Repression and reactivation of the variant surface glycoprotein gene in Trypanosoma brucei

AbstractRapid repression of variant surface glycoprotein (VSG) synthesis is an early event during the in vitro transformation of Trypanosoma brucei from coated bloodstream forms to uncoated procyclic cells. Repression occurs at the transcriptional level and is triggered by the combined action of two signals: a reduction in temperature from 37 to 27°C and the addition of the citric acid cycle intermediates citrate and cis-aconitate. It is shown that synthesis of VSG mRNA can be reactivated up to 8 h after triggering differentiation by releasing either one or both of the signals. After 30 h repression is irreversible. The results suggest that transformation of bloodstream forms to procyclic cells proceeds through a reversible phase to an irreversible committed state. A reversible repression of VSG mRNA synthesis is also observed upon inhibition of protein synthesis in bloodstream forms at 37°C

Identification of a novel betaherpesvirus in Mus musculus

Rodent betaherpesviruses vary considerably in genomic content, and these variations can result in a distinct pathogenicity. Therefore, the identification of unknown betaherpesviruses in house mice (Mus musculus), the most important rodent host species in basic research, is of importance. During a search for novel herpesviruses in house mice using herpesvirus consensus PCR and attempts to isolate viruses in tissue culture, we identified a previously unknown betaherpesvirus. The primary PCR search in mouse organs revealed the presence of known strains of murine cytomegalovirus (Murid herpesvirus 1) and of Mus musculus rhadinovirus 1 only. However, the novel virus was detected after incubation of organ pieces in fibroblast tissue culture and subsequent PCR analysis of the supernatants. Long-distance PCR amplification including the DNA polymerase and glycoprotein B genes revealed a 3.4 kb sequence that was similar to sequences of rodent cytomegaloviruses. Pairwise sequence comparisons and phylogenetic analyses showed that this newly identified murine virus is most similar to the English isolate of rat cytomegalovirus, thereby raising the possibility that two distinct CMV lineages have evolved in both Mus musculus and Rattus norvegicus

Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach

Targeting the highly conserved herpes DNA polymerase (DPOL) gene with PCR using panherpes degenerate primers is a powerful tool to universally detect unknown herpesviruses. However, vertebrate hosts are often infected with more than one herpesvirus in the same tissue, and pan-herpes DPOL PCR often favors the amplification of one viral sequence at the expense of the others. Here we present two different technical approaches that overcome this obstacle: (i) Pan-herpes DPOL PCR is carried out in the presence of an oligonucleotide substituted with locked nucleic acids (LNA).This suppresses the amplification of a specific herpesvirus DPOL sequence by a factor of approximately 1000, thereby enabling the amplification of a second, different DPOL sequence. (ii) The less conserved glycoprotein B (gB) gene is targeted with several sets of degenerate primers that are restricted to gB genes of different herpesvirus subfamilies or genera. These techniques enable the amplification of gB and DPOL sequences of multiple viruses from a single specimen. The partial gB and DPOL sequences can be connected by long-distance PCR, producing final contiguous sequences of approximately 3.5 kbp. Such sequences include parts of two genes and therefore allow for a robust phylogenetic analysis. To illustrate this principle, six novel herpesviruses of the genera Rhadinovirus, Lymphocryptovirus and Cytomegalovirus were discovered in multi-infected samples of non-human primates and phylogenetically characterized

High genotypic diversity and a novel variant of human cytomegalovirus revealed by combined UL33/UL55 genotyping with broad-range PCR

The known strains of human cytomegalovirus (HCMV) represent genotypic variants of a single species, and HCMV genotypic variability has been studied in order to reveal correlations between different disease patterns and the presence of certain HCMV genotypes, either as single or as multiple infections. The methods used for the detection of HCMV genotypes have not always been sophisticated enough to achieve complete comprehensiveness, mainly because only one genotype is usually detected in a certain specimen, due to primer specificity and genome copy number. To improve detection of variant HCMV genotypes in mixed infections, we developed PCR assays with degenerate primers targeting two variable HCMV genes, glycoprotein B (gB, UL55) and the G-protein-coupled receptor gene UL33. Primers were designed to bind conserved sites in the genomes of HCMV variants and great ape CMVs. To analyse if samples contained one or more HCMV genotypic variants, PCR assays were supplemented with oligonucleotides containing locked nucleic acids. This broad-range PCR methodology and subsequent sequence analysis detected all gB/UL55 and UL33 genotypic variants known to date in primary clinical specimens, but also revealed that many samples contained genotype mixtures. Importantly, a novel UL33 genotypic variant could be discovered in several specimens, and one HCMV isolate was plaque-purified containing the novel UL33 genotype and a so far undescribed variant of gB

A novel adenovirus of Western lowland gorillas (Gorilla gorilla gorilla)

Adenoviruses (AdV) broadly infect vertebrate hosts including a variety of primates. We identified a novel AdV in the feces of captive gorillas by isolation in cell culture, electron microscopy and PCR. From the supernatants of infected cultures we amplified DNA polymerase (DPOL), preterminal protein (pTP) and hexon gene sequences with generic pan primate AdV PCR assays. The sequences in-between were amplified by long-distance PCRs of 2 - 10 kb length, resulting in a final sequence of 15.6 kb. Phylogenetic analysis placed the novel gorilla AdV into a cluster of primate AdVs belonging to the species Human adenovirus B (HAdV-B). Depending on the analyzed gene, its position within the cluster was variable. To further elucidate its origin, feces samples of wild gorillas were analyzed. AdV hexon sequences were detected which are indicative for three distinct and novel gorilla HAdV-B viruses, among them a virus nearly identical to the novel AdV isolated from captive gorillas. This shows that the discovered virus is a member of a group of HAdV-B viruses that naturally infect gorillas. The mixed phylogenetic clusters of gorilla, chimpanzee, bonobo and human AdVs within the HAdV-B species indicate that host switches may have been a component of the evolution of human and non-human primate HAdV-B viruses

Identification of a novel human polyomavirus in organs of the gastrointestinal tract

Peer reviewedPublisher PD

Genome Sequence of Bovine Polyomavirus 1 Detected in a Salers Cow (Bos taurus) from Catalonia, Spain

We identified a variant of the first bovine polyomavirus (BPyV1; family Polyomaviridae) in a lymph node of a Salers cow. As the 2 previously published genome sequences of this virus originated from fetal bovine serum and ground beef, respectively, this is the first BPyV1 genome that could be traced back to an individual

A new multi-dimensional general relativistic neutrino hydrodynamics code for core-collapse supernovae. I. Method and code tests in spherical symmetry

We present a new general relativistic (GR) code for hydrodynamic supernova simulations with neutrino transport in spherical and azimuthal symmetry (1D/2D). The code is a combination of the CoCoNuT hydro module, which is a Riemann-solver based, high-resolution shock-capturing method, and the three-flavor, energy-dependent neutrino transport scheme VERTEX. VERTEX integrates the neutrino moment equations with a variable Eddington factor closure computed from a model Boltzmann equation and uses the ray-by-ray plus approximation in 2D, assuming the neutrino distribution to be axially symmetric around the radial direction, and thus the neutrino flux to be radial. Our spacetime treatment employs the ADM 3+1 formalism with the conformal flatness condition for the spatial three-metric. This approach is exact in 1D and has been shown to yield very accurate results also for rotational stellar collapse. We introduce new formulations of the energy equation to improve total energy conservation in relativistic and Newtonian hydro simulations with Eulerian finite-volume codes. Moreover, a modified version of the VERTEX scheme is developed that simultaneously conserves energy and lepton number with better accuracy and higher numerical stability. To verify our code, we conduct a series of tests, including a detailed comparison with published 1D results for stellar core collapse. Long-time simulations of proto-neutron star cooling over several seconds both demonstrate the robustness of the new CoCoNuT-VERTEX code and show the approximate treatment of GR effects by means of an effective gravitational potential as in PROMETHEUS-VERTEX to be remarkably accurate in 1D. (abridged)Comment: 36 pages, 19 eps figures; submitted to ApJS (minor revisions; some typos corrected

Fractal diffusion in high temperature polymer electrolyte fuel cell membranes

© 2018 Author(s). The performance of fuel cells depends largely on the proton diffusion in the proton conducting membrane, the core of a fuel cell. High temperature polymer electrolyte fuel cells are based on a polymer membrane swollen with phosphoric acid as the electrolyte, where proton conduction takes place. We studied the proton diffusion in such membranes with neutron scattering techniques which are especially sensitive to the proton contribution. Time of flight spectroscopy and backscattering spectroscopy have been combined to cover a broad dynamic range. In order to selectively observe the diffusion of protons potentially contributing to the ion conductivity, two samples were prepared, where in one of the samples the phosphoric acid was used with hydrogen replaced by deuterium. The scattering data from the two samples were subtracted in a suitable way after measurement. Thereby subdiffusive behavior of the proton diffusion has been observed and interpreted in terms of a model of fractal diffusion. For this purpose, a scattering function for fractal diffusion has been developed. The fractal diffusion dimension dw and the Hausdorff dimension df have been determined on the length scales covered in the neutron scattering experiments