Dynamics of dissolved and particulate organic carbon in a saline and semiarid stream of southeast Spain (Chicamo stream)

Annual variations in the concentration of dissolved (DOC) and particulate organic carbon (CPOC = Coarse; FPOC = Fine; UPOC = Ultrafine) were studied in a 100 m-reach of the Chicamo stream, an intermittent saline stream in southeast Spain. DOC represented the most important fraction of organic carbon flowing in the Chicamo stream (>98%), with concentrations of about 1.7 mgC l^–1 during most of the year, reaching 2.5 mgC l^–1 in summer. One high flow episode during a rain storm in winter was characterized by a considerably increased concentration of DOC (9.4 mgC l^–1). CPOC was the dominant POC fraction. Positive and significant correlations were found for DOC and discharge, which support the idea of allochthonous inputs due to floods. There was no significant correlation between POC and discharge. No significant correlations were found for DOC or POC with the physico-chemical parameters measured, while a negative significant correlation was found between DOC and temperature. The export of total organic carbon from the drainage basin of the Chicamo stream was low (6.2 × 10^–4 gC m^–2 yr^–1) and typical of streams in arid and semi-arid regions. The results of a Principal Component Analysis defined three different phases. The first consisted of short periods, during which floods provide pulses of allochthonous organic carbon and nutrients, the second a dry phase (summer), defined by biotic interactions, during which the stream could acts as a `sink' of organic matter, and the third and final phase which is characterised by hydrological stability.     

A TGFβRII frameshift-mutation-derived CTL epitope recognised by HLA-A2-restricted CD8+ T cells

Microsatellite instability (MSI) is recognised as genome-wide alterations in repetitive DNA sequences caused by defects in the DNA mismatch repair machinery. Such mutation patterns have been found in almost all analysed malignancies from patients with hereditary non-polyposis colorectal cancer, and in approximately 15% of sporadic colorectal cancers. In cancers with the MSI phenotype, microsatellite-like sequences in coding regions of various cancer-related genes, including transforming growth factor beta receptor type II (TGF betaRII), are targets for mutations. The TGF betaRII gene harbours a 10-bp polyadenine tract, and mutations within this region are found in 90% of colorectal cancers with MSI. The frameshift mutations result in new amino acid sequences in the C-terminal part of the proteins, prematurely terminating where a novel stop codon appears. In this study we have defined new cytotoxic T lymphocyte (CTL) epitope (RLSSCVPVA), carrying a good HLA-A*0201 binding motif, and resulting from the most common frameshift mutation in TGF betaRII. A CTL line and several CTL clones were generated from an HLA-A2+ normal donor by repeated stimulation of T cells with dendritic cells pulsed with the peptide. One of the CTL clones was able to kill an HLA-A2+ colon cancer cell line harbouring mutant TGF betaRII. This epitope may be a valuable component in cancer vaccines directed at MSI-positive carcinomas.     

Selective cytotoxic T-lymphocyte targeting of tumor immune escape variants

Defects in major histocompatibility complex (MHC) class I-restricted antigen presentation are frequently observed in human cancers and result in escape of tumors from cytotoxic T lymphocyte (CTL) immune surveillance in mice. Here, we show the existence of a unique category of CTLs that can prevent this escape. The CTLs target an alternative repertoire of peptide epitopes that emerge in MHC class I at the surface of cells with impaired function of transporter associated with antigen processing (TAP), tapasin or the proteasome. These peptides, although derived from self antigens such as the commonly expressed Lass5 protein (also known as Trh4), are not presented by normal cells. This explains why they act as immunogenic neoantigens. The newly discovered epitopes can be exploited for immune intervention against processing-deficient tumors through adoptive T-cell transfer or peptide vaccination.     

Structural basis for target protein recognition by the protein disulfide reductase thioredoxin

Thioredoxin is ubiquitous and regulates various target proteins through disulfide bond reduction. We report the structure of thioredoxin (HvTrxh2 from barley) in a reaction intermediate complex with a protein substrate, barley alpha-amylase/subtilisin inhibitor (BASI). The crystal structure of this mixed disulfide shows a conserved hydrophobic motif in thioredoxin interacting with a sequence of residues from BASI through van der Waals contacts and backbone-backbone hydrogen bonds. The observed structural complementarity suggests that the recognition of features around protein disulfides plays a major role in the specificity and protein disulfide reductase activity of thioredoxin. This novel insight into the function of thioredoxin constitutes a basis for comprehensive understanding of its biological role. Moreover, comparison with structurally related proteins shows that thioredoxin shares a mechanism with glutaredoxin and glutathione transferase for correctly positioning substrate cysteine residues at the catalytic groups but possesses a unique structural element that allows recognition of protein disulfides.     

Temperature dependence of predation depends on the relative performance of predators and prey

The temperature dependence of predation rates is a key issue for understanding and predicting the responses of ecosystems to climate change. Using a simple mechanistic model, we demonstrate that differences in the relative performances of predator and prey can cause strong threshold effects in the temperature dependence of attack rates. Empirical data on the attack rate of northern pike (Esox lucius) feeding on brown trout (Salmo trutta) confirm this result. Attack rates fell sharply below a threshold temperature of +11°C, which corresponded to a shift in relative performance of pike and brown trout with respect to maximum attack and escape swimming speeds. The average attack speed of pike was an order of magnitude lower than the escape speed of brown trout at 5°C, but approximately equal at temperatures above 11°C. Thresholds in the temperature dependence of ecological rates can create tipping points in the responses of ecosystems to increasing temperatures. Thus, identifying thresholds is crucial when predicting future effects of climate warming.     

Proteogenomic Refinement of the Neomegalonema perideroedesT Genome Annotation

Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema) which belongs to the Alphaproteobacteria. N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species—being the only sequenced member of its proposed family—the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. Here, a proteomic dataset for the refinement of the N. perideroedes genome annotations is generated which clearly indicates the shortcomings of high‐throughput in silico genome annotation.     

Human Brain Reacts to Transcranial Extraocular Light

Transcranial extraocular light affects the brains of birds and modulates their seasonal changes in physiology and behavior. However, whether the human brain is sensitive to extraocular light is unknown. To test whether extraocular light has any effect on human brain functioning, we measured brain electrophysiology of 18 young healthy subjects using event-related potentials while they performed a visual attention task embedded with emotional distractors. Extraocular light delivered via ear canals abolished normal emotional modulation of attention related brain responses. With no extraocular light delivered, emotional distractors reduced centro-parietal P300 amplitude compared to neutral distractors. This phenomenon disappeared with extraocular light delivery. Extraocular light delivered through the ear canals was shown to penetrate at the base of the scull of a cadaver. Thus, we have shown that extraocular light impacts human brain functioning calling for further research on the mechanisms of action of light on the human brain.     

Land-use history of the Axlarp area in the Småland uplands,southern Sweden: palaeoecological and archaeological investigations

The results of pollen analysis, magnetic measurements (SIRM), and archaeological and historical investigations, in the Axlarp area are presented. With respect to natural conditions and the distribution of prehistoric features, this area is typical of the higher parts of the Småland uplands, which, agriculturally, is a marginal region of southern Sweden. The study shows that farming in the Axlarp area began at ca. 700 B.C. (dates in calibrated/calendar years). The period 700 B.C.-A.D. 500 was characterized by shifting cultivation of Hordeum and Triticum and much pasture. Between A.D. 500 and A.D. 1200 farming declined but some pasturage was still practised, possibly on a seasonal basis. Two farms were established in the Middle Ages, probably between A.D. 1200–1300. Cereals were sown in stone-cleared fields and pastoral farming and hay making was carried out. One farm was deserted during the 15th or early 16th century and the other developed into the hamlet Axlarp whose farmers practised a three-course cropping system. Land-use history as recorded in the pollen diagram can be related to activities associated with these farms. Cereals grown after A.D. 1200 included Hordeum and Avena, and possibly Triticum and Secale. There are no indications of slash-and-burn cultivation in the area.