bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of histidine kinases that act as sensors in the perception of salt stress in
Synechocystis
sp. PCC 6803
Authors: Marin Kay , Suzuki Iwane , Yamaguchi Katsushi , Ribbeck Kathrin , Yamamoto Hiroshi , Kanesaki Yu , Hagemann Martin , Murata Norio
Published: July 2003

In plants and microorganisms, salt stress regulates the expression of large
numbers of genes. However, the machinery that senses salt stress remains to be
characterized. In this study we identified sensory histidine kinases that are
involved in the perception of salt stress in the cyanobacterium
Synechocystis
sp. strain PCC 6803. A library of strains with
mutations in all 43 histidine kinases was screened by DNA microarray analysis
of genomewide gene expression under salt stress. The results suggested that
four histidine kinases, namely, Hik16, Hik33, Hik34, and Hik41, perceived and
transduced salt signals. However, Hik33, Hik34, and Hik16 acting with Hik41
regulated the expression of different sets of genes. These histidine kinases
regulated the expression of ≈20% of the salt-inducible genes, whereas the
induction of the remaining salt-inducible genes was unaffected by mutations in
any of the histidine kinases, suggesting that additional sensory mechanisms
might operate in the perception of salt stress. We also used DNA microarrays
to investigate the effect of various salts on gene expression. Our results
indicate that Hik33 responds to sodium salts and not to KCl, whereas the
Hik16/Hik41 system responds only to NaCl.
Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy
Authors: Yersin A. , Hirling H. , Steiner P. , Magnin S. , Regazzi R. , Hüni B. , Huguenot P. , De Los Rios P. , Dietler G. , Catsicas S. , Kasas S.
Published: July 2003

Measuring the biophysical properties of macromolecular complexes at work is a major challenge of modern biology. The protein complex composed of vesicle-associated membrane protein 2, synaptosomal-associated protein of 25 kDa, and syntaxin 1 [solubleN-ethyl-maleimide-sensitive factor attachment protein receptor (SNARE) complex] is essential for docking and fusion of neurotransmitter-filled synaptic vesicles with the presynaptic membrane. To better understand the fusion mechanisms, we reconstituted the synaptic SNARE complex in the imaging chamber of an atomic force microscope and measured the interaction forces between its components. Each protein was tested against the two others, taken either individually or as binary complexes. This approach allowed us to determine specific interaction forces and dissociation kinetics of the SNAREs and led us to propose a sequence of interactions. A theoretical model based on our measurements suggests that a minimum of four complexes is probably necessary for fusion to occur. We also showed that the regulatory protein neuronal Sec1 injected into the atomic force microscope chamber prevented the complex formation. Finally, we measured the effect of tetanus toxin protease on the SNARE complex and its activity by on-line registration during tetanus toxin injection. These experiments provide a basis for the functional study of protein microdomains and also suggest opportunities for sensitive screening of drugs that can modulate protein–protein interactions.
Chimeric recombinases with designed DNA sequence recognition
Authors: Akopian Aram , He Jiuya , Boocock Martin R. , Stark W. Marshall
Published: July 2003

Site-specific recombination typically occurs only between DNA sequences
that have co-evolved with a natural recombinase enzyme to optimize sequence
recognition, catalytic efficiency, and regulation. Here, we show that the
sequence recognition and the catalysis functions of a recombinase can be
specified by unrelated protein domains. We describe chimeric recombinases with
a catalytic domain from an activated multiple mutant of the bacterial enzyme
Tn
3
resolvase, fused to a DNA recognition domain from the mouse
transcription factor Zif268. These proteins catalyze efficient recombination
specifically at synthetic target sites recognized by two Zif268 domains. Our
results demonstrate the functional autonomy of the resolvase catalytic domain
and open the way to creating “custom-built” recombinases that act
at chosen natural target sequences.
Cognitive processes underlying human mate choice: The relationship between self-perception and mate preference in Western society
Authors: Buston Peter M. , Emlen Stephen T.
Published: July 2003

This study tested two hypotheses concerning the cognitive processes underlying human mate choice in Western society: (i) mate preference is conditional in that the selectivity of individuals' mate preference is based on their perception of themselves as long-term partners, and (ii) the decision rule governing such conditional mate preference is based on translating perception of oneself on a given attribute into a comparable selectivity of preference for the same attribute in a mate. Both hypotheses were supported. A two-part questionnaire was completed by 978 heterosexual residents of Ithaca, New York, aged 18–24; they first rated the importance they placed on 10 attributes in a long-term partner and then rated their perception of themselves on those same attributes. Both women and men who rated themselves highly were significantly more selective in their mate preference. When the 10 attributes were grouped into four evolutionarily relevant categories (indicative of wealth and status, family commitment, physical appearance, and sexual fidelity), the greatest amount of variation in the selectivity of mate preference in each category was explained by self-perception in the same category of attributes. We conclude that, in Western society, humans use neither an “opposites-attract” nor a “reproductive-potentials-attract” decision rule in their choice of long-term partners but rather a “likes-attract” rule based on a preference for partners who are similar to themselves across a number of characteristics.
Inhibition of apoptosis in normal and transformed intestinal epithelial cells by cAMP through induction of inhibitor of apoptosis protein (IAP)-2
Authors: Nishihara Hiroshi , Kizaka-Kondoh Shinae , Insel Paul A. , Eckmann Lars
Published: July 2003

Cyclooxygenase (COX)-2, a rate-limiting enzyme of prostaglandin (PG) production, is overexpressed in colorectal adenomas and adenocarcinomas, and its inhibition by nonsteroidal antiinflammatory drugs protects against colorectal cancer. Mechanisms of cancer promotion by COX-2 are not fully understood, but signaling through prostaglandin (PG)E2receptors is a contributing factor. The major PGE2receptors on epithelial cells, EP2and EP4, increase cAMP production, which promotes growth and inhibits apoptosis in some cell types. Here, we show that cAMP agonists, including PGE2, cholera toxin, and a membrane-permeant cAMP analog, protect normal and transformed intestinal epithelial cells from apoptosis induced by diverse stimuli. This protection is associated with cAMP-mediated, rapid induction of cellular inhibitor of apoptosis protein (c-IAP)-2 and delayed induction of LIVIN, but not of six other members of the IAP family. Concurrently and characteristic of IAP functions, the activity, but not generation, of the cleaved form of the central executioner caspase 3 is inhibited. Induction of c-IAP2 expression by cAMP agonists is accompanied by phosphorylation of cAMP response element binding protein and cAMP response element-dependent activation of transcriptional reporters. Furthermore, inhibition of COX-2 in cells overexpressing the enzyme decreases c-IAP2 expression and promotes apoptosis, both of which are reversible by PGE2addition, suggesting that COX-2-promoted antiapoptosis is mediated by release of PGE2and subsequent cAMP-dependent c-IAP2 induction. These results help to explain the cancer chemoprotective effects of nonsteroidal antiinflammatory drugs by defining a mechanism through which cAMP signaling can promote the development of colorectal and possibly other epithelial cancers by means of disruption of normal apoptotic processes.
Angiopoietin-2 induces human glioma invasion through the activation of matrix metalloprotease-2
Authors: Hu Bo , Guo Ping , Fang Quan , Tao Huo-Quan , Wang Degui , Nagane Motoo , Su Huang Hui-Jein , Gunji Yuji , Nishikawa Ryo , Alitalo Kari , Cavenee Webster K. , Cheng Shi-Yuan
Published: July 2003

A hallmark of highly malignant human gliomas is their infiltration of the
brain. We analyzed a large number of primary human glioma biopsies and found
high levels of expression of an angiogenic regulator, angiopoietin-2 (Ang2),
in the invasive areas, but not in the central regions, of those tumors. In the
invasive regions where Ang2 was overexpressed, increased levels of matrix
metalloprotease-2 (MMP-2) were also apparent. Consonant with these features,
intracranial xenografts of glioma cells engineered to express Ang2 were highly
invasive into adjacent brain parenchyma compared with isogenic control tumors.
In regions of the Ang2-expressing tumors that were actively invading the
brain, high levels of expression of MMP-2 and increased angiogenesis were also
evident. A link between these two features was apparent, because stable
expression of Ang2 by U87MG cells or treatment of several glioma cell lines
with recombinant Ang2
in vitro
caused activation of MMP-2 and
acquisition of increased invasiveness. Conversely, MMP inhibitors suppressed
Ang2-stimulated activation of MMP-2 and Ang2-induced cell invasion. These
results suggest that Ang2 plays a critical role in inducing tumor cell
infiltration, and that this invasive phenotype is caused by activation of
MMP-2.
Bacteria–host communication: The language of hormones
Authors: Sperandio Vanessa , Torres Alfredo G. , Jarvis Bruce , Nataro James P. , Kaper James B.
Published: July 2003

The interbacterial communication system known as quorum sensing (QS)
utilizes hormone-like compounds referred to as autoinducers to regulate
bacterial gene expression. Enterohemorrhagic
Escherichia coli
(EHEC)
serotype O157:H7 is the agent responsible for outbreaks of bloody diarrhea in
several countries. We previously proposed that EHEC uses a QS regulatory
system to “sense” that it is within the intestine and activate
genes essential for intestinal colonization. The QS system used by EHEC is the
LuxS/autoinducer 2 (AI-2) system extensively involved in interspecies
communication. The autoinducer AI-2 is a furanosyl borate diester whose
synthesis depends on the enzyme LuxS. Here we show that an EHEC
luxS
mutant, unable to produce the bacterial autoinducer, still responds to a
eukaryotic cell signal to activate expression of its virulence genes. We have
identified this signal as the hormone epinephrine and show that β- and
α-adrenergic antagonists can block the bacterial response to this
hormone. Furthermore, using purified and
in vitro
synthesized AI-2 we
showed that AI-2 is not the autoinducer involved in the bacterial signaling.
EHEC produces another, previously undescribed autoinducer (AI-3) whose
synthesis depends on the presence of LuxS. These results imply a potential
cross-communication between the
luxS
/AI-3 bacterial QS system and the
epinephrine host signaling system. Given that eukaryotic cell-to-cell
signaling typically occurs through hormones, and that bacterial cell-to-cell
signaling occurs through QS, we speculate that QS might be a
“language” by which bacteria and host cells communicate.
Socioeconomics drive urban plant diversity
Authors: Hope Diane , Gries Corinna , Zhu Weixing , Fagan William F. , Redman Charles L. , Grimm Nancy B. , Nelson Amy L. , Martin Chris , Kinzig Ann
Published: July 2003

Spatial variation in plant diversity has been attributed to heterogeneity
in resource availability for many ecosystems. However, urbanization has
resulted in entire landscapes that are now occupied by plant communities
wholly created by humans, in which diversity may reflect social, economic, and
cultural influences in addition to those recognized by traditional ecological
theory. Here we use data from a probability-based survey to explore the
variation in plant diversity across a large metropolitan area using spatial
statistical analyses that incorporate biotic, abiotic, and human variables.
Our prediction for the city was that land use, along with distance from urban
center, would replace the dominantly geomorphic controls on spatial variation
in plant diversity in the surrounding undeveloped Sonoran desert. However, in
addition to elevation and current and former land use, family income and
housing age best explained the observed variation in plant diversity across
the city. We conclude that a functional relationship, which we term the
“luxury effect,” may link human resource abundance (wealth) and
plant diversity in urban ecosystems. This connection may be influenced by
education, institutional control, and culture, and merits further study.
The ErbB2/ErbB3 heterodimer functions as an oncogenic unit: ErbB2 requires ErbB3 to drive breast tumor cell proliferation
Authors: Holbro Thomas , Beerli Roger R. , Maurer Francisca , Koziczak Magdalena , Barbas Carlos F. , Hynes Nancy E.
Published: July 2003

ErbB2 is a receptor tyrosine kinase whose activity in normal cells depends
on dimerization with another ligand-binding ErbB receptor. In contrast,
amplification of
c-erbB2
in tumors results in dramatic overexpression
and constitutive activation of the receptor. Breast cancer cells
overexpressing ErbB2 depend on its activity for proliferation, because
treatment of these cells with ErbB2-specific antagonistic antibodies or kinase
inhibitors blocks tumor cells in the G
1
phase of the cell cycle.
Intriguingly, loss of ErbB2 signaling is accompanied by a decrease in the
phosphotyrosine content of ErbB3. On the basis of these results, it has been
proposed that ErbB3 might be a partner for ErbB2 in promoting cellular
transformation. To test this hypothesis and directly examine the role of the
“kinase dead” ErbB3, we specifically ablated its expression with a
designer transcription factor (E3). By infection of ErbB2-overexpressing
breast cancer cells with a retrovirus expressing E3, we show that ErbB3 is an
essential partner in the transformation process. Loss of functional ErbB2 or
ErbB3 has similar effects on cell proliferation and cell cycle regulators.
Furthermore, expression of constitutively active protein kinase B rescues the
proliferative block induced as a consequence of loss of ErbB2 or ErbB3
signaling. These results demonstrate that ErbB2 overexpression and activity
alone are insufficient to promote breast tumor cell division. Furthermore, we
identify ErbB3's role, which is to couple active ErbB2 to the
phosphatidylinositol 3-kinase/protein kinase B pathway. Thus, the ErbB2/ErbB3
dimer functions as an oncogenic unit to drive breast tumor cell
proliferation.
Vacuole membrane fusion
Authors: Bayer Martin J. , Reese Christoph , Bühler Susanne , Peters Christopher , Mayer Andreas
Published: July 2003

Pore models of membrane fusion postulate that cylinders of integral membrane proteins can initiate a fusion pore after conformational rearrangement of pore subunits. In the fusion of yeast vacuoles, V-ATPase V0 sectors, which contain a central cylinder of membrane integral proteolipid subunits, associate to form a transcomplex that might resemble an intermediate postulated in some pore models. We tested the role of V0 sectors in vacuole fusion. V0 functions in fusion and proton translocation could be experimentally separated via the differential effects of mutations and inhibitory antibodies. Inactivation of the V0 subunit Vph1p blocked fusion in the terminal reaction stage that is independent of a proton gradient. Δvph1 mutants were capable of docking and trans-SNARE pairing and of subsequent release of lumenal Ca2+, but they did not fuse. The Ca2+-releasing channel appears to be tightly coupled to V0 because inactivation of Vph1p by antibodies blocked Ca2+ release. Vph1 deletion on only one fusion partner sufficed to severely reduce fusion activity. The functional requirement for Vph1p correlates to V0 transcomplex formation in that both occur after docking and Ca2+ release. These observations establish V0 as a crucial factor in vacuole fusion acting downstream of trans-SNARE pairing.
PAK1 phosphorylation of MEK1 regulates fibronectin-stimulated MAPK activation
Authors: Slack-Davis Jill K. , Eblen Scott T. , Zecevic Maja , Boerner Scott A. , Tarcsafalvi Adel , Diaz H. Bruce , Marshall Mark S. , Weber Michael J. , Parsons J. Thomas , Catling Andrew D.
Published: July 2003

Activation of the Ras–MAPK signal transduction pathway is necessary for biological responses both to growth factors and ECM. Here, we provide evidence that phosphorylation of S298 of MAPK kinase 1 (MEK1) by p21-activated kinase (PAK) is a site of convergence for integrin and growth factor signaling. We find that adhesion to fibronectin induces PAK1-dependent phosphorylation of MEK1 on S298 and that this phosphorylation is necessary for efficient activation of MEK1 and subsequent MAPK activation. The rapid and efficient activation of MEK and phosphorylation on S298 induced by cell adhesion to fibronectin is influenced by FAK and Src signaling and is paralleled by localization of phospho-S298 MEK1 and phospho-MAPK staining in peripheral membrane–proximal adhesion structures. We propose that FAK/Src-dependent, PAK1-mediated phosphorylation of MEK1 on S298 is central to the organization and localization of active Raf–MEK1–MAPK signaling complexes, and that formation of such complexes contributes to the adhesion dependence of growth factor signaling to MAPK.
A novel role for dp115 in the organization of tER sites in Drosophila
Authors: Kondylis Vangelis , Rabouille Catherine
Published: July 2003

Here, we describe that depletion of the Drosophila homologue of p115 (dp115) by RNA interference in Drosophila S2 cells led to important morphological changes in the Golgi stack morphology and the transitional ER (tER) organization. Using conventional and immunoelectron microscopy and confocal immunofluorescence microscopy, we show that Golgi stacks were converted into clusters of vesicles and tubules, and that the tERs (marked by Sec23p) lost their focused organization and were now dispersed throughout the cytoplasm. However, we found that this morphologically altered exocytic pathway was nevertheless largely competent in anterograde protein transport using two different assays. The effects were specific for dp115. Depletion of the Drosophila homologues of GM130 and syntaxin 5 (dSed5p) did not lead to an effect on the tER organization, though the Golgi stacks were greatly vesiculated in the cells depleted of dSed5p. Taken together, these studies suggest that dp115 could be implicated in the architecture of both the Golgi stacks and the tER sites.
Regulation of phospholipase D1 subcellular cycling through coordination of multiple membrane association motifs
Authors: Du Guangwei , Altshuller Yelena M. , Vitale Nicolas , Huang Ping , Chasserot-Golaz Sylvette , Morris Andrew J. , Bader Marie-France , Frohman Michael A.
Published: July 2003

The signaling enzyme phospholipase D1 (PLD1) facilitates membrane vesicle trafficking. Here, we explore how PLD1 subcellular localization is regulated via Phox homology (PX) and pleckstrin homology (PH) domains and a PI4,5P2-binding site critical for its activation. PLD1 localized to perinuclear endosomes and Golgi in COS-7 cells, but on cellular stimulation, translocated to the plasma membrane in an activity-facilitated manner and then returned to the endosomes. The PI4,5P2-interacting site sufficed to mediate outward translocation and association with the plasma membrane. However, in the absence of PX and PH domains, PLD1 was unable to return efficiently to the endosomes. The PX and PH domains appear to facilitate internalization at different steps. The PH domain drives PLD1 entry into lipid rafts, which we show to be a step critical for internalization. In contrast, the PX domain appears to mediate binding to PI5P, a lipid newly recognized to accumulate in endocytosing vesicles. Finally, we show that the PH domain–dependent translocation step, but not the PX domain, is required for PLD1 to function in regulated exocytosis in PC12 cells. We propose that PLD1 localization and function involves regulated and continual cycling through a succession of subcellular sites, mediated by successive combinations of membrane association interactions.
New normalization methods for cDNA microarray data
Authors: Wilson D.L. , Buckley M.J. , Helliwell C.A. , Wilson I.W.
Published: July 2003

Motivation: The focus of this paper is on two new normalization methods for cDNA microarrays. After the image analysis has been performed on a microarray and before differentially expressed genes can be detected, some form of normalization must be applied to the microarrays. Normalization removes biases towards one or other of the fluorescent dyes used to label each mRNA sample allowing for proper evaluation of differential gene expression.

Results: The two normalization methods that we present here build on previously described non-linear normalization techniques. We extend these techniques by firstly introducing a normalization method that deals with smooth spatial trends in intensity across microarrays, an important issue that must be dealt with. Secondly we deal with normalization of a new type of cDNA microarray experiment that is coming into prevalence, the small scale specialty or ‘boutique’ array, where large proportions of the genes on the microarrays are expected to be highly differentially expressed.

Availability: The normalization methods described in this paper are available via http://www.pi.csiro.au/gena/ in a software suite called tRMA: tools for R Microarray Analysis upon request of the authors. Images and data used in this paper are also available via the same link.

Contact: dwilson@gmp.usyd.edu.au

* To whom correspondence should be addressed.
Increased coverage obtained by combination of methods for
protein sequence database searching
Authors: Webber Caleb , Barton Geoffrey J.
Published: July 2003

Motivation: Sequence alignment methods that compare two sequences (pairwise methods) are important tools for the detection of biological sequence relationships. In genome annotation, multiple methods are often run and agreement between methods taken as confirmation. In this paper, we assess the advantages of combining search methods by comparing seven pairwise alignment methods, including three local dynamic programming algorithms (PRSS, SSEARCH and SCANPS), two global dynamic programming algorithms (GSRCH and AMPS) and two heuristic approximations (BLAST and FASTA), individually and by pairwise intersection and union of their result lists at equal p-value cut-offs.

Results: When applied singly, the dynamic programming methods SCANPS and SSEARCH gave significantly better coverage (p=0.01) compared to AMPS, GSRCH, PRSS, BLAST and FASTA.

Results ranked by BLAST p-values gave significantly better coverage compared to ranking by BLAST e-values.

Of 56 combinations of eight methods considered, 19 gave significant increases in coverage at low error compared to the parent methods at an equal p-value cutoff.

The union of results by BLAST (p-value) and FASTA at an equal p-value cutoff gave significantly better coverage than either method individually.

The best overall performance was obtained from the intersection of the results from SSEARCH and the GSRCH62 global alignment method. At an error level of five false positives, this combination found 444 true positives, a significant 12.4% increase over SSEARCH applied alone.

Contact: geoff@compbio.dundee.ac.uk

* To whom correspondence should be addressed.
MeKE: discovering the functions of gene products
from biomedical literature via sentence alignment
Authors: Chiang Jung-Hsien , Yu Hsu-Chun
Published: July 2003

Motivation: Research on roles of gene products in cells is accumulating and changing rapidly, but most of the results are still reported in text form and are not directly accessible by computers. To expedite the progress of functional bioinformatics, it is, therefore, important to efficiently process large amounts of biomedical literature and transform the knowledge extracted into a structured format usable by biologists and medical researchers. Our aim was to develop an intelligent text-mining system that will extract from biomedical documents knowledge about the functions of gene products and thus facilitate computing with function.

Results: We have developed an ontology-based text-mining system to efficiently extract from biomedical literature knowledge about the functions of gene products. We also propose methods of sentence alignment and sentence classification to discover the functions of gene products discussed in digital texts.

Availability: http://ismp.csie.ncku.edu.tw/~yuhc/meke/

Contact: jchiang@mail.ncku.edu.tw

* To whom correspondence should be addressed.
The binding interface
database (BID): a compilation
of amino acid hot spots in protein interfaces
Authors: Fischer T. B. , Arunachalam K. V. , Bailey D. , Mangual V. , Bakhru S. , Russo R. , Huang D. , Paczkowski M. , Lalchandani V. , Ramachandra C. , Ellison B. , Galer S. , Shapley J. , Fuentes E. , Tsai J.
Published: July 2003

Summary: To make information about protein interactive function easily accessible, we are mining the primary scientific literature for detailed data about protein interfaces. The Binding Interface Database (BID) organizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles. Currently data on 170 interacting protein pairs are available with over 1300 mutations described.

Availability: The BID database is freely available at http://tsailab.org/BID/ To have your protein of interest entered, contact Tiffany Fischer (tiffbrink@neo.tamu.edu) or Jerry Tsai at the email below

Contact: JerryTsai@TAMU.edu

* To whom correspondence should be addressed.
Alignment of BLAST high-scoring segment pairs
based on the longest increasing subsequence algorithm
Authors: Zhang Hongyu
Published: July 2003

Motivation:The popular BLAST algorithm is based on a local similarity search strategy, so its high-scoring segment pairs (HSPs) do not have global alignment information. When scientists use BLAST to search for a target protein or DNA sequence in a huge database like the human genome map, the existence of repeated fragments, homologues or pseudogenes in the genome often makes the BLAST result filled with redundant HSPs. Therefore, we need a computational strategy to alleviate this problem.

Results: In the gene discovery group of Celera Genomics, I developed a two-step method, i.e. a BLAST step plus an LIS step, to align thousands of cDNA and protein sequences into the human genome map. The LIS step is based on a mature computational algorithm, Longest Increasing Subsequence (LIS) algorithm. The idea is to use the LIS algorithm to find the longest series of consecutive HSPs in the BLAST output. Such a BLAST+LIS strategy can be used as an independent alignment tool or as a complementary tool for other alignment programs like Sim4 and GenWise. It can also work as a general purpose BLAST result processor in all sorts of BLAST searches. Two examples from Celera were shown in this paper.

Contact: me@hongyu.org

* Present address: Ceres Inc., 3007 Malibu Canyon Road, Malibu, CA 90265, USA.
GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the
identification of T-DNA insertion mutants in Arabidopsis
thaliana
Authors: Li Yong , Rosso Mario G. , Strizhov Nicolai , Viehoever Prisca , Weisshaar Bernd
Published: July 2003

Summary: GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project. Sequences flanking the T-DNA insertion sites were aligned to the A.thaliana genome sequence, annotated with information about the FST, the insertion site and the line from which the FST was derived. A web interface permits text-based as well as sequence-based searches for relevant insertions. GABI-Kat SimpleSearch aims to help biologists to quickly find T-DNA insertion mutants for their research.

Availability: http://www.mpiz-koeln.mpg.de/GABI-Kat/

Contact: weisshaa@mpiz-koeln.mpg.de

* To whom correspondence should be addressed.

† Present address: Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, D-22607 Hamburg, Germany.

‡ Present address: Bielefeld University, Faculty of Biology, PO Box, D-33501 Bielefeld, Germany.
The connectivity structure, giant strong component
and centrality of metabolic networks
Authors: Ma Hong-Wu , Zeng An-Ping
Published: July 2003

Motivation:Structural and functional analysis of genome-based large-scale metabolic networks is important for understanding the design principles and regulation of the metabolism at a system level. The metabolic network is conventionally considered to be highly integrated and very complex. A rational reduction of the metabolic network to its core structure and a deeper understanding of its functional modules are important.

Results: In this work, we show that the metabolites in a metabolic network are far from fully connected. A connectivity structure consisting of four major subsets of metabolites and reactions, i.e. a fully connected sub-network, a substrate subset, a product subset and an isolated subset is found to exist in metabolic networks of 65 fully sequenced organisms. The largest fully connected part of a metabolic network, called ‘the giant strong component (GSC)’, represents the most complicated part and the core of the network and has the feature of scale-free networks. The average path length of the whole network is primarily determined by that of the GSC. For most of the organisms, GSC normally contains less than one-third of the nodes of the network. This connectivity structure is very similar to the‘ bow-tie’ structure of World Wide Web. Our results indicate that the bow-tie structure may be common for large-scale directed networks. More importantly, the uncovered structure feature makes a structural and functional analysis of large-scale metabolic network more amenable. As shown in this work, comparing the closeness centrality of the nodes in the GSC can identify the most central metabolites of a metabolic network. To quantitatively characterize the overall connection structure of the GSC we introduced the term ‘overall closeness centralization index (OCCI)’. OCCI correlates well with the average path length of the GSC and is a useful parameter for a system-level comparison of metabolic networks of different organisms.

Contact: aze@gbf.de

Supplementary Information: http://genome.gbf.de/bioinformatics/

* To whom correspondence should be addressed.
Computational analysis of stop codon readthrough in D.melanogaster
Authors: Sato Misaki , Umeki Hitomi , Saito Rintaro , Kanai Akio , Tomita Masaru
Published: July 2003

Motivation: Readthrough is an unusual process in which a stop codon is misread or skipped. Recently it has been shown that some translation is regulated by the readthrough reactions although the complete mechanism is not clear. Therefore, the discovery of ‘readthrough genes’ is important for further investigation of their cellular roles, which may provide additional insights into the mechanism of translational regulation.

Results: We constructed a system that lists candidates of readthrough genes based on the existence of a ‘protein motif’ at the 3′ untranslated region (UTR). Using this system, we extracted 85 candidates from 4082 nucleic acid sequences of Drosophila melanogaster in GenBank database. The sequences of these candidates had a slightly more stable secondary structure and different base preferences compared to the non-candidates. As these features are known to have an effect on readthrough events, we would like to suggest that these candidates contain actual readthrough genes.

Availability: Source code of the system is available upon request.

Contact: rsaito@sfc.keio.ac.jp

* To whom correspondence should be addressed.
Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation
Authors: Ayyanathan Kasirajan , Lechner Mark S. , Bell Peter , Maul Gerd G. , Schultz David C. , Yamada Yoshihiko , Tanaka Kazuhiro , Torigoe Kiyoyuki , Rauscher Frank J.
Published: July 2003

Heterochromatin protein 1 (HP1) is a key component of constitutive heterochromatin inDrosophilaand is required for stable epigenetic gene silencing classically observed as position effect variegation. Less is known of the family of mammalian HP1 proteins, which may be euchromatic, targeted to expressed loci by repressor-corepressor complexes, and retained there by Lys 9-methylated histone H3 (H3-MeK9). To characterize the physical properties of euchromatic loci bound by HP1, we developed a strategy for regulated recruitment of HP1 to an expressed transgene in mammalian cells by using a synthetic, hormone-regulated KRAB repression domain. We show that its obligate corepressor, KAP1, can coordinate all the machinery required for stable gene silencing. In the presence of hormone, the transgene is rapidly silenced, spatially recruited to HP1-rich nuclear regions, assumes a compact chromatin structure, and is physically associated with KAP1, HP1, and the H3 Lys 9-specific methyltransferase, SETDB1, over a highly localized region centered around the promoter. Remarkably, silencing established by a short pulse of hormone is stably maintained for >50 population doublings in the absence of hormone in clonal-cell populations, and the silent transgenes in these clones show promoter hypermethylation. Thus, like variegation inDrosophila, recruitment of mammalian HP1 to a euchromatic promoter can establish a silenced state that is epigenetically heritable.
The serine/threonine kinase Pim-2 is a transcriptionally regulated apoptotic inhibitor
Authors: Fox Casey J. , Hammerman Peter S. , Cinalli Ryan M. , Master Stephen R. , Chodosh Lewis A. , Thompson Craig B.
Published: July 2003

Growth factor withdrawal results in the termination of factor-dependent transcription. One transcript that declines rapidly following growth factor deprivation of hematopoietic cells is the serine/threonine kinasepim-2. When constitutively expressed, Pim-2 conferred long-term resistance to a variety of apoptotic stimuli including growth factor withdrawal and endogenous levels of Pim-2 contributed to growth factor-mediated apoptotic resistance. Pim-2 expression maintained cell size and mitochondrial potential independently of the PI3K/Akt/TOR pathway. Pim-2-dependent maintenance of cell size and survival correlated with its ability to maintain rapamycin-resistant phosphorylation of the translational repressor 4E-BP1 and phosphorylation of the BH3 protein BAD. These results establish Pim-2 as a direct link between growth factor-induced transcription and a novel, kinase-dependent pathway that promotes cell-autonomous survival.
Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling
Authors: Inoki Ken , Li Yong , Xu Tian , Guan Kun-Liang
Published: July 2003

Tuberous sclerosis complex (TSC) is a genetic disease caused by mutation in eitherTSC1orTSC2. The TSC1 and TSC2 gene products form a functional complex and inhibit phosphorylation of S6K and 4EBP1. These functions of TSC1/TSC2 are likely mediated by mTOR. Here we report that TSC2 is a GTPase-activating protein (GAP) toward Rheb, a Ras family GTPase. Rheb stimulates phosphorylation of S6K and 4EBP1. This function of Rheb is blocked by rapamycin and dominant-negative mTOR. Rheb stimulates the phosphorylation of mTOR and plays an essential role in regulation of S6K and 4EBP1 in response to nutrients and cellular energy status. Our data demonstrate that Rheb acts downstream of TSC1/TSC2 and upstream of mTOR to regulate cell growth.
Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes
Authors: Nelander Sven , Mostad Petter , Lindahl Per
Published: July 2003

Genes that are expressed in the same subset of cells potentially constitute a module regulated by shared cis-regulatory elements and a distinct set of transcription factors. Identifying such units is an important entry point to the molecular study of cell differentiation. We developed a general method to classify cell type-specific genes from expressed sequence tag (EST) data, and we optimized it for identification of smooth muscle cell (SMC)-specific genes. Expression profiles were derived from the quantitative distribution of EST data in mouse, and genes were classified based on their profile similarity to known reference genes, in this case smooth muscle myosin heavy chain. A large majority (>90%) of known SMC-specific genes were identified, together with novel candidates. Extensive experimental validation confirmed SMC-specific expression of candidates, for example, lipoma preferred partner (LPP) and a novel SMC-specific putative monoamine oxidase, SMAO. Our method performed considerably better than other computational methods in an objective cross validation comparison. The total number of SMC-specific genes is estimated to be ∼50.
Integrated Mapping, Chromosomal Sequencing and Sequence Analysis ofCryptosporidium parvum
Authors: Bankier Alan T. , Spriggs Helen F. , Fartmann Berthold , Konfortov Bernard A. , Madera Martin , Vogel Christine , Teichmann Sarah A. , Ivens Al , Dear Paul H.
Published: July 2003

The apicomplexanCryptosporidium parvumis one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and ∼0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical map, we devised a novel and general strategy, enabling accurate placement of clones regardless of clone artefacts. Analysis reveals a compact genome, unusually rich in membrane proteins. As inPlasmodium falciparum, the mean size of the predicted proteins is larger than that in other sequenced eukaryotes. We find several predicted proteins of interest as potential therapeutic targets, including one exhibiting similarity to the chloroquine resistance protein ofPlasmodium. Coding sequence analysis argues against the conventional phylogenetic position ofCryptosporidiumand supports an earlier suggestion that this genus arose from an early branching within the Apicomplexa. In agreement with this, we find no significant synteny and surprisingly little protein similarity withPlasmodium. Finally, we find two unusual and abundant repeats throughout the genome. Among sequenced genomes, one motif is abundant only inC. parvum, whereas the other is shared with (but has previously gone unnoticed in) all known genomes of the Coccidia and Haemosporida. These motifs appear to be unique in their structure, distribution and sequences.
Small-angle neutron scattering and differential scanning calorimetry study of associative behaviour of branched poly(ethylene oxide)/poly(propylene oxide) copolymer in aqueous solution
Authors: Pleštil J. , Pospíšil H. , Sikora A. , Krakovský I. , Kuklin A. I.
Published: July 2003

Tetronic RED 9040, a reverse-type [poly(propylene oxide) as terminal blocks] octablock star copolymer with four poly(ethylene oxide)/poly(propylene oxide) arms attached to the ethylenediamine core was studied in D2O at concentrations between 1 and 60 g dL−1in the temperature range from 283 to 353 K. Depending on concentration and temperature, various structures (unimers, random network, micelles, micellar aggregates, micellar networks) were indicated by small-angle neutron scattering (SANS). Some structure characteristics of unimers, micelles and micellar networks have been determined by fitting model scattering functions to the SANS data. A competition between the increasing association number and dehydration of the micelles is suggested as a possible explanation of the observed non-monotonic temperature dependence of the structure parameters of concentrated systems. A partial phase diagram was suggested on the basis of SANS and differential scanning calorimetry (DSC) data and visual inspection of the solutions.
Time-resolved small-angle X-ray scattering and wide-angle X-ray diffraction studies on the nanostructure of melt-processable molecular composites
Authors: Janicki Jaroslaw
Published: July 2003

Novel melt-processable molecular composites were obtained from isotactic polypropylene (iPP) and liquid-crystalline oligoester (LCO). The nanostructure and thermal behaviour of molecular composites were examined by real-time synchrotron small-angle X-ray scattering and wide-angle X-ray diffraction methods, and differential scanning calorimetry. The synthesized oligoester, with low melting temperature (391 K), exhibits the ability to form a thermotropic mesophase. It was shown that strong rigid rod-like macromolecules of LCO are dispersed at the molecular scale in iPP matrix and act as reinforcing fibres.
Combined small- and wide-angle X-ray scattering study of early stages of polymer crystallization
Authors: Panine P. , Urban V. , Boesecke P. , Narayanan T.
Published: July 2003

The early stage of melt crystallization in low-density polyethylene was investigated by simultaneous time-resolved small-angle and wide-angle X-ray scattering (SAXS/WAXS) techniques. The high detectivity of the two-dimensional detectors together with the large photon flux of an undulator source permitted the collection of SAXS and WAXS patterns with nearly single-photon sensitivity and sub-second time resolution. As a result, the crystalline fraction well below 0.001 can be reliably detected and the apparent induction time is considerably reduced (<10 s). The time evolution of both the SAXS invariant and the degree of crystallinity follow the well established Avrami-type growth law. Despite the orders of magnitude improvement in sensitivity, the difference in the onset time of SAXS and WAXS signals is not significant. The behaviour of the SAXS data in the very early stages is not consistent with spinodal decomposition mechanism as described by the linearized Cahn–Hilliard theory.
HRTEM study of orthorhombic zirconia in MgO-PSZ
Authors: Liu Zongwen , Bando Yoshio , Drennan John , Spargo Alan E. C.
Published: July 2003

High-resolution transmission electron microscopy (HRTEM) was used to study the phase of orthorhombic ZrO2formed in magnesia partially stabilized zirconia (MgO-PSZ) during HRTEM specimen preparation. Based on the three reported crystal structures of orthorhombic ZrO2, with the space groupsPbcm,Pbc21andPbca, here it is shown that orthorhombic ZrO2formed in MgO-PSZ has thePbcmstructure.
Theoreticalversusexperimental geometries in S-bridged manganese carbonyl complexes
Authors: Van der Maelen Uría Juan F. , Ruiz Javier , García-Granda Santiago
Published: July 2003

The experimental geometry obtained from single-crystal X-ray diffraction for a number of binuclear S-bridged manganese complexes is compared with the results of theoretical calculations made at theab initiolevel by using Hartree–Fock and density functional theory methods with medium-size and large basis sets. The optimized geometries obtained were somewhat relaxed when compared with the experimental ones, with very similar bond and torsion angles but longer bond lengths. The mean square deviation for bond lengths (angles) was found to be between 0.046 Å (1.1°) and 0.004 Å (0.7°) depending on the theoretical model used.
Airport offices: facilitating nomadic workers
Authors: Breure Adrianne , van Meel Juriaan
Published: July 2003

With the globalisation of the economy, more people travel for business purposes, doing much of their work while on the move. Business travellers spend a lot of time at airports and are likely to want to use this time productively. Already, airports have transformed from people processors into places where you can shop, dine, drink and sleep, so why not work there? This article shows that business travellers spend a large part of their waiting time checking their e‐mail, making phone calls, reading reports and working on their laptop. The question is whether they need special facilities to perform these activities. Do business travellers need a dedicated workplace with facilities ranging from colour printers and Internet access, to showers and a good cappuccino? Or just a place to sit with a network connection? This article tries to answer this question by studying the activities and needs of business travellers during their stay at an airport. It is based on a survey and in‐depth interviews among Dutch business travellers.
The journey to work: a descriptive UK case study
Authors: McLennan Peter , Bennetts Martin
Published: July 2003

A descriptive survey of the journey to work is used to investigate the facilities manager’s scope for addressing the use of public transport as a workplace together with the health and well‐being implications of commuting. The results from a self‐administered descriptive survey of a random sample comprising 127 employees are the data used to explore these issues with a 83 per cent response rate (106/127). The results indicate that 87 per cent used an automobile to commute and 32 per cent reported the journey was stressful. This later finding is consistent with other commuting studies and suggests that facilities managers should consider more fully the impact that commuting has on employee health and well‐being.
Plans, commitments and practical norms of reason
Authors: Sharpe Keiran
Published: July 2003

This paper uses the “planning” or “narrative” approach to agency – which has recently been developed by philosophers Bratman, Gauthier, McClennen and Velleman – to do two things. First, the paper criticises the standard, decision‐theoretic view of “rational” agent action and, second, it sketches a positive model of agency in which agents employ (quasi‐)Kantian maxims to guide their conduct.
Sustainable human resource strategy
Authors: Mariappanadar Sugumar
Published: July 2003

Sustainable human resource (HR) strategies could help companies manage their human resources HRs to achieve “net optimality” of companies' objectives as well as a stable community. Using a theoretical model, an attempt is made to explain the “externality” of retrenchment and highlight the need for sustainable HR strategies to achieve the “unitary economics” of human life. Further, the sustainable benefit of HR conservation and HR recuperation in understanding the HR asset, and how this can be used in reducing the externality effect of retrenchment and downsizing strategies on the social and emotional web of the community is discussed.
Misplaced marketing: Mismanagement of misfocused trade association leaders
Authors: Rotfeld Herbert Jack
Published: July 2003

Focuses on the mismanagement by trade association leaders who focus on wrong areas. Suggests that they would do well to remember their experience as a member rather than as a leader in order for them to maintain their marketing perspective.
Services marketing: taking up the sustainable development challenge
Authors: van der Zwan Frank , Bhamra Tracy
Published: July 2003

There is a window of opportunity within the area of design for sustainability for services marketing academics and practitioners to offer their knowledge and experience to manufacturing companies and academics. Over the last decade there has been a growing interest in services within the field of sustainable development. Services are viewed as a dematerialized alternative to existing products, with reduced environmental impact (i.e. less material and less energy use to fulfil a certain need). The services considered by academics in the field of sustainable development are those related to products or those substituting products. These services are often called “eco‐efficient services”. Academics focusing on the development of eco‐efficient services can use elements of theory and experience available within the services marketing discipline. Services marketing academics and practitioners can help in developing blueprints and processes to facilitate manufacturing companies to shift towards a more service‐intensive way of doing business. This paper calls for cross‐disciplinary collaboration.