Importance of the penultimate positive charge in mouse hepatitis coronavirus A59 membrane protein

The coronavirus membrane (M) protein carboxy tail interacts with the nucleocapsid during virus assembly. Previous studies demonstrated that the two terminal residues are important, and the charged residue (R227) in the penultimate position in the mouse hepatitis coronavirus (MHV) A59 M protein was suggested to participate in intermolecular interactions with negative charges in the nucleocapsid (N) protein. To determine the significance of the positive charge at position 227, we substituted the arginine with lysine (K), aspartic acid (D), glutamic acid (E), or alanine (A) and studied these by reverse genetics in the context of a MHV full-length infectious clone. Viruses with wild-type phenotype were readily recovered with the K or A substitutions. In contrast, negative-charge substitutions were not tolerated as well. In all recovered R227D viruses the negative charge was replaced with heterologous residues resulting from apparent template switching during negative-strand synthesis of subgenomic RNA 7. An additional second-site compensatory V202I substitution was present in some viruses. Recovered R227E viruses had second-site changes within the M protein carboxy tail that were partially compensatory. Significantly, most of the second site changes in the R227E mutant viruses were previously shown to compensate for the removal of negative charges in the N protein. Our results strongly indicate that a positive charge is not absolutely required. It is clear that other regions within the tail must also be involved in helping mediate interactions between the M protein and the nucleocapsid.     

Open LED Illuminator: A Simple and Inexpensive LED Illuminator for Fast Multicolor Particle Tracking in Neurons

Dual-color live cell fluorescence microscopy of fast intracellular trafficking processes, such as axonal transport, requires rapid switching of illumination channels. Typical broad-spectrum sources necessitate the use of mechanical filter switching, which introduces delays between acquisition of different fluorescence channels, impeding the interpretation and quantification of highly dynamic processes. Light Emitting Diodes (LEDs), however, allow modulation of excitation light in microseconds. Here we provide a step-by-step protocol to enable any scientist to build a research-grade LED illuminator for live cell microscopy, even without prior experience with electronics or optics. We quantify and compare components, discuss our design considerations, and demonstrate the performance of our LED illuminator by imaging axonal transport of herpes virus particles with high temporal resolution.     

Characterization of antigenic determinants on human solubilized apolipoprotein B. Conformational requirements for lipids

The expression of low density lipoprotein (LDL) antigenic determinants in the delipidated and solubilized apolipoprotein B (apo-B) free of sodium dodecyl sulfate (SDS) has been studied. Of the six distinct determinants which react with previously characterized monoclonal antibodies against LDL (Milne, R.W., Theolis , R., Jr., Verdery , R.B., and Marcel , Y.L. (1983) Arteriosclerosis 3, 23-30), only one, that recognized by antibody 1D1 , was expressed on the soluble apo-B, indicating that soluble apo-B may be partly denatured. The average immunoreactivity of apo-B with antibody 1D1 was similar to or lower than that of intact LDL (mean 36%, range 93-20%). Therefore, delipidation and solubilization did not expose on apo-B any additional site reactive with 1D1 . When apo-B was equilibrated with either SDS micelles or with cholesterol-lecithin liposomes, the immunoreactivity of the determinant recognized by antibody 2D8 was partially regenerated, but not that of the others. In contrast, incubation of apo-B with microemulsions containing a hydrophobic core of cholesteryl esters also restored the antigenicity of the determinants reacting with antibodies 3F5 , 4G3 , and 5E11 . However, the regeneration of these antigenic determinants could only be achieved when solubilized apo-B was treated with SDS prior to equilibration with microemulsion preparations. In conclusion, three types of antigenic determinants have been identified on apo-B. The first type, such as that recognized by antibody 1D1 , is expressed both on LDL and on apo-B and is constituted by the primary and secondary structure of apo-B. The second type, an example being that recognized by 2D8 , is a conformational determinant which requires the presence of amphipathic lipids such as lecithin and cholesterol or SDS micelles. The third type, which reacts with antibodies 3F5 , 4G3 , and 5E11 , represents different conformational determinants which require the association of apo-B with lipid structures having a cholesteryl ester hydrophobic core. It may be significant that the latter determinants are those close to the LDL receptor-binding site on apo-B and that this domain of apo-B has a complex tertiary and quaternary structure as evidenced by the conformational requirements of the antigenic determinants.     

Dependence of H2O2 Formation by Rat Heart Mitochondria on Substrate Availability and Donor Age

We have examined the substrate specificity and inhibitor sensitivity of H₂O₂ formation by rat heart mitochondria. Active H₂O₂ production requires both a high fractional reduction of Complex I (indexed by NADH/NAD⁺ + NADH ratio) and a high membrane potential, . These conditions are achieved with supraphysiological concentrations of succinate. With physiological concentrations of NAD-linked substrates, rates of H₂O₂ formation are much lower (less than 0.1% of respiratory chain electron flux) but may be stimulated by the Complex III inhibitor antimycin A, but not by myxothiazol. Addition of Mn²⁺ to give 10 nmol/mg of mitochondrial protein enhances H₂O₂ production with all substrate combinations, possibly by repleting mitochondrial superoxide dismutase with this cation. Contrary to previously published work, no increased activity of H₂O₂ production was found with heart mitochondria from senescent (24 month) rats, relative to young adults (6 month).     

Short term effects on bone quality associated with consumption of soy protein isolate and other dietary protein sources in rapidly growing female rats

Beneficial effects of soy protein consumption on bone quality have been reported. The effects of other dietary protein sources such as whey protein hydrolysate (WPH) and rice protein isolate (RPI) on bone growth have been less well examined. The current study compared effects of feeding soy protein isolate (SPI), WPH and RPI for 14 d on tibial bone mineral density (BMD) and bone mineral content (BMC) in intact and ovariectomized (OVX) rapidly growing female rats relative to animals fed casein (CAS). The effects of estrogenic status on responses to SPI were also explored. Tibial peripheral quantitative computerized tomography (pQCT) showed all three protein sources had positive effects on either BMD or BMC relative to CAS (P < 0.05), but SPI had greater effects in both intact and OVX female rats. SPI and E2 had positive effects on BMD and BMC in OVX rats (P < 0.05). However, trabecular BMD was lower in a SPI + E2 group compared to a CAS + E2 group. In OVX rats, SPI increased serum bone formation markers, and serum from SPI-fed rats stimulated osteoblastogenesis in ex vivo. SPI also suppressed the bone resorption marker RatLaps (P < 0.05). Both SPI and E2 increased alkaline phosphatase gene expression in bone, but only SPI decreased receptor activator of nuclear factor-kappaB ligand (RANKL) and estrogen receptor gene expression (P < 0.05). These data suggest beneficial bone effects of a soy diet in rapidly growing animals and the potential for early soy consumption to increase peak bone mass.     

SeqHound: biological sequence and structure database as a platform for bioinformatics research

Background  

SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment.     

Response of strawberry to inoculation with arbuscular mycorrhizal fungi under very high soil phosphorus conditions

A field study was done to assess the potential benefit of arbuscular mycorrhizal (AM) inoculation of elite strawberry plants on plant multiplication, under typical strawberry nursery conditions and, in particular, high soil P fertility (Mehlich-3 extractible P=498 mg kg⁻¹). Commercially in vitro propagated elite plants of five cultivars (‘Chambly,’ ‘Glooscap,’ ‘Joliette,’ ‘Kent,’ and ‘Sweet Charlie’) were transplanted in noninoculated growth substrate or in substrate inoculated with Glomus intraradices or with a mixture of species (G. intraradices, Glomus mosseae, and Glomus etunicatum) at the acclimation stage and were grown for 6 weeks before transplantation in the field. We found that AM fungi can impact on plant productivity in a soil classified as excessively rich in P. Inoculated mother plants produced about 25% fewer daughter plants than the control in Chambly (P=0.03), and Glooscap produced about 50% more (P=0.008) daughter plants when inoculated with G. intraradices, while the productivity of other cultivars was not significantly decreased. Daughter plant shoot mass was not affected by treatments, but their roots had lower, higher, or similar mass, depending on the cultivar–inoculum combination. Root mass was unrelated to plant number. The average level of AM colonization of daughter plants produced by noninoculated mother plants did not exceed 2%, whereas plants produced from inoculated mothers had over 10% of their root length colonized 7 weeks after transplantation of mother plants and ∼6% after 14 weeks (harvest), suggesting that the AM fungi brought into the field by inoculated mother plants had established and spread up to the daughter plants. The host or nonhost nature of the crop species preceding strawberry plant production (barley or buckwheat) had no effect on soil mycorrhizal potential, on mother plant productivity, or on daughter plant mycorrhizal development. Thus, in soil excessively rich in P, inoculation may be the only option for management of the symbiosis.     

DNA damage levels and biochemical repair capacities associated with XRCC1 deficiency

Base excision repair (BER) is the major corrective pathway for most spontaneous, oxidative, and alkylation DNA base and sugar damage. X-ray cross-complementing 1 (XRCC1) has been suggested to function at nearly every step of this repair process, primarily through direct protein-protein interactions. Using whole cell extract (WCE) repair assays and DNA damage measurement techniques, we examined systematically the quantitative contribution of XRCC1 to specific biochemical steps of BER and single-strand break repair (SSBR). Our studies reveal that XRCC1-deficient Chinese hamster ovary WCEs exhibit normal base excision activity for 8-oxoguanine (8-OH-dG), 5-hydroxycytosine, ethenoadenine, and uracil lesions. Moreover, XRCC1 mutant EM9 cells possess steady-state levels of endogenous 8-OH-dG base damage similar to those of their wild-type counterparts. Abasic site incision activity was found to be normal in XRCC1-deficient cell extracts, as were the levels of abasic sites in isolated chromosomal DNA from mutant cells. While one- and five-nucleotide gap filling was not affected by XRCC1 status, a significant approximately 2-4-fold reduction in nick ligation activity was observed in EM9 WCEs. Our results herein suggest that the primary biochemical defect associated with XRCC1 deficiency is in the ligation step of BER/SSBR, and that XRCC1 plays no significant role in endogenous base damage and abasic site repair, or in promoting the polymerase gap-filling step.     

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules

A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.