Complete probabilistic analysis of RNA shapes

Background  

Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived.     

Transformation of nuclear and plastomic plant genomes by biolistic particle bombardment

Microprojectile bombardment is a powerful method for the transformation of various organisms and tissues. For plants, the biolistic approach is primarily used for transformation of cereals and other monocotyledons, as well as for dicotyledonous plants shown to be recalcitrant to Agrobacterium-based transformation of organellar genomes, and transformation of plant and algal chloroplasts has recently been reported. In this protocol paper we provide methods for nuclear and plastomic transformation of plants using the biolistic technique.     

A long‐term record of Quercus decline,logging and fires in a southern Swedish Fagus‐Picea forest

Abstract. We reconstructed forest development and disturbance events (fire and logging) during the last 1000 yr with tree‐ring data, pollen and charcoal analysis from a semi‐natural Fagus sylvatica‐Picea abies forest (ca. 1 km²) in the hemiboreal zone. According to pollen analysis, Quercus robur together with Pinus sylvestris was abundant in the forest until the turn of the 18th/19th centuries when these species disappeared completely (Quercus) or nearly completely (Pinus) and were replaced by Fagus and Picea. The disappearance of Quercus was corroborated by the remarkable discovery of a single Quercus stump that had been cut in the 18th century and had become overgrown and preserved by a very old Picea. In total 11 fires were dated from 1555 to 1748 from fire scars in several Pinus stumps cut 100 ‐ 200 yr ago. Since the last fire in 1748, no Quercus or Pinus have regenerated in the core of the reserve apart from single pines in neighbouring managed forest (80 yr ago). During the period of documented fires Fagus was protected from fires in a refuge made up of large boulders. Picea colonized the region at the time when the fires ceased 250 yr ago. We hypothesize that most of the fires were probably of human origin because of their patchiness and high frequency compared to the natural background levels of lightning ignitions in the region. On a 300‐yr time scale, logging and fire suppression seem to strongly overshadow the effect of climate change on forest composition and dynamics.     

Functional properties of recombinant factor V mutated in a potential calcium-binding site

Activated coagulation factor V (FVa) is a cofactor of activated factor X (FXa) in prothrombin activation. FVa is composed of a light chain (LC) and a heavy chain (HC) that are noncovalently associated in a calcium-dependent manner. We constructed a recombinant FV Asp111Asn/Asp112Asn mutant (rFV-NN) to abolish calcium binding to a potential calcium-binding site in FVa in order to study the specific role of these residues in the expression of FVa activity. Whereas thrombin-activated recombinant FV wild type (rFV-wt) presented with stable FVa activity, incubation of rFV-NN with thrombin resulted in a temporary increase in FVa activity, which was rapidly lost upon prolonged incubation. Loss of FVa activity was most likely due to dissociation of HC and LC since, upon chromatography of rFVa-NN on a SP-Sepharose column, the HC did not bind significantly to the resin whereas the LC bound and could be eluted at high ionic strength. In contrast, rFVa-wt adhered to the column, and both the HC and LC coeluted at high ionic strength. In the presence of phospholipid vesicles, the loss of rFVa-NN activity was partially prevented by FXa, active site inhibited FXa, and prothombin in a dose-dependent manner. We conclude that the introduced amino acid substitutions result in a loss of the high-affinity (calcium-dependent) interaction of the HC and LC of FVa. We propose that the introduced substitutions disrupt the calcium-binding site in FV, thereby yielding a FV molecule that rapidly loses activity following thrombin-catalyzed activation most likely via dissociation of the HC and LC.     

Physiological and autonomic stress responses after prolonged sleep restriction and subsequent recovery sleep in healthy young men

Sleep and Biological Rhythms - Sleep restriction is increasingly common and associated with the development of health problems. We investigated how the neuroendocrine stress systems respond to...     

Immuno-histochemical and -cytochemical Evidence Suggesting the Presence of Campylobacter jejuni and Campylobacter coli in Cases of Porcine Intestinal Adenomatosis

Antisera against a number of Campylobacter species were used in immuno-histochemical and -cytochemical studies on cases of porcine intestinal adenomatosis. Avidin-biotin-complex (ABC) and streptavidin immunoperoxidase methods were used on formalin-fixed, paraffin-embedded and frozen sections. Protein A gold method was used on formaldehyde fixed and frozen sections for immuno-cytochemistry. The antisera used were raised in rabbits by subcutaneous or intravenous injection of living or formalin treated organisms. Antisera against different serotypes of the thermotolerant, catalase positive Campylobacters, Campylobacter jejuni and Campylobacter coli gave positive reactions in the immuno-histochemical studies. The staining was found in intestinal epithelial cells both in the ileum and in the colon and was restricted to the apical cytoplasm of adenomatous epithelial cells. The staining had a granular pattern, the positive structures sometimes having the shape of Campylobacter. Epithelial cells in areas with normal differentiation of goblet cells did not stain. In contrast, no staining resulted with antisera against Campylobacter sputorum subsp. mucosalis and Campylobacter hyointestinalis. Immuno-cytochemistry, using antisera against Campylobacter jejuni showed that the positive staining in altered epithelial cells were restricted to intracellular organisms having a structure resembling Campylobacter spp.     

Decoupling of reproductive rates and parental expenditure in a polyandrous butterfly

Current theory postulates that the operational sex ratio (OSR)determines the relative degree of mating competition in thetwo sexes and is in turn influenced by a sexual difference inthe potential reproductive rate (PRR) denned as 1/time out,where time out is the time an individual must spend recoveringfrom a bout of mating activity and/or caring for offspring.In bushcricket mating systems where males provide females witha nuptial gift, relative energy expenditure in offspring influencesthe PRR of males and females and underlies a diet-mediated shiftin the OSR. Here we investigated if there is a similar positiverelationship between relative parental nutrient expenditurein offspring and PRR in the polyandrous butterfly Pieris napi,where female fecundity is strongly dependent on male nuptialgifts at mating. By varying the amount of nutrients femalesreceive at mating and relating this to number of offspring produced,we show that male P. napi have, on average, a nutrient expenditurein offspring equaling that of females. In spite of this, themale reproductive rate is 8–13 times higher than thatof females. Hence the relative degree of parental expenditurein offspring is largely decoupled from the degree of matingcompetition in P. napi. Two alternative explanations are advancedto account for the difference between the butterfly and thebushcricket mating systems.     

Bi-specific TCR-anti CD3 redirected T-cell targeting of NY-ESO-1- and LAGE-1-positive tumors

NY-ESO-1 and LAGE-1 are cancer testis antigens with an ideal profile for tumor immunotherapy, combining up-regulation in many cancer types with highly restricted expression in normal tissues and sharing a common HLA-A*0201 epitope, 157–165. Here, we present data to describe the specificity and anti-tumor activity of a bifunctional ImmTAC, comprising a soluble, high-affinity T-cell receptor (TCR) specific for NY-ESO-1_157–165 fused to an anti-CD3 scFv. This reagent, ImmTAC-NYE, is shown to kill HLA-A2, antigen-positive tumor cell lines, and freshly isolated HLA-A2- and LAGE-1-positive NSCLC cells. Employing time-domain optical imaging, we demonstrate in vivo targeting of fluorescently labelled high-affinity NYESO-specific TCRs to HLA-A2-, NY-ESO-1_157–165-positive tumors in xenografted mice. In vivo ImmTAC-NYE efficacy was tested in a tumor model in which human lymphocytes were stably co-engrafted into NSG mice harboring tumor xenografts; efficacy was observed in both tumor prevention and established tumor models using a GFP fluorescence readout. Quantitative RT-PCR was used to analyze the expression of both NY-ESO-1 and LAGE-1 antigens in 15 normal tissues, 5 cancer cell lines, 10 NSCLC, and 10 ovarian cancer samples. Overall, LAGE-1 RNA was expressed at a greater frequency and at higher levels than NY-ESO-1 in the tumor samples. These data support the clinical utility of ImmTAC-NYE as an immunotherapeutic agent for a variety of cancers.     

Interferon-Inducible Mechanism of Dendritic Cell-Mediated HIV-1 Dissemination Is Dependent on Siglec-1/CD169

Human immunodeficiency virus type 1 (HIV-1) interactions with myeloid dendritic cells (DCs) can result in virus dissemination to CD4⁺ T cells via a trans infection pathway dependent on virion incorporation of the host cell derived glycosphingolipid (GSL), GM3. The mechanism of DC-mediated trans infection is extremely efficacious and can result in infection of multiple CD4⁺ T cells as these cells make exploratory contacts on the DC surface. While it has long been appreciated that activation of DCs with ligands that induce type I IFN signaling pathway dramatically enhances DC-mediated T cell trans infection, the mechanism by which this occurs has remained unclear until now. Here, we demonstrate that the type I IFN-inducible Siglec-1, CD169, is the DC receptor that captures HIV in a GM3-dependent manner. Selective downregulation of CD169 expression, neutralizing CD169 function, or depletion of GSLs from virions, abrogated DC-mediated HIV-1 capture and trans infection, while exogenous expression of CD169 in receptor-naïve cells rescued GSL-dependent capture and trans infection. HIV-1 particles co-localized with CD169 on DC surface immediately following capture and subsequently within non-lysosomal compartments that redistributed to the DC – T cell infectious synapses upon initiation of T cell contact. Together, these findings describe a novel mechanism of pathogen parasitization of host encoded cellular recognition machinery (GM3 – CD169 interaction) for DC-dependent HIV dissemination.