Characterization of SARS-CoV main protease and identification of biologically active small molecule inhibitors using a continuous fluorescence-based assay

Severe acute respiratory syndrome associated coronavirus main protease (SARS-CoV Mpro) has been proposed as a prime target for anti-SARS drug development. We have cloned and overexpressed the SARS-CoV Mpro in Escherichia coli, and purified the recombinant Mpro to homogeneity. The kinetic parameters of the recombinant SARS-CoV Mpro were characterized by high performance liquid chromatography-based assay and continuous fluorescence-based assay. Two novel small molecule inhibitors of the SARS-CoV Mpro were identified by high-throughput screening using an internally quenched fluorogenic substrate. The identified inhibitors have Ki values at low microM range with comparable anti-SARS-CoV activity in cell-based assays.     

Association of the herpes simplex virus type 1 Us11 gene product with the cellular kinesin light-chain-related protein PAT1 results in the redistribution of both polypeptides

The herpes simplex virus type 1 (HSV-1) Us11 gene encodes a multifunctional double-stranded RNA (dsRNA)-binding protein that is expressed late in infection and packaged into the tegument layer of the virus particle. As a tegument component, Us11 associates with nascent capsids after its synthesis late in the infectious cycle and is delivered into newly infected cells at times prior to the expression of viral genes. Us11 is also an abundant late protein that regulates translation through its association with host components and contains overlapping nucleolar retention and nuclear export signals, allowing its accumulation in both nucleoli and the cytosol. Thus, at various times during the viral life cycle and in different intracellular compartments, Us11 has the potential to execute discrete tasks. The analysis of these functions, however, is complicated by the fact that Us11 is not essential for viral replication in cultured cells. To discover new host targets for the Us11 protein, we searched for cellular proteins that interact with Us11 and have identified PAT1 as a Us11-binding protein according to multiple, independent experimental criteria. PAT1 binds microtubules, participates in amyloid precursor protein trafficking, and has homology to the kinesin light chain (KLC) in its carboxyl terminus. The carboxyl-terminal dsRNA-binding domain of Us11, which also contains the nucleolar retention and nuclear export signals, binds PAT1, whereas 149 residues derived from the KLC homology region of PAT1 are important for binding to Us11. Both PAT1 and Us11 colocalize within a perinuclear area in transiently transfected and HSV-1-infected cells. The 149 amino acids derived from the KLC homology region are required for colocalization of the two polypeptides. Furthermore, although PAT1 normally accumulates in the nuclear compartment, Us11 expression results in the exclusion of PAT1 from the nucleus and its accumulation in the perinuclear space. Similarly, Us11 does not accumulate in the nucleoli of infected cells that overexpress PAT1. These results establish that Us11 and PAT1 can associate, resulting in an altered subcellular distribution of both polypeptides. The association between PAT1, a cellular trafficking protein with homology to KLC, and Us11, along with a recent report demonstrating an interaction between Us11 and the ubiquitous kinesin heavy chain (R. J. Diefenbach et al., J. Virol. 76:3282-3291, 2002), suggests that these associations may be important for the intracellular movement of viral components.     

A prostate-derived cDNA that is mapped to human chromosome 19 encodes a novel protein

The epithelial cells of prostate gland secrete various secretory products that play an important role in the growth and differentiation of prostate gland. These secretory products have also been implicated in neuroendocrine differentiation of benign prostatic hyperplasia and prostate malignancy. We have cloned a prostate-derived cDNA encoding a novel protein with a predicted molecular weight of 78 kDa (P(78)), and precisely mapped the cDNA sequence to chromosome 19. The P(78) gene has a complex genomic structure with 18 exons and 17 introns. The P(78) contains two conserved structural domains with limited similarity to domain D of synapsin I. The P(78) mRNA was expressed in various human cell lines. Western blot analysis using antibody specific for the P(78) revealed the presence of the P(78) protein in the prostate cancer cell lines with much lower level in metastatic prostate cancer cell lines compared to that in a primary prostate cancer cell line.     

Multi-decadal trends in biomarkers in harp seal teeth from the North Atlantic reveal the influence of prey availability on seal trophic position

Arctic food webs are being impacted by borealisation and environmental change. To quantify the impact of these multiple forcings, it is crucial to accurately determine the temporal change in key ecosystem metrics, such as trophic position of top predators. Here, we measured stable nitrogen isotopes (δ¹⁵N) in amino acids in harp seal teeth from across the North Atlantic spanning a period of 60 years to robustly assess multi-decadal trends in harp seal trophic position, accounting for changes in δ¹⁵N at the base of the food web. We reveal long-term variations in trophic position of harp seals which are likely to reflect fluctuations in prey availability, specifically fish- or invertebrate-dominated diets. We show that the temporal trends in harp seal trophic position differ between the Northwest Atlantic, Greenland Sea and Barents Sea, suggesting divergent changes in each local ecosystem. Our results provide invaluable data for population dynamic and ecotoxicology studies.     

Structure of the Red Fluorescence Band in Chloroplasts

Using Weber's method of "matrix analysis" for the estimation of the number of fluorescent species contributing to the emission of a sample, it is shown that the fluorescence¹ band in spinach chloroplast fragments at room temperature originates in two species of chlorophyll a. Emission spectra obtained upon excitation with different wavelengths of light (preferentially absorbed in chlorophyll a or b) are presented. Upon cooling to - 196°C, the fluorescence efficiency increases about twentyfold. Two additional bands, that now appear at 696 and 735 mµ, suggest the participation of four molecular species. Emission spectra observed at different concentrations of chloroplast fragments with excitation in chlorophyll a and b and excitation spectra for different concentrations of chloroplast fragments and measurements at 685 and 760 mµ are presented. Two of the four emission bands may belong to pigment system I and two to system II. The 685, 696, and 738 mµ bands respond differently to temperature changes. In the -196°C to -150°C range, the intensity of the 685 mµ band remains constant, and that of the 696 mµ band decreases twice as fast as that of the 738 mµ band.     

Crude ethanolic extract, lignoid fraction and yangambin from Ocotea duckei (Lauraceae) show antileishmanial activity

Crude ethanolic extract, lignoid fraction and the purified compound yangambin were obtained from Ocotea duckei (Lauraceae) and their antileishmanial activity was tested against promastigote forms of Leishmania chagasi and Leishmania amazonensis cultivated in Schneider medium, supplemented with 20% of fetal bovine serum. All substances presented antileishmanial activity with IC50 values of 135.7 microg/mL for the crude ethanolic extract, 26.5 microg/mL for the lignoid fraction and 49.0 microg/mL for yangambin on L. chagasi. For L. amazonensis the IC50 values were 143.7 microg/mL, 48.2 microg/mL and 64.9 microg/mL for the crude ethanolic extract, the lignoid fraction, and the purified compound yangambin, respectively. The crude ethanolic extract, lignoid fraction, and yangambin caused an inhibition higher than Glucantime, a reference drug used for the treatment of leishmaniasis.     

Identification and classification of host cell proteins during biopharmaceutical process development

As significant improvements in volumetric antibody productivity have been achieved by advances in upstream processing over the last decade, and harvest material has become progressively more difficult to recover with these intensified upstream operations, the segregation of upstream and downstream processing has remained largely unchanged. By integrating upstream and downstream process development, product purification issues are given consideration during the optimization of upstream operating conditions, which mitigates the need for extensive and expensive clearance strategies downstream. To investigate the impact of cell culture duration on critical quality attributes, CHO-expressed IgG1 was cultivated in two 2 L bioreactors with samples taken on days 8, 10, 13, 15, and 17. The material was centrifuged, filtered and protein A purified on a 1 ml HiTrap column. Host cell protein (HCP) identification by mass spectrometry (MS) was applied to this system to provide insights into cellular behavior and HCP carryover during protein A purification. It was shown that as cultivation progressed from day 8 to 17 and antibody titer increased, product quality declined due to an increase in post-protein A HCPs (from 72 to 475 peptides detected by MS) and a decrease in product monomer percentage (from 98% to 95.5%). Additionally, the MS data revealed an increase in the abundance of several classes of post-protein A HCPs (e.g., stress response proteins and indicators of cell age), particularly on days 15 and 17 of culture, which were associated with significant increases in total overall HCP levels. This provides new insight into the specific types of HCPs that are retained during mAb purification and may be used to aid process development strategies.     

Description of whistles of Irrawaddy dolphins (Orcaella brevirostris) from the waters of Matang,Peninsular Malaysia

The whistles of Irrawaddy dolphins (Orcaella brevirostris) from the waters of Matang, western Peninsular Malaysia are described. Duration, frequency and frequency modulation variables were measured from 163 whistles recorded using a broadband towed hydrophone. Irrawaddy dolphins produced whistles with a mean duration of 0.366 s (S.D. ± 0.217 s). The fundamental frequency of whistles extended from 3040 to 17,123 Hz with low levels of frequency modulation. These dolphins produced whistles that were comparable to those of conspecifics recorded from the waters of Kalimantan, but were generally different from the related Australian snubfin dolphin (O. heinsohni). They also differed from the whistles of the sympatric Indo-Pacific humpback dolphin (Sousa chinensis). Characteristics of Irrawaddy dolphin whistles may be useful in future passive acoustic monitoring studies to investigate differences in sympatric species and their habitat.