bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping the Dynamics of New Forms of Technological Governance in Agriculture: Methodological Considerations
Authors: Higgins Vaughan , Kitto Simon
Published: July 2004

This paper reflects on the conceptual issues involved in developing a methodology to study the role of computer-based technologies, and particularly farm planning and management software, in governing the practices of farmers. It represents the first stage of a larger project that explores how farm planning and management practices are governed through, and reconfigured by, such technology. In recent years, computer software has been encouraged by a range of government and nongovernment agencies and organisations as a useful technical means of supporting farm decisionmaking and improving farmers' managerial capacities, thereby improving their competitive position. The key question of this paper is how to conceptualise and study this link. Existing literature in the area tends to draw on either rationalist – technological determinist or social constructionist accounts which, we suggest, are limited in understanding such software as a type of governmental technology that has productive effects. We argue that a methodology drawing upon insights from governmentality and actor-network theory enables the role of software in programmes of agricultural governance to be more robustly explored as a sociotechnical process. Specifically, a ‘sociology of translation’ is outlined to demonstrate how computer software can be analysed as a material technology of government that constitutes and shapes the capacities of ‘users’ as calculable agents. In order to demonstrate how such a methodology might work in practice, we apply a translation methodology to decision-support software designed to improve the planning practices of dairy farmers in the State of Victoria, Australia.
What Makes a Good Sustainable Development Plan? An Analysis of Factors That Influence Principles of Sustainable Development
Authors: Conroy Maria Manta , Berke Philip R
Published: July 2004

A key question faced by practitioners trying to plan for sustainable development is: what can be done in planning practice to influence promotion of sustainable development? This research addresses that question by investigating three dimensions of the planning process (political support for the concept, participation, and resource commitment), the organization of local land-use plans, and state planning mandates to determine how they influence the support plan policies have for principles of sustainable development. We use plan content analysis as well as survey data for forty-two communities across the United States to analyze factors which influence such support. Our findings highlight that the presence of a state planning mandate, most applicable to US planning, as well as having a variety of groups participating in the planning process, are key factors that increase overall plan support for the sustainable development principles. Recommendations for planning practice are offered based on our findings.
Transfer of photosynthesis genes to and from
Prochlorococcus
viruses
Authors: Lindell Debbie , Sullivan Matthew B. , Johnson Zackary I. , Tolonen Andrew C. , Rohwer Forest , Chisholm Sallie W.
Published: July 2004

Comparative genomics gives us a new window into phage–host interactions and their evolutionary implications. Here we report the presence of genes central to oxygenic photosynthesis in the genomes of three phages from two viral families (
Myoviridae
and
Podoviridae
) that infect the marine cyanobacterium
Prochlorococcus
. The genes that encode the photosystem II core reaction center protein D1 (
psbA
), and a high-light-inducible protein (HLIP) (
hli
) are present in all three genomes. Both myoviruses contain additional
hli
gene types, and one of them encodes the second photosystem II core reaction center protein D2 (
psbD
), whereas the other encodes the photosynthetic electron transport proteins plastocyanin (
petE
) and ferredoxin (
petF
). These uninterrupted, full-length genes are conserved in their amino acid sequence, suggesting that they encode functional proteins that may help maintain photosynthetic activity during infection. Phylogenetic analyses show that phage D1, D2, and HLIP proteins cluster with those from
Prochlorococcus
, indicating that they are of cyanobacterial origin. Their distribution among several
Prochlorococcus
clades further suggests that the genes encoding these proteins were transferred from host to phage multiple times. Phage HLIPs cluster with multicopy types found exclusively in
Prochlorocococus
, suggesting that phage may be mediating the expansion of the
hli
gene family by transferring these genes back to their hosts after a period of evolution in the phage. These gene transfers are likely to play a role in the fitness landscape of hosts and phages in the surface oceans.
A point mutation in the regulatory light chain reduces the step size of skeletal muscle myosin
Authors: Sherwood Jennifer J. , Waller Guillermina S. , Warshaw David M. , Lowey Susan
Published: July 2004

Current evidence favors the theory that, when the globular motor domain of myosin attaches to actin, the light chain binding domain or “lever arm” rotates, and thereby generates movement of actin filaments. Myosin is uniquely designed for such a role in that a long α-helix (≈9 nm) extending from the C terminus of the catalytic core is stabilized by two calmodulin-like molecules, the regulatory light chain (RLC) and the essential light chain (ELC). Here, we introduce a single-point mutation into the skeletal myosin RLC, which results in a large (≈50%) reduction in actin filament velocity (
V
actin
) without any loss in actin-activated MgATPase activity. Single-molecule analysis of myosin by optical trapping showed a comparable 2-fold reduction in unitary displacement or step size (
d
), without a significant change in the duration of the strongly attached state (τ
on
) after the power stroke. Assuming that
V
actin
≈
d
/τ
on
, we can account for the change in velocity primarily by a change in the step size of the lever arm without incurring any change in the kinetic properties of the mutant myosin. These results suggest that a principal role for the many light chain isoforms in the myosin II class may be to modulate the flexural rigidity of the light chain binding domain to maximize tension development and movement during muscle contraction.
A large conformational change of the translocation ATPase SecA
Authors: Osborne Andrew R. , Clemons William M. , Rapoport Tom A.
Published: July 2004

The ATPase SecA mediates the posttranslational translocation of a wide range of polypeptide substrates through the SecY channel in the cytoplasmic membrane of bacteria. We have determined the crystal structure of a monomeric form of
Bacillus subtilis
SecA at a 2.2-Å resolution. A comparison with the previously determined structures of SecA reveals a nucleotide-independent, large conformational change that opens a deep groove similar to that in other proteins that interact with diverse polypeptides. We propose that the open form of SecA represents an activated state.
A force-dependent switch reverses type IV pilus retraction
Authors: Maier Berenike , Koomey Michael , Sheetz Michael P.
Published: July 2004

Type IV pilus dynamics is important for virulence, motility, and DNA transfer in a wide variety of prokaryotes. The type IV pilus system constitutes a very robust and powerful molecular machine that transports pilus polymers as well as DNA through the bacterial cell envelope. In
Neisseria gonorrhoeae
, pilus retraction is a highly irreversible process that depends on PilT, an AAA ATPase family member. However, when levels of PilT are reduced, the application of high external forces (
F
= 110 ± 10 pN) induces processive pilus elongation. At forces of >50 pN, single pili elongate at a rate of
v
= 350 ± 50 nm/s. For forces of <50 pN, elongation velocity depends strongly on force and relaxation causes immediate retraction. Both pilus retraction and force-induced elongation can be modeled by chemical kinetics with same step length for the rate-limiting translocation step. The model implies that a force-dependent molecular switch can induce pilus elongation by reversing the retraction mechanism.
Sampling design for an integrated socioeconomic and ecological survey by using satellite remote sensing and ordination
Authors: Binford Michael W. , Lee Tae Jeong , Townsend Robert M.
Published: July 2004

Environmental variability is an important risk factor in rural agricultural communities. Testing models requires empirical sampling that generates data that are representative in both economic and ecological domains. Detrended correspondence analysis of satellite remote sensing data were used to design an effective low-cost sampling protocol for a field study to create an integrated socioeconomic and ecological database when no prior information on ecology of the survey area existed. We stratified the sample for the selection of tambons from various preselected provinces in Thailand based on factor analysis of spectral land-cover classes derived from satellite data. We conducted the survey for the sampled villages in the chosen tambons. The resulting data capture interesting variations in soil productivity and in the timing of good and bad years, which a purely random sample would likely have missed. Thus, this database will allow tests of hypotheses concerning the effect of credit on productivity, the sharing of idiosyncratic risks, and the economic influence of environmental variability.
Innervation of ectopic endometrium in a rat model of endometriosis
Authors: Berkley Karen J. , Dmitrieva Natalia , Curtis Kathleen S. , Papka Raymond E.
Published: July 2004

Endometriosis (ENDO) is a disorder in which vascularized growths of endometrial tissue occur outside the uterus. Its symptoms include reduced fertility and severe pelvic pain. Mechanisms that maintain the ectopic growths and evoke symptoms are poorly understood. One factor not yet considered is that the ectopic growths develop their own innervation. Here, we tested the hypothesis that the growths develop both an autonomic and a sensory innervation. We used a rat model of surgically induced ENDO whose growths mimic those in women. Furthermore, similar to women with ENDO, such rats exhibit reduced fertility and increased pelvic nociception. The ENDO was induced by autotransplanting, on mesenteric cascade arteries, small pieces of uterus that formed vascularized cysts. The cysts and healthy uterus were harvested from proestrous rats and immunostained using the pan-neuronal marker PGP9.5 and specific markers for calcitonin gene-related peptide (CGRP) (sensory C and Aδ fibers), substance P (SP) (sensory C and Aδ fibers) and vesicular monoamine transporter (sympathetic fibers). Cysts (like the uterus) were robustly innervated, with many PGP9.5-stained neurites accompanying blood vessels and extending into nearby luminal epithelial layers. CGRP-, SP-, and vesicular monoamine transporter-immunostained neurites also were observed, with CGRP and SP neurites extending the furthest into the cyst lining. These results demonstrate that ectopic endometrial growths develop an autonomic and sensory innervation. This innervation could contribute not only to symptoms associated with ENDO but also to maintenance of the ectopic growths.
Facial appearance and impressions of ‘credibility’: The effects of facial babyishness and age on person perception
Authors: Masip Jaume , Garrido Eugenio , Herrero Carmen
Published: July 2004

The babyface overgeneralization effect is perceiving that people whose facial features resemble those of children have childlike traits, and treating them accordingly. This experiment sought to replicate the US findings with a South‐European sample, to examine the impact of facial maturity on impressions of truthfulness, and to examine the influence of age on person perception. Three‐hundred and twenty‐four Spanish undergraduates were shown a photograph and had to rate it on a series of behavioural‐tendency and trait scales measuring honesty, truthfulness, strength, dominance, intelligence, naivety, and warmth. The photographs were babyfaced, intermediate, and mature faced computer‐manipulated versions of three pictures of the same individual at three different ages. Results indicate that the experimental manipulations significantly affected most of the dependent variables. Babyfaced individuals were perceived as the most truthful, and children as the most deceitful. However, when the deceit concerned a sexual abuse allegation, children were rated as the least deceitful. These results support the existence of (a) the babyface overgeneralization effect, (b) the stereotype that children are unreliable witnesses, and (c) the belief that children never lie about sexual abuse offenses. They also suggest that facial babyishness and age may be static perceived deception cues that may account for the demeanour bias found in nonverbal research on the detection of deceit.
DarkSUSY: computing supersymmetric dark matter properties numerically
Authors: P Gondolo  , J Edsjö  , P Ullio  , L Bergström  , M Schelke  , E A Baltz
Published: July 2004

The question of the nature of the dark matter in the Universe remains one of the most outstanding unsolved problems in basic science. One of the best motivated particle physics candidates is the lightest supersymmetric particle, assumed to be the lightest neutralino—a linear combination of the supersymmetric partners of the photon, theZboson and neutral scalar Higgs particles. Here we describe DarkSUSY, a publicly available advanced numerical package for neutralino dark matter calculations. In DarkSUSY one can compute the neutralino density in the Universe today using precision methods which include resonances, pair production thresholds and coannihilations. Masses and mixings of supersymmetric particles can be computed within DarkSUSY or with the help of external programs such as FeynHiggs, ISASUGRA and SUSPECT. Accelerator bounds can be checked to identify viable dark matter candidates. DarkSUSY also computes a large variety of astrophysical signals from neutralino dark matter, such as direct detection in low-background counting experiments and indirect detection through antiprotons, antideuterons, gamma-rays and positrons from the galactic halo or high-energy neutrinos from the centre of the Earth or of the Sun. Here we describe the physics behind the package. A detailed manual will be provided with the computer package.
Cross-talk of Integrin α3β1 and Tissue Factor in Cell Migration
Authors: Dorfleutner Andrea , Hintermann Edith , Tarui Takehiko , Takada Yoshikazu , Ruf Wolfram
Published: July 2004

In cancer and angiogenesis, coagulation-independent roles of tissue factor (TF) in cell migration are incompletely understood. Immobilized anti-TF extracellular domain antibodies induce cell spreading, but this phenomenon is epitope specific and is not induced by anti-TF 5G9. Spreading on anti-TF is β1 integrin–dependent, indicating functional interactions of the TF extracellular domain 5G9 epitope (a presumed integrin-binding site) and integrins. Recombinant TF extracellular domain supports adhesion of cells expressing αvβ3 or certain β1 integrin heterodimers (α3β1, α4β1, α5β1, α6β1, α9β1) and adhesion is blocked by specific anti-integrin antibodies or mutations in the integrin ligand-binding site. Although several studies have linked TF to cell migration, we here demonstrate that TF specifically regulates α3β1-dependent migration on laminin 5. Expression of TF suppresses α3β1-dependent migration, but only when the TF cytoplasmic domain is not phosphorylated. Suppression of migration can be reversed by 5G9, presumably by disrupting integrin interaction, or by the protease ligand VIIa, known to induce PAR-2–dependent phosphorylation of TF. In both cases, release of α3β1 inhibition is prevented by mutation of critical phosphorylation sites in the TF cytoplasmic domain. Thus, TF influences integrin-mediated migration through cooperative intra- and extracellular interactions and phosphorylation regulates TF's function in cell motility.
Importance of Mitochondrial Dynamics During Meiosis and Sporulation
Authors: Gorsich Steven W. , Shaw Janet M.
Published: July 2004

Opposing fission and fusion events maintain the yeast mitochondrial network. Six proteins regulate these membrane dynamics during mitotic growth—Dnm1p, Mdv1p, and Fis1p mediate fission; Fzo1p, Mgm1p, and Ugo1p mediate fusion. Previous studies established that mitochondria fragment and rejoin at distinct stages during meiosis and sporulation, suggesting that mitochondrial fission and fusion are required during this process. Here we report that strains defective for mitochondrial fission alone, or both fission and fusion, complete meiosis and sporulation. However, visualization of mitochondria in sporulating cultures reveals morphological defects associated with the loss of fusion and/or fission proteins. Specifically, mitochondria collapse to one side of the cell and fail to fragment during presporulation. In addition, mitochondria are not inherited equally by newly formed spores, and mitochondrial DNA nucleoid segregation defects give rise to spores lacking nucleoids. This nucleoid inheritance defect is correlated with an increase in petite spore colonies. Unexpectedly, mitochondria fragment in mature tetrads lacking fission proteins. The latter finding suggests either that novel fission machinery operates during sporulation or that mechanical forces generate the mitochondrial fragments observed in mature spores. These results provide evidence of fitness defects caused by fission mutations and reveal new phenotypes associated with fission and fusion mutations.
Enhanced Membrane Fusion in Sterol-enriched Vacuoles Bypasses the Vrp1p Requirement
Authors: Tedrick Kelly , Trischuk Tim , Lehner Richard , Eitzen Gary
Published: July 2004

Organization of lipids into membrane microdomains is a vital mechanism of protein processing. Here we show that overexpression of ERG6, a gene involved in ergosterol synthesis, elevates sterol levels 1.5-fold on the vacuole membrane and enhances their homotypic fusion. The mechanism of sterol-enhanced fusion is not via more efficient sorting, but instead promotes increased kinetics of fusion subreactions. We initially isolated ERG6 as a suppressor of a vrp1Δ growth defect selective for vacuole function. VRP1 encodes verprolin, an actin-binding protein that colocalizes to vacuoles. The vrp1Δ mutant has fragmented vacuoles in vivo and isolated vacuoles do not fuse in vitro, indicative of a Vrp1p requirement for membrane fusion. ERG6 overexpression rescues vrp1Δ vacuole fusion in a cytosol-dependent manner. Cytosol prepared from the vrp1Δ strain remains active; therefore, cytosol is not resupplying Vrp1p. Las17p (Vrp1p functional partner) antibodies, which inhibit wild-type vacuole fusion, do not inhibit the fusion of vacuoles from the vrp1Δ-ERG6 overexpression strain. Vacuole-associated actin turnover is decreased in the vrp1Δ strain, but recovered by ERG6 overexpression linking sterol enrichment to actin remodeling. Therefore, the Vrp1p/Las17p requirement for membrane fusion is bypassed by increased sterols, which promotes actin remodeling as part the membrane fusion mechanism.
Autocrine Extracellular Signal-regulated Kinase (ERK) Activation in Normal Human Keratinocytes: Metalloproteinase-mediated Release of Amphiregulin Triggers Signaling from ErbB1 to ERK
Authors: Kansra Sanjay , Stoll Stefan W. , Johnson Jessica L. , Elder James T.
Published: July 2004

ErbB signaling through extracellular signal-regulated kinase (ERK) has been implicated in regulating the expression of ErbB ligands in hyperproliferative skin disorders and wound healing. Here, we characterize the process of autocrine ERK activation in cultured normal human keratinocytes (NHKs) subjected to growth factor (GF) deprivation. Basal ERK phosphorylation was lower after 48 h than after 24 h of GF deprivation, and lowest at 30–60 min after an additional medium change. ERK phosphorylation was markedly increased by low concentrations of epidermal growth factor (EGF) (0.2–1 ng/ml) that provoked only a limited increase in ErbB1 tyrosine phosphorylation and internalization. Basal ErbB tyrosine phosphorylation and ERK phosphorylation were inhibited by two different ErbB receptor tyrosine kinase inhibitors, by the ErbB1-specific neutralizing monoclonal antibody 225 IgG, by two different metalloproteinase inhibitors, and by neutralizing antibodies against amphiregulin (AR). In contrast, these responses were unaffected by neutralizing antibodies against other ErbB1 ligands or the ErbB2 inhibitors geldanamycin and AG825. The time course of autocrine ERK phosphorylation correlated with the appearance of soluble AR, and two different metalloproteinase inhibitors blocked AR release. These results define an amphiregulin- and ErbB1-dependent mechanism by which autocrine ERK activation is maintained in NHKs, even when ErbB1 autophosphorylation and internalization are limited.
The ArfGAP Glo3 Is Required for the Generation of COPI Vesicles
Authors: Lewis Stephen M. , Poon Pak Phi , Singer Richard A. , Johnston Gerald C. , Spang Anne
Published: July 2004

The small GTPase Arf and coatomer (COPI) are required for the generation of retrograde transport vesicles. Arf activity is regulated by guanine exchange factors (ArfGEF) and GTPase-activating proteins (ArfGAPs). The ArfGAPs Gcs1 and Glo3 provide essential overlapping function for retrograde vesicular transport from the Golgi to the endoplasmic reticulum. We have identified Glo3 as a component of COPI vesicles. Furthermore, we find that a mutant version of the Glo3 protein exerts a negative effect on retrograde transport, even in the presence of the ArfGAP Gcs1. Finally, we present evidence supporting a role for ArfGAP protein in the generation of COPI retrograde transport vesicles.
Interactive gene-order comparison for multiple small genomes
Authors: Kaluszka Aaron , Gibas Cynthia
Published: July 2004

Summary: The Genome Organization Analysis Tool (GOAT) is a program that performs comparative sequence analysis on ordered gene lists from annotated genomes, provides visual and tabular output, and provides means of accessing and analyzing related gene sequence data, for the purpose of comparing genome organization at the gene-order level. GOAT can be used to compare any two or more genomes or chromosomes on demand, or configured to provide access to precomputed comparisons of a specific group of genome sequences.

Availability: Demonstration web server and software download, subject to the Virginia Tech Noncommercial License are available at http://gaia.biotech.vt.edu/goat/

Supplementary information: Updates, installation and configuration information are available at http://gaia.biotech.vt.edu/goat
Preferred in vivo ubiquitination sites
Authors: Catic André , Collins Cal , Church George M. , Ploegh Hidde L.
Published: July 2004

Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their substrate and which lysines are targeted for ubiquitin conjugation is largely an enigma. The object of this study is to identify preferred ubiquitination sites. Genetic approaches to study this question have proven difficult, because of the redundancy of ligases and the lack of strictly required motifs. However, a better understanding of acceptor site selection could help to predict ubiquitination sites and clarify yet unsolved structure–function relationships of the transfer reaction.

Results: In an effort to define preferences for ubiquitination, we systematically analyzed structure and sequence of 135 known ubiquitination sites in 95 proteins in Saccharomyces cerevisiae. The results show clear structural preferences for ubiquitin ligation to target proteins, and compartment-specific amino acid patterns in close proximity to the modified side chain.

Supplementary information:  http://www.people.fas.harvard.edu/~catic
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences
Authors: Bilgen Mehmet , Karaca Mehmet , Onus A. Naci , Ince Ayşe Gül
Published: July 2004

Motivation: One of the most interesting features of genomes (both coding and non-coding regions) is the presence of relatively short tandemly repeated DNA sequences known as tandem repeats (TRs). We developed a new PC-based stand-alone software analysis program, combining sequence motif searches with keywords such as organs, tissues, cell lines or development stages for finding exact, inexact and compound, TRs. Tandem Repeats Analyzer 1.5 (TRA) has several advanced repeat search parameters/options over other repeat finder programs as it does not only accept GenBank, FASTA and expressed sequence tag (EST) sequence files but also does analysis of multifiles with multisequences. Advanced user-defined parameters/options let the researchers use different motif lengths search criteria for varying motif lengths simultaneously. The outputs show statistical results to be evaluated by the user. The discovery of TRs in ESTs could be useful for both gene mapping and association studies and discovering TRs located in coding regions of important genes that are expressed under various conditions of environment, stress, organ, tissue and development stage.

Results: In this paper, we demonstrated applications of TRA using 175 899 ESTs sequences for three Arabidopsis spp. downloaded from GenBank. The EST-SSRs/ESTs ratios were found 43.1%, 15.3% and 2.34% in A.lyrata, A.thaliana and A.halleri, respectively. Analysis revealed that organs, tissues and development stages possessed different amounts of repeats and repeat compositions. This indicated that the distribution of TRs among the tissues or organs may not be random differing from the untranscribed repeats found in genomes.

Availability: The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA
An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites
Authors: Selivanov Vitaly A. , Puigjaner Joaquim , Sillero Antonio , Centelles Josep J. , Ramos-Montoya Antonio , Lee Paul W.-N. , Cascante Marta
Published: July 2004

Motivation: Analysis of the conversion of 13C glucose within the metabolic network allows the evaluation of the biochemical fluxes in interconnecting metabolic pathways. Such analyses require solving hundreds of equations with respect to individual isotopomer concentrations, and this assumes applying special software even for constructing the equations. The algorithm, proposed by others could be improved.

Method: A C-code linked to the program written in Mathematica (Wolfram Research Inc.), constructs and solves differential equations for all isotopomer concentrations, using the general enzyme characteristics (Km, equilibrium constant, etc.). This code uses innovative algorithm of determination for the isotopomers–products, thus essentially decreasing the computation time. Feasible metabolic fluxes are provided by the parameters of enzyme kinetics found from the data fitting.

Results: The software effectively evaluates metabolic fluxes based on the measured isotopomer distribution, as was illustrated by the analysis of glycolysis and pentose phosphate cycle. The mechanism of transketolase and transaldolase catalysis was shown to induce a specific kind of isotopomer re-distribution, which, despite the significance of its effect, usually is not taken into account.

Availability: The software could be freely downloaded from the site: http://bq.ub.es/bioqint/label_distribution/
GenePicker: replicate analysis of Affymetrix gene expression microarrays
Authors: Finocchiaro Giacomo , Parise Paola , Minardi Simone P. , Alcalay Myriam , Müller Heiko
Published: July 2004

Summary: GenePicker allows efficient analysis of Affymetrix gene expression data performed in replicate, through definition of analysis schemes, data normalization, t-test/ANOVA, Change-Fold Change-analysis and yields lists of differentially expressed genes with high confidence. Comparison of noise and signal analysis schemes allows determining a signal-to-noise ratio in a given experiment. Change Call, Fold Change and Signal mean ratios are used in the analysis. While each parameter alone yields gene lists that contain up to 30% false positives, the combination of these parameters nearly eliminates the false positives as verified by northern blotting, quantitative PCR in numerous independent experiments as well as by the analysis of spike-in data.

Availability:  http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html

Supplementary information:  http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html
Gene selection using a two-level hierarchical Bayesian model
Authors: Bae Kyounghwa , Mallick Bani K.
Published: July 2004

Summary: The fundamental problem of gene selection via cDNA data is to identify which genes are differentially expressed across different kinds of tissue samples (e.g. normal and cancer). cDNA data contain large number of variables (genes) and usually the sample size is relatively small so the selection process can be unstable. Therefore, models which incorporate sparsity in terms of variables (genes) are desirable for this kind of problem. This paper proposes a two-level hierarchical Bayesian model for variable selection which assumes a prior that favors sparseness. We adopt a Markov chain Monte Carlo (MCMC) based computation technique to simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer.

Supplementary information:  http://stat.tamu.edu/people/faculty/bmallick.html
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
Authors: Gisel Andreas , Panetta Maria , Grillo Giorgio , Licciulli Vito Flavio , Liuni Sabino , Saccone Cecilia , Pesole Graziano
Published: July 2004

Summary: DNAfan (DNA Feature ANalyzer) is a tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets. Fragments are defined by annotated gene feature keys and co- or non-occurring patterns within the feature or close to it. A gene feature parser and a pattern-based filter tool localizes and extracts the specific subset of sequences. The selected sequence data can subsequently be retrieved for analyses or further processed with DNAfan to find the occurrence of specific patterns or structural motifs. DNAfan is a powerful tool for pattern analysis. Its filter features restricts the pattern search to a well-defined set of sequences, allowing drastic reduction in false positive hits.

Availability:  http://bighost.ba.itb.cnr.it:8080/Framework
Water–DNA interactions as studied by X–ray and neutron fibre diffraction
Authors: Fuller Watson , Forsyth Trevor , Mahendrasingam Arumugam
Published: July 2004

X–ray fibre–diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration–driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real–time X–ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre–diffraction studies of DNA is complemented by information from X–ray single–crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.
Autophosphorylation of the 16 kDa and 70 kDa antigens (Hsp 16·3 and Hsp 70) of Mycobacterium tuberculosis
Authors: Preneta Rachel , Papavinasasundaram K. G. , Cozzone Alain J. , Duclos Bertrand
Published: July 2004

Several antigens ofMycobacterium tuberculosis, identified by monoclonal antibodies, have been previously cloned and are being exploited in the development of improved vaccines and diagnostic reagents. In this study, the molecular characteristics of two of these antigens, the immunodominant proteins Hsp 16·3 and Hsp 70, were analysed in further detail by assessing their capacity to undergo protein phosphorylation, a chemical modification frequently used by organisms to adjust to environmental variations. Hsp 16·3 was overproduced in anEscherichia coliexpression system and purified to homogeneity. Upon incubation in the presence of radioactive ATP, it was shown to possess autophosphorylation activity. Two-dimensional analysis of its phosphoamino acid content revealed that it was modified exclusively at serine residues. In addition, cross-linking experiments demonstrated that it could tightly bind to ATP. Purified Hsp 70 was also shown to autophosphorylate but phosphorylation occurred exclusively at threonine residues. This reaction was found to be strongly stimulated by calcium ions. These data indicate that both structural and functional similarities exist between Hsp 16·3 (Acr) andα-crystallin, a eukaryotic protein which plays an important role in maintaining the transparency of the vertebrate eye, and that the functional properties of Hsp 70 fromM. tuberculosisare similar to those of other bacterial members of the Hsp 70 family, particularly theE. colihomologue DnaK.
Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate
Authors: Kapatral Vinayak , Campbell John W. , Minnich Scott A. , Thomson Nicholas R. , Matsumura Philip , Prüß Birgit M.
Published: July 2004

This paper focuses on global gene regulation by FlhD/FlhC in enteric bacteria. Even though Yersinia enterocolitica FlhD/FlhC can complement an Escherichia coli
flhDC mutant for motility, it is not known if the Y. enterocolitica FlhD/FlhC complex has an effect on metabolism similar to E. coli. To study metabolic gene regulation, a partial Yersinia enterocolitica 8081c microarray was constructed and the expression patterns of wild-type cells were compared to an flhDC mutant strain at 25 and 37 °C. The overlap between the E. coli and Y. enterocolitica FlhD/FlhC regulated genes was 25 %. Genes that were regulated at least fivefold by FlhD/FlhC in Y. enterocolitica are genes encoding urocanate hydratase (hutU), imidazolone propionase (hutI), carbamoylphosphate synthetase (carAB) and aspartate carbamoyltransferase (pyrBI). These enzymes are part of a pathway that is involved in the degradation of l-histidine to l-glutamate and eventually leads into purine/pyrimidine biosynthesis via carbamoylphosphate and carbamoylaspartate. A number of other genes were regulated at a lower rate. In two additional experiments, the expression of wild-type cells grown at 4 or 25 °C was compared to the same strain grown at 37 °C. The expression of the flagella master operon flhD was not affected by temperature, whereas the flagella-specific sigma factor fliA was highly expressed at 25 °C and reduced at 4 and 37 °C. Several other flagella genes, all of which are under the control of FliA, exhibited a similar temperature profile. These data are consistent with the hypothesis that temperature regulation of flagella genes might be mediated by the flagella-specific sigma factor FliA and not the flagella master regulator FlhD/FlhC.
Genetic analysis of Treponema denticola ATCC 35405 biofilm formation
Authors: Vesey Peter M. , Kuramitsu Howard K.
Published: July 2004

Treponema denticola is a major aetiological organism implicated in periodontal disease. The interaction of T. denticola with other oral bacteria, in particular Porphyromonas gingivalis, in biofilm formation is thought to be an important step in the onset of periodontal disease. The interaction between T. denticola and P. gingivalis has been examined using a panel of T. denticola mutants and their effects on mixed biofilm formation tested in a static biofilm model. T. denticola ATCC 35405 did not form detectable biofilms on various inert surfaces. However, the spirochaete was demonstrated to form a biofilm with preattached P. gingivalis 381. T. denticola cfpA, which lacks the cytoplasmic filament, was unable to produce a mixed biofilm with P. gingivalis. A T. denticola flgE mutant which lacks the flagella hook protein and is therefore non-motile displayed a reduced, but readily detectable, ability to form a mixed biofilm as did the T. denticola mutant which does not possess the major outer sheath protein (Msp). The T. denticola lrrA mutant was only moderately defective in forming mixed biofilms with P. gingivalis. However, the T. denticola methyl-accepting chemotaxis protein (DmcA) did not appear to play a major role in mixed biofilm formation. In contrast, T. denticola lacking the PrtP protein for prolyl-phenylalanine-specific protease, showed an increased ability to form mixed biofilms and a prolonged viability in the biofilm.
The nitrogen-fixing gene (nifH) of Rhodopseudomonas palustris: a case of lateral gene transfer?
Authors: Cantera Jose Jason L. , Kawasaki Hiroko , Seki Tatsuji
Published: July 2004

Nitrogen fixation is catalysed by some photosynthetic bacteria. This paper presents a phylogenetic comparison of a nitrogen fixation gene (nifH) with the aim of elucidating the processes underlying the evolutionary history of Rhodopseudomonas palustris. In the NifH phylogeny, strains of Rps. palustris were placed in close association with Rhodobacter spp. and other phototrophic purple non-sulfur bacteria belonging to the α-Proteobacteria, separated from its close relatives Bradyrhizobium japonicum and the phototrophic rhizobia (Bradyrhizobium spp. IRBG 2, IRBG 228, IRBG 230 and BTAi 1) as deduced from the 16S rRNA phylogeny. The close association of the strains of Rps. palustris with those of Rhodobacter and Rhodovulum, as well as Rhodospirillum rubrum, was supported by the mol% G+C of their nifH gene and by the signature sequences found in the sequence alignment. In contrast, comparison of a number of informational and operational genes common to Rps. palustris CGA009, B. japonicum USDA 110 and Rhodobacter sphaeroides 2.4.1 suggested that the genome of Rps. palustris is more related to that of B. japonicum than to the Rba. sphaeroides genome. These results strongly suggest that the nifH of Rps. palustris is highly related to those of the phototrophic purple non-sulfur bacteria included in this study, and might have come from an ancestral gene common to these phototrophic species through lateral gene transfer. Although this finding complicates the use of nifH to infer the phylogenetic relationships among the phototrophic bacteria in molecular diversity studies, it establishes a framework to resolve the origins and diversification of nitrogen fixation among the phototrophic bacteria in the α-Proteobacteria.
Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin
Authors: Yarzábal Andrés , Appia-Ayme Corinne , Ratouchniak Jeanine , Bonnefoy Violaine
Published: July 2004

The regulation of the expression of the rus operon, proposed to encode an electron transfer chain from the outer to the inner membrane in the obligate acidophilic chemolithoautroph Acidithiobacillus ferrooxidans, has been studied at the RNA and protein levels. As observed by Northern hybridization, real-time PCR and reverse transcription analyses, this operon was more highly expressed in ferrous iron- than in sulfur-grown cells. Furthermore, it was shown by immunodetection that components of this respiratory chain are synthesized in ferrous iron- rather than in sulfur-growth conditions. Nonetheless, weak transcription and translation products of the rus operon were detected in sulfur-grown cells at the early exponential phase. The results strongly support the notion that rus-operon expression is induced by ferrous iron, in agreement with the involvement of the rus-operon-encoded products in the oxidation of ferrous iron, and that ferrous iron is used in preference to sulfur.
The complex structure of polyhydroxybutyrate (PHB) granules: four orthologous and paralogous phasins occur in Ralstonia eutropha
Authors: Pötter Markus , Müller Helena , Reinecke Frank , Wieczorek Roman , Fricke Florian , Bowien Botho , Friedrich Bärbel , Steinbüchel Alexander
Published: July 2004

Analysis of the genome sequence of the polyhydroxyalkanoate- (PHA) accumulating bacteriumRalstonia eutrophastrain H16 revealed three homologues (PhaP2, PhaP3 and PhaP4) of the phasin protein PhaP1. PhaP1 is known to constitute the major component of the layer at the surface of poly(3-hydroxybutyrate), poly(3HB), granules. PhaP2, PhaP3 and PhaP4 exhibited 42, 49 and 45 % identity or 61, 62 and 63 % similarity to PhaP1, respectively. The calculated molecular masses of PhaP1, PhaP2, PhaP3 and PhaP4 were 20·0, 20·2, 19·6 and 20·2 kDa, respectively. RT-PCR analysis showed thatphaP2,phaP3andphaP4were transcribed under conditions permissive for accumulation of poly(3HB). 2D PAGE of the poly(3HB) granule proteome and analysis of the detected proteins by MALDI-TOF clearly demonstrated that PhaP1, PhaP3 and PhaP4 are bound to the poly(3HB) granules in the cells. PhaP3 was expressed at a significantly higher level in PhaP1-negative mutants. Occurrence of an unknown protein with an N-terminal amino-acid sequence identical to that of PhaP2 in crude cellular extracts ofR. eutrophahad previously been shown by others. Although PhaP2 could not be localizedin vivoon poly(3HB) granules,in vitroexperiments clearly demonstrated binding of PhaP2 to these granules. Further analysis of complete or partial genomes of other poly(3HB)-accumulating bacteria revealed the existence of multiple phasin homologues inRalstonia solanacearum,Burkholderia fungorumandAzotobacter vinelandii. These new and unexpected findings should affect our current models of PHA-granule structure and may also have a considerable impact on the establishment of heterologous production systems for PHAs.
Ffz1, a new transporter specific for fructose from Zygosaccharomyces bailii
Authors: Pina Carlos , Gonçalves Paula , Prista Catarina , Loureiro-Dias Maria C.
Published: July 2004

The basis of fructophily in the yeastZygosaccharomyces bailiihas been shown to reside in the performance of transport systems for hexoses. In this study, a gene encoding a fructose-specific transporter was characterized. The strategy involved the functional complementation of aSaccharomyces cerevisiaestrain that does not take up hexoses (hxt-nullstrain). This strain was transformed with a genomic library ofZ. bailii. One transformant capable of growing on fructose, but not on glucose, was obtained. This transformant did not transportd-[14C]glucose, and the kinetic parameters ford-[14C]fructose wereVmax=3·3 mmol h−1 g−1andKm=80·4 mM. As in the original strain ofZ. bailii, fructose uptake was not inhibited by the presence of other hexoses or uranyl. The plasmid responsible for the observed phenotype was found to carry an ORF encoding a 616 amino acid protein with the characteristics of a membrane transporter, which was designatedFFZ1(fructose facilitatorZygosaccharomyces). The impairment in function observed in anS. cerevisiaetransformant expressing a truncated Ffz1 protein lacking 67 amino acids at the C-terminus suggests an important role for this terminal part in the proper structure of the transporter.
Fungal cell wall chitinases and glucanases
Authors: Adams David J.
Published: July 2004

The fungal cell wall is a complex structure composed of chitin, glucans and other polymers, and there is evidence of extensive cross-linking between these components. The wall structure is highly dynamic, changing constantly during cell division, growth and morphogenesis. Hydrolytic enzymes, closely associated with the cell wall, have been implicated in the maintenance of wall plasticity and may have roles during branching and cross-linking of polymers. Most fungal cell wall hydrolases identified to date have chitinase or glucanase activity and this short article reviews the apparent functions of these enzymes in unicellular and filamentous fungi, and the mechanisms that regulate enzyme activity in yeasts.
The SPI2-encoded SseA chaperone has discrete domains required for SseB stabilization and export, and binds within the C-terminus of SseB and SseD
Authors: Zurawski Daniel V. , Stein Murry A.
Published: July 2004

SseA, a keySalmonellavirulence determinant, is a small, basic pI protein encoded within theSalmonellapathogenicity island 2 and serves as a type III secretion system chaperone for SseB and SseD. Both SseA partners are subunits of the surface-localized translocon module that delivers effectors into the host cell; SseB is predicted to compose the translocon sheath and SseD is a putative translocon pore subunit. In this study, SseA molecular interactions with its partners were characterized further. Yeast two-hybrid screens indicate that SseA binding requires a C-terminal domain within both partners. An additional central domain within SseD was found to influence binding. The SseA-binding region within SseB was found to encompass a predicted amphipathic helix of a type participating in coiled-coil interactions that are implicated in the assembly of translocon sheaths. Deletions that impinge upon this putative coiled-coiled domain prevent SseA binding, suggesting that SseA occupies a portion of the coiled-coil. SseA occupancy of this motif is envisioned to be sufficient to prevent premature SseB self-association inside bacteria. Domain mapping on the chaperone was also performed. A deletion of the SseA N-terminus, or site-directed mutations within this region, allowed stabilization of SseB, but its export was disrupted. Therefore, the N-terminus of SseA provides a function that is essential for SseB export, but dispensable for partner binding and stabilization.
Functional analysis of the ALD gene family of Saccharomyces cerevisiae during anaerobic growth on glucose: the NADP+-dependent Ald6p and Ald5p isoforms play a major role in acetate formation
Authors: Saint-Prix Florence , Bönquist Linda , Dequin Sylvie
Published: July 2004

InSaccharomyces cerevisiae, acetate is formed by acetaldehyde dehydrogenase (ACDH), a key enzyme of the pyruvate dehydrogenase (PDH) bypass, which fulfils the essential task of generating acetyl-CoA in the cytosol. The role of the five members of the ACDH family (ALDgenes) was investigated during anaerobic growth on glucose. Single and multiplealdΔ mutants were generated in the wine-yeast-derived V5 and laboratory CEN.PK strains and analysed under standard (YPD 5 % glucose) and wine (MS 20 % glucose) fermentation conditions. The deletion ofALD6andALD5decreased acetate formation in both strains, demonstrating for the first time that the mitochondrial Ald5p isoform is involved in the biosynthesis of acetate during anaerobic growth on glucose. Acetate production of theald4Δ mutant was slightly decreased in the CEN.PK strain during growth on YPD only. In contrast, the deletion ofALD2orALD3had no effect on acetate production. The absence of Ald6p was compensated by the mitochondrial isoforms and this involves the transcriptional activation ofALD4. Consistent with this, growth retardation was observed inald6Δald4Δ, and this effect was amplified by the additional deletion ofALD5. AaldΔ null mutant, devoid of ACDH activity, was viable and produced similar levels of acetate to theald6Δald4Δald5Δ strain, excluding a role of Ald2p and Ald3p. Thus, acetate is mainly produced by the cytosolic PDH bypass via Ald6p and by a mitochondrial route involving Ald5p. An unknown alternative pathway can compensate for the loss of Ald6p, Ald4p and Ald5p.