bluuebunny/crossref_metadata_2025_split huggingface dataset:
HSP90 and eNOS partially co‐localize and change cellular localization in relation to different ECM components in 2D and 3D cultures of adult rat cardiomyocytes
Authors: Di Felice Valentina , Cappello Francesco , Montalbano Antonella , Ardizzone Nella Maria , De Luca Angela , Macaluso Filippo , Amelio Daniela , Cerra Maria Carmela , Zummo Giovanni 
Published: November 2007

Background information. Cultivation techniques promoting three‐dimensional organization of mammalian cells are of increasing interest, since they confer key functionalities of the native ECM (extracellular matrix) with a power for regenerative medicine applications. Since ECM compliance influences a number of cell functions, Matrigel‐based gels have become attractive tools, because of the ease with which their mechanical properties can be controlled. In the present study, we took advantage of the chemical and mechanical tunability of commonly used cell culture substrates, and co‐cultures to evaluate, on both two‐ and three‐dimensional cultivated adult rat cardiomyocytes, the impact of ECM chemistry and mechanics on the cellular localization of two interacting signalling proteins: HSP90 (heat‐shock protein of 90 kDa) and eNOS (endothelial nitric oxide synthase).Results. Freshly isolated rat cardiomyocytes were cultured on fibronectin, Matrigel gel or laminin, or in co‐culture with cardiac fibroblasts, and tested for both integrity and viability. As validation criteria, integrity of both plasma membrane and mitochondria was evaluated by transmission electron microscopy. Cell sensitivity to microenvironmental stimuli was monitored by immunofluorescence and confocal microscopy. We found that HSP90 and eNOS expression and localization are affected by changes in ECM composition. Elaboration of the images revealed, on Matrigel‐cultured cardiomyocytes, areas of high co‐localization between HSP90 and eNOS and co‐localization coefficients, which indicated the highest correlation with respect to the other substrates.Conclusions. Our three‐dimensional adult cardiomyocyte cultures are suitable for both analysing cell—ECM interactions at electron and confocal microscopy levels and monitoring micro‐environment impact on cardiomyocyte phenotype.
A novel motility pattern in quail spermatozoa with implications for the mechanism of flagellar beating
Authors: Woolley David M. 
Published: November 2007

Background information. The spermatozoon of the quail (Coturnix coturnix L., var japonica) has a ‘9+2’ flagellum that is unusually long. When it moves in a viscous medium, near to the coverslip, it develops a meander waveform. Because of the high viscosity, the meander bends are static in relation to the field of view; bend propagation is therefore manifest as the forward movement of the flagellum through the meander shape. At the same time, the origin of the oscillation typically shifts proximally in a stepwise fashion. These movements have been analysed in the hope of contributing to the resolution of problems in flagellar mechanics.Results. (1) Meander waves originate from spontaneous sigmoid bend complexes. (2) On a given flagellum, fully developed meander bends are uniform in their large angle, curvature and propagation speed; interbends can vary in length and shape. (3) No intra‐axonemal sliding is transmitted through formed bends; sliding related to new bends is accommodated proximally. (4) Sliding reversal is initiated at a threshold shear angle of approx. 1 rad. (5) The arc wavespeed is the product of the arc wavelength and the beat frequency. (6) Physical obstruction to bend development causes a pause in the oscillation. (7) New bend initiation can thus be dissociated from bend propagation on the distal flagellum. (8) The steps in the forward advance of the oscillation site occur during the early phase of bend growth.Conclusions. (1) The main conclusion is that, in meander waves, the mechanical basis of the oscillation appears to be that the propulsive thrust arising from bend propagation acts as a bending stress to trigger sliding reversal, thus perpetuating the rhythmic beating. (2) Oscillations can originate at any position, provided the position is distal to a location where doublet sliding is restrained. (3) Meander waves are an example of new bend development without ‘paradoxical’ classes of sliding.
Identification of a bipartite focal adhesion localization signal in RhoU/Wrch‐1, a Rho family GTPase that regulates cell adhesion and migration
Authors: Ory Stéphane , Brazier Hélène , Blangy Anne 
Published: November 2007

Background information. Rho GTPases are important regulators of cytoskeleton dynamics and cell adhesion. RhoU/Wrch‐1 is a Rho GTPase which shares sequence similarities with Rac1 and Cdc42 (cell division cycle 42), but has also extended N‐ and C‐terminal domains. The N‐terminal extension promotes binding to SH3 (Src homology 3)‐domain‐containing adaptors, whereas the C‐terminal extension mediates membrane targeting through palmitoylation of its non‐conventional CAAX box. RhoU/Wrch‐1 possesses transforming activity, which is negatively regulated by its N‐terminal extension and depends on palmitoylation.Results. In the present study, we have shown that RhoU is localized to podosomes in osteoclasts and c‐Src‐expressing cells, and to focal adhesions of HeLa cells and fibroblasts. The N‐terminal extension and the palmitoylation site were dispensable, whereas the C‐terminal extension and effector binding loop were critical for RhoU targeting to focal adhesions. Moreover, the number of focal adhesions was reduced and their distribution changed upon expression of activated RhoU. Conversely, RhoU silencing increased the number of focal adhesions. As RhoU was only transiently associated with adhesion structures, this suggests that RhoU may modify adhesion turnover and cell migration rate. Indeed, we found that migration distances were increased in cells expressing activated RhoU and decreased when RhoU was knocked‐down.Conclusions. Our data indicate that RhoU localizes to adhesion structures, regulates their number and distribution and increases cell motility. It also suggests that the RhoU effector binding and C‐terminal domains are critical for these functions.
Clustering of change patterns using Fourier coefficients
Authors: Kim Jaehee , Kim Haseong 
Published: November 2007

Abstract
Motivation: To understand the behavior of genes, it is important to explore how the patterns of gene expression change over a time period because biologically related gene groups can share the same change patterns. Many clustering algorithms have been proposed to group observation data. However, because of the complexity of the underlying functions there have not been many studies on grouping data based on change patterns. In this study, the problem of finding similar change patterns is induced to clustering with the derivative Fourier coefficients. The sample Fourier coefficients not only provide information about the underlying functions, but also reduce the dimension. In addition, as their limiting distribution is a multivariate normal, a model-based clustering method incorporating statistical properties would be appropriate.
Results: This work is aimed at discovering gene groups with similar change patterns that share similar biological properties. We developed a statistical model using derivative Fourier coefficients to identify similar change patterns of gene expression. We used a model-based method to cluster the Fourier series estimation of derivatives. The model-based method is advantageous over other methods in our proposed model because the sample Fourier coefficients asymptotically follow the multivariate normal distribution. Change patterns are automatically estimated with the Fourier representation in our model. Our model was tested in simulations and on real gene data sets. The simulation results showed that the model-based clustering method with the sample Fourier coefficients has a lower clustering error rate than K-means clustering. Even when the number of repeated time points was small, the same results were obtained. We also applied our model to cluster change patterns of yeast cell cycle microarray expression data with alpha-factor synchronization. It showed that, as the method clusters with the probability-neighboring data, the model-based clustering with our proposed model yielded biologically interpretable results. We expect that our proposed Fourier analysis with suitably chosen smoothing parameters could serve as a useful tool in classifying genes and interpreting possible biological change patterns.
Availability: The R program is available upon the request.
Contact: jaehee@duksung.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Straightening Caenorhabditis elegans images
Authors: Peng Hanchuan , Long Fuhui , Liu Xiao , Kim Stuart K. , Myers Eugene W. 
Published: November 2007

Abstract
Motivation: Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must ‘straighten’ the worms if they are to be compared under a canonical coordinate system.
Results: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a ‘backbone’ that models the anterior–posterior axis of the worm. We formulate the backbone as a parametric cubic spline defined by a series of control points. We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images.
Contact: pengh@janelia.hhmi.org
Supplementary information: The example data sets and programs are available upon request.
The consumption of zooplankton by early life stages of fish in the North Sea
Authors: Heath Michael R. 
Published: November 2007

Abstract
Heath, M. R. 2007. The consumption of zooplankton by early life stages of fish in the North Sea. – ICES Journal of Marine Science, 64: 1650–1663. Previous work has shown that during the 1970s, fish and carnivorous macrozooplankton together consumed ∼22 gC m−2 year−1 of mesozooplankton, principally copepods. Consumption declined to ∼17 gC m−2 year−1 during the 1990s, mainly because of a reduction in fish production. The zooplankton production required to meet this demand seems to be approximately accounted for by estimates of new primary production, but there are additional sinks for zooplankton production attributable to predation by, for example, gelatinous species. Additionally, the consumption of zooplankton by early life stages of fish is difficult to assess and could be larger than implied by the earlier analysis. Here, the role of fish early life stages in zooplankton consumption is re-assessed, and found to be approximately double that previously estimated. Some 28% of the zooplankton consumption by fish is now estimated to be attributable to early life stages, resulting in an estimate of zooplankton consumption by the fish community as a whole 14% higher. Taken overall, the consumption of zooplankton production by fish and other planktivorous predators is now estimated to be 19–25 gC m−2 year−1.
Cyclotron resonance of electrons and holes in graphene monolayers
Authors: Chuang Kai-Chieh , Deacon Russell S , Nicholas Robin J , Novoselov Kostya S , Geim Andre K 
Published: November 2007

We report studies of cyclotron resonance in monolayer graphene. Cyclotron resonances are detected by observing changes in the photoconductive response of the sample. An electron velocity at the Dirac point of 1.093×10
6
m s
−1
is obtained, which is the fastest velocity recorded for all known carbon materials. In addition, a significant asymmetry exists between band structure for electrons and holes, which gives rise to a 5% difference between the velocities at energies of 125 meV away from the Dirac point.
Solution structure of the region 51–160 of human KIN17 reveals an atypical winged helix domain
Authors: Carlier Ludovic , Couprie Joël , le Maire Albane , Guilhaudis Laure , Milazzo‐Segalas Isabelle , Courçon Marie , Moutiez Mireille , Gondry Muriel , Davoust Daniel , Gilquin Bernard , Zinn‐Justin Sophie 
Published: November 2007

AbstractHuman KIN17 is a 45‐kDa eukaryotic DNA‐ and RNA‐binding protein that plays an important role in nuclear metabolism and in particular in the general response to genotoxics. Its amino acids sequence contains a zinc finger motif (residues 28–50) within a 30‐kDa N‐terminal region conserved from yeast to human, and a 15‐kDa C‐terminal tandem of SH3‐like subdomains (residues 268–393) only found in higher eukaryotes. Here we report the solution structure of the region 51–160 of human KIN17. We show that this fragment folds into a three‐α‐helix bundle packed against a three‐stranded β‐sheet. It belongs to the winged helix (WH) family. Structural comparison with analogous WH domains reveals that KIN17 WH module presents an additional and highly conserved 310‐helix. Moreover, KIN17 WH helix H3 is not positively charged as in classical DNA‐binding WH domains. Thus, human KIN17 region 51–160 might rather be involved in protein–protein interaction through its conserved surface centered on the 310‐helix.
Characterization of substrate binding and catalysis in the potential antibacterial target N‐acetylglucosamine‐1‐phosphate uridyltransferase (GlmU)
Authors: Mochalkin Igor , Lightle Sandra , Zhu Yaqi , Ohren Jeffrey F. , Spessard Cindy , Chirgadze Nickolay Y. , Banotai Craig , Melnick Michael , McDowell Laura 
Published: November 2007

AbstractN‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) catalyzes the first step in peptidoglycan biosynthesis in both Gram‐positive and Gram‐negative bacteria. The products of the GlmU reaction are essential for bacterial survival, making this enzyme an attractive target for antibiotic drug discovery. A series of Haemophilus influenzae GlmU (hiGlmU) structures were determined by X‐ray crystallography in order to provide structural and functional insights into GlmU activity and inhibition. The information derived from these structures was combined with biochemical characterization of the K25A, Q76A, D105A, Y103A, V223A, and E224A hiGlmU mutants in order to map these active‐site residues to catalytic activity of the enzyme and refine the mechanistic model of the GlmU uridyltransferase reaction. These studies suggest that GlmU activity follows a sequential substrate‐binding order that begins with UTP binding noncovalently to the GlmU enzyme. The uridyltransferase active site then remains in an open apo‐like conformation until N‐acetylglucosamine‐1‐phosphate (GlcNAc‐1‐P) binds and induces a conformational change at the GlcNAc‐binding subsite. Following the binding of GlcNAc‐1‐P to the UTP‐charged uridyltransferase active site, the non‐esterified oxygen of GlcNAc‐1‐P performs a nucleophilic attack on the α‐phosphate group of UTP. The new data strongly suggest that the mechanism of phosphotransfer in the uridyltransferase reaction in GlmU is primarily through an associative mechanism with a pentavalent phosphate intermediate and an inversion of stereochemistry. Finally, the structural and biochemical characterization of the uridyltransferase active site and catalytic mechanism described herein provides a basis for the structure‐guided design of novel antibacterial agents targeting GlmU activity.
Therapeutic alliance, patient behaviour and dropout in a drug rehabilitation programme: the moderating effect of clinical subpopulations
Authors: Cournoyer Louis‐Georges , Brochu Serge , Landry Michel , Bergeron Jacques 
Published: November 2007

ABSTRACTAim Treatment dropout is an important concern for professionals working in mental health. While this problem is common, the highest attrition rates have been observed in drug rehabilitation programmes. The present study focuses on the therapeutic alliance, a process variable that has been associated repeatedly with positive treatment outcome in the scientific literature. Respondent behaviour indicative of commitment or resistance to treatment was examined in combination with therapist prognoses.Design A total of 248 subjects, classified into three subpopulations (justice,n = 50; mental health,n = 53; comparison group,n = 145), participated in the study. Analyses aimed at predicting dropout were conducted using Cox proportional‐hazards regressions. The moderating effect of sub‐population was tested.Measurements Respondents completed a multi‐dimensional measure of alliance [California Psychotherapeutic Alliance Scale (CALPAS‐P)]. Therapists rated the behaviour of respondents in treatment and made prognoses about perseverance and improvement.Findings An increased risk of dropout was predicted when patients viewed themselves as less committed and perceived the therapist as less understanding and less involved. Therapist prognosis of perseverance was also predictive of dropout. The relationship between patient/therapist evaluations and dropout is affected differently across subpopulations by means of a moderation effect.Conclusion This paper demonstrates the capacity to predict dropout by measuring therapeutic alliance, therapist prognoses and therapist appraisal of patient behaviour. Moreover, the moderation effect of clinical subpopulation on treatment process variables and dropout is supported in the context of drug rehabilitation programmes.
Papain‐like cysteine proteases: key players at molecular battlefields employed by both plants and their invaders
Authors: SHINDO TAKAYUKI , VAN DER HOORN RENIER A. L. 
Published: November 2007

ABSTRACTPapain‐like cysteine proteases (PLCPs) play crucial roles in plant–pathogen/pest interactions. During these parasitic interactions, PLCPs act on non‐self substrates, provoking the selection of counteracting inhibitors and other means to evade proteolysis. We review examples of PLCPs acting on molecular battlefields in the extracellular space, plant cytoplasm and herbivore gut. Examples are maize Mir1 (Maize inbred resistance 1), tomato Rcr3 (Required for Cladosporium resistance‐3), Pseudomonas AvrRpt2 and AurPphB, insect DvCAL1 (Diabrotica virgifera cathepsin L‐like protease‐1) and nematode MiCpl1 (Meloidogyne incognita cathepsin L‐like protease 1). The data suggest that PLCPs cleave specific proteins and that their translocation, activation and inhibition of PLCPs are tightly regulated.
Investigation of X‐ and Y‐specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle
Authors: Anderung C. , Hellborg L. , Seddon J. , Hanotte O. , Götherström A. 
Published: November 2007

SummaryInitially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X‐chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y‐chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X‐chromosome individuals, recombinant X‐chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.
Association of a single‐nucleotide substitution in TYRP1 with roux in Japanese quail (Coturnix japonica)
Authors: Nadeau N. J. , Mundy N. I. , Gourichon D. , Minvielle F. 
Published: November 2007

SummaryWe investigated TYRP1 as a candidate locus for the recessive, sex‐linked roux (brr) phenotype in Japanese quail. A screen of the entire coding sequence of TYRP1 in roux and wild‐type quail revealed a non‐synonymous T‐to‐C substitution in exon 3, leading to a Phe282Ser mutation. This was perfectly associated with plumage phenotype: all roux birds were homozygous for Ser282. Co‐segregation of the Phe282Ser mutation with the roux phenotype was confirmed in three brr/BR+ × brr/– backcrosses. We found no significant difference in TYRP1 expression between roux and wild‐type birds, suggesting that this association is not due to linkage disequilibrium with an unknown regulatory mutation. In addition, the Phe282 amino acid appears to be of functional significance, as it is highly conserved across the vertebrates. This is the first demonstration that TYRP1 has a role in pigmentation in birds.
Bone marrow microvessel density in chronic myeloproliferative disorders: a study of 115 patients with clinicopathological and molecular correlations
Authors: Boveri Emanuela , Passamonti Francesco , Rumi Elisa , Pietra Daniela , Elena Chiara , Arcaini Luca , Pascutto Cristiana , Castello Alessandro , Cazzola Mario , Magrini Umberto , Lazzarino Mario 
Published: November 2007

SummaryPhiladelphia‐negative chronic myeloproliferative disorders (CMD) include polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF). Angiogenesis is critical in the pathogenesis of PMF. We studied angiogenesis in 115 patients with CMD (23 PV, 24 ET, 46 PMF, 12 post‐PV and 10 post‐ET myelofibrosis) by assessment of microvessel density (MVD) in bone marrow (BM). Kruskall–Wallis analysis of variance showed that patients with PMF had significantly higher values of MVD than those with PV (P < 0·001), ET (P < 0·001) and controls (P < 0·001). Mann–Whitney U‐test demonstrated that patients with PMF at the prefibrotic stage had significantly higher MVD values than those with ET (P = 0·02). Patients with post‐PV myelofibrosis showed significantly higher MVD values than those with PV (P < 0·001), as did patients with post‐ET myelofibrosis compared with ET (P < 0·001). In patients with CMD, the multivariate generalized linear regression model showed that the JAK2 (V617F) mutational burden (P = 0·01), serum lactate dehydrogenase level (P = 0·003), and anaemia (P < 0·001) independently correlated with MVD. In summary, this study indicates that assessment of BM angiogenesis, as measured by MVD, may be a useful additional tool in the histopathological definition of CMD.
Serum lactate dehydrogenase activity as a biomarker in children with sickle cell disease
Authors: O’Driscoll Sandra , Height Susan E. , Dick Moira C. , Rees David C. 
Published: November 2007

SummarySerum lactate dehydrogenase (LDH) levels were studied in children with HbSS and HbSC in a single institution, and their relationship to cerebral vasculopathy as assessed by transcranial Doppler scanning (TCD). All children with HbSS (n = 97) and HbSC (n = 18) who underwent a TCD scan in 2006 were studied. LDH levels were higher in HbSS patients than HbSC (581 IU/l vs. 305 IU/l, P < 0·001). In children with HbSS, LDH correlated significantly with haemoglobin, reticulocytes, aspartate transaminase and creatinine. LDH also correlated positively and significantly with TCD measurements in the middle and anterior cerebral artery circulations in the children with HbSS.