Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.     

The consequences of uncertainties in land use, climate and vegetation responses on the terrestrial carbon

The IPCC SRES narratives were implemented in IMAGE 2.2 to evaluate thefuture condition of the climate system (including the biosphere). A series of scenario experiments was used to assess possible ranges in emissions and concentrations of greenhouse gases, climate change and impacts. These experiments focussed on the role of the terrestrial carbon cycle. The experiments show that the SRES narratives dominate human emissions and not natural processes. In contrary, atmospheric CO2 concentration strongly differs between the experiments. Atmospheric CO2 concentrations range for A1B from 714 to 1009 ppmv CO2 in 2100. The spread of this range is comparable with the full SRES range as implemented in IMAGE 2.2 (515-895 μmol/mol CO2). The most important negative and positive feedback processes in IMAGE 2.2 on the build-up of CO2 concentrations are CO2 fertilisation and soil respiration respectively. Indirect effects of these processes furtherchange land-use patterns, deforestation rates and alter the natural C fluxes. The cumulative effects of these changes have a pronounced influence on the final CO2 concentrations. Our scenario experiments highlight the importance of a proper parameterisation of feedback processes, C-cycle and land use in determining the future states of the climate system.     

Structural characterization of canine PYY

PYY was purified from canine colonic mucosa by sequential steps of reverse phase HPLC and ion-exchange FPLC. Microsequence, amino acid and mass spectral analyses of the purified peptide and its tryptic fragments were consistent with the structure: YPAKPEAPGEDASPEELSRYYASLRHYLNLVTRQRY-amide. Canine PYY(1-36) has the identical sequence as porcine and rat PYY but differs from human PYY at position 3, with Ala instead of Ile, and position 18, with Ser instead of Asn. A smaller form, PYY(3-36), was also purified and characterized. It may differ in its biological activity from the intact peptide and could act as a partial antagonist or agonist of PYY(1-36).     

Alveolar bone loss in wild baboons

Radiograph-based methods were used to assess alveolar bone loss in 12 juvenile and 18 adult baboons (Papio hamadryas, sensu lato) living in the Awash National Park, Ethiopia. Alveolar bone loss, as measured from the cementoenamel junction to the alveolar crest, averaged about 1 mm in juveniles and about 1.5 mm in adults. Densitometry of alveolar bone from the radiographs provides a baseline for comparisons with other adult baboons. Periodontal disease surveys of baboon populations using such methods may identify potential etiological agents. Such knowledge may contribute to a better understanding of periodontal disease etiology in humans. © 1993 Wiley-Liss, Inc.     

Nectar Yeasts in the Tall Larkspur Delphinium barbeyi (Ranunculaceae) and Effects on Components of Pollinator Foraging Behavior

Microorganisms frequently colonize the nectar of angiosperm species. Though capable of altering a suite of traits important for pollinator attraction, few studies exist that test the degree to which they mediate pollinator foraging behavior. The objective of our study was to fill this gap by assessing the abundance and diversity of yeasts associated with the perennial larkspur Delphinium barbeyi (Ranunculaceae) and testing whether their presence affected components of pollinator foraging behavior. Yeasts frequently colonized D. barbeyi nectar, populating 54–77% of flowers examined depending on site. Though common, the yeast community was species-poor, represented by a single species, Metschnikowia reukaufii. Female-phase flowers of D. barbeyi were more likely to have higher densities of yeasts in comparison to male-phase flowers. Pollinators were likely vectors of yeasts, as virgin (unvisited) flowers rarely contained yeasts compared to flowers open to pollinator visitation, which were frequently colonized. Finally, pollinators responded positively to the presence of yeasts. Bombus foragers both visited and probed more flowers inoculated with yeasts in comparison to uninoculated controls. Taken together, our results suggest that variation in the occurrence and density of nectar-inhabiting yeasts have the potential to alter components of pollinator foraging behavior linked to pollen transfer and plant fitness.     

Power of QTL detection by either fixed or random models in half-sib designs

The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio of QTL variance to total genetic variance (λ = 0.1), marker spacing (10 cM), and QTL allele frequency (0.5). A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ) of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log₁₀ of type I error profiles were quite flat at close marker spacing (1 cM), confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.     

Novel fluid shear‐based dissociation device for improved single cell dissociation of spheroids and cell aggregates

Biological industries commonly rely on bioreactor systems for the large‐scale production of cells. Cell aggregation, clumping, and spheroid morphology of certain suspension cells make their large‐scale culture challenging. Growing stem cells as spheroids is indispensable to retain their stemness, but large spheroids (>500 µm diameter) suffer from poor oxygen and nutrient diffusion, ultimately resulting in premature cell death in the centers of the spheroids. Despite this, most large‐scale bioprocesses do not have an efficient method for dissociating cells into single cells, but rely on costly enzymatic dissociation techniques. Therefore, we tested a proof‐of‐concept fluid shear‐based mechanical dissociator that was designed to dissociate stem cell spheroids and aggregates. Our prototype was able to dissociate cells while retaining high viability and low levels of apoptosis. The dissociator also did not impact long‐term cell growth or spheroid formation. Thus, the dissociator introduced here has the potential to replace traditional dissociation methods. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:293–298, 2018