bluuebunny/crossref_metadata_2025 huggingface dataset:
Broadly heterogeneous activation of the master regulator for sporulation in
Bacillus subtilis
Authors: Chastanet Arnaud , Vitkup Dennis , Yuan Guo-Cheng , Norman Thomas M. , Liu Jun S. , Losick Richard M.
Published: April 2010

A model system for investigating how developmental regulatory networks determine cell fate is spore formation in
Bacillus subtilis
. The master regulator for sporulation is Spo0A, which is activated by phosphorylation via a phosphorelay that is subject to three positive feedback loops. The ultimate decision to sporulate is, however, stochastic in that only a portion of the population sporulates even under optimal conditions. It was previously assumed that activation of Spo0A and hence entry into sporulation is subject to a bistable switch mediated by one or more feedback loops. Here we reinvestigate the basis for bimodality in sporulation. We show that none of the feedback loops is rate limiting for the synthesis and phosphorylation of Spo0A. Instead, the loops ensure a just-in-time supply of relay components for rising levels of phosphorylated Spo0A, with phosphate flux through the relay being limiting for Spo0A activation and sporulation. In addition, genes under Spo0A control did not exhibit a bimodal pattern of expression as expected for a bistable switch. In contrast, we observed a highly heterogeneous pattern of Spo0A activation that increased in a nonlinear manner with time. We present a computational model for the nonlinear increase and propose that the phosphorelay is a noise generator and that only cells that attain a threshold level of phosphorylated Spo0A sporulate.
Quantum computing with defects
Authors: Weber J. R. , Koehl W. F. , Varley J. B. , Janotti A. , Buckley B. B. , Van de Walle C. G. , Awschalom D. D.
Published: April 2010

Identifying and designing physical systems for use as qubits, the basic units of quantum information, are critical steps in the development of a quantum computer. Among the possibilities in the solid state, a defect in diamond known as the nitrogen-vacancy (NV
-1
) center stands out for its robustness—its quantum state can be initialized, manipulated, and measured with high fidelity at room temperature. Here we describe how to systematically identify other deep center defects with similar quantum-mechanical properties. We present a list of physical criteria that these centers and their hosts should meet and explain how these requirements can be used in conjunction with electronic structure theory to intelligently sort through candidate defect systems. To illustrate these points in detail, we compare electronic structure calculations of the NV
-1
center in diamond with those of several deep centers in 4H silicon carbide (SiC). We then discuss the proposed criteria for similar defects in other tetrahedrally coordinated semiconductors.
Transmembrane polar interactions are required for signaling in the
Escherichia coli
sensor kinase PhoQ
Authors: Goldberg Shalom D. , Clinthorne Graham D. , Goulian Mark , DeGrado William F.
Published: April 2010

PhoQ is the transmembrane sensor histidine kinase of the bacterial
phoPQ
two-component system, which detects and responds to divalent cations and to antimicrobial peptides, and can trigger virulence. Despite their ubiquitous importance in bacterial signaling, the structure and mechanism of the sensor kinases are not fully understood. In particular, the mechanism by which the signal is propagated through the transmembrane (TM) region remains unclear. We have identified a critical asparagine residue in the second TM helix of PhoQ. Replacement of this Asn202 with a variety of hydrophobic amino acids results in a protein that is blind to signal, fails to activate transcription of PhoQ-dependent genes, and abrogates transcription when coexpressed with wild-type PhoQ. Analysis of other two-component kinase sequences indicated that many such proteins contain similarly conserved polar residues, and the structure of one such domain shows a polar residue proximal to an extended cavity near the center of the TM bundle. We therefore examined the role of Asn202 in PhoQ. Our analysis indicated that its kinase function is dependent on the polarity of Asn202, rather than its precise structure or position in the TM region; it can be displaced up or down one turn of TM helix 2, or even moved to the adjacent TM helix 1. The presence of polar TM amino acids among many diverse sensor kinases suggest a widespread mechanism of two-component signal transduction; we speculate that they might stabilize underpacked water-containing cavities that can accommodate conformational changes required for switching from phosphatase to kinase-competent conformations.
IL-23 suppresses innate immune response independently of IL-17A during carcinogenesis and metastasis
Authors: Teng Michele W. L. , Andrews Daniel M. , McLaughlin Nicole , von Scheidt Bianca , Ngiow Shin Foong , Möller Andreas , Hill Geoffrey R. , Iwakura Yoichiro , Oft Martin , Smyth Mark J.
Published: April 2010

IL-23 is an important molecular driver of Th17 cells and has strong tumor-promoting proinflammatory activity postulated to occur via adaptive immunity. Conversely, more recently it has been reported that IL-17A elicits a protective inflammation that promotes the activation of tumor-specific CD8+T cells. Here we show the much broader impact of IL-23 in antagonizing antitumor immune responses primarily mediated by innate immunity. Furthermore, the majority of this impact was independent of IL-17A, which did not appear critical for many host responses to tumor initiation or metastases. IL-23–deficient mice were resistant to experimental tumor metastases in three models where host NK cells controlled disease. Immunotherapy with IL-2 was more effective in mice lacking IL-23, and again the protection afforded was NK cell mediated and independent of IL-17A. Further investigation revealed that loss of IL-23 promoted perforin and IFN-γ antitumor effector function in both metastasis models examined. IL-23-deficiency also strikingly protected mice from tumor formation in two distinct mouse models of carcinogenesis where the dependence on host IL-12p40 and IL-17A was quite different. Notably, in the 3′-methylcholanthrene (MCA) induction of fibrosarcoma model, this protection was completely lost in the absence of NK cells. Overall, these data indicate the general role that IL-23 plays in suppressing natural or cytokine-induced innate immunity, promoting tumor development and metastases independently of IL-17A.
Molecular basis for SH3 domain regulation of F-BAR–mediated membrane deformation
Authors: Rao Yijian , Ma Qingjun , Vahedi-Faridi Ardeschir , Sundborger Anna , Pechstein Arndt , Puchkov Dmytro , Luo Lin , Shupliakov Oleg , Saenger Wolfram , Haucke Volker
Published: April 2010

Members of the Bin/amphiphysin/Rvs (BAR) domain protein superfamily are involved in membrane remodeling in various cellular pathways ranging from endocytic vesicle and T-tubule formation to cell migration and neuromorphogenesis. Membrane curvature induction and stabilization are encoded within the BAR or Fer-CIP4 homology-BAR (F-BAR) domains, α-helical coiled coils that dimerize into membrane-binding modules. BAR/F-BAR domain proteins often contain an SH3 domain, which recruits binding partners such as the oligomeric membrane-fissioning GTPase dynamin. How precisely BAR/F-BAR domain-mediated membrane deformation is regulated at the cellular level is unknown. Here we present the crystal structures of full-length syndapin 1 and its F-BAR domain. Our data show that syndapin 1 F-BAR-mediated membrane deformation is subject to autoinhibition by its SH3 domain. Release from the clamped conformation is driven by association of syndapin 1 SH3 with the proline-rich domain of dynamin 1, thereby unlocking its potent membrane-bending activity. We hypothesize that this mechanism might be commonly used to regulate BAR/F-BAR domain-induced membrane deformation and to potentially couple this process to dynamin-mediated fission. Our data thus suggest a structure-based model for SH3-mediated regulation of BAR/F-BAR domain function.
H-NOX–mediated nitric oxide sensing modulates symbiotic colonization by
Vibrio fischeri
Authors: Wang Yanling , Dufour Yann S. , Carlson Hans K. , Donohue Timothy J. , Marletta Michael A. , Ruby Edward G.
Published: April 2010

The bioluminescent bacterium
Vibrio fischeri
initiates a specific, persistent symbiosis in the light organ of the squid
Euprymna scolopes.
During the early stages of colonization,
V. fischeri
is exposed to host-derived nitric oxide (NO). Although NO can be both an antimicrobial component of innate immunity and a key signaling molecule in eukaryotes, potential roles in beneficial host–microbe associations have not been described.
V. fischeri hnoX
encodes a heme NO/oxygen-binding (H-NOX) protein, a member of a family of bacterial NO- and/or O
2
-binding proteins of unknown function. We hypothesized that H-NOX acts as a NO sensor that is involved in regulating symbiosis-related genes early in colonization. Whole-genome expression studies identified 20 genes that were repressed in an NO- and H-NOX–dependent fashion. Ten of these, including hemin-utilization genes, have a promoter with a putative ferric-uptake regulator (Fur) binding site. As predicted, in the presence of NO, wild-type
V. fischeri
grew more slowly on hemin than a
hnoX
deletion mutant. Host-colonization studies showed that the
hnoX
mutant was also 10-fold more efficient in initially colonizing the squid host than the wild type; similarly, in mixed inoculations, it outcompeted the wild-type strain by an average of 16-fold after 24 h. However, the presence of excess hemin or iron reversed this dominance. The advantage of the mutant in colonizing the iron-limited light-organ tissues is caused, at least in part, by its greater ability to acquire host-derived hemin. Our data suggest that
V. fischeri
normally senses a host-generated NO signal through H-NOX
Vf
and modulates the expression of its iron uptake capacity during the early stages of the light-organ symbiosis.
CryoEM structure of Hsp104 and its mechanistic implication for protein disaggregation
Authors: Lee Sukyeong , Sielaff Bernhard , Lee Jungsoon , Tsai Francis T. F.
Published: April 2010

Hsp104 is a ring-forming AAA+ machine that recognizes both aggregated proteins and prion-fibrils as substrates and, together with the Hsp70 system, remodels substrates in an ATP-dependent manner. Whereas the ability to disaggregate proteins is dependent on the Hsp104 M-domain, the location of the M-domain is controversial and its exact function remains unknown. Here we present cryoEM structures of two Hsp104 variants in both crosslinked and noncrosslinked form, in addition to the structure of a functional Hsp104 chimera harboring T4 lysozyme within the M-domain helix L2. Unexpectedly, we found that our Hsp104 chimera has gained function and can solubilize heat-aggregated β-galactosidase (β-gal) in the absence of the Hsp70 system. Our fitted structures confirm that the subunit arrangement of Hsp104 is similar to other AAA+ machines, and place the M-domains on the Hsp104 exterior, where they can potentially interact with large, aggregated proteins.
Dynamics and processes of copy number instability in human γ-globin genes
Authors: Neumann Rita , Lawson Victoria E. , Jeffreys Alec J.
Published: April 2010

Copy number variation in the human genome is prevalent but relatively little is known about the dynamics of DNA rearrangement. We therefore used the duplicated γ-globin genes as a simple system to explore de novo copy number changes. Rearrangements that changed gene number were seen in both germline and somatic DNA, and mainly arose by unequal sister chromatid exchange between homologous sequences, with evidence from recurrent mosaic rearrangements that many, if not all, of these events in sperm arise before meiosis. Unequal exchange frequencies are apparently controlled primarily by the degree of sequence identity shared by the duplicate genes, leading to substantial variation between haplotypes in copy number instability. Additional, more complex rearrangements generated by mechanisms not involving homologous recombination, and in some cases showing DNA transfer between chromosomes, were also detected but were rare. Sequence changes were also seen in γ-globin DNA molecules, with strong evidence that some were genuine de novo base substitutions. They were present in sperm at a frequency far higher than predicted from current estimates of germline mutation rates, raising interesting questions about base mutation dynamics in the male germline.
Helper-independent
piggyBac
plasmids for gene delivery approaches: Strategies for avoiding potential genotoxic effects
Authors: Urschitz Johann , Kawasumi Miyuri , Owens Jesse , Morozumi Kazuto , Yamashiro Hideaki , Stoytchev Ilko , Marh Joel , Dee James A. , Kawamoto Kris , Coates Craig J. , Kaminski Joseph M. , Pelczar Pawel , Yanagimachi Ryuzo , Moisyadi Stefan
Published: April 2010

Efficient integration of functional genes is an essential prerequisite for successful gene delivery such as cell transfection, animal transgenesis, and gene therapy. Gene delivery strategies based on viral vectors are currently the most efficient. However, limited cargo capacity, host immune response, and the risk of insertional mutagenesis are limiting factors and of concern. Recently, several groups have used transposon-based approaches to deliver genes to a variety of cells. The
piggyBac
(pB) transposase in particular has been shown to be well suited for cell transfection and gene therapy approaches because of its flexibility for molecular modification, large cargo capacity, and high transposition activity. However, safety considerations regarding transposase gene insertions into host genomes have rarely been addressed. Here we report our results on engineering helper-independent pB plasmids. The single-plasmid gene delivery system carries both the
piggyBac
transposase (pBt) expression cassette as well as the transposon cargo flanked by terminal repeat element sequences. Improvements to the helper-independent structure were achieved by developing new plasmids in which the pBt gene is rendered inactive after excision of the transposon from the plasmid. As a consequence, potentially negative effects that may develop by the persistence of an active pBt gene posttransposition are eliminated. The results presented herein demonstrate that our helper-independent plasmids represent an important step in the development of safe and efficient gene delivery methods that should prove valuable in gene therapy and transgenic approaches.
Perifornical Urocortin-3 mediates the link between stress-induced anxiety and energy homeostasis
Authors: Kuperman Yael , Issler Orna , Regev Limor , Musseri Ifat , Navon Inbal , Neufeld-Cohen Adi , Gil Shosh , Chen Alon
Published: April 2010

In response to physiological or psychological challenges, the brain activates behavioral and neuroendocrine systems linked to both metabolic and emotional outputs designed to adapt to the demand. However, dysregulation of integration of these physiological responses to challenge can have severe psychological and physiological consequences, and inappropriate regulation, disproportional intensity, or chronic or irreversible activation of the stress response is linked to the etiology and pathophysiology of mood and metabolic disorders. Using a transgenic mouse model and lentiviral approach, we demonstrate the involvement of the hypothalamic neuropeptide Urocortin-3, a specific ligand for the type-2 corticotropin-releasing factor receptor, in modulating septal and hypothalamic nuclei responsible for anxiety-like behaviors and metabolic functions, respectively. These results position Urocortin-3 as a neuromodulator linking stress-induced anxiety and energy homeostasis and pave the way toward better understanding of the mechanisms that mediate the reciprocal relationships between stress, mood and metabolic disorders.
Genetic suppression of the circadian
Clock
mutation by the melatonin biosynthesis pathway
Authors: Shimomura Kazuhiro , Lowrey Phillip L. , Vitaterna Martha Hotz , Buhr Ethan D. , Kumar Vivek , Hanna Peter , Omura Chiaki , Izumo Mariko , Low Sharon S. , Barrett R. Keith , LaRue Silvia I. , Green Carla B. , Takahashi Joseph S.
Published: April 2010

Most laboratory mouse strains including C57BL/6J do not produce detectable levels of pineal melatonin owing to deficits in enzymatic activity of arylalkylamine
N
-acetyltransferase (AANAT) and
N
-acetylserotonin
O
-methyl transferase (ASMT), two enzymes necessary for melatonin biosynthesis. Here we report that alleles segregating at these two loci in C3H/HeJ mice, an inbred strain producing melatonin, suppress the circadian period-lengthening effect of the
Clock
mutation. Through a functional mapping approach, we localize mouse
Asmt
to chromosome X and show that it, and the
Aanat
locus on chromosome 11, are significantly associated with pineal melatonin levels. Treatment of suprachiasmatic nucleus (SCN) explant cultures from

Period2
Luciferase

(

Per2
Luc

)
Clock
/+ reporter mice with melatonin, or the melatonin agonist, ramelteon, phenocopies the genetic suppression of the
Clock
mutant phenotype observed in living animals. These results demonstrate that melatonin suppresses the
Clock
/+ mutant phenotype and interacts with
Clock
to affect the mammalian circadian system.
Esperanto y anarquismo en la Argentina de principios del siglo XX
Authors: Stefano Mariana di
Published: April 2010

El artículo analiza, desde una perspectiva glotopolítica, una polémica sobre el esperanto desarrollada en el diario anarquista de la Argentina La Protesta, en 1917, entre libertarios pro- y anti- esperantistas. Se estudian las ideologías lingüísticas de ambos grupos a través de la identificación de los ideologemas que sostienen las argumentaciones. A partir de categorías propias de la Política y Planeamiento Lingüísticos, se caracteriza el conflicto en el nivel de la planificación del estatus de la lengua, que generó debates tanto sobre la selección de la variedad (el esperanto) como sobre la implementación (se cuestiona la legitimidad de emprender una política lingüística). El análisis traza, por último, una relación entre las ideologías lingüísticas y sistemas ideológicos más amplios y encuentra un vínculo entre los grupos anarquistas ortodoxos y el rechazo del esperanto, y entre los proclives a la organización y la defensa de esta lengua.
Co-receptor choice by Vα14i NKT cells is driven by Th-POK expression rather than avoidance of CD8-mediated negative selection
Authors: Engel Isaac , Hammond Kirsten , Sullivan Barbara A. , He Xi , Taniuchi Ichiro , Kappes Dietmar , Kronenberg Mitchell
Published: April 2010

Mouse natural killer T (NKT) cells with an invariant Vα14-Jα18 rearrangement (Vα14 invariant [Vα14i] NKT cells) are either CD4+CD8− or CD4−CD8−. Because transgenic mice with forced CD8 expression in all T cells exhibited a profound NKT cell deficit, the absence of CD8 has been attributed to negative selection. We now present evidence that CD8 does not serve as a coreceptor for CD1d recognition and that the defect in development in CD8 transgene homozygous mice is the result of a reduction in secondary T cell receptor α rearrangements. Thymocytes from mice hemizygous for the CD8 transgene have a less severe rearrangement defect and have functional CD8+ Vα14i NKT cells. Furthermore, we demonstrate that the transcription factor Th, Poxviruses and Zinc finger, and Krüppel family (Th-POK) is expressed by Vα14i NKT cells throughout their differentiation and is necessary both to silence CD8 expression and for the functional maturity of Vα14i NKT cells. We therefore suggest that Th-POK expression is required for the normal development of Vα14i NKT cells and that the absence of CD8 expression by these cells is a by-product of such expression, as opposed to the result of negative selection of CD8-expressing Vα14i NKT cells.
Biphasic Aire expression in early embryos and in medullary thymic epithelial cells before end-stage terminal differentiation
Authors: Nishikawa Yumiko , Hirota Fumiko , Yano Masashi , Kitajima Hiroyuki , Miyazaki Jun-ichi , Kawamoto Hiroshi , Mouri Yasuhiro , Matsumoto Mitsuru
Published: April 2010

The roles of autoimmune regulator (Aire)–expressing medullary thymic epithelial cells (mTECs) in the organization of the thymic microenvironment for establishing self-tolerance are enigmatic. We sought to monitor the production and maintenance of Aire-expressing mTECs by a fate-mapping strategy in which bacterial artificial chromosome transgenic (Tg) mice expressing Cre recombinase under the control of the Aire regulatory element were crossed with a GFP reporter strain. We found that, in addition to its well recognized expression within mature mTECs, Aire was expressed in the early embryo before emergence of the three germ cell layers. This observation may help to explain the development of ectodermal dystrophy often seen in patients with AIRE deficiency. With the use of one Tg line in which Cre recombinase expression was confined to mTECs, we found that Aire+CD80high mTECs further progressed to an Aire−CD80intermediate stage, suggesting that Aire expression is not constitutive from after its induction until cell death but instead is down-regulated at the beginning of terminal differentiation. We also demonstrated that many mTECs of Aire-expressing lineage are in close contact with thymic dendritic cells. This close proximity may contribute to transfer of tissue-restricted self-antigens expressed by mTECs to professional antigen-presenting cells.
S1P1 receptor directs the release of immature B cells from bone marrow into blood
Authors: Allende Maria L. , Tuymetova Galina , Lee Bridgin G. , Bonifacino Eliana , Wu Yun-Ping , Proia Richard L.
Published: April 2010

S1P1 receptor expression is required for the egress of newly formed T cells from the thymus and exit of mature T and B cells from secondary lymphoid organs. In this study, we deleted the expression of the S1P1 receptor gene (S1pr1) in developing B cells in the bone marrow. Although B cell maturation within the bone marrow was largely normal in the B cell–specific S1pr1 knockout (B-S1pr1KO) mice, their newly generated immature B cells appeared in the blood at abnormally low numbers as compared with control mice. In the bone marrow of B-S1pr1KO mice, immature B cells in contact with the vascular compartment displayed increased apoptosis as compared with control mice. Forced expression of CD69, a negative regulator of S1P1 receptor expression, in developing bone marrow B cells also reduced the number of immature B cells in the blood. Attenuation of CXCR4 signaling, which is required for the proper retention of developing B cells in bone marrow, did not release immature B cells into the blood of B-S1pr1KO mice as effectively as in control mice. Our results indicate that the S1P1 receptor provides a signal necessary for the efficient transfer of newly generated immature B cells from the bone marrow to the blood.
Regulation of medullary thymic epithelial cell differentiation and function by the signaling protein Sin
Authors: Danzl Nichole M. , Donlin Laura T. , Alexandropoulos Konstantina
Published: April 2010

Medullary thymic epithelial cells (mTECs) play an important role in T cell tolerance and prevention of autoimmunity. Mice deficient in expression of the signaling protein Sin exhibit exaggerated immune responses and multitissue inflammation. Here, we show that Sin is expressed in the thymic stroma, specifically in mTECs. Sin deficiency led to thymic stroma–dependent autoimmune manifestations shown by radiation chimeras and thymic transplants in nude mice, and associated with defective mTEC-mediated elimination of thymocytes in a T cell receptor transgenic model of negative selection. Lack of Sin expression correlated with a disorganized medullary architecture and fewer functionally mature mTECs under steady–state conditions. Additionally, Sin deficiency inhibited the expansion of mTECs in response to in vivo administration of keratinocyte growth factor (KGF). These results identify Sin as a novel regulator of mTEC development and T cell tolerance, and suggest that Sin is important for homeostatic maintenance of the medullary epithelium in the adult thymus.
Atrial fibrillation in heart failure is associated with an increased risk of death only in patients with ischaemic heart disease
Authors: Raunsø Jakob , Pedersen Ole Dyg , Dominguez Helena , Hansen Morten Lock , Møller Jacob Eifer , Kjærgaard Jesper , Hassager Christian , Torp‐Pedersen Christian , Køber Lars ,   on behalf of the EchoCardiography and Heart Outcome Study (ECHOS) investigators
Published: April 2010

Aims

The prognostic importance of atrial fibrillation (AF) in heart failure (HF) populations is controversial and may depend on patient selection. In the present study, we investigated the prognostic impact of AF in a large population with HF of various aetiologies.

Methods and results

We included 2881 patients admitted to hospital with symptoms of worsening HF over a 4‐year period (2001–2004), all patients were participants in the Echocardiography and Heart Outcome Study (ECHOS). Patients were followed for up to 7 years for all‐cause mortality stratified according to heart rhythm (sinus rhythm, paroxysmal, or chronic AF) and according to the presence of ischaemic heart disease (IHD). During follow‐up, 1934 patients (67%) died. In HF patients with a history of IHD, chronic AF was associated with an increased risk of death [hazard ratio (HR) 1.44; 95% confidence interval (CI): 1.18–1.77; P < 0.001). In contrast, in patients without IHD, chronic AF was not associated with an increased mortality risk (HR 0.88; 95% CI: 0.71–1.09; P = 0.25). There was significant interaction between the aetiology of HF and the prognostic importance of chronic AF (Pinteraction = 0.003).

Conclusion

In patients with HF, AF is associated with an increased risk of death only in patients with underlying IHD.
A simulated archival tagging programme for albacore (Thunnus alalunga) in the Northeast Atlantic, including an analysis of factors affecting tag recovery
Authors: Cosgrove Ronan , Arregi Igor , Brophy Deirdre , Arrizabalaga Haritz , Ortiz de Zarate Victoria , Griffin Nigel
Published: April 2010

Cosgrove, R., Arregi, I., Brophy, D., Arrizabalaga, H., Ortiz de Zarate, V., and Griffin, N. 2010. A simulated archival tagging programme for albacore (Thunnus alalunga) in the Northeast Atlantic, including an analysis of factors affecting tag recovery. – ICES Journal of Marine Science, 67: 1216–1221. An archival tagging programme in the Northeast Atlantic would assist in testing the hypothesis that subpopulations of juvenile albacore exist within the region and provide important information on fish behaviour in relation to environmental variables. No information was available, however, on the ability of juvenile albacore to carry costly implanted archival tags, or on rates of tag recovery. A simulated archival tagging study on albacore using simulated or “dummy” archival tags was therefore carried out in the Bay of Biscay from 2005 to 2008. In all, 353 fish were tagged and released, and 9 fish (2.55%) were recaptured. A comprehensive ICCAT database of conventionally tagged fish in the Northeast Atlantic was also analysed to determine whether optimal conditions at the time of release could be identified and used to boost recovery rates in future tagging programmes. A binary logistic regression model using a response variable with two possible outcomes, recaptured or not recaptured, was developed, then tested on two datasets to deal with association between variables. Effort and fishing gear were significant in the first dataset, and length class and fishing gear in the second. The last two factors can be manipulated, and a recapture rate of >5% was predicted if derived optimal tagging conditions are followed in future tagging programmes.
Antibodies to CBir1 Are Associated With Glycogen Storage Disease Type Ib
Authors: Davis Michael K , Valentine John F , Weinstein David A , Polyak Steven
Published: April 2010

Objectives:

Glycogen storage disease (GSD) type Ib is a congenital disorder of glycogen metabolism that is associated with neutropenia, neutrophil and monocyte dysfunction, and an inflammatory bowel disease (IBD) that mimics a Crohn disease phenotype. The enteric microflora is implicated in the pathogenesis of IBD; however, its role in the development of GSD‐associated IBD is unknown. Antibody reactivity to Saccharomyces cerevisiae antibodies (ASCA), Escherichia coli outer membrane porin C (anti‐OmpC), and bacterial flagellin (anti‐CBir1) have been associated with Crohn disease in the general population, but they have an undetermined association in children and adults with GSD‐Ib. Our goal was to examine the association of ASCA, anti‐OmpC, and anti‐CBir1 with the clinical features of GSD‐Ib enterocolitis.

Patients and Methods:

A retrospective review identified 19 patients with GSD‐Ib with or without a known diagnosis of enterocolitis. Radiographic, endoscopic, and serologic data were collected and assays for ASCA, anti‐OmpC, and anti‐CBir1 obtained.

Results:

Seven patients had combined radiographic, endoscopic, and histologic evidence of intestinal inflammation; the majority had ileocolonic involvement. Seventeen of 19 (89%) patients had elevated anti‐CBir1 levels (6/7 in the IBD group and 11/12 in the no clinical evidence of IBD group). Thirteen of 19 (68%) had elevated anti‐OmpC levels (5/7 in the IBD group and 8/12 in the no clinical evidence of IBD group). Eleven of 19 (58%) patients had elevated ASCA IgA levels (4/7 in the IBD group and 7/12 in the no clinical evidence of IBD group).

Conclusions:

Nearly all of the patients with GSD‐Ib had elevated anti‐CBir1 levels. The antibody did not differentiate those with and without a diagnosis of GSD‐Ib‐associated IBD. Seroreactivity to flagellin may represent immune dysfunction rather than active enterocolitis in this patient population. Long‐term follow‐up of the group without known IBD is required to determine whether these antibodies can predict intestinal inflammation.
Gastric Emptying Time of Oral Contrast Material in Children and Adolescents Undergoing Abdominal Computed Tomography
Authors: Berger‐Achituv Sivan , Zissin Rivka , Shenkman Ze'ev , Gutermacher Michael , Erez Ilan
Published: April 2010

Objectives:

Considering the hazards of pulmonary aspiration of oral contrast material (OCM) during general anesthesia, we investigated the gastric emptying time (GET) of OCM in children and adolescents undergoing abdominal computed tomography (CT).

Patients and Methods:

Included in the study were 101 consecutive patients ages 3.1 to 17.9 years (mean age 12.2 ± 3.3 years), who underwent contrast‐enhanced abdominal CT for suspected acute appendicitis (n = 90), abdominal trauma (n = 10), or suspected ileus (n = 1). Oral iodinated ioxithalamate was given for bowel opacification. Background data (age, sex, weight, chronic diseases, and medication intake), time of initiation and completion of OCM, and time of CT scanning were recorded. To estimate the GET of OCM, CT images were reviewed to examine whether the stomach was empty or full of OCM at the time of imaging.

Results:

The Kaplan‐Meier curve showed that 75% of the patients had OCM in the stomach 48 ± 5.2 minutes after its completion, 50% after 74 ± 7.9 minutes, and 25% after 135 ± 32.5 minutes; 1 patient still had OCM after 162 minutes. Except for the length of time taken to drink the contrast material (≤90 minutes was associated with slower empting of the stomach; log rank, P = 0.03), GET of OCM was not correlated with sex (P = 0.16), age (P = 0.15), weight (P = 0.13), or type of diagnosis (P = 0.41).

Conclusions:

Given the variability of GET of OCM and if clinically feasible, we advocate waiting at least 3 hours between completion of OCM ingestion and general anesthesia induction.
Iron, Zinc, and Copper Nutritional Status in Children Infected With Helicobacter pylori
Authors: Janjetic Mariana A , Goldman Cinthia G , Balcarce Norma E , Rua Eduardo Cueto , González Andrea Beltrán , Fuda Julián A , Meseri Emiliano I , Torti Horacio E , Barrado Julieta , Zubillaga Marcela B , López Laura B , Boccio José R
Published: April 2010

Objective:

Helicobacter pylori colonizes the gastric mucosa of about half of the world's population and it has been related to extragastrointestinal diseases. The present study sought to evaluate the association between H pylori infection and iron, zinc, and copper nutritional status in symptomatic children.

Patients and Methods:

A cross‐sectional study was carried out in 395 children (4–16 years) with upper gastrointestinal symptoms, who were tested for H pylori infection by the 13C‐urea breath test. Iron status was determined by hemoglobin, serum ferritin, and serum transferrin receptors. Copper and zinc serum concentrations were also evaluated. Epidemiological data, dietary assessment, and anthropometric indicators were analyzed as potential confounding factors.

Results:

Prevalence of H pylori infection was 24.3%. Anemia and iron deficiency (ID) were found in 12.0% and 14.3% of the H pylori–positive and 8.9% and 11.0% of the H pylori–negative children, respectively. There was no association between H pylori infection and anemia (odds ratio = 1.54 [95% confidence interval [CI] 0.73%–3.24%]) or ID (odds ratio = 1.35 [95% CI 0.67–2.70]). Crude β coefficients showed that H pylori has no significant effect on hemoglobin, serum ferritin, serum transferrin receptors, copper, and zinc concentrations. However, adjusted results suggested that H pylori–infected children had an increase of 9.74 μg/dL (95% CI 2.12–17.37 μg/dL) in copper concentrations.

Conclusions:

This study revealed that H pylori infection was not associated with iron deficiency, anemia, or zinc concentrations; however, a positive relation with copper status was found after adjusting for confounding factors. The contribution of H pylori infection to higher copper concentrations needs to be confirmed by additional studies.
Postoperative Outcome of Colectomy for Pediatric Patients With Ulcerative Colitis
Authors: Patton Dana , Gupta Neera , Wojcicki Janet M , Garnett Elizabeth A , Nobuhara Kerilyn , Heyman Melvin B
Published: April 2010

Background:

Few studies have reported on the surgical outcomes of colectomy in pediatric patients with ulcerative colitis (UC).

Patients and Methods:

We conducted a retrospective chart review of all pediatric patients diagnosed with UC who underwent colectomy at UCSF between 1980 and 2005 to identify early (within 30 days) and later complications of surgery.

Results:

Complete medical records were available for 31 patients [12.4 ± 3.3 (range 6–19) years] with UC who underwent colectomy at UCSF Children's Hospital. Total colectomy with ileal pouch anal anastomosis (IPAA) was performed in 21 of the 31 patients (12 without diverting ileostomy). Five of the 31 patients had an initial colectomy with IPAA and J‐pouch performed later; 4 had an initial subtotal colectomy for urgent indications. Only one of 31 had IPAA with S‐pouch. The median number of early postoperative complications was 1.0; 4 required additional surgery to treat complications. The most common early complications were small intestinal obstruction in 6 (19%) and wound infection in 4 (13%). Preoperative medications included corticosteroids in 25 (81%), 6‐mercaptopurine/azathioprine in 10 (32%), and 5‐aminosalicylates in 19 (61%). Medication exposure was not related to postoperative complications. Late complications included pouchitis in 12 (39%), anastomotic, anal, or rectal strictures in 5 (16%), and fistulas in 5 (16%); 1 (3%) was subsequently diagnosed as having Crohn disease.

Conclusions:

Postcolectomy morbidity is common among pediatric patients with UC. Preoperative medications were not associated with postoperative complications. Investigations to determine preoperative factors affecting surgical outcomes and long‐term satisfaction following this surgery in a large pediatric cohort are needed.
Detection and correction of underassigned rotational symmetry prior to structure deposition
Authors: Poon Billy K. , Grosse-Kunstleve Ralf W. , Zwart Peter H. , Sauter Nicholas K.
Published: April 2010

Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit.
Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions
Authors: Trapani Stefano , Schoehn Guy , Navaza Jorge , Abergel Chantal
Published: April 2010

The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme fromCandida albicans(∼190 kDa) and that of the orthologousStreptomyces coelicolorprotein.
Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer fromAmphitrite ornata
Authors: de Serrano Vesna , D'Antonio Jennifer , Franzen Stefan , Ghiladi Reza A.
Published: April 2010

As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelidAmphitrite ornatapossess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 Å resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H2O2-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure–function relationships.
Structural analysis of mycobacterial branched-chain aminotransferase: implications for inhibitor design
Authors: Castell Alina , Mille Christian , Unge Torsten
Published: April 2010

The branched-chain aminotransferase (BCAT) ofMycobacterium tuberculosishas been characterized as being essential to the survival of the bacterium. The enzyme is pyridoxal 5′-phosphate-dependent and belongs to the aminotransferase IIIa subfamily, to which the human BCATs also belong. The overall sequence similarity is high within the subfamily and the sequence identity among the active-site residues is high. In order to identify structurally unique features ofM. tuberculosisBCAT, X-ray structural and functional analyses of the closely related BCAT fromM. smegmatiswere carried out. The crystal structures include the apo form at 2.2 Å resolution and a 1.9 Å structure of the holo form cocrystallized with the inhibitorO-benzylhydroxylamine (Obe). The analyses highlighted the active-site residues Tyr209 and Gly243 as being structurally unique characteristics of the mycobacterial BCATs relative to the human BCATs. The inhibitory activities of Obe and ammonium sulfate were verified in an inhibition assay. Modelling of the inhibitor Obe in the substrate pocket indicated potential for the design of a mycobacterial-specific inhibitor.
Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography
Authors: Gardberg Anna S. , Del Castillo Alexis Rae , Weiss Kevin L. , Meilleur Flora , Blakeley Matthew P. , Myles Dean A. A.
Published: April 2010

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3-protonated perdeuterated crystals ofPyrococcus furiosusrubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 Å resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the σ level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 Å resolution RT neutron data for perdeuterated rubredoxin are ∼8 times more likely overall to provide high-confidence positions for D atoms than 1.1 Å resolution X-ray data at 100 K or RT. At or above the 1.0σ level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 Å resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0σ level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.
Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plantColeus blumeiBenth.
Authors: Janiak Verena , Petersen Maike , Zentgraf Matthias , Klebe Gerhard , Heine Andreas
Published: April 2010

Hydroxy(phenyl)pyruvate reductase [H(P)PR] belongs to the family of D-isomer-specific 2-hydroxyacid dehydrogenases and catalyzes the reduction of hydroxyphenylpyruvates as well as hydroxypyruvate and pyruvate to the corresponding lactates. Other non-aromatic substrates are also accepted. NADPH is the preferred cosubstrate. The crystal structure of the enzyme fromColeus blumei(Lamiaceae) has been determined at 1.47 Å resolution. In addition to the apoenzyme, the structure of a complex with NADP+was determined at a resolution of 2.2 Å. H(P)PR is a dimer with a molecular mass of 34 113 Da per subunit. The structure is similar to those of other members of the enzyme family and consists of two domains separated by a deep catalytic cleft. To gain insights into substrate binding, several compounds were docked into the cosubstrate complex structure using the programAutoDock. The results show two possible binding modes with similar docking energy. However, only binding modeAprovides the necessary environment in the active centre for hydride and proton transfer during reduction, leading to the formation of the (R)-enantiomer of lactate and/or hydroxyphenyllactate.
Hereditary causes of kidney tumours
Authors: Axwijk Priscilla Helene , Kluijt Irma , De Jong Daphne , Gille Hans , Teertstra Jelle , Horenblas Simon
Published: April 2010

Eur J Clin Invest 2010; 40 (5): 433–439

Background  In most cases of renal cell carcinoma there is no family history of renal cancer and no hereditary cause of the disease. Hereditary renal cancer accounts for about 2–4% of cases. Recognition of this subgroup by clinicians is important because of the possibility of severe medical consequences for patients and their relatives.

Materials and methods  We review the latest data about different genetic conditions characterized by an increased risk of developing renal cancer and we formulate tools to recognize high‐risk families.

Results  In general, a positive family history, young age at diagnosis of renal cancer, multiple and/or bilateral renal tumours and combined occurrence of different histological types of renal tumours should raise suspicion of a hereditary renal tumour syndrome. In addition, the presence of specific extrarenal symptoms in patients could assist in differentiating between tumour syndromes.

Conclusions  A detailed medical and family history, along with physical examination are key factors to diagnose hereditary renal cancer syndromes. When a genetic predisposition for renal cancer is suspected, referral to a Family Cancer Clinic is warranted to initiate genetic examination and counselling on preventive options.
Applying systematic conservation planning principles to palustrine and inland saline wetlands of New Zealand
Authors: AUSSEIL ANNE‐GAELLE E. , LINDSAY CHADDERTON W. , GERBEAUX PHILIPPE , THEO STEPHENS R.T. , LEATHWICK JOHN R.
Published: April 2010

1. Previous attempts to identify nationally important wetlands for biodiversity in New Zealand were based on expert panel opinions because quantitative approaches were hampered by a lack of data. We apply principles of systematic conservation planning to remote sensing data within a geographical information system (GIS) to identify nationally important palustrine and inland saline wetlands.

2. A catchment‐based classification was used to divide New Zealand into 29 biogeographic units. To meet representation goals, all wetland classes need to be protected within each unit.

3. We mapped current and historic wetlands down to a minimum size of 0.5 ha. Over 7000 current wetlands were mapped using standardised satellite imagery and a collection of point or polygon data. Historical extent was estimated from soil information refined using a digital elevation model. The current extent of wetlands is 10% of the historic extent, which is consistent with previous estimates.

4. A classification was produced using fuzzy expert rules within a GIS to identify seven wetland classes: bog, fen, swamp, marsh, pakihi/gumland, seepage and inland saline. Swamps and pakihi/gumland are the most common, but the former has sustained the greatest reduction in area with only 6% of its historical extent remaining. A preliminary field assessment of classification accuracy in the Otago region found only 60% agreement, mainly because of the misclassification of marshes into swamps.

5. Wetland condition was estimated using six measures of human disturbance (natural cover, human‐made impervious cover, introduced fish, woody weeds, artificial drainage and nitrate leaching risk) applied at three spatial scales: the wetland’s catchment, a 30‐m buffer around the wetland and the wetland itself. Measures were transformed and combined into a single condition index. More than 60% of remaining wetlands had condition indices <0.5, probably indicating moderate to severe degradation and loss of native biodiversity.

6. Sites were ranked within each biogeographic unit using the wetland classification to ensure a representative set of wetland diversity. Rankings were determined by combining condition and complementarity to calculate conservation effectiveness that was then weighted by irreplaceability. Highest ranked sites in each biogeographic unit were usually the largest remaining wetlands that contained multiple wetland classes. This reflects their potential to protect a diverse range of wetland classes and a high proportion of the remaining habitat.