Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication

The development of surrogate markers capable of detecting residual ongoing human immunodeficiency virus type 1 (HIV-1) replication in patients receiving highly active antiretroviral therapy is an important step in understanding viral dynamics and in developing new treatment strategies. In this study, we evaluated the utility of circular forms of the viral genome for the detection of recent infection of cells by HIV-1. We measured the fate of both one-long terminal repeat (1-LTR) and 2-LTR circles following in vitro infection of logarithmically growing CD4+ T cells under conditions in which cell death was not a significant contributing factor. Circular forms of the viral genome were found to be highly stable and to decrease in concentration only as a function of dilution resulting from cell division. We conclude that these DNA circles are not intrinsically unstable in all cell types and suggest that the utility of 2-LTR circle assays in measuring recent HIV-1 infection of susceptible cells in vivo needs to be reevaluated.     

Multiple cross mapping (MCM) markedly improves the localization of a QTL for ethanol-induced activation

This study examines the use of multiple cross mapping (MCM) to reduce the interval for an ethanol response QTL on mouse chromosome 1. The phenotype is the acute locomotor response to a 1.5-g/kg i.p. dose of ethanol. The MCM panel consisted of the six unique intercrosses that can be obtained from the C57BL/6J (B6), DBA/2J (D2), BALB/cJ (C) and LP/J (LP) inbred mouse strains (N ≥ 600/cross). Ethanol response QTL were detected only with the B6xD2 and B6xC intercrosses. For both crosses, the D2 and C alleles were dominant and decreased ethanol response. The QTL information was used to develop an algorithm for sorting and editing the chromosome 1 Mit microsatellite marker set ( http://www.jax.org ) . This process yielded a cluster of markers between 82 and 85 cM (MGI). Evidence that the QTL was localized in or near this interval was obtained by the analysis of a sample ( n  = 550) of advanced cross heterogenous stock animals. In addition, it was observed that one of the BXD recombinant inbred strains (BXD-32) had a recombination in the interval of interest which produced the expected change in behavior. Overall, the data obtained suggest that the information available within existing genetic maps coupled with MCM data can be used to reduce the QTL interval. In addition, the MCM data set can be used to interrogate gene expression data to estimate which polymorphisms within the interval of interest are relevant to the QTL.     

Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15)N and (13)CO) NMR relaxation and computational molecular dynamics

The nano-pico second backbone dynamics of the ribonuclease binase, homologous to barnase, is investigated with (15)N, (13)C NMR relaxation at 11.74 and 18.78 T and with a 1.1 ns molecular dynamics simulation. The data are compared with the temperature factors reported for the X-ray structure of this enzyme. The molecular dynamics and X-ray data correspond well and predict motions in the loops 56-61 and 99-104 that contain residues that specifically recognize substrate and are catalytic (His101), respectively. In contrast, the (15)N relaxation data indicate that these loops are mostly ordered at the nano-pico second time scale. Nano-pico second motions in the recognition loop 56-61 are evident from (13)CO-(13)C cross relaxation data, but the mobility of the catalytic loop 99-104 is not detected by (13)CO cross relaxation either. From the results of this and previous work [Wang, L., Pang, Y., Holder, T., Brender, J. R., Kurochkin, A., and Zuiderweg, E. R. P. (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 7684-7689], the following dynamical characterization of the active site area of binase emerges: a beta sheet, rigid at all probed time scales, supports the catalytic residue Glu 72. Both substrate-encapsulating loops are mobile on both fast and slow time scales, but the fast motions of the loop which contains the other catalytic residue, His 101, as predicted by B-factors and computational molecular dynamics is not detected by NMR relaxation. This work strongly argues for the use of several measures in the study of protein dynamics.     

The effects of fungicides on the phylloplane yeast populations of creeping bentgrass

The effects of fungicides on population size and the development of fungicide resistance in the phylloplane yeast flora of bentgrass was investigated. In the spring of 2001, azoxystrobin, chlorothalonil, flutolanil, and propiconazole were applied separately over a 6-week period to creeping bentgrass (Agrostis palustris Huds.). Total and fungicide-resistant yeast populations were assessed by dilution plating onto either potato dextrose agar or potato dextrose agar amended with the test fungicides. Total yeast populations in the fungicide-treated plots were significantly lower than the check plots on three out of four sample dates. In the fall, azoxystrobin or propiconazole were applied twice to the bentgrass over 3 weeks. Significantly larger total yeast populations were observed compared with resistant or highly resistant populations for each treatment on every sample date. Total yeast populations were significantly higher in the check plots compared with either the propiconazole- or azoxystrobin-treated plots on the first three of five sample dates. A collection of yeasts (N = 114) with no prior exposure to fungicides were more sensitive to chlorothalonil, propiconazole, flutolanil, and iprodione than a second group (N = 115) isolated from fungicide-treated turfgrass. These results suggest that fungicide resistance among phylloplane yeasts is widespread and could be an important factor in the development of biological control agents for turfgrass diseases.     

Cooperativity and flexibility of cystic fibrosis transmembrane conductance regulator transmembrane segments participate in membrane localization of a charged residue

Polytopic protein topology is established in the endoplasmic reticulum (ER) by sequence determinants encoded throughout the nascent polypeptide. Here we characterize 12 topogenic determinants in the cystic fibrosis transmembrane conductance regulator, and identify a novel mechanism by which a charged residue is positioned within the plane of the lipid bilayer. During cystic fibrosis transmembrane conductance regulator biogenesis, topology of the C-terminal transmembrane domain (TMs 7-12) is directed by alternating signal (TMs 7, 9, and 11) and stop transfer (TMs 8, 10, and 12) sequences. Unlike conventional stop transfer sequences, however, TM8 is unable to independently terminate translocation due to the presence of a single charged residue, Asp(924), within the TM segment. Instead, TM8 stop transfer activity is specifically dependent on TM7, which functions both to initiate translocation and to compensate for the charged residue within TM8. Moreover, even in the presence of TM7, the N terminus of TM8 extends significantly into the ER lumen, suggesting a high degree of flexibility in establishing TM8 transmembrane boundaries. These studies demonstrate that signal sequences can markedly influence stop transfer behavior and indicate that ER translocation machinery simultaneously integrates information from multiple topogenic determinants as they are presented in rapid succession during polytopic protein biogenesis.     

Automated evaluation and normalization of immunohistochemistry on tissue microarrays with a DNA microarray scanner

Hundreds of tissue samples may be assembled in a tissue microarray format for simultaneous immunostaining assessment of protein expression profiling. A DNA microarray two-color laser scanner was used for automated analysis of tissue microarray indirect immunofluorescence. On sections from both a human lung adenocarcinoma and a squamous cell carcinoma tissue microarray, fluorescence intensity for two epidermal growth factor receptors (EGFR and c-erbB2) correlates with diagnostic pathologic assessment, indicating that immunohistochemistry quantitation can be achieved. Importantly, double-label indirect immunofluorescence detection with the cDNA scanner demonstrates that one reference antigen can normalize tumor marker immunosignal for the cellular content of tissue microarray tissue cores. Therefore, DNA microarray scanners and associated image analysis software provide general and efficient analysis of tissue microarray immunostaining, including estimation of specific protein expression levels.