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At least 721 records · Page 40Linked to original sources
PubMed2002

Shapes of phospholipid [correction of phosholipid] vesicles with beadlike protrusions.

Giant phospholipid vesicles obtained by the method of electroformation were observed by the phase contrast microscope. Most of these vesicles contain a protrusion which shortens in a slow shape transformation process until it is absorbed into the main vesicle body. We are concerned with the last stages of this shape transformation process, where the protrusions attain a beadlike shape. The number of "beads" decreases one by one in consecutive steps, and it is demonstrated that each such step consists of two distinguishable phases. During the first phase the beadlike shape does not change and the necks connecting the "beads" are narrow. During the second phase the width of the protrusion necks increases. On the basis of the assumption that these shape transformations are driven by the decrease of the equilibrium difference between the outer and the inner membrane monolayers areas, the system behavior is analyzed in terms of the generalized bilayer couple model. The theoretical results confirm the observed time sequence: at a given number of "beads" the protrusion has in the first phase the shape that consists of spheres connected by infinitesimal necks, and during the second phase the protrusion is a single prolate unit with open necks. The discrepancies between the observed and the predicted widths of the necks are interpreted by the repulsive forces between the neighboring "beads" induced by the membrane thermal fluctuations. The analysis presented extends the existing catalog of vesicle shapes to the region of larger differences between the areas of membrane monolayers, and confirms the applicability of the generalized bilayer couple model to the description of the shape behavior of phospholipid vesicles containing beadlike protrusions.

Computer Simulation↗
PubMed2006

Associations of the IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFN (gamma) R1 cytokine receptor genes with AIDS progression in a French AIDS cohort.

We have performed an extensive analysis of Th1/Th2 cytokine receptors IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFNgammaR1 gene polymorphisms to evaluate their impact on AIDS progression. The coding regions and promoters of these genes were sequenced in the genetics of resistance to immunodeficiency virus cohort, composed of 327 HIV-1-positive patients with extreme progression phenotypes, slow and rapid progressors, and of 446 healthy control subjects, all of them of Caucasian descent. Overall, 104 single nucleotide polymorphisms and four insertions/deletions with a minor allelic frequency higher than 1% were identified, 21 of them being newly characterized. We observed weak associations for 13 polymorphisms of IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFNgammaR1, and 11 haplotypes of IL2Ralpha, IL4Ralpha, and IFNgammaR1. However, we could not relate these positive signals to any relevant biological information on the gene function. To affirm these putative associations in AIDS, further confirmation on other AIDS cohorts will be needed. This complete catalog of polymorphisms in IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFNgammaR1 cytokine receptor genes should also be useful for investigating associations in other immune-related diseases.

Acquired Immunodeficiency Syndrome↗
PubMed2005

Evaluation of flood and landslide risk to the population of Italy.

We have compiled a database of floods and landslides that occurred in Italy between AD 1279 and 2002 and caused deaths, missing persons, injuries, and homelessness. Analysis of the database indicates that more than 50,593 people died, went missing, or were injured in 2580 flood and landslide events. Harmful events were inventoried in 26.3% of the 8103 Italian municipalities. Fatal events were most frequent in the Alpine regions of northern Italy and were caused by both floods and landslides. In southern Italy, landslides were the principal agents of fatalities and were most numerous in the Campania region. Casualties were most frequent in the autumn. Fast-moving landslides, including rock falls, rockslides, rock avalanches, and debris flows, caused the largest number of deaths. In order to assess the overall risk posed by these processes, we merged the historical catalogs and identified 2682 "hydrogeomorphological" events that triggered single or multiple landslides and floods. We estimated individual risk through the calculation of mortality rates for both floods and landslides and compared these rates to the death rates for other natural, medical, and human-induced hazards in Italy. We used the frequency distribution of events with fatalities to ascertain the magnitude and frequency of the societal risks posed by floods and landslides. We quantified these risks in a Bayesian model that describes the probabilities of fatal flood and landslide events in Italy.

Bayes Theorem↗
PubMed1998

Animal Burrowing Attributes Affecting Hazardous Waste Management.

/ Animal burrowing is critical to the formation of soils and contributes to the interface between geological materials and organic life. It also influences the management of hazardous materials at nuclear waste facilities and elsewhere. For example, residues and waste products from the production of nuclear weapons are released onto the ground surface and within engineered burial structures. Soil bioturbation has exposed radionuclides and other hazardous materials to wind and rain, thereby risking inhalation and injury to humans and wildlife on and off site. Soil bioturbation can expand soil depths and spatial distributions of the source term of hazardous waste, potentially increasing chronic exposures to wildlife and humans over the long term. Ample evidence indicates that some of the large quantities of hazardous materials around the world have been released from soil repositories, where they have also contaminated and harmed biota. Key burrowing parameters influencing these outcomes include the catalog of resident species, and their abundance, typical burrow volumes (void space created by soil displacement), burrow depth profiles, maximum depth of excavation, constituents and structural qualities of excavated soil mounds, and proportion of the ground covered by excavated soil. Other important parameters include rate of mound construction, depth of den chambers, and volume of burrow backfill. Soil bioturbation compromised the integrity of some hazardous waste management systems using soil, but the environmental impact remains largely unknown. Designers and operators of waste management facilities, as well as risk assessors, need to understand how burrowing animals influence hazardous waste storage.KEY WORDS: Burrowing; Environmental impact; Radioactivity; Risk; Soil bioturbation; Hazardous waste

Journal Article↗
PubMed2005

[Spectrum of chronic pancreatitis. On the way to etiological classification].

Chronic pancreatitis is a fibroinflammatory disease that is induced by injuries to the interstitial, ductal, and/or acinar cells. The most important causes are alcohol abuse, gene mutations, autoimmune processes, special anatomic changes, and obstructive duct lesions. The morphologic spectrum of the various types of chronic pancreatitis related to the above causes shows features that increasingly allow an etiological distinction and categorization to be made. A catalog of five criteria is presented for distinguishing chronic pancreatitis from ductal adenocarcinoma of the pancreas.

Alcoholism↗
PubMed2005

Palindrome content of the yeast Saccharomyces cerevisiae genome.

Palindromic sequences are important DNA motifs involved in the regulation of different cellular processes, but are also a potential source of genetic instability. In order to initiate a systematic study of palindromes at the whole genome level, we developed a computer program that can identify, locate and count palindromes in a given sequence in a strictly defined way. All palindromes, defined as identical inverted repeats without spacer DNA, can be analyzed and sorted according to their size, frequency, GC content or alphabetically. This program was then used to prepare a catalog of all palindromes present in the chromosomal DNA of the yeast Saccharomyces cerevisiae. For each palindrome size, the observed palindrome counts were significantly different from those in the randomly generated equivalents of the yeast genome. However, while the short palindromes (2-12 bp) were under-represented, the palindromes longer than 12 bp were over-represented, AT-rich and preferentially located in the intergenic regions. The 44-bp palindrome found between the genes CDC53 and LYS21 on chromosome IV was the longest palindrome identified and contained only two C-G base pairs. Avoidance of coding regions was also observed for palindromes of 4-12 bp, but was less pronounced. Dinucleotide analysis indicated a strong bias against palindromic dinucleotides that could explain the observed short palindrome avoidance. We discuss some possible mechanisms that may influence the evolutionary dynamics of palindromic sequences in the yeast genome.

DNA, Intergenic↗
PubMed2002

Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly.

Genetic and environmental factors affect the efficiency of pork production by influencing gene expression during porcine reproduction, tissue development, and growth. The identification and functional analysis of gene products important to these processes would be greatly enhanced by the development of a database of expressed porcine gene sequence. Two normalized porcine cDNA libraries (MARC 1PIG and MARC 2PIG), derived respectively from embryonic and reproductive tissues, were constructed, sequenced, and analyzed. A total of 66,245 clones from these two libraries were 5?-end sequenced and deposited in GenBank. Cluster analysis revealed that within-library redundancy is low, and comparison of all porcine ESTs with the human database suggests that the sequences from these two libraries represent portions of a significant number of independent pig genes. A Porcine Gene Index (PGI), comprising 15,616 tentative consensus sequences and 31,466 singletons, includes all sequences in public repositories and has been developed to facilitate further comparative map development and characterization of porcine genes (http://www.tigr.org/tdb/ssgi/). The clones and sequences from these libraries provide a catalog of expressed porcine genes and a resource for development of high-density hybridization arrays for transcriptional profiling of porcine tissues. In addition, comparison of porcine ESTs with sequences from other species serves as a valuable resource for comparative map development. Both arrayed cDNA libraries are available for unrestricted public use.

Animals↗
PubMed2001

Assignment of 64 genes expressed in 28-day-old pig embryo to radiation hybrid map.

A swine resource family was constructed at the National Institute of Animal Industry, Japan, in order to determine the genetic regions responsible for economically important traits, including fetus development. To identify genes expressed in the early stage of embryo development, we cataloged and mapped genes expressed in a 28-day-old normal pig embryo. In this effort, we have mapped 64 genes, which have map information in human genome onto a swine radiation hybrid (RH) map, IMpRH. These mappings provided additional chromosomal homologies between swine and human to improve the comparative map between the two species. The distribution of the genes assigned to swine chromosomes are as follows: 9 genes were assigned on SSC6; 6 genes each assigned on SSC5 and SSC14; 5 genes each assigned on SSC3, SSC4, and SSC8; 4 genes each assigned on SSC1, SSC7, SSC9, and SSC15; 3 genes each assigned on SSC2, SSC13 and SSCX; and 1 gene each assigned on SSC10, SSC11, and SSC16. Moreover, the present findings revealed 18 new chromosomal homologies between pig and human. Briefly, SSC3 regions were indicated to correspond with HSA1 and HSA10; SSC4 with HSA6; SSC5 with HSA2, HSA15, and HSA16; SSC6 with HSA3, HSA6, and HSA20; SSC7 with HSA11; SSC8 with HSA3, HSA6, and HSA7; SSC9 with HSA8; SSC13 with HSA1; SSC14 with HSA13; SSC15 with HSA19; SSC16 with HSA9.

Animals↗
PubMed1999

[The German Ophthalmology Society in the internet. Resources and interest].

OBJECTIVE: The German Ophthalmologic Society is rising to the challenges of the information age by offering comprehensive information resources online. METHODS: The society's board decided on the development of an Internet website in October 1996. Since February 1997, the website has been available under the Internet address www.dog.org. The amount of information offered has been growing fast during the following 12 months. RESULTS: On its website, the DOG offers information about itself, membership, further education, and a catalog of important addresses, patient information, official recommendations, and the program and abstracts of the annual sessions. The ICD10-aug was integrated into the website as a database application. A discussion group is reserved for ophthalmologists who can use this platform to share ideas and discuss clinical topics. CONCLUSIONS: The website of the DOG consists of over 4,900 files that represent the activities of the society. The website's access log indicates steady interest in the information offered. Over 53,000 users visited the DOG website. The discussion group is used by 71 members from 10 countries (all numbers as of 9/98).

Germany↗
PubMed1999

[Effective use of medical-scientific internet resources].

PROBLEM: The Internet is not structured hierarchically and therefore it distinguishes from today's common knowledge sources. The rapidly growing number of medical websites offers comprehensive but not easy to find information resources and continuing education opportunities for ophthalmologists. METHODS AND RESULTS: The efficiency of an Internet search is related to knowledge about existing search strategies. Several search systems are described (search engines, catalogs, databases, indices, etc.). Additional advice about efficient usage (Meta-Search, use of Boolean operators, phrase search, etc.) is provided. The suggested search strategies are evaluated regarding their specific results, update status, and the usability of search engines used. New applications such as SemioMap and Intelligent Agents are described. CONCLUSION: Today the Internet provides practitioners and scientists who are able to use efficient search strategies with easy and fast to use information resources. The total number of scientific-medical documents on the Web is growing very quickly. More and more, their content is related to current problems in patient treatment and future trends in clinical research.

Education, Medical, Continuing↗
PubMed2005

Determining localized garment insulation values from manikin studies: computational method and results.

The localized thermal insulation value expresses a garment's thermal resistance over the region which is covered by the garment, rather than over the entire surface of a subject or manikin. The determination of localized garment insulation values is critical to the development of high-resolution models of sensible heat exchange. A method is presented for determining and validating localized garment insulation values, based on whole-body insulation values (clo units) and using computer-aided design and thermal analysis software. Localized insulation values are presented for a catalog consisting of 106 garments and verified using computer-generated models. The values presented are suitable for use on volume element-based or surface element-based models of heat transfer involving clothed subjects.

Body Temperature Regulation↗
PubMed2005

Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii.

The beet cyst nematode Heterodera schachtii is an important pathogen worldwide, but its molecular characterization has been limited to studying individual genes of interest. We undertook a high-throughput genomic approach and drastically increased the number of available sequences for this parasite. A total of 2,662 expressed sequence tags were grouped into 1,212 clusters representing a nonredundant catalog of H. schachtii genes. Implementing a bioinformatic workflow, we identified 50 sequences coding for candidate secreted proteins. All of these contain a putative signal peptide required for entry into the secretory pathway and lack any transmembrane domain. Included are previously postulated cell-wall-degrading enzymes and other parasitism-related genes. Moreover, we provide the first report of an arabinogalactan endo-1,4-beta-galactosidase enzyme (EC 3.2.1.89) in animals. As sequence data increase at a rapid rate, developing high-throughput genomic screening is a necessity. The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies.

Animals↗
PubMed2004

Sequence evaluation of four specific cDNA libraries for developmental genomics of sunflower.

Four different cDNA libraries were constructed from sunflower protoplasts growing under embryogenic and non-embryogenic conditions: one standard library from each condition and two subtractive libraries in opposite sense. A total of 22,876 cDNA clones were obtained and 4800 ESTs were sequenced, giving rise to 2479 high quality ESTs representing an unigene set of 1502 sequences. This set was compared with ESTs represented in public databases using the programs BLASTN and BLASTX, and its members were classified according to putative function using the catalog in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Some 33% of sequences failed to align with existing plant ESTs and therefore represent putative novel genes. The libraries show a low level of redundancy and, on average, 50% of the present ESTs have not been previously reported for sunflower. Several potentially interesting genes were identified, based on their homology with genes involved in animal zygotic division or plant embryogenesis. We also identified two ESTs that show significantly different levels of expression under embryogenic and non-embryogenic conditions. The libraries described here represent an original and valuable resource for the discovery of yet unknown genes putatively involved in dicot embryogenesis and improving our knowledge of the mechanisms involved in polarity acquisition by plant embryos.

DNA, Complementary↗
PubMed2004

A whole genome perspective on the phylogeny of the plant virus family Tombusviridae.

Most current classifications of viruses are based on single gene analysis of capsid protein or polymerase. The comparison of entire genomes is a more balanced approach that should provide a more complete picture of relatedness. We have used a singular value decomposition (SVD)-based analysis to generate phylogenetic trees using whole genome protein sequences from a family of single-stranded RNA plant viruses. Our dataset includes the 26 species of the family Tombusviridae, 25 of which have complete genome sequences cataloged in GenBank. The resulting phylogenetic tree agrees well with current taxonomic classifications, but with significant exceptions. One previously unassigned virus within this family, Maize necrotic streak virus, is definitively placed within the genus Tombusvirus by this analysis. In addition, the analysis defines two distinct subsets within the genus Necrovirus. Future datasets will be expanded to include other icosahedral positive strand RNA plant viruses, and then perhaps all positive strand RNA plant viruses.

Amino Acid Sequence↗
PubMed2000

Reidentification of facultatively alkaliphilic Bacillus firmus OF4 as Bacillus pseudofirmus OF4.

With a view toward verifying the original classification of alkaliphilic Bacillus firmus OF4, physiological and biochemical characteristics were more extensively catalogued than in original studies, and this catalog was supplemented with 16S rDNA sequence homology and more extensive DNA-DNA hybridization analyses. Phylogenetic analysis of this alkaliphile based on the comparison of multiple 16S rDNA sequences from Bacillus species indicated that this strain is most closely related to Bacillus pseudofirmus. Consistently, in the DNA-DNA hybridization analysis of the alkaliphile and Bacillus reference strains, the highest level of DNA-DNA relatedness (96%) was found between the alkaliphile and the B. pseudofirmus type strain (DSM 8715(T)). The findings support the conclusion that this alkaliphile strain is more closely related to B. pseudofirmus than to B. firmus, and we propose the future use of the designation B. pseudofirmus OF4.

Bacillus↗
PubMed1998

Biochemistry and biotechnology of mesophilic and thermophilic nitrile metabolizing enzymes.

Mesophilic nitrile-degrading enzymes are widely dispersed in the Bacteria and lower orders of the eukaryotic kingdom. Two distinct enzyme systems, a nitrilase catalyzing the direct conversion of nitriles to carboxylic acids and separate but cotranscribed nitrile hydratase and amidase activities, are now well known. Nitrile hydratases are metalloenzymes, incorporating FeIII or CoII ions in thiolate ligand networks where they function as Lewis acids. In comparison, nitrilases are thiol-enzymes and the two enzyme groups have little or no apparent sequence or structural homology. The hydratases typically exist as alpha beta dimers or tetramers in which the alpha- and beta-subunits are similar in size but otherwise unrelated. Nitrilases however, are usually found as homomultimers with as many as 16 subunits. Until recently, the two nitrile-degrading enzyme classes were clearly separated by functional differences, the nitrile hydratases being aliphatic substrate specific and lacking stereoselectivity, whereas the nitrilases are enantioselective and aromatic substrate specific. The recent discovery of novel enzymes in both classes (including thermophilic representatives) has blurred these functional distinctions. Purified mesophilic nitrile-degrading enzymes are typically thermolabile in buffered solution, rarely withstanding exposure to temperatures above 50 degrees C without rapid inactivation. However, operational thermostability is often increased by addition of aliphatic acids or by use of immobilized whole cells. Low molecular stability has frequently been cited as a reason for the limited industrial application of "nitrilases"; such statements notwithstanding, these enzymes have been successfully applied for more than a decade to the kiloton production of acrylamide and more recently to the smaller-scale production of nicotinic acid, R-(-)-mandelic acid and S-(+)-ibuprofen. There is also a rapidly growing catalog of other potentially useful conversions of complex nitriles in which the regioselectivity of the enzyme coupled with the ability to achieve high conversion efficiencies without detriment to other sensitive functionalities is a distinct process advantage.

Acrylamide↗
PubMedDate not supplied

Congenitally malformed hearts from a population of children undergoing cardiac transplantation: comments on sequential segmental analysis and dissection.

Our aim is to examine the types of cardiac malformations found in a population of children undergoing cardiac transplantation, and to discuss a method for examining cardiac explants based on intrinsic morphology. We describe in detail the congenital malformations found in 65 cardiac explants acquired from a population of children over a period of 15 years. The specimens were examined and diagnosed using the method of sequential segmental analysis. The most prevalent type of cardiac malformation was severe obstruction of the left heart (29. 2%), followed by double-outlet right ventricle (15.4%), complete transposition (13.8%), hearts with left-hand ventricular topology (10.8%), ventricular septal defect(s) (9.2%), tricuspid valvar agenesis (4.6%), and tetralogy of Fallot (4.6%). These abnormalities accounted for 87.6% of the specimens studied. We also cataloged the extracardiac malformations found at autopsy in those patients who died despite the transplantation. Extracardiac malformations were identified in 10 of the 19 patients who came to autopsy. Three had heterotaxy syndrome with isomerism of the atrial appendages, one with right and two with left isomerism. Other anomalies included tracheoesophageal fistula, pulmonary sequestration, extrahepatic biliary atresia, duodenal atresia, choanal atresia, and vascular malformations.Our study shows that even the most complicated cardiac malformations can readily be diagnosed in an explanted heart using the segmental approach based on observed morphology.

Adolescent↗
PubMed2001

High-density single-nucleotide polymorphism (SNP) map of the 150-kb region corresponding to the human ATP-binding cassette transporter A1 (ABCA1) gene.

Highly dense catalogs of human genetic variations, in combination with high-throughput genotyping technologies, are expected to clarify individual genetic differences in pharmacological responsiveness and predispositions to common diseases. Here we report single-nucleotide polymorphisms (SNPs) present among 48 Japanese individuals at the locus for the human ATP-binding cassette transporter A1 (ABCA1) gene. ABCA1 plays a key role in apolipoprotein-mediated cholesterol transport, and mutations in this gene are responsible for Tangier disease and familial high-density lipoprotein deficiency associated with reduced cholesterol efflux. We identified a total of 162 SNPs, 149 of which were novel, within the 150-kb region encompassing the entire ABCA1 gene. Eight of the SNPs lie within coding elements, two in 5' flanking regions, 147 in introns, and five in 3' untranslated regions, but none were found in 5' untranslated or 3' flanking regions. The ratio of transitions to transversions was approximately 2.37 to 1. Our dense SNP map of this region could serve as a powerful resource for studies of complex genetic diseases that may be associated with ABCA1 and of individual responses to drug therapy.

ATP Binding Cassette Transporter 1↗