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At least 883 records · Page 49Linked to original sources
PubMed1999

Recent advances on proteins of plant terminal membranes.

Since the beginning of the 1990s, our knowledge of the protein equipment of plant membranes progresses at an accelerating pace, owing to the irruption of molecular biology tools and genetics strategies in plant biology. Map-based cloning strategies and exploration of EST databases rapidly enrich the catalog of cDNA or gene sequences expected to code for membrane proteins. The accumulation of 'putative' membrane proteins reinforces the need for structural, functional and physiological information. Indeed, ambiguities often exist concerning the association to a membrane, the membrane identity and the topology of the protein inserted in the membrane. The combination of directed mutagenesis and heterologous expression of plant genes in various systems and plant reverse genetics has opened the possibility to study molecular and physiological functions. This review will emphasize how these tools have been essential for the exciting recent discoveries on plant terminal membrane proteins. These discoveries concern a variety of transport systems for ions, organic solutes including auxin, water channels, a large collection of systems suspected to act as receptors of chemical signals, proteins thought to control vesicle trafficking and enzymatic systems.

Animals↗
PubMed2001

Bone marrow stem cell protection from chemotherapy by low--molecular-weight compounds.

The stem cells of the bone marrow have the capacity for both self-renewal and derivation of all the blood cell lineages. Consequently, toxicity to these cells can result in neutropenia, agranulocytosis, thrombocytopenia, pancytopenia, or aplastic anemia. Many anticancer drugs adversely affect the bone marrow, and neutropenia is a common limiting factor in dose escalation. In this review, we discuss agents that appear to have potential as bone marrow sparing agents. Computerized catalogs of the National Library of Medicine and Medline were searched for reports on low-molecular-weight compounds that detailed effects on the hematopoietic progenitor cells. The most promising agents are the endogenous peptides p-glutamic acid-glutamic acid-aspartic acid-cysteine-lysine and acetyl-serine-aspartic acid-lysine-proline, and the exogenous compounds amifostine and ammonium trichloro[dioxoethylene-O,O']tellurate, but several others are also discussed. These compounds preserve stem cell function in the presence of antineoplastic drugs of diverse pharmacological classes, and they do so by various mechanisms of action. Their present status in clinical practice is also detailed. More needs to be learned about their mechanisms of action and therapeutic potential, but the results are encouraging for some of these compounds and more clinical trials should be expected.

Amifostine↗
PubMed1994

Cardiomyopathy in childhood and adult life, with emphasis on hypertrophic cardiomyopathy.

Over 60 entries in the genetic catalog have cardiomyopathy features--32 autosomal dominant, 35 autosomal recessive and X-linked. Over 40 present in, or can have survival into, adult life. Major clinicopathologic categories of these cardiomyopathic disorders included: sudden death (13 entities); cardiac conduction disturbance important feature; associated myopathy or motor dysfunction; storage diseases with cardiac involvement; cardiac amyloidoses; and, other categories. Genes, abnormality of which can cause hypertrophic cardiomyopathy (HCM), have been identified on chromosomes 1, 14 and 15, the locus on chromosome 14 involving the B-myosin heavy chain gene, but at least one unidentified locus is known to exist and there is a suggestive locus on chromosome 16, so that HCM is not a single disease but a group of disorders with clinicopatholopic similarities. To investigate these aspects of HCM in some detail, sixty-six patients with "sharply demarcated" differential myocardial fiber bundle hypertrophy (DMBH), considered to be of significant degree, from a pediatric autopsy data base of approximately 8,000 cases, were reviewed. Twenty-three of the patients died suddenly, without antecedent significant cardiac dysfunction, seven had clinical congestive heart failure of varying duration, three were stillborn, six showed evidence of aspiration of amniotic sac content (three had history of fetal distress), five had ischemic bowel disease, three (two with clinical cerebral palsy and one with Ondine's curse syndrome) had cerebral atrophy and sclerosis and one had extensive more acute encephalomalacia, and a variety of other major "causes of death" were present. Whether all infants and children with DMBH meeting the criteria used, who do not have congenital heart disease, have dominant hypertrophic cardiomyopathy (HCM) cannot be established by studies of this type, but the "concentration" of a gene or genes for HCM in pediatric autopsy series because the strong effect of HCM on life expectancy is relevant to this possibility. The data raise the question that stillbirth, fetal distress with aspiration of amniotic sac content, ischemic bowel disease and cerebral atrophy and sclerosis may be hitherto underappreciated features of HCM in childhood, and that patients with HCM may be peculiarly liable to die with certain types of septic shock, such as acute meningococcemia. In the material of this study, sudden death was statistically more frequent in females than in males in childhood (p < .029).

Adolescent↗
PubMed1998

Radiation therapy port films: a quality assurance study.

PURPOSE: The purpose of this study was to assess the port film acceptance rate in a large community practice setting and to catalog the reasons for rejection. METHODS: Between December 1993 and July 1996, a quality assurance monitor log was maintained on 4,150 patients who underwent a total of 4,450 treatment courses. Port films were taken at the beginning and at the half way point in the treatment course. A total of 20,735 port films were compared with the matching simulation films. We recorded the site being treated, the radiation oncologist who reviewed the films and the reason for rejection. RESULTS: The monthly acceptance rate varied from a low of 67% to a high of 83%, with a gradual upward trend. The single most common reason for rejecting films was a centering problem-12% of all films taken were rejected for this reason. The next most common problems were block placement or body setup errors that caused 3.4% and 2.7% of the films to be rejected, respectively. Average acceptance rates between 10 different sites (abdomen, brain, breast, chest, extremities, head and neck, pelvis, prostate, rectum and spine) varied from 68% to 80%. Individual differences between 12 radiation oncologists reviewing the films varied from 67% to 87%. CONCLUSIONS: A detailed analysis of field localization errors allowed us to identify areas where improvement was needed and suggested that specific guidelines for acceptance would help reduce the variability noted in the acceptance rate between sites and physicians.

Analysis of Variance↗
PubMed2003

Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis.

We present a simple method to detect pathogenicity islands and anomalous gene clusters in bacterial genomes. The method uses iterative discriminant analysis to define genomic regions that deviate most from the rest of the genome in three compositional criteria: G+C content, dinucleotide frequency and codon usage. Using this method, we identify many virulence-related gene islands, e.g. encoding protein secretion systems, adhesins, toxins, and other anomalous gene clusters, such as prophages. The program and the whole dataset, including the catalogs of genes in the detected anomalous segments, are publicly available at http://compbio.sibsnet.org/projects/pai-ida/. This program can be used in searching for virulence-related factors in newly sequenced bacterial genomes.

Algorithms↗
PubMed2001

Expressed sequence tags from a NaCl-treated Suaeda salsa cDNA library.

Past efforts to improve plant tolerance to osmotic stress have had limited success owing to the genetic complexity of stress responses. The first step towards cataloging and categorizing genetically complex abotic stress responses is the rapid discovery of genes by the large-scale partial sequencing of randomly selected cDNA clones or expressed sequence tags (ESTs). Suaeda salsa, which can survive seawater-level salinity, is a favorite halophytic model for salt tolerant research. We constructed a NaCl-treated cDNA library of Suaeda salsa and sequenced 1048 randomly selected clones, out of which 1016 clones produced readable sequences (773 showed homology to previously identified genes, 227 matched unknown protein coding regions, 16 anomalous sequences or sequences of bacterial origin were excluded from further analysis). By sequence analysis we identified 492 unique clones: 315 showed homology to previously identified genes, 177 matched unknown protein coding regions (101 of which have been found before in other organisms and 76 are completely novel). All our EST data are available on the Internet. We believe that our dbEST and the associated DNA materials will be a useful source to scientists engaging in stress-tolerance study.

Blotting, Northern↗
PubMed1999

Identification of 167 polymorphisms in 88 genes from candidate neurodegeneration pathways.

Catalogs of intra-gene polymorphisms are needed to facilitate wide-ranging candidate gene-based association studies in common complex diseases. With this in mind, we have scanned multiple alignments of expressed sequence tags and of genomic DNA sequences (PCR products from four to eight unrelated individuals) to find polymorphisms in 195 genes putatively involved in neurodegenerative illness (including components of oxidative stress, excitotoxicity, inflammation, apoptosis and aging). This led to the discovery of 167 polymorphisms in 88 genes. These comprised 163 single nucleotide polymorphisms, one insertion/deletion, and three other variations involving more than one base pair. The polymorphisms were distributed in the exons (87), introns (70), and gene flanking regions (10). Of the exonic polymorphisms, 17 would give rise to non-synonymous amino acid substitutions. These findings now provide a valuable resource for association studies in neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease.

Evolution, Molecular↗
PubMed1984

The phylogeny of purple bacteria: the alpha subdivision.

The technique of oligonucleotide cataloging shows the purple photosynthetic eubacteria to comprise three major subdivisions, temporarily called alpha, beta, and gamma--previously designated groups I-III by Gibson et al. (1979). Each subdivision contains a number of non-photosynthetic genera in addition to the photosynthetic ones. The alpha subdivision, the subject of the present report, contains most but not all of the species that fall into the classically defined genera Rhodospirillum, Rhodopseudomonas and Rhodomicrobium. Intermingled with these are a variety of non-photosynthetic species from genera such as Agrobacterium, Rhizobium, Azospirillum, Nitrobacter, Erythrobacter, Phenylobacterium, Aquaspirillum, and Paracoccus. The phylogenetic substructure of the alpha subdivision is presented and the evolutionary significance of the admixture of biochemical phenotypes is discussed.

Base Sequence↗
PubMed1989

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction.

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Bacteria↗
PubMed2003

Oral manifestations of systemic disease.

Most systemic diseases can affect the oral cavity. Some oral changes are nonspecific, whereas others directly lead to the diagnosis of a particular disorder. A systems approach is used here to catalog these oral changes. In some instances it is difficult to separate the oral manifestations of pharmacotherapy for a particular disease from that entity. The oral manifestations of pharmacotherapy are presented for selected disease processes. This article introduces the most common oral manifestations of systemic disease.

Bone Diseases↗
PubMed1993

Heritability and diagnosis of congenital abnormalities in food animals.

The heritability and diagnosis of congenital abnormalities in food animals have been reviewed from the viewpoint of practitioners, clinicians, and researchers. At least 632 putative mutant genes have been cataloged and listed according to the principal body system affected and mode of inheritance (see Tables 1 and 2). Implications of recent advances in genetic methodology are noted.

Animals↗
PubMedDate not supplied

Taxonomy of phototrophic green and purple bacteria: a review.

The presently existing classification for the green and purple bacteria comprises physiological-ecological assemblages of phototrophic bacteria with anoxygenic photosynthesis. The taxonomic units of the different levels were based entirely on common phenotypic traits, including morphological, cytological, physiological and biochemical characteristics. Since degrees of resemblance form the basis of the grouping, this classification cannot reflect the genetic or evolutionary relatedness of these bacteria, neither among themselves nor with other bacteria. The advantage of the artificial system, however, is the use of features which can be established in most laboratories and which allow the comparison and identification of newly isolated strains with those already studied and described. The four existing families correspond to the four major recognized, ecophysiological groups, the Chlorobiaceae and Chloroflexaceae among the green bacteria, and the Chromatiaceae and Rhodospirillaceae among the purple bacteria. Our knowledge of all these groups is incomplete; this is reflected by the fact that seven new species have been described during the past three years (6th Newsletter on phot. bacteria, Trüper and Hansen, 1982). The description of the new genus and species Erythrobacter longus (Shiba and Simidu, 1982) is also interesting, as it comprises aerobic chemoorganotrophic marine bacteria which form bacteriochlorophyll a and carotenoids; however, no strains were able to grow phototrophilcally. Significant success is currently being obtained in the different approaches toward elucidating the genetic relationships within and outside of the purple and green bacteria. Detailed studies of the lipopolysaccharides of several species and genera of the Rhodospirillaceae (Weckesser et al., 1979, and more recent paper) have proven to be very useful for the recognition of relationships or dissimilarities between the species of a genus or between different genera. Amino acid sequence studies of cytochromes c from Rhodospirillaceae, other bacteria and eukaryotic organisms (Dickerson, 1980) have led to the recognition of four different groups of cytochrome c molecules (long, medium and two groups of short protein chains). The subdivision of the Rhodospirillaceae into three species groups, each possessing one of the three types of cytochrome c, proved to be in total agreement with the results of oligonucleotide cataloging of the 16 S ribosomal RNA of these bacteria (Gibson et al., 1979). The latter method also revealed that several chemotropic bacteria, including the nitrifying bacteria, are more closely related to certain purple bacteria than different species of the purple bacteria among themselves (Seewaldt et al., 1982).(ABSTRACT TRUNCATED AT 400 WORDS)

Bacteria↗
PubMedDate not supplied

Novel intergenic repeats of Escherichia coli K-12.

An online catalog of intergenic DNA repeat sequence elements is added to the EcoGene Escherichia coli K-12 genome sequence annotation and analysis project (bmb.med.miami.edu/EcoGene). A library of noncoding (intergenic) DNA sequences depleted of known intergenic repeat classes was searched for DNA sequence similarities to identify novel DNA repeat sequence classes.

Base Sequence↗
PubMed1998

Macromolecular matchmaking: advances in two-hybrid and related technologies.

The success of the original yeast two-hybrid system has stimulated the development of a number of 'hybrid technologies' in yeast (and now prokaryotes and mammals) to widen the scope of the protein-protein interactions that can be analyzed, and to enable comparable studies of the interactions of proteins with DNA, RNA or small chemical ligands. In addition, the application of the two-hybrid system to entire genomes is being used to create protein linkage maps which catalog the network of interactions of an organism's complete proteome.

Biochemistry↗
PubMed2000

Discovery and modeling of transcriptional regulatory regions.

A complex network of regulatory controls governs the patterns of gene expression. Enabled by the tools of molecular cloning, initial experimental queries into the gene regulatory network elucidated a wide array of transcription factors and their cognate binding sites from hundreds of genes. The recent fusion of genome-scale experimental tools, a more comprehensive gene catalog, and concomitant advances in computational methodology, has extended the range of questions being posed. The potential to further our understanding of the biochemical mechanisms of transcriptional regulation and to accelerate the delineation of regulatory control regions in the human genome is enormous.

Animals↗
PubMed2003

In search of the minimal Escherichia coli genome.

Recent plans announced for the systematic cataloging of the minimal Escherichia coli gene set, the phenotypes of all mutations, the expression levels of every transcript and gene product, and the interactions of all genetic loci or their gene products point the way towards a new frontier in the biology of model organisms. Powerful tools for this endeavor are emerging, and efforts to organize the E. coli community are under way. The anticipated benefit is a functional model of the bacterial cell.

Cloning, Molecular↗
PubMed1986

Platelet granule disorders.

The present review has cataloged the inherited and acquired disorders of platelet granules. Unfortunately, a mere listing of different conditions in which dense bodies, alpha granules, or both are decreased, absent, or fused does little to define their importance in human platelet physiology or as a causative factor in hemorrhagic disease. The inherited disorders serve as the best index of granule involvement in platelet hemostatic function. Our experience with storage pool deficiency in patients with Hermansky-Pudlak syndrome has suggested that in many individuals virtual absence of dense bodies and their contents does not present a serious threat to hemostasis. Placing HPS patients on aspirin did not cause spontaneous hemorrhage, suggesting that secretion of dense body contents and synthesis of endoperoxides and thromboxane A2 are not absolutely essential for platelet function. However, the literature strongly suggests that many patients with HPS and SPD face a serious risk from bleeding, and hemorrhage may cause death. We can only conclude that some patients with HPS have platelet defects or other hemostatic problems that render SPD a far more serious threat than in other patients who appear to have the same disease. Dense bodies of and by themselves do not appear absolutely required for platelet function. Isolated deficiency of alpha granules presents the same enigma. Only a few patients with this rare inherited disease have been reported. They are generally considered to have mild to severe hemorrhagic problems. However, the past medical history of our two patients with GPS has recently been reviewed and platelet function studies repeated. Despite the mild thrombocytopenia, they are free of any significant bleeding episodes and their platelet function appears virtually normal. Our findings do not support the concept that alpha granules are essential for platelet function. The only condition that seems to support a critical role for storage organelles in hemostasis is the combined alpha-granule, dense body deficiency in one patient reported by Weiss. This patient does have bleeding problems. However, it is difficult to draw conclusions based on a single patient, and the discovery of other patients will help to clarify the hemostatic problem of patients with dual storage organelle deficiencies. In the meantime, we have prepared platelets from normal individuals free of storage granules by sedimentation through gradients containing cytochalasin B. The function of the normal agranular platelets is compromised, but they do respond to some aggregating agents.(ABSTRACT TRUNCATED AT 400 WORDS)

Blood Platelet Disorders↗
PubMed2001

Targeted use of exoglycosidase digestion for the structural elucidation of neutral O-linked oligosaccharides.

Exoglycosidase digestion in combination with the catalog-library approach (CLA) is used with matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) to obtain the complete structure of oligosaccharides. The CLA is a collision-induced dissociation (CID)-based method used to determine the structure of O-linked neutral oligosaccharides. It provides both linkage and stereochemical information. Exoglycosidases are used to confirm independently the validity of the CLA. In some cases, the CLA provides structural information on all but a single residue. Exoglycosidase is used to refine these structures. In this way, exoglycosidase use is targeted employing only a small number of enzymes. Exoglycosidase arrays, which have been used with N-linked oligosaccharides, is avoided despite the larger variations in structures of O-linked species.

Animals↗