Diversity among bacteria isolated from the deep subsurface

Culturable bacteria from the deep subsurface (179 m) at Cerro Negro, New Mexico were isolated and characterized. The average number of viable aerobic bacteria was estimated to be 5×10⁵g^–1 of sediment, but only about 0.1% of these could be recovered on agar medium when incubated under aerobic conditions. Of 158 strains isolated from this depth, 92 were characterized by cellular fatty acid profiles (FAME), 36 by analysis of partial 16S rDNA sequences, and 44 by rep-PCR genome fingerprint analysis using three different sets of oligonucleotide primers (REP, BOX, or ERIC). These analyses showed the majority of isolates (67%) were Gram-positive bacteria and primarily members of genera with a high %G+C DNA. The remaining isolates were -subdivisionProteobacteria (19%) and members of the flavobacteria group (14%). The diversity indices based on these different methods of characterization were very high suggesting this subsurface habitat harbors a highly diverse microbial community.     

Phylogenetic reconstruction of the Drosophila obscura group, on the basis of mitochondrial DNA

We have constructed restriction-site maps of the mtDNAs in 13 species and one subspecies of the Drosophila obscura group. The traditional division of this group into two subgroups (affinis and obscura) does not correspond to the phylogeny of the group, which shows two well- defined clusters (the Nearctic affinis and pseudoobscura subgroups) plus a very heterogeneous set of anciently diverged species (the Palearctic obscura subgroup). The mtDNA of Drosophila exhibits a tendency to evolve toward high A+T values. This leads to a "saturation" effect that (1) begets an apparent decrease in the rate of evolution as the time since the divergence of taxa increases and (2) reduces the value that mtDNA restriction analysis has for the phylogenetic reconstruction of Drosophila species that are not closely related.      

Neurodegenerative disease induced by the wild mouse ecotropic retrovirus is markedly accelerated by long terminal repeat and gag-pol sequences from nondefective Friend murine leukemia virus.

The wild mouse ecotropic retrovirus (WM-E) induces a spongiform neurodegenerative disease in mice after a variable incubation period of 2 months to as long as 1 year. We isolated a molecular clone of WM-E (15-1) which was weakly neurovirulent (incidence, 8%) but was highly leukemogenic (incidence, 45%). Both lymphoid and granulocytic leukemias were observed, and these leukemias were often neuroinvasive. A chimeric virus was constructed containing the env and 3' pol sequences of 15-1 and long terminal repeat (LTR), gag, and 5' pol sequences from a clone of Friend murine leukemia virus (FB29). FB29 has been shown previously to replicate to high levels in the central nervous system (CNS) but is not itself neurovirulent. This finding was confirmed at the DNA level in the current study. Surprisingly, intraperitoneal inoculation of neonatal IRW mice with the chimeric virus (FrCasE) caused an accelerated neurodegenerative disease with an incubation period of only 16 days and was uniformly fatal by 23 days postinoculation. Introduction of the LTR of 15-1 into the FrCasE genome yielded a virus (FrCasEL) with a degree of neurovirulence intermediate between those of 15-1 and FrCasE. No differences were found in the levels of viremia or the relative levels of viral DNA in the spleens of mice inoculated with 15-1, FrCasE, or FrCasEL. However, the levels of viral DNA in the CNS correlated with the relative degrees of neurovirulence of the respective viruses (FrCasE greater than FrCasEL greater than 15-1). Thus, the env and 3' pol sequences of WM-E (15-1) were required for neurovirulence, but elements within the LTR and gag-pol regions of FB29 had a profound influence on the level of CNS infection and the rate of development of neurodegeneration.     

Intracellular calcium buffering capacity in isolated squid axons

Changes in ionized calcium were studied in axons isolated from living squid by measuring absorbance of the Ca binding dye Arsenazo III using multiwavelength differential absorption spectroscopy. Absorption changes measured in situ were calibrated in vitro with media of ionic composition similar to axoplasm containing CaEGTA buffers. Calcium loads of 50-2,500 μmol/kg axoplasm were induced by microinjection, by stimulation in 112 mM Ca seawater, or by soaking in choline saline with 1-10 mM Ca. Over this range of calcium loading of intact axoplasm, the ionized calcium in the axoplasm rose about 0.6 nM/μM load. Similar loading in axons preteated with carbonyl cyanide 4- trifluoromethoxyphenylhydrazone (FCCP) to inhibit the mitochondrial proton gradient increased ionized calcium by 5-7 percent of the imposed load, i.e. 93-95 percent of the calcium load was buffered by a process insensitive to FCCP. This FCCP- insensitive buffer system was not saturated by the largest calcium loads imposed, indicating a capacity of at least several millimolar. Treatment of previously loaded axons with FCCP or apyrase plus cyanide produced rises in ionized calcium which could be correlated with the extent of the load. Analysis of results indicated that, whereas only 6 percent of the endogenous calcium in fresh axons is stored in the FCCP-sensitive (presumably mitochondrial) buffer system, about 30 percent of an imposed exogenous load in the range of 50-2,500 μM is taken up by this system.     

A General Synthetic Method of 5-Carboranyluracil Nucleosides with Potential Antiviral Activity and use in Neutron Capture Therapy

Abstract

Previous biochemical and pharmacological studies indicated that 5-o-carboranyl-2′-deoxyuridine is a lead candidate for boron neutron capture therapy. This prompted the development of a rapid and stereoselective N ¹-glycosylation reaction of silylated 5-o-carboranyluracil with a variety of protected sugars. The key intermediate, 5-o-carboranyluracil (6), was prepared from 5-iodouracil in six steps. A novel coupling procedure of the 2,4-dimethoxy-5-ethynylpyrimidine (4) with decaborane without activator was used. Silylated 6 was coupled with a variety of carbohydrates under mild conditions to produce several carborane containing nucleosides. In each case, the stereochemistry and stereoselectivity of the glycosylation reaction was not affected by the presence of the carborane at the 5-position of the uracil and produced exclusively closo [closo-1,2-C₂B₁₀H₁₂ cage] nucleosides. This was confirmed by X-ray structure determination of racemic 5-carboranyl-2′,3′-dideoxy-3′-thiauridine. This compound demonstrated an anti-conformation with the oxathiolane ring in a pseudo C-2′-endo conformation. The toxicity profile of the new compounds and their precursors was determined in three cell culture systems, two of human origin (PBM and CEM cells) and one of monkey origin (Vero cells). The compounds were also evaluated for their potential antiviral activity against human immunodeficiency virus and herpes simplex virus in vitro. 5-o-Carboranyl-xylofuranosyluracil (12) demonstrated low toxicity in culture and in mice.     

Hyaluronan suppresses prostate tumor cell proliferation through diminished expression of N-cadherin and aberrant growth factor receptor signaling

Hyaluronan (HA) production has been functionally implicated in prostate tumorigenesis and metastasis. We previously used prostate tumor cells overexpressing the HA synthesizing enzyme HAS3 or the clinically relevant hyaluronidase Hyal1 to show that excess HA production suppresses tumor growth, while HA turnover accelerates spontaneous metastasis from the prostate. Here, we examined pathways responsible for effects of HAS3 and Hyal1 on tumor cell phenotype. Detailed characterization of cell cycle progression revealed that expression of Hyal1 accelerated cell cycle re-entry following synchronization, whereas HAS3 alone delayed entry. Hyal1 expressing cells exhibited a significant reduction in their ability to sustain ERK phosphorylation upon stimulation by growth factors, and in their expression of the cyclin-dependent kinase inhibitor p21. In contrast, HAS3 expressing cells showed prolonged ERK phosphorylation and increased expression of both p21 and p27, in asynchronous and synchronized cultures. Changes in cell cycle regulatory proteins were accompanied by HA-induced suppression of N-cadherin, while E-cadherin expression and β-catenin expression and distribution remained unchanged. Our results are consistent with a model in which excess HA synthesis suppresses cell proliferation by promoting homotypic E-cadherin mediated cell–cell adhesion, consequently signaling to elevate cell cycle inhibitor expression and suppress G1- to S-phase transition.     

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Background  

Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear.     

Novel human histamine H(3) receptor antagonists

High throughput screening, using the recombinant human H(3) receptor, was used to identify novel histamine H(3) receptor antagonists. Evaluation of the lead compounds ultimately afforded potent, selective, orally bioavailable compounds (e.g., 38) with favorable blood-brain barrier penetration.     

Monoclonal antibodies specific for wild mouse neurotropic retrovirus: detection of comparable levels of virus replication in mouse strains susceptible and resistant to paralytic disease.

We used AKR/J mice to produce monoclonal antibodies specific for a neurotropic ecotropic (WM-E) virus initially isolated from wild mice. The rationale for this approach involved the observation that these mice were immunologically hyporesponsive to endogenous ecotropic virus (Akv) but fully responsive to type-specific determinants of WM-E. Hybridoma cell lines derived from mice immunized with both denatured and viable virus produced antibodies with specificity for three viral membrane-associated polypeptides, gp70, p15(E), and p15gag. Epitopes specific for WM-E virus were detected in each of these polypeptides. Cross-reactivity with Friend ecotropic virus (Friend murine leukemia virus) was observed with some gp70- and p15gag-specific antibodies, but no reactivity with endogenous Akv ecotropic virus was seen. The majority of these antibodies did not react with either xenotropic or mink cell focus-forming viruses. Two WM-E-specific anti-gp70 antibodies reacting with different determinants had virus-neutralizing activity in the absence of complement, suggesting that the respective epitopes may participate in receptor binding or virus penetration events. We used these monoclonal antibodies in initial studies to examine the replication of WM-E virus in neonatally inoculated AKR/J mice which are fully resistant to the paralytic disease induced by this virus. Since these mice express high levels of endogenous ecotropic virus, standard assays for ecotropic virus cannot be used to study this question. We present evidence that the resistance to disease does not involve a resistance to virus replication, since these mice expressed levels of viremia and virus replication in spleen and lumbar spinal cord comparable to susceptible NFS/N mice at a time when the latter began to manifest clinical signs of lower-motor-neuron pathology.     

Protective efficacy of nonneutralizing monoclonal antibodies in acute infection with murine leukemia virus.

We have used an experimental retrovirus infection to study the roles played by different antibodies in resistance to both infection and disease. A molecularly cloned chimeric murine leukemia virus was used to induce acute lethal neurological disease in neonatal mice. A panel of monoclonal antibodies directed against the Gag and Env proteins was tested for protective efficacy. In vitro neutralization assays demonstrated that anti-Env antibodies gave different degrees of neutralization, while no anti-Gag neutralized the virus. In vivo experimental endpoints were onset of clinical signs and premoribund condition. As expected, different anti-Env antibodies demonstrated different degrees of protection which correlated with their neutralizing abilities. Surprisingly, anti-Gag antibodies directed against both p15 (MA protein) and p30 (CA protein) were also protective, significantly delaying the onset of disease. No protection was seen with either of two control antibodies. The protection with anti-Gag was dose related and time dependent and was also produced with Fab fragments. Treatment with anti-Gag did not prevent viremia but resulted in a slight slowing in viremia kinetics and decreased levels of virus in the central nervous systems of mice protected from disease. These data indicate that nonneutralizing antiretroviral antibodies can influence the outcome of retroviral disease. The data also suggest a functional role for cell surface expression of Gag proteins on murine leukemia virus-infected cells.