bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculation of the minimum number of replicate spots required
for detection of significant gene expression fold change in
microarray experiments
Authors: Black Michael A. , Doerge R. W.
Published: December 2002

Motivation: We present statistical methods for determining the number of per gene replicate spots required in microarray experiments. The purpose of these methods is to obtain an estimate of the sampling variability present in microarray data, and to determine the number of replicate spots required to achieve a high probability of detecting a significant fold change in gene expression, while maintaining a low error rate. Our approach is based on data from control microarrays, and involves the use of standard statistical estimation techniques.

Results: After analyzing two experimental data sets containing control array data, we were able to determine the statistical power available for the detection of significant differential expression given differing levels of replication. The inclusion of replicate spots on microarrays not only allows more accurate estimation of the variability present in an experiment, but more importantly increases the probability of detecting genes undergoing significant fold changes in expression, while substantially decreasing the probability of observing fold changes due to chance rather than true differential expression.

Availability: The methods presented here are based on standard techniques, and are available in most statistical software packages. We used the software R to perform the computations for this work.

Contact: doerge@purdue.edu; blackma@stat.purdue.edu

* To whom correspondence should be addressed at Department of Statistics, 1399 Mathematical Sciences Building, Purdue University, West Lafayette, IN 47907-1399, USA.
A decomposition model to track gene expression signatures: preview on
observer-independent classification of ovarian cancer
Authors: Martoglio Ann-Marie , Miskin James W. , Smith Stephen K. , MacKay David J. C.
Published: December 2002

Motivation: A number of algorithms and analytical models have been employed to reduce the multidimensional complexity of DNA array data and attempt to extract some meaningful interpretation of the results. These include clustering, principal components analysis, self-organizing maps, and support vector machine analysis. Each method assumes an implicit model for the data, many of which separate genes into distinct clusters defined by similar expression profiles in the samples tested. A point of concern is that many genes may be involved in a number of distinct behaviours, and should therefore be modelled to fit into as many separate clusters as detected in the multidimensional gene expression space. The analysis of gene expression data using a decomposition model that is independent of the observer involved would be highly beneficial to improve standard and reproducible classification of clinical and research samples.

Results: We present a variational independent component analysis (ICA) method for reducing high dimensional DNA array data to a smaller set of latent variables, each associated with a gene signature. We present the results of applying the method to data from an ovarian cancer study, revealing a number of tissue type-specific and tissue type-independent gene signatures present in varying amounts among the samples surveyed. The observer independent results of such molecular analysis of biological samples could help identify patients who would benefit from different treatment strategies. We further explore the application of the model to similar high-throughput studies.

Availability: Supporting details of the decomposition model can be found at http://www.inference.phy.cam.ac.uk/mackay/abstracts/icagenes.html and the ovarian cancer study data can be found at http://www.path.cam.ac.uk/~angio/publications/martoglioetal2002/ovcaica.html.

Contact: amm53@cam.ac.uk; mackay@mrao.cam.ac.uk

* To whom correspondence should be addressed.

† These authors contributed equally to this work.
Partial least squares proportional hazard regression for
application to DNA microarray survival data
Authors: Nguyen Danh V. , Rocke David M.
Published: December 2002

Motivation: Microarrays are increasingly used in cancer research. When gene transcription data from microarray experiments also contains patient survival information, it is often of interest to predict the survival times based on the gene expression. In this paper we consider the well-known proportional hazard (PH) regression model for survival analysis. Ordinarily, the PH model is used with a few covariates and many observations (subjects). We consider here the case that the number of covariates, p, exceeds the number of samples, N, a setting typical of gene expression data from DNA microarrays.

Results: For a given vector of response values which are survival times and p gene expressions (covariates) we examine the problem of how to predict the survival probabilities, when N ≪ p. The approach taken to cope with the high dimensionality is to reduce the dimension using partial least squares with the response variable as the vector of survival times. After dimension reduction, the extracted PLS gene components are then used as covariates in a PH regression to predict the survival probabilities. We demonstrate the use of the methodology on two cDNA gene expression data sets, both containing survival data. The first data set contains 40 diffuse large B-cell lymphoma (DLBCL) tissue samples and the second data set contains 49 tissue samples from patients with locally advanced breast cancer in a prospective study.

Availability: The methodology can be implemented using a combination of standard statistical methods, available, for example, in SAS. Sample SAS macro codes to implement the methods will be available at http://stat.tamu.edu/~dnguyen/supplemental.html

Contact: dnguyen@stat.tamu.edudmrocke@ucdavis.edu

* To whom correspondence should be addressed.
Modeling the percolation of annotation errors in a
database of protein sequences
Authors: Gilks Walter R. , Audit Benjamin , De Angelis Daniela , Tsoka Sophia , Ouzounis Christos A.
Published: December 2002

Public sequence databases contain information on the sequence, structure and function of proteins. Genome sequencing projects have led to a rapid increase in protein sequence information, but reliable, experimentally verified, information on protein function lags a long way behind. To address this deficit, functional annotation in protein databases is often inferred by sequence similarity to homologous, annotated proteins, with the attendant possibility of error. Now, the functional annotation in these homologous proteins may itself have been acquired through sequence similarity to yet other proteins, and it is generally not possible to determine how the functional annotation of any given protein has been acquired. Thus the possibility of chains of misannotation arises, a process we term ‘error percolation’. With some simple assumptions, we develop a dynamical probabilistic model for these misannotation chains. By exploring the consequences of the model for annotation quality it is evident that this iterative approach leads to a systematic deterioration of database quality.

Contact: WRG: wally.gilks@mrc-bsu.cam.ac.uk; BA and CAO: audit@ebi.ac.uk; ouzounis@ebi.ac.uk

* To whom correspondence should be addressed.

† Both these authors contributed equally to this work.
Local structure-based sequence profile database for local
and global protein structure predictions
Authors: Yang An-Suei , Wang Lu-yong
Published: December 2002

Motivation: A large body of evidence suggests that protein structural information is frequently encoded in local sequences—sequence–structure relationships derived from local structure/sequence analyses could significantly enhance the capacities of protein structure prediction methods. In this paper, the prediction capacity of a database (LSBSP2) that organizes local sequence–structure relationships encoded in local structures with two consecutive secondary structure elements is tested with two computational procedures for protein structure prediction. The goal is twofold: to test the folding hypothesis that local structures are determined by local sequences, and to enhance our capacity in predicting protein structures from their amino acid sequences.

Results: The LSBSP2 database contains a large set of sequence profiles derived from exhaustive pair-wise structural alignments for local structures with two consecutive secondary structure elements. One computational procedure makes use of the PSI-BLAST alignment program to predict local structures for testing sequence fragments by matching the testing sequence fragments onto the sequence profiles in the LSBSP2 database. The results show that 54% of the test sequence fragments were predicted with local structures that match closely with their native local structures. The other computational procedure is a filter system that is capable of removing false positives as possible from a set of PSI-BLAST hits. An assessment with a large set of non-redundant protein structures shows that the PSI-BLAST + filter system improves the prediction specificity by up to two-fold over the prediction specificity of the PSI-BLAST program for distantly related protein pairs. Tests with the two computational procedures above demonstrate that local sequence–structure relationships can indeed enhance our capacity in protein structure prediction. The results also indicate that local sequences encoded with strong local structure propensities play an important role in determining the native state folding topology.

Availability: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website:www.columbia.edu/~ay1/

Contact: ay1@columbia.edu

* To whom correspondence should be addressed.
Structure–dependent sequence alignment for remotely
related proteins
Authors: Yang An-Suei
Published: December 2002

Motivation: The quality of a model structure derived from a comparative modeling procedure is dictated by the accuracy of the predicted sequence–template alignment. As the sequence–template pairs are increasingly remote in sequence relationship, the prediction of the sequence–template alignments becomes increasingly problematic with sequence alignment methods. Structural information of the template, used in connection with the sequence relationship of the sequence–template pair, could significantly improve the accuracy of the sequence–template alignment. In this paper, we describe a sequence–template alignment method that integrates sequence and structural information to enhance the accuracy of sequence–template alignments for distantly related protein pairs.

Results: The structure-dependent sequence alignment (SDSA) procedure was optimized for coverage and accuracy on a training set of 412 protein pairs; the structures for each of the training pairs are similar (RMSD<∼4Å) but the sequence relationship is undetectable (average pair-wise sequence identity = 8%). The optimized SDSA procedure was then applied to extend PSI-BLAST local alignments by calculating the global alignments under the constraint of the residue pairs in the local alignments. This composite alignment procedure was assessed with a testing set of 1421 protein pairs, of which the pair-wise structures are similar (RMSD<∼4Å) but the sequences are marginally related at best in each pair (average pair-wise sequence identity = 13%). The assessment showed that the composite alignment procedure predicted more aligned residues pairs with an average of 27% increase in correctly aligned residues over the standard PSI-BLAST alignments for the protein pairs in the testing set.

Availability: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website: http://www.columbia.edu/~ay1/

Contact: ay1@columbia.edu
PFDB: a generic protein family database integrating the CATH domain
structure database with sequence based protein family resources
Authors: Shepherd Adrian J. , Martin Nigel J. , Johnson Roger G. , Kellam Paul , Orengo Christine A.
Published: December 2002

Motivation: The PFDB (Protein Family Database) is a new database designed to integrate protein family-related data with relevant functional and genomic data. It currently manages biological data for three projects—the CATH protein domain database (Orengo et al., 1997; Pearl et al., 2001), the VIDA virus domains database (Albà et al., 2001) and the Gene3D database (Buchan et al., 2001). The PFDB has been designed to accommodate protein families identified by a variety of sequence based or structure based protocols and provides a generic resource for biological research by enabling mapping between different protein families and diverse biochemical and genetic data, including complete genomes.

Results: A characteristic feature of the PFDB is that it has a number of meta-level entities (for example aggregation, collection and inclusion) represented as base tables in the final design. The explicit representation of relationships at the meta-level has a number of advantages, including flexibility—both in terms of the range of queries that can be formulated and the ability to integrate new biological entities within the existing design. A potential drawback with this approach—poor performance caused by the number of joins across meta-level tables—is avoided by implementing the PFDB with materialized views using the mature relational database technology of Oracle 8i. The resultant database is both fast and flexible.

This paper presents the principles on which the database has been designed and implemented, and describes the current status of the database and query facilities supported.

Availability: http://bsmsn01.biochem.ucl.ac.uk/

* To whom correspondence should be addressed.
A hierarchical approach to aligning collinear regions of genomes
Authors: Roytberg Mikhail A. , Ogurtsov Aleksey Y. , Shabalina Svetlana A. , Kondrashov Alexey S.
Published: December 2002

Motivation: As a first approximation, similarity between two long orthologous regions of genomes can be represented by a chain of local similarities. Within such a chain, pairs of successive similarities are collinear (non-conflicting), i.e. segments involved in the nth similarity precede in both sequences segments involved in the (n+1)th similarity. However, when all similarities between two long sequences are considered, usually there are many conflicts between them. Although some conflicts can be avoided by masking transposons or low-complexity sequences, selecting only those similarities that reflect orthology and, thus, belong to the evolutionarily true chain is not trivial.

Results: We propose a simple, hierarchical algorithm of finding the true chain of local similarities. Starting from similarities with low P-values, we resolve each pairwise conflict by deleting a similarity with a higher P-value. This greedy approach constructs a chain of similarities faster than when a chain optimal with respect to some global criterion is sought, and makes more sense biologically.

Availability: A software tool OWEN based on the proposed approach is described in the accompanying note and is freely available at ftp://ftp.ncbi.nih.gov/pub/kondrashov/owen

Contact: kondrashov@ncbi.nlm.nih.gov

Supplementary information: Algorithm Chain and examples of chains of local similarities are available at ftp://ftp.ncbi.nih.gov/pub/kondrashov/owen/extra

* To whom correspondence should be addressed.
SNPper: retrieval and analysis of human SNPs
Authors: Riva A. , Kohane I. S.
Published: December 2002

Motivation: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for the study of the human genome. SNPs can be used as markers to create high-density genetic maps, as causal candidates for diseases, or to reconstruct the history of our genome. SNP-based studies rely on the availability of large numbers of validated, high-frequency SNPs whose position on the chromosomes is known with precision. Although large collections of SNPs exist in public databases, researchers need tools to effectively retrieve and manipulate them.

Results: We describe the implementation and usage of SNPper, a web-based application to automate the tasks of extracting SNPs from public databases, analyzing them and exporting them in formats suitable for subsequent use. Our application is oriented toward the needs of candidate-gene, whole-genome and fine-mapping studies, and provides several flexible ways to present and export the data. The application has been publicly available for over a year, and has received positive user feedback and high usage levels.

Availability: SNPper is freely available at http://snpper.chip.org/. Registration is optional and provides access to some advanced features.

Contact: Alberto.Riva@TCH.Harvard.edu

* To whom correspondence should be addressed.
Oligodb—interactive design of oligo DNA for transcription
profiling of human genes
Authors: Mrowka Ralf , Schuchhardt Johannes , Gille Christoph
Published: December 2002

Motivation: The increasing use of customized oligo-DNA-microarrays has created a demand for convenient design of oligo nucleotides. The oligo-nucleotides have to serve as specific templates in the hybridization reaction.

Results: We have devised a web-based system for interactive design of suitable oligos for transcription profiling experiments with user-defined parameters. Oligodb is based on predicted human gene transcripts from the ENSEMBL project. The web interface allows the user to retrieve oligos for human transcripts in a flexible manner. Criteria for selecting the oligos are low similarity to all other known human genes, the absence of stable secondary structures, the length of the oligo, and the absence of low complexity regions. Furthermore, the user may select oligos corresponding to the desired position in the 5’–3’ direction of the transcript, and based on the melting temperature. All data and results are tightly web-linked to the corresponding data entries of ENSEMBL project.

Availability: The working Oligodb system is to be found at http://oligodb.charite.de

Contact: ralf.mrowka@charite.de

* To whom correspondence should be addressed.
PCR designer for restriction analysis of various types of
sequence mutation
Authors: Ke Xiayi , Collins Andrew , Ye Shu
Published: December 2002

Summary: Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.

Availability: The computer software, with related documentation, is available at http://cedar.genetics.soton.ac.uk/public_html/primer.html

Contact: xiayi@well.ox.ac.uk

* To whom correspondence should be addressed.
Design of endonuclease restriction sites into primers for PCR cloning
Authors: Hou Jianghui
Published: December 2002

Summary: I present a software system PCRCLNG that facilitates the design of endonuclease restriction sites into the 5′-end of PCR primers. The product amplified using these primers can be directly cloned into vectors. The program estimates the annealing temperature for each primer and selects the primer pairs with comparable annealing temperature. Finally the software determines whether the PCR product can be cloned into the vector to generate in-frame gene fusion.

Availability: PCRCLNG is available for non-commercial users free of charge as a set of executables and source codes upon request from the author.

Contact: jianghui.hou@ed.ac.uk
RED: the analysis, management and dissemination of
expressed sequence tags
Authors: Everitt R. , Minnema S. E. , Wride M. A. , Koster C. S. , Hance J. E. , Mansergh F. C. , Rancourt D. E.
Published: December 2002

Summary: The Rancourt EST Database (RED) is a web-based system for the analysis, management, and dissemination of expressed sequence tags (ESTs). RED represents a flexible template DNA sequence database that can be easily manipulated to suit the needs of other laboratories undertaking mid-size sequencing projects.

Availability: http://www.ucalgary.ca/~rancourt

Contact: reveritt@ucalgary.ca

* To whom correspondence should be addressed.

1 Present address: Cardiff University, Biomedical Sciences Building, Museum Avenue, PO Box 911, Cardiff CF10 3US, Wales, UK.
GENECOUNTING: haplotype analysis with missing genotypes
Authors: Zhao Jing Hua , Lissarrague Sebastien , Essioux Laurent , Sham Pak Chung
Published: December 2002

Summary: A general algorithm is described for haplotype analysis of unrelated individuals with missing genotypes. It can handle problems involving multiple polymorphic markers with missing data.

Availability: GENECOUNTING is available fromhttp://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.stm

Contact: j.zhao@public-health.ucl.ac.uk;p.sham@iop.kcl.ac.uk

* To whom correspondence should be addressed.
DNACompress: fast and effective DNA sequence compression
Authors: Chen Xin , Li Ming , Ma Bin , Tromp John
Published: December 2002

Summary: While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs.

Availability: http://dna.cs.ucsb.edu/DNACompress

Contact: chxin@cs.ucsb.edumli@cs.ucsb.edu

* To whom correspondence should be addressed.
ADME-AP: a database of ADME associated proteins
Authors: Sun L. Z. , Ji Z. L. , Chen X. , Wang J. F. , Chen Y. Z.
Published: December 2002

Summary: Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates.

Availability: http://xin.cz3.nus.edu.sg/group/admet/admet.asp

Contact: yzchen@cz3.nus.edu.sg

* To whom correspondence should be addressed.
PoPMuSiC, rationally designing point
mutations in protein structures
Authors: Kwasigroch J. M. , Gilis D. , Dehouck Y. , Rooman M.
Published: December 2002

Summary: PoPMuSiC is an efficient tool for rational computer-aided design of single-site mutations in proteins and peptides. Two types of queries can be submitted. The first option allows to estimate the changes in folding free energy for specific point mutations given by the user. In the second option, all possible point mutations in a given protein or protein region are performed and the most stabilizing or destabilizing mutations, or the neutral mutations with respect to thermodynamic stability, are selected. For each sequence position or secondary structure the deviation from the most stable sequence is moreover evaluated, which helps to identify the most suitable sites for the introduction of mutations.

Availability: http://babylone.ulb.ac.be/popmusic

Contact: jean.marc.kwasigroch@ulb.ac.be

* To whom correspondence should be addressed.
OWEN: aligning long collinear regions of genomes
Authors: Ogurtsov Aleksey Y. , Roytberg Mikhail A. , Shabalina Svetlana A. , Kondrashov Alexey S.
Published: December 2002

Summary: OWEN is an interactive tool for aligning two long DNA sequences that represents similarity between them by a chain of collinear local similarities. OWEN employs several methods for constructing and editing local similarities and for resolving conflicts between them. Alignments of sequences of lengths over 106 can often be produced in minutes. OWEN requires memory below 20 L, where L is the sum of lengths of the compared sequences.

Availability: Pre-compiled versions of OWEN for Windows, Linux for PC, SunOS for Sun, and Irix for SGI, user manual, and examples of alignments are freely available atftp://ftp.ncbi.nih.gov/pub/kondrashov/owen

Contact: ogurtsov@ncbi.nlm.nih.gov

* To whom correspondence should be addressed.
The GeneAround GO viewer
Authors: Tanoue Junko , Yoshikawa Masatoshi , Uemura Shunsuke
Published: December 2002

Summary: We have developed a system for visualizing the Gene Ontology™ hierarchy. The graphical browser interactively displays diagrams of the inheritance relationship for each term to help understand the meanings of terms when handling gene annotation data.

Availability: The GeneAround GO viewer is open to the public at http://db.aist-nara.ac.jp/genearound/

Contact: genearound@is.aist-nara.ac.jp

* To whom correspondence should be addressed at Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, JAPAN.
Finding Genes That Underlie Complex Traits
Authors: Glazier Anne M. , Nadeau Joseph H. , Aitman Timothy J.
Published: December 2002

Phenotypic variation among organisms is central to evolutionary adaptations underlying natural and artificial selection, and also determines individual susceptibility to common diseases. These types of complex traits pose special challenges for genetic analysis because of gene-gene and gene-environment interactions, genetic heterogeneity, low penetrance, and limited statistical power. Emerging genome resources and technologies are enabling systematic identification of genes underlying these complex traits. We propose standards for proof of gene discovery in complex traits and evaluate the nature of the genes identified to date. These proof-of-concept studies demonstrate the insights that can be expected from the accelerating pace of gene discovery in this field.
A Distinct Signaling Pathway Used by the IgG-Containing B Cell Antigen Receptor
Authors: Wakabayashi Chisato , Adachi Takahiro , Wienands Jürgen , Tsubata Takeshi
Published: December 2002

The immunoglobulin G (IgG)–containing B lymphocyte antigen receptor (IgG-BCR) transmits a signal distinct from that of IgM-BCR or IgD-BCR, although all three use the same signal-transducing component, Igα/Igβ. Here we demonstrate that the inhibitory coreceptor CD22 down-modulates signaling through IgM-BCR and IgD-BCR, but not that through IgG-BCR, because of the IgG cytoplasmic tail, which prevents CD22 phosphorylation. These results suggest that the cytoplasmic tail of IgG specifically enhances IgG-BCR signaling by preventing CD22-mediated signal inhibition. Enhanced signaling through IgG-BCR may be involved in efficient IgG production, which is crucial for immunity to pathogens.
Sir2-Dependent Activation of Acetyl-CoA Synthetase by Deacetylation of Active Lysine
Authors: Starai V. J. , Celic I. , Cole R. N. , Boeke J. D. , Escalante-Semerena J. C.
Published: December 2002

Acetyl-coenzyme A (CoA) synthetase (Acs) is an enzyme central to metabolism in prokaryotes and eukaryotes. Acs synthesizes acetyl CoA from acetate, adenosine triphosphate, and CoA through an acetyl–adenosine monophosphate (AMP) intermediate. Immunoblotting and mass spectrometry analysis showed that
Salmonella enterica
Acs enzyme activity is posttranslationally regulated by acetylation of lysine-609. Acetylation blocks synthesis of the adenylate intermediate but does not affect the thioester-forming activity of the enzyme. Activation of the acetylated enzyme requires the nicotinamide adenine dinucleotide–dependent protein deacetylase activity of the CobB Sir2 protein from
S. enterica.
We propose that acetylation modulates the activity of all the AMP-forming family of enzymes, including nonribosomal peptide synthetases, luciferase, and aryl- and acyl-CoA synthetases. These findings extend our knowledge of the roles of Sir2 proteins in gene silencing, chromosome stability, and cell aging and imply that lysine acetylation is a common regulatory mechanism in eukaryotes and prokaryotes.
Rates of Behavior and Aging Specified by Mitochondrial Function During Development
Authors: Dillin Andrew , Hsu Ao-Lin , Arantes-Oliveira Nuno , Lehrer-Graiwer Joshua , Hsin Honor , Fraser Andrew G. , Kamath Ravi S. , Ahringer Julie , Kenyon Cynthia
Published: December 2002

To explore the role of mitochondrial activity in the aging process, we have lowered the activity of the electron transport chain and adenosine 5′-triphosphate (ATP) synthase with RNA interference (RNAi) in
Caenorhabditis elegans.
These perturbations reduced body size and behavioral rates and extended adult life-span. Restoring messenger RNA to near-normal levels during adulthood did not elevate ATP levels and did not correct any of these phenotypes. Conversely, inhibiting respiratory-chain components during adulthood only did not reset behavioral rates and did not affect life-span. Thus, the developing animal appears to contain a regulatory system that monitors mitochondrial activity early in life and, in response, establishes rates of respiration, behavior, and aging that persist during adulthood.
Control of Facial Muscle Development by MyoR and Capsulin
Authors: Lu Jian-rong , Bassel-Duby Rhonda , Hawkins April , Chang Priscilla , Valdez Renee , Wu Hai , Gan Lin , Shelton John M. , Richardson James A. , Olson Eric N.
Published: December 2002

Members of the MyoD family of basic helix-loop-helix (bHLH) transcription factors control the formation of all skeletal muscles in vertebrates, but little is known of the molecules or mechanisms that confer unique identities to different types of skeletal muscles. MyoR and capsulin are related bHLH transcription factors expressed in specific facial muscle precursors. We show that specific facial muscles are missing in mice lacking both
MyoR
and
capsulin
, reflecting the absence of MyoD family gene expression and ablation of the corresponding myogenic lineages. These findings identify
MyoR
and
capsulin
as unique transcription factors for the development of specific head muscles.
Genetic Structure of Human Populations
Authors: Rosenberg Noah A. , Pritchard Jonathan K. , Weber James L. , Cann Howard M. , Kidd Kenneth K. , Zhivotovsky Lev A. , Feldman Marcus W.
Published: December 2002

We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.
NPAS2: A Gas-Responsive Transcription Factor
Authors: Dioum Elhadji M. , Rutter Jared , Tuckerman Jason R. , Gonzalez Gonzalo , Gilles-Gonzalez Marie-Alda , McKnight Steven L.
Published: December 2002

Neuronal PAS domain protein 2 (NPAS2) is a mammalian transcription factor that binds DNA as an obligate dimeric partner of BMAL1 and is implicated in the regulation of circadian rhythm. Here we show that both PAS domains of NPAS2 bind heme as a prosthetic group and that the heme status controls DNA binding in vitro. NPAS2-BMAL1 heterodimers, existing in either the apo (heme-free) or holo (heme-loaded) state, bound DNA avidly under favorably reducing ratios of the reduced and oxidized forms of nicotinamide adenine dinucleotide phosphate. Low micromolar concentrations of carbon monoxide inhibited the DNA binding activity of holo-NPAS2 but not that of apo-NPAS2. Upon exposure to carbon monoxide, inactive BMAL1 homodimers were formed at the expense of NPAS2-BMAL1 heterodimers. These results indicate that the heterodimerization of NPAS2, and presumably the expression of its target genes, are regulated by a gas through the heme-based sensor described here.
Formation of a One-Dimensional Array of Oxygen in a Microporous Metal-Organic Solid
Authors: Kitaura Ryo , Kitagawa Susumu , Kubota Yoshiki , Kobayashi Tatsuo C. , Kindo Koichi , Mita Yoshimi , Matsuo Akira , Kobayashi Michihiro , Chang Ho-Chol , Ozawa Tadashi C. , Suzuki Megumi , Sakata Makoto , Takata Masaki
Published: December 2002

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O
2
locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O–O stretching Raman band and magnetic susceptibilities are characteristic of the confined O
2
molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).
Oral Delivery ofMycobacterium bovisBCG in a Lipid Formulation Induces Resistance to Pulmonary Tuberculosis in Mice
Authors: Aldwell Frank E. , Tucker Ian G. , de Lisle Geoffrey W. , Buddle Bryce M.
Published: December 2002

A lipid-based formulation has been developed for oral delivery ofMycobacterium bovisbacille Calmette-Guérin (BCG) vaccine. The formulatedM. bovisBCG was fed to BALB/c mice to test for immune responses and protection againstM. bovisinfection. The immune responses included antigen-specific cytokine responses, spleen cell proliferation, and lymphocyte-mediated macrophage inhibition ofM. bovis. Oral delivery of formulatedM. bovisBCG to mice induced strong splenic gamma interferon levels and macrophage inhibition of virulentM. boviscompared with results with nonformulatedM. bovisBCG. Formulated oralM. bovisBCG significantly reduced the bacterial burden in the spleen and lungs of mice following aerosol challenge with virulentM. bovis. Our data suggest that oral delivery of formulatedM. bovisBCG is an effective means of inducing protective immune responses against tuberculosis. Lipid-based, orally delivered mycobacterial vaccines may be a safe and practical method of controlling tuberculosis in humans and animals.
Effective Induction of Acquired Resistance toListeria monocytogenesby Immunizing Mice with In Vivo-Infected Dendritic Cells
Authors: Sashinami Hiroshi , Nakane Akio , Iwakura Yoichiro , Sasaki Mutsuo
Published: December 2002

Splenic dendritic cells (DCs) obtained from mice at 48 h afterListeria monocytogenesinfection exhibited up-regulation of CD80 and produced higher titers of gamma interferon (IFN-γ) and interleukin-12 (IL-12) than did DCs obtained from uninfected mice. Mice immunized with DCs obtained from mice that had been infected withL. monocytogenes48 h before acquired host resistance to lethal infection withL. monocytogenesat 4 and 8 weeks. Immunization with DCs from heat-killedL. monocytogenesfailed to induce resistance. Acquired antilisterial resistance is specific, since the immunized mice could not be protected fromSalmonella entericaserovar Typhimurium infection. Infected DCs stimulated proliferation of naive CD4+and CD8+cells in vitro, suggesting that in vivo-infected DCs activate CD8+T cells, which are critical in acquired antilisterial resistance, as well as CD4+T cells. When wild-type mice were immunized with DCs from IFN-γ-deficient mice, they were protected against a lethalL. monocytogeneschallenge. In contrast, when mice were immunized with DCs from anti-IL-12 p40 monoclonal antibody-injected mice, they failed to gain acquired antilisterial resistance. These results suggest that DC-derived IL-12, but not IFN-γ, may play a critical role in induction of acquired antilisterial resistance. Our present results suggest that splenic DCs obtained from mice infected withL. monocytogenesin vivo may be an effective immunogen with which to induce antigen-specific immunity.
Pathogenicity and Immune Response Measured in Mice following Intranasal Challenge with EnterotoxigenicEscherichia coliStrains H10407 and B7A
Authors: Byrd Wyatt , Mog Steven R. , Cassels Frederick J.
Published: December 2002

The pathogenicity and immunogenicity induced in BALB/c mice by intranasal (i.n.) inoculation of enterotoxigenicEscherichia coli(ETEC) strains H10407 (O78:H11:CFA/I:LT+:ST+) and B7A (O148:H28:CS6:LT+:ST+) (two ETEC strains previously used in human challenge trials) were studied. The i.n. inoculation of BALB/c mice with large doses of ETEC strains H10407 and B7A caused illness and death. The H10407 strain was found to be consistently more virulent than the B7A strain. Following i.n. challenge with nonlethal doses of H10407 and B7A, the bacteria were cleared from the lungs of the mice at a steady rate over a 2-week period. Macrophages and neutrophils were observed in the alveoli and bronchioles, and lymphocytes were observed in the septa, around vessels, and in the pleura of the lungs in mice challenged with H10407 and B7A. In mice i.n. challenged with H10407, serum immunoglobulin G (IgG) and IgM antibodies were measured at high titers to the CFA/I and O78 lipopolysaccharide (LPS) antigens. In mice i.n. challenged with B7A, low serum IgG antibody titers were detected against CS6, and low serum IgG and IgM antibody titers were detected against O148 LPS. The serum IgG and IgM antibody titers against the heat-labile enterotoxin were equivalent in the H10407- and B7A-challenged mice. The CFA/I and O78 LPS antigens gave mixed T-helper cell 1-T-helper cell 2 (Th1-Th2) responses in which the Th2 response was greater than the Th1 response (i.e., stimulated primarily an antibody response). These studies indicate that the i.n. challenge of BALB/c mice with ETEC strains may provide a useful animal model to better understand the immunogenicity and pathogenicity of ETEC and its virulence determinants. This model may also be useful in providing selection criteria for vaccine candidates for use in primate and human trials.
The Hyaluronic Acid Capsule of
Streptococcus uberis
Is Not Required for the Development of Infection and Clinical Mastitis
Authors: Field Terence R. , Ward Philip N. , Pedersen Lars H. , Leigh James A.
Published: December 2002

The frequency at which the genes responsible for capsule biosynthesis occurred in field isolates of
Streptococcus uberis
was determined. Of the two genotypes detected (
hasABC
and
hasC
), the capsular genotype (
hasABC
) was more common. This genotype was present at a higher frequency in a population isolated from mastitis cases than in a population isolated from cattle bedding. The virulence of a mutant strain of
S. uberis
(TRF0-6) that lacked the ability to produce a hyaluronic acid capsule due to an insertion within its single copy of
hasA
(P. N. Ward, T. R. Field, W. G. F. Ditcham, E. Maguin, and J. A. Leigh, Infect. Immun.
69:
392-399, 2001) was compared to that of the capsular parental strain (0140J). Strains TRF0-6 and 0140J infected all mammary gland quarters following experimental challenge. The wild type and the mutant induced overt signs of disease in four out of four and in six out of eight mammary gland quarters, respectively. Both the wild type and the
hasA
mutant were resistant to killing by bovine neutrophils following cultivation in bovine milk. The ability to withstand the bactericidal action of neutrophils following growth in milk was therefore independent of the capsule and coincided with the ability of supernatants from such cultures to prevent the bactericidal action of neutrophils. This investigation revealed that, in the absence of the capsule,
S. uberis
is able to withstand the bactericidal effect of bovine neutrophils and induce mastitis in dairy cows.
Role of S-Layer Protein Antigenic Diversity in the Immune Responses of Sheep Experimentally Challenged with
Campylobacter fetus
subsp.
fetus
Authors: Grogono-Thomas R. , Blaser M. J. , Ahmadi M. , Newell D. G.
Published: December 2002

Surface layer proteins (SLPs) are essential for induction of abortion by
Campylobacter fetus
subsp.
fetus
in experimentally challenged ewes. These proteins are encoded by multiple
sap
genes and vary in size and antigenicity. The role of SLP antigenic variation during experimental ovine infection was investigated. Following subcutaneous challenge, the SLPs were highly antigenic, and antibodies were detected in serum, milk, bile, and urine. Fecal anti-SLP antibodies were detected only in animals challenged orally. Ewes challenged with wild-type strain 23D with variable SLPs developed detectable circulating anti-SLP immunoglobulin G (IgG) antibodies by 2 weeks postchallenge. In contrast, ewes challenged with mutants of 23D that had fixed expression of a single SLP developed antibodies within 1 week postchallenge, suggesting that antigenic variation in SLPs may delay the host antibody response. Although not statistically significant, the data from challenge experiments in which vaccinated ewes were used suggested that SLP-expressing vaccines could protect animals from abortion and that this effect was independent of the SLP expressed, indicating involvement of conserved epitopes in the SLP. The conserved 184-amino-acid N-terminal region of the SLP, identified from previously published sequences, was epitope mapped with rabbit anti-SLP antisera by using overlapping synthetic 20-mer peptides. Two putative epitopes were identified at amino acids 81 to 110 and 141 to 160. Amino acids 81 to 100 also bound serum IgG antibodies from experimentally challenged sheep. Conserved antigenic regions of the SLP that induce protective immune responses may enable development of synthetic vaccine candidates for
C. fetus
subsp.
fetus
-associated ovine abortion.
Two-Component Systems in
Haemophilus influenzae
: a Regulatory Role for ArcA in Serum Resistance
Authors: De Souza-Hart J. A. , Blackstock W. , Di Modugno V. , Holland I. B. , Kok M.
Published: December 2002

Knockout mutations were constructed in the
arcA
gene of a virulent type b strain of
Haemophilus influenzae
, and the behavior of the resulting mutants was investigated in a number of conditions that mimicked distinct steps in the natural infection pathway. In
arcA
mutants, synthesis of capsule and lipooligosaccharide (LOS) and growth in synthetic media were unaltered compared to synthesis of capsule and LOS and growth in synthetic media in the wild-type
H. influenzae
type b parent strain. However, the virulence of the
arcA
mutants for BALB/c mice was significantly reduced. Upon exposure to human blood or serum, the
arcA
mutants showed markedly reduced survival compared with the survival of its wild-type parent. Serum resistance could be fully restored by complementation in
cis
with the
H. influenzae arcA
gene but not by complementation in
cis
with the homologous gene from
Escherichia coli
. The proteomes of wild-type and mutant bacteria were markedly different, especially under anaerobic conditions, underscoring the global regulatory role of ArcAB in
H. influenzae
. Evaluation of antibody titers and classical complement activities in various serum samples pointed to complement-mediated bactericidal activity as the factor that distinguishes between the
arcA
mutant and wild-type phenotypes. Comparative analysis of the membrane fractions of the
arcA
mutants and the wild-type strain revealed several ArcA-regulated proteins, some of which may be implicated in the serum hypersensitivity phenotype.
4-1BB (CD137) Differentially Regulates Murine In Vivo Protein- and Polysaccharide-Specific Immunoglobulin Isotype Responses toStreptococcus pneumoniae
Authors: Wu Zheng-Qi , Khan Abdul Q. , Shen Yi , Wolcott Karen M. , Dawicki Wojciech , Watts Tania H. , Mittler Robert S. , Snapper Clifford M.
Published: December 2002

4-1BB (CD137) is induced on activated CD4+and CD8+T cells and delivers a costimulatory signal upon binding the 4-1BB ligand (4-1BBL) expressed on antigen-presenting cells. Induction of 4-1BB is dependent on activation via the T-cell receptor (TCR) and possibly CD28. It was previously demonstrated that both an in vivo protein (pneumococcal surface protein A [PspA])- and polysaccharide (phosphorylcholine [PC] determinant of teichoic acid)-specific immunoglobulin (Ig) isotype response toStreptococcus pneumoniaewas dependent on CD4+TCRαβ+T cells and B7-dependent costimulation through CD28. We thus postulated that 4-1BB costimulation would also play a role in regulating the in vivo anti-PspA and anti-PC response toS. pneumoniae. We demonstrate that mice genetically deficient in 4-1BBL elicit a markedly reduced IgM and IgG anti-PC but normal primary and secondary IgG anti-PspA responses toS. pneumoniaerelative to those for wild-type mice. However, injection of an agonistic anti-4-1BB monoclonal antibody (MAb), while having no significant effect on the anti-PC response, strongly inhibits the primary anti-PspA response, the generation of PspA-specific memory, and germinal center formation but does not induce a lasting state of tolerance. In contrast, anti-4-1BB MAb has no effect on the anti-PspA response when injected only at the time of secondary immunization. Delay of the addition of anti-4-1BB leads to progressively less inhibition of the primary response up to day 8. This inhibition is independent of CD8+T cells and is associated with the expansion of CD4+T cells with an activated phenotype, which is partly dependent on B7-dependent costimulation. These data are the first to suggest a stimulatory role for endogenous 4-1BB-4-1BBL interactions during a humoral immune response to a pathogen and further underscore significant differences in costimulation requirements for an in vivo protein- versus polysaccharide-specific Ig isotype response to an extracellular bacterium.