bluuebunny/crossref_metadata_2025 huggingface dataset:
HLA‐B and HLA‐C alleles and haplotypes in the Dravidian tribal populations of southern India
Authors: Thomas R. , Nair S.B. , Banerjee M.
Published: June 2004

Abstract:  The Dravidians are believed to be the earliest inhabitants of India. Their subsequent migration and admixture with invading racial groups has been of scientific interest for population geneticists. In the present study, seven highly endogamous and extremely isolated colonies of Dravidian tribal populations (n = 105) from Kerala in South India were analysed and compared with random non‐tribal Dravidian (RND) samples (n = 78) of southern India using the polymerase chain reaction with sequence‐specific primer method for HLA‐B and HLA‐C typing. The tribal group comprises Adiya, Kanikkar, Kattunaikka, Kuruma, Kurichiya, Malapandaram and Paniya, while the RND group includes Malayalam‐speaking individuals from various non‐tribal castes of Kerala selected randomly. Some of the most frequent HLA‐B alleles in the RND population were similar to the North Indian population and included B*07, B*61 (B*40), B*44, B*51, B*35 and B*52. Although B*61 was the most frequent allele in our total study population, the frequency fluctuated in individual populations. HLA‐Cw*14 was one of the most frequent alleles while HLA‐Cw*17 was totally absent in all populations studied. The haplotype B*61‐Cw*14 was present in all the study groups except in Kurichiya, and the haplotype B*51‐Cw*14 was only absent in Kattunaikka. Phylogenetic tree and correspondence analysis indicate that all the Dravidian tribal communities group together as a separate cluster, while the RND group of individuals from South India lie close to the North Indian population. This suggests that the RND population of South India might have a crypto‐Dravidian origin, while the smaller Dravidian tribal communities have a distinct Dravidian origin.
An HLA‐A*2607 variant (A*260702) independently identified in two unrelated French families
Authors: Lafarge X. , Fizet D. , Masson D. , Moine A.
Published: June 2004

Abstract In this report, we describe the identification of a new variant of the A*2607 allele, named A*260702. This variant was detected independently in two unrelated potential bone marrow donors living in two different regions of France. Molecular typing and mono‐allelic sequencing revealed that this allele differs from the original A*2607 allele by a single‐nucleotide substitution in codon 56 (GGG → GGT). This nucleotide change does not affect the amino acid sequence, both triplets coding for a glycine.
Transforming growth factor‐β1 gene polymorphism modifies the histological and clinical manifestations in Japanese patients with IgA nephropathy
Authors: Sato F. , Narita I. , Goto S. , Kondo D. , Saito N. , Ajiro J. , Saga D. , Ogawa A. , Kadomura M. , Akiyama F. , Kaneko Y. , Ueno M. , Sakatsume M. , Gejyo F.
Published: June 2004

Abstract Transforming growth factor (TGF)‐β1, a multifunctional cytokine, which regulates proliferation and differentiation of a variety of cell types, has the central role in the development and progression of renal injury in both animal models and human. Although it has been suggested that genetic variations in the TGF‐β1 gene are associated with the activity of the gene product, their clinical significance in glomerular disease is unknown. We investigated whether the polymorphisms of C‐509T and T869C in TGF‐β1 account for interindividual variation in manifestations of IgA nephropathy (IgAN) using 626 Japanese subjects including 329 patients with histologically proven IgAN and 297 healthy controls with normal urinalysis. The frequencies of genotypes, alleles, and major haplotypes were similar between the patients and controls. The C‐509T and T869C polymorphisms were in tight linkage disequilibrium, and the major haplotypes were C‐C and T‐T, which accounted for more than 95% of the total. In patients with –509CC and in those with the 869CC, urinary protein excretion was higher than in those with other genotypes, whereas no difference in other clinical manifestations was noted. Moreover, patients with –509CC and those with 869CC genotypes presented with a significant higher score of mesangial cell proliferation than in those with other genotypes. These results suggest that TGF‐β1 gene polymorphisms are specifically associated with heavy proteinuria and mesangial cell proliferation in Japanese patients with IgAN, although they do not confer susceptibility to this disease.
Two‐step consumption of yolk granules during the development of quail embryos
Authors: Yoshizaki Norio , Soga Marie , Ito Yasushi , Mao Kun Ming , Sultana Fowzia , Yonezawa Satoshi
Published: June 2004

The mechanism of yolk consumption was studied morphologically and biochemically in Japanese quail Coturnix japonica. The amount of yolk granules in the yolk (or ‘yolk cell’) decreased in two steps during embryonic development. In the first step, during days 0–4 of incubation, the yolk‐granule weight decreased at a rate of 13 mg/day. This decrease was due to segregation by endodermal cells that were newly formed in the developing yolk sac. In the second step after day 6, the decrease was drastic at a rate of 29.8 mg/day during days 6–12 and very slow thereafter. The decrease at the second step was due to the enzymatic digestion of yolk granules by cathepsin D that coexisted in yolk spheres. This digesting reaction was triggered by the solubilization of the granules with high concentrations of salts that were supplied after disruption of the limiting membrane of yolk spheres. The ‘yolk cell’ seemed to die around day 5 of incubation. Thus the digestion products might be taken up together with yolk lipids by endocytosis into the endodermal cells and transported to blood vessels.
Minostransposon causes germline transgenesis of the ascidianCiona savignyi
Authors: Matsuoka Terumi , Awazu Satoko , Satoh Nori , Sasakura Yasunori
Published: June 2004

An ascidian,Ciona savignyi, is regarded as a good experimental animal for genetics because of its small and compact genome for which a draft sequence is available, its short generation time and its interesting phylogenic position. ENU‐based mutagenesis has been carried out using this animal. However, insertional mutagenesis using transposable elements (transposons) has not yet been introduced. Recently, one of the Tc1/marinersuperfamily transposons,Minos, was demonstrated to cause germline transgenesis in the related speciesCiona intestinalis. In this report, we show thatMinoshas the ability to transpose from DNA to DNA inCiona savignyiin transposition assays. Although the activity was slightly weaker than inCiona intestinalis,Minosstill caused germline transgenesis inCiona savignyi. In addition, one insertion seemed to have caused an enhancer trapping. These results indicate thatMinosprovides a potential tool for transgenic techniques such as insertional mutagenesis inCiona savignyi.
Developmentally regulated expression of mouse HtrA3 and its role as an inhibitor of TGF‐β signaling
Authors: Tocharus Jiraporn , Tsuchiya Akiho , Kajikawa Miwa , Ueta Yoshifumi , Oka Chio , Kawaichi Masashi
Published: June 2004

The expression of mouse HtrA1 is developmentally regulated and restricted in embryo tissues which depend largely on TGF‐β signaling for their differentiation. We examined whether mouse HtrA3, another HtrA family member very close to HtrA1, shows similar expression patterns. HtrA3 and ‐1 were expressed mostly in the same embryonic organs but exhibited complementary patterns in various tissues; the lens epithelial cells in day 12.5 embryo expressed HtrA3 whereas the ciliary body and pigment retina expressed HtrA1. In the vertebrae of day 14.5 embryo, HtrA3 was expressed in the tail region, but HtrA1 was predominantly expressed in the thoracic and lumbar regions.

Similar to HtrA1, HtrA3 bound to various TGF‐β proteins and inhibited the signaling of BMP‐4, ‐2 and TGF‐β1. HtrA3 did not inhibit signaling originated from a constitutively active BMP receptor, indicating that the inhibition occurred upstream of the cell surface receptor. HtrA3 also showed proteolytic activities indistinguishable from those of HtrA1 toward β‐casein and some extracellular matrix (ECM) proteoglycans. The protease activity was absolutely required for the TGF‐β signal inhibition activity.

All these data suggest that HtrA3 and ‐1 have the overlapping biological activities but can function in complementary fashion in certain types of tissues.
Bayesian selection of threshold autoregressive models
Authors: Campbell Edward P.
Published: June 2004

Abstract. An approach to Bayesian model selection in self‐exciting threshold autoregressive (SETAR) models is developed within a reversible jump Markov chain Monte Carlo (RJMCMC) framework. Our approach is examined via a simulation study and analysis of the Zurich monthly sunspots series. We find that the method converges rapidly to the optimal model, whilst efficiently exploring suboptimal models to quantify model uncertainty. A key finding is that the parsimony of the model selected is influenced by the specification of prior information, which can be examined and subjected to criticism. This is a strength of the Bayesian approach, allowing physical understanding to constrain the model selection algorithm.
Adjustments in Different Government Systems
Authors: Spolaore Enrico
Published: June 2004

This paper develops a model in which agents have a conflict of interest over what instrument to use for policy adjustment in response to shocks. Three different government systems are analyzed: cabinet systems, in which one decision‐maker has full control over adjustment policies; consensus systems, in which adjustment policies must be agreed upon by all agents; and checks‐and‐balances systems, in which one agent decides what instrument should be used for adjustment, but the remaining agents may veto its use. All three systems may lead to inefficient policies. The cabinet system adjusts too often. The other systems may fail to adjust when adjustment is optimal. The relative performance of the three systems depends on the degree of political fragmentation and the size distribution of shocks.
Protection versus Promotion: An Empirical Investigation
Authors: Mitra Devashish , Thomakos Dimitrios D. , Ulubaşoğlu Mehmet A.
Published: June 2004

Using Turkish industry‐level data from 1983 to 1990, we find that politically organized industries receive both higher protection and promotion than unorganized ones. Tariff rates are decreasing (increasing) in the import‐penetration ratio and the absolute value of the import‐demandelasticity for organized (unorganized) industries. Subsidy rates are decreasing (increasing) in the output‐supply elasticity for organized (unorganized) industries. The results are consistent with the predictions of the Grossman–Helpman model and its extension in this paper. The mix of protection and promotion is inversely related to the ratio of their respective marginal deadweight cost measures.
Donor Strategy under the Fungibility of Foreign Aid
Authors: Lahiri Sajal , Raimondos‐Møller Pascalis
Published: June 2004

We develop a political–economic model of aid fungibility: a part of aid is diverted away from its intended target by lobby groups. The size of this diversion – the degree of aid fungibility – is determined endogenously by the recipient government. The donor can affect the equilibrium degree of fungibility by choosing both the size of aid and the timing of its decision. We derive a condition under which the donor's reaction to fungibility is to reduce the amount of aid. Under this condition, if the donor acts as a follower, both the donor and the target group are better off.
Tongue Sandwiches and Bagel Days: Sex, Food and Mind‐Body Dualism
Authors: Baxter Lynne , Hughes Christina
Published: June 2004

The substantive content of our paper is that of mind‐body dualism, which we explore through food metaphors. However, our primary aim is to use these food metaphors to explore the difficulties in going beyond dualistic thinking. We do this by focusing on dualism as a learnt state of being. Accordingly, and using an analysis of pedagogies of the everyday that takes account of particular communities of practice, we seek to demonstrate the (re)production of dualistic frameworks in organizational life. Our conclusion returns to a political agenda that is concerned to go beyond the inevitable hierarchization implicit in dualistic construction. Here we present the case for the retention of the binary and we indicate the work that now needs to take place if we are interested in developing interpretations that express the fluidity of gendered identities.
Doing Gender, Doing Entrepreneurship: An Ethnographic Account of Intertwined Practices
Authors: Bruni Attila , Gherardi Silvia , Poggio Barbara
Published: June 2004

Traditional literature and research on entrepreneurship relies on a model of economic rationality alleged to be universal and agendered. This article presents a description of the processes that position people as ‘men’ and ‘women’ within entrepreneurial practices and as ‘entrepreneurs’ within gender practices, relying on an ethnographic study carried out in small enterprises in Italy. Our analysis shows how gender and entrepreneurship are enacted as situated practices and how the codes of a gendered identity are kept, changed and transgressed by constantly sliding between different symbolic spaces. In particular we highlight five processes of the symbolic construction of gender and entrepreneurship: managing the dual presence, doing ceremonial and remedial work, boundary‐keeping, footing and gender commodification. We then propose a final metaphor which conveys a summary image of these processes. In concluding, we link our analysis to the original purpose of our investigation, highlighting not only how entrepreneurship is equated with the masculine, but also how alternative and possible forms of entrepreneurship exist, in the same way as different forms of gender.
New Zealand Maritime Glaciation: Millennial-Scale Southern Climate Change Since 3.9 Ma
Authors: Carter Robert M. , Gammon Paul
Published: June 2004

Ocean Drilling Program Site 1119 is ideally located to intercept discharges of sediment from the mid-latitude glaciers of the New Zealand Southern Alps. The natural gamma ray signal from the site's sediment core contains a history of the South Island mountain ice cap since 3.9 million years ago (Ma). The younger record, to 0.37 Ma, resembles the climatic history of Antarctica as manifested by the Vostok ice core. Beyond, and back to the late Pliocene, the record may serve as a proxy for both mid-latitude and Antarctic polar plateau air temperature. The gamma ray signal, which is atmospheric, also resembles the ocean climate history represented by oxygen isotope time series.
Involvement of Mammalian Mus81 in Genome Integrity and Tumor Suppression
Authors: McPherson John Peter , Lemmers Bénédicte , Chahwan Richard , Pamidi Ashwin , Migon Eva , Matysiak-Zablocki Elzbieta , Moynahan Mary Ellen , Essers Jeroen , Hanada Katsuhiro , Poonepalli Anuradha , Sanchez-Sweatman Otto , Khokha Rama , Kanaar Roland , Jasin Maria , Hande M. Prakash , Hakem Razqallah
Published: June 2004

Mus81-Eme1 endonuclease has been implicated in the rescue of stalled replication forks and the resolution of meiotic recombination intermediates in yeast. We used gene targeting to study the physiological requirements of Mus81 in mammals.
Mus81
–/–
mice are viable and fertile, which indicates that mammalian Mus81 is not essential for recombination processes associated with meiosis. Mus81-deficient mice and cells were hypersensitive to the DNA cross-linking agent mitomycin C but not to γ-irradiation. Remarkably, both homozygous
Mus81
–/–
and heterozygous
Mus81
+/–
mice exhibited a similar susceptibility to spontaneous chromosomal damage and a profound and equivalent predisposition to lymphomas and other cancers. These studies demonstrate a critical role for the proper biallelic expression of the mammalian
Mus81
in the maintenance of genomic integrity and tumor suppression.
Matching Behavior and the Representation of Value in the Parietal Cortex
Authors: Sugrue Leo P. , Corrado Greg S. , Newsome William T.
Published: June 2004

Psychologists and economists have long appreciated the contribution of reward history and expectation to decision-making. Yet we know little about how specific histories of choice and reward lead to an internal representation of the “value” of possible actions. We approached this problem through an integrated application of behavioral, computational, and physiological techniques. Monkeys were placed in a dynamic foraging environment in which they had to track the changing values of alternative choices through time. In this context, the monkeys' foraging behavior provided a window into their subjective valuation. We found that a simple model based on reward history can duplicate this behavior and that neurons in the parietal cortex represent the relative value of competing actions predicted by this model.
Oxoiron(IV) in Chloroperoxidase Compound II Is Basic: Implications for P450 Chemistry
Authors: Green Michael T. , Dawson John H. , Gray Harry B.
Published: June 2004

With the use of x-ray absorption spectroscopy, we have found that the Fe-O bond in chloroperoxidase compound II (CPO-II) is much longer than expected for an oxoiron(IV) (ferryl) unit; notably, the experimentally determined bond length of 1.82(1) Å accords closely with density functional calculations on a protonated ferryl (Fe
IV
-OH, 1.81 Å). The basicity of the CPO-II ferryl [p
K
a
> 8.2 (where
K
a
is the acid dissociation constant)] is attributable to strong electron donation by the axial thiolate. We suggest that the CPO-II protonated ferryl is a good model for the rebound intermediate in the P450 oxygenation cycle;with elevated p
K
a
values after one-electron reduction, thiolate-ligated ferryl radicals are competent to oxygenate saturated hydrocarbons at potentials that can be tolerated by folded polypeptide hosts.
Soil Carbon Sequestration Impacts on Global Climate Change and Food Security
Authors: Lal R.
Published: June 2004

The carbon sink capacity of the world's agricultural and degraded soils is 50 to 66% of the historic carbon loss of 42 to 78 gigatons of carbon. The rate of soil organic carbon sequestration with adoption of recommended technologies depends on soil texture and structure, rainfall, temperature, farming system, and soil management. Strategies to increase the soil carbon pool include soil restoration and woodland regeneration, no-till farming, cover crops, nutrient management, manuring and sludge application, improved grazing, water conservation and harvesting, efficient irrigation, agroforestry practices, and growing energy crops on spare lands. An increase of 1 ton of soil carbon pool of degraded cropland soils may increase crop yield by 20 to 40 kilograms per hectare (kg/ha) for wheat, 10 to 20 kg/ha for maize, and 0.5 to 1 kg/ha for cowpeas. As well as enhancing food security, carbon sequestration has the potential to offset fossilfuel emissions by 0.4 to 1.2 gigatons of carbon per year, or 5 to 15% of the global fossil-fuel emissions.
Selective Growth of Metal Tips onto Semiconductor Quantum Rods and Tetrapods
Authors: Mokari Taleb , Rothenberg Eli , Popov Inna , Costi Ronny , Banin Uri
Published: June 2004

We show the anisotropic selective growth of gold tips onto semiconductor (cadmium selenide) nanorods and tetrapods by a simple reaction. The size of the gold tips can be controlled by the concentration of the starting materials. The new nanostructures display modified optical properties caused by the strong coupling between the gold and semiconductor parts. The gold tips show increased conductivity as well as selective chemical affinity for forming self-assembled chains of rods. Such gold-tipped nanostructures provide natural contact points for self-assembly and for electrical devices and can solve the difficult problem of contacting colloidal nanorods and tetrapods to the external world.
The Hedgehog Response Network: Sensors, Switches, and Routers
Authors: Lum Lawrence , Beachy Philip A.
Published: June 2004

The Hedgehog (Hh) signaling pathway is intimately linked to cell growth and differentiation, with normal roles in embryonic pattern formation and adult tissue homeostasis and pathological roles in tumor initiation and growth. Recent advances in our understanding of Hh response have resulted from the identification of new pathway components and new mechanisms of action for old pathway components. The most striking new finding is that signal transmission from membrane to cytoplasm proceeds through recruitment, by the seven-transmembrane protein Smoothened, of an atypical kinesin, which routes pathway activation by interaction with other components of a complex that includes the latent zinc finger transcription factor, Ci.
Ultrahigh-Resolution Spin-Echo Measurement of Surface Potential Energy Landscapes
Authors: Jardine Andrew P. , Dworski Shechar , Fouquet Peter , Alexandrowicz Gil , Riley David J. , Lee Gabriel Y. H. , Ellis John , Allison William
Published: June 2004

We demonstrate two approaches that use the recently developed helium spin-echo technique to measure surface potential energy landscapes. For helium–lithium fluoride (100), we use the selective adsorption phenomenon to obtain the complete experimental band structure of atoms in a corrugated surface potential. For carbon monoxide–copper (001), we measure the diffusion-induced energy broadening in the scattered helium beam and extract properties of the adsorbate-substrate potential. The measurements are made possible by the resolution of our new spectrometer, which improves on existing resolution by three orders of magnitude. We show that it is possible to produce benchmark energy landscapes to assist evaluation and development of first-principles theory in the problematic van der Waals/weak chemisorption regime.
Tragedy Averted
Authors: Laubichler Manfred D.
Published: June 2004

Karl Pearson
The Scientific Life in a Statistical Age. by Theodore M. Porter. Princeton University Press, Princeton, NJ, 2004. 352 pp. $35, £22.95. ISBN 0-691-11445-5.

Porter explores the development of Pearson's interests from his early work in philosophy and cultural history through his crucial contributions to the foundations of modern statistics.
The Cometary and Interstellar Dust Analyzer at Comet 81P/Wild 2
Authors: Kissel J. , Krueger F. R. , Silén J. , Clark B. C.
Published: June 2004

The CIDA (Cometary and Interstellar Dust Analyzer) instrument on the Stardust spacecraft is a time-of-flight mass spectrometer used to analyze ions formed when fast dust particles strike the instrument's target. In the spectra of 45 presumably interstellar particles, quinone derivates were identified as constituents in the organic component. The 29 spectra obtained during the flyby of Comet 81P/Wild 2 confirm the predominance of organic matter. In moving from interstellar to cometary dust, the organic material seems to lose most of its hydrogen and oxygen as water and carbon monoxide. These are now present in the comet as gas phases, whereas the dust is rich in nitrogen-containing species. No traces of amino acids were found. We detected sulfur ions in one spectrum, which suggests that sulfur species are important in cometary organics.
Microarray-Based Analysis of theStaphylococcus aureusσBRegulon
Authors: Bischoff Markus , Dunman Paul , Kormanec Jan , Macapagal Daphne , Murphy Ellen , Mounts William , Berger-Bächi Brigitte , Projan Steven
Published: June 2004

Microarray-based analysis of the transcriptional profiles of the genetically distinctStaphylococcus aureusstrains COL, GP268, and Newman indicate that a total of 251 open reading frames (ORFs) are influenced by σBactivity. While σBwas found to positively control 198 genes by a factor of ≥2 in at least two of the three genetic lineages analyzed, 53 ORFs were repressed in the presence of σB. Gene products that were found to be influenced by σBare putatively involved in all manner of cellular processes, including cell envelope biosynthesis and turnover, intermediary metabolism, and signaling pathways. Most of the genes and/or operons identified as upregulated by σBwere preceded by a nucleotide sequence that resembled the σBconsensus promoter sequence ofBacillus subtilis. A conspicuous number of virulence-associated genes were identified as regulated by σBactivity, with many adhesins upregulated and prominently represented in this group, while transcription of various exoproteins and toxins were repressed. The data presented here suggest that the σBofS. aureuscontrols a large regulon and is an important modulator of virulence gene expression that is likely to act conversely to RNAIII, the effector molecule of theagrlocus. We propose that this alternative transcription factor may be of importance for the invading pathogen to fine-tune its virulence factor production in response to changing host environments.
Telomere Exchange between Linear Replicons ofBorrelia burgdorferi
Authors: Huang Wai Mun , Robertson Margaret , Aron John , Casjens Sherwood
Published: June 2004

Spirochetes in the genusBorreliacarry a linear chromosome and numerous linear plasmids that have covalently closed hairpin telomeres. The overall organization of the large chromosome ofBorrelia burgdorferiappears to have been quite stable over recent evolutionary time; however, a large fraction of natural isolates carry differing lengths of DNA that extend the right end of the chromosome between about 7 and 20 kbp relative to the shortest chromosomes. We present evidence here that a rather recent nonhomologous recombination event in theB. burgdorferistrain Sh-2-82 lineage has replaced its right chromosomal telomere with a large portion of the linear plasmid lp21, which is present in the strain B31 lineage. At least two successive rounds of addition of linear plasmid genetic material to the chromosomal right end appear to have occurred at the Sh-2-82 right telomere, suggesting that this is an evolutionary mechanism by which plasmid genetic material can become part of the chromosome. The unusual nonhomologous nature of this rearrangement suggests that, barring horizontal transfer, it can be used as a unique genetic marker for this lineage ofB. burgdorferichromosomes.
Presence of a Novel Phosphopentomutase and a 2-Deoxyribose 5-Phosphate Aldolase Reveals a Metabolic Link between Pentoses and Central Carbon Metabolism in the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
Authors: Rashid Naeem , Imanaka Hiroyuki , Fukui Toshiaki , Atomi Haruyuki , Imanaka Tadayuki
Published: June 2004

Numerous bacteria and mammalian cells harbor two enzymes, phosphopentomutase (PPM) and 2-deoxyribose 5-phosphate aldolase (DERA), involved in the interconversion between nucleosides and central carbon metabolism. In this study, we have examined the presence of this metabolic link in the hyperthermophilic archaeon,
Thermococcus kodakaraensis
KOD1. A search of the genome sequence of this strain revealed the presence of a closely related orthologue (TK2104) of bacterial DERA genes while no orthologue related to previously characterized PPM genes could be detected. Expression, purification, and characterization of the TK2104 protein product revealed that this gene actually encoded a DERA, catalyzing the reaction through a class I aldolase mechanism. As PPM activity was detected in
T. kodakaraensis
cells, we partially purified the protein to examine its N-terminal amino acid sequence. The sequence corresponded to a gene (TK1777) similar to phosphomannomutases within COG1109 but not COG1015, which includes all previously identified PPMs. Heterologous gene expression of TK1777 and characterization of the purified recombinant protein clearly revealed that the gene indeed encoded a PPM. Both enzyme activities could be observed in
T. kodakaraensis
cells under glycolytic and gluconeogenic growth conditions, whereas the addition of ribose, 2-deoxyribose, and 2′-deoxynucleosides in the medium did not lead to a significant induction of these activities. Our results clearly indicate the presence of a metabolic link between pentoses and central carbon metabolism in
T. kodakaraensis
, providing an alternative route for pentose biosynthesis through the functions of DERA and a structurally novel PPM.
Identification of Inducers of the
Yersinia enterocolitica
Phage Shock Protein System and Comparison to the Regulation of the RpoE and Cpx Extracytoplasmic Stress Responses
Authors: Maxson Michelle E. , Darwin Andrew J.
Published: June 2004

Known inducers of the phage shock protein (Psp) system suggest that it is an extracytoplasmic stress response, as are the well-studied RpoE and Cpx systems. However, a random approach to identify conditions and proteins that induce the Psp system has not been attempted. It is also unknown whether the proteins or mutations that induce Psp are specific or if they also activate the RpoE and Cpx systems. This study addressed these issues for the
Yersinia enterocolitica
Psp system. Random transposon mutagenesis identified null mutations and overexpression mutations that increase Φ(
pspA
-
lacZ
) operon fusion expression. The results suggest that Psp may respond exclusively to extracytoplasmic stress. Null mutations affected glucosamine-6-phosphate synthetase (
glmS
), which plays a role in cell envelope biosynthesis, and the F
0
F
1
ATPase (
atp
operon). The screen also revealed that in addition to several secretins, the overexpression of three novel putative inner membrane proteins (IMPs) induced the Psp response. We also compared induction of the
Y. enterocolitica
Psp, RpoE, and Cpx responses. Overexpression of secretins or the three IMPs or the presence of an
atpB
null mutation only induced the Psp response. Similarly, known inducers of the RpoE and Cpx responses did not significantly induce the Psp response. Only the
glmS
null mutation induced all three responses. Therefore, Psp is induced distinctly from the RpoE and Cpx systems. The specific IMP inducers may be valuable tools to probe specific signal transduction events of the Psp response in future studies.
Regulation of Expression of Cellulosomes and Noncellulosomal (Hemi)Cellulolytic Enzymes in
Clostridium cellulovorans
during Growth on Different Carbon Sources
Authors: Han Sung Ok , Cho Hee-Yeon , Yukawa Hideaki , Inui Masayuki , Doi Roy H.
Published: June 2004

Cellulosomes and noncellulosomal (hemi)cellulolytic enzymes are produced by
Clostridium cellulovorans
to degrade plant cell walls. To understand their synergistic relationship, changes in mRNA and protein expression in cellulosomes and noncellulosomal (hemi)cellulolytic enzymes (hereafter called noncellulosomal enzymes) of cultures grown on cellobiose, cellulose, pectin, xylan, and corn fiber or mixtures thereof were examined. Cellulase expression, favored particularly by the presence of Avicel, was found with all substrates. Comparison of cellulosome and noncellulosomal enzymes showed that expression profiles were strongly affected by the carbon source. High xylanase or pectate lyase expression was observed when
C. cellulovorans
was grown on xylan or pectin, respectively. Mixed carbon substrates (cellulose-pectin-xylan mixture or corn fiber) induced a wider variety of enzymes than a single carbon source, such as cellobiose, pectin, or xylan. Cellulosomal proteome profiles were more affected by the carbon source than the noncellulosomal enzymes. Transcription and protein analyses revealed that cellulosomes and noncellulosomal enzymes were expressed simultaneously on mixed carbon sources, but their degree of inducibility varied when the substrate was either cellulose or cellobiose. Cellulosomes and noncellulosomal enzymes had synergistic activity on various carbon substrates. These results indicated that expression of plant cell wall-degrading enzymes is highly influenced by the available carbon source and that synergy between cellulosomes and noncellulosomal enzymes contribute to plant cell wall degradation.
Structure of
Pseudomonas aeruginosa
Populations Analyzed by Single Nucleotide Polymorphism and Pulsed-Field Gel Electrophoresis Genotyping
Authors: Morales Gracia , Wiehlmann Lutz , Gudowius Peter , van Delden Christian , Tümmler Burkhard , Martínez José Luis , Rojo Fernando
Published: June 2004

Pseudomonas aeruginosa
has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of
P. aeruginosa
, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (
oriC
,
oprL
,
fliC
,
alkB2
,
citS
,
oprI
, and
ampC
). The combination of these SNPs plus the type of
fliC
present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of
P. aeruginosa
strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The
P. aeruginosa
chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the
P. aeruginosa
population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.
Multiple Paths for Nonphysiological Transport of K
+
in
Escherichia coli
Authors: Buurman Ed T. , McLaggan Debbie , Naprstek Josef , Epstein Wolfgang
Published: June 2004

Mutants of
Escherichia coli
lacking all of the known saturable K
+
transport systems, “triple mutants,” require elevated K
+
concentrations for growth. K
+
transport activity in such mutants, called TrkF activity, has low substrate specificity and a low rate that increases with increasing external pH. Attempts to isolate mutants requiring even higher concentrations of K
+
failed, implying that either TrkF is essential or is composed of multiple minor K
+
transport activities. Instead, we sought mutations that allowed triple mutants to grow at lower K
+
concentrations. Mutations so identified include ones altering MscL, the large mechanosensitive channel, or Opp, the oligopeptide permease. However, a possible contribution of wild-type Opp and MscL to TrkF activity was not proven. In contrast, expression of wild-type ProP, TrkG, and TrkH proteins increased uptake when encoded on multicopy plasmids. In all of these situations, the driving force for K
+
appeared to be the transmembrane electric potential, and in most cases substrate specificity was low; these are characteristics of TrkF activity. These results support the view that TrkF is composed of multiple, “aberrant” K
+
transport activities, i.e., paths that, regardless of their physiological function, allow K
+
to cross the cell membrane by a uniport process.
Energetics of Gliding Motility in
Mycoplasma mobile
Authors: Jaffe Jacob D. , Miyata Makoto , Berg Howard C.
Published: June 2004

Mycoplasma mobile
glides on surfaces at up to 7 μm/s by an unknown mechanism. We studied the energetics that power gliding by using a novel, growth medium-free system. We found that cells could glide in defined media if the glass substrate is preconditioned by exposure to horse serum. The active component that potentiates gliding is sensitive to proteinase K treatment. We used the defined medium system to test the effect of various inhibitors, ionophores, and poisons on motility of
M. mobile
. Valinomycin, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP),
N,N
′-dicyclohexylcarbodiimide, phenamil, amiloride, rifampin, and puromycin had no short-term effects on gliding. We also confirmed that we were able to modulate the membrane potential with valinomycin and FCCP by using a potential-sensitive dye. Shifting the pH likewise had no effect on motility. These results rule out the use of conventional ion motive forces to power gliding. Arsenate had a dramatic inhibitory effect on gliding, and both the speed and the fraction of cells moving tracked ATP levels. Sodium orthovanadate had a slight but significant inhibitory effect on gliding. Taken together, these results suggest that the motor system of
M. mobile
is likely an ATPase or is directly coupled to an ATPase.
Autoinduction ofBacillus subtilis phoPROperon Transcription Results from Enhanced Transcription from EσA- and EσE-Responsive Promoters by Phosphorylated PhoP
Authors: Paul Salbi , Birkey Stephanie , Liu Wei , Hulett F. Marion
Published: June 2004

ThephoPRoperon encodes a response regulator, PhoP, and a histidine kinase, PhoR, which activate or repress genes of theBacillus subtilisPho regulon in response to an extracellular phosphate deficiency. Induction ofphoPRupon phosphate starvation required activity of both PhoP and PhoR, suggesting autoregulation of the operon, a suggestion that is supported here by PhoP footprinting on thephoPRpromoter. Primer extension analyses, using RNA from JH642 or isogenicsigEorsigBmutants isolated at different stages of growth and/or under different growth conditions, suggested that expression of thephoPRoperon represents the sum of five promoters, each responding to a specific growth phase and environmental controls. The temporal expression of thephoPRpromoters was investigated using in vitro transcription assays with RNA polymerase holoenzyme isolated at different stages of Pho induction, from JH642 or isogenicsigEorsigBmutants. In vitro transcription studies using reconstituted EσA, EσB, and EσEholoenzymes identified PA4and PA3as EσApromoters and PE2as an EσEpromoter. Phosphorylated PhoP (PhoP∼P) enhanced transcription from each of these promoters. EσBwas sufficient for in vitro transcription of the PB1promoter. P5was active only in asigBmutant strain. These studies are the first to report a role for PhoP∼P in activation of promoters that also have activity in the absence of Pho regulon induction and an activation role for PhoP∼P at an EσEpromoter. Information concerning PB1and P5creates a basis for further exploration of the regulatory coordination or overlap of the PhoPR and SigB regulons during phosphate starvation.
Vibrio fischeri
Flagellin A Is Essential for Normal Motility and for Symbiotic Competence during Initial Squid Light Organ Colonization
Authors: Millikan Deborah S. , Ruby Edward G.
Published: June 2004

The motile bacterium
Vibrio fischeri
is the specific bacterial symbiont of the Hawaiian squid
Euprymna scolopes
. Because motility is essential for initiating colonization, we have begun to identify stage-specific motility requirements by creating flagellar mutants that have symbiotic defects.
V. fischeri
has six flagellin genes that are uniquely arranged in two chromosomal loci,
flaABCDE
and
flaF
. With the exception of the
flaA
product, the predicted gene products are more similar to each other than to flagellins of other
Vibrio
species. Immunoblot analysis indicated that only five of the six predicted proteins were present in purified flagella, suggesting that one protein, FlaF, is unique with respect to either its regulation or its function. We created mutations in two genes,
flaA
and
flaC
. Compared to a
flaC
mutant, which has wild-type flagellation, a strain having a mutation in the
flaA
gene has fewer flagella per cell and exhibits a 60% decrease in its rate of migration in soft agar. During induction of light organ symbiosis, colonization by the
flaA
mutant is impaired, and this mutant is severely outcompeted when it is presented to the animal as a mixed inoculum with the wild-type strain. Furthermore,
flaA
mutant cells are preferentially expelled from the animal, suggesting either that FlaA plays a role in adhesion or that normal motility is an advantage for retention within the host. Taken together, these results show that the flagellum of
V. fischeri
is a complex structure consisting of multiple flagellin subunits, including FlaA, which is essential both for normal flagellation and for motility, as well as for effective symbiotic colonization.
Displacements of Prohead Protease Genes in the Late Operons of Double-Stranded-DNA Bacteriophages
Authors: Liu Jing , Mushegian Arcady
Published: June 2004

Most of the known prohead maturation proteases in double-stranded-DNA bacteriophages are shown, by computational methods, to fall into two evolutionarily independent clans of serine proteases, herpesvirus assemblin-like and ClpP-like. Phylogenetic analysis suggests that these two types of phage prohead protease genes displaced each other multiple times while preserving their exact location within the late operons of the phage genomes.
Spike Structure at the Interface between GlidingMycoplasma mobileCells and Glass Surfaces Visualized by Rapid-Freeze-and-Fracture Electron Microscopy
Authors: Miyata Makoto , Petersen Jennifer D.
Published: June 2004

Mycoplasma mobileis a flask-shaped bacteria that binds to a substrate and glides towards its tapered end, the so-called “head-like protrusion,” by an unknown mechanism. To search for cellular structures underlying this motility, the cell-substrate interface of actively gliding cells was visualized by rapid-freeze-and-freeze-fracture rotary-shadow electron microscopy. Novel structures, called “spikes,” were observed to protrude from the cell membrane and attach to the glass surface at their distal end. The spikes were on average 50 nm in length and 4 nm in diameter, most abundant around the head, and not observed in a nonbinding mutant. The spikes may be involved in the mechanism of binding, gliding, or both.
Insulation of the σFRegulatory System inBacillus subtilis
Authors: Carniol Karen , Kim Tae-Jong , Price Chester W. , Losick Richard
Published: June 2004

The transcription factors σFand σBare related RNA polymerase sigma factors that govern dissimilar networks of adaptation to stress conditions inBacillus subtilis. The two factors are controlled by closely related regulatory pathways, involving protein kinases and phosphatases. We report that insulation of the σFpathway from the σBpathway involves the integrated action of both the cognate kinase and the cognate phosphatase.
Independent Regulation of Two Genes in
Escherichia coli
by Tetracyclines and Tet Repressor Variants
Authors: Kamionka Annette , Sehnal Miriam , Scholz Oliver , Hillen Wolfgang
Published: June 2004

We report a regulation system in
Escherichia coli
for independent regulation of two distinct reporter genes by application of Tet repressors with different specificities. One Tet repressor variant comprises wild-type
tet
operator (
tetO
) recognition and exclusive induction with the novel inducer 4-dedimethylamino-anhydrotetracycline. The other Tet repressor variant shows
tetO-
4C recognition and induction with tetracycline. We demonstrate that both variants are independently active in vivo and allow selective regulation of two genes in the same cell without any cross talk.
TheponAGene ofEnterococcus faecalisJH2-2 Codes for a Low-Affinity Class A Penicillin-Binding Protein
Authors: Duez Colette , Hallut Séverine , Rhazi Noureddine , Hubert Séverine , Amoroso Ana , Bouillenne Fabrice , Piette André , Coyette Jacques
Published: June 2004

A soluble derivative of theEnterococcus faecalisJH2-2 class A PBP1 (*PBP1) was overproduced and purified. It exhibited a glycosyltransferase activity on theEscherichia coli14C-labeled lipid II precursor. As add-peptidase, it could hydrolyze thiolester substrates with efficiencies similar to those of other class A penicillin-binding proteins (PBPs) and bind β-lactams, but withk2/K(a parameter accounting for the acylation step efficiency) values characteristic of penicillin-resistant PBPs.
Genital condylomata in a patient receiving infliximab for Crohn’s disease
Authors: Somasekar A , Alcolado R
Published: June 2004

Infliximab is a monoclonal antibody against tumour necrosis factor-alpha. Recent studies have shown that it is effective in treating patients with refractory Crohn’s disease and in those with Crohn’s fistulae. Though this drug is found to be safe in clinical trials, sporadic reports of serious complications have been recorded in the literature. The case of a patient who developed profuse genital warts after infliximab treatment is reported. The literature is reviewed and information is presented on side effects and complications as a result of infliximab therapy.
Evolving immunotherapeutic strategies in bladder and renal cancer
Authors: Griffiths T R L , Mellon J K
Published: June 2004

For patients with urological cancers, immunotherapy is currently a treatment option for metastatic renal cell carcinoma, and those with “high risk” superficial bladder cancers. In this review, our current understanding of tumour immune escape is discussed. The principles and role of current immunotherapies for these tumours are described, and new areas of immunotherapeutic promise are highlighted.
Lemierre’s syndrome: more than a historical curiosa
Authors: Riordan T , Wilson M
Published: June 2004

Lemierre’s syndrome is a severe illness caused by the anaerobic bacterium, Fusobacterium necrophorum which typically occurs in healthy teenagers and young adults. The infection originates in the throat and spreads via a septic thrombophlebitis of the tonsillar vein and internal jugular vein. The ensuing bacteraemia is complicated by septic emboli to a range of sites such as lung, joints, and bones. Although rare, there is evidence of a resurgence in the condition in recent years, possibly associated with reduced use of antibiotic therapy for sore throats. The typical clinical picture is characteristic but many clinicians are unaware of the condition and diagnosis is often delayed with potentially fatal consequences.
A novel multimedia tool to improve bedside teaching of cardiac auscultation
Authors: Woywodt A , Herrmann A , Kielstein J T , Haller H , Haubitz M , Purnhagen H
Published: June 2004

Training in cardiac auscultation is a core element of undergraduate teaching but recent studies have documented a remarkable decline in auscultatory skills. Therefore there is an interest in new ways to teach cardiac auscultation. In analogy to phonocardiography, an electronic system for simultaneous auscultation and visualisation of murmurs was sought. For this purpose, an electronic stethoscope was linked to a laptop computer and software created to visualise auscultatory findings. In a preliminary trial in undergraduate students, this approach greatly facilitated teaching. Amalgamating traditional phonocardiography with a multimedia approach, this system represents a novel tool for bedside teaching of cardiac auscultation.