The Role of Programmed Cell Death Ligand-1 (PD-L1/CD274) in the Development of Graft versus Host Disease

Programmed cell death ligand-1 (PD-L1/CD274) is an immunomodulatory molecule involved in cancer and complications of bone marrow transplantation, such as graft rejection and graft-versus-host disease. The present study was designed to assess the dynamic expression of this molecule after hematopoietic stem cell transplantation in relation to acute graft-versus-host disease. Female BALB/c mice were conditioned with busulfan and cyclophosphamide and transplanted with either syngeneic or allogeneic (male C57BL/6 mice) bone marrow and splenic cells. The expression of PD-L1 was evaluated at different time points employing qPCR, western blot and immunohistochemistry. Allogeneic- but not syngeneic-transplanted animals exhibited a marked up-regulation of PD-L1 expression in the muscle and kidney, but not the liver, at days 5 and 7 post transplantation. In mice transplanted with allogeneic bone marrow cells, the enhanced expression of PD-L1 was associated with high serum levels of IFNγ and TNFα at corresponding intervals. Our findings demonstrate that PD-L1 is differently induced and expressed after allogeneic transplantation than it is after syngeneic transplantation, and that it is in favor of target rather than non-target organs at the early stages of acute graft-versus-host disease. This is the first study to correlate the dynamics of PD-L1 at the gene-, protein- and activity levels with the early development of acute graft-versus-host disease. Our results suggest that the higher expression of PD-L1 in the muscle and kidney (non-target tissues) plays a protective role in skeletal muscle during acute graft-versus-host disease.     

Isolation and characterization of nuclear genes coding for subunits of the yeast ubiquinol-cytochrome c reductase complex

Nuclear genes coding for the M_r 17000, 14000 and 11000 subunits of the ubiquinol-cytochrome c reductase complex (complex III) in yeast have been isolated from a clone bank of yeast nuclear DNA by use of a mRNA hybridization-competition assay. This is based on our observations that levels of mRNAs for these subunits are much reduced during glucose repression and in cytoplasmic petite mutants and the procedure should be of general application for the isolation of other inducible or repressible genes coding for mRNAs present at low levels in the cell. A first characterization of the clones is presented. The genes are not closely linked in the genome and those coding for M_r 14000 and 11000 subunits are present in unique genomic environments, which suggests that there are only single copies of each in the nuclear genome.     

Degradation of phytochrome A and the high irradiance response in Arabidopsis: a kinetic analysis

The ability to respond to far‐red‐rich light is essential for seedlings germinating below dense canopies. Physiological and genetic studies have demonstrated that phytochrome A is the only photoreceptor mediating responses to far‐red light. However, all phytochromes including phytochrome A are believed to be activated by red light and to be inactivated by far‐red light. To address the fundamental question of why phytochrome A has its highest physiological activity at presumably inactivating wavelengths, we analysed light‐induced degradation of phytochrome A in Arabidopsis. Rate constants were obtained for all reaction events in a two‐step model of degradation. Based on biochemical data, the model includes a tagging mechanism preceding degradation. The parameterized model describes Pr accumulation, wavelength dependencies of degradation kinetics and steady‐state levels as well as Pfr‐induced Pr degradation. Subsequently, experimentally derived fluence rate response curves, action spectrum and response curves to dichromatic irradiation were compared to simulations based on the model of degradation. Two kinetically defined phytochrome subspecies, untagged Pfr and tagged Pr, have steady‐state levels closely matching the physiological response curves. Therefore, sensing of far‐red light by phytochrome A can be quantitatively explained based exclusively on regulated protein degradation.     

Nuclear replication activities during imbibition of abscisic acid- and gibberellin-deficient tomato (Lycopersicon esculentum Mill.) seeds

The role of cis-abscisic acid (ABA) and gibberellins (GAs) in the induction of cell-cycle activities has been studied during imbibition and subsequent germination of tomato seeds. Using flow cytometry, nuclear replication activity was investigated in embryo root tips isolated from seeds of the ABA-deficient mutant sit ^w , the GA-deficient mutant gib-1, and the wild-type (MM) tomato (Lycopersicon esculentum Mill. cv. Moneymaker) upon imbibition in water, 10 μM GA₄₊₇, 5 μM ABA or 5 μM ABA+10 μM GA₄₊₇. The nuclei of fully matured dry MM, sit ^w and gib-1 seeds predominantly showed 2C DNA signals, indicating that the cell-cycle activity of most root-tip cells had been arrested at the G₁ phase of nuclear division. However, ABA-deficient sit ^w seeds contained a significantly higher amount of G₂ cells (4C DNA) compared with the other genotypes, suggesting that, during maturation, cell-cycle activity in sit ^w seeds is less efficiently arrested in G₁. Upon imbibition in water, an induction of the 4C signal, indicating nuclear replication, was observed in the root tip cells of both MM and sit ^w embroys. The augmentation in the 4C signal occurred before visible germination. Gib-1 seeds did not show cell-cycle activity and did not germinate in water. Upon imbibition in GA₄₊₇, both cell-cycle activity and subsequent germination were enhanced in MM and sit ^w seeds, and were induced in gib-1. In ABA, the germination of MM and sit ^w seeds was inhibited while nuclear replication of these seeds was not affected. It is concluded that GA influences germination by acting upon processes that precede cell-cycle activation, while ABA affects growth by acting upon processes that follow cell-cycle activation.     

A Bayesian Modelling Approach with Balancing Informative Prior for Analysing Imbalanced Data

When a dataset is imbalanced, the prediction of the scarcely-sampled subpopulation can be over-influenced by the population contributing to the majority of the data. The aim of this study was to develop a Bayesian modelling approach with balancing informative prior so that the influence of imbalance to the overall prediction could be minimised. The new approach was developed in order to weigh the data in favour of the smaller subset(s). The method was assessed in terms of bias and precision in predicting model parameter estimates of simulated datasets. Moreover, the method was evaluated in predicting optimal dose levels of tobramycin for various age groups in a motivating example. The bias estimates using the balancing informative prior approach were smaller than those generated using the conventional approach which was without the consideration for the imbalance in the datasets. The precision estimates were also superior. The method was further evaluated in a motivating example of optimal dosage prediction of tobramycin. The resulting predictions also agreed well with what had been reported in the literature. The proposed Bayesian balancing informative prior approach has shown a real potential to adequately weigh the data in favour of smaller subset(s) of data to generate robust prediction models.     

Landscape composition and spatial prediction of alveolar echinococcosis in southern Ningxia, China

Background

Alveolar echinococcosis (AE) presents a serious public health challenge within China. Mass screening ultrasound surveys can detect pre-symptomatic AE, but targeting areas identified from hospital records is inefficient regarding AE. Prediction of undetected or emerging hotspots would increase detection rates. Voles and lemmings of the subfamily Arvicolinae are important intermediate hosts in sylvatic transmission systems. Their populations reach high densities in productive grasslands where food and cover are abundant. Habitat availability is thought to affect arvicoline population dynamic patterns and definitive host–intermediate host interactions. Arvicoline habitat correlates with AE prevalence in Western Europe and southern Gansu Province, China.

Methods and Findings

Xiji County, Ningxia Hui Autonomous Region, borders southern Gansu. The aims of this study were to map AE prevalence across Xiji and test arvicoline habitat as a predictor. Land cover was mapped using remotely sensed (Landsat) imagery. Infection status of 3,205 individuals screened in 2002–2003 was related, using generalised additive mixed models, to covariates: gender; farming; ethnicity; dog ownership; water source; and areal cover of mountain pasture and lowland pasture. A Markov random field modelled additional spatial variation and uncertainty. Mountain pasture and lowland pasture were associated with below and above average AE prevalence, respectively.

Conclusions

Low values of the normalised difference vegetation index indicated sub-optimality of lowland pasture for grassland arvicolines. Unlike other known endemic areas, grassland arvicolines probably did not provide the principal reservoir for Echinococcus multilocularis in Xiji. This result is consistent with recent small mammal surveys reporting low arvicoline densities and high densities of hamsters, pikas and jerboas, all suitable intermediate hosts for E. multilocularis, in reforested lowland pasture. The risk of re-emergence is discussed. We recommend extending monitoring to: southern Haiyuan County, where predicted prevalence was high; southern Xiji County, where prediction uncertainty was high; and monitoring small mammal community dynamics and the infection status of dogs.     

Gene expression programs during Brassica oleracea seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level

During seed maturation and germination, major changes in physiological status, gene expression, and metabolic events take place. Using chlorophyll sorting, osmopriming, and different drying regimes, Brassica oleracea seed lots of different maturity, stress tolerance, and germination behavior were created. Through careful physiological analysis of these seed lots combined with gene expression analysis using a dedicated cDNA microarray, gene expression could be correlated to physiological processes that occurred within the seeds. In addition, gene expression was studied during early stages of seed germination, prior to radicle emergence, since very little detailed information of gene expression during this process is available. During seed maturation expression of many known seed maturation genes, such as late-embryogenesis abundant or storage-compound genes, was high. Notably, a small but distinct subgroup of the maturation genes was found to correlate to seed stress tolerance in osmoprimed and dried seeds. Expression of these genes rapidly declined during priming and/or germination in water. The majority of the genes on the microarray were up-regulated during osmopriming and during germination on water, confirming the hypothesis that during osmopriming, germination-related processes are initiated. Finally, a large group of genes was up-regulated during germination on water, but not during osmopriming. These represent genes that are specific to germination in water. Germination-related gene expression was found to be partially reversible by physiological treatments such as slow drying of osmoprimed seeds. This correlated to the ability of seeds to withstand stress.     

The nature and perception of fluctuations in human musical rhythms

Although human musical performances represent one of the most valuable achievements of mankind, the best musicians perform imperfectly. Musical rhythms are not entirely accurate and thus inevitably deviate from the ideal beat pattern. Nevertheless, computer generated perfect beat patterns are frequently devalued by listeners due to a perceived lack of human touch. Professional audio editing software therefore offers a humanizing feature which artificially generates rhythmic fluctuations. However, the built-in humanizing units are essentially random number generators producing only simple uncorrelated fluctuations. Here, for the first time, we establish long-range fluctuations as an inevitable natural companion of both simple and complex human rhythmic performances. Moreover, we demonstrate that listeners strongly prefer long-range correlated fluctuations in musical rhythms. Thus, the favorable fluctuation type for humanizing interbeat intervals coincides with the one generically inherent in human musical performances.     

Structure of the dimeric RC–LH1–PufX complex from Rhodobaca bogoriensis investigated by electron microscopy

Electron microscopy and single-particle averaging were performed on isolated reaction centre (RC)—antenna complexes (RC–LH1–PufX complexes) of Rhodobaca bogoriensis strain LBB1, with the aim of establishing the LH1 antenna conformation, and, in particular, the structural role of the PufX protein. Projection maps of dimeric complexes were obtained at 13 Å resolution and show the positions of the 2 × 14 LH1 α- and β-subunits. This new dimeric complex displays two open, C-shaped LH1 aggregates of 13 αβ polypeptides partially surrounding the RCs plus two LH1 units forming the dimer interface in the centre. Between the interface and the two half rings are two openings on each side. Next to the openings, there are four additional densities present per dimer, considered to be occupied by four copies of PufX. The position of the RC in our model was verified by comparison with RC–LH1–PufX complexes in membranes. Our model differs from previously proposed configurations for Rhodobacter species in which the LH1 ribbon is continuous in the shape of an S, and the stoichiometry is of one PufX per RC.     

Remodelling chromatin to shape development of plants

Establishment and dynamic regulation of a higher order chromatin structure is an essential component of development. Chromatin remodelling complexes such as the SWI2/SNF2 family of ATP-dependent chromatin remodellers can alter chromatin architecture by changing nucleosome positioning or substituting histones with histone variants. These remodellers often act in concert with chromatin modifiers such as the polycomb group proteins which confer repressive states through modification of histone tails. These mechanisms are highly conserved across the eukaryotic kingdom although in plants, owing to the maintenance of dedifferentiated cell states that allow for post-embyronic changes in development, strict control of chromatin remodelling is even more paramount. Recent and ongoing studies in the model plant Arabidopsis thaliana have found that while the major families of the SWI2/SNF2 ATPase chromatin remodellers are represented, a number of redundancies and divergent functions have emerged that show a break from the roles of their metazoan counterparts. This review focusses on the SNF2 and CHD families of ATP-dependent remodellers and their roles in plant development.