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Biomedical subjects

D Block

Publications and source records attributed to D Block.

At least 19 recordsLinked to original sources

Genquire: genome annotation browser/editor.

UNLABELLED: We present a software package, Genquire, that allows visualization, querying, hand editing, and de novo markup of complete or partially annotated genomes. The system is written in Perl/Tk and uses, where possible, existing BioPerl data models and methods for representation and manipulation of the sequence and annotation objects. An adaptor API is provided to allow Genquire to display a wide range of databases and flat files, and a plugins API provides an interface to other sequence analysis software. AVAILABILITY: Genquire v3.03 is open-source software. The code is available for download and/or contribution at http://www.bioinformatics.org/Genquire

Chromosome Mapping↗

Mode selective control of drift wave turbulence.

Experiments on spatiotemporal open-loop synchronization of drift wave turbulence in a magnetized cylindrical plasma are reported. The synchronization effect is modeled by a rotating current profile with prescribed mode structure. Numerical simulations of an extended Hasegawa-Wakatani model show good agreement with experimental results.

Journal Article↗

Synchronization of drift waves.

Based on a thorough experimental study of the equilibrium plasma state and the description of coherent drift modes in the framework of a linear, nonlocal model, the response of drift modes to different external driver signal is reported. Purely temporal perturbations as well as corotating and counter-rotating electric fields of various mode numbers are applied to the system. Drift mode synchronization and periodic pulling, typical for driven nonlinear oscillator systems, are investigated in detail. The full spatio-temporal behavior of periodic pulling is observed with multiprobe arrays.

Journal Article↗

Toxicity of fipronil and its degradation products to Procambarus sp.: field and laboratory studies.

Fipronil is a phenylpyrazole insecticide that is the active ingredient in the pesticide Icon 6.2 FS which is applied to rice seeds targeting the rice water weevil. An arthropod-selective insecticide, fipronil blocks the GABA-gated chloride channel and is unique in that several of its degradation products have been indicated to be equal or more potent than fipronil. After application of rice seeds (2-3 days postplant) to flooded rice fields, water is typically pumped from the rice fields and can be used for the culture of crayfish (Procambarus sp.). Because fipronil is selective for arthropods, is transported via organic sediment, and crayfish consume organic sediment, 96-h LC(50) experiments were conducted with fipronil and three of its environmental derivatives in crayfish under conditions without carrier solvents in water of similar pH, alkalinity, and hardness as observed in south Louisiana crayfish culture ponds. Measured LC(50)s for fipronil to red swamp (Procambarus clarkii) and white river (Procambarus zonangulus) crayfish were 14.3 (95% CI; 5.1-23.4) and 19.5 (95% CI; 11.1-27.9) microg/L, respectively. LC(50)s of fipronil sulfone (11.2; 9.2-13.2 microg/L), fipronil sulfide (15.5; 13-18 microg/L); and the photoproduct, desulfinyl fipronil (68.6; 46-95.2 microg/L) displayed very high toxicity in crayfish. In situ toxicity studies using caged crayfish in culturing ponds receiving effluent from drained rice fields indicated that effluent from rice fields planted with Icon-treated seed was significantly more toxic compared to untreated surface water (40% survival compared to 83% survival). Hazard quotient comparisons using measured water concentrations in the field and laboratory-based LC(50)s indicated that fipronil and its metabolites in water resulting from Icon-treated rice seed planting poses a significant risk to crayfish survival.

Animals↗

New concepts in systemic autoimmunity testing.

Diagnosis of systemic autoimmune diseases is highly complex, and it is becoming increasingly difficult to make assumptions about the functional roles and diagnostic significance of autoantibodies. The latter is mainly due to the fact that results from different assay systems are not interchangeable. A laboratory "gold standard" which helps the clinician to differentiate irrelevant autoimmune phenomena from significant autoimmune diseases at an early stage, is clearly missed. To meet this challenge, a rheuma entrance screening (RES) assay toolbox is proposed based on fully-automated enzyme immunoassay (EIA) technology on one system for the clinical and routine laboratory. The RES concept is intended to cover the most important syndromes of systemic rheumatic diseases, i.e. collagenosis, early rheumatoid arthritis, early osteoarthritis, anti-phospholipid syndrome and inflammation. The serological part of diagnosis of these diseases comprises testing for anti-nuclear antibodies (ANA), rheumatoid factor (RF), low levels of C-reactive protein (CRP), and disease-specific anti-phospholipid antibodies, e.g. anti-beta-2 glycoprotein I (anti-beta2 GPI). To eliminate the known problems of varying assay systems in this field, a novel, objective, rapid and reproducible approach to screen for such analytes in patient serum or plasma more efficiently is the application of EIAs on the fully-automated immunoassay analyser COBAS CORE (Roche Diagnostics GmbH, Mannheim, Germany). The combined use of the RES (COBAS CORE HEp2 ANA EIA, COBAS CORE RF EIA Quant, COBAS CORE CRP EIA Quant and COBAS CORE Anti-beta2 GPI EIA) is intended for patients sent to the laboratory with the primary suspicion of harbouring a systemic rheumatic disease.

Algorithms↗

Spaceflight effects on cultured embryonic chick bone cells.

A model calcifying system of primary osteoblast cell cultures derived from normal embryonic chicken calvaria has been flown aboard the shuttle, Endeavour, during the National Aeronautics and Space Administration (NASA) mission STS-59 (April 9-20, 1994) to characterize unloading and other spaceflight effects on the bone cells. Aliquots of cells (approximately 7 x 10(6)) grown in Dulbecco's modified Eagle's medium (DMEM) + 10% fetal bovine serum (FBS) were mixed with microcarrier beads, inoculated into cartridge culture units of artificial hollow fiber capillaries, and carried on the shuttle. To promote cell differentiation, cartridge media were supplemented with 12.5 microg/ml ascorbate and 10 mM beta-glycerophosphate for varying time periods before and during flight. Four cartridges contained cells from 17-day-old embryos grown for 5 days in the presence of ascorbate prior to launch (defined as flight cells committed to the osteoblastic lineage) and four cartridges supported cells from 14-day-old embryos grown for 10 days with ascorbate before launch (uncommitted flight cells). Eight cartridges prepared in the same manner were maintained under normal gravity throughout the flight (control cells) and four additional identical cartridges under normal gravity were terminated on the day of launch (basal cells). From shuttle launch to landing, all cartridges were contained in closed hardware units maintaining 5% CO2, 37 degrees C, and media delivery at a rate of approximately 1.5 ml/6 h. During day 3 and day 5 of flight, duplicate aliquots of conditioned media and accumulated cell products were collected in both the flight and the control hardware units. At the mission end, comparisons among flight, basal, and control samples were made in cell metabolism, gene expression for type I collagen and osteocalcin, and ultrastructure. Both committed and uncommitted flight cells were metabolically active, as measured by glucose uptake and lactate production, at approximately the same statistical levels as control counterparts. Flight cells elaborated a less extensive extracellular matrix, evidenced by a reduced collagen gene expression and collagen protein appearance compared with controls. Osteocalcin was expressed by all cells, a result indicating progressive differentiation of both flight and control osteoblasts, but its message levels also were reduced in flight cells compared with ground samples. This finding suggested that osteoblasts subjected to flight followed a slower progression toward a differentiated function. The summary of data indicates that spaceflight, including microgravity exposure, demonstrably affects bone cells by down-regulating type I collagen and osteocalcin gene expression and thereby inhibiting expression of the osteogenic phenotype notably by committed osteoblasts. The information is important for insight into the response of bone cells to changes of gravity and of force in general.

Animals↗

Two non-contiguous regions contribute to nidogen binding to a single EGF-like motif of the laminin gamma 1 chain.

High affinity binding of nidogen to laminin is mediated by an EGF-like repeat gamma 1III4 of the mouse laminin gamma 1 chain and has now been restricted to two short noncontiguous regions of its 56 residue sequence by use of synthetic peptides and recombinant mutants. Disulfide loop a,b of the repeat and a modified loop a,c could completely inhibit binding, with a 5000-fold or 300-fold reduced affinity respectively. Synthetic loops c and d lacked inhibitory activity. Some binding contribution of Tyr819 in loop c was, however, shown by mutation and side chain modification. Together with studies of loop chimeras, this indicated a distinct cooperativity between the two binding sites. The major binding site of loop a was localized to the heptapeptide NIDPNAV (position 798-804). A change of Asp800 to Asn or Ala803 to Val caused a strong reduction in binding activity, while only small effects were observed for the changes Pro801 to Gln and Ile799 to Val. The latter replacement corresponds to the single substitution found in the same region of the Drosophila laminin gamma 1 chain. However, the changes Asn802 to Ser or Val804 to Ser, both known to exist in the laminin gamma 2 chain, were deleterious mutations. This demonstrated conservation of binding structures in laminins of distantly related species, but not between homologous chains of laminin isoforms.

Amino Acid Sequence↗

Placental teratoma.

The rare teratoma of the placenta has been compared to the fetus amorphus, two distinguishing characteristics being the teratoma's lack of structural organization and lack of large vessels entering the tumor. A case of placental teratoma and theories of origin are discussed.

Adult↗

Fasted state impedes recovery of porcine hepatic oxygen consumption after warm hepatic ischemia.

The most effective means to prepare the hepatic donor liver for harvest, preservation, and transplantation are not known. Studies have shown that in combination with an injury to the liver, fasting reduces hepatic function. This study randomized 20 market pigs, 20 to 45 kg, to an overnight fast (fed group) or a 42-hour fast (fasted group). Under general anesthetic perfusion of the portal vein and hepatic artery were controlled. Studies were performed at high flow (30 ml/min/kg portal flow and 10 ml/min/kg arterial flow) and after a 90-minute period of warm ischemia (no flow). Flow was restored at 25% of the original (low flow), then increased to 50% of the original (medium flow). After the ischemic insult, the fed group improved hepatic oxygen consumption at a faster rate than the fasted group (p less than 0.05 by ANOVA). In addition, significant differences were noted between the fed and fasted groups in the amount of insulin delivered by the portal venous system to the liver (p less than 0.001 by ANOVA). Hepatic oxygen consumption was related to insulin delivery (r2 = 0.46; p less than 0.001) for both groups. The data suggest that acute changes in the nutritional status of both the donor and the recipient may affect hepatic recovery from ischemia.

Amino Acids↗

Attitudes of mothers toward sex education.

Data are presented on the attitudes of mothers from the entire social class spectrum toward content and timing of sex education for children (CT-Attitudes), and also toward sex education in school (S-Attitudes) in two California communities in 1969. Findings underscore the necessity to consider these two attitudinal variables separately. As a result of their separation for study purposes, it was possible to arrive at a four-fold typology or grouping of mothers: 1) CT liberals in favor, and 2) CT liberals opposed to sex education in schools, 3) CT conservatives in favor, and 4) CT conservatives opposed to school programs of sex education. It is inferred that educational planners need to pay due regard to the sentiments of all four maternal groups and all social classes in developing sex education programs for families and for school children.

Adolescent↗