bluuebunny/crossref_metadata_2025 huggingface dataset:
Israel in the Book of Isaiah
Authors: Kratz Reinhard G.
Published: August 2006

The name ‘Israel’ is employed by all sections of Isaiah in various ways and with various meanings. As such, the book takes part in the fundamental transformation the name has undergone both in the history of Israel and in the literary history of the Old and New Testaments as it evolved from a political to a theological concept, from the Israel of history to the Israel of faith. According to an insightful thesis proposed by Leonard Rost, this development took its point of departure from the prophets of the eighth century BCE and has left especially deep traces in First and Second Isaiah. The name Israel can thus serve as a leitmotif that allows us to retrace the development of Isaianic prophecy as well as the various stages of the book’s origins.
A user-centred design and evaluation of IR interfaces
Authors: Ahmed S. M. Zabed , McKnight Cliff , Oppenheim Charles
Published: August 2006

This paper presents a user-centred design and evaluation methodology for ensuring the usability of IR interfaces. The methodology is based on sequentially performing: a competitive analysis, user task analysis, heuristic evaluation, formative evaluation and a summative comparative evaluation. These techniques are described, and their application to iteratively design a prototype IR interface, which was then evaluated, is described. After each round of testing, the prototype was modified as needed. The user-centred methodology had a major impact in improving the interface. Results from the summative comparative evaluation suggest that users’ performance improved significantly in our prototype interface compared with a similar competitive system. They were also more satisfied with the prototype design. This methodology provides a starting point for techniques that let IR researchers and practitioners design better IR interfaces that are both easy to learn to use and remember. The paper concludes with some principles of interface design for IR systems.
Why appoint professionals?
Authors: Attar K. E.
Published: August 2006

Students have provided cheap successful labour for routine retrospective cataloguing projects. The current article examines a library project which went further, using university students with minimum training to catalogue its undergraduate stock from the book in hand to AACR2, level 2, allegedly to professional standard. The article discusses the faults made in MARC coding, descriptive cataloguing and subject cataloguing, noting the nature of the errors and their results. The investigation concludes that intelligence alone does not guarantee library ability, and that cataloguing beyond the creation of minimum records is not an intuitive task to be picked up without training. Hidden expenses are attached. A derisory attitude towards library skills is unjustified, and a place remains for qualified librarians to do qualified library work.
Terminological control of ‘Anonymous Groups’ for catalogues of audiovisual television documents
Authors: Caldera-Serrano Jorge
Published: August 2006

This article discusses the exceptional nature of the description of moving images for television archives, deriving from their audiovisual nature, and of the specifications in the queries of journalists as users of the Document Information System. It is suggested that there is a need to control completely ‘Anonymous Groups’ - groups without any established name - using current guidelines for authority data control. The article describes how ‘Proper Names’ access points can be established for the appropriate interrogation of moving image databases.
Time Preference and Learning Versus Selection
Authors: Klochko Marianna A.
Published: August 2006

With few exceptions, economic theory assumes that people’s valuations of the future - the discount applied to the future as opposed to the present - are fixed and exogenously set. The relevance of this assumption derives from the fact that this parameter of individual preference is critical in determining the likelihood that a person will engage in cooperative action, including the likelihood that they will abide by democratic norms and participate constructively in the development of efficient and competitive markets. Using a sample of Ukrainian youth - those who have emigrated to the West to complete their studies as compared to those who have remained in Ukraine - I question the validity of this assumption. Although the data reveals that those students who travel to the West are an unrepresentative sample of Ukraine’s student population generally in terms of the time discount they apply to the future, the data also suggest that the discount they apply to the future changes as a function of their length of stay in the West.
Coordination and Status Influence
Authors: Clark C. Robert , Clark Samuel , Polborn Mattias K.
Published: August 2006

We develop a model to explain why the influence of higher-status individuals is often accepted even when status is not an indication of superior information or competence. We propose such acceptance as a rational strategy in cases where coordination is important. In our model agents must select from among a set of alternatives after witnessing the choices of some group of initial movers, one of whom is assumed to be of high status. These agents would like to select the better alternative, but would also like to coordinate with as many others as possible. If a high-status individual is more prominent, he or she can be used as a coordination device. We determine in what situations agents weigh the behavior of higher-status agents more heavily than that of other agents, and whether the total utility of agents is improved as a result of the existence of high-status individuals.
Effect of Lactic Acid Bacteria on Beef Steak Microbial Flora Stored Under Modified Atmosphere and on Listeria Monocytogenes in Broth Cultures
Authors: Djenane D. , Martínez L. , Sánchez-Escalante A. , Montañés L. , Blanco D. , Yangüela J. , Beltrán J. A. , Roncalés P.
Published: August 2006

Beef steaks were inoculated with one or other of two protective strains of lactic acid bacteria, the bacteriocinogenic Lactobacillus sakei CTC 372 or the uncharacterised Lactobacillus CTC 711. They were stored under modified atmospheres (20–40% CO2). Inoculation of meat with both strains inhibited the growth of the spoilage bacteria. Neither CO2 in the pack atmosphere, inoculation with protective strains, nor a combination of both, affected formation of metmyoglobin or the development of off-odours. The formation of metmyoglobin in meat pigments and the sensory odour scores were compatible to those of fresh meat which had not undergone either oxidative deterioration or microbial spoilage. Listeria monocytogenes were inhibited in broth by meat surface microbiota containing either of the protective strains. With an initial population of 5.6 log cfu/mL, after 7 days incubation at 3°C, Listeria monocytogenes were recovered at log mean population of 2.8 log cfu/mL when neither protective strain was present. At 8°C, the population of Listeria monocytogenes recovered were reduced by about 2.5 or 1.5 log cfu/mL in the presence of Lactobacillus sakei CTC 372 or Lactobacillus CTC 711, respectively. At 25°C, the population of Listeria monocytogenes recovered from broth containing either protective strain were about 5 log cfu/mL less than the population recovered from broth containing Listeria monocytogenes only.
Firmness of Mandarin at Different Picking Dates
Authors: Gómez A. Hernández , Wang J. , Pereira A. García
Published: August 2006

The objective of this work was to characterise the firmness of ‘Satsuma’ mandarin fruit ( Citrus reticulate) at different picking dates. The firmness of mandarin was monitored using non-destructive impulse response (I-R) and traditional compression test. The dominant frequency (f), stiffness coefficient (SC) and elasticity coefficient (EC) as a function of picking date were expressed. The mandarin at different picking dates is characterised for a decrease in the f, SC and EC. The higher f, SC and EC corresponded to the firmer mandarin. A good correlation was established between the impulse response parameters (SC and EC) and compression force (CF) and determination coefficients were 0.89 and 0.90, respectively. The low correlation was found between SC (or EC) and sugar content (or pH). SC and EC were better firmness prediction, and the results implied that these two parameters could be used to distinguish different picking dates and firmness.
Note: Stability of Calcium Bioaccessibility and Sensory Parameters During the Storage of Fortified Juices
Authors: Haro J. F. , Martínez C. , Ros G. , Vidal M. L.
Published: August 2006

Changes in calcium bioaccessibility and sensory attributes of four different calcium compounds (calcium hydroxide lactate, emulsified calcium triphosphate, calcium pidolate and calcium amino acid chelate) added to a citric juice were studied at 0, 6 and 12 months of storage. Type of calcium compound showed significant differences ( p 0.05) in calcium bioaccessibility at the three periods of the study. The maximum value at month 0 and month 6 corresponded to the calcium amino acid chelate (45.09±0.59%) followed by calcium pidolate (38.09±0.28%), calcium lactate (32.4±2.17%) and calcium triphosphate (31.21±4.43%). There were no changes in calcium bioaccessibility through time of storage in any juice added with the different calcium salts, however organoleptic changes were critical in the most available samples at month 6. According to these results three of the salts (calcium hydroxide lactate, calcium pidolate and calcium triphosphate) were equally valid for adding to a citric fruit juice for up to 12 months of storage.
Physical Properties of Frozen Pork Thawed by High Pressure Assisted Thawing Process
Authors: Park S. H. , Ryu H. S. , Hong G. P. , Min S. G.
Published: August 2006

The effects of a high pressure assisted thawing process (HPATP) at 50, 100, 150 and 200MPa at 15ºC on the physical properties of frozen pork, M. longissimus dorsi, were investigated. Treated samples increased pH significantly, compared to atmospheric thawing ones (control). HPATP samples had higher water holding capacities and lower thawing losses than the control. Cooking losses of HPATP treatment decreased at 50 and 100MPa. HPATP had no significant effect ( p 0.05) on Warner-Bratzler shear force below 150MPa. There were no differences in colour at 100MPa, however, both L*-and b*-values increased significantly from 150MPa whereas a*-value decreased. According to the results, HPATP treatment improved the quality of frozen pork below 100MPa, effectively.
Departing the margins
Authors: Higgs Paul , Gilleard Chris
Published: August 2006

The contemporary experience of retirement in the most prosperous nations reorganizes the relationship of social class to old age. Later life can now be seen in terms of lifestyle and identity rather than being primarily a reflection of previous occupation. From being a residual category of social policy, the widespread introduction of retirement pensions not only ‘decommodified’ later life but was successful in taking older people out of a life-cycle-determined poverty. This decommodification had the effect of removing later life from the social relations of social class. During the ‘golden age’ of welfare, old age became dependent on class but was effectively outside it. ‘Old people’ were simply pensioners dependent on conditions set up during their working lives. Using Beck’s schema of the transition from first modernity into second modernity, retirement, particularly in Australia, the UK and the USA, has become recommodified as a potential consumer lifestyle sustained by pension fund capitalism and by the individualization of pension risk. Contemporary later life thus complicates the nature of social class as retirees become constitutive rather than residues of the class system.
‘Another world is possible’
Authors: Bramble Tom
Published: August 2006

The past decade has seen the emergence of a mass ‘alter-globalization’ movement in many regions of the world. One element in this movement has been the World Social Forum and its continental, regional, national and local spinoffs. In the first half of this article I provide a critical analysis of the social forum experience, particularly the World Social Forum, and outline both those aspects of the experience that are commonly agreed to be successes as well as those that are frequently held to be their failings or limitations. In the second half of the article, I report on a survey of the participants at two Australian social forums in 2004, which details their backgrounds, motivations, attitudes, experience and ambitions. Comparison is made with their closest parallels - the activists from the new social movements of the 1970s and 1980s previously examined by Offe, Touraine, Melucci and others.
Analysis of Piezoelectric Composite Beams and Plates with Multiple Delaminations
Authors: Raja S. , Adya H. P. Prathima , Viswanath S.
Published: August 2006

In the present work, the effect of delamination or debonding on the static and dynamic characteristics of laminated piezoelectric beams and plates is studied. A four-noded quadrilateral shear flexible plate element is developed to model the damages in composite substrate and in piezoelectric layers. The elastic stiffness and electro-elastic stiffness degradations are introduced at the elemental level through coupled constitutive relations. The undamaged structure is modeled as a single laminate while the delaminated region is modeled as sublaminates whose interface contains the desired delamination or debonding. The continuity of displacement is maintained across the delaminated edge by imposing the strain-based multipoint constraints. Numerical studies are conducted on composite specimens with surface bonded active layers. The results are presented to evaluate the performance of these smart structures in the presence of delamination. For actuators, the performance is measured in terms of the achievable deflection control and in sensors as a measurable output voltage.

It is observed that actuator and sensor debonding degrade the capabilities of active materials significantly. Therefore, the study concludes that a damage tolerant approach is essential for the design of smart structural systems to account for damage-induced uncertainty in the functional properties of smart actuators and sensors.
Feature Extraction for Defect Detection in Strands by Guided Ultrasonic Waves
Authors: Rizzo Piervincenzo , di Scalea Francesco Lanza
Published: August 2006

Multi-wire strands are widely used in civil structures as tensioning members in prestressed concrete, cable-stayed and suspension bridges. In recent years, various researchers including the authors have investigated guided ultrasonic waves as a tool for monitoring the health of the strands. Magnetostrictive ultrasonic transducers have been successfully used to excite and detect the guided waves in these components.

This study improves the general guided-wave technique with magnetostrictive transducers for the detection and sizing of defects in strands. The improvement consists of extracting sensitive and robust features of the wave signals, and then using these features to construct a damage index (D.I.). The proposed D.I. is unaffected by accidental variations in the excitation power or by changes in the electromechanical coupling efficiency of the transducers. The specific defect under investigation is a notch cut at varying depths in a strand that is subjected to a typical operational load. Features extracted after discrete wavelet processing of the wave signals result in a D.I. that is robust against noise and is linearly related to the notch depth in a logarithmic scale. In particular, the variance of the signal’s wavelet coefficients results in the largest sensitivity to notch depth.
Practitioner consensus in the use of cognitive behaviour therapy for individuals with a learning disability
Authors: Haddock Katie , Jones Robert S. P.
Published: August 2006

Cognitive behaviour therapy (CBT) has been acknowledged as one of the most successful treatments for mental health problems. However, only a small number of practitioners engage in CBT with people with learning disabilities. A group of eight clinical psychologists who currently use CBT with this population gave details about their work in an attempt to gain a consensus on how to adapt CBT.The collective experiences of a wider group of experts produced a wealth of knowledge and suggestions to promote the use of CBT with this client group. Results suggested that although CBT needs to be creatively delivered, it does not necessarily need extensive adaptation.
The barriers to social inclusion as perceived by people with intellectual disabilities
Authors: Abbott Suzanne , Mcconkey Roy
Published: August 2006

Very little research has been done on social inclusion from the perspective of people with intellectual disabilities, including perceived barriers and remedies. Focus groups were held with 68 persons, mostly tenants in supported living or shared group homes. Qualitative data were obtained using a mix of workshop activities and small group discussions. Four main barriers were identified: lack of necessary knowledge and skills; role of support staff and service mangers; location of house; and community factors such as lack of amenities and attitudes. Participants were able to identify a range of solutions for these barriers. Most of their proposals were in line with the aims of current government policy and good practice.These findings reinforce the contribution individuals could make to the planning of local services for themselves and others.This advocacy has been an essential element in reducing the social isolation of other marginalized groups.
MultiSeq: unifying sequence and structure data for evolutionary analysis
Authors: Roberts Elijah , Eargle John , Wright Dan , Luthey-Schulten Zaida
Published: August 2006

Background

Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes.

Results

Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins.

Conclusion

MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/
Profiling helper T cell subset gene expression in deer mice
Authors: Oko Lauren , Aduddell-Swope Bethany , Willis Derall , Hamor Robyn , Coons Teresa A , Hjelle Brian , Schountz Tony
Published: August 2006

Background

Deer mice (Peromyscus maniculatus) are the most common mammals in North America and are reservoirs for several zoonotic agents, including Sin Nombre virus (SNV), the principal etiologic agent of hantavirus cardiopulmonary syndrome (HCPS) in North America. Unlike human HCPS patients, SNV-infected deer mice show no overt pathological symptoms, despite the presence of virus in the lungs. A neutralizing IgG antibody response occurs, but the virus establishes a persistent infection. Limitations of detailed analysis of deer mouse immune responses to SNV are the lack of reagents and methods for evaluating such responses.

Results

We developed real-time PCR-based detection assays for several immune-related transcription factor and cytokine genes from deer mice that permit the profiling of CD4+helper T cells, including markers of Th1 cells (T-bet, STAT4, IFNγ, TNF, LT), Th2 cells (GATA-3, STAT6, IL-4, IL-5) and regulatory T cells (Fox-p3, IL-10, TGFβ1). These assays compare the expression of in vitro antigen-stimulated and unstimulated T cells from individual deer mice.

Conclusion

We developed molecular methods for profiling immune gene expression in deer mice, including a multiplexed real-time PCR assay for assessing expression of several cytokine and transcription factor genes. These assays should be useful for characterizing the immune responses of experimentally- and naturally-infected deer mice.
Getting by on credit: how district health managers in Ghana cope with the untimely release of funds
Authors: Asante Augustine D , Zwi Anthony B , Ho Maria T
Published: August 2006

Background

District health systems in Africa depend largely on public funding. In many countries, not only are these funds insufficient, but they are also released in an untimely fashion, thereby creating serious cash flow problems for district health managers. This paper examines how the untimely release of public sector health funds in Ghana affects district health activities and the way district managers cope with the situation.

Methods

A qualitative approach using semi-structured interviews was adopted. Two regions (Northern and Ashanti) covering the northern and southern sectors of Ghana were strategically selected. Sixteen managers (eight directors of health services and eight district health accountants) were interviewed between 2003/2004. Data generated were analysed for themes and patterns.

Results

The results showed that untimely release of funds disrupts the implementation of health activities and demoralises district health staff. However, based on their prior knowledge of when funds are likely to be released, district health managers adopt a range of informal mechanisms to cope with the situation. These include obtaining supplies on credit, borrowing cash internally, pre-purchasing materials, and conserving part of the fourth quarter donor-pooled funds for the first quarter of the next year. While these informal mechanisms have kept the district health system in Ghana running in the face of persistent delays in funding, some of them are open to abuse and could be a potential source of corruption in the health system.

Conclusion

Official recognition of some of these informal managerial strategies will contribute to eliminating potential risks of corruption in the Ghanaian health system and also serve as an acknowledgement of the efforts being made by local managers to keep the district health system functioning in the face of budgetary constraints and funding delays. It may boost the confidence of the managers and even enhance service delivery.
A nanoparticle-based immobilization assay for prion-kinetics study
Authors: Kouassi Gilles K , Irudayaraj Joseph
Published: August 2006

Magnetic and gold coated magnetic nanoparticles were synthesized by co-precipitation of ferrous and ferric chlorides, and by the micromicelles method, respectively. Synthesized nanoparticles were functionalized to bear carboxyl and amino acid moieties and used as prion protein carriers after carbodiimide activation in the presence of N-hydroxysuccinimide. The binding of human recombinant prion protein (huPrPrec) to the surface of these nanoparticles was confirmed by FTIR and the size and structures of the particles were characterized by transmission electron microscopy. Findings indicate that the rate of prion binding increased only slightly when the concentration of prion in the reaction medium was increased. Rate constants of binding were very similar on Fe3O4@Au and Fe3O4-LAA when the concentrations of protein were 1, 2, 1.5, 2.25 and 3.57 μg/ml. For a 5 μg/ml concentration of huPrPrec the binding rate constant was higher for the Fe3O4-LAA particles. This study paves the way towards the formation of prion protein complexes onto a 3-dimensional structure that could reveal obscure physiological and pathological structure and prion protein kinetics.
Differential susceptibility of naïve, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission
Authors: Groot Fedde , van Capel Toni MM , Schuitemaker Joost HN , Berkhout Ben , de Jong Esther C
Published: August 2006

Background

Dendritic cells (DC) have been proposed to facilitate sexual transmission of HIV-1 by capture of the virus in the mucosa and subsequent transmission to CD4+T cells. Several T cell subsets can be identified in humans: naïve T cells (TN) that initiate an immune response to new antigens, and memory T cells that respond to previously encountered pathogens. The memory T cell pool comprises central memory (TCM) and effector memory cells (TEM), which are characterized by distinct homing and effector functions. The TEMcell subset, which can be further divided into effector Th1 and Th2 cells, has been shown to be the prime target for viral replication after HIV-1 infection, and is abundantly present in mucosal tissues.

Results

We determined the susceptibility of TN, TCMand TEMcells to DC-mediated HIV-1 transmission and found that co-receptor expression on the respective T cell subsets is a decisive factor for transmission. Accordingly, CCR5-using (R5) HIV-1 was most efficiently transmitted to TEMcells, and CXCR4-using (X4) HIV-1 was preferentially transmitted to TNcells.

Conclusion

The highly efficient R5 transfer to TEMcells suggests that mucosal T cells are an important target for DC-mediated transmission. This may contribute to the initial burst of virus replication that is observed in these cells. TNcells, which are the prime target for DC-mediated X4 virus transmission in our study, are considered to inefficiently support HIV-1 replication. Our results thus indicate that DC may play a decisive role in the susceptibility of TNcells to X4 tropic HIV-1.
Sodium Channel Expression in the Ventral Posterolateral Nucleus of the Thalamus after Peripheral Nerve Injury
Authors: Zhao Peng , Waxman Stephen G , Hains Bryan C
Published: August 2006

Peripheral nerve injury is known to up-regulate the expression of rapidly-repriming Nav1.3 sodium channel within first-order dorsal root ganglion neurons and second-order dorsal horn nociceptive neurons, but it is not known if pain-processing neurons higher along the neuraxis also undergo changes in sodium channel expression. In this study, we hypothesized that after peripheral nerve injury, third-order neurons in the ventral posterolateral (VPL) nucleus of the thalamus undergo changes in expression of sodium channels. To test this hypothesis, adult male Sprague-Dawley rats underwent chronic constriction injury (CCI) of the sciatic nerve. Ten days after CCI, when allodynia and hyperalgesia were evident, in situ hybridization and immunocytochemical analysis revealed up-regulation of Nav1.3 mRNA, but no changes in expression of Nav1.1, Nav1.2, or Nav1.6 in VPL neurons, and unit recordings demonstrated increased background firing, which persisted after spinal cord transection, and evoked hyperresponsiveness to peripheral stimuli. These results demonstrate that injury to the peripheral nervous system induces alterations in sodium channel expression within higher-order VPL neurons, and suggest that misexpression of the Nav1.3 sodium channel increases the excitability of VPL neurons injury, contributing to neuropathic pain.
Fertility of frozen-thawed stallion semen cannot be predicted by the currently used laboratory methods
Authors: Kuisma P , Andersson M , Koskinen E , Katila T
Published: August 2006

The aim of the project was to use current simple and practical laboratory tests and compare results with the foaling rates of mares inseminated with commercially produced frozen semen. In Exp. 1, semen was tested from 27 and in Exp. 2 from 23 stallions; 19 stallions participated in both experiments. The mean number of mares per stallion in both experiments was 37 (min. 7, max. 121). Sperm morphology was assessed and bacterial culture performed once per stallion. In Exp. 1, progressive motility after 0, 1, 2, 3, and 4 h of incubation using light microscopy, motility characteristics measured with an automatic sperm analyzer, plasma membrane integrity using carboxyfluorescein diacetate/propidium iodide (CFDA/PI) staining and light microscopy, plasma membrane integrity using PI staining and a fluorometer, plasma membrane integrity using a resazurin reduction test, and sperm concentration were evaluated. In Exp. 2, the same tests as in Exp. 1 and a hypo-osmotic swelling test (HOST) using both light microscopy and a fluorometer were performed immediately after thawing and after a 3-h incubation. Statistical analysis was done separately to all stallions and to those having ≥ 20 mares; in addition, stallions with foaling rates < 60 or ≥ 60% were compared. In Exp. 1, progressive motility for all stallions after a 2 – 4-h incubation correlated with the foaling rate (correlation coefficients 0.39 – 0.51), (p < 0.05). In stallions with > 20 mares, the artificial insemination dose showed a correlation coefficient of -0.58 (p < 0.05). In Exp. 2, the HOST immediately after thawing showed a negative correlation with foaling rate (p < 0.05). No single test was consistently reliable for predicting the fertilizing capacity of semen, since the 2 experiments yielded conflicting results, although the same stallions sometimes participated in both. This shows the difficulty of frozen semen quality control in commercially produced stallion semen, and on the other hand, the difficulty of conducting fertility trials in horses.
Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsisrosettes
Authors: Gibon Yves , Usadel Bjoern , Blaesing Oliver E , Kamlage Beate , Hoehne Melanie , Trethewey Richard , Stitt Mark
Published: August 2006

Background

Genome-wide transcript profiling and analyses of enzyme activities from central carbon and nitrogen metabolism show that transcript levels undergo marked and rapid changes during diurnal cycles and after transfer to darkness, whereas changes in activities are smaller and delayed. In the starchless pgm mutant, where sugars are depleted every night, there are accentuated diurnal changes in transcript levels. Enzyme activities in this mutant do not show larger diurnal changes; instead, they shift towards the levels found in the wild type after several days of darkness. This indicates that enzyme activities change slowly, integrating the changes in transcript levels over several diurnal cycles.

Results

To generalize this conclusion, 137 metabolites were profiled using gas and liquid chromatography coupled to mass spectroscopy. The amplitudes of the diurnal changes in metabolite levels in pgm were (with the exception of sugars) similar or smaller than in the wild type. The average levels shifted towards those found after several days of darkness in the wild type. Examples include increased levels of amino acids due to protein degradation, decreased levels of fatty acids, increased tocopherol and decreased myo-inositol. Many metabolite-transcript correlations were found and the proportion of transcripts correlated with sugars increased dramatically in the starchless mutant.

Conclusion

Rapid diurnal changes in transcript levels are integrated over time to generate quasi-stable changes across large sectors of metabolism. This implies that correlations between metabolites and transcripts are due to regulation of gene expression by metabolites, rather than metabolites being changed as a consequence of a change in gene expression.
Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts
Authors: Hahne Florian , Arlt Dorit , Sauermann Mamatha , Majety Meher , Poustka Annemarie , Wiemann Stefan , Huber Wolfgang
Published: August 2006

Highthroughput cell-based assays with flow cytometric readout provide a powerful technique for identifying components of biologic pathways and their interactors. Interpretation of these large datasets requires effective computational methods. We present a new approach that includes data pre-processing, visualization, quality assessment, and statistical inference. The software is freely available in the Bioconductor package prada. The method permits analysis of large screens to detect the effects of molecular interventions in cellular systems.
Development of heart valves requiresGata4expression in endothelial-derived cells
Authors: Rivera-Feliciano José , Lee Kyu-Ho , Kong Sek Won , Rajagopal Satish , Ma Qing , Springer Zhangli , Izumo Seigo , Tabin Clifford J. , Pu William T.
Published: August 2006

Cardiac malformations due to aberrant development of the atrioventricular(AV) valves are among the most common forms of congenital heart disease. At localized swellings of extracellular matrix known as the endocardial cushions,the endothelial lining of the heart undergoes an epithelial to mesenchymal transition (EMT) to form the mesenchymal progenitors of the AV valves. Further growth and differentiation of these mesenchymal precursors results in the formation of portions of the atrial and ventricular septae, and the generation of thin, pliable valves. Gata4, which encodes a zinc finger transcription factor, is expressed in the endothelium and mesenchyme of the AV valves. Using a Tie2-Cre transgene, we selectively inactivated Gata4 within endothelial-derived cells. Mutant endothelium failed to undergo EMT, resulting in hypocellular cushions. Mutant cushions had decreased levels of Erbb3, an EGF-family receptor essential for EMT in the atrioventricular cushions. In Gata4 mutant embryos, Erbb3downregulation was associated with impaired activation of Erk, which is also required for EMT. Expression of a Gata4 mutant protein defective in interaction with Friend of Gata (FOG) cofactors rescued the EMT defect, but resulted in a decreased proliferation of mesenchyme and hypoplastic cushions that failed to septate the ventricular inlet. We demonstrate two novel functions of Gata4 in development of the AV valves. First, Gata4 functions as an upstream regulator of an Erbb3-Erk pathway necessary for EMT, and second, Gata4 acts to promote cushion mesenchyme growth and remodeling.
Temporal regulation of shoot development inArabidopsis thalianabymiR156and its targetSPL3
Authors: Wu Gang , Poethig R. Scott
Published: August 2006

SPL3, SPL4 and SPL5 (SPL3/4/5) are closely related members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE family of transcription factors in Arabidopsis, and have a target site for the microRNA miR156 in their 3 ′ UTR. The phenotype of Arabidopsis plants constitutively expressing miR156-sensitive and miR156-insensitive forms of SPL3/4/5 revealed that all three genes promote vegetative phase change and flowering, and are strongly repressed by miR156. Constitutive expression of miR156a prolonged the expression of juvenile vegetative traits and delayed flowering. This phenotype was largely corrected by constitutive expression of a miR156-insensitive form of SPL3. The juvenile-to-adult transition is accompanied by a decrease in the level of miR156 and an increase in the abundance of SPL3 mRNA. The complementary effect of hasty on the miR156 and SPL3 transcripts, as well as the miR156-dependent temporal expression pattern of a 35S::GUS-SPL3 transgene, suggest that the decrease in miR156 is responsible for the increase in SPL3 expression during this transition. SPL3 mRNA is elevated by mutations in ZIPPY/AGO7, RNA DEPENDENT RNA POLYMERASE 6 (RDR6) and SUPPRESSOR OF GENE SILENCING 3 (SGS3), indicating that it is directly or indirectly regulated by RNAi. However, our results indicate that RNAi does not contribute to the temporal expression pattern of this gene. We conclude that vegetative phase change in Arabidopsis is regulated by an increase in the expression of SPL3 and probably also SPL4and SPL5, and that this increase is a consequence of a decrease in the level of miR156.
Small molecule-induced ablation and subsequent regeneration of larval zebrafish melanocytes
Authors: Yang Chao-Tsung , Johnson Stephen L.
Published: August 2006

We developed a method to efficiently ablate a single cell type, the zebrafish melanocyte, and study the mechanisms of its regeneration. We found that a small molecule, (2-morpholinobutyl)-4-thiophenol (MoTP), specifically ablates zebrafish larval melanocytes or melanoblasts, and that this melanocytotoxicity is dependent on tyrosinase activity, which presumably converts MoTP to cytotoxic quinone species. Following melanocyte ablation by MoTP treatment, we demonstrate by BrdU incorporation experiments that regenerated melanocytes are derived from the division of otherwise quiescent melanocyte precursors or stem cells. We further show that larval melanocyte regeneration requires the kit receptor tyrosine kinase. Our results suggest that a small number of melanocyte precursors or stem cells unevenly distributed in larvae are drawn upon to reconstitute the larval melanocyte population following melanocyte ablation by MoTP.
COUP-TFI controls Notch regulation of hair cell and support cell differentiation
Authors: Tang Louisa S. , Alger Heather M. , Pereira Fred A.
Published: August 2006

The orphan nuclear receptor COUP-TFI (Nr2f1) regulates many aspects of mammalian development, but little is known about its role in cochlear hair cell and Deiter's support cell development. The COUP-TFI knockout(COUP-TFI-/-) has a significant increase in hair cell (HC)number in the mid-to-apical turns. The total number of hair cells is not increased over wild type, perhaps because of displaced hair cells and a shortened cochlear duct. This implicates a defect of convergent-extension in the COUP-TFI-/- duct. In addition, excess proliferation in the COUP-TFI-/- sensory epithelium indicates that the origin of the extra HCs in the apex is complex. Because loss-of-function studies of Notch signaling components have similar phenotypes, we investigated Notch regulation of hair cell differentiation in COUP-TFI-/-mice and confirmed misregulation of Notch signaling components, including Jag1, Hes5 and in a manner consistent with reduced Notch signaling,and correlated with increases in hair cell and support cell differentiation. The disruption of Notch signaling by a γ-secretase inhibitor in an in vitro organ culture system of wild-type cochleae resulted in a reduction in expression of the Notch target gene Hes5 and an increase in hair cell differentiation. Importantly, inhibition of Notch activity resulted in a greater increase in hair cell differentiation in COUP-TFI-/- cochlear cultures than in wild-type cultures,suggesting a hypersensitivity to Notch inactivation in COUP-TFI-/- cochlea, particularly at the apical turn. Thus, we present evidence that reduced Notch signaling contributes to increases in hair cell and support cell differentiation in COUP-TFI-/- mice, and suggest that COUP-TFI is required for Notch regulation of hair cell and support cell differentiation.
Mesodermal expression ofTbx1is necessary and sufficient for pharyngeal arch and cardiac outflow tract development
Authors: Zhang Zhen , Huynh Tuong , Baldini Antonio
Published: August 2006

The development of the segmented pharyngeal apparatus involves complex interaction of tissues derived from all three germ layers. The role of mesoderm is the least studied, perhaps because of its apparent lack of anatomical boundaries and positionally restricted gene expression. Here, we report that the mesoderm-specific deletion of Tbx1, a T-box transcription factor, caused severe pharyngeal patterning and cardiovascular defects, while mesoderm-specific restoration of Tbx1 expression in a mutant background corrected most of those defects in the mouse. We show that some organs, e.g. the thymus, require Tbx1 expression in the mesoderm and in the epithelia. In addition, these experiments revealed that different pharyngeal arches require Tbx1 in different tissues. Finally, we show that Tbx1 in the mesoderm is required to sustain cell proliferation. Thus, the mesodermal transcription program is not only crucial for cardiovascular development, but is also key in the development and patterning of pharyngeal endoderm.
The transcription factor ZBP-89 controls generation of the hematopoietic lineage in zebrafish and mouse embryonic stem cells
Authors: Li Xiangen , Xiong Jing-Wei , Shelley C. Simon , Park Heiyoung , Arnaout M. Amin
Published: August 2006

Hematopoietic development is closely linked to that of blood vessels and the two processes are regulated in large part by transcription factors that control cell fate decisions and cellular differentiation. Both blood and blood vessels derive from a common progenitor, termed the hemangioblast, but the factor(s) specifying the development and differentiation of this stem cell population into the hematopoietic and vascular lineages remain ill defined. Here, we report that knockdown of the Krüppel-like transcription factor ZBP-89 in zebrafish embryos results in a bloodless phenotype, caused by disruption of both primitive and definitive hematopoiesis, while leaving primary blood vessel formation intact. Injection of ZBP-89 mRNA into cloche zebrafish embryos, which lack both the hematopoietic and endothelial lineages, rescues hematopoiesis but not vasculogenesis. Injection of mRNA for Stem Cell Leukemia (SCL), a transcription factor that directs hemangioblast development into blood cell precursors, rescues the bloodless phenotype in ZBP-89 zebrafish morphants. Forced expression of ZBP-89 induces the expansion of hematopoietic progenitors in wild-type zebrafish and in mouse embryonic stem cell cultures but inhibits angiogenesis in vivo and in vitro. These findings establish a unique regulatory role for ZBP-89, positioned at the interface between early blood and blood vessel development.
Derivation and large-scale expansion of multipotent astroglial neural progenitors from adult human brain
Authors: Walton Noah M. , Sutter Benjamin M. , Chen Huan-Xin , Chang Lung-Ji , Roper Steven N. , Scheffler Bjorn , Steindler Dennis A.
Published: August 2006

The isolation and expansion of human neural cell types has become increasingly relevant in restorative neurobiology. Although embryonic and fetal tissue are frequently envisaged as providing sufficiently primordial cells for such applications, the developmental plasticity of endogenous adult neural cells remains largely unclear. To examine the developmental potential of adult human brain cells, we applied conditions favoring the growth of neural stem cells to multiple cortical regions, resulting in the identification and selection of a population of adult human neural progenitors(AHNPs). These nestin+ progenitors may be derived from multiple forebrain regions, are maintainable in adherent conditions, co-express multiple glial and immature markers, and are highly expandable, allowing a single progenitor to theoretically form sufficient cells for∼4×107 adult brains. AHNPs longitudinally maintain the ability to generate both glial and neuronal cell types in vivo and in vitro,and are amenable to genetic modification and transplantation. These findings suggest an unprecedented degree of inducible plasticity is retained by cells of the adult central nervous system.
Kermit 2/XGIPC, an IGF1 receptor interacting protein, is required for IGF signaling inXenopuseye development
Authors: Wu Jinling , O'Donnell Michael , Gitler Aaron D. , Klein Peter S.
Published: August 2006

GIPC is a PDZ-domain-containing protein identified in vertebrate and invertebrate organisms through its interaction with a variety of binding partners including many membrane proteins. Despite the multiple reports identifying GIPC, its endogenous function and the physiological significance of these interactions are much less studied. We have previously identified the Xenopus GIPC homolog kermit as a frizzled 3 interacting protein that is required for frizzled 3 induction of neural crest in ectodermal explants. We identified a second Xenopus GIPC homolog, named kermit 2 (also recently described as an IGF receptor interacting protein and named XGIPC). Despite its high amino acid similarity with kermit, kermit 2/XGIPC has a distinct function in Xenopus embryos. Loss-of-function analysis indicates that kermit 2/XGIPC is specifically required for Xenopuseye development. Kermit 2/XGIPC functions downstream of IGF in eye formation and is required for maintaining IGF-induced AKT activation. A constitutively active PI3 kinase partially rescues the Kermit 2/XGIPC loss-of-function phenotype. Our results provide the first in vivo loss of function analysis of GIPC in embryonic development and also indicate that kermit 2/XGIPC is a novel component of the IGF pathway, potentially functioning through modulation of the IGF1 receptor.
Intraspecific variation in tracheal volume in the American locust,Schistocerca americana, measured by a new inert gas method
Authors: Lease Hilary M. , Wolf Blair O. , Harrison Jon F.
Published: August 2006

The volume of a tracheal system influences breath-holding capacity and provides an index of an insect's investment in its respiratory system. Here,we describe a new, generally applicable method to measure tracheal volume that enables repeatable determinations on live animals. Animals are isolated in a closed chamber of a known volume and equilibrated with a helium:oxygen gas mixture. The chamber is then rapidly flushed with a nitrogen:oxygen gas mixture to eliminate the helium surrounding the animal, and sealed. After a period of time sufficient to allow equilibration of helium between tracheal system and chamber air, a gas sample is taken from the chamber, and tracheal volumes are calculated from the helium content of the sample, using a gas chromatograph. We show that relative investment in the tracheal system increases with age/size in the grasshopper; tracheal volume scales with mass to the power 1.3. This increased proportional investment in the tracheal system provides a mechanistic basis for the enhanced respiratory capacity of older grasshoppers. Tracheal volumes decrease strongly as grasshoppers grow within an instar stage, explaining reduced safety margins for oxygen delivery. Finally, tracheal volumes are smaller in gravid females than males, probably due to compression of air sacs by eggs.