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At least 1,225 records · Page 68Linked to original sources
PubMed2004

National Science Foundation-sponsored workshop report. Draft plan for soybean genomics.

Recent efforts to coordinate and define a research strategy for soybean (Glycine max) genomics began with the establishment of a Soybean Genetics Executive Committee, which will serve as a communication focal point between the soybean research community and granting agencies. Secondly, a workshop was held to define a strategy to incorporate existing tools into a framework for advancing soybean genomics research. This workshop identified and ranked research priorities essential to making more informed decisions as to how to proceed with large scale sequencing and other genomics efforts. Most critical among these was the need to finalize a physical map and to obtain a better understanding of genome microstructure. Addressing these research needs will require pilot work on new technologies to demonstrate an ability to discriminate between recently duplicated regions in the soybean genome and pilot projects to analyze an adequate amount of random genome sequence to identify and catalog common repeats. The development of additional markers, reverse genetics tools, and bioinformatics is also necessary. Successful implementation of these goals will require close coordination among various working groups.

Computational Biology↗
PubMed2005

Exploring the plant transcriptome through phylogenetic profiling.

Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species- and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.

Arabidopsis↗
PubMed2005

Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction.

To better understand the molecular basis of the defense response against the rice blast fungus (Magnaporthe grisea), a large-scale expressed sequence tag (EST) sequencing approach was used to identify genes involved in the early infection stages in rice (Oryza sativa). Six cDNA libraries were constructed using infected leaf tissues harvested from 6 conditions: resistant, partially resistant, and susceptible reactions at both 6 and 24 h after inoculation. Two additional libraries were constructed using uninoculated leaves and leaves from the lesion mimic mutant spl11. A total of 68,920 ESTs were generated from 8 libraries. Clustering and assembly analyses resulted in 13,570 unique sequences from 10,934 contigs and 2,636 singletons. Gene function classification showed that 42% of the ESTs were predicted to have putative gene function. Comparison of the pathogen-challenged libraries with the uninoculated control library revealed an increase in the percentage of genes in the functional categories of defense and signal transduction mechanisms and cell cycle control, cell division, and chromosome partitioning. In addition, hierarchical clustering analysis grouped the eight libraries based on their disease reactions. A total of 7,748 new and unique ESTs were identified from our collection compared with the KOME full-length cDNA collection. Interestingly, we found that rice ESTs are more closely related to sorghum (Sorghum bicolor) ESTs than to barley (Hordeum vulgare), wheat (Triticum aestivum), and maize (Zea mays) ESTs. The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies.

Disease Susceptibility↗
PubMed1999

A computer-assisted personalized approach in an undergraduate plant physiology class

We used Computer-Assisted Personalized Approach (CAPA), a networked teaching and learning tool that generates computer individualized homework problem sets, in our large-enrollment introductory plant physiology course. We saw significant improvement in student examination performance with regular homework assignments, with CAPA being an effective and efficient substitute for hand-graded homework. Using CAPA, each student received a printed set of similar but individualized problems of a conceptual (qualitative) and/or quantitative nature with quality graphics. Because each set of problems is unique, students were encouraged to work together to clarify concepts but were required to do their own work for credit. Students could enter answers multiple times without penalty, and they were able to obtain immediate feedback and hints until the due date. These features increased student time on task, allowing higher course standards and student achievement in a diverse student population. CAPA handles routine tasks such as grading, recording, summarizing, and posting grades. In anonymous surveys, students indicated an overwhelming preference for homework in CAPA format, citing several features such as immediate feedback, multiple tries, and on-line accessibility as reasons for their preference. We wrote and used more than 170 problems on 17 topics in introductory plant physiology, cataloging them in a computer library for general access. Representative problems are compared and discussed.

Journal Article↗
PubMed2001

Chloroplast and mitochondrial proteases in Arabidopsis. A proposed nomenclature.

The identity and scope of chloroplast and mitochondrial proteases in higher plants has only started to become apparent in recent years. Biochemical and molecular studies suggested the existence of Clp, FtsH, and DegP proteases in chloroplasts, and a Lon protease in mitochondria, although currently the full extent of their role in organellar biogenesis and function remains poorly understood. Rapidly accumulating DNA sequence data, especially from Arabidopsis, has revealed that these proteolytic enzymes are found in plant cells in multiple isomeric forms. As a consequence, a systematic approach was taken to catalog all these isomers, to predict their intracellular location and putative processing sites, and to propose a standard nomenclature to avoid confusion and facilitate scientific communication. For the Clp protease most of the ClpP isomers are found in chloroplasts, whereas one is mitochondrial. Of the ATPase subunits, the one ClpD and two ClpC isomers are located in chloroplasts, whereas both ClpX isomers are present in mitochondria. Isomers of the Lon protease are predicted in both compartments, as are the different forms of FtsH protease. DegP, the least characterized protease in plant cells, has the most number of isomers and they are predicted to localize in several cell compartments. These predictions, along with the proposed nomenclature, will serve as a framework for future studies of all four families of proteases and their individual isomers.

Arabidopsis↗
PubMed2001

New molecular phenotypes in the dst mutants of Arabidopsis revealed by DNA microarray analysis.

In this study, DNA microarray analysis was used to expand our understanding of the dst1 mutant of Arabidopsis. The dst (downstream) mutants were isolated originally as specifically increasing the steady state level and the half-life of DST-containing transcripts. As such, txhey offer a unique opportunity to study rapid sequence-specific mRNA decay pathways in eukaryotes. These mutants show a threefold to fourfold increase in mRNA abundance for two transgenes and an endogenous gene, all containing DST elements, when examined by RNA gel blot analysis; however, they show no visible aberrant phenotype. Here, we use DNA microarrays to identify genes with altered expression levels in dst1 compared with the parental plants. In addition to verifying the increase in the transgene mRNA levels, which were used to isolate these mutants, we were able to identify new genes with altered mRNA abundance in dst1. RNA gel blot analysis confirmed the microarray data for all genes tested and also was used to catalog the first molecular differences in gene expression between the dst1 and dst2 mutants. These differences revealed previously unknown molecular phenotypes for the dst mutants that will be helpful in future analyses. Cluster analysis of genes altered in dst1 revealed new coexpression patterns that prompt new hypotheses regarding the nature of the dst1 mutation and a possible role of the DST-mediated mRNA decay pathway in plants.

Amino Acid Sequence↗
PubMed2005

A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.

The complete genome sequence of cultivated rice (Oryza sativa) provides an unprecedented opportunity to understand the biology of this model cereal. An essential and necessary step in this effort is the determination of the coding information and expression patterns of each sequenced chromosome. Here, we report an analysis of the transcriptional activity of rice chromosome 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Six representative rice organ types were examined using this microarray to catalog the transcribed regions of rice chromosome 4 and to reveal organ- and developmental stage-specific transcription patterns. This analysis provided expression support for 82% of the gene models in the chromosome. Transcriptional activities in 1643 nonannotated regions were also detected. Comparison with cytologically defined chromatin features indicated that in juvenile-stage rice the euchromatic region is more actively transcribed than is the transposon-rich heterochromatic portion of the chromosome. Interestingly, increased transcription of transposon-related gene models in certain heterochromatic regions was observed in mature-stage rice organs and in suspension-cultured cells. These results suggest a close correlation between transcriptional activity and chromosome organization and the developmental regulation of transcription activity at the chromosome level.

Chromosome Mapping↗
PubMed1999

Enumeration of four-connected three-dimensional nets. I. Conversion of all edges of simple three-connected two-dimensional nets into crankshaft chains.

Various topological approaches to mathematical analysis, classification and enumeration of four-connected three-dimensional (3D) nets are listed. Four-connected 3D nets are being generated systematically by conversion of edges of a vertical stack of congruent three-connected two-dimensional (2D) nets into chains. This paper describes 57 3D nets obtained by converting into crankshaft chains all edges of the simpler 2D nets in the catalog of the Consortium of Theoretical Frameworks. Atomic coordinates are given for distance-least-squares modeling in the highest space group. Nine nets occur in known structures: tridymite, Zn(2)P(2)O(8).organic, aluminophosphates AlPO-5 (International Zeolite Association Structure Commission code AFI), AlPO-8 (AEI), AlPO-11 (AEL), AlPO-25 (ATV), AlPO-41 (AFO), AlPO-54 (VFI) and AlPO-H2 (AHT).

Journal Article↗
PubMed2002

Integrated surface model optimization for freehand three-dimensional echocardiography.

The major obstacle of three-dimensional (3-D) echocardiography is that the ultrasound image quality is too low to reliably detect features locally. Almost all available surface-finding algorithms depend on decent quality boundaries to get satisfactory surface models. We formulate the surface model optimization problem in a Bayesian framework, such that the inference made about a surface model is based on the integration of both the low-level image evidence and the high-level prior shape knowledge through a pixel class prediction mechanism. We model the probability of pixel classes instead of making explicit decisions about them. Therefore, we avoid the unreliable edge detection or image segmentation problem and the pixel correspondence problem. An optimal surface model best explains the observed images such that the posterior probability of the surface model for the observed images is maximized. The pixel feature vector as the image evidence includes several parameters such as the smoothed grayscale value and the minimal second directional derivative. Statistically, we describe the feature vector by the pixel appearance probability model obtained by a nonparametric optimal quantization technique. Qualitatively, we display the imaging plane intersections of the optimized surface models together with those of the ground-truth surfaces reconstructed from manual delineations. Quantitatively, we measure the projection distance error between the optimized and the ground-truth surfaces. In our experiment, we use 20 studies to obtain the probability models offline. The prior shape knowledge is represented by a catalog of 86 left ventricle surface models. In another set of 25 test studies, the average epicardial and endocardial surface projection distance errors are 3.2 +/- 0.85 mm and 2.6 +/- 0.78 mm, respectively.

Algorithms↗
PubMed1994

Mutations in the H1 and 1A domains in the keratin 1 gene in epidermolytic hyperkeratosis.

In the autosomal dominant disorder epidermolytic hyperkeratosis, the structural integrity of the keratin intermediate filaments is altered in the suprabasal layers of the epidermis. We and others have used genetic linkage studies and mutation analysis to establish that single amino acid substitutions in either the keratin 1 or keratin 10 chains can cause epidermolytic hyperkeratosis. However, a larger database of mutations is required to better understand the relationship between specific mutations in these keratin chains and their effect on keratin filament structure. A larger database will also provide a catalog that may be useful for genetic counseling purposes. In this paper, we report the identification of three new mutations of the keratin 1 chain of epidermolytic hyperkeratosis probands in highly conserved residues in the H1 or beginning of the 1A rod domain segments. These correspond to regions involved in molecular overlaps between neighboring molecules in keratin filaments. Using an in vitro assay, synthetic peptides bearing these substitutions show diminished capacity to disassemble preformed filaments in vitro in comparison to the wild type peptides. Moreover, analyses of all mutations in epidermolytic hyperkeratosis known to date demonstrate remarkable clustering in the molecular overlap region. We conclude that non-conservative substitutions in the overlap region are likely to interfere with normal keratin filament structure and function, leading to pathology.

Amino Acid Sequence↗
PubMed1995

Mutations in the 1A domain of keratin 9 in patients with epidermolytic palmoplantar keratoderma.

Epidermolytic palmoplantar keratoderma is an autosomal dominant skin disorder characterized by hyperkeratosis of the palms and soles. Ultrastructurally the disease exhibits abnormal keratin filament networks and tonofilament clumping like that found in the keratin disorders of epidermolysis bullosa simplex and epidermolytic hyperkeratosis. The disease has been mapped to chromosome 17q11-q23 in the region of the type 1 keratin gene locus and more recently mutations have been found in the palmoplantar specific keratin, keratin 9. We have analyzed six unrelated incidences of epidermolytic palmoplantar keratoderma for mutations in their keratin 9 genes. In two of these, we have identified mutations that alter critical residues within the highly conserved helix initiation motif at the beginning of the rod domain of keratin 9. In a three-generation Middle Eastern kindred we found a C to T transition at codon 162 that results in an arginine to tryptophan substitution at position 10 of the 1A alpha-helical domain, thus confirming this codon as a hot spot for mutation in keratin 9. The other mutation found involves a T to C transition at codon 167 that results in the expression of a serine residue in place of the normal leucine at position 15 of the 1A segment and is the first documentation of this mutation in this gene. The identification of these substitutions extends the current catalog of disease causing mutations in keratin 9.

Base Sequence↗
PubMed2005

Insights into genotype-phenotype correlation in pachyonychia congenita from the human intermediate filament mutation database.

Keratins are the intermediate filament proteins specifically expressed by epithelial cells. The Human Genome Project has uncovered a total of 54 functional keratin genes that are differentially expressed in specific epithelial structures of the body, many of which involve the epidermis and its appendages. Pachyonychia congenita (PC) is a group of autosomal dominant genodermatoses affecting the nails, thick skin and other ectodermal structures, according to specific sub-type. The major clinical variants of the disorder (PC-1 and PC-2) are known to be caused by dominant-negative mutations in one of four differentiation-specific keratins: K6a, K6b, K16, and K17. A total of 20 human keratin genes are currently linked to single-gene disorders or are predisposing factors in complex traits. In addition, a further six intermediate filament genes have been linked to other non-epithelial genetic disorders. We have established a comprehensive mutation database that catalogs all published independent occurrences of intermediate filament mutations (http://www.interfil.org), with details of phenotypes, published papers, patient support groups and other information. Here, we review the genotype-phenotype trends emerging from the spectrum of mutations in these genes and apply these correlations to make predictions about PC phenotypes based on the site of mutation and keratin pair involved.

Age of Onset↗
PubMed2004

Narrow-band ultraviolet B radiation: a review of the current literature.

BACKGROUND: Narrow-Band radiation (NB-UVB) is a relatively new treatment modality for psoriasis and many practitioners may be unaware of its effectiveness and applications. OBJECTIVE: The purpose of this study is to review the literature and compare NB-UVB to both broad-band ultraviolet B radiation (BB-UVB) and psoralen plus ultraviolet A radiation (PUVA) for the treatment of psoriasis and other dermatoses. METHODS: A comprehensive Medline search of the literature was done on all citations electronically cataloged since the mid 1960s. RESULTS: NB-UVB is superior to BB-UVB, but less effective than PUVA for the treatment of psoriasis, and is beneficial for the treatment of many other dermatoses. CONCLUSION: NB-UVB is a useful and important adjust to the treatment of psoriasis.

Humans↗
PubMed2005

Congenital generalized lipodystrophy: profile of the disease and gender differences in two siblings.

Congenital generalized Lipodystrophy (BSCL) or Berardinelli-Seip syndrome (Mendelian inheritance in man, catalog no. 269700) is a rare autosomal recessive syndrome characterized by paucity of body fat since birth and insulin resistance. The pathophysiology of this condition is unclear, but defects in insulin function and impaired adipogenesis have been described as important factors in the etiology of the disease. Recently, two gene loci have been identified to harbor the mutations causing this disorder: BSCL1 mapped to human chromosome 9q34 (1, 2) and BSCL2 mapped to human chromosome 11q13 (1, 3). This report describes the natural history of the disease in two siblings (female and male) of Lebanese origin who have mutations in the BSCL2 locus (669delGTATC).

Child↗
PubMed1987

Suprabasal expression of a 64-kilodalton keratin (no. 3) in developing human corneal epithelium.

We have previously shown that a basic 64-kilodalton (no. 3 in the catalog of Moll et al.) and an acidic 55-kilodalton (no. 12) keratin are characteristic of suprabasal cell layers in cultured rabbit corneal epithelial colonies, and therefore may be regarded as markers for an advanced stage of corneal epithelial differentiation. Moreover, using an AE5 mouse monoclonal antibody, we showed that the 64-kilodalton keratin marker is expressed suprabasally in limbal epithelium but uniformly (basal layer included) in central corneal epithelium, suggesting that corneal basal cells are in a more differentiated state than limbal basal cells. In conjunction with previous data implicating the centripetal migration of corneal epithelial cells, our data support a model of corneal epithelial maturation in which corneal epithelial stem cells are located in the limbus, the transitional zone between the cornea and conjunctiva. In the present study, we analyzed the expression of the 64-kilodalton keratin in developing human corneal epithelium by immunohistochemical staining. At 8 weeks of gestation, the presumptive corneal epithelium is composed of a single layer of cuboidal cells with an overlying periderm; neither of these cell layers is AE5 positive. At 12-13 weeks of gestation, some superficial cells of the three- to four-layered epithelium become AE5 positive, providing the earliest sign of overt corneal epithelial differentiation. At 36 weeks, although the epithelium is morphologically mature (four to six layers), AE5 produces a suprabasal staining pattern, this being in contrast to the adult epithelium which exhibits uniform staining.(ABSTRACT TRUNCATED AT 250 WORDS)

Aging↗
PubMed1985

Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species.

The nucleotide sequences of the 5S ribosomal RNAs of the bacteria Agrobacterium tumefaciens, Alcaligenes faecalis, Pseudomonas cepacia, Aquaspirillum serpens and Acinetobacter calcoaceticus have been determined. The sequences fit in a generally accepted model for 5S RNA secondary structure. However, a closer comparative examination of these and other bacterial 5S RNA primary structures reveals the potential of additional base pairing and of multiple equilibria between a set of slightly different alternative secondary structures in one area of the molecule. The phylogenetic position of the examined bacteria is derived from a 5S RNA sequence alignment by a clustering method and compared with the position derived on the basis of 16S ribosomal RNA oligonucleotide catalogs.

Bacteria↗
PubMed1991

Immunohistochemical study of cytokeratin distribution in the collecting duct of the human kidney.

In order to assess the expression of different cytokeratins in the collecting duct cells (CDCs) of the human kidney, three consecutive sections were stained with periodic acid-Schiff, CAM 5.2 and AE-1 (CAM 5.2 recognizes cytokeratins #19,18,8 and AE-1 #19,16,15,14,10 of Moll's catalog.), respectively. By comparing these sections, it was found that most CDCs in the inner medulla were both CAM 5.2- and AE-1-positive, whereas in the outer medulla and cortex, 77% of the CDCs were both CAM 5.2- and AE-1-positive, 15% CAM 5.2-positive and AE-1-negative, 8% both CAM 5.2- and AE-1-negative, and 0.4% CAM 5.2-negative and AE-1-positive. Recent studies have shown that most CDCs express low-molecular-weight cytokeratins #7,8,18 and 19 (17, 18, 19, 20). Of these cytokeratins, CAM 5.2 recognizes cytokeratins #8,18,19 and AE-1 recognizes cytokeratin #19. Therefore, most CDCs belong to one of the following three major types; 1. Those positive for cytokeratins #8,18 and 19 (CAM 5.2- and AE-1-positive), 2. Those positive for cytokeratins #8 and 18 and negative for #19 (CAM 5.2-positive and AE-1-negative) and 3. Those negative for cytokeratins #8,18 and 19 (CAM 5.2- and AE-1-negative). A few CAM 5.2-negative and AE-1-positive cells were thought to express high-molecular-weight cytokeratins. The significance of these various cytokeratin expressions is discussed.

Adult↗
PubMed1996

Effect sizes and p values: what should be reported and what should be replicated?

Despite publication of many well-argued critiques of null hypothesis testing (NHT), behavioral science researchers continue to rely heavily on this set of practices. Although we agree with most critics' catalogs of NHT's flaws, this article also takes the unusual stance of identifying virtues that may explain why NHT continues to be so extensively used. These virtues include providing results in the form of a dichotomous (yes/no) hypothesis evaluation and providing an index (p value) that has a justifiable mapping onto confidence in repeatability of a null hypothesis rejection. The most-criticized flaws of NHT can be avoided when the importance of a hypothesis, rather than the p value of its test, is used to determine that a finding is worthy of report, and when p approximately equal to .05 is treated as insufficient basis for confidence in the replicability of an isolated non-null finding. Together with many recent critics of NHT, we also urge reporting of important hypothesis tests in enough descriptive detail to permit secondary uses such as meta-analysis.

Psychophysiology↗