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At least 793 records · Page 44Linked to original sources

Ufr/s variation in Escherichia coli K12: a reversible double-mutation or alternate chromosome expression in non-complementing diploids?

A novel form of bacterial variation found in an FhuA- mutant of Escherichia coli K12 was characterized by the alternation of (1) simultaneous resistance to lipopolysaccharide-specific phage U3 and to FhuA-specific agents (Ufr phenotype); and (2) a return to the sensitivity pattern of the initial strain (Ufs). In Ufr cells, loss of the U3 receptor permitted C21 adsorption without modifying the sensitivity to other tested phages or colicins. Genetic analysis revealed that Ufr variants were altered at two distinct loci. Ufr bacteria, though derived from a strain F- devoid of classical gene transfer mechanisms, were transiently able to promote mating between themselves and, to some extent, with other bacteria, including Rec-. Heterogenic matings resulted in the formation of persistent heterozygotes segregating Ufr- and Ufs-like bacteria. Pedigree analysis and subcloning of heterozygotic isolates indicate that they were diploids, as was the initial Ufr strain. Functional genetic complementation between these two genomes was only transient and the alternative forms were likely to result from the expression of a single chromosome of the heterozygotes. Mutation occurred in either form without causing any change in the alternative form.

Bacteriophages↗

Immunological and genetic characterization of 2-deoxygalactose-resistant, galactokinase-deficient mutants of Chinese hamster cells: evidence for structural mutations at the galK locus.

Ten independent mutants resistant to 2-deoxygalactose and without any detectable galactokinase activity (null-galactokinase mutations) were isolated from mutagenized Chinese hamster somatic cells. They were analyzed for the presence of serologically cross-reacting material (CRM) with antiserum generated against highly purified Chinese hamster galactokinase. All 10 mutants contain cross-reacting material (i.e., were CRM+), indicating that all the mutations affect the correct expression of a product of the galactokinase structural gene. Complementation analysis among them shows that the 10 mutations fall in one functional genetic unit.

Animals↗

Interleukin-10 receptor signaling through the JAK-STAT pathway. Requirement for two distinct receptor-derived signals for anti-inflammatory action.

Interleukin-10 (IL-10) is a cytokine that has pleiotropic effects on a variety of different cell types. Although many of the biologic responses induced by IL-10 are also induced by other cytokines, such as IL-6, IL-10 is relatively unique in its ability to potently inhibit production of pro-inflammatory cytokines in macrophages. In this study, we have used gain-of-function and loss-of-function genetic approaches to define the intracellular components involved in the different biologic actions of IL-10. Herein, we demonstrate that the ability of IL-10 to inhibit tumor necrosis factor alpha (TNFalpha) production in lipopolysaccharide-stimulated macrophages requires the presence of Stat3, Jak1, and two distinct regions of the IL-10 receptor intracellular domain. Macrophages deficient in Stat3 or Jak1 were unable to inhibit lipopolysaccharide-induced TNFalpha production following treatment with murine IL-10. Structure-function analysis of the intracellular domain of the IL-10 receptor alpha chain showed that whereas two redundant Stat3 recruitment sites (427YQKQ430 and 477YLKQ480) were required for all IL-10-dependent effects on either B cells or macrophages, expression of IL-10-dependent anti-inflammatory function required the presence on the intracellular domain of the IL-10 receptor of a carboxyl-terminal sequence containing at least one functionally critical serine. These results thus demonstrate that IL-10-induced inhibition of TNFalpha production requires two distinct regions of the IL-10 receptor intracellular domain and thereby establish a distinctive molecular basis for the developmental versus the anti-inflammatory actions of IL-10.

Animals↗

Rhizosphere Dialogue: Microorganisms Mediated by Root Exudates Alleviate Drought Stress in Grasses.

Drought stress threatens the ecological functions and economic value of grasses, posing a major challenge to their sustainable production. Plants co-evolve with rhizosphere microbial communities, sometimes described as the plant's second genome, that can contribute to drought adaptation. Drought alters root architecture, hormonal and redox regulation and belowground carbon allocation, thereby modifying the quantity and composition of root exudation and reshaping the rhizosphere environment. This review uses the rhizosphere dialogue as an integrative framework to link these plant responses with microbial recruitment and subsequent feedback to the host. We summarise three linked stages of this dialogue: drought-induced changes in root exudation; microbial recruitment and colonisation through chemotaxis, attachment, biofilm formation, and root colonisation; and microbiome-mediated feedback that improves plant water relations, hormonal and redox homoeostasis, nutrient acquisition, and root function. We highlight microbial extracellular polymeric substances, 1-aminocyclopropane-1-carboxylate deaminase, and microbial volatile organic compounds as key mediators of drought alleviation. We then discuss how this framework may inform rational synthetic microbial community (SynCom) design, microbiome-informed breeding, artificial intelligence and machine-learning assisted strain prioritisation, rhizosphere legacy effects, and real-time monitoring. Future work should distinguish active exudate-mediated recruitment from drought-driven environmental filtering and integrate multi-omics, plant genetics, functional validation, and multi-location field trials to determine whether rhizosphere dialogue can become a predictive framework for climate-resilient grass production.

drought stress↗

Cloning, characterization, and embryonic expression analysis of the Drosophila melanogaster gene encoding insulin/relaxin-like peptide.

Insulin is one of the key peptide hormones that regulates growth and metabolism in vertebrates. Evolutionary conservation of many elements of the insulin/IGF signaling network makes it possible to study the basic genetic function of this pathway in lower metazoan models such as Drosophila. Here we report the cloning and characterization of the gene for Drosophila insulin/relaxin-like peptide (DIRLP). The predicted protein structure of DIRLP greatly resembles typical insulin structure and contains features that differentiate it from the Drosophila juvenile hormone, another member of the insulin family. The Dirlp gene is represented as a single copy in the Drosophila melanogaster genome (compared to multiple copies for Drosophila juvenile hormone) and shows evolutionary conservation of genetic structure. The gene was mapped to the Drosophila chromosome 3, region 67D2. In situ hybridization of whole-mount Drosophila embryos with Dirlp antisense RNA probe reveals early embryonic mesodermal/ventral furrow expression pattern, consistent with earlier observation of the insulin protein immunoreactivity in Drosophila embryos. The in situ hybridization pattern was found to be identical to that obtained during immunohistochemistry analysis of the Drosophila embryos using various insulin monoclonal and polyclonal antibodies that do not recognize Drosophila juvenile hormone, supporting the idea that Dirlp is a possible Drosophila insulin ortholog. Identification of the gene for DIRLP provides a new approach for study of the regulatory pathway of the insulin family of peptides.

Amino Acid Sequence↗

The TINS Lecture. Understanding the roles of Otx1 and Otx2 in the control of brain morphogenesis.

The murine homologs of the orthodenticle (otd) gene of Drosophila, Otx1 and Otx2, have an important role in brain morphogenesis. Analysis of Otx1 and Otx2 null mice reveals that Otx1 is required primarily for corticogenesis and sense-organ development,while Otx2 is necessary for specification and maintenance of anterior neural plate as well as for proper gastrulation. Cross-phylum recoveries of Otx1 abnormalities by Drosophila otd, and vice versa, indicate that genetic functions required in mammalian-brain development evolved in a primitive ancestor of flies and mice. Knock-in mouse models in which Otx2 was replaced with Otx1, and vice versa, provide evidence that the existence of Otx1-/- and Otx2-/- divergent phenotypes largely reflects differences in expression patterns rather than in the biochemical activity of OTX1 and OTX2. In evolutionary terms, some of these findings lead us to hypothesize a fascinating and crucial role for Otx genes that contributes to the genetic program required for the specification of the development of the vertebrate head.

Animals↗

Phenotype analysis using network motifs derived from changes in regulatory network dynamics.

The intrinsic dynamic response of a transcriptional regulatory network depends directly on molecular interactions in the cellular transcription, translation, and degradation machineries. These interactions can be incorporated into dynamic mathematical models of the biochemical system using the biophysical relationship with the model parameters. Modifications of such interactions bring changes to the biological behavior of the cells, and therefore, many normal and pathological cellular states depend on them. It is important for analysis, prediction, diagnosis, and treatment of cellular function to have an experimentally derived model with parameters that adequately represent the molecular interactions of interest. Finding the model and parameters of a transcriptional regulatory network is a difficult task that has been approached at different levels and with different techniques. We develop here a new analysis method (based on previous work on network inference, modeling, and parameter identification) that finds the most changed parameters from yeast oligonucleotide microarray expression patterns in cases where a phenotype difference exists between two samples. We then relate and examine the changed parameters with their associated genes, corresponding genetic functional categories, and particular subnetworks and connectivities. The biophysical bases for these changes are also identified by studying the relationship of the changed parameters with the transcription, translation, and degradation mechanisms. The method is improved to cases where there are two or more transcription factors influencing transcription, and a statistical analysis is performed to give a measurement of the uniqueness and robustness of the parameter fit.

Algorithms↗

Quantification of multiple gene expression in individual cells.

Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. So far, these assessments can only be performed at the population level. Therefore, they determine the average gene expression within a population, overlooking possible cell-to-cell heterogeneity that could lead to different cell behaviors/cell fates. Understanding individual cell behavior requires multiple gene expression analyses of single cells, and may be fundamental for the understanding of all types of biological events and/or differentiation processes. We here describe a new reverse transcription-polymerase chain reaction (RT-PCR) approach allowing the simultaneous quantification of the expression of 20 genes in the same single cell. This method has broad application, in different species and any type of gene combination. RT efficiency is evaluated. Uniform and maximized amplification conditions for all genes are provided. Abundance relationships are maintained, allowing the precise quantification of the absolute number of mRNA molecules per cell, ranging from 2 to 1.28 x 10(9) for each individual gene. We evaluated the impact of this approach on functional genetic read-outs by studying an apparently homogeneous population (monoclonal T cells recovered 4 d after antigen stimulation), using either this method or conventional real-time RT-PCR. Single-cell studies revealed considerable cell-to-cell variation: All T cells did not express all individual genes. Gene coexpression patterns were very heterogeneous. mRNA copy numbers varied between different transcripts and in different cells. As a consequence, this single-cell assay introduces new and fundamental information regarding functional genomic read-outs. By comparison, we also show that conventional quantitative assays determining population averages supply insufficient information, and may even be highly misleading.

Base Sequence↗

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

Experimental investigations of eukaryotic enhancers suggest that multiple binding sites and trans-acting regulatory factors are often required for wild-type enhancer function. Genetic analysis of the stripe 2 enhancer of even-skipped (eve), an important developmental gene in Drosophila, provides support for this view. Given the importance of even-skipped expression in early Drosophila development, it might be predicted that many structural features of the stripe 2 enhancer will be evolutionarily conserved, including the DNA sequences of protein binding sites and the spacing between them. To test this hypothesis, we compared sequences of the stripe 2 enhancer between four species of Drosophila: D. melanogaster, D. yakuba, D. erecta and D. pseudoobscura. Our analysis revealed a large number of nucleotide substitutions in regulatory protein binding sites for bicoid, hunchback, Kruppel and giant, as well as a systematic change in the size of the enhancer. Some of the binding sites in D. melanogaster are either absent or modified in other species. One functionally important bicoid-binding site in D. melanogaster appears to be recently evolved. We, therefore, investigated possible functional consequences of sequence differences among these stripe 2 enhancers by P-element-mediated transformation. This analysis revealed that the eve stripe 2 enhancer from each of the four species drove reporter gene expression at the identical time and location in D. melanogaster embryos. Double staining of native eve protein and transgene mRNA in early embryos showed that the reporter gene mimicked native eve expression and, in every case, produced sharply defined stripes at the blastoderm stage that were coincident with eve stripe 2 protein. We argue that stripe 2 eve expression in Drosophila evolution can be viewed as being under constant stabilizing selection with respect to the location of the anterior and posterior borders of the stripe. We further hypothesize that the stripe 2 enhancer is functionally robust, so that its evolution may be governed by the fixation of both slightly deleterious and adaptive mutations in regulatory protein binding sites as well as in the spacing between binding sites. This view allows for a slow but continual turnover of functionally important changes in the stripe 2 enhancer.

Animals↗

In vivo selection of combinatorial libraries and designed affinity maturation of polydactyl zinc finger transcription factors for ICAM-1 provides new insights into gene regulation.

Zinc finger DNA-binding domains can be combined to create new proteins of desired DNA-binding specificity. By shuffling our repertoire of modified zinc finger domains to create randomly generated polydactyl zinc finger proteins with transcriptional regulatory domains, we developed large combinatorial libraries of zinc finger transcription factors (TFZFs). Millions of TFZFs can then be simultaneously screened in mammalian cells. Here, we successfully isolated specific TFZFs that significantly positively and negatively modulate the transcription of the ICAM-1 gene in primary and cancer cells, which are relevant to ICAM-1 biology and tumor development. We show that TFZFs can work in a general and in a cell-type specific manner depending on the regulatory domain and the zinc finger protein. We show that a TFZF that interacts directly with the ICAM-1 promoter at an overlapping NF-kappaB binding enhancer can overcome or synergistically cooperate with NF-kappaB induction of ICAM-1. For this TFZF, rational design was used to optimize the binding of the zinc finger protein to its DNA element and the resulting TFZF demonstrated a direct correlation between increased affinity and efficiency of target gene regulation. Thus, combining library and affinity maturation approaches generated superior TFZFs that may find further applications in therapeutic research and in ICAM-1 biology, and also provided novel mechanistic insights into the biology of transcription factors. Transcription factor libraries provide genome-wide approaches that can be applied towards the development of TFZFs specific for virtually any gene or desired phenotype and may lead to the discovery of new genetic functions and pathways.

Binding Sites↗

The human myelin basic protein gene is included within a 179-kilobase transcription unit: expression in the immune and central nervous systems.

Two human Golli (for gene expressed in the oligodendrocyte lineage)-MBP (for myelin basic protein) cDNAs have been isolated from a human oligodendroglioma cell line. Analysis of these cDNAs has enabled us to determine the entire structure of the human Golli-MBP gene. The Golli-MBP gene, which encompasses the MBP transcription unit, is approximately 179 kb in length and consists of 10 exons, seven of which constitute the MBP gene. The human Golli-MBP gene contains two transcription start sites, each of which gives rise to a family of alternatively spliced transcripts. At least two Golli-MBP transcripts, containing the first three exons of the gene and one or more MBP exons, are produced from the first transcription start site. The second family of transcripts contains only MBP exons and produces the well-known MBPs. In humans, RNA blot analysis revealed that Golli-MBP transcripts were expressed in fetal thymus, spleen, and human B-cell and macrophage cell lines, as well as in fetal spinal cord. These findings clearly link the expression of exons encoding the autoimmunogen/encephalitogen MBP in the central nervous system to cells and tissues of the immune system through normal expression of the Golli-MBP gene. They also establish that this genetic locus, which includes the MBP gene, is conserved among species, providing further evidence that the MBP transcription unit is an integral part of the Golli transcription unit and suggest that this structural arrangement is important for the genetic function and/or regulation of these genes.

Alternative Splicing↗

Pharmacogenetics of responses to alcohol and genes that influence alcohol drinking.

OBJECTIVE: There is now compelling evidence for genetic influence on susceptibility to alcoholism. This article presents results from studies qualifying alcoholism as a pharmacogenetic disorder of the brain. METHOD: Studies from the author's research group and other investigators, of human subjects and experimental animal models, are reviewed. Included are experiments on the pharmacogenetics (elimination and metabolism) and pharmacodynamics (initial response, tolerance and dependence) of ethanol. RESULTS: Studies in humans have reliably shown that the genes for the principal enzymes of alcohol metabolism influence drinking behavior and alcoholism risk. Notably, the functional genetic variants of alcohol dehydrogenase that exhibit high alcohol oxidizing activity, and the genetic variant of aldehyde dehydrogenase that exhibits low acetaldehyde oxidizing activity, protect against heavy drinking and alcoholism. Extensive studies of inbred and selectively bred experimental rodent models with alcohol drinking preference, tolerance development and alcohol withdrawal susceptibility have shown strong genetic influence on these responses to ethanol. Neuroanatomical, neurochemical and genetic studies have shown the involvement of serotonin, dopamine, glutamate, gamma-aminobutyric acid and opioid pathways in these actions of ethanol. Genetic studies, including association and genome-wide survey studies in both humans and rodents, implicate serotonin 1b receptor, dopamine D2 receptor, tryptophan hydroxylase and neuropeptide Y as candidate targets of genetic susceptibility in these pharmacodynamic actions of ethanol. CONCLUSIONS: There are genetic predisposing factors for alcoholism. Nonspecific susceptibility factors include personality traits characterized by behavioral inhibition (e.g., novelty-seeking and impulsivity). These genetically influenced traits interact with other, also genetically influenced, traits involved in the metabolism and pharmacodynamic effects of alcohol, and this interaction forms the basis for nominating alcoholism as a pharmacogenetic disease. Clearly, there are also many environmental factors that influence drinking behavior. Individuals have different sets of susceptibility genes and experience different kinds of environmental provocation. These factors underlie the heterogeneity and complexity of the clinical phenotype of alcoholism.

Alcohol Dehydrogenase↗

Genetics of Type 1 diabetes mellitus.

Type 1 diabetes or insulin-dependent diabetes mellitus (IDDM) is the archetypal example of a T cell-mediated autoimmune disease characterised by selective destruction of a single cell type: the insulin-producing beta-cells of the pancreatic islets of Langerhans. The pathogenic equation for IDDM presents a complex interrelation of genetic and environmental factors, most of which have yet to be identified. Based on the observed familial aggregation of IDDM, it is certain that there is a decided heritable genetic susceptibility for developing autoimmune diabetes. The well-known association of IDDM with certain human histocompatibility leukocyte antigen (HLA) alleles of the major histocompatibility complex (MHC) was a major step toward understanding the role of inheritance in IDDM. Landmark molecular biological investigations of diabetes HLA susceptibility genes provided great potential for insights into the molecular basis for the autoimmune nature of the disease, beginning a story that continues to unfold. Although the association of certain HLA alleles with IDDM is very strong, this genetic locus is estimated to account for less than 50% of genetic contributions to disease susceptibility. The search for non-HLA susceptibility genes has received great attention in recent years. Albeit genome wide searches are wrought with controversy, such studies have suggested the association of numerous non-MHC loci with Type 1 diabetes that will require careful follow-up investigation. Cell biological and genetic functional analyses will provide clues that are indispensable for further progress. The necessary studies include research on immunological abnormalities that are present many years before the clinical onset of Type 1 diabetes.

Alleles↗

Genetic variants of the extra-large stimulatory Gs protein alpha-subunit and risk of thrombotic and haemorrhagic disorders.

A polymorphism of the gene encoding the extra-large stimulatory G-protein alpha-subunit (XLalphas), originally identified in three patients with a bleeding tendency, involved a 36-bp insertion and two missense changes. A paternally-inherited insertion displayed a moderate platelet Gsalpha over-expression, which lead to platelet hypo-reactivity. These data prompted us to investigate the genetic, functional and clinical relevance of this polymorphism in the Mediterranean population. We included 414 healthy subjects and three case/control studies: 263 consecutive patients with a first episode of primary intracerebral haemorrhage, 195 patients with deep venous thrombosis, and 104 patients with cerebrovascular disease. Controls were selected by approximating criteria to match selected risk factors to patients. Moreover, we performed studies of platelet function. We developed a simple method to determine the methylated allele, by digestion of genomic DNA with Sma I before polymerase chain reaction amplification. We identified two new rare variants, resulting from the loss of repeat units 7 and 5. The AB genotype was present in 3.6% of healthy population and the prevalence of the B allele was similar among cases and controls. Accordingly, the non-methylated B allele did not modify either the expression of platelet Gsalpha or the platelet response to Gs-agonists. Thus, our study suggests a minor functional role of XLalphas polymorphism in thrombotic or in haemorrhagic disorders.

Aged↗

Targeted disruption of gene function in Drosophila by RNA interference (RNA-i): a role for nautilus in embryonic somatic muscle formation.

The expression of the MyoD gene homolog, nautilus (nau), in the Drosophila embryo defines a subset of mesodermal cells known as the muscle "pioneer" or "founder" cells. These cells are thought to establish the future muscle pattern in each hemisegment. Founders appear to recruit fusion-competent mesodermal cells to establish a particular muscle fiber type. In support of this concept every somatic muscle in the embryo is associated with one or more nautilus-positive cells. However, because of the lack of known (isolated) nautilus mutations, no direct test of the founder cell hypothesis has been possible. We now have utilized toxin ablation and genetic interference by double-stranded RNA (RNA interference or RNA-i) to determine both the role of the nautilus-expressing cells and the nautilus gene, respectively, in embryonic muscle formation. In the absence of nautilus-expressing cells muscle formation is severely disrupted or absent. A similar phenotype is observed with the elimination of the nautilus gene product by genetic interference upon injection of nautilus double-stranded RNA. These results define a crucial role for nautilus in embryonic muscle formation. The application of RNA interference to a variety of known Drosophila mutations as controls gave phenotypes essentially indistinguishable from the original mutation. RNA-i provides a powerful approach for the targeted disruption of a given genetic function in Drosophila.

Animals↗

Genetic regulation of AIF1 shapes immune and liver injury profiles in chronic alcohol use.

BACKGROUNDIn chronic alcohol consumers, immune cells may drive the progression from mild liver injury to more severe alcohol-associated liver disease (ALD), including alcohol-associated hepatitis (AAH) and cancer. Liver macrophages, both resident and infiltrating, express allograft inflammatory factor 1 (AIF1), which is upregulated during inflammation and enhances immune activation.METHODSUsing serum and urine samples from 868 individuals classified as having alcohol use disorder or not, based on DSM-IV/V criteria, along with serum and liver biopsy tissue from a second cohort of 27 patients diagnosed with AAH, we evaluated the impact of the AIF1 promoter single-nucleotide polymorphism (SNP) (rs3132451; C/C, C/G, G/G) on liver function markers and immune cell profiles.RESULTSAIF1 transcript levels were genotype dependent: C/C homozygotes expressed 5.2% of the levels observed in G/G individuals, while C/G heterozygotes expressed 46%. Unlike most SNPs associated with harmful effects, the G/G genotype is highly prevalent, present in about 70% of patients. Among chronic alcohol users, G/G individuals exhibited elevated markers of liver injury and a more than 3-fold increase in hepatic immune cells, including infiltrating AIF1+ macrophages and neutrophils. Despite similar durations of alcohol misuse, G/G individuals had higher Model for End-Stage Liver Disease scores compared with C/G individuals, indicating a significantly greater 90-day mortality risk. Notably, some immune abnormalities, such as elevated neutrophils, persisted in G/G males even after alcohol abstinence.CONCLUSIONThese findings suggest that functional genetic variation in AIF1 may contribute to the severity and persistence of ALD.TRIAL REGISTRATIONClinicalTrials.gov NCT02231840.FUNDINGResearch support was provided from the National Institute on Alcohol Abuse and Alcoholism of the NIH under grants 1ZIAAA000440-02 and R24AA025017.

Humans↗

Trp53-dependent DNA-repair is affected by the codon 72 polymorphism.

Trp53 is arguably the most critical tumour suppressor gene product that inhibits malignant transformation. Besides mutations that inactivate Trp53 functions, genetic polymorphisms have been suggested to be risk factors for cancer. A polymorphic site at codon 72 in exon 4 encodes either an arginine amino acid (Trp53(72R)) or a proline residue (Trp53(72P)). Previous studies have shown that the Trp53(72R) form is more efficient in apoptosis induction, whereas the Trp53(72P) form was suggested to induce G1 arrest better. Here we report that Trp53(72P) is more efficient than Trp53(72R) in specifically activating several Trp53-dependent DNA-repair target genes in several cellular systems. Moreover, using isogenic cell lines and several DNA-repair assays, we show that Trp53(72P) cells have a significantly higher DNA-repair capacity than the Trp53(72R) cells. Furthermore, Trp53(72P)-expressing cells exhibit reduced micronuclei formation compared to Trp53(72R)-expressing cells, suggesting that genomic instability is reduced in these cells. Together, the data highlight the functional differences between the Trp53 polymorphic variants, and suggest that their expression status may influence cancer risk.

Animals↗

Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat.

Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The publicly available collection of expressed sequence tags (ESTs) from several grass species can be used in the analysis of both structural and functional relationships in these genomes. We analyzed over 260000 EST sequences from five different cereals for their potential use in developing simple sequence repeat (SSR) markers. The frequency of SSR-containing ESTs (SSR-ESTs) in this collection varied from 1.5% for maize to 4.7% for rice. In addition, we identified several ESTs that are related to the SSR-ESTs by BLAST analysis. The SSR-ESTs and the related sequences were clustered within each species in order to reduce the redundancy and to produce a longer consensus sequence. The consensus and singleton sequences from each species were pooled and clustered to identify cross-species matches. Overall a reduction in the redundancy by 85% was observed when the resulting consensus and singleton sequences (3569) were compared to the total number of SSR-EST and related sequences analyzed (24 606). This information can be useful for the development of SSR markers that can amplify across the grass genera for comparative mapping and genetics. Functional analysis may reveal their role in plant metabolism and gene evolution.

Computational Biology↗