bluuebunny/crossref_metadata_2025 huggingface dataset:
NFAT is a nerve activity sensor in skeletal muscle and controls activity-dependent myosin switching
Authors: McCullagh Karl J. A. , Calabria Elisa , Pallafacchina Giorgia , Ciciliot Stefano , Serrano Antonio L. , Argentini Carla , Kalhovde John M. , Lømo Terje , Schiaffino Stefano
Published: July 2004

Calcineurin (Cn) signaling has been implicated in nerve activity-dependent fiber type specification in skeletal muscle, but the downstream effector pathway has not been established. We have investigated the role of the transcription factor nuclear factor of activated T cells (NFAT), a major target of Cn, by using an
in vivo
transfection approach in regenerating and adult rat muscles. NFAT transcriptional activity was monitored with two different NFAT-dependent reporters and was found to be higher in slow compared to fast muscles. NFAT activity is decreased by denervation in slow muscles and is increased by electrostimulation of denervated muscles with a tonic low-frequency impulse pattern, mimicking the firing pattern of slow motor neurons, but not with a phasic high-frequency pattern typical of fast motor neurons. To determine the role of NFAT, we transfected regenerating and adult rat muscles with a plasmid coding for VIVIT, a specific peptide inhibitor of Cn-mediated NFAT activation. VIVIT was found to block the expression of slow myosin heavy chain (MyHC-slow) induced by slow motor neuron activity in regenerating slow soleus muscle and to inhibit the expression of MyHC-slow transcripts and the activity of a MyHC-slow promoter in adult soleus. The role of NFAT was confirmed by the finding that a constitutively active NFATc1 mutant stimulates the MyHC-slow, inhibits the fast MyHC-2B promoter in adult fast muscles, and induces MyHC-slow expression in regenerating muscles. These results support the notion that Cn-NFAT signaling acts as a nerve activity sensor in skeletal muscle
in vivo
and controls nerve activity-dependent myosin switching.
The
Spn4
gene of
Drosophila
encodes a potent furin-directed secretory pathway serpin
Authors: Richer Martin J. , Keays Clairessa A. , Waterhouse Jennifer , Minhas Jessey , Hashimoto Carl , Jean François
Published: July 2004

Proprotein convertases (PCs) are an important class of host-cell serine endoproteases implicated in many physiological and pathological processes. Owing to their expanding roles in the proteolytic events required for generating infectious microbial pathogens and for tumor growth and invasiveness, there is increasing interest in identifying endogenous PC inhibitors. Here we report the identification of Spn4A, a previously uncharacterized secretory pathway serine protease inhibitor (serpin) from
Drosophila melanogaster
that contains a consensus furin cleavage site, -Arg
P4
-Arg-Lys-Arg
P1↓
-, in its reactive site loop (RSL). Our biochemical and kinetics analysis revealed that recombinant Spn4A inhibits human furin (
K
i
, 13 pM;
k
ass
, 3.2 × 10
7
M
–1
·s
–1
) and
Drosophila
PC2 (
K
i
, 3.5 nM;
k
ass
, 9.2 × 10
4
M
–1
·s
–1
) by a slow-binding mechanism characteristic of serpin molecules and forms a kinetically trapped SDS-stable complex with each enzyme. For both PCs, the stoichiometry of inhibition by Spn4A is nearly 1, which is characteristic of known physiological serpin–protease interactions. Mass analysis of furin–Spn4A reaction products identified the actual reactive site center of Spn4A to be -Arg
P4
-Arg-Lys-Arg
P1↓
-. Moreover, we demonstrate that Spn4A's highly effective PC inhibition properties are critically dependent on the unusual length of its RSL, which is composed of 18 aa instead of the typical 17-residue RSL found in most other inhibitory serpins. The identification of Spn4A, the most potent and effective natural serpin of PCs identified to date, suggests that Spn4A could be a prototype of endogenous serpins involved in the precise regulation of PC-dependent proteolytic cleavage events in the secretory pathway of eukaryotic cells.
NFAT5/TonEBP mutant mice define osmotic stress as a critical feature of the lymphoid microenvironment
Authors: Go William Y. , Liu Xuebin , Roti Michelle A. , Liu Forrest , Ho Steffan N.
Published: July 2004

Osmotic stress responses are critical not only to the survival of unicellular organisms but also to the normal function of the mammalian kidney. However, the extent to which cells outside the kidney rely on osmotic stress responses
in vivo
remains unknown. Nuclear factor of activated T cells 5 (NFAT5)/tonicity enhancer binding protein (TonEBP), the only known osmosensitive mammalian transcription factor, is expressed most abundantly in the thymus and is induced upon lymphocyte activation. Here we report that NFAT5/TonEBP is not only essential for normal cell proliferation under hyperosmotic conditions but also necessary for optimal adaptive immunity. Targeted deletion of exons 6 and 7 of the
Nfat5
gene, which encode a critical region of the DNA-binding domain, gave rise to a complete loss of function in the homozygous state and a partial loss of function in the heterozygous state. Complete loss of function resulted in late gestational lethality. Furthermore, hypertonicity-induced NFAT5/TonEBP transcriptional activity and hsp70.1 promoter function were completely eliminated, and cell proliferation under hyperosmotic culture conditions was markedly impaired. Partial loss of NFAT5/TonEBP function resulted in lymphoid hypocellularity and impaired antigen-specific antibody responses in viable heterozygous animals. In addition, lymphocyte proliferation
ex vivo
was reduced under hypertonic, but not isotonic, culture conditions. Direct measurement of tissue osmolality further revealed lymphoid tissues to be hyperosmolar. These results indicate that lymphocyte-mediated immunity is contingent on adaptation to physiologic osmotic stress, thus providing insight into the lymphoid microenvironment and the importance of the NFAT5/TonEBP osmotic stress response pathway
in vivo
.
Charge equilibration between two distinct sites in double helical DNA
Authors: Delaney Sarah , Yoo Jae , Stemp Eric D. A. , Barton Jacqueline K.
Published: July 2004

DNA assemblies containing a pendant dipyridophenazine complex of Ru(II) along with two oxidative traps, a site containing the nucleoside analog methylindole (5′-GMG-3′) and a 5′-GGG-3′ site, have been constructed to explore long-range charge transport through the base pair stack. With these chemically well defined assemblies, in combination with the flash/quench technique, formation of the methylindole cation radical and the neutral guanine radical is monitored directly by using transient absorption spectroscopy, and yields of oxidative damage are quantitated biochemically by gel electrophoresis. In these assemblies the base radicals form with a rate of ≥10
7
s
–1
. The rate of base radical formation does not change upon the addition of a second radical trap, the 5′-GGG-3′ site; however, the yield of methylindole oxidation is significantly lower. This observation indicates that the 5′-GGG-3′ site is effective in competing for the migrating charge and provides a second trapping site. Switching the orientation of the two trapping sites does not affect the yield of oxidized products at either site. Therefore, in DNA both forward and reverse charge transport occur so as to provide equilibration across the duplex on a timescale that is fast compared with trapping at a particular site. Further evidence of charge equilibration results from incorporating an intervening base-stacking perturbation and monitoring the fate of the injected charge. These experiments underscore the dynamic nature of DNA charge transport and reveal the importance of considering radical propagation in both directions along the DNA duplex.
Protozoan predation, diversifying selection, and the evolution of antigenic diversity in
Salmonella
Authors: Wildschutte Hans , Wolfe David M. , Tamewitz Aletheia , Lawrence Jeffrey G.
Published: July 2004

Extensive population-level genetic variability at the
Salmonella rfb
locus, which encodes enzymes responsible for synthesis of the O-antigen polysaccharide, is thought to have arisen through frequency-dependent selection (FDS) by means of exposure of this pathogen to host immune systems. The FDS hypothesis works well for pathogens such as
Haemophilus influenzae
and
Neisseria meningitis
, which alter the composition of their O-antigens during the course of bloodborne infections. In contrast,
Salmonella
remains resident in epithelial cells or macrophages during infection and does not have phase variability in its O-antigen. More importantly,
Salmonella
shows host–serovar specificity, whereby strains bearing certain O-antigens cause disease primarily in specific hosts; this behavior is inconsistent with FDS providing selection for the origin or maintenance of extensive polymorphism at the
rfb
locus. Alternatively, selective pressure may originate from the host intestinal environment itself, wherein diversifying selection mediated by protozoan predation allows for the continued existence of
Salmonella
able to avoid consumption by host-specific protozoa. This selective pressure would result in high population-level diversity at the
Salmonella rfb
locus without phase variation. We show here that intestinal protozoa recognize antigenically diverse
Salmonella
with different efficiencies and demonstrate that differences solely in the O-antigen are sufficient to allow for prey discrimination. Combined with observations of the differential distributions of both serotypes of bacterial species and their protozoan predators among environments, our data provides a framework for the evolution of high genetic diversity at the
rfb
locus and host-specific pathogenicity in
Salmonella
.
Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates
Authors: Lewin Jörn , Schmitt Armin O. , Adorján Péter , Hildmann Thomas , Piepenbrock Christian
Published: July 2004

Motivation: Methylation of cytosines in DNA plays an important role in the regulation of gene expression, and the analysis of methylation patterns is fundamental for the understanding of cell differentiation, aging processes, diseases and cancer development. Such analysis has been limited, because technologies for detailed and efficient high-throughput studies have not been available. We have developed a novel quantitative methylation analysis algorithm and workflow based on direct DNA sequencing of PCR products from bisulfite-treated DNA with high-throughput sequencing machines. This technology is a prerequisite for success of the Human Epigenome Project, the first large genome-wide sequencing study for DNA methylation in many different tissues. Methylation in tissue samples which are compositions of different cells is a quantitative information represented by cytosine/thymine proportions after bisulfite conversion of unmethylated cytosines to uracil and PCR. Calculation of quantitative methylation information from base proportions represented by different dye signals in four-dye sequencing trace files needs a specific algorithm handling imbalanced and overscaled signals, incomplete conversion, quality problems and basecaller artifacts.

Results: The algorithm we developed has several key properties: it analyzes trace files from PCR products of bisulfite-treated DNA sequenced directly on ABI machines; it yields quantitative methylation measurements for individual cytosine positions after alignment with genomic reference sequences, signal normalization and estimation of effectiveness of bisulfite treatment; it works in a fully automated pipeline including data quality monitoring; it is efficient and avoids the usual cost of multiple sequencing runs on subclones to estimate DNA methylation. The power of our new algorithm is demonstrated with data from two test systems based on mixtures with known base compositions and defined methylation. In addition, the applicability is proven by identifying CpGs that are differentially methylated in real tissue samples.
A model-based optimization framework for the inference on gene regulatory networks from DNA array data
Authors: Thomas Reuben , Mehrotra Sanjay , Papoutsakis Eleftherios T. , Hatzimanikatis Vassily
Published: July 2004

Motivation: Identification of the regulatory structures in genetic networks and the formulation of mechanistic models in the form of wiring diagrams is one of the significant objectives of expression profiling using DNA microarray technologies and it requires the development and application of identification frameworks.

Results: We have developed a novel optimization framework for identifying regulation in a genetic network using the S-system modeling formalism. We show that balance equations on both mRNA and protein species led to a formulation suitable for analyzing DNA-microarray data whereby protein concentrations have been eliminated and only mRNA relative concentrations are retained. Using this formulation, we examined if it is possible to infer a set of possible genetic regulatory networks consistent with observed mRNA expression patterns. Two origins of changes in mRNA expression patterns were considered. One derives from changes in the biophysical properties of the system that alter the molecular-interaction kinetics and/or message stability. The second is due to gene knock-outs. We reduced the identification problem to an optimization problem (of the so-called mixed-integer non-linear programming class) and we developed an algorithmic procedure for solving this optimization problem. Using simulated data generated by our mathematical model, we show that our method can actually find the regulatory network from which the data were generated. We also show that the number of possible alternate genetic regulatory networks depends on the size of the dataset (i.e. number of experiments), but this dependence is different for each of the two types of problems considered, and that a unique solution requires fewer datasets than previously estimated in the literature. This is the first method that also allows the identification of every possible regulatory network that could explain the data, when the number of experiments does not allow identification of unique regulatory structure.

Availability: The implementation of the algorithm in AMPL is available on request from the authors.
Accuracy improvement for identifying translation initiation sites in microbial genomes
Authors: Zhu Huai-Qiu , Hu Gang-Qing , Ouyang Zheng-Qing , Wang Jin , She Zhen-Su
Published: July 2004

Motivation: At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3′ end), but a much lower accuracy of the translation initiation site (TIS, 5′ end). The latter is important to the analysis and the understanding of the putative protein of a gene and the regulatory machinery of the translation. Improving the accuracy of prediction of TIS is one of the remaining open problems.

Results: In this paper, we develop a four-component statistical model to describe the TIS of prokaryotic genes. The model incorporates several features with biological meanings, including the correlation between translation termination site and TIS of genes, the sequence content around the start codon; the sequence content of the consensus signal related to ribosomal binding sites (RBSs), and the correlation between TIS and the upstream consensus signal. An entirely non-supervised training system is constructed, which takes as input a set of annotated coding open reading frames (ORFs) by any gene finder, and gives as output a set of organism-specific parameters (without any prior knowledge or empirical constants and formulas). The novel algorithm is tested on a set of reliable datasets of genes from Escherichia coli and Bacillus subtillis. MED-Start may correctly predict 95.4% of the start sites of 195 experimentally confirmed E.coli genes, 96.6% of 58 reliable B.subtillis genes. Moreover, the test results indicate that the algorithm gives higher accuracy for more reliable datasets, and is robust to the variation of gene length. MED-Start may be used as a postprocessor for a gene finder. After processing by our program, the improvement of gene start prediction of gene finder system is remarkable, e.g. the accuracy of TIS predicted by MED 1.0 increases from 61.7 to 91.5% for 854 E.coli verified genes, while that by GLIMMER 2.02 increases from 63.2 to 92.0% for the same dataset. These results show that our algorithm is one of the most accurate methods to identify TIS of prokaryotic genomes.

Availability: The program MED-Start can be accessed through the website of CTB at Peking University: http://ctb.pku.edu.cn/main/SheGroup/MED_Start.htm
Effects of pooling mRNA in microarray class comparisons
Authors: Shih Joanna H. , Michalowska Aleksandra M. , Dobbin Kevin , Ye Yumei , Qiu Ting Hu , Green Jeffrey E.
Published: July 2004

Motivation: In microarray experiments investigators sometimes wish to pool RNA samples before labeling and hybridization due to insufficient RNA from each individual sample or to reduce the number of arrays for the purpose of saving cost. The basic assumption of pooling is that the expression of an mRNA molecule in the pool is close to the average expression from individual samples. Recently, a method for studying the effect of pooling mRNA on statistical power in detecting differentially expressed genes between classes has been proposed, but the different sources of variation arising in microarray experiments were not distinguished. Another paper recently did take different sources of variation into account, but did not address power and sample size for class comparison.

In this paper, we study the implication of pooling in detecting differential gene expression taking into account different sources of variation and check the basic assumption of pooling using data from both the cDNA and Affymetrix GeneChip microarray experiments.

Results: We present formulas for the required number of subjects and arrays to achieve a desired power at a specified significance level. We show that due to the loss of degrees of freedom for a pooled design, a large increase in the number of subjects may be required to achieve a power comparable to that of a non-pooled design. The added expense of additional samples for the pooled design may outweigh the benefit of saving on microarray cost. The microarray data from both platforms show that the major assumption of pooling may not hold.

Supplementary information: Supplementary material referenced in the text is available at http://linus.nci.nih.gov/brb/TechReport.htm
MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks
Authors: Masseroli Marco , Stella Andrea , Meani Natalia , Alcalay Myriam , Pinciroli Francesco
Published: July 2004

Motivation: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank.

Results: We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms.

Availability: MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/
A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome
Authors: Accardo M. C. , Giordano E. , Riccardo S. , Digilio F. A. , Iazzetti G. , Calogero R. A. , Furia M.
Published: July 2004

Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome.

Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules.

Availability: Additional information is available at http://www.bioinformatica.unito.it/bioinformatics/snoRNAs
SARGE: a tool for creation of putative genetic networks
Authors: Shaw O. J. , Harwood C. , Steggles L. J. , Wipat A.
Published: July 2004

Summary: SARGE is a tool for creating, visualizing and manipulating a putative genetic network from time series microarray data. The tool assigns potential edges through time-lagged correlation, incorporates a clustering mechanism, an interactive visual graph representation and employs simulated annealing for network optimization.

Availability: The application is available as a .jar file from http://www.bioinformatics.cs.ncl.ac.uk/sarge/index.html
DAGchainer: a tool for mining segmental genome duplications and synteny
Authors: Haas Brian J. , Delcher Arthur L. , Wortman Jennifer R. , Salzberg Steven L.
Published: July 2004

Summary: Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG). These chains of collinear gene pairs can represent segmentally duplicated regions and genes within a single genome or syntenic regions between related genomes. Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer.
CSB.DB: a comprehensive systems-biology database
Authors: Steinhauser Dirk , Usadel Björn , Luedemann Alexander , Thimm Oliver , Kopka Joachim
Published: July 2004

Summary: The open access comprehensive systems-biology database (CSB.DB) presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life's complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The central part of CSB.DB, which we describe in this applications note, is a set of co-response databases that currently focus on the three key model organisms, Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels, CSB.DB allows to infer hypotheses on the functional interaction of genes. These hypotheses are novel and not accessible through analysis of sequence homology. The database enables the search for pairs of genes and larger units of genes, which are under common transcriptional control. In addition, statistical tools are offered to the user, which allow validation and comparison of those co-responses that were discovered by gene queries performed on the currently available set of pre-selectable datasets.

Availability: All co-response databases can be accessed through the CSB.DB Web server (http://csbdb.mpimp-golm.mpg.de/).
Defining chronic conditions for primary care with ICPC-2
Authors: O'Halloran Julie , Miller Graeme C , Britt Helena
Published: July 2004

Background. With the increasing prevalence of chronic conditions, there is need for a standardized definition of chronicity for use in research, to evaluate the population prevalence and general practice management of chronic conditions.

Objectives. Our aims were to determine the characteristics required to define chronicity, apply them to a primary care classification and provide a defined codeset of chronic conditions.

Methods. A literature review evaluated characteristics used to define chronic conditions. The final set of characteristics was applied to the International Classification of Primary Care-Version 2 (ICPC-2) through more specific terms available in ICPC-2 PLUS, an extended terminology classified to ICPC-2. A set of ICPC-2 rubrics was delineated as representing chronic conditions.

Results. Factors found to be relevant to a definition of chronic conditions for research were: duration; prognosis; pattern; and sequelae. Within ICPC-2, 129 rubrics were described as ‘chronic’, and another 20 rubrics had elements of chronicity. Duration was the criterion most frequently satisfied (98.4% of chronic rubrics), while 88.2% of rubrics met at least three of the four criteria.

Conclusion. Monitoring the prevalence and management of chronic conditions is of increasing importance. This study provided evidence for multifaceted definitions of chronicity. While all characteristics examined could be used by those interested in chronicity, the list has been designed to identify chronic conditions managed in Australian general practice, and is therefore not a nomenclature of all chronic conditions. Subsequent analysis of chronic conditions using pre-existing data sets will provide a baseline measure of chronic condition prevalence and management in general practice.
Application of structural analysis to the mechanical behaviour of the cornea
Authors: Anderson Kevin , El-Sheikh Ahmed , Newson Timothy
Published: July 2004

Structural engineering analysis tools have been used to improve the understanding of the biomechanical behaviour of the cornea. The research is a multi-disciplinary collaboration between structural engineers, mathematical and numerical analysts, ophthalmologists and clinicians. Mathematical shell analysis and nonlinear finite-element modelling have been used in conjunction with laboratory experiments to study the behaviour of the cornea under different loading states and to provide improved predictions of the mechanical response to disease and injury. The initial study involved laboratory tests and mathematical back analysis to determine the corneal material properties and topography. These data were then used to facilitate the construction of accurate finite-element models that are able to reliably trace the performance of cornea upon exposure to disease, injury or elevated intra-ocular pressure. The models are being adapted to study the response to keratoconus (a disease causing loss of corneal tissue) and to tonometry procedures, which are used to measure the intra-ocular pressure. This paper introduces these efforts as examples of the application of structural engineering analysis tools and shows their potential in the field of corneal biomechanics.
The mechanism of biomineralization of bone-like apatite on synthetic hydroxyapatite: anin vitroassessment
Authors: Kim Hyun-Min , Himeno Teruyuki , Kawashita Masakazu , Kokubo Tadashi , Nakamura Takashi
Published: July 2004

The mechanism of biomineralization of bone-like apatite on synthetic hydroxyapatite (HA) has been investigatedin vitro, in which the HA surface was surveyed as a function of soaking time in simulated body fluid (SBF). In terms of surface structure by transmission electron microscopy with energy-dispersive X-ray spectrometry, the HA whose Ca/P atomic ratio was 1.67 revealed three different characteristic soaking periods in SBF, i.e. the first soaking period, in which the HA surface increased the Ca/P ratio up to 1.83 to form an amorphous phase of Ca-rich calcium phosphate; the second soaking period, in which the HA surface decreased the Ca/P ratio up to 1.47 to form an amorphous phase of Ca-poor calcium phosphate; and the third soaking period, in which the HA surface gradually increased the Ca/P ratio up to 1.65 to eventually produce the bone-like nano-cerystallites of apatite, which grew forming complex crystal assemblies with a further increase in immersion time. Analysis using electrophoresis spectroscopy indicated that, immediately after immersion in SBF, the HA revealed a highly negative surface potential, which increased to reach a maximum positive value in the first soaking period. The surface potential then decreased to again reach a negative value in the second soaking period and thereafter converge to a constant negative value in the third soaking period. This implies that the HA induces biomineralization of apatite by smartly varying its surface potential to trigger an electrostatic interaction, first with positive calcium ions and second with negative phosphate ions in the SBF.
Design of biomimetic fibrillar interfaces: 1. Making contact
Authors: Glassmaker N. J. , Jagota A. , Hui C.-Y. , Kim J.
Published: July 2004

This paper explores the contact behaviour of simple fibrillar interfaces designed to mimic natural contact surfaces in lizards and insects. A simple model of bending and buckling of fibrils shows that such a structure can enhance compliance considerably. Contact experiments on poly(dimethylsiloxane) (PDMS) fibrils confirm the model predictions. Although buckling increases compliance, it also reduces adhesion by breaking contact between fibril ends and the substrate. Also, while slender fibrils are preferred from the viewpoint of enhanced compliance, their lateral collapse under the action of surface forces limits the aspect ratio achievable. We have developed a quantitative model to understand this phenomenon, which is shown to be in good agreement with experiments.
Design of biomimetic fibrillar interfaces: 2. Mechanics of enhanced adhesion
Authors: Hui C.-Y. , Glassmaker N. J. , Tang T. , Jagota A.
Published: July 2004

This study addresses the strength and toughness of generic fibrillar structures. We show that the stress
σ
c
required to pull a fibril out of adhesive contact with a substrate has the form
σ
c
=
σ
0
Φ(
χ
). In this equation,
σ
0
is the interfacial strength, Φ(
χ
) is a dimensionless function satisfying 0=Φ(
χ
)=1 and
χ
is a dimensionless parameter that depends on the interfacial properties, as well as the fibril stiffness and radius. Pull-off is flaw sensitive for
χ
≫1, but is
flaw insensitive
for
χ
<1. The important parameter
χ
also controls the stability of a homogeneously deformed non-fibrillar (flat) interface. Using these results, we show that the work to fail a unit area of fibrillar surface can be much higher than the intrinsic work of adhesion for a flat interface of the same material. In addition, we show that cross-sectional fibril dimensions control the pull-off force, which increases with decreasing fibril radius. Finally, an increase in fibril length is shown to increase the work necessary to separate a fibrillar interface.

Besides our calculations involving a single fibril, we study the concept of equal load sharing (ELS) for a perfect interface containing many fibrils. We obtain the practical work of adhesion for an idealized fibrillated interface under equal load sharing. We then analyse the peeling of a fibrillar surface from a rigid substrate and establish a criterion for ELS.
The use of gas–phase substrates to study enzyme catalysis at low hydration
Authors: Dunn Rachel V. , Daniel Roy M.
Published: July 2004

Although there are varying estimates as to the degree of enzyme hydration required for activity, a threshold value of
ca
. 0.2 g of water per gram of protein has been widely accepted. The evidence upon which this is based is reviewed here. In particular, results from the use of gas–phase substrates are discussed. Results using solid–phase enzyme–substrate mixtures are not altogether in accord with those obtained using gas–phase substrates. The use of gaseous substrates and products provides an experimental system in which the hydration of the enzyme can be easily controlled, but which is not limited by diffusion.

All the results show that increasing hydration enhances activity. The results using gas–phase substrates do not support the existence of a critical hydration value below which enzymatic activity is absent, and suggest that enzyme activity is possible at much lower hydrations than previously thought; they do not support the notion that significant hydration of the surface polar groups is required for activity. However, the marked improvement of activity as hydration is increased suggests that water does play a role, perhaps in optimizing the structure or facilitating the flexibility required for maximal activity.
Structure and interactions in simple solutions
Authors: Bowron D. T.
Published: July 2004

Neutron scattering with hydrogen/deuterium isotopic substitution techniques has been used to investigate the full range of structural interactions in a dilute 0.02 mol fraction solution of tertiary butanol in water, both in the absence and in the presence of a small amount of sodium chloride. Emphasis is given to the detailed pictures of the intermolecular interactions that have been derived using the empirical potential structure refinement technique. Analysis has been performed to the level of the spatial density distribution functions that illustrate the orientational dependence of the intermolecular interactions between all combinations of molecular and ionic components. The results show the key structural motifs involved in the interactions between the various components in a complex aqueous system. They underline the structural versatility of the water molecule in accommodating a range of different kinds of interactions while retaining its characteristic first–neighbour interaction geometry. Within this framework, the results highlight the complex interplay between the polar, non–polar and charged molecular interactions that exist in the system.
Water–protein interactions from high–resolution protein crystallography
Authors: Nakasako Masayoshi
Published: July 2004

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein–water interface have been investigated by cryogenic X–ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen–bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three–dimensional chain connection of a hydrogen–bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico–chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.
Protein hydration dynamics in solution: a critical survey
Authors: Halle Bertil
Published: July 2004

The properties of water in biological systems have been studied for well over a century by a wide range of physical techniques, but progress has been slow and erratic. Protein hydration—the perturbation of water structure and dynamics by the protein surface—has been a particularly rich source of controversy and confusion. Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. Recent oxygen–17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. The high mobility of hydration water ensures that all thermally activated processes at the protein–water interface, such as binding, recognition and catalysis, can proceed at high rates. The MRD–derived picture of a highly mobile hydration layer is consistent with recent molecular dynamics simulations, but is incompatible with results deduced from intermolecular nuclear Overhauser effect spectroscopy, dielectric relaxation and fluorescence spectroscopy. It is also inconsistent with the common view of hydration effects on protein hydrodynamics. Here, we show how these discrepancies can be resolved.
Protein structure, stability and solubility in water and other solvents
Authors: Nick Pace C. , Treviño Saul , Prabhakaran Erode , Martin Scholtz J.
Published: July 2004

Proteins carry out the most difficult tasks in living cells. They do so by interacting specifically with other molecules. This requires that they fold to a unique, globular conformation that is only marginally more stable than the large ensemble of unfolded states. The folded state is stabilized mainly by the burial and tight packing of over 80% of the peptide groups and non–polar side chains. If life as we know it is to exist in a solvent other than water, the folded state must be stable and soluble in the new solvent. Our analysis suggests that proteins will be unstable in most polar solvents such as ethanol, extremely stable in non–polar solvents such as cyclohexane, and even more stable in a vacuum. Our solubility studies suggest that protein solubility will be markedly lower in polar solvents such as ethanol and that proteins will be essentially insoluble in non–polar solvents such as cyclohexane. For these and other reasons it seems unlikely that the life we know could exist in any solvent system other than water.
Life at low water activity
Authors: Grant W. D.
Published: July 2004

Two major types of environment provide habitats for the most xerophilic organisms known: foods preserved by some form of dehydration or enhanced sugar levels, and hypersaline sites where water availability is limited by a high concentration of salts (usually NaCl). These environments are essentially microbial habitats, with high–sugar foods being dominated by xerophilic (sometimes called osmophilic) filamentous fungi and yeasts, some of which are capable of growth at a water activity (
a
w
) of 0.61, the lowest
a
w
value for growth recorded to date. By contrast, high–salt environments are almost exclusively populated by prokaryotes, notably the haloarchaea, capable of growing in saturated NaCl (
a
w
0.75). Different strategies are employed for combating the osmotic stress imposed by high levels of solutes in the environment. Eukaryotes and most prokaryotes synthesize or accumulate organic so–called ‘compatible solutes’ (osmolytes) that have counterbalancing osmotic potential. A restricted range of bacteria and the haloarchaea counterbalance osmotic stress imposed by NaCl by accumulating equivalent amounts of KCl. Haloarchaea become entrapped and survive for long periods inside halite (NaCl) crystals. They are also found in ancient subterranean halite (NaCl) deposits, leading to speculation about survival over geological time periods.
The effect of water on protein dynamics
Authors: Zaccai G.
Published: July 2004

Neutron diffraction and spectroscopy were applied to describe the hydration and dynamics of a soluble protein and a natural membrane from extreme halophilic Archaea. The quantitative dependence of protein motions on water activity was clearly illustrated, and it was established that a minimum hydration shell is required for the systems to access their functional resilience, i.e. a dynamics state that allows biological activity.
Probing the role of water in protein conformation and function
Authors: Rand R. P.
Published: July 2004

Life began in a bath of water and has never escaped it. Cellular function has forced the evolution of many mechanisms ensuring that cellular water concentration has never changed significantly. To free oneself of any conceptual distinction among all small molecules, solutes and solvents, means that experiments to probe water's specific role in molecular function can be designed like any classical chemical reaction. Such an ‘osmotic stress’ strategy will be described in general and for an enzyme, hexokinase. Water behaves like a reactant that competes with glucose in binding to hexokinase, and modulates its conformational change and activity. This ‘osmotic stress’ strategy, now applied to many very different systems, shows that water plays a significant role, energetically, in most macromolecular reactions. It can be required to fill obligatory space, it dominates nearest non–specific interactions between large surfaces, it can be a reactant modulating conformational change; all this in addition to its more commonly perceived static role as an integral part of stereospecific intramolecular structure.
Introduction
Authors: Daniel Roy M. , Finney John L. , Stoneham Marshall
Published: July 2004

It is generally taken for granted that water is essential for life. Looking for water on Mars has been a preoccupation for decades, and there are an infinite number of meetings on the general topic of ‘water in biology’. Yet these rarely ask precisely
why
water is important. And if we cannot answer that question, then perhaps it might be replaced by some other medium in some other life form that can still metabolize and reproduce. In fact, there is recent evidence that the molecular–level requirements for water may have been overstated. Our Discussion Meeting aimed to take a constructively sceptical view, encouraging diversity of attitude by bringing together interested scientists from a range of disciplines.
Medium or message? A new look at standards, structures, and schemata for managing electronic resources
Authors: Farb Sharon E. , Riggio Angela
Published: July 2004

This article examines several library metadata standards, structures and schema relevant to the challenge of managing electronic resources. Among the standards, structures and schema to be discussed are MARC, METS, Dublin Core, EAD, XrML, and ODRL. The authors’ analysis reveals that there is currently no one standard, structure or schema that adequately addresses the complexity of e‐resource management. The article concludes with an outline and proposal for a new metadata schema designed to manage electronic resources.
Repurposing MARC metadata: using digital project experience to develop a metadata management design
Authors: Kurth Martin , Ruddy David , Rupp Nathan
Published: July 2004

Metadata and information technology staff in libraries that are building digital collections typically extract and manipulate MARC metadata sets to provide access to digital content via non‐MARC schemes. Metadata processing in these libraries involves defining the relationships between metadata schemes, moving metadata between schemes, and coordinating the intellectual activity and physical resources required to create and manipulate metadata. Actively managing the non‐MARC metadata resources used to build digital collections is something most of these libraries have only begun to do. This article proposes strategies for managing MARC metadata repurposing efforts as the first step in a coordinated approach to library metadata management. Guided by lessons learned from Cornell University library mapping and transformation activities, the authors apply the literature of data resource management to library metadata management and propose a model for managing MARC metadata repurposing processes through the implementation of a metadata management design.
PSU Gateway Library: electronic library in transition
Authors: Moyo Lesley M.
Published: July 2004

Developments in information technology have led to changes in the mode of delivery of library services, and in the perceptions of the role of librarians in the information‐seeking context. In particular, the proliferation of electronic resources has led to the emergence of new service paradigms and new roles for librarians. The Gateway Library at Penn State University (PSU) is an electronic library in transition, with new technology‐based services evolving to address the ever growing and changing needs of the academic community. It facilitates access to and navigation of electronic resources in an integrated technology environment.
The theory of planned behavior and Internet purchasing
Authors: George Joey F.
Published: July 2004

Several opinion polls have found that many consumers resist making purchases via the Internet because of their concerns about the privacy of the personal information they provide to Internet merchants. Using the theory of planned behavior as its basis, this study investigated the relationships among beliefs about Internet privacy and trustworthiness, along with beliefs about perceived behavioral control and the expectations of important others, and online purchasing behavior. Data were collected from 193 college students. Analysis of the data indicates that beliefs about trustworthiness positively affect attitudes toward buying online, which in turn positively affect purchasing behavior. Beliefs about self‐efficacy regarding purchasing positively affect perceived behavioral control, which in turn affects online purchasing behavior. In short, respondents who believed in the trustworthiness of the Internet and in their own abilities to buy online were more likely to make Internet purchases than were those without such beliefs.
Project‐based knowledge maps: combining project mining and XML‐enabled topic maps
Authors: Liu Duen‐Ren , Hsu Chouyin
Published: July 2004

Many enterprises implement various business projects on the Internet in the global knowledge economy. The task of managing distributed and heterogeneous project knowledge is very important in increasing the knowledge assets of enterprises. Accordingly, this work presents a project‐based knowledge map system to properly organize project knowledge into topic maps, from which users can obtain in‐depth concepts to facilitate further project development. A two‐phase data mining approach involving the ISO/ISEC 13250 topic maps and Extensible Markup Language (XML) is used to establish the proposed system, which can determine knowledge patterns from previous projects and transform these patterns into a navigable knowledge map. The map can help users to locate required information and also offers subject‐related information easily and rapidly over the Internet.