Active bacteria (CTC+) in temperate lakes: temporal and cross-system variations

The temporal variation in the abundance and proportion of highlyrespiration-active bacteria in the eutrophic lakes Esrum andFrederiksborg Slotssø was determined with the redox dye5-cyano-2,3-ditolyl tetrazolium chloride (CTC). In addition,a comparative late summer study was undertaken across a gradientof nutrient enrichment in Danish lakes. The purpose was to investigatethe importance of substrate (chlorophyll) and temperature forthe control of CTC-active cells (CTC+). The abundance of CTC+cells was much lower and more variable than the total numberof cells counted after 4',6-diamidino-2-phenylindole (DAPI)staining. The proportion of CTC+ cells in Lake Esrum and FrederiksborgSlotssø was normally <5%, and between 2.5 and 20%in 14 other lakes. The abundance as well as the proportion ofCTC+ cells increased with chlorophyll in Lake Esrum and FrederiksborgSlotssø, and chlorophyll explained 43% of the variabilityin CTC+ abundance. In the comparative study, the abundance ofCTC+ cells increased along the chlorophyll gradient, which explained49% of the variability. The results showed that the abundanceand, to a lesser degree, the proportion of CTC+ bacteria werecontrolled by substrate supply. One consequence of the low abundanceof active bacteria is that in situ growth rates scaled to CTC+cells are 3- to 7-fold higher than those scaled to DAPI counts.It is suggested that studies on factors controlling bacterioplanktonactivity at the single-cell level should be investigated scaledto active cells.     

Genomic signatures of experimental adaptive radiation in Drosophila

Abiotic environmental factors play a fundamental role in determining the distribution, abundance and adaptive diversification of species. Empowered by new technologies enabling rapid and increasingly accurate examination of genomic variation in populations, researchers may gain new insights into the genomic background of adaptive radiation and stress resistance. We investigated genomic variation across generations of large‐scale experimental selection regimes originating from a single founder population of Drosophila melanogaster, diverging in response to ecologically relevant environmental stressors: heat shock, heat knock down, cold shock, desiccation and starvation. When compared to the founder population, and to parallel unselected controls, there were more than 100,000 single nucleotide polymorphisms (SNPs) displaying consistent allelic changes in response to selective pressures across generations. These SNPs were found in both coding and noncoding sequences, with the highest density in promoter regions, and involved a broad range of functionalities, including molecular chaperoning by heat‐shock proteins. The SNP patterns were highly stressor‐specific despite considerable variation among line replicates within each selection regime, as reflected by a principal component analysis, and co‐occurred with selective sweep regions. Only ~15% of SNPs with putatively adaptive changes were shared by at least two selective regimes, while less than 1% of SNPs diverged in opposite directions. Divergent stressors driving evolution in the experimental system of adaptive radiation left distinct genomic signatures, most pronounced in starvation and heat‐shock selection regimes.     

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.