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At least 1,171 records · Page 65Linked to original sources
PubMed2004

Identification of novel pathogenicity genes by PCR signature-tagged mutagenesis and related technologies.

Microbial pathogens possess a repertoire of virulence determinants that make unique contributions to bacterial fitness during infection. In this chapter, we focus on the recent progress and adaptations of signature-tagged mutagenesis (STM) by PCR instead of hybridization. This is a PCR-based STM mutation-based screening method using a population of bacterial mutants for the simultaneous identification of multiple virulence genes in microbial pathogens by negative selection. Modifications of STM developed in our laboratory have been applied to Pseudomonas aeruginosa PAO1. Screening of a collection of 6912 STM mutants in the rat chronic lung model of infection identified 214 P. aeruginosa STM mutants defective in virulence. For further studies, and to illustrate better the strategies that need to be utilized, we present detailed analysis of nine selected STM mutants. The data obtained indicate that in vivo, defects in virulence give a wide variety of phenotypes: defects in known virulence factors have been found, thereby validating the method; defects have also been found in orthologs with predicted functions, and in some genes whose functions cannot be predicted from databases. A general strategy and a simple scenario is discussed using the nine STM mutants selected for further characterization. PCR-based STM represent a genomics-based method for in vivo high-throughput screening of new virulence factors.

Bacteria↗
PubMed2006

Massively parallel signature sequencing.

Massively parallel signature sequencing is an ultra-high throughput sequencing technology. It can simultaneously sequence millions of sequence tags, and, therefore, is ideal for whole genome analysis. When applied to expression profiling, it reveals almost every transcript in the sample and provides its accurate expression level. This chapter describes the technology and its application in establishing stem cell transcriptome databases.

Cell Culture Techniques↗
PubMed2005

A distinctive molecular signature of multiple sclerosis derived from MALDI-TOF/MS and serum proteomic pattern analysis: detection of three biomarkers.

Although multiple sclerosis (MS) is an immune-mediated disorder, serological testing to aid in its diagnosis has not been developed. To test the hypothesis that the pathological changes in MS can be detected by analyzing a molecular signature of serum proteomic patterns, we tested sera from 25 newly diagnosed relapsing-remitting MS patients and 25 healthy controls with matrix-assisted laser desorption/ ionization time of flight (MALDI-TOF) mass spectrometry, following albumin depletion and desalting. Analysis of MALDI-TOF/mass spectrometry data, using proteomic spectral pattern recognition software, revealed a distinct proteomic pattern in the MS group determined by 3 biomarkers at 8687, 8773, and 8818 mass-to-charge ratios. Although our data are representative of analysis on a small number of samples and are preliminary, we conclude that MALDI-TOF/mass spectrometry, in combination with serum proteomic pattern analysis, could be useful in the diagnosis of MS, and a larger, masked trial to identify proteomic spectral patterns characteristic of relapsing-remitting, primary progressive and secondary progressive variants of MS is justified.

Biomarkers↗
PubMed2005

Expressed genome molecular signatures of heart failure.

Traditional gene expression studies typically focus on one or a few genes of interest. An important limitation of single-gene studies is that they present a portrait of disease that is essentially static. However, disease is a dynamic process, driven by a combination of genetic, epigenetic and environmental factors. Recently, genomic technologies have permitted better characterization of the dynamic aspect of disease progression. Genome-wide expression profiles of cardiovascular diseases, heart failure in particular, using microarrays have been published and are providing new insights into this complex disease. Tissue biopsies required for traditional microarray studies, however, are often invasive and not readily available. By contrast, blood samples are relatively non-invasive and are readily available. In a number of recent studies, blood cells appear to be a viable substitute for tissue biopsy. Blood cells have the ability to mirror the body's tissues and organs in health and disease; thus, we hypothesize that blood cells can indicate at the molecular level the presence of disease. Here we review microarray gene expression profiling of blood RNA for a number of different diseases. Sieving through gene expression molecular signatures has identified groups of genes characteristic of each and has identified biomarkers associated with specific diseases.

Expressed Sequence Tags↗
PubMed2004

Memory reconsolidation and extinction have distinct temporal and biochemical signatures.

Memory retrieval is not a passive phenomenon. Instead, it triggers a number of processes that either reinforce or alter stored information. Retrieval is thought to activate a second memory consolidation cascade (reconsolidation) that requires protein synthesis. Here, we show that the temporal dynamics of memory reconsolidation are dependent on the strength and age of the memory, such that younger and weaker memories are more easily reconsolidated than older and stronger memories. We also report that reconsolidation and extinction, two opposing processes triggered by memory retrieval, have distinct biochemical signatures: pharmacological antagonism of either cannabinoid receptor 1 or L-type voltage-gated calcium channels blocks extinction but not reconsolidation. These studies demonstrate the dynamic nature of memory processing after retrieval and represent a first step toward a molecular dissection of underlying mechanisms.

Animals↗
PubMed2004

Molecular signatures of lymphoma.

Hematologic malignancies have historically been characterized by morphologic, immunophenotypic, molecular, and genetic features. However, morphologically identical tumors can have clearly distinct clinical outcomes, suggesting underlying biological heterogeneity. Recent advances in microarray technology have helped the classification of lymphoid malignancies evolve to a new refined level. In addition to the discovery of new disease subclasses defined by unique molecular profiles, gene expression patterns can be correlated with specific genetic abnormalities and prognoses. Furthermore, the discovery of new disease subtypes has provided further insight into lymphoma biology and pathogenesis. Unique gene signatures can highlight key deregulated pathways that are active in molecular disease categories, and in some cases these findings have elucidated new targets for novel therapeutic approaches. This review summarizes the current status of molecular profiling in non-Hodgkin lymphomas. In this review, we have endeavored to include data from multiple investigator groups and tried to cover the breadth of lymphoid tumors, excluding acute and chronic leukemias.

Biomarkers, Tumor↗
PubMed2006

Signatures of demographic history and natural selection in the human major histocompatibility complex Loci.

Many lines of evidence show that several HLA loci have experienced balancing selection. However, distinguishing among demographic and selective explanations for patterns of variation observed with HLA genes remains a challenge. In this study we address this issue using data from a diverse set of human populations at six classical HLA loci and, employing a comparative genomics approach, contrast results for HLA loci to those for non-HLA markers. Using a variety of analytic methods, we confirm and extend evidence for selection acting on several HLA loci. We find that allele frequency distributions for four of the six HLA loci deviate from neutral expectations and show that this is unlikely to be explained solely by demographic factors. Other features of HLA variation are explained in part by demographic history, including decreased heterozygosity and increased LD for populations at greater distances from Africa and a similar apportionment of genetic variation for HLA loci compared to putatively neutral non-HLA loci. On the basis of contrasts among different HLA loci and between HLA and non-HLA loci, we conclude that HLA loci bear detectable signatures of both natural selection and demographic history.

Evolution, Molecular↗
PubMed2007

Arrayed identification of DNA signatures.

Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium system from Illumina and the Affymetrix GeneChips are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine re-sequencing of human genomes as a tool for personalized medicine, however, remain to be developed.

Base Sequence↗
PubMed2006

Chemical signature of two Permian volcanic ash deposits within a bentonite bed from Melo, Uruguay.

A Permian bentonite deposit at Melo, Uruguay is composed of a calcite-cemented sandstone containing clay pseudomorphs of glass shards (0-0.50 m) overlying a pink massive clay deposit (0.50-2.10 m). The massive bed is composed of two layers containing quartz and smectite or pure smectite respectively. The smectite is remarkably homogeneous throughout the profile: it is a complex mixed layer composed of three layer types whose expandability with ethylene glycol (2EG 1EG or 0EG sheets in the interlayer zone which correspond to low-, medium- and high-charge layers respectively) varies with the cation saturating the interlayer zone. The smectite homogeneity through the profile is the signature of an early alteration process in a lagoonal water which was over saturated with respect to calcite. Compaction during burial has made the bentonite bed a K-depleted closed system in which diagenetic illitization was inhibited. Variations in major, REE and minor element abundances throughout the massive clay deposit suggest that it originated from two successive ash falls. The incompatible element abundances are consistent with that of a volcanic glass fractionated from a rhyolite magma formed in a subduction/collision geological context.

Journal Article↗
PubMed2006

An epidermal neural crest stem cell (EPI-NCSC) molecular signature.

Here, we report the first transcriptome for mouse epidermal neural crest stem cells (EPI-NCSC, formerly eNCSCs). In addition, our study resolves conflicting opinions in the literature by showing that EPI-NCSC are distinct from other types of skin-resident stem cells/progenitors. Finally, with the three gene profiles, we have established a foundation and provide a valuable resource for future mouse NCSC research. EPI-NCSC represent a novel type of multipotent adult stem cell that originates from the embryonic neural crest and resides in the bulge of hair follicles. We performed gene profiling by LongSAGE (long serial analysis of gene expression) with mRNA from EPI-NCSC, embryonic NCSC, and in vitro differentiated embryonic neural crest progeny. We have identified important differentially expressed genes, including novel genes and disease genes. Furthermore, using stringent criteria, we have defined an NCSC molecular signature that consists of a panel of 19 genes and is representative of both EPI-NCSC and NCSC. EPI-NCSC have characteristics that combine advantages of embryonic and adult stem cells. Similar to embryonic stem cells, EPI-NCSC have a high degree of innate plasticity, they can be isolated at high levels of purity, and they can be expanded in vitro. Similar to other types of adult stem cell, EPI-NCSC are readily accessible by minimal invasive procedure. Multipotent adult mammalian stem cells are of great interest because of their potential value in future cell replacement therapy by autologous transplantation, which avoids graft rejection.

Animals↗
PubMed2005

Tetrahydrogestrinone induces a genomic signature typical of a potent anabolic steroid.

Tetrahydrogestrinone (THG) is a recently identified compound having the greatest impact in the world of sports. In order to obtain a highly accurate and sensitive assessment of the potential anabolic/androgenic activity of THG, we have used microarrays to identify its effect on the expression of practically all the 30,000 genes in the mouse genome and compared it with the effect of dihydrotestosterone (DHT), the most potent natural androgen. Quite remarkably, we found that 671 of the genes modulated by THG in the mouse muscle levator ani are modulated in a similar fashion by DHT, while in the gastrocnemius muscle and prostate, 95 and 939 genes respectively, are modulated in common by the two steroids. On the other hand, THG is more potent than DHT in binding to the androgen receptor, while, under in vivo conditions, THG possesses 20% of the potency of DHT in stimulating prostate, seminal vesicle and levator ani muscle weight in the mouse. The present microarray data provide an extremely precise and unquestionable signature of the androgenic/anabolic activity of THG, an approach which should apply to the analysis of the activity of any anabolic steroid.

Anabolic Agents↗
PubMedDate not supplied

Microarray analyses of peripheral blood cells identifies unique gene expression signature in psoriatic arthritis.

Psoriatic arthritis (PsA) is a chronic and erosive form of arthritis of unknown cause. We aimed to characterize the PsA phenotype using gene expression profiling and comparing it with healthy control subjects and patients rheumatoid arthritis (RA). Peripheral blood cells (PBCs) of 19 patients with active PsA and 19 age- and sex-matched control subjects were used in the analyses of PsA, with blood samples collected in PaxGene tubes. A significant alteration in the pattern of expression of 313 genes was noted in the PBCs of PsA patients on Affymetrix U133A arrays: 257 genes were expressed at reduced levels in PsA, and 56 genes were expressed at increased levels, compared with controls. Downregulated genes tended to cluster to certain chromosomal regions, including those containing the psoriasis susceptibility loci PSORS1 and PSORS2. Among the genes with the most significantly reduced expression were those involved in downregulation or suppression of innate and acquired immune responses, such as SIGIRR, STAT3, SHP1, IKBKB, IL-11RA, and TCF7, suggesting inappropriate control that favors proin-flammatory responses. Several members of the MAPK signaling pathway and tumor suppressor genes showed reduced expression. Three proinflammatory genes--S100A8, S100A12, and thioredoxin--showed increased expression. Logistic regression and recursive partitioning analysis determined that one gene, nucleoporin 62 kDa, could correctly classify all controls and 94.7% of the PsA patients. Using a dataset of 48 RA samples for comparison, the combination of two genes, MAP3K3 followed by CACNA1S, was enough to correctly classify all RA and PsA patients. Thus, PBC gene expression profiling identified a gene expression signature that differentiated PsA from RA, and PsA from controls. Several novel genes were differentially expressed in PsA and may prove to be diagnostic biomarkers or serve as new targets for the development of therapies.

Adult↗
PubMed2003

Computational methods for sequence mapping of large combinatorial libraries and deduced sequence signatures.

Here we describe a computational approach for the high-throughput sequence mapping of combinatorial libraries obtained by DNA shuffling. Original algorithms and their software implementation were developed for the automated and reliable analysis of hybridization data of differentially labeled oligonucleotide probes with PCR products spotted on DNA microarrays. This novel approach allows a context-dependent sequence attribution tolerant to fluctuations in experimental conditions and is well adapted to hybridization signals of variable qualities resulting from high-throughput PCR amplification from colonies. In addition, the analysis permits the calculation of sequence signatures that are characteristic of combinatorial library structure, defects, and diversity. The approach is of interest for the characterization and the equalization (library reduction to nonredundant structures) of combinatorial libraries involved in directed evolution and could be extrapolated to high-throughput polymorphism analysis.

Biotechnology↗
PubMed1996

Generation of sequence signatures from DNA amplification fingerprints with mini-hairpin and microsatellite primers.

DNA amplification fingerprinting (DAF) with mini-hairpins harboring arbitrary "core" sequences at their 3' termini were used to fingerprint a variety of templates, including PCR products and whole genomes, to establish genetic relationships between plant tax at the interspecific and intraspecific level, and to identify closely related fungal isolates and plant accessions. No correlation was observed between the sequence of the arbitrary core, the stability of the mini-hairpin structure and DAF efficiency. Mini-hairpin primers with short arbitrary cores and primers complementary to simple sequence repeats present in microsatellites were also used to generate arbitrary signatures from amplification profiles (ASAP). The ASAP strategy is a dual-step amplification procedure that uses at least one primer in each fingerprinting stage. ASAP was able to reproducibly amplify DAF products (representing about 10-15 kb of sequence) following careful optimization of amplification parameters such as primer and template concentration. Avoidance of primer sequences partially complementary to DAF product termini was necessary in order to produce distinct fingerprints. This allowed the combinatorial use of oligomers in nucleic acid screening, with numerous ASAP fingerprinting reactions based on a limited number of primer sequences. Mini-hairpin primers and ASAP analysis significantly increased detection of polymorphic DNA, separating closely related bermudagrass (Cynodon) cultivars and detecting putatively linked markers in bulked segregant analysis of the soybean (Glycine max) supernodulation (nitrate-tolerant symbiosis) locus.

DNA Fingerprinting↗
PubMed1999

Defined oligonucleotide tag pools and PCR screening in signature-tagged mutagenesis of essential genes from bacteria.

We describe a fast and simple method for signature-tagged mutagenesis (STM) using defined oligonucleotides for tag construction into mini-Tn5 and PCR instead of hybridization for rapid screening of bacterial mutants in vivo. A collection of 12 unique 21-mers were synthesized as complementary DNA strands to tag bacterial mutants constructed by insertional mutagenesis using pUTmini-Tn5Km2 plasmids. Tags were tested in a combination of assays by PCR and compared to hybridization for specificity and for large-scale screening. Each defined tag has the same melting temperature, an invariable region to optimize PCRs and a variable region for specific amplification by PCR. A series of "suicide" plasmids carrying mini-Tn5s, each with a specific tag, were transferred into Pseudomonas aeruginosa, giving 12 libraries of mutants; groups of 12 mutants were pooled and arrayed into 96-well microplates, representing approximately one-sixth of the P. aeruginosa 5.9-Mb genome. This simple STM method can be adapted to any bacterial system and used for genome scanning in various growth conditions.

Base Sequence↗
PubMed2004

Extracting hydrogen-bond signature patterns from protein structure data.

Classification of protein sequences and structures into families is a fundamental task in biology, and it is often used as a basis for designing experiments for gaining further knowledge. Some relationships between proteins are detected by the similarities in their sequences, and many more by the similarities in their structures. Despite this, there are a number of examples of functionally similar molecules without any recognisable sequence or structure similarities, and there are also a number of protein molecules that share common structural scaffolds but exhibit different functions. Newer methods of comparing molecules are required in order to detect similarities and dissimilarities in protein molecules. In this article, it is proposed that the precise 3-dimensional disposition of key residues in a protein molecule is what matters for its function, or what conveys the "meaning" for a biological system, but not what means it uses to achieve this. The concept of comparing two molecules through their intramolecular interaction networks is explored, since these networks dictate the disposition of amino acids in a protein structure. First, signature patterns, or fingerprints, of interaction networks in pre-classified protein structural families are computed using an approach to find structural equivalences and consensus hydrogen bonds. Five examples from different structural classes are illustrated. These patterns are then used to search the entire Protein Data Bank, an approach through which new, unexpected similarities have been found. The potential for finding relationships through this approach is highlighted. The use of hydrogen-bond fingerprints as a new metric for measuring similarities in protein structures is also described.

Algorithms↗
PubMed2006

The microbial signature of drinking waters: myth or reality?

This paper presents a new software developed for analyzing single strand conformation polymorphism (SSCP) electrophoresis patterns delivered by the genetic analyzer ABI310 (Applied Biosystems). SSCP is a molecular typing technique based on the PCR amplification of microbial 16S rDNA and used for the monitoring of complex microbial ecosystems dynamics. The software--a home-made MATLAB toolbox called MODIMECO--developed for the analysis of SSCP patterns is presented. MODIMECO includes a number of basic signal processing abilities as well as largely used statistical tools such as the well known principal component analysis. The use of the SSCP for assessing the hypothesis of the existence of a microbial signature of drinking waters illustrates the typical advantages of using such software tools. Results are discussed and conclusions drawn.

DNA, Bacterial↗
PubMed1993

Neuropsychiatric update of the crime "profile" and "signature" in single or serial homicides: rule out limbic psychotic trigger reaction.

A neuropsychiatric and -psychological update of the crime "profile" and "signature" is a necessary addition to the traditional sociopsychological model likely to miss limbic system dysfunctioning. Thus, occurrence of a brief (c. 20 minutes) limbic seizure has been proposed based on behaviors of 12 white male homicidal loners, who showed a dozen symptoms and signs: Limbic Psychotic Trigger Reaction. Readily overlooked can be (a) a transient psychosis (hallucinations and/or delusions), (b) autonomic hyperactivation (e.g., loss of bladder control, nausea, ejaculation), (c) motiveless, out-of-character, unplanned, and well-remembered homicidal acts, (d) committed with a flat affect (not emotionally or impulsively provoked), (e) typically involving a stranger who happened to provide an objectively harmless and only subjectively important stimulus. (f) Such an individualized stimulus triggered the memory revival of mild to moderate but repeatedly experienced hurts. Such a specific sequence of events implicates the specific mechanism of limbic seizure, "kindling," which does not necessarily involve motor convulsions. Repetition of such limbic episodes with "criminal acts" is conceivable under specific circumstances including cases in which the triggering stimulus is associated with pleasurable delusions (e.g., of grandiose power or wealth) or constitutes a specific aspect of a basic drive motive. For example, eating or sexual activities might be planned but degenerate into a limbic episode with a specific core symptomatology.

Diagnosis, Differential↗