Multidrug-resistant tumor cells with decreased malignancy: a role for integrin alphavbeta3

We studied whether acquisition of multidrug resistance (MDR) by tumor cells can alter their integrin profile and malignant behavior. Hamster fibroblast cell line HET-SR-2SC-LNM was selected for MDR, yielding the 2SC/20 subline. Compared with the parental cells, the 2SC/20 subline weakly adhered to denatured collagen (dCol) which correlated with decreased expression of alphavbeta3, a dCol receptor. Importantly, 2SC/20 subline demonstrated significantly decreased activity of collagenase MMP-2, lower ability to invade Matrigel, and attenuated metastasis in syngeneic animals. We provide evidence for the first time that selection for MDR can be associated with down-regulation of alphavbeta3 integrin, supporting our recent proof of the pro-apoptotic role of this integrin (Oncogene 20 (2001) 4710). Lack of alphavbeta3 expression may link cell survival under toxic conditions with decreased malignancy of the resulting drug resistant tumor.     

Codon usage in Xanthophyllomyces dendrorhous (formerly Phaffia rhodozyma)

By sequence analysis of 96 randomly selected clones in a cDNA library of Xanthophyllomyces dendrorhous, ten novel, full-length clones encoding cytoplasmic ribosomal proteins (rp) were found. The deduced amino acid sequences showed significant homology to their counterparts from eukaryotic origin including mammals, fungi and plants. Some ribosmal protein encoding cDNAs appeared several times, but by Southern blot analysis it was shown they are encoded by a single copy gene. The nucleotide sequences of ten full length cDNAs were used to investigate the codon usage in X. dendrorhous.     

The Effect of Chilling of the Physiological and Simulated Apex of 2- and 3-leaf Plants of Pisum sativum L. cv. Alaska on Lateral Shoot Growth, C-14 IAA Movement and P-32 Accumulation

The apex of a 3-leaf pea plant was chilled in cold chambers maintained at 5–7°C. The lateral shoots 1 through 5 grew, and shoot 5 eventually dominated other lateral shoots. The apex when returned to the ambient temperature did not reimpose apical dominance. The growing lateral shoots competed with the stem apex. The apices of 2- and 3-leaf plants were chilled and P-32 distribution in these plants was studied in the entire plant, at various intervals of time. Phosphorus-32 accumulation followed the growth pattern of the plant. The lateral shoots accumulated P-32 activity and very little activity was accumulated by the apex. The dominating shoots 2 and 5 accumulated the maximum amount of activity in 2- and 3-leaf plants, respectively. Labeled-IAA moved basipetally through the stem when applied to the cut stump simulating the apex. By cold treatment the translocation of IAA was influenced more than its absorption. The plant seems to metabolize this compound in the later periods of application. The plant now becomes “insensitive” to auxin and the lateral shoots grow.     

Protease-sensitive scrapie prion protein in aggregates of heterogeneous sizes

The pathological prion protein PrP(Sc) is the only known component of the infectious prion. In cells infected with prions, PrP(Sc) is formed posttranslationally by the refolding of the benign cell surface glycoprotein PrP(C) into an aberrant conformation. The two PrP isoforms possess very different properties, as PrP(Sc) has a protease-resistant core, forms very large amyloidic aggregates in detergents, and is only weakly immunoreactive in its native form. We now show that prion-infected rodent brains and cultured cells contain previously unrecognized protease-sensitive PrP(Sc) varieties. In both ionic (Sarkosyl) and nonionic (n-octyl beta-D-glucopyranoside) detergents, the novel protease-sensitive PrP(Sc) species formed aggregates as small as 600 kDa, as measured by gel filtration. The denaturation dependence of PrP(Sc) immunoreactivity correlated with the size of the aggregate. The small PrP(Sc) aggregates described here are consistent with the previous demonstration of scrapie infectivity in brain fractions with a sedimentation coefficient as small as 40 S [Prusiner et al. (1980) J. Neurochem. 35, 574-582]. Our results demonstrate for the first time that prion-infected tissues contain protease-sensitive PrP(Sc) molecules that form low MW aggregates. Whether these new PrP(Sc) species play a role in the biogenesis or the pathogenesis of prions remains to be established.     

Characterization of putative hydrophobic substrate binding site residues of a Delta class glutathione transferase from Anopheles dirus

To date, investigations of the hydrophobic substrate site of the insect Delta class glutathione transferase are limited in number. In the present study, putative hydrophobic site residues of AdGSTD4-4 have been proposed and characterized. These residues are Gln-112, Thr-174, Phe-212, Arg-214, Tyr-215 and Phe-216. It was found that Gln-112 does not contribute significantly to the catalytic properties of AdGSTD4-4. Arg-214, Tyr-215 and Phe-216 made contributions to catalytic properties and the rate-limiting step. Thr-174 and Phe-212 appeared to be important in enzymatic catalysis by stabilizing the active site β1-α1 loop on which the critical catalytic residue Ser-9 is located. The aromatic Phe-212 pi cloud appears to be important for interactions with its hydrophobic size representing an almost equally important factor. The data suggests that these residues are not directly involved in catalysis but exert their influence through secondary interactions. In addition, active site rearrangements occur to bring different residues into play even for conjugation through the same mechanisms. Therefore, due to the conformational rearrangements topologically equivalent residues observed in crystal structures may not perform equivalent roles in catalysis in different GST classes.     

GeneTrack--a genomic data processing and visualization framework

MOTIVATION: High-throughput 'ChIP-chip' and 'ChIP-seq' methodologies generate sufficiently large data sets that analysis poses significant informatics challenges, particularly for research groups with modest computational support. To address this challenge, we devised a software platform for storing, analyzing and visualizing high resolution genome-wide binding data. GeneTrack automates several steps of a typical data processing pipeline, including smoothing and peak detection, and facilitates dissemination of the results via the web. Our software is freely available via the Google Project Hosting environment at http://genetrack.googlecode.com     

CFTR mutations in Turkish and North African cystic fibrosis patients in Europe: implications for screening

AIMS: To obtain more insight into the variability of the CFTR mutations found in immigrant cystic fibrosis (CF) patients who are living in Europe now, and to estimate the test sensitivity of different frequently used methods of DNA analysis to detect CF carriers or patients among these Turkish or North African immigrants. METHODS: A survey among 373 European CF centers asking which CFTR mutations had been found in Turkish and North African CF patients. RESULTS: 31 and 26 different mutations were reported in Turkish and North African patients, identifying 64.2% (113/176) and 87.4% (118/135) alleles, respectively (p < 0.001). The mean sensitivity (detection rate) of three most common CFTR mutation panels to detect these mutations differed between Turkish and North African people, 44.9% (79/176) versus 69.6% (94/135) (p < 0.001), and can be increased to 57.4% (101/176) and 79.3% (107/135) (p < 0.001), respectively, by expanding these panels with 13 mutations which have been found on two or more alleles. CONCLUSION: 35.8% and 12.6%, respectively, of CF alleles in Turkish and North African patients living in Europe now had not been identified. Among these populations, the test sensitivity of common CFTR mutation panels is insufficient for use in screening programs in Europe, even after expansion with frequent Turkish and North African mutations. This raises questions about whether and how to implement CF carrier and neonatal screening in a multiethnic society.     

Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate: coenzyme a ligase for expanded substrate range

Environmental aromatic acids are transformed to chemical energy in bacteria that possess the requisite secondary pathways. Some of these pathways rely on the activation of the aromatic acid by coenzyme A (CoA) thioesterification catalyzed by an aromatic acid: CoA ligase. Adaptation of such pathways to the bioremediation of man-made pollutants such as polychlorinated biphenyl (PCB) and dichlorodiphenyltrichloroethane (DDT) requires that the chlorinated benzoic acid byproduct that is formed be able to be eliminated by further degradation. To take advantage of natural benzoic acid degrading pathways requiring initial ring activation by thioesterification, the pathway aromatic acid:CoA ligase must be an effective catalyst with the chlorinated benzoic acid. This study, which focuses on the 4-chlorobenzoate:CoA ligase (CBL) of the 4-monochlorobiphenyl degrading bacterium Alcaligenes sp. strain ALP83, was carried out to determine if the 4-chlorobenzoate binding site of this enzyme can be transformed by rational design to recognize the chlorobenzoic acids formed in the course of breakdown of other environmental PCB congeners. The fundamental question addressed in this study is whether it is possible to add or subtract space from the substrate-binding pocket of this ligase (to complement the topology of the unnatural aromatic substrate) without causing disruption of the ligase catalytic machinery. Herein, we report the results of a substrate specificity analysis that, when interpreted within the context of the X-ray crystal structures, set the stage for the rational design of the ligase for thioesterification of two PCB-derived chlorobenzoic acids. The ligase was first optimized to catalyze CoA thioesterification of 3,4-dichlorobenzoic acid, a poor substrate, by truncating Ile303, a large hydrophobic residue that packs against the ring meta-C(H) group. The structural basis for the approximately 100-fold enhancement in the rate of 3,4-dichlorobenzoate thioesterification catalyzed by the I303A and I303G CBL mutants was validated by determination of the crystal structure of the 3,4-dichlorobenzoate-bound enzymes. Determinations of the structures of I303 mutant complexes of 3-chlorobenzoate, a very poor substrate, revealed nonproductive binding as a result of the inability of the substrate ring C(4)H group to fill the pocket that binds the C(4)Cl group of the native substrate. The C(4)Cl pocket of the CBL I303A mutant was then reduced in size by strategic amino acid replacement. A 54-fold improvement in catalytic efficiency was observed for the CBL F184W/I303A/V209T triple mutant. The results of this investigation are interpreted as evidence that the plasticity of the ligase catalytic scaffold is sufficient to allow expansion of substrate range by rational design. The combination of structural and kinetic analyses of the constructed mutants proved to be an effective approach to engineering the ligase for novel substrates.     

Reproductive biology of the endemic goby, Lentipes concolor, from Makamaka'ole Stream, Maui and Waikolu Stream, Moloka'i

Constant pressure in Hawai'i to use limited freshwater resources has resulted in increasing concern for the future of the native stream fauna. Hawaiian freshwater gobies have an amphidromous life cycle with a marine larva period and require streams which flow continuously to the ocean for the critical reproductive periods and during recruitment. As such, the stream fauna is particularly sensitive to any anthropogenic perturbations which disrupt the continuity of stream flows. The objective of this 2-year study was to compare the life cycles of the goby, Lentipes concolor, from a heavily diverted stream on Moloka'i and a relatively undisturbed stream on Maui. In Makamaka'ole Stream, Maui, the population of L. concolor was reproductively active all year with females potentially spawning 2–3 times annually. The timing of spawning did not occur consistently during the wet or dry season but coincided with high stream flow conditions regardless of time-of-year. In Waikolu Stream, Moloka'i, the reproductive pattern was more variable with the number of reproductively active females ranging from 0% to 100%. In general the number of eggs was greater and egg size smaller for female L. concolor in Waikolu Stream than in Makamaka'ole Stream. However, female reproductive condition of L. concolor from Maui was consistently higher than from fish on Moloka'i. Reproduction of L. concolor in Makamaka'ole Stream was correlated with the seasonal pattern of flow rates with peaks in female reproductive condition associated with periods of elevated discharge. No correlation between reproduction and discharge occurred in Waikolu Stream. There were considerable differences between the magnitude of discharge in the two streams. Waikolu Stream experienced prolonged periods of extremely low flows which have become common since the Moloka'i Irrigation System began diverting water from the stream in 1960. In Makamaka'ole Stream, L. concolor was capable of reproducing throughout the year and adjusting fecundity in response to stream flow conditions. In contrast, the population in Waikolu Stream appeared to have a ‘boom or bust’ reproductive pattern; the population had reduced or no reproduction when stream flow conditions reached extreme low levels, but the population succesfully reproduced during higher flow months. The diversion structure in Waikolu Stream has dampened the natural seasonal discharge cycle, exacerbated natural low flow conditions, and increased the likelihood of prolonged periods of extremely low flow. Stream management practices in the Hawaiian Islands must take into account the complex life cycles and sensitivity to variable stream flow conditions of the native fauna. This revised version was published online in July 2006 with corrections to the Cover Date.