bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-based clustering and data transformations for gene
expression data
Authors: Yeung K. Y. , Fraley C. , Murua A. , Raftery A. E. , Ruzzo W. L. 
Published: September 2002

Abstract
Motivation: Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particular, model-based clustering assumes that the data is generated by a finite mixture of underlying probability distributions such as multivariate normal distributions. The issues of selecting a ‘good’ clustering method and determining the ‘correct’ number of clusters are reduced to model selection problems in the probability framework. Gaussian mixture models have been shown to be a powerful tool for clustering in many applications.
Results: We benchmarked the performance of model-based clustering on several synthetic and real gene expression data sets for which external evaluation criteria were available. The model-based approach has superior performance on our synthetic data sets, consistently selecting the correct model and the number of clusters. On real expression data, the model-based approach produced clusters of quality comparable to a leading heuristic clustering algorithm, but with the key advantage of suggesting the number of clusters and an appropriate model. We also explored the validity of the Gaussian mixture assumption on different transformations of real data. We also assessed the degree to which these real gene expression data sets fit multivariate Gaussian distributions both before and after subjecting them to commonly used data transformations. Suitably chosen transformations seem to result in reasonable fits.
Availability: Mclust is available at http://www.stat.washington.edu/fraley/mclust. The software for the diagonal model is under development.
Contact: kayee@cs.washington.edu
Supplementary information: http://www.cs.washington.edu/homes/kayee/model
* To whom all correspondence should be addressed.
PIRA PCR designer for restriction analysis of single nucleotide
polymorphisms
Authors: Ke Xiayi , Collins Andrew , Ye Shu 
Published: September 2002

Abstract
Summary: Primer-introduced restriction analysis (PIRA-PCR) is widely used to detect Single Nucleotide Polymorphisms (SNPs). To create artificial Restriction Fragment Length Polymorphism (RFLP), a mismatch is usually introduced near the \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(3{^\prime}\) \end{document}end of the primer that is close to the mutation of interest. We describe in this report a www-based computer program that screens for the suitable mismatches, designs the primers, lists the appropriate restriction enzymes and other related information.
Availability: The computer program, with related descriptions, is available at http://cedar.genetics.soton.ac.uk/public_html/primer2.html.
Contact: xke@soton.ac.uk
InterProScan – an integration platform for the
signature-recognition methods in InterPro
Authors: Zdobnov Evgeni M. , Apweiler Rolf 
Published: September 2002

Abstract
Summary: InterProScan is a tool that scans given protein sequences against the protein signatures of the InterPro member databases, currently – PROSITE, PRINTS, Pfam, ProDom and SMART. The number of signature databases and their associated scanning tools as well as the further refinement procedures make the problem complex. InterProScan is designed to be a scalable and extensible system with a robust internal architecture.
Availability: The Perl-based InterProScan implementation is available from the EBI ftp server (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request. We provide the public web interface (http://www.ebi.ac.uk/interpro/scan.html) as well as email submission server (interproscan@ebi.ac.uk).
Contact: Evgueni.Zdobnov@EBI.ac.uk
* To whom correspondence should be addressed.
BioLayout—an automatic graph layout algorithm for
similarity visualization
Authors: Enright Anton J. , Ouzounis Christos A. 
Published: September 2002

Abstract
Summary: Graph layout is extensively used in the field of mathematics and computer science, however these ideas and methods have not been extended in a general fashion to the construction of graphs for biological data. To this end, we have implemented a version of the Fruchterman Rheingold graph layout algorithm, extensively modified for the purpose of similarity analysis in biology. This algorithm rapidly and effectively generates clear two (2D) or three-dimensional (3D) graphs representing similarity relationships such as protein sequence similarity. The implementation of the algorithm is general and applicable to most types of similarity information for biological data.
Availability: BioLayout is available for most UNIX platforms at the following web-site: http://www.ebi.ac.uk/research/cgg/services/layout
Contact: enright@ebi.ac.uk
Why are complementary DNA strands symmetric?
Authors: Baisnée Pierre-François , Hampson Steve , Baldi Pierre 
Published: September 2002

Abstract
Motivation: Over sufficiently long windows, complementary strands of DNA tend to have the same base composition. A few reports have indicated that this first-order parity rule extends at higher orders to oligonucleotide composition, at least in some organisms or taxa. However, the scientific literature falls short of providing a comprehensive study of reverse-complement symmetry at multiple orders and across the kingdom of life. It also lacks a characterization of this symmetry and a convincing explanation or clarification of its origin.
Results: We develop methods to measure and characterize symmetry at multiple orders, and analyze a wide set of genomes, encompassing single- and double-stranded RNA and DNA viruses, bacteria, archae, mitochondria, and eukaryota. We quantify symmetry at orders 1 to 9 for contiguous sequences and pools of coding and non-coding upstream regions, compare the observed symmetry levels to those predicted by simple statistical models, and factor out the effect of lower-order distributions. We establish the universality and variability range of first-order strand symmetry, as well as of its higher-order extensions, and demonstrate the existence of genuine high-order symmetric constraints. We show that ubiquitous reverse-complement symmetry does not result from a single cause, such as point mutation or recombination, but rather emerges from the combined effects of a wide spectrum of mechanisms operating at multiple orders and length scales.
Contact: baisnee@ics.uci.eduhampson@ics.uci.edupfbaldi@ics.uci.edu
Data: http://promoter.ics.uci.edu/RevCompSym/
* To whom correspondence should be addressed.
Tagging gene and protein names in biomedical text
Authors: Tanabe Lorraine , Wilbur W. John 
Published: September 2002

Abstract
Motivation: The MEDLINE database of biomedical abstracts contains scientific knowledge about thousands of interacting genes and proteins. Automated text processing can aid in the comprehension and synthesis of this valuable information. The fundamental task of identifying gene and protein names is a necessary first step towards making full use of the information encoded in biomedical text. This remains a challenging task due to the irregularities and ambiguities in gene and protein nomenclature. We propose to approach the detection of gene and protein names in scientific abstracts as part-of-speech tagging, the most basic form of linguistic corpus annotation.
Results: We present a method for tagging gene and protein names in biomedical text using a combination of statistical and knowledge-based strategies. This method incorporates automatically generated rules from a transformation-based part-of-speech tagger, and manually generated rules from morphological clues, low frequency trigrams, indicator terms, suffixes and part-of-speech information. Results of an experiment on a test corpus of 56K MEDLINE documents demonstrate that our method to extract gene and protein names can be applied to large sets of MEDLINE abstracts, without the need for special conditions or human experts to predetermine relevant subsets.
Availability: The programs are available on request from the authors.
Contact: tanabe@ncbi.nlm.nih.gov
TFBS: Computational framework for transcription factor binding site analysis
Authors: Lenhard Boris , Wasserman Wyeth W. 
Published: September 2002

Abstract
Motivation: TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system.
Availability and Supplementary Information: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/
Contact: Boris.Lenhard@cgb.ki.se
* To whom correspondence should be addressed.
Multiple Deletions of the Osmolyte Transporters BetL, Gbu, and OpuC of
Listeria monocytogenes
Affect Virulence and Growth at High Osmolarity
Authors: Wemekamp-Kamphuis Henrike H. , Wouters Jeroen A. , Sleator Roy D. , Gahan Cormac G. M. , Hill Colin , Abee Tjakko 
Published: September 2002

ABSTRACT

The success of
Listeria monocytogenes
as a food-borne pathogen owes much to its ability to survive a variety of stresses, both in the food environment and, after ingestion, within the animal host. Growth at high salt concentrations is attributed mainly to the accumulation of organic solutes such as glycine betaine and carnitine. We characterized
L. monocytogenes
LO28 strains with single, double, and triple deletions in the osmolyte transport systems BetL, Gbu, and OpuC. When single deletion mutants were tested, Gbu was found to have the most drastic effect on the rate of growth in brain heart infusion (BHI) broth with 6% added NaCl. The highest reduction in growth rate was found for the triple mutant LO28BCG (Δ
betL
Δ
opuC
Δ
gbu
), although the mutant was still capable of growth under these adverse conditions. In addition, we analyzed the growth and survival of this triple mutant in an animal (murine) model. LO28BCG showed a significant reduction in its ability to cause systemic infection following peroral coinoculation with the wild-type parent. Altering OpuC alone resulted in similar effects (R. D. Sleator, J. Wouters, C. G. M. Gahan, T. Abee, and C. Hill, Appl. Environ. Microbiol. 67:2692-2698, 2001), leading to the assumption that OpuC may play an important role in listerial pathogenesis. Analysis of the accumulation of osmolytes revealed that betaine is accumulated up to 300 μmol/g (dry weight) when grown in BHI broth plus 6% NaCl whereas no carnitine accumulation could be detected. Radiolabeled-betaine uptake studies revealed an inability of BGSOE (Δ
betL
Δ
gbu
) and LO28BCG to transport betaine. Indeed, for LO28BCG, no accumulated betaine was found, but carnitine was accumulated in this strain up to 600 μmol/g (dry weight) of cells, indicating the presence of a possible fourth osmolyte transporter.
Fourier-Transform Infrared Microspectroscopy, a Novel and Rapid Tool for Identification of Yeasts
Authors: Wenning Mareike , Seiler Herbert , Scherer Siegfried 
Published: September 2002

ABSTRACT

Fourier-transform infrared (FT-IR) microspectroscopy was used in this study to identify yeasts. Cells were grown to microcolonies of 70 to 250 μm in diameter and transferred from the agar plate by replica stamping to an IR-transparent ZnSe carrier. IR spectra of the replicas on the carrier were recorded using an IR microscope coupled to an IR spectrometer, and identification was performed by comparison to reference spectra. The method was tested by using small model libraries comprising reference spectra of 45 strains from 9 genera and 13 species, recorded with both FT-IR microspectroscopy and FT-IR macrospectroscopy. The results show that identification by FT-IR microspectroscopy is equivalent to that achieved by FT-IR macrospectroscopy but the time-consuming isolation of the organisms prior to identification is not necessary. Therefore, this method also provides a rapid tool to analyze mixed populations. Furthermore, identification of 21
Debaryomyces hansenii
and 9
Saccharomyces cerevisiae
strains resulted in 92% correct identification at the strain level for
S. cerevisiae
and 91% for
D. hansenii
, which demonstrates that the resolution power of FT-IR microspectroscopy may also be used for yeast typing at the strain level.
Engineering of Primary Carbon Metabolism for Improved Antibiotic Production in
Streptomyces lividans
Authors: Butler Michael J. , Bruheim Per , Jovetic Srdjan , Marinelli Flavia , Postma Pieter W. , Bibb Mervyn J. 
Published: September 2002

ABSTRACT

Deletions were made in
Streptomyces lividans
in either of two genes (
zwf1
and
zwf2
) encoding isozymes of glucose-6-phosphate dehydrogenase, the first enzyme in the oxidative pentose phosphate pathway (PPP). Each mutation reduced the level of Zwf activity to approximately one-half that observed in the wild-type strain. When the mutants were transformed with multicopy plasmids carrying the pathway-specific transcriptional activator genes for either the actinorhodin (ACT) or undecylprodigiosin (RED) biosynthetic pathway, they produced higher levels of antibiotic than the corresponding wild-type control strains. The presumed lower flux of carbon through the PPP in each of the Δ
zwf
mutants may allow more efficient glucose utilization via glycolysis, resulting in higher levels of antibiotic production. This appears to occur without lowering the concentration of NADPH (the major biochemical product of the oxidative PPP activity) to a level that would limit antibiotic biosynthesis. Consistent with this hypothesis, deletion of the gene (
devB
) encoding the enzyme that catalyzes the next step in the oxidative PPP (6-phosphogluconolactonase) also resulted in increased antibiotic production. However, deletion of both
zwf
genes from the
devB
mutant resulted in reduced levels of ACT and RED production, suggesting that some of the NADPH made by the PPP is utilized, directly or indirectly, for antibiotic biosynthesis. Although applied here to the model antibiotics ACT and RED, such mutations may prove to be useful for improving the yield of commercially important secondary metabolites.
Relationship between Bacterial Community Composition and Bottom-Up versus Top-Down Variables in Four Eutrophic Shallow Lakes
Authors: Muylaert Koenraad , Van der Gucht Katleen , Vloemans Nele , Meester Luc De , Gillis Moniek , Vyverman Wim 
Published: September 2002

ABSTRACT

Bacterial community composition was monitored in four shallow eutrophic lakes during one year using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified prokaryotic rDNA genes. Of the four lakes investigated, two were of the clearwater type and had dense stands of submerged macrophytes while two others were of the turbid type characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had high nutrient levels (total phosphorus, >100 μg liter
−1
) while the other lakes had relatively low nutrient levels (total phosphorus, <100 μg liter
−1
). For each lake, seasonal changes in the bacterial community were related to bottom-up (resources) and top-down (grazers) variables by using canonical correspondence analysis (CCA). Using an artificial model dataset to which potential sources of error associated with the use of relative band intensities in DGGE analysis were added, we found that preferential amplification of certain rDNA genes over others does not obscure the relationship between bacterial community composition and explanatory variables. Besides, using this artificial dataset as well as our own data, we found a better correlation between bacterial community composition and explanatory variables by using relative band intensities compared to using presence/absence data. While bacterial community composition was related to phytoplankton biomass in the high-nutrient lakes no such relation was found in the low-nutrient lakes, where the bacterial community is probably dependent on other organic matter sources. We used variation partitioning to evaluate top-down regulation of bacterial community composition after bottom-up regulation has been accounted for. Using this approach, we found no evidence for top-down regulation of bacterial community composition in the turbid lakes, while grazing by ciliates and daphnids (
Daphnia
and
Ceriodaphnia
) was significantly related to changes in the bacterial community in the clearwater lakes. Our results suggest that in eutrophic shallow lakes, seasonality of bacterial community structure is dependent on the dominant substrate source as well as on the food web structure.
Growth at Low Ammonium Concentrations and Starvation Response as Potential Factors Involved in Niche Differentiation among Ammonia-Oxidizing Bacteria
Authors: Bollmann Annette , Bär-Gilissen Marie-José , Laanbroek Hendrikus J. 
Published: September 2002

ABSTRACT

In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with
Nitrosomonas europaea
suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with
N. europaea
and the ammonia oxidizer G5-7, a close relative of
Nitrosomonas oligotropha
belonging to
Nitrosomonas
cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of
N. europaea
. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete
N. europaea
at growth-limiting substrate concentrations of about 10 μM ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However,
N. europaea
displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation,
N. europaea
became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The
Nitrosomonas
cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of
N. europaea
, belonging to
Nitrosomonas
cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of
N. europaea
to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.
Differences in Attachment of
Salmonella enterica
Serovars and
Escherichia coli
O157:H7 to Alfalfa Sprouts
Authors: Barak J. D. , Whitehand L. C. , Charkowski A. O. 
Published: September 2002

ABSTRACT

Numerous
Salmonella enterica
and
Escherichia coli
O157:H7 outbreaks have been associated with contaminated sprouts. We examined how
S. enterica
serovars,
E. coli
serotypes, and nonpathogenic bacteria isolated from alfalfa sprouts grow on and adhere to alfalfa sprouts. Growth on and adherence to sprouts were not significantly different among different serovars of
S. enterica
, but all
S. enterica
serovars grew on and adhered to alfalfa sprouts significantly better than
E. coli
O157:H7.
E. coli
O157:H7 was essentially rinsed from alfalfa sprouts with repeated washing steps, while 1 to 2 log CFU of
S. enterica
remained attached per sprout.
S. enterica
Newport adhered to 3-day-old sprouts as well as
Pantoea agglomerans
and 10-fold more than
Pseudomonas putida
and
Rahnella aquatilis
, whereas the growth rates of all four strains throughout seed sprouting were similar.
S. enterica
Newport and plant-associated bacteria adhered 10- to 1,000-fold more than
E. coli
O157:H7; however, three of four other
E. coli
serotypes, isolated from cabbage roots exposed to sewage water following a spill, adhered to sprouts better than
E. coli
O157:H7 and as well as the
Pseudomonas
and
Rahnella
strains. Therefore, attachment to alfalfa sprouts among
E. coli
serotypes is variable, and nonpathogenic strains of
E. coli
to be used as surrogates for the study of pathogenic
E. coli
may be difficult to identify and should be selected carefully, with knowledge of the biology being examined.
Cloning, Sequencing, and Characterization of the Hexahydro-1,3,5-Trinitro-1,3,5-Triazine Degradation Gene Cluster from
Rhodococcus rhodochrous
Authors: Seth-Smith Helena M. B. , Rosser Susan J. , Basran Amrik , Travis Emma R. , Dabbs Eric R. , Nicklin Steve , Bruce Neil C. 
Published: September 2002

ABSTRACT

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive which presents an environmental hazard as a major land and groundwater contaminant.
Rhodococcus rhodochrous
strain 11Y was isolated from explosive contaminated land and is capable of degrading RDX when provided as the sole source of nitrogen for growth. Products of RDX degradation in resting-cell incubations were analyzed and found to include nitrite, formaldehyde, and formate. No ammonium was excreted into the medium, and no dead-end metabolites were observed. The gene responsible for the degradation of RDX in strain 11Y is a constitutively expressed cytochrome P450-like gene,
xplA
, which is found in a gene cluster with an adrenodoxin reductase homologue,
xplB
. The cytochrome P450 also has a flavodoxin domain at the N terminus. This study is the first to present a gene which has been identified as being responsible for RDX biodegradation. The mechanism of action of XplA on RDX is thought to involve initial denitration followed by spontaneous ring cleavage and mineralization.
Simultaneous Fluorescent Gram Staining and Activity Assessment of Activated Sludge Bacteria
Authors: Forster Scott , Snape Jason R. , Lappin-Scott Hilary M. , Porter Jonathan 
Published: September 2002

ABSTRACTWastewater treatment is one of the most important commercial biotechnological processes, and yet the component bacterial populations and their associated metabolic activities are poorly understood. The novel fluorescent dye hexidium iodide allows assessment of Gram status by differential absorption through bacterial cell walls. Differentiation between gram-positive and gram-negative wastewater bacteria was achieved after flow cytometric analysis. This study shows that the relative proportions of gram-positive and gram-negative bacterial cells identified by traditional microscopy and hexidium iodide staining were not significantly different. Dual staining of cells for Gram status and activity proved effective in analyzing mixtures of cultured bacteria and wastewater populations. Levels of highly active organisms at two wastewater treatment plants, both gram positive and gram negative, ranged from 1.5% in activated sludge flocs to 16% in the activated sludge fluid. Gram-positive organisms comprised <5% of the total bacterial numbers but accounted for 19 and 55% of the highly active organisms within flocs at the two plants. Assessment of Gram status and activity within activated sludge samples over a 4-day period showed significant differences over time. This method provides a rapid, quantitative measure of Gram status linked with in situ activity within wastewater systems.