Cryptic transcripts from a ubiquitous plasmid origin of replication confound tests for cis-regulatory function.

A vast amount of research on the regulation of gene expression has relied on plasmid reporter assays. In this study, we show that plasmids widely used for this purpose constitutively produce substantial amounts of RNA from a TATA-containing cryptic promoter within the origin of replication. Readthrough of these RNAs into the intended transcriptional unit potently stimulated reporter activity when the inserted test sequence contained a 3' splice site (ss). We show that two human sequences, originally reported to be internal ribosome entry sites and later to instead be promoters, mimic both types of element in dicistronic reporter assays by causing these cryptic readthrough transcripts to splice in patterns that allow efficient translation of the downstream cistron. Introduction of test sequences containing 3' ss into monocistronic luciferase reporter vectors widely used in the study of transcriptional regulation also created the false appearance of promoter function via the same mechanism. Across a large number of variants of these plasmids, we found a very highly significant correlation between reporter activity and levels of such spliced readthrough transcripts. Computational estimation of the frequency of cryptic 3' ss in genomic sequences suggests that misattribution of cis-regulatory function may be a common occurrence

Search for magnetic monopoles using proportional counters filled with helium gas

Slow magnetic monopoles in cosmic rays have been searched at sea level with the detector which consists of seven layers of proportional counters filled with a mixture of He + 20% CH4. The velocities and the energy losses of the incident particles are measured. The upper limit of flux for the monopoles in the velocity range of 1 x 0.001 Beta 4 x 0.001 is 2.78 x 10 to the minus 12th power square centimeters sr sec of 90% confidence level

Microbe-surface interactions in biofouling and biocorrosion processes

The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions. [Int Microbiol 2005; 8(3):157-168

Anomalous Angular Dependence of the Dynamic Structure Factor near Bragg Reflections: Graphite

The electron energy-loss function of graphite is studied for momentum transfers q beyond the first Brillouin zone. We find that near Bragg reflections the spectra can change drastically for very small variations in q. The effect is investigated by means of first principle calculations in the random phase approximation and confirmed by inelastic x-ray scattering measurements of the dynamic structure factor S(q,\omega). We demonstrate that this effect is governed by crystal local field effects and the stacking of graphite. It is traced back to a strong coupling between excitations at small and large momentum transfers

Proportional drift tubes for large area muon detectors

A proportional drift chamber which consists of eight rectangular drift tubes with cross section of 10 cm x 5 cm, a sense wire of 100 micron phi gold-plated tungsten wire and the length of 6 m, was tested using cosmic ray muons. Spatial resolution (rms) is between 0.5 and 1 mm over drift space of 50 mm, depending on incident angle and distance from sense wire

Toca 511 gene transfer and treatment with the prodrug, 5-fluorocytosine, promotes durable antitumor immunity in a mouse glioma model.

BackgroundToca 511 (vocimagene amiretrorepvec) is a retroviral replicating vector encoding an optimized yeast cytosine deaminase (CD). Tumor-selective expression of CD converts the prodrug, 5-fluorocytosine (5-FC), into the active chemotherapeutic, 5-fluorouracil (5-FU). This therapeutic approach is being tested in a randomized phase II/III trial in recurrent glioblastoma and anaplastic astrocytoma (NCT0241416). The aim of this study was to identify the immune cell subsets contributing to antitumor immune responses following treatment with 5-FC in Toca 511-expressing gliomas in a syngeneic mouse model.MethodsFlow cytometry was utilized to monitor and characterize the immune cell infiltrate in subcutaneous Tu-2449 gliomas in B6C3F1 mice treated with Toca 511 and 5-FC.ResultsTumor-bearing animals treated with Toca 511 and 5-FC display alterations in immune cell populations within the tumor that result in antitumor immune protection. Attenuated immune subsets were exclusive to immunosuppressive cells of myeloid origin. Depletion of immunosuppressive cells temporally preceded a second event which included expansion of T cells which were polarized away from Th2 and Th17 in the CD4+ T cell compartment with concomitant expansion of interferon gamma-expressing CD8+ T cells. Immune alterations correlated with clearance of Tu-2449 subcutaneous tumors and T cell-dependent protection from future tumor challenge.ConclusionsTreatment with Toca 511 and 5-FC has a concentrated effect at the site of the tumor which causes direct tumor cell death and alterations in immune cell infiltrate, resulting in a tumor microenvironment that is more permissive to establishment of a T cell mediated antitumor immune response

Quantized representation of some nonlinear integrable evolution equations on the soliton sector

The Hirota algorithm for solving several integrable nonlinear evolution equations is suggestive of a simple quantized representation of these equations and their soliton solutions over a Fock space of bosons or of fermions. The classical nonlinear wave equation becomes a nonlinear equation for an operator. The solution of this equation is constructed through the operator analog of the Hirota transformation. The classical N-solitons solution is the expectation value of the solution operator in an N-particle state in the Fock space.Comment: 12 page

Criteria for the experimental observation of multi-dimensional optical solitons in saturable media

Criteria for experimental observation of multi-dimensional optical solitons in media with saturable refractive nonlinearities are developed. The criteria are applied to actual material parameters (characterizing the cubic self-focusing and quintic self-defocusing nonlinearities, two-photon loss, and optical-damage threshold) for various glasses. This way, we identify operation windows for soliton formation in these glasses. It is found that two-photon absorption sets stringent limits on the windows. We conclude that, while a well-defined window of parameters exists for two-dimensional solitons (spatial or spatiotemporal), for their three-dimensional spatiotemporal counterparts such a window \emph{does not} exist, due to the nonlinear loss in glasses.Comment: 8 pages, to appear in Phys. Rev.