‐3A
Authors: Montaville Pierre , Coudevylle Nicolas , Radhakrishnan Anand , Leonov Andrei , Zweckstetter Markus , Becker Stefan
Published: April 2008

Phosphatidylinositol‐4,5‐bisphosphate (PIP2) is a key player in the neurotransmitter release process. Rabphilin‐3A is a neuronal C2 domain tandem containing protein that is involved in this process. Both its C2 domains (C2A and C2B) are able to bind PIP2. The investigation of the interactions of the two C2 domains with the PIP2 headgroup IP3 (inositol‐1,4,5‐trisphosphate) by NMR showed that a well‐defined binding site can be described on the concave surface of each domain. The binding modes of the two domains are different. The binding of IP3 to the C2A domain is strongly enhanced by Ca2+ and is characterized by a KD of 55 μM in the presence of a saturating concentration of Ca2+ (5 mM). Reciprocally, the binding of IP3 increases the apparent Ca2+‐binding affinity of the C2A domain in agreement with a Target‐Activated Messenger Affinity (TAMA) mechanism. The C2B domain binds IP3 in a Ca2+‐independent fashion with low affinity. These different PIP2 headgroup recognition modes suggest that PIP2 is a target of the C2A domain of rabphilin‐3A while this phospholipid is an effector of the C2B domain.
Correlation between 13Cα chemical shifts and helix content of peptide ensembles
Authors: Weinstock Daniel S. , Narayanan Chitra , Baum Jean , Levy Ronald M.
Published: April 2008

Replica exchange molecular dynamics simulations are used to generate three ensembles of an S‐peptide analog (AETAAAKFLREHMDS). Percent helicity of the peptide ensembles calculated using STRIDE is compared to percent helicity calculated from 13Cα chemical shift deviations (CSD) from random coil in order to test the assumption that CSD can be correlated to percent helicity. The two estimates of helicity, one based on structure and the other on CSD, are in close to quantitative agreement, except at the edges of helical stretches where disagreements of as much as 50% can be found. These disagreements can occur by CSDs both as an under‐ and an overestimate of peptide helicity. We show that underestimation arises due to ensemble averaging of positive CSDs from conformers with torsion angles in the helical region of Ramachandran space with negative CSDs corresponding to conformers of the peptide in the extended region. In contrast, overestimation comes about due to the fact that a large number of conformations with torsion angles in the helical region are not counted as helical by STRIDE due to a lack of correlated helical torsion angles in neighboring residues.
Toward quantification of protein backbone–backbone hydrogen bonding energies: An energetic analysis of an amide‐to‐ester mutation in an α‐helix within a protein
Authors: Gao Jianmin , Kelly Jeffery W.
Published: April 2008

Amide‐to‐ester backbone mutagenesis enables a specific backbone–backbone hydrogen bond (H‐bond) in a protein to be eliminated in order to quantify its energetic contribution to protein folding. To extract a H‐bonding free energy from an amide‐to‐ester perturbation free energy (ΔG folding,wt − ΔG folding,mut), it is necessary to correct for the putative introduction of a lone pair–lone pair electrostatic repulsion, as well as for the transfer free energy differences that may arise between the all amide sequence and the predominantly amide sequence harboring an ester bond. Mutation of the 9–10 amide bond within the V9F variant of the predominantly helical villin headpiece subdomain (HP35) to an ester or an E‐olefin backbone bond results in a less stable but defined wild‐type fold, an attribute required for this study. Comparing the folding free energies of the ester and E‐olefin mutants, with correction for the desolvation free energy differences (ester and E‐olefin) and the loss of an n‐to‐π* interaction (E‐olefin), yields an experimentally based estimate of +0.4 kcal/mol for the O–O repulsion energy in an α‐helical context, analogous to our previous experimentally based estimate of the O–O repulsion free energy in the context of a β‐sheet. The small O–O repulsion energy indicates that amide‐to‐ester perturbation free energies can largely be attributed to the deletion of the backbone H‐bonds after correction for desolvation differences. Quantitative evaluation of H‐bonding in an α‐helix should now be possible, an important step toward deciphering the balance of forces that enable spontaneous protein folding.
Long‐term effects of universal preventive interventions on prescription drug misuse
Authors: Spoth Richard , Trudeau Linda , Shin Chungyeol , Redmond Cleve
Published: April 2008

Background  This is a supplemental report on tests of the long‐term effects of universal preventive interventions conducted during middle school on 17–21‐year‐olds' prescription drug misuse.

Design/setting/participants  Two randomized controlled prevention trials were conducted in public schools in the rural midwestern United States. Study 1 began in 1993, with 667 6th‐graders; follow‐ups with 12th‐graders and 21‐year‐olds included 457 and 483 participants, respectively. Study 2 began in 1998 with 7th‐graders (total sample across waves 2127); follow‐ups with 11th‐ and 12th‐graders included 1443 and 1212 participants, respectively.

Interventions  In study 1, schools were assigned to the Iowa Strengthening Families Program (ISFP), Preparing for the Drug Free Years, or a control condition. In study 2, schools were assigned to the school‐based Life Skills Training (LST) plus a revised ISFP, called SFP 10–14 (LST + SFP 10–14), LST‐only, or a control condition.

Measurements  Self reports of lifetime and past‐year prescription drug misuse.

Findings  In study 1, ISFP 12th‐graders' past year narcotic misuse was significantly less than controls, as were ISFP 21‐year‐olds' life‐time narcotic and barbiturate misuse rates. In study 2, LST + SFP 10–14 showed significant effects on life‐time prescription drug misuse at the 11th‐grade follow‐up, while effects at the 12th‐grade follow‐up were marginally significant.

Conclusions  Consistent with intervention effects on other substance use outcomes reported earlier, results suggest that universal interventions have potential for pubic health impact by reducing some types of prescription drug misuse among adolescents and young adults.
Distribution and pathway for phloem‐dependent movement of Melon necrotic spot virus in melon plants
Authors: GOSALVEZ‐BERNAL BLANCA , GENOVES AINHOA , ANTONIO NAVARRO JOSE , PALLAS VICENTE , SANCHEZ‐PINA M. AMELIA
Published: April 2008

The translocation of Melon necrotic spot virus (MNSV) within tissues of inoculated and systemically infected Cucumis melo L. ‘Galia’ was studied by tissue‐printing and in situ hybridization techniques. The results were compatible with the phloem vascular components being used to spread MNSV systemically by the same assimilate transport route that runs from source to sink organs. Virus RNAs were shown to move from the inoculated cotyledon toward the hypocotyl and root system via the external phloem, whereas the upward spread through the stem to the young tissues took place via the internal phloem. Virus infection was absent from non‐inoculated source tissues as well as from both shoot and root apical meristems, but active sink tissues such as the young leaves and root system were highly infected. Finally, our results suggest that the MNSV invasion of roots is due to virus replication although a destination‐selective process is probably necessary to explain the high levels of virus accumulation in roots. This efficient invasion of the root system is discussed in terms of natural transmission of MNSV by the soil‐borne fungal vector.
Glutathione‐binding proteins of Setaria digitata: antibody responses in human infected with Wuchereria bancrofti
Authors: BAL MADHUSMITA , DAS MANOJ K.
Published: April 2008

Glutathione‐s‐transferase activity was determined in filarial parasites. The activity was detected in adult stages of cattle parasite Setaria digitata. It was absent in other stages of Setaria and also in infective larval stages of Wuchereria bancrofti and Brugia malayi. The activity was enhanced about twenty five fold following purification of adult setaria extracts on glutathione agarose column. Antibody (IgG and IgM) levels to the affinity purified proteins (SdGBP) were detected predominantly (90%) in Wuchereria bancrofti infected individuals compared with normal residents of endemic regions. IgA and IgE responses could not be detected. Filarial sera in contrast to non‐filarial caused reduction in the enzymatic activities of Sd GBP. Micro‐filaraemic sera after dielhylcarhamazine treatment resulted in enhanced reduction of enzymatic activity.
Childhood cirrhosis, hepatopulmonary syndrome and liver transplantation
Authors: Tumgor Gokhan , Arikan Cigdem , Yuksekkaya Hasan Ali , Cakir Murat , Levent Erturk , Yagci Rasit Vural , Kilic Murat , Aydogdu Sema
Published: April 2008

Abstract:  Objectives:  The hepatopulmonary syndrome (HPS) is characterized as a triad: liver disease, intrapulmonary vascular dilatatiton, and arterial hypoxemia. The aim of this study is to analyze outcome of children with HPS in liver transplant era.

Methods:  Between September 1996 and November 2006, 172 cirrhotic patients (median age 5 years; range 0.2–22 years, M/F; 97/75) were followed at Ege University Pediatric Gastroenterology, Hepatology and Nutrition Unit. All patients were evaluated by chest radiography, arterial blood gas analysis, and alveolar‐arterial oxygen tension difference, contrast echocardiography (CEE) after and before the liver transplantation.

Results:  HPS was diagnosed in 33 patients (19%) by CEE. None of them had pulmonary hypertension. HPS was not found related to etiology of the liver disease. Portal hypertension was found related to the development of HPS (75.7% in patients with HPS and 54.6% in others, p = 0.02). 17 of 33 patients with HPS underwent liver transplantation. Preoperative and postoperative period of these patients was uneventful. Patients were extubated in the operating room except for two. Median follow up of transplanted children was 1.9 year (range; 0.75–10 years). Arterial blood gas analysis and CEE positivity regressed in all of them by postoperative 6th month.

Conclusions:  HPS is a serious and important complication of cirrhotic children that leads to tissue hypoxia and central cyanosis. HPS seems reversible after liver transplantation in all patients.
Relative Efficiency of Prilled Urea, Urea Super Granules, Sulphur Coated Urea and Nitrification Inhibitor N‐Serve Blended Urea for Direct Seeded Rice
Authors: Thomas J. , Prasad R.
Published: April 2008

A two year field study conducted at the Indian Agricultural Research Institute, New Delhi, India showed that for direct seeded rice (drilled in moist bed) blending of urea with nitrification inhibitor N‐Serve was the most advantageous; it gave significantly higher grain and straw yield nitrogen uptake by rice than urea super‐granules (USG), urea briquettes (UB), sulphur coated urea (SCU), neem cake coated urea (NCU) and prilled urea. USG or UB were next in order and significantly superior to SCU, NCU and prilled urea, which were equally effective. Nitrogen application to rice left a significant residual effect on succeeding wheat, but various sources of nitrogen studied did not differ significantly in this respect.