bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae
Authors: Paiva Sandra , Devaux Frederic , Barbosa Sonia , Jacq Claude , Casal Margarida 
Published: February 2004

AbstractTo identify new genes involved in acetate uptake in Saccharomyces cerevisiae, an analysis of the gene expression profiles of cells shifted from glucose to acetic acid was performed. The gene expression reprogramming of yeast adapting to a poor non‐fermentable carbon source was observed, including dramatic metabolic changes, global activation of translation machinery, mitochondria biogenesis and the induction of known or putative transporters. Among them, the gene ADY2/YCR010c was identified as a new key element for acetate transport, being homologous to the Yarrowia lipolytica GPR1 gene, which has a role in acetic acid sensitivity. Disruption of ADY2 in S. cerevisiae abolished the active transport of acetate. Microarray analyses of ady2Δ strains showed that this gene is not a critical regulator of acetate response and that its role is directly connected to acetate transport. Ady2p is predicted to be a membrane protein and is a valuable acetate transporter candidate. Copyright © 2004 John Wiley & Sons, Ltd.
Large‐scale screening of yeast mutants for sensitivity to the IMP dehydrogenase inhibitor 6‐azauracil
Authors: Riles Linda , Shaw Randal J. , Johnston Mark , Reines Daniel 
Published: February 2004

AbstractMutations in several genes encoding components of the RNA polymerase II elongation machinery render S. cerevisiae cells sensitive to the drug 6‐azauracil (6AU), an inhibitor of IMP dehydrogenase and orotidylate decarboxylase. It is thought that a reduction in nucleotide levels following drug treatment causes transcriptional elongation to be more dependent on a fully functional RNA polymerase. To gain insight into the basis of the 6AU‐sensitive phenotype and discern its specificity, we screened almost 3000 deletion mutants for growth in the presence of drug; 42 (1.5%) were reproducibly sensitive to the drug. The sensitive mutants included several missing known transcription elongation factors, but the majority were in genes involved in other cellular processes. Not all of the 6AU‐sensitive strains displayed cross‐sensitivity to mycophenolic acid (MPA), another drug that inhibits IMP dehydrogenase and has been employed as a screening agent for elongation mutants, showing that these two drugs are mechanistically distinct. Several of the mutants were tested for the ability to induce transcription of IMP dehydrogenase‐encoding genes, in response to 6‐AU and MPA treatment. As expected, mutants defective in transcriptional elongation factors were unable to fully induce IMPDH expression. However, most of the 6AU‐sensitive strains had normal levels of IMPDH expression. Thus, although 6AU‐sensitivity often results from defects in the elongation machinery, mutations that compromise processes other than transcription and induction of IMPDH also lead to sensitivity to this drug. Copyright © 2004 John Wiley & Sons, Ltd.
Overexpression of ovine leptin in Pichia pastoris: physiological yeast response to leptin production and characterization of the recombinant hormone
Authors: Laborde C. , Chemardin P. , Bigey F. , Combarnous Y. , Moulin G. , Boze H. 
Published: February 2004

AbstractOvine leptin was cloned in the methylotrophic yeast Pichia pastoris using a pPIC9K vector. Leptin was produced and secreted into the culture medium using the Saccharomyces cerevisiae α‐mating factor prepro signal by five clones. Expression levels of leptin varied from clone to clone, depending on the copy number of the ob gene. Highest expression was observed with the single‐copy clone S27 (250 mg/l). The modifications of culture conditions in batch and fed‐batch culture increase the yield of protein. The use of higher cell concentration (63 g/l) before induction of oLept associate with a regulation of pH at 3.2, which decreases the effects of proteolysis, increases the expression level of the oLept to 402 mg/l. Moreover, compared with the non‐producer clone, we observed a drastic decrease in growth rate and biomass yield in the leptin‐producing clones. At the end of the fed‐batch phase at pH 3.2 with clone S27, mortality rate reached 17.3%. Results showed that recombinant leptin production induced metabolic stress, and a negative impact on biomass yield and growth rate. We characterized the recombinant leptin produced by clone S27. It exhibited a molecular mass of 16 kDa, an N‐terminal amino acid sequence identical to that of ovine leptin but with an additional tyrosine introduced by the cloning site. Moreover, it was found to be biologically active in vitro. The available production of a large quantity of oLept will strengthen the functional study for theorical and practical purposes. Copyright © 2004 John Wiley & Sons, Ltd.
The role of Ynt1 in nitrate and nitrite transport in the yeast Hansenula polymorpha
Authors: Machín Felix , Medina Braulio , Navarro Francisco J. , Pérez M. Dolores , Veenhuis Marten , Tejera Paula , Lorenzo Helena , Lancha Ana , Siverio José M. 
Published: February 2004

AbstractYnt1 is the only high‐affinity nitrate uptake system in Hansenula polymorpha. Nitrate uptake was directly correlated with the Ynt1 levels and shown to be independent of nitrate reductase (NR) activity levels. Ynt1 failed to transport chlorate and, as a result, strains lacking YNT1 were sensitive to chlorate, as is the wild‐type. Nitrite uptake in a wild‐type strain was partially inhibited by nitrate to levels shown by a YNT1‐disrupted strain in which, in turn, nitrite transport was not inhibited by nitrate. It is concluded that nitrite uptake takes place by two different transport systems: Ynt1 and a nitrite‐specific transporter(s). The nitrite‐specific transport system was induced by nitrate; consistently, no induction was observed in strains lacking the transcription factor YNA1, which is involved in nitrate and nitrite induction of the nitrate assimilatory structural genes. Ynt1 presents its optimal rate for nitrite uptake at pH 6, while pH 4 was optimal for the specific nitrite uptake system(s). At pH 5.5, the contribution of Ynt1 to high‐affinity nitrate and nitrite uptake was around 95% and 60%, respectively. The apparent Km of Ynt1 for nitrate and nitrite is in the µM range, as is the specific nitrite uptake system for nitrite. The analysis of the effect of the reduced nitrogen sources on nitrate assimilation revealed that glutamine inactivates nitrate and nitrite transport, dependent on Ynt1, but not the nitrite‐specific system. Copyright © 2004 John Wiley & Sons, Ltd.
Neonatal ventral hippocampus lesion alters the dopamine content in the limbic regions in postpubertal rats
Authors: Alquicer Glenda , Silva‐Gómez Adriana B. , Peralta Fernando , Flores Gonzalo 
Published: February 2004

AbstractThe neonatal ventral Hippocampus (nVH) lesion in rats has been used as a model to test the hypothesis that early neurodevelopmental abnormalities lead to behavioral changes putatively linked to schizophrenia. The schizophrenic patients tend to social isolation. In addition, considerable evidence from behavioral and neurochemistry studies strongly implicate the dopamine (DA) system and the medial part of the prefrontal cortex (mPFC) in the pathophysiology of the social isolation syndrome. In order to assess effects of the postweaning social isolation (pwSI) on the DA system of the nVH lesions, we investigated the DA content and its metabolite, DOPAC in different limbic subregions in rats postpubertally at postnatal day (P) 78 following nVH lesions at P7 with and without pwSI for 8 weeks. The DA and DOPAC were measured by HPLC with electrochemical detection. The nVH lesion induces increase in the DA content in the hippocampus with no effect in the mPFC, nucleus accumbens and caudate‐putamen, while the pwSI induces major increase in the DA content in limbic subregions such as the mPFC, nucleus accumbens and hipocampus with opposite effect in the caudate‐putamen. These results suggest that while pwSI has an effect in the postpubertal content of DA in both sham and nVH lesions in rats, the nVH‐lesioned rats appear to be affected to a greater extent than the sham animals underscoring the influence of pwSI differences in the development of behaviors in the nVH‐lesioned animals.
The effect of tibiofemoral joint kinematics on patellofemoral contact pressures under simulated muscle loads
Authors: Li G. , DeFrate L. E. , Zayontz S. , Park S. E. , Gill T. J. 
Published: February 2004

AbstractAltered patellofemoral joint contact pressures are thought to contribute to patellofemoral joint symptoms. However, little is known about the relationship between tibiofemoral joint kinematics and patellofemoral joint contact pressures. The objective of this paper was to investigate the effect of tibiofemoral joint kinematics on patellofemoral joint pressures using an established in vitro robotic testing experimental setup. Eight cadaveric knee specimens were tested at 0°, 30°, 60°, 90°, and 120° of flexion under an isolated quadriceps load of 400 N and a combined quadriceps/hamstrings load of 400 N/200 N. Tibiofemoral joint kinematics were measured by the robot and contact pressures by a TekScan pressure sensor. The isolated quadriceps loading caused anterior translation and internal rotation of the tibia up to 60° of flexion and posterior translation and external rotation of the tibia beyond 60°. The co‐contraction of the hamstring muscles caused a posterior translation and external rotation of the tibia relative to the motion of the tibia under the quadriceps load. Correspondingly, the contact pressures were elevated significantly at all flexion angles. For example, at 60° of flexion, the hamstrings co‐contraction increased the posterior tibial translation by approximately 2.8 mm and external tibial rotation by approximately 3.6°. The peak contact pressure increased from 1.4 ± 0.8 to 1.7 ± 1.0 MPa, a 15% increase. The elevated contact pressures after hamstrings co‐contraction indicates an intrinsic relation between the tibiofemoral joint kinematics and the patellofemoral joint biomechanics. An increase in posterior tibial translation and external rotation is accompanied by an increase in contact pressure in the patellofemoral joint. These results imply that excessive strength conditioning with the hamstring muscles might not be beneficial to the patellofemoral joint. Knee pathology that causes an increase in tibial posterior translation and external rotation might contribute to degeneration of the patellofemoral joint. These results suggest that conservative treatment of posterior cruciate ligament injury should be reconsidered. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
A silencer element in the cartilage oligomeric matrix protein gene regulates chondrocyte‐specific expression
Authors: Issack Paul S. , Liu Chuan‐Ju , Prazak Lisa , di Cesare Paul E. 
Published: February 2004

AbstractThe molecular mechanisms by which mesenchymal cells differentiate into chondrocytes are poorly understood. The cartilage oligomeric matrix protein gene (COMP) encodes a noncollagenous extracellular matrix protein whose expression pattern correlates with chondrocyte differentiation and arthritis. We have used the COMP promoter as a model to identify regulatory sequences necessary for chondrocyte‐specific expression and to identify cell type‐specific proteins that bind these sequences. We have previously cloned 1.9 kilobases of the 5′ flanking promoter sequence of the murine COMP gene and by deletion analysis have identified two spatially distant chondrocyte‐specific regulatory regions. One element is situated proximally (−125 to −75), and a second region is located distally (−1925 to −592) relative to the transcription start site. In the present study, we performed a finer deletion analysis of the region of the COMP promoter from −1925 to −592 and identified a silencer region situated between −1775 and −1725. This silencer binds sequence‐specific protein complexes; the intensity of these complexes is greater in two different fibroblast cell lines (NIH3T3 and 10T1/2) than in chondrocytic RCS cells. Competition experiments localized the binding site of these protein complexes from −1775 to −1746; deletion of this 30‐bp site results in a selective increase in COMP promoter activity in fibroblasts. Four tandem repeats of this 30‐bp site are sufficient to confer negative transcriptional regulation on a heterologous promoter (SV40) in NIH3T3 fibroblasts. These results suggest that negative regulation of transcription is an important mechanism for chondrocyte‐specific expression of the COMP gene. © 2003 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Theoretical model and experimental results for the nonlinear elastic behavior of human annulus fibrosus
Authors: Wagner Diane R. , Lotz Jeffrey C. 
Published: February 2004

AbstractThe physical properties of the annulus fibrosus are critical to the intervertebral disc's biomechanical function; alterations with degeneration and aging can contribute directly to joint dysfunction and pain. A constitutive model that links the mechanical structure of the annulus to its material properties is important for many bioengineering purposes. To this end, we developed a strain energy function with separate terms to represent the matrix, the fibers, and the interactions between the constituents. Additionally, we measured the tensile and compressive stress–strain response of the annulus in the circumferential direction. We simultaneously applied the strain energy function to these new data and to data from a wide range of experimental protocols reported in the literature. By choosing experimental protocols that use an unloaded reference configuration, we developed a comprehensive formulation for the multiaxial annular elastic behavior. As a partial validation, this formulation predicted experimental results that were not included in model parameter specification. We anticipate that this constitutive formulation will be useful for computational simulations of the disc's biomechanical response and for elucidating structure–function relationships of the annulus fibrosus. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Reflexes in the shoulder muscles elicited from the human coracoacromial ligament
Authors: Diederichsen Louise Pyndt , Nørregaard Jesper , Krogsgaard Michael , Fischer‐Rasmussen Torsten , Dyhre‐Poulsen Poul 
Published: February 2004

AbstractMorphological studies have demonstrated mechanoreceptors in the capsuloligamentous structures of the shoulder joint, however knowledge of the role these joint receptors play in the control of shoulder stability is limited. We therefore investigated the effect of electrically induced afferent activity from mechanoreceptors in the coracoacromial ligament (CAL) on the activity of voluntary activated shoulder muscles in healthy humans. In study I, wire electrodes, for electrical stimulation, were inserted into the CAL in eight normal shoulders. In study II, a needle electrode was inserted into the CAL in seven normal shoulders. Electric activity was recorded from eight shoulder muscles by surface and intramuscular electrodes. During isometric contractions, electrical stimulation was applied to the CAL at two different stimulus intensities, a weak stimulus (stim‐1) and a stronger stimulus (stim‐2).In both experiments, electrical stimulation of the CAL elicited a general inhibition in the voluntary activated shoulder muscles. In study I the average latencies (mean ± SE) of the muscular inhibition were 66 ± 4 ms (stim‐1) and 62 ± 4 ms (stim‐2) during isometric flexion and 73 ± 3 ms (stim‐1) and 73 ± 5 ms (stim‐2) during isometric extension. In study II the average latency (mean ± SE) of the response was 66 ± 4 ms (stim‐1) during isometric flexion. Our results demonstrated a response, probably of reflex origin, from mechanoreceptors in the CAL to the shoulder muscles. The existence of this synaptic connection between mechanoreceptors in CAL and the shoulder muscles suggest a role of these receptors in muscle coordination and in the functional joint stability. © 2004 Orthopaedic Research Society. Published y Elsevier Ltd. All rights reserved.
Michael Brawne: 1925–2003
Authors: CAROLIN PETER , ALLIES BOB , CORREA CHARLES , DOWSON PHILIP , CLEGG PETER , STONEHOUSE ROGER , DE GREY SPENCER , HAWKES DEAN 
Published: February 2004

Architect, author and teacher, Michael Brawne was also an arq contributor and referee. His article ‘Research, design and Popper’ published in our second issue (1/2, pp 10–15) was an analysis of the similarity between architectural design and scientific research based on Karl Popper's hypothetico-deductive theory. It cut straight to the heart of the declared subject of this journal. Reading it again, one can almost hear Michael – with his characteristically precise enunciation (and often exquisitely drawly voice) – elucidating his argument.The following celebration of Michael and his contribution to architecture speaks eloquently about the man and his teaching but surprisingly little about his completed buildings – especially those of the '60s and '70s. There was something very rigorous about these. Indeed, Charles Correa asserts that the houses in Hampstead are ‘among the half-dozen most important pieces of architecture’ constructed in the UK over the last 50 years.It was in the first Hampstead house that, in 1962, there emerged the surface mounted vertical mullions that were to appear again – always subtly related to the internal spatial arrangement – in later projects. And there was his use on the upper levels of his buildings of steeply sloping Cor-Ten sheet (something that today's generation, who seem to have rediscovered this problematic material, could well learn from). In plan, his buildings often made a powerful use of the diagonal (the Cambridge influence perhaps?) and occasionally revealed his admiration for Alvar Aalto's work. This thoughtful, highly distinctive body of work extended from country cottage conversions and extensions to competition designs such as his ‘groundscraper’ high-density housing entry for the Portsdown competition.And what of Michael's exhibition designs? Following the 1965 publication of his book, The New Museum, it was a field in London which he seemed to dominate for much of the late '60s and the '70s – with shows such as the stunning Art in Revolution at the Hayward Gallery in 1971 and the exquisite Age of Neo-Classicism at the Royal Academy in the following year. In the mid '90s, his work for ecclesiastical museums in Germany was equally elegant and well-judged. And, over the last six years, recalling his artist father, he turned to making sculpture at Bath College.Michael Brawne is remembered here by some of his contemporaries, fellow teachers and students. The first contribution, by Bob Allies, is reproduced by permission from The Independent newspaper in which it appeared on 16 August 2003.
Pseudo-periodic partitions of biological sequences
Authors: Li Lugang , Jin Renchao , Kok Poh-Lin , Wan Honghui 
Published: February 2004

Abstract
Motivation: Algorithm development for finding typical patterns in sequences, especially multiple pseudo-repeats (pseudo-periodic regions), is at the core of many problems arising in biological sequence and structure analysis. In fact, one of the most significant features of biological sequences is their high quasi-repetitiveness. Variation in the quasi-repetitiveness of genomic and proteomic texts demonstrates the presence and density of different biologically important information. It is very important to develop sensitive automatic computational methods for the identification of pseudo-periodic regions of sequences through which we can infer, describe and understand biological properties, and seek precise molecular details of biological structures, dynamics, interactions and evolution.
Results: We develop a novel, powerful computational tool for partitioning a sequence to pseudo-periodic regions. The pseudo-periodic partition is defined as a partition, which intuitively has the minimal bias to some perfect-periodic partition of the sequence based on the evolutionary distance. We devise a quadratic time and space algorithm for detecting a pseudo-periodic partition for a given sequence, which actually corresponds to the shortest path in the main diagonal of the directed (acyclic) weighted graph constructed by the Smith–Waterman self-alignment of the sequence. We use several typical examples to demonstrate the utilization of our algorithm and software system in detecting functional or structural domains and regions of proteins. A big advantage of our software program is that there is a parameter, the granularity factor, associated with it and we can freely choose a biological sequence family as a training set to determine the best parameter. In general, we choose all repeats (including many pseudo-repeats) in the SWISS-PROT amino acid sequence database as a typical training set. We show that the granularity factor is 0.52 and the average agreement accuracy of pseudo-periodic partitions, detected by our software for all pseudo-repeats in the SWISS-PROT database, is as high as 97.6%.
Availability: The program is available upon request from Honghui Wan and will be also available at http://www.mindgen.org
affy—analysis of Affymetrix GeneChip data at the probe level
Authors: Gautier Laurent , Cope Leslie , Bolstad Benjamin M. , Irizarry Rafael A. 
Published: February 2004

Abstract
Motivation: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used.
Results: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.
Hybrid simulation of cellular behavior
Authors: Kiehl Thomas R. , Mattheyses Robert M. , Simmons Melvin K. 
Published: February 2004

Abstract
Motivation: To be valuable to biological or biomedical research, in silico methods must be scaled to complex pathways and large numbers of interacting molecular species. The correct method for performing such simulations, discrete event simulation by Monte Carlo generation, is computationally costly for large complex systems. Approximation of molecular behavior by continuous models fails to capture stochastic behavior that is essential to many biological phenomena.
Results: We present a novel approach to building hybrid simulations in which some processes are simulated discretely, while other processes are handled in a continuous simulation by differential equations. This approach preserves the stochastic behavior of cellular pathways, yet enables scaling to large populations of molecules. We present an algorithm for synchronizing data in a hybrid simulation and discuss the trade-offs in such simulation. We have implemented the hybrid simulation algorithm and have validated it by simulating the statistical behavior of the well-known lambda phage switch. Hybrid simulation provides a new method for exploring the sources and nature of stochastic behavior in cells.
Supplementary information: The SBML file for the lambda phage tests will be made available at the OUP site.