bluuebunny/crossref_metadata_2025 huggingface dataset:
Use-dependent amplification of presynaptic Ca
2+
signaling by axonal ryanodine receptors at the hippocampal mossy fiber synapse
Authors: Shimizu Hidemi , Fukaya Masahiro , Yamasaki Miwako , Watanabe Masahiko , Manabe Toshiya , Kamiya Haruyuki
Published: August 2008

Presynaptic Ca
2+
stores have been suggested to regulate Ca
2+
dynamics within the nerve terminals at certain types of the synapse. However, little is known about their mode of activation, molecular identity, and detailed subcellular localization. Here, we show that the ryanodine-sensitive stores exist in axons and amplify presynaptic Ca
2+
accumulation at the hippocampal mossy fiber synapses, which display robust presynaptic forms of plasticity. Caffeine, a potent drug inducing Ca
2+
release from ryanodine-sensitive stores, causes elevation of presynaptic Ca
2+
levels and enhancement of transmitter release from the mossy fiber terminals. The blockers of ryanodine receptors, TMB-8 or ryanodine, reduce presynaptic Ca
2+
transients elicited by repetitive stimuli of mossy fibers but do not affect those evoked by single shocks, suggesting that ryanodine receptors amplify presynaptic Ca
2+
dynamics in an activity dependent manner. Furthermore, we generated the specific antibody against the type 2 ryanodine receptor (RyR2; originally referred to as the cardiac type) and examined the cellular and subcellular localization using immunohistochemistry. RyR2 is highly expressed in the stratum lucidum of the CA3 region and mostly colocalizes with axonal marker NF160 but not with terminal marker VGLUT1. Immunoelectron microscopy revealed that RyR2 is distributed around smooth ER within the mossy fibers but is almost excluded from their terminal portions. These results suggest that axonal localization of RyR2 at sites distant from the active zones enables use dependent Ca
2+
release from intracellular stores within the mossy fibers and thereby facilitates robust presynaptic forms of plasticity at the mossy fiber-CA3 synapse.
Deficiency in ubiquitin ligase TRIM2 causes accumulation of neurofilament light chain and neurodegeneration
Authors: Balastik Martin , Ferraguti Francesco , Pires-da Silva André , Lee Tae Ho , Alvarez-Bolado Gonzalo , Lu Kun Ping , Gruss Peter
Published: August 2008

TRIM RING finger proteins have been shown to play an important role in cancerogenesis, in the pathogenesis of some human hereditary disorders, and in the defense against viral infection, but the function of the majority of TRIM proteins remains unknown. Here, we show that TRIM RING finger protein TRIM2, highly expressed in the nervous system, is an UbcH5a-dependent ubiquitin ligase. We further demonstrate that TRIM2 binds to neurofilament light subunit (NF-L) and regulates NF-L ubiquitination. Additionally, we show that mice deficient in TRIM2 have increased NF-L level in axons and NF-L-filled axonal swellings in cerebellum, retina, spinal cord, and cerebral cortex. The axonopathy is followed by progressive neurodegeneration accompanied by juvenile-onset tremor and ataxia. Our results demonstrate that TRIM2 is an ubiquitin ligase and point to a mechanism regulating NF-L metabolism through an ubiquitination pathway that, if deregulated, triggers neurodegeneration.
Cox-dependent fatty acid metabolites cause pain through activation of the irritant receptor TRPA1
Authors: Materazzi Serena , Nassini Romina , Andrè Eunice , Campi Barbara , Amadesi Silvia , Trevisani Marcello , Bunnett Nigel W. , Patacchini Riccardo , Geppetti Pierangelo
Published: August 2008

Prostaglandins (PG) are known to induce pain perception indirectly by sensitizing nociceptors. Accordingly, the analgesic action of nonsteroidal anti-inflammatory drugs (NSAIDs) results from inhibition of cyclooxygenases and blockade of PG biosynthesis. Cyclopentenone PGs, 15-d-PGJ2, PGA2, and PGA1, formed by dehydration of their respective parent PGs, PGD2, PGE2, and PGE1, possess a highly reactive α,β-unsaturated carbonyl group that has been proposed to gate the irritant transient receptor potential A1 (TRPA1) channel. Here, by using TRPA1 wild-type (TRPA1+/+) or deficient (TRPA1−/−) mice, we show that cyclopentenone PGs produce pain by direct stimulation of nociceptors via TRPA1 activation. Cyclopentenone PGs caused a robust calcium response in dorsal root ganglion (DRG) neurons of TRPA1+/+, but not of TRPA1−/−mice, and a calcium-dependent release of sensory neuropeptides from the rat dorsal spinal cord. Intraplantar injection of cyclopentenone PGs stimulated c-fos expression in spinal neurons of the dorsal horn and evoked an instantaneous, robust, and transient nociceptive response in TRPA1+/+but not in TRPA1−/−mice. The classical proalgesic PG, PGE2, caused a slight calcium response in DRG neurons, increased c-fos expression in spinal neurons, and induced a delayed and sustained nociceptive response in both TRPA1+/+and TRPA1−/−mice. These results expand the mechanism of NSAID analgesia from blockade of indirect nociceptor sensitization by classical PGs to inhibition of direct TRPA1-dependent nociceptor activation by cyclopentenone PGs. Thus, TRPA1 antagonism may contribute to suppress pain evoked by PG metabolites without the adverse effects of inhibiting cyclooxygenases.
A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress
Authors: Ghosh Debjani , Srivastava Gyan P. , Xu Dong , Schulz Laura C. , Roberts R. Michael
Published: August 2008

When SIN1 (MAPKAP1) was used as the bait in a two-hybrid screen of a human bone marrow cDNA library, its most frequent partner was poly(rC) binding protein 2 (PCBP2/hnRNP-E2), which associates with the N-terminal domain of SIN1 and can be coimmunoprecipitated with SIN1 and the cytoplasmic domain of the IFN receptor IFNAR2 from HeLa cells. SIN1, but not PCBP2, also associates with the receptors that bind TNFα. PCBP2 is known to bind pyrimidine-rich repeats within the 3′ UTR of mRNAs and has been implicated in control of RNA stability and translation and selective cap-independent transcription. RNAi silencing of either SIN1 or PCBP2 renders cells sensitive to basal and stress-induced apoptosis. Stress in the form of TNFα and H
2
O
2
treatments rapidly raises the cell content of SIN1 and PCBP2, an effect reversible by inhibiting MAPK14. A meta analysis of human microarray information with an algorithm that discerns similarities in gene-regulatory profiles shows that SIN1 and PCBP2 are generally coregulated with large numbers of genes implicated in both cell survival and death and in cellular stress responses, including RNA translation and processing. We predict that SIN1 is a scaffold protein that organizes antiapoptotic responses in stressed cells, whereas PCBP2, its binding partner, provides for the selective expression of cell survival factors through posttranslational events.
Bmi1 is critical for lung tumorigenesis and bronchioalveolar stem cell expansion
Authors: Dovey Jennifer Shepard , Zacharek Sima J. , Kim Carla F. , Lees Jacqueline A.
Published: August 2008

Understanding the pathways that control epithelial carcinogenesis is vital to the development of effective treatments. The Polycomb group family member Bmi1 is overexpressed in numerous epithelial tumors, but its role in their development has not been established. We now show a key role for
Bmi1
in lung adenocarcinoma. Whereas lung development occurs normally in
Bmi1
-deficient mice, loss of
Bmi1
decreases the number and progression of lung tumors at a very early point in an oncogenic
K-ras
-initiated mouse model of lung cancer. This correlates with a defect in the ability of
Bmi1
-deficient putative bronchiolalveolar stem cells (BASCs) to proliferate in response to the oncogenic stimulus. Notably, in the absence of oncogenic
K-ras
,
Bmi1
-deficient BASCs show impaired proliferation and self-renewal capacity in culture and after lung injury
in vivo
. Abrogated lung cancer development and BASC self-renewal occur partially in a p19
ARF
-dependent manner. Our data suggest that
Bmi1
deficiency suppresses tumor development by limiting the expansion potential of BASCs, the apparent lung cancer cells of origin. Because Bmi1 is elevated in additional tumor types, this suggests that Bmi1 plays a key role in regulating proliferation of both stem cells and tumor cells in diverse adult epithelial tissues.
Epac signaling is required for hippocampus-dependent memory retrieval
Authors: Ouyang Ming , Zhang Lei , Zhu J. Julius , Schwede Frank , Thomas Steven A.
Published: August 2008

Previously we uncovered a critical role for norepinephrine and β
1
-adrenergic signaling in hippocampus-dependent memory retrieval. Because the β
1
receptor couples to G
s
, we examine here whether cAMP is also required for contextual memory retrieval. Using pharmacologic and genetic approaches to manipulate cAMP and downstream signaling, we demonstrate that cAMP and two of its targets, protein kinase A (PKA) and exchange protein activated by cAMP (Epac), are both required for retrieval. These findings demonstrate that cAMP signaling through Epac (as well as PKA) plays an essential role in cognition.
The nonequilibrium mechanism for ultrasensitivity in a biological switch: Sensing by Maxwell's demons
Authors: Tu Yuhai
Published: August 2008

The
Escherichia coli
flagellar motor senses the intracellular concentration of the response regulator CheY-P and responds by varying the bias between its counterclockwise (CCW) and clockwise (CW) rotational states. The response is ultrasensitive with a large Hill coefficient (≈10). Recently, the detailed distribution functions of the CW and the CCW dwell times have been measured for different CW biases. Based on a general result on the properties of the dwell-time statistics for all equilibrium models, we show that the observed dwell-time statistics imply that the flagellar motor switch operates out of equilibrium, with energy dissipation. We propose a dissipative allosteric model that generates dwell-time statistics consistent with the experimental results. Our model reveals a general nonequilibrium mechanism for ultrasensitivity wherein the switch operates with a small energy expenditure to create high sensitivity. In contrast to the conventional equilibrium models, this mechanism does not require one to assume that CheY-P binds to the CCW and CW states with different affinities. The estimated energy consumption by the flagellar motor switch suggests that the transmembrane proton motive force, which drives the motor's rotation, may also power its switching. The existence of net transitional fluxes between microscopic states of the switch is predicted, measurement of these fluxes can test the nonequilibrium model directly. Both the results on the general properties of the dwell-time statistics and the mechanism for ultrasensitivity should be useful for understanding a diverse class of physical and biological systems.
Neural basis of the cognitive map: Path integration does not require hippocampus or entorhinal cortex
Authors: Shrager Yael , Kirwan C. Brock , Squire Larry R.
Published: August 2008

The hippocampus and entorhinal cortex have been linked to both memory functions and to spatial cognition, but it has been unclear how these ideas relate to each other. An important part of spatial cognition is the ability to keep track of a reference location using self-motion cues (sometimes referred to as path integration), and it has been suggested that the hippocampus or entorhinal cortex is essential for this ability. Patients with hippocampal lesions or larger lesions that also included entorhinal cortex were led on paths while blindfolded (up to 15 m in length) and were asked to actively maintain the path in mind. Patients pointed to and estimated their distance from the start location as accurately as controls. A rotation condition confirmed that performance was based on self-motion cues. When demands on long-term memory were increased, patients were impaired. Thus, in humans, the hippocampus and entorhinal cortex are not essential for path integration.
Inelastic x-ray scattering of dense solid oxygen: Evidence for intermolecular bonding
Authors: Meng Yue , Eng Peter J. , Tse John S. , Shaw Dawn M. , Hu Michael Y. , Shu Jinfu , Gramsch Stephen A. , Kao Chi-chang , Hemley Russell J. , Mao Ho-kwang
Published: August 2008

The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O
2
molecules interact predominantly through the half-filled 1π

g

* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1π

g

* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O
2
molecules at the transition to the ε-phase. The ε-phase, which consists of (O
2
)
4
clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O
2
)
4
clusters develop upon compression of the ε-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.
RBC Adhesion to Vascular Endothelial Cells: More Potent than RBC Aggregation in Inducing Circulatory Disorders
Authors: YEDGAR SAUL , KAUL DHANANJAY K. , BARSHTEIN GREGORY
Published: August 2008

Growing evidence has suggested that the adhesion of red blood cells (RBCs) to blood vessel wall endothelial cells (ECs) is a potent catalyst of microcirculatory disorders, but direct in vivo documentation has been lacking. In a recent study we have demonstrated the elevation of vascular resistance by RBCs with increased adhesion to ECs and normal deformability in the absence of aggregation. Unlike the previous chapter (i.e., the “point”), the findings and considerations discussed in this chapter (the “counterpoint) imply that RBC/EC adhesion is a more potent determinant of circulatory disorders than RBC aggregation.
Increased Arachidonic Acid‐Induced Thromboxane Generation Impairs Skeletal Muscle Arteriolar Dilation with Genetic Dyslipidemia
Authors: GOODWILL ADAM. G. , STAPLETON PHOEBE A. , JAMES MILINDA E. , D'AUDIFFRET ALEXANDRE C. , FRISBEE JEFFERSON C.
Published: August 2008

Objective:The aim of this study was to determine if arachidonic acid (AA)‐induced skeletal muscle arteriolar dilation is altered with hypercholesterolemia in ApoE and low‐density lipoprotein receptor (LDLR) gene deletion mice fed a normal diet. This study also determined contributors to altered AA‐induced dilation between dyslipidemic mice and controls, C57/Bl/6J (C57).

Methods:Gracilis muscle arterioles were isolated, with mechanical responses assessed following a challenge with AA under control conditions and after elements of AA metabolism pathways were inhibited. Conduit arteries from each strain were used to assess AA‐induced production of PGI2and TxA2.

Results:Arterioles from ApoE and LDLR exhibited a blunted dilation to AA versus C57. While responses were cyclo‐oxygenase‐dependent in all strains, inhibition of thromboxane synthase or blockade of PGH2/TxA2receptors improved dilation in ApoE and LDLR only. AA‐induced generation of PGI2was comparable across strains, although TxA2generation was increased in ApoE and LDLR. Arteriolar reactivity to PGI2and TxA2was comparable across strains. Treatment with TEMPOL improved dilation and reduced TxA2production with AA in ApoE and LDLR.

Conclusions:These results suggest that AA‐induced arteriolar dilation is constrained in ApoE and LDLR via an increased production of TxA2. While partially due to elevated oxidant stress, additional mechanisms contribute that are independent of acute alterations in oxidant tone.
Drug use in prisons in Kyrgyzstan: a study about the effect of health promotion among prisoners
Authors: Moller L. F. , Van Den Bergh B. J. , Karymbaeva S. , Esenamanova A. , Muratalieva R.
Published: August 2008

In Kyrgyzstan the prevalence of injecting drug behaviour is among the highest found throughout the world. Health promotion training, improved health care and needle/syringe exchange (NSE) programmes have been shown to decrease risk behaviour among injecting drug users. In Kyrgyzstan, an intervention study with training of prison staff and prisoners was performed in one prison. Before and after the training, a random selection of the prisoners answered a questionnaire about drug use, risk behaviour and health care. The survey was carried out in both the intervention prison and in a reference prison. The number of drug users, the use of drugs and risk behaviour were improved significantly within half a year and, especially, the injection and use of drugs decreased in the intervention group. The study clearly shows that increased focus, improved healthcare and training of prisoners and staff on drug use and harm reduction can reduce both use of drugs and risk behaviour.
High and variable use of primary care in prison. A qualitative study to understand help‐seeking behaviour
Authors: Feron Jean‐Marc , Hong Nguyen Tan Lac , Pestiaux Dominique , Lorant Vincent
Published: August 2008

Background. High and variable rates of attendance at GP consultations in prisons are observed. The aim of the study is to have a clearer understanding of social factors influencing inmates’ help‐seeking behaviour and demand for primary health care. Methods. A qualitative study was carried out in five Belgian prisons (three Dutch‐speaking and two French‐speaking). Twenty‐five male inmates were interviewed face‐to‐face and 18 caregivers (7 nurses and 11 GPs) in focus groups. Results. Five main social factors explain inmates’ help‐seeking behaviour and demand for primary health care: (1) inmates’ negative perception of imprisonment increases help‐seeking behaviour; (2) inmates use their rights to health care as strategies to maintain some form of control over their lives; (3) the doctor’s role distorts expression of need and demand; (4) health professionals’ control over inmates’ lives creates mistrust and a controlling therapeutic relationship; and (5) lack of alternatives to health care. These factors are mutually dependent and cause a confrontation in the inmates’ and clinicians’ agendas. Conclusion. The most important recommendation is to understand what the inmates are really seeking in their demands. This information can be used to develop appropriate alternatives in terms of human support and well‐being facilities. The therapeutic and security roles of health care workers should be separated, in order to increase the trust that is central to the therapeutic relationship between them and inmates.
Prisons and HCV: a review and a report on an experience in New South Wales Australia
Authors: Batey R. G. , Jones T. , McAllister C.
Published: August 2008

Prison populations in Western countries are characterised by a high hepatitis C prevalence. This reflects a high rate of imprisonment for drug related offences. Prison entrants who are HCV‐negative face a significant risk of acquiring hepatitis C. Effective prevention strategies and successful treatment of a significant percentage of hepatitis C‐positive inmates could reduce the risk of transmission in the prison context significantly. Several reports of treating hepatitis C in prisoners in major facilities have
been published. We report our experience of establishing a liver clinic service in two regional prisons in New South Wales, Australia. Liver biopsy requirements to access treatment in Australia meant that only 46 of 196 reviewed patients were able to commence treatment in our 5‐year experience. Treatment completion rate was 61% and end of treatment viral response was 57%. The removal of liver biopsy requirements in Australia in April 2006 has freed up access to treatment and our results encourage further effort to optimise the process of assessment and treatment in this high‐risk population.
Colour versus quantity as cues in reverse-reward-competent squirrel monkeys (Saimiri sciureus)
Authors: Anderson James R. , Awazu Shunji , Fujita Kazuo
Published: August 2008

To assess the relative salience of colour and quantity cues, squirrel monkeys previously trained to reach for the smaller of two quantities of food in a reverse-reward contingency task received colour discrimination training. After initial failure to discriminate between two colours of dots under a differential reinforcement regime, they learned the task when the S− colour was associated with zero reward. The monkeys then showed good retention on the original reverse-reward task of 1 versus 4 with pairs of dots presented in S+ or S− colours. However, on “mismatch” trials of 1S− versus 4S+, only 2 of 4 monkeys tested showed a preference—1 monkey chose based on quantity, the other based on colour. Individual differences and the possible roles of overshadowing and blocking are discussed.
The Arabidopsis AtNPR1 Inversely Modulates Defense Responses Against Fungal, Bacterial, or Viral Pathogens While Conferring Hypersensitivity to Abiotic Stresses in Transgenic Rice
Authors: Quilis Jordi , Peñas Gisela , Messeguer Joaquima , Brugidou Christophe , Segundo Blanca San
Published: August 2008

The nonexpressor of pathogenesis-related (PR) genes (NPR1) protein plays an important role in mediating defense responses activated by pathogens in Arabidopsis. In rice, a disease-resistance pathway similar to the Arabidopsis NPR1-mediated signaling pathway one has been described. Here, we show that constitutive expression of the Arabidopsis NPR1 (AtNPR1) gene in rice confers resistance against fungal and bacterial pathogens. AtNPR1 exerts its protective effects against fungal pathogens by priming the expression of salicylic acid (SA)-responsive endogenous genes, such as the PR1b, TLP (PR5), PR10, and PBZ1. However, expression of AtNPR1 in rice has negative effects on viral infections. The AtNPR1-expressing rice plants showed a higher susceptibility to infection by the Rice yellow mottle virus (RYMV) which correlated well with a misregulation of RYMV-responsive genes, including expression of the SA-regulated RNA-dependent RNA polymerase 1 gene (OsRDR1). Moreover, AtNPR1 negatively regulates the expression of genes playing a role in the plant response to salt and drought stress (rab21, salT, and dip1), which results in a higher sensitivity of AtNPR1 rice to the two types of abiotic stress. These observations suggest that AtNPR1 has both positive and negative regulatory roles in mediating defense responses against biotic and abiotic stresses.
MHC-correlated odour preferences in humans and the use of oral contraceptives
Authors: Roberts S. Craig , Gosling L. Morris , Carter Vaughan , Petrie Marion
Published: August 2008

Previous studies in animals and humans show that genes in the major histocompatibility complex (MHC) influence individual odours and that females often prefer odour of MHC-dissimilar males, perhaps to increase offspring heterozygosity or reduce inbreeding. Women using oral hormonal contraceptives have been reported to have the opposite preference, raising the possibility that oral contraceptives alter female preference towards MHC similarity, with possible fertility costs. Here we test directly whether contraceptive pill use alters odour preferences using a longitudinal design in which women were tested before and after initiating pill use; a control group of non-users were tested with a comparable interval between test sessions. In contrast to some previous studies, there was no significant difference in ratings between odours of MHC-dissimilar and MHC-similar men among women during the follicular cycle phase. However, single women preferred odours of MHC-similar men, while women in relationships preferred odours of MHC-dissimilar men, a result consistent with studies in other species, suggesting that paired females may seek to improve offspring quality through extra-pair partnerships. Across tests, we found a significant preference shift towards MHC similarity associated with pill use, which was not evident in the control group. If odour plays a role in human mate choice, our results suggest that contraceptive pill use could disrupt disassortative mate preferences.
Impacts of protein–protein interaction domains on organism and network complexity
Authors: Xia Kai , Fu Zheng , Hou Lei , Han Jing-Dong J.
Published: August 2008

It has been a puzzle that genome or proteome sizes are not correlated with the complexity of the organisms. Although alternative splicing and noncoding and regulatory elements explain some of the differences, the complexity of the protein interaction network and regulatory network may provide additional explanations. Here, we collected 642 domains that mediate protein–protein interactions (PPIs) and examined the evolution of the PPI domains and its impact on organismal complexity and PPI network complexity. In agreement with previous more general studies of protein domains, a significant expansion of PPI domains per proteome was found in metazoa. We also found both the number and coverage of PPI domains per protein increased. However, a better correlation with complexity was seen with increasing PPI domain coverage per protein, so that proteins in complex organisms are more compact and specialized in PPI. Such a structural adaptation of the proteins is correlated with the number of interactions that the proteins can make in PPI networks, and seems to be a more favorable way to increase network connectivity than other structural adaptations.
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
Authors: Zhu Qian-Hao , Spriggs Andrew , Matthew Louisa , Fan Longjiang , Kennedy Gavin , Gubler Frank , Helliwell Chris
Published: August 2008

Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as post-transcriptional or transcriptional regulators in plants. miRNA function is essential for normal plant development and therefore is likely to be important in the growth of the rice grain. To investigate the roles of miRNAs in rice grain development, we carried out deep sequencing of the small RNA populations of rice grains at two developmental stages. In a data set of ∼5.5 million sequences, we found representatives of all 20 conserved plant miRNA families. We used an approach based on the presence of miRNA and miRNA* sequences to identify 39 novel, nonconserved rice miRNA families expressed in grains. Cleavage of predicted target mRNAs was confirmed for a number of the new miRNAs. We identified a putative mirtron, indicating that plants may also use spliced introns as a source of miRNAs. We also identified a miRNA-like long hairpin that generates phased 21 nt small RNAs, strongly expressed in developing grains, and show that these small RNAs act in trans to cleave target mRNAs. Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner.
Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties
Authors: Bacolla Albino , Larson Jacquelynn E. , Collins Jack R. , Li Jian , Milosavljevic Aleksandar , Stenson Peter D. , Cooper David N. , Wells Robert D.
Published: August 2008

Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra- and trinucleotide repeats revealed an inverse correlation between the stability of folded-back hairpin and quadruplex structures and the sequence representation for repeats ≥30 bp in length in nine vertebrate genomes. Alternatively, the predicted energies of base-stacking interactions correlated directly with the longest length distributions in vertebrate genomes. Genome-wide analyses indicated that unstable sequences, such as CAG:CTG and CCG:CGG, were over-represented in coding regions and that micro/minisatellites were recruited in genes involved in transcription and signaling pathways, particularly in the nervous system. Microsatellite instability (MSI) is a hallmark of cancer, and length polymorphism within genes can confer susceptibility to inherited disease. Sequences that manifest the highest MSI values also displayed the strongest base-stacking interactions; analyses of 62 tri- and tetranucleotide repeat-containing genes associated with human genetic disease revealed enrichments similar to those noted for micro/minisatellite-containing genes. We conclude that DNA structure and base-stacking determined the number and length distributions of microsatellite repeats in vertebrate genomes over evolutionary time and that micro/minisatellites have been recruited to participate in both gene and protein function.
The solution structure of the C‐terminal domain of NfeD reveals a novel membrane‐anchored OB‐fold
Authors: Kuwahara Yohta , Ohno Ayako , Morii Taichi , Yokoyama Hideshi , Matsui Ikuo , Tochio Hidehito , Shirakawa Masahiro , Hiroaki Hidekazu
Published: August 2008

Nodulation formation efficiency D (NfeD) is a member of a class of membrane‐anchored ClpP‐class proteases. There is a second class of NfeD homologs that lack the ClpP domain. The genes of both NfeD classes usually are part of an operon that also contains a gene for a prokaryotic homolog of stomatin. (Stomatin is a major integral‐membrane protein of mammalian erythrocytes.) Such NfeD/stomatin homolog gene pairs are present in more than 290 bacterial and archaeal genomes, and their protein products may be part of the machinery used for quality control of membrane proteins. Herein, we report the structure of the isolated C‐terminal domain of PH0471, a Pyrococcus horikoshii NfeD homolog, which lacks the ClpP domain. This C‐terminal domain (termed NfeDC) contains a five‐strand β‐barrel, which is structurally very similar to the OB‐fold (oligosaccharide/oligonucleotide–binding fold) domain. However, there is little sequence similarity between it and previously characterized OB‐fold domains. The NfeDC domain lacks the conserved surface residues that are necessary for the binding of an OB‐fold domain to DNA/RNA, an ion. Instead, its surface is composed of residues that are uniquely conserved in NfeD homologs and that form the structurally conserved surface turns and β‐bulges. There is also a conserved tryptophan present on the surface. We propose that, in general, NfeDC domains may interact with other spatially proximal membrane proteins and thereby regulate their activities.
Assignment‐free solution NMR method reveals CesT as an unswapped homodimer
Authors: Rumpel Sigrun , Lakshmi Raghavendran , Becker Stefan , Zweckstetter Markus
Published: August 2008

The X‐ray structure of the homodimeric chaperone CesT is the only structure among the type three secretion system (TTSS) chaperones that shows a domain swap. This swap has potential importance for the mechanism of effector translocation through a TTSS. Here we present two nuclear magnetic resonance strategies exploiting pre‐existing structural models and residual dipolar couplings (RDCs), which reveal the unswapped 35.4‐kDa dimer to be present in solution. Particularly efficient is the discrimination of a swapped and unswapped structural state performed simultaneously to automatic backbone assignment using only HN‐RDCs and carbonyl backbone chemical shifts. This direct approach may prove to be generally useful to rapidly differentiate two structural models.
Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb‐C and its complement target C3d
Authors: Haspel Nurit , Ricklin Daniel , Geisbrecht Brian V. , Kavraki Lydia E. , Lambris John D.
Published: August 2008

The C3–inhibitory domain of Staphylococcus aureus extracellular fibrinogen‐binding protein (Efb‐C) defines a novel three‐helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb‐C bound to its cognate subdomain of human C3 (C3d) identified Arg‐131 and Asn‐138 of Efb‐C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb‐C and the single‐point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb‐C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb‐C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb‐C to C3d, resulting in its potent complement inhibitory properties.
An electrostatic network and long‐range regulation of Src kinases
Authors: Ozkirimli Elif , Yadav Shalini S. , Miller W. Todd , Post Carol Beth
Published: August 2008

The regulatory mechanism of Src tyrosine kinases includes conformational activation by a change in the catalytic domain tertiary structure and in domain–domain contacts between the catalytic domain and the SH2/SH3 regulatory domains. The kinase is activated when tyrosine phosphorylation occurs on the activation loop, but without phosphorylation of the C‐terminal tail. Activation also occurs by allostery when contacts between the catalytic domain (CD) and the regulatory SH3 and SH2 domains are released as a result of exogenous protein binding. The aim of this work is to examine the proposed role of an electrostatic network in the conformational transition and to elucidate the molecular mechanism for long‐range, allosteric conformational activation by using a combination of experimental enzyme kinetics and nonequilibrium molecular dynamics simulations. Salt dependence of the induction phase is observed in kinetic assays and supports the role of an electrostatic network in the transition. In addition, simulations provide evidence that allosteric activation involves a concerted motion coupling highly conserved residues, and spanning several nanometers from the catalytic site to the regulatory domain interface to communicate between the CD and the regulatory domains.
Bile acids repress E‐cadherin through the induction of Snail and increase cancer invasiveness in human hepatobiliary carcinoma
Authors: Fukase Koji , Ohtsuka Hideo , Onogawa Tohru , Oshio Hiroshi , Ii Takayuki , Mutoh Mitsuhisa , Katayose Yu , Rikiyama Toshiki , Oikawa Masaya , Motoi Fuyuhiko , Egawa Shinichi , Abe Takaaki , Unno Michiaki
Published: August 2008

Although some kinds of bile acids have been implicated in colorectal cancer development, the mechanism of cancer progression remains unexplored in hepatobiliary cancer. From our personal results using complementary DNA microarray, we found that chenodeoxycholic acid (CDCA) induced Snail expression in human carcinoma cell lines derived from hepatocellular carcinoma and cholangiocarcinoma. Snail expression plays an important role in the regulation of E‐cadherin and in the acquisition of invasive potential in many types of human cancers including hepatocellular carcinoma. We found that CDCA and lithocholic acid (LCA) induced Snail expression in a concentration‐dependent manner and down‐regulated E‐cadherin expression in hepatocellular carcinoma and cholangiocarcinoma cell lines. Moreover, Snail short interference RNA (siRNA) treatment reduced the down‐regulation of E‐cadherin by CDCA or LCA. Luciferase analysis demonstrated that the promoter region from –111 to –24 relative to the transcriptional start site was necessary for this induction and, at least in part, nuclear factor Y (NF‐Y) and stimulating protein 1 (Sp1) might be an inducer of Snail expression in response to bile acids. In addition, using an in vitro wound healing assay and invasion assay, we observed that CDCA and LCA induced cell migration and invasion. These results suggest that bile acids repress E‐cadherin through the induction of transcription factor Snail and increase cancer invasiveness in human hepatocellular carcinoma and cholangiocarcinoma. Inhibition of this bile acid‐stimulated pathway may prove useful as an adjuvant in the therapy of hepatocellular carcinoma. (Cancer Sci 2008; 99: 1785–1792)
Flexible dosing of Tincture of Opium in the management of opioid withdrawal: pharmacokinetics and pharmacodynamics
Authors: Somogyi Andrew A. , Larsen Mie , Abadi Reza M. , Jittiwutikarn Jaroon , Ali Robert , White Jason M.
Published: August 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• In parts of South‐East Asia, Tincture of Opium (TOP) is a culturally acceptable alternative to methadone in the treatment of opioid withdrawal.

• We have previously shown that TOP has a therapeutic effect when administered to opioid‐dependent patients in Northern Thailand.

• However, before TOP could be used clinically, an evaluation of the dosing regimen had to be undertaken.

WHAT THIS STUDY ADDS

• This study extends the previous study by evaluating the clinical effectiveness of a dosing regimen in which the TOP dose was adjusted according to prior self‐reported opium use.

• Adequate suppression of withdrawal can be achieved, with minimal side‐effects, in opioid‐dependent individuals receiving flexible dosing of TOP.

• This study provides preliminary evidence for the effectiveness of TOP in the management of opioid withdrawal.

AIMS

The aim was to evaluate the clinical effectiveness, pharmacodynamics and pharmacokinetics of a range of Tincture of Opium (TOP) doses in the management of opioid withdrawal.

METHODS

Forty‐five opium‐dependent Thai subjects were allocated to three dosing groups (6.66, 13.3 and 20 mg morphine equivalents, twice daily) depending on their self‐reported prior opium use. On day 5 of dosing subjects underwent an interdosing interval study where blood, withdrawal scores, heart rate and blood pressure (BP) were collected at 0, 1, 3 and 8 h. Plasma morphine concentrations were quantified by high‐performance liquid chromatography, and plasma morphine‐3‐glucuronide (M3G) and morphine‐6‐glucuronide (M6G) concentrations by LCMS.

RESULTS

Thirty‐two subjects completed the study. Withdrawal scores were low for all subjects (range 9–23% of maximum response). There were dose‐dependent changes in both systolic and diastolic BP (P = 0.021 and P = 0.01, respectively), but these were not considered clinically significant. There were no effects of dose on respiratory rate. Plasma morphine concentrations changed significantly across the interdosing interval (P = 0.0001), rising to a maximum at 1 h after dosing. Plasma morphine concentrations also differed according to dose (P < 0.05). The mean ratios of the morphine glucuronides were found to be: M3G/M6G = 7.7, M3G/morphine = 35.6 and M6G/morphine = 4.9, values comparable to those previously reported.

CONCLUSION

The management of opioid withdrawal can be achieved, with minimal adverse effects, by using flexible dosing of TOP.
Intravitreal bevacizumab (Avastin®) injection for neovascular glaucoma: a survey on 23 cases throughout 12‐month follow‐up
Authors: Costagliola Ciro , Cipollone Ugo , Rinaldi Michele , Della Corte Michele , Semeraro Francesco , Romano Mario R.
Published: August 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Neovascular glaucoma (NVG) is a form of secondary glaucoma in which fibrovascular tissue grows, leading to progressive angle closure with elevation of intraocular pressure.

• NVG is poorly responsive to the conventional treatment and has a poor visual prognosis.

WHAT THIS STUDY ADDS

• The present study, performed in 23 patients (26 eyes), shows that three intravitreal injections of bevacizumab scheduled at 4‐week intervals are able to result in significant regression of neovascularization, with best response achieved after the third injection.

• Our study suggests that bevacizumab is effective in rapidly controlling neovascularization and in preventing angle closure.

• Improvements are demonstrated to last at 12 months, and additional interest comes from the lack of any significant adverse effects.

AIMS

Neovascular glaucoma (NVG) represents one of the most severe forms of secondary glaucoma, caused by a number of ocular and systemic conditions, which share the common element of retinal ischaemia/hypoxia that initiates the subsequent release of angiogenesis factors, with consequent development of new abnormal vessels through the ciliary body. The aim was to examine the potential efficacy and safety of intravitreal injection of bevacizumab (IVB) (Avastin®) in the treatment of NVG in patients who had already undergone the standard retinal ablative procedure.

METHODS

This was a prospective pilot trial. Clinical data of 26 eyes from 23 patients, including diagnosis, visual acuity, iris fluorescein angiography stage and intraocular pressure (IOP), were collected. Three injections of bevacizumab were scheduled for each recruited eye at 4‐week intervals from the start. All investigations were repeated the day before the IVB (1.25 mg/0.05 ml) and at the 1‐, 3‐, 6‐, 9‐ and 12‐month follow‐up.

RESULTS

Regression of corneal oedema together with significant pain reduction was achieved in all eyes already after the first IVB, without any noteworthy improvement of visual acuity. At the end of the scheduled protocol (three IVB), regression of iris neovascularization was documented in all patients, together with significant improvement of visual acuity. The IOP reduction from baseline ranged from 30 to 0 mmHg (12.1 ± 8 mmHg).

CONCLUSIONS

Intravitreal bevacizumab, as adjunctive treatment to the standard retinal ablative procedure, seems promising for the management of conditions responsible of retinal ischaemia/hypoxia associated with NVG.
Source–sink dynamics sustain central stonerollers (Campostoma anomalum) in a heavily urbanized catchment
Authors: WAITS ERIC R. , BAGLEY MARK J. , BLUM MICHAEL J. , MCCORMICK FRANK H. , LAZORCHAK JAMES M.
Published: August 2008

1. The influence of spatial structure on population dynamics within river–stream networks is poorly understood. Utilizing spatially explicit analyses of temporal genetic variance, we tested whether persistence of central stonerollers (Campostoma anomalum) reflects differences in habitat quality and location within a highly modified urban catchment in southwestern Ohio, U.S.A.

2. Estimates of genetic diversity did not vary with habitat quality. Nevertheless, evidence of weak but temporally stable genetic structure, location‐dependent effective population sizes and rates of immigration among sites, together suggest that persistence of central stonerollers within the catchment may be attributable to source–sink dynamics driven by habitat heterogeneity.

3. Under this scenario, migrant‐pool colonization from areas of relatively high habitat quality in the upper catchment sustains the presence of central stonerollers at degraded sites in the main stem and dampens population subdivision within the catchment. However, because intact habitat is restricted to the upper portion of the catchment, it is not possible to preclude net downstream dispersal as a mechanism contributing to source–sink dynamics. The slight genetic structure that persists appears to reflect weak isolation by distance diminished by high rates of immigration.

4. This study suggests that without a systems perspective of the conditions that sustain populations in degraded waterways, environmental assessments may underestimate levels of impairment. Conservation and management of stream fishes could be improved by maintaining habitat in areas that are net exporters of migrants or by remediation of impaired habitat.
Effects of gelatinisation level, gum and transglutaminase on the quality characteristics of rice noodle
Authors: Yalcin Seda , Basman Arzu
Published: August 2008

The aim of the present study was to investigate the effects of gelatinisation level, gum (locust bean gum, xanthan gum, 3%) and/or transglutaminase (TG, 0.5%) on quality characteristics of rice noodle. In order to improve the dough forming ability, rice flour was gelatinised at levels of 15%, 20%, 25% and 30%. Noodle samples were evaluated in terms of cooking loss, total organic matter (TOM), water absorption, swelling volume, maximum force, colour, sensory properties, pasting properties. Noodle sample with a gelatinisation level of 25% had better cooking and sensory properties. Gum and/or TG were added to this noodle formula. The noodle samples including xanthan gum had better cooking and sensory properties. TG caused a significant decrease in TOM. The samples including locust bean gum had significantly higher maximum force values. Xanthan gum caused decreases in some Rapid ViscoAnalyzer viscosity values of the noodle samples, while locust bean gum caused increases.
The effect of pectin concentration on viscoelastic and sensory properties of processed cheese
Authors: Macků Ivana , Buňka František , Pavlínek Vladimír , Leciánová Petra , Hrabě Jan
Published: August 2008

The effect of pectin addition on viscoelastic properties of model processed cheeses with 40% w/w dry matter and 50% w/w fat in dry matter after 42 days of storage at temperature 6 ± 2 °C has been investigated using dynamic oscillation rheometry (plate–plate geometry; frequency range 0.1–50.0 Hz; temperature 20 °C). The role of pectin concentration (0.2%, 0.4%, 0.6% and 0.8% w/w) has been studied. Also, the sensory evaluation of samples has been made to assess cheese appearance, rigidity, spreadability and flavour. All samples with the pectin addition were more rigid and less spreadable compared with processed cheeses without pectin. With the increasing concentration of pectin the storage (G′) and loss (G″) moduli rose at the whole tested frequency range (0.1–50.0 Hz). Growing pectin content resulted in the decrease in loss tangent (the nature of gel was changed to more elastic material). The dependence of processed cheese rigidity on pectin concentration (in range 0–0.8% w/w) was not linear. The appearance and flavour were not worse by pectin addition.
The effect of cutting and fish‐orientation systems on the deheading yield of carp
Authors: Dowgiallo Andrzej
Published: August 2008

Applied research into carp‐deheading yield indicated that the V‐cut with two circular knives averaged 77.9%; the V‐cut with one cup‐type knife – 75.6%, and the straight cut at a 79° angle to the fish backbone – 77.4%. The yield averages for deheaded and gutted carp were 63.6%, 62.4% and 62.9%, respectively. Standard analysis of variance demonstrated that there were no statistically significant differences between the mean yields of these three deheading systems. Furthermore, the potential influence of the fish‐orientation system in close connection with the cutting systems on the deheading yield was analysed. This indicated that, with the same yields, the straight‐cutting system simplifies the precise orientation of the fish in relation to the cutting knives.
Differences in chemical, microbial and sensory quality parameters of the marinated ascidiaMicrocosmus sabatieriRoule, 1885 during storage at 6 °C under vacuum conditions
Authors: Stamatis Nikolaos , Arkoudelos John , Vafidis Dimitris
Published: August 2008

Chemical, microbial and sensory quality aspects of the marinated ascidiaMicrocosmus sabatieriRoule, 1885, were examined over a 150‐day period at 6 °C, under vacuum and air (control) packaging conditions using three different formulations (with 12% sodium chloride and 3%, 5% or 7% acetic acid). Significant differences were found between chemical and sensory analysis of three different marinated groups (P > 0.05) during the storage period. There were also significant differences in pseudomonads, lactic acid bacteria and yeast and moulds of the marinated groups by which lower bacterial counts were determined.N‐3 polyunsaturated fatty acids concentrations decreased significantly (P < 0.05), while total viable counts, ammonia and total saturated fatty acid concentrations increased significantly (P > 0.05) in all three groups during storage. The differences in fatty acid and ammonia concentrations were found to be useful as indexes of freshness and decomposition of marinatedM. sabatieriin storage. Shelf life ofM. sabatierimarinades was found to be 5 and 4 months under vacuum and air (control) packaging conditions respectively, at 6 °C.