NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure

Background

Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Due to extremely low signal levels, however, Raman microscopy requires sophisticated image processing techniques for noise reduction and signal extraction. To date, efficient, automated algorithms for resolving sub-cellular features in noisy, multi-dimensional image sets have not been explored extensively.

Results

We show that hybrid z-score normalization and standard regression (Z-LSR) can highlight the spectral differences within the cell and provide image contrast dependent on spectral content. In contrast to typical Raman imaging processing methods using multivariate analysis, such as single value decomposition (SVD), our implementation of the Z-LSR method can operate nearly in real-time. In spite of its computational simplicity, Z-LSR can automatically remove background and bias in the signal, improve the resolution of spatially distributed spectral differences and enable sub-cellular features to be resolved in Raman microscopy images of mouse macrophage cells. Significantly, the Z-LSR processed images automatically exhibited subcellular architectures whereas SVD, in general, requires human assistance in selecting the components of interest.

Conclusions

The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without compromise in image quality or information loss in associated spectra. These results motivate further use of label free microscopy techniques in real-time imaging of live immune cells.     

Subjecting the theory of the small‐island effect to Ockham’s razor

Species–area curves from islands and other isolates often differ in shape from sample‐area curves generated from mainlands or sections of isolates (or islands), especially at finer scales. We examine two explanations for this difference: (1) the small‐island effect (SIE), which assumes the species–area curve is composed of two distinctly different curve patterns; and (2) a sigmoid or depressed isolate species–area curve with no break‐points (in arithmetic space). We argue that the application of Ockham’s razor – the principle that the simplest, most economical explanation for a hypothesis should be accepted over less parsimonious alternatives – leads to the conclusion that the latter explanation is preferable. We hold that there is no reason to assume the ecological factors or patterns that affect the shapes of isolate (or island) curves cause two distinctly different patterns. This assumption is not required for the alternative, namely that these factors cause a single (though depressed) isolate species–area curve with no break‐points. We conclude that the theory of the small‐island effect, despite its present standing as an accepted general pattern in nature, should be abandoned.     

Choice of Allocations and Constructs for Attributional or Consequential Life Cycle Assessment and Input‐Output Analysis

The divide between attributional and consequential research perspectives partly overlaps with the long‐standing methodological discussions in the life cycle assessment (LCA) and input‐output analysis (IO) research communities on the choice of techniques and models for dealing with situations of coproduction. The recent harmonization of LCA allocations and IO constructs revealed a more diverse set of coproduction models than had previously been understood. This increased flexibility and transparency in inventory modeling warrants a re‐evaluation of the treatment of coproduction in analyses with attributional and consequential perspectives. In the present article, the main types of coproductions situations and of coproduction models are reviewed, along with key desirable characteristics of attributional and consequential studies. A concordance analysis leads to clear recommendations, which call for important refinements to current guidelines for both LCA/IO practitioners and database developers. We notably challenge the simple association between, on the one hand, attributional LCA and partition allocation, and on the one hand, consequential LCA and substitution modeling.     

Regulation of tissue inhibitor of metalloproteinases-1 in rat Sertoli cells: induction by germ cell residual bodies, interleukin-1alpha, and second messengers

In the testis, FSH has been shown to induce the expression and secretion of tissue inhibitor of metalloproteinases-1 (TIMP-1) from Sertoli cells in vitro. This study was performed to elucidate further the cellular origin of testicular TIMP-1 and its expression by hormonal and paracrine factors. This is the first report on the expression of testicular TIMP-1 in vivo. TIMP-1 mRNA in whole testis was decreased after hypophysectomy and strongly increased by the injection of FSH-S17 to hypophysectomized rats. Primary cultures of both peritubular and Sertoli cells showed basal expression of TIMP-1 mRNA. In contrast, we were unable to detect TIMP-1 mRNA in Leydig cells, freshly isolated immature germ cells (primary spermatocytes and spermatids), or residual bodies. We further show that treatment of Sertoli cells with 8-(4-chlorophenyl)thio-cAMP (8-CPTcAMP) in combination with 12-O-tetradecanoylphorbol 13-acetate (TPA) or Ca(2+) inducers (calcium ionophore A23187 or thapsigargin) had additive (TPA) and synergistic effects (Ca(2+)) on the level of TIMP-1 mRNA and secreted protein. We also show that both the level of TIMP-1 mRNA and secreted protein from Sertoli cells were strongly increased by residual bodies, as well as by the cytokine interleukin-1alpha. TIMP-1 was not up-regulated by either 8-CPTcAMP or interleukin-1alpha in peritubular cells. In contrast to the regulated secretory fraction of TIMP-1, we also detected constitutively expressed immunoreactive TIMP-1 in the nucleus of Sertoli cells, suggesting a role of nuclear TIMP-1 in these cells. In conclusion, our data show that secretion of TIMP-1 from Sertoli cells is highly regulated by hormonal and local processes in the testis, indicating that TIMP-1 is of physiological importance during both testicular development and spermatogenesis.     

E. coli initiator tRNA analogs with different nucleotides in the discriminator base position.

The effect of base changes at the fourth position from the 3'-terminus of Escherichia coli initiator tRNAMet has been studied to test the 'discriminator hypothesis' which proposed that the nucleotide in this position might have a role in the specificity of the aminoacylation reaction. E. coli initiator tRNA lacking the 3'-terminal tetranucleotide was prepared by partial digestion with S1 nuclease. To construct tRNA analogs with different bases in the fourth position this truncated tRNA was joined by RNA ligase to each of four chemically synthesized 2',3'-ethoxy-methylidene tetranucleotides pACCA(em), pCCCA(em), pGCCA(em), and pUCCA(em). In vitro aminoacylation studies showed that all four molecules accepted methionine, albeit with different Vmax values.     

Seasonal carbon allocation to arbuscular mycorrhizal fungi assessed by microscopic examination, stable isotope probing and fatty acid analysis

Background and Aim

Climate change models are limited by lack of baseline data, in particular carbon (C) allocation to – and dynamics within – soil microbial communities. We quantified seasonal C-assimilation and allocation by plants, and assessed how well this corresponds with intraradical arbuscular mycorrhizal fungal (AMF) storage and structural lipids (16:1ω5 NLFA and PLFA, respectively), as well as microscopic assessments of AMF root colonization.

Methods

Coastal Hypochoeris radicata plants were labeled with ¹³CO₂ in February, July and October, and ¹³C-allocation to fine roots and NLFA 16:1ω5, as well as overall lipid contents and AM colonization were quantified.

Results

C-allocation to fine roots and AMF storage lipids differed seasonally and mirrored plant C-assimilation, whereas AMF structural lipids and AM colonization showed no seasonal variation, and root colonization exceeded 80 % throughout the year. Molecular analyzes of the large subunit rDNA gene indicated no seasonal AMF community shifts.

Conclusions

Plants allocated C to AMF even at temperatures close to freezing, and fungal structures persisted in roots during times of low C-allocation. The lack of seasonal differences in PLFA and AM colonization indicates that NLFA analyses should be used to estimate fungal C-status. The implication of our findings for AM function is discussed.     

The antimicrobial peptide LL-37 activates innate immunity at the airway epithelial surface by transactivation of the epidermal growth factor receptor

Antimicrobial peptides produced by epithelial cells and neutrophils represent essential elements of innate immunity, and include the defensin and cathelicidin family of antimicrobial polypeptides. The human cathelicidin cationic antimicrobial protein-18 is an antimicrobial peptide precursor predominantly expressed in neutrophils, and its active peptide LL-37 is released from the precursor through the action of neutrophil serine proteinases. LL-37 has been shown to display antimicrobial activity against a broad spectrum of microorganisms, to neutralize LPS bioactivity, and to chemoattract neutrophils, monocytes, mast cells, and T cells. In this study we show that LL-37 activates airway epithelial cells as demonstrated by activation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) and increased release of IL-8. Epithelial cell activation was inhibited by the MAPK/ERK kinase (MEK) inhibitors PD98059 and U0126, by the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor AG1478, by blocking anti-EGFR and anti-EGFR-ligand Abs, and by the metalloproteinase inhibitor GM6001. These data suggest that LL-37 transactivates the EGFR via metalloproteinase-mediated cleavage of membrane-anchored EGFR-ligands. LL-37 may thus constitute one of the mediators by which neutrophils regulate epithelial cell activity in the lung.     

Genetic code: introducing pyrrolysine

Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG. Initial studies suggest that pyrrolysine may be co-translationally inserted during protein synthesis, probably by a mechanism analogous to that operating during selenocysteine incorporation.     

Vacuoles release sucrose via tonoplast-localised SUC4-type transporters

Arabidopsis thaliana has seven genes for functionally active sucrose transporters. Together with sucrose transporters from other dicot and monocot plants, these proteins form four separate phylogenetic groups. Group-IV includes the Arabidopsis protein SUC4 (synonym SUT4) and related proteins from monocots and dicots. These Group-IV sucrose transporters were reported to be either tonoplast- or plasma membrane-localised, and in heterologous expression systems were shown to act as sucrose/H(+) symporters. Here, we present comparative analyses of the subcellular localisation of the Arabidopsis SUC4 protein and of several other Group-IV sucrose transporters, studies on tissue specificity of the Arabidopsis SUC4 promoter, phenotypic characterisations of Atsuc4.1 mutants and AtSUC4 overexpressing (AtSUC4-OX) plants, and functional comparisons of Atsuc4.1 and AtSUC4-OX vacuoles. Our data show that SUC4-type sucrose transporters from different plant families (Brassicaceae, Cucurbitaceae and Solanaceae) localise exclusively to the tonoplast, demonstrating that vacuolar sucrose transport is a common theme of all SUC4-type proteins. AtSUC4 expression is confined to the stele of Arabidopsis roots, developing anthers and meristematic tissues in all aerial parts. Analyses of the carbohydrate content of WT and mutant seedlings revealed reduced sucrose content in AtSUC4-OX seedlings. This is in line with patch-clamp analyses of AtSUC4-OX vacuoles that characterise AtSUC4 as a sucrose/H(+) symporter directly in the tonoplast membrane.