ISOLATION AND PARTIAL CHARACTERIZATION OF NITRATE ASSIMILATION MUTANTS OF DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE)1

Fifteen nitrate assimilation-deficient mutants of the euryhaline green alga, Dunaliella tertiolecta Butcher were selected by their chlorate resistance. Ten mutants, unable to grow on NO₃^? but able to grow on NO₂^?, had no detectable nitrate reductase activity. Five mutants, unable to grow on either NO₃^? or NO₂^?, had depressed levels of both nitrate and nitrite reductase. A method for assaying methyl viologen-nitrate reductase in the presence of nitrite reductase is described.     

Functional Overlay: An Illegitimate Diagnosis?

Functional overlay is not a recognized psychiatric diagnosis. Evaluating functional overlay and differentiating between this concept and organic conditions is important in medicolegal areas in which financial values are placed on pain and disability. Functional overlay is not malingering: the former is based on preconscious or unconscious mechanisms, the latter is consciously induced.In considering psychologic reactions to pain and disability, a gradient of simulation, malingering, symptom exaggeration, overvaluation, functional overlay and hysteria is useful. The dynamics of overlay are a combination of anxiety from body-image distortion and depression from decreased efficiency of the body, as well as the resulting psychosocial disruption in a patient''s life.     

An assay for adenyl cyclase based on a combination of sodium borate electrophoresis and paper chromatography.

We describe a method for the assay of adenyl cyclase in whole tissue homogenates. Adenosine 3′:5′-cyclic monophosphate (cAMP) formed from α-³²P-, ¹⁴C- or ³H-labeled adenosine 5′-triphosphate (ATP) substrate is isolated from all known ATP metabolites and an unknown metabolite by electrophoresis in 1% sodium borate for 40 min, followed by overnight descending chromatography in 95% ethanol:1 m ammonium acetate (70:30). The purity of the cAMP isolated is established by chromatographic techniques as well as by utilizing a purified cyclic nucleotide phosphodiesterase. The method described here also makes possible the measurement of phosphodiesterase activity in homogenates. It is rapid enough to allow routine assay of 180 samples per day, although the number of samples processed depends on the number of electrophoretic and chromatographic units available.     

Chapter 15: Disease Gene Prioritization

Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest possible causal links. A fair amount of this evidence comes from high-throughput experimentation. Thus, well-developed methods are necessary to reliably deal with the quantity of information at hand. Existing gene prioritization techniques already significantly improve the outcomes of targeted experimental studies. Faster and more reliable techniques that account for novel data types are necessary for the development of new diagnostics, treatments, and cure for many diseases.

This article is part of the “Translational Bioinformatics" collection for PLOS Computational Biology.

What to Learn in This Chapter

• Identification of specific disease genes is complicated by gene pleiotropy, polygenic nature of many diseases, varied influence of environmental factors, and overlying genome variation.
• Gene prioritization is the process of assigning likelihood of gene involvement in generating a disease phenotype. This approach narrows down, and arranges in the order of likelihood in disease involvement, the set of genes to be tested experimentally.
• The gene “priority" in disease is assigned by considering a set of relevant features such as gene expression and function, pathway involvement, and mutation effects.
• In general, disease genes tend to 1) interact with other disease genes, 2) harbor functionally deleterious mutations, 3) code for proteins localizing to the affected biological compartment (pathway, cellular space, or tissue), 4) have distinct sequence properties such as longer length and a higher number of exons, 5) have more orthologues and fewer paralogues.
• Data sources (directly experimental, extracted from knowledge-bases, or text-mining based) and mathematical/computational models used for gene prioritization vary widely.

     

Association between pygmy right whales (Caperea marginata) and areas of high marine productivity off Australia and New Zealand

Abstract

Opportunistic sightings and strandings of Caperea marginata (n=196) from the vicinity of Australia and New Zealand (1884 to early 2007) were used to relate geographic and temporal patterns to oceanographic and broad-scale climatic variability. Records were not uniformly distributed along the coast and more (69%) were from Australia than New Zealand. Seven coastal whale ‘hotspots’ were identified which accounted for 61% of records with locality data. Half of the hotspot records were from southeast (37) and northwest (20) Tasmania—others each had 9–15 events. Upwelling and/or high zooplankton abundance has been documented near all whale hotspots. Records of C. marginata occurred in all months, with 75% in spring and summer. Inter-annual variability showed broad agreement between increased whale records (usually in spring/summer) and strongly positive ‘Niño 3.4’ during 1980–1995 but not thereafter. Coastal upwelling and productivity increase during climatic phenomena such as El Niño and are likely to be quickly beneficial to plankton-feeding whales such as C. marginata.     

Quinolone action against human topoisomerase IIalpha: stimulation of enzyme-mediated double-stranded DNA cleavage

Several important antineoplastic drugs kill cells by increasing levels of topoisomerase II-mediated DNA breaks. These compounds act by two distinct mechanisms. Agents such as etoposide inhibit the ability of topoisomerase II to ligate enzyme-linked DNA breaks. Conversely, compounds such as quinolones have little effect on ligation and are believed to stimulate the forward rate of topoisomerase II-mediated DNA cleavage. The fact that there are two scissile bonds per double-stranded DNA break implies that there are two sites for drug action in every enzyme-DNA cleavage complex. However, since agents in the latter group are believed to act by locally perturbing DNA structure, it is possible that quinolone interactions at a single scissile bond are sufficient to distort both strands of the double helix and generate an enzyme-mediated double-stranded DNA break. Therefore, an oligonucleotide system was established to further define the actions of topoisomerase II-targeted drugs that stimulate the forward rate of DNA cleavage. Results indicate that the presence of the quinolone CP-115,953 at one scissile bond increased the extent of enzyme-mediated scission at the opposite scissile bond and was sufficient to stimulate the formation of a double-stranded DNA break by human topoisomerase IIalpha. These findings stand in marked contrast to those for etoposide, which must be present at both scissile bonds to stabilize a double-stranded DNA break [Bromberg, K. D., et al. (2003) J. Biol. Chem. 278, 7406-7412]. Moreover, they underscore important mechanistic differences between drugs that enhance DNA cleavage and those that inhibit ligation.     

Successful immunotherapy with matrix metalloproteinase-derived peptides in adjuvant arthritis depends on the timing of peptide administration

We have recently found that matrix metalloproteinases (MMPs) are targets for T-cell and B-cell reactivity in experimental arthritis. In the present article, we investigate whether modulation of MMP-specific T-cell responses could influence the course of adjuvant arthritis (AA). Lewis rats were treated nasally with MMP peptides prior to or after AA induction. Administration of the MMP-10 or the MMP-16 peptide prior to AA induction reduced the arthritic symptoms. In contrast, administration of the MMP-10 peptide after AA induction aggravated the arthritic symptoms. The present study shows the possible usefulness of MMP peptides for immunotherapy. However, a clear understanding of proper timing of peptide administration is crucial for the development of such therapies.     

Violacein biotransformation by basidiomycetes and bacteria

AIMS: The biotransformation study of the pigment (violacein) produced by Chromobacterium violaceum, was verified by its decolorization utilizing six different organisms in liquid and solid media. METHODS AND RESULTS: Lentinus edodes showed the fastest violacein decolorization (8th d) in solid medium whereas in a liquid medium, violacein was rapidly decolorized in 2 h by Azotobacter vinelandii. Adsorption experiments indicated no significant contribution for the decolorization process for all organisms in both media. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The results showed poor lignin peroxidase activity in both media but manganese peroxidase and laccase activity varied according to the organism used. Siderophores presence was also detected in all organisms mainly in the liquid medium experiment.     

Self-association of mucin

Aggregation phenomena in aqueous solutions of purified human tracheobronchial mucin have been studied by rheological methods, steady-state fluorescence, quasielastic light scattering, and spin probe techniques. At temperatures below 30 degrees C and concentrations above 15 mg/mL and in the absence of chaotropic agents, mucin solutions are viscoelastic gels. A gel-sol transition is observed at temperatures above 30 degrees C that is manifested by the diminishing storage modulus and a loss tangent above unity throughout the studied frequency range of the oscillatory shear. No decline in the mucin molecular weight is observed by size-exclusion chromatography above 30 degrees C in the absence of redox agents or proteolytic enzymes. Aggregation of hydrophobic protein segments of the mucin chains at 37 degrees C is indicated by QELS experiments. The decreasing polarity of the microenvironment of pyrene solubilized into mucin solutions at temperatures above 30 degrees C, concomitant with the gel-sol transition, shows the hydrophobicity of the formed aggregates. ESR spectra of the fatty acid spin probe, 16-doxylstearic acid indicate that the aggregate-aqueous interface becomes more developed at elevated temperatures.     

Nociceptive mechanisms modulate ozone-induced human lung function decrements

We have previously suggested that ozone(O₃)-induced pain-relatedsymptoms and inhibition of maximal inspiration are due to stimulationof airway C fibers (M. J. Hazucha, D. V. Bates, and P. A. Bromberg.J. Appl.Physiol. 67: 1535-1541, 1989). If this were so,pain suppression or inhibition by opioid-receptor agonists shouldpartially or fully reverseO₃-induced symptomatic and lung functional responses. The objectives of this study were to determine whether O₃-induced pain limitsmaximal inspiration and whether endogenous opioids contribute tomodulation of the effects of inhaledO₃ on lung function. Theparticipants in this double-blind crossover study were healthyvolunteers (18-59 yr) known to be "weak" (WR;n = 20) and "strong"O₃ responders (SR;n = 42). They underwent either two 2-hexposures to air or two 2-h exposures to 0.42 parts/millionO₃ with moderate intermittentexercise. Immediately afterpost-O₃ spirometry, the WR wererandomly given either naloxone (0.15 mg/kg iv) or saline, whereas SRrandomly received either sufentanil (0.2 µg/kg iv) or saline.O₃ exposure significantly(P < 0.001) impaired lung function.In SR, sufentanil rapidly, although not completely, reversed both thechest pain and spirometric effects (forced expiratory volume in 1 s;P < 0.0001) compared with saline.Immediate postexposure administration of saline or naloxone had nosignificant effect on WR. Plasma -endorphin levels were not relatedto an individual's O₃responsiveness. Cutaneous pain variables showed a nonsignificantweak association with O₃responsiveness. These observations demonstrate that nociceptive mechanisms play a key role in modulatingO₃-induced inhibition ofinspiration but not in causing lack of spirometric response toO₃ exposure in WR.