Increasing abundance of bowhead whales in West Greenland

In April 2006, a dedicated survey of bowhead whales (Balaena mysticetus) was conducted on the former whaling ground in West Greenland to determine the current wintering population abundance. This effort included a double platform aerial survey design, satellite tracking of the movements of nine whales, and estimation of high-resolution surface time from 14 whales instrumented with time-depth recorders. Bowhead whales were estimated to spend an average of 24% (cv=0.03) of the time at or above 2m depth, the maximum depth at which they can be seen on the trackline. This resulted in a fully corrected abundance estimate of 1229 (95% CI: 495-2939) bowhead whales when the availability factor was applied and sightings missed by observers were corrected. This surprisingly large population estimate is puzzling given that the change in abundance cannot be explained by a recent or rapid growth in population size. One possible explanation is that the population, which demonstrates high age and sex segregation, has recently attained a certain threshold size elsewhere, and a higher abundance of mature females appears on the winter and spring feeding ground in West Greenland. This in combination with the latest severe reduction in sea ice facilitating access to coastal areas might explain the surprising increase in bowhead whale abundance in West Greenland.     

Ecosystem properties of semiarid savanna grassland in West Africa and its relationship with environmental variability

The Dahra field site in Senegal, West Africa, was established in 2002 to monitor ecosystem properties of semiarid savanna grassland and their responses to climatic and environmental change. This article describes the environment and the ecosystem properties of the site using a unique set of in situ data. The studied variables include hydroclimatic variables, species composition, albedo, normalized difference vegetation index (NDVI), hyperspectral characteristics (350–1800 nm), surface reflectance anisotropy, brightness temperature, fraction of absorbed photosynthetic active radiation (FAPAR), biomass, vegetation water content, and land‐atmosphere exchanges of carbon (NEE) and energy. The Dahra field site experiences a typical Sahelian climate and is covered by coexisting trees (~3% canopy cover) and grass species, characterizing large parts of the Sahel. This makes the site suitable for investigating relationships between ecosystem properties and hydroclimatic variables for semiarid savanna ecosystems of the region. There were strong interannual, seasonal and diurnal dynamics in NEE, with high values of ~?7.5 g C m^?2 day^?1 during the peak of the growing season. We found neither browning nor greening NDVI trends from 2002 to 2012. Interannual variation in species composition was strongly related to rainfall distribution. NDVI and FAPAR were strongly related to species composition, especially for years dominated by the species Zornia glochidiata. This influence was not observed in interannual variation in biomass and vegetation productivity, thus challenging dryland productivity models based on remote sensing. Surface reflectance anisotropy (350–1800 nm) at the peak of the growing season varied strongly depending on wavelength and viewing angle thereby having implications for the design of remotely sensed spectral vegetation indices covering different wavelength regions. The presented time series of in situ data have great potential for dryland dynamics studies, global climate change related research and evaluation and parameterization of remote sensing products and dynamic vegetation models.     

YKL-40 is differentially expressed in human embryonic stem cells and in cell progeny of the three germ layers

The secreted glycoprotein YKL-40 participates in cell differentiation, inflammation, and cancer progression. High YKL-40 expression is reported during early human development, but its functions are unknown. Six human embryonic stem cell (hESC) lines were cultured in an atmosphere of low or high oxygen tension, in culture medium with or without basic fibroblast growth factor, and on feeder layers comprising mouse embryonic fibroblasts or human foreskin fibroblasts to evaluate whether hESCs and their progeny produced YKL-40 and to characterize YKL-40 expression during differentiation. Secreted YKL-40 protein and YKL-40 mRNA expression were measured by enzyme-linked immunosorbent assay (ELISA) and quantitative RT-PCR. Serial-sectioned colonies were stained for YKL-40 protein and for pluripotent hESC (OCT4, NANOG) and germ layer (HNF-3β, PDX1, CD34, p63, nestin, PAX6) markers. Double-labeling showed YKL-40 expression in OCT4-positive hESCs, PAX6-positive neuroectodermal cells, and HNF-3β-positive endodermal cells. The differentiating progeny showed strong YKL-40 expression. Abrupt transition between YKL-40 and OCT4-positive hESCs and YKL-40-positive ecto- and neuroectodermal lineages was observed within the same epithelial-like layer. YKL-40-positive cells within deeper layers lacked contact with OCT4-positive cells. YKL-40 may be important in initial cell differentiation from hESCs toward ectoderm and neuroectoderm, with retained epithelial morphology, whereas later differentiation into endoderm and mesoderm involves a transition into the deeper layers of the colony.     

Apoptosome-independent activation of the lysosomal cell death pathway by caspase-9

The apoptosome, a heptameric complex of Apaf-1, cytochrome c, and caspase-9, has been considered indispensable for the activation of caspase-9 during apoptosis. By using a large panel of genetically modified murine embryonic fibroblasts, we show here that, in response to tumor necrosis factor (TNF), caspase-8 cleaves and activates caspase-9 in an apoptosome-independent manner. Interestingly, caspase-8-cleaved caspase-9 induced lysosomal membrane permeabilization but failed to activate the effector caspases whereas apoptosome-dependent activation of caspase-9 could trigger both events. Consistent with the ability of TNF to activate the intrinsic apoptosis pathway and the caspase-9-dependent lysosomal cell death pathway in parallel, their individual inhibition conferred only a modest delay in TNF-induced cell death whereas simultaneous inhibition of both pathways was required to achieve protection comparable to that observed in caspase-9-deficient cells. Taken together, the findings indicate that caspase-9 plays a dual role in cell death signaling, as an activator of effector caspases and lysosomal membrane permeabilization.     

Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips was three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.     

The C-terminus is critical for the functional expression of the human serotonin transporter

The plasma membrane serotonin transporter (SERT) has an important role in terminating serotonergic neurotransmission by re-uptake of 5-HT from the synaptic cleft. The expression of SERT on the cell surface is therefore a critical factor. In this study, we examined the role of the carboxyl terminus of SERT in trafficking to the plasma membrane. 5-HT uptake activity was used to measure the effects of systematic deletions or alanine substitutions in the C-terminus. We found that deletion of 16 amino acids in the distal C-terminus had no effect on uptake activity, whereas further deletion was detrimental for the function of SERT. Cell surface biotinylation was used to determine the role of the C-terminus in localization and trafficking. We showed that the C-terminus is crucial for the delivery of SERT to the plasma membrane and that the deletion of this part of the transporter results in a lack of mature glycosylation and impaired trafficking to the plasma membrane. Furthermore, the C-terminally truncated mutants were shown to have a dominant negative effect on wild-type SERT uptake activity.     

PYY(3-36) reduces food intake and body weight and improves insulin sensitivity in rodent models of diet-induced obesity

The gut hormone peptide YY (PYY) was recently proposed to comprise an endogenous satiety factor. We have studied acute anorectic functions of PYY(3-36) in mice and rats, as well as metabolic effects of chronic PYY(3-36) administration to diet-induced obese (DIO) mice and rats. A single intraperitoneal injection of PYY(3-36) inhibited food intake in mice, but not in rats. We next investigated the effects of increasing doses (100, 300, and 1,000 microg.kg-1.day-1) of PYY(3-36) administered subcutaneously via osmotic minipumps on food intake and body weight in DIO C57BL/6J mice. Whereas only the highest dose (1,000 microg.kg-1.day-1) of PYY(3-36) significantly reduced food intake over the first 3 days, body weight gain was dose dependently reduced, and on day 28 the group treated with 1,000 microg.kg-1.day-1 PYY(3-36) weighed approximately 10% less than the vehicle-treated group. Mesenteric, epididymal, retroperitoneal, and inguinal fat pad weight was dose dependently reduced. Subcutaneous administration of PYY(3-36) (250 and 1,000 microg.kg-1.day-1) for 28 days reduced body weight and improved glycemic control in glucose-intolerant DIO rats. Neither 250 nor 1,000 microg/kg PYY(3-36) elicited a conditioned taste aversion in male rats.     

Screening for cellulose and hemicellulose degrading enzymes from the fungal genus Ulocladium

The fungal genus Ulocladium consists mostly of saprotrophic species and can readily be isolated from dead vegetation, rotten wood, paper, textiles and other cellulose containing materials. Thus, they must produce cellulolytic and hemicellulolytic enzymes. In this study fifty Ulocladium strains from ten different species were tested for enzyme activities on 14 different azurine-cross-linked (AZCL) substrates and analyzed by multivariate analysis. The tested strains of Ulocladium were found to produce a broad enzyme profile. Most species in Ulocladium were able to produced high amounts of enzymes that degraded amylose, arabinoxylan, β-glucan, cellulose and xylan; however, variations between species as well as between individual strains in each species were seen. Overall, the enzyme profiles were found to be species specific, but also source of isolation impacted the enzymes produced. The results suggest that species identity as well as isolation source must be considered when screening microorganisms for enzymes.     

Dermatan Sulfate Epimerase 1-Deficient Mice Have Reduced Content and Changed Distribution of Iduronic Acids in Dermatan Sulfate and an Altered Collagen Structure in Skin

Dermatan sulfate epimerase 1 (DS-epi1) and DS-epi2 convert glucuronic acid to iduronic acid in chondroitin/dermatan sulfate biosynthesis. Here we report on the generation of DS-epi1-null mice and the resulting alterations in the chondroitin/dermatan polysaccharide chains. The numbers of long blocks of adjacent iduronic acids are greatly decreased in skin decorin and biglycan chondroitin/dermatan sulfate, along with a parallel decrease in iduronic-2-O-sulfated-galactosamine-4-O-sulfated structures. Both iduronic acid blocks and iduronic acids surrounded by glucuronic acids are also decreased in versican-derived chains. DS-epi1-deficient mice are smaller than their wild-type littermates but otherwise have no gross macroscopic alterations. The lack of DS-epi1 affects the chondroitin/dermatan sulfate in many proteoglycans, and the consequences for skin collagen structure were initially analyzed. We found that the skin collagen architecture was altered, and electron microscopy showed that the DS-epi1-null fibrils have a larger diameter than the wild-type fibrils. The altered chondroitin/dermatan sulfate chains carried by decorin in skin are likely to affect collagen fibril formation and reduce the tensile strength of DS-epi1-null skin.Chondroitin sulfate (CS) is an unbranched polymer chain composed of alternating glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc) units (36, 49). In dermatan sulfate (DS), d-glucuronic acid is converted to its epimer l-iduronic acid (IdoA) (25). The extent of this modification, which varies from a few percent of the glucuronic acid being epimerized to a predominant presence of iduronic acid, depends on the variable epimerase activity in tissues and on the core protein attached to the chain in CS/DS proteoglycans (PGs) (41, 47). The same CS/DS PG has a different iduronic acid content, depending on the cell type and tissue of origin (4, 5). The name CS/DS denotes the hybrid GlcA-IdoA nature of the chain. It has long been known that the distribution of iduronic acids within the chain is not random but follows two patterns: either they are clustered together, forming long iduronic acid blocks, or they are isolated, i.e., interspersed among surrounding glucuronic acids (11). DS epimerase 1 (DS-epi1) and DS-epi2, encoded in mouse by the Dse and Dsel (Dse-like) genes, respectively, are present in organisms ranging from Xenopus tropicalis to humans but not in worms and flies (23, 34). During DS biosynthesis, epimerization is followed by the action of eight C-specific O-sulfotranferases, which transfer a sulfate group to C-2 of both IdoA and GlcA and to C-4, C-6, and C-4/C-6 of GalNAc (18). These modification reactions, individually affecting only part of the available substrate, produce structural variability in the CS/DS chain. Considerable efforts have been made to characterize specific sequences in the CS/DS chains responsible for binding to protein and the subsequent mediation of a biological effect (28). For instance, (IdoA-2OS-GalNAc-4OS)₃- and GalNAc-4/6-diOS-containing structures bind and activate heparin cofactor II, which is the major antithrombotic system in the subendothelial layer (48). IdoA/GlcA-2OS-GalNAc-6OS-containing structures bind to pleiotrophin, mediating neuritogenic activity (3, 44). IdoA-GalNAc-4OS-containing structures bind to basic fibroblast growth factor, and the complex has been shown to be active in wound healing (46).CS/DS PGs are mainly found in the extracellular matrix. They belong to four families: lecticans, e.g., versican, aggrecan, brevican, and neurocan; collagens, e.g., collagen IX; basement membrane PGs, e.g., SMC3, collagen XV, and perlecan, containing both heparan sulfate (HS) and CS/DS; and small leucine-rich repeat PGs. Some PGs of the first three groups are referred to as CS PGs. The actual presence of iduronic acid, depending on the tissue examined and on the developmental stage, has been overlooked in many cases (37, 44). The archetypical small leucine-rich repeat PG family members decorin, biglycan, fibromodulin, and lumican bind fibrillar collagens and affect collagen fibril and scaffold formation in connective tissues (15). Decorin and biglycan are substituted with one and two CS/DS chains, respectively. Decorin is involved in collagen type I fibril formation and matrix assembly in a wide range of connective tissues and binds near the C terminus of collagen monomers, delaying their accretion to the growing fibrils. We have identified an SYIRIADTNIT sequence in decorin as essential for binding to collagen (16). The role of the decorin CS/DS chain in vivo has not been explored, although in vitro studies suggest that IdoA promotes the binding of CS/DS to collagen (31) and is required for self-association of CS/DS chains (6, 10, 22).Here the function of DS-epi1 in mice was disrupted. DS-epi1-deficient mice show CS/DS with a marked deficiency in iduronic acid-containing structures. The deletion of DS-epi1 is likely to affect many types of PGs and to result in a complex phenotype. We focus on skin alterations presumably caused by altered decorin/biglycan CS/DS chains.     

Longitudinal immune monitoring of patients receiving intratumoral injection of a MART-1 T-cell receptor-transduced cell line (C-Cure 709)

Background aimsAdoptive transfer of tumor-specific lymphocytes is a promising strategy in the treatment of cancer. We conducted intratumoral administration of an allogeneic irradiated continuous T-cell line (C-Cure 709) expressing an HLA-A2-restricted MART-1-specific T-cell receptor (TCR) into HLA-A2⁺ melanoma patients. The C-Cure 709 cell line is cytotoxic against MART-1⁺ HLA-A2⁺ melanoma cell lines and secretes several immune stimulatory cytokines upon stimulation.MethodsAnti-tumor immune responses against the commonly expressed tumor antigen (Ag) MART-1 were longitudinally analyzed in peripheral blood by fluorescence-activated cell sorting (FACS) before and after intratumoral injection of C-Cure 709.ResultsNo treatment-induced increase in Ag-specific T-cell frequencies was observed in peripheral blood, and the phenotype of MART-1-specific T cells was very stable during the treatment. Interestingly, despite a very stable frequency of MART-1-specific T cells over the course of treatment, clonotype mapping revealed that the response was in fact highly diverse and dynamic, with new clonotypes emerging during treatment. Only a few clonotypes were recurrently detected in consecutive samples. One MART-1-specific T-cell clone disappearing from peripheral blood was later detected in a metastatic lesion.ConclusionsSequence analyzes of the CDR3 region revealed conserved structural characteristics in the MART-1-specific TCR used by T-cell clones.