Implications of genetic heterogeneity in cancer

DNA sequencing studies have established that many cancers contain tens of thousands of clonal mutations throughout their genomes, which is difficult to reconcile with the very low rate of mutation in normal human cells. This observation provides strong evidence for the mutator phenotype hypothesis, which proposes that a genome-wide elevation in the spontaneous mutation rate is an early step in carcinogenesis. An elevated mutation rate implies that cancers undergo continuous evolution, generating multiple subpopulations of cells that differ from one another in DNA sequence. The extensive heterogeneity in DNA sequence and continual tumor evolution that would occur in the context of a mutator phenotype have important implications for cancer diagnosis and therapy.     

To what extent are task-switching deficits in children with attention-deficit/hyperactivity disorder independent of impaired inhibition?

Executive functions, higher-order cognitive functions needed for goal-directed behavior, have been studied extensively in the search for endophenotypes for ADHD, yet results have been inconclusive. We examine the performance of children with ADHD in task switching as an as yet understudied potential endophenotype. A group of 20 children with ADHD and a group of 23 children without ADHD (ages 7?C12) performed a task-switching paradigm and a Go/No-Go Task. Children with ADHD displayed significantly greater specific switch costs, that is, compared to control children they were especially impaired directly after task switches. There were no group differences with respect to the general switch costs, which are estimated by comparing performance on single task blocks to the block where both tasks are intermixed. Specific switch costs and Go/No-Go error rate were significantly correlated; yet, group differences in the task-switching paradigm remained significant even when inhibition was controlled for. This pattern of results suggests that children with ADHD are neither generally impaired in executive function nor only impaired with respect to inhibition. Instead, they display a highly specific deficit with regard to the flexible suppression and amplification of different task rules according to the context. Our conclusion that task switching has the potential to be added to the list of ADHD endophenotypes is strengthened by the independence of task-switching deficits and inhibition.     

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2012 - 31 May 2012

This article documents the addition of 123 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brenthis ino, Cichla orinocensis, Cichla temensis, Epinephelus striatus, Gobio gobio, Liocarcinus depurator, Macrolophus pygmaeus, Monilinia vaccinii-corymbosi, Pelochelys cantorii, Philotrypesis josephi, Romanogobio vladykovi, Takydromus luyeanus and Takydromus viridipunctatus. These loci were cross-tested on the following species: Cichla intermedia, Cichla ocellaris, Cichla pinima, Epinephelus acanthistius, Gobio carpathicus, Gobio obtusirostris, Gobio sp. 1, Gobio volgensis, Macrolophus costalis, Macrolophus melanotoma, Macrolophus pygmaeus, Romanogobio albipinnatus, Romanogobio banaticus, Romanogobio belingi, Romanogobio kesslerii, Romanogobio parvus, Romanogobio pentatrichus, Romanogobio uranoscopus, Takydromus formosanus, Takydromus hsuehshanesis and Takydromus stejnegeri.     

Managed metapopulations: do salmon hatchery 'sources' lead to in-river 'sinks' in conservation?

Maintaining viable populations of salmon in the wild is a primary goal for many conservation and recovery programs. The frequency and extent of connectivity among natal sources defines the demographic and genetic boundaries of a population. Yet, the role that immigration of hatchery-produced adults may play in altering population dynamics and fitness of natural populations remains largely unquantified. Quantifying, whether natural populations are self-sustaining, functions as sources (population growth rate in the absence of dispersal, λ>1), or as sinks (λ<1) can be obscured by an inability to identify immigrants. In this study we use a new isotopic approach to demonstrate that a natural spawning population of Chinook salmon, (Oncorhynchus tshawytscha) considered relatively healthy, represents a sink population when the contribution of hatchery immigrants is taken into consideration. We retrieved sulfur isotopes ((34)S/(32)S, referred to as δ(34)S) in adult Chinook salmon otoliths (ear bones) that were deposited during their early life history as juveniles to determine whether individuals were produced in hatcheries or naturally in rivers. Our results show that only 10.3% (CI = 5.5 to 18.1%) of adults spawning in the river had otolith δ(34)S values less than 8.5‰, which is characteristic of naturally produced salmon. When considering the total return to the watershed (total fish in river and hatchery), we estimate that 90.7 to 99.3% (CI) of returning adults were produced in a hatchery (best estimate = 95.9%). When population growth rate of the natural population was modeled to account for the contribution of previously unidentified hatchery immigrants, we found that hatchery-produced fish caused the false appearance of positive population growth. These findings highlight the potential dangers in ignoring source-sink dynamics in recovering natural populations, and question the extent to which declines in natural salmon populations are undetected by monitoring programs.     

IL-2 receptor beta-chain signaling controls immunosuppressive CD4+ T cells in the draining lymph nodes and lung during allergic airway inflammation in vivo

IL-2 influences both survival and differentiation of CD4(+) T effector and regulatory T cells. We studied the effect of i.n. administration of Abs against the alpha- and the beta-chains of the IL-2R in a murine model of allergic asthma. Blockade of the beta- but not the alpha-chain of the IL-2R after allergen challenge led to a significant reduction of airway hyperresponsiveness. Although both treatments led to reduction of lung inflammation, IL-2 signaling, STAT-5 phosphorylation, and Th2-type cytokine production (IL-4 and IL-5) by lung T cells, IL-13 production and CD4(+) T cell survival were solely inhibited by the blockade of the IL-2R beta-chain. Moreover, local blockade of the common IL-2R/IL-15R beta-chain reduced NK cell number and IL-2 production by lung CD4(+)CD25(+) and CD4(+)CD25(-) T cells while inducing IL-10- and TGF-beta-producing CD4(+) T cells in the lung. This cytokine milieu was associated with reduced CD4(+) T cell proliferation in the draining lymph nodes. Thus, local blockade of the beta-chain of the IL-2R restored an immunosuppressive cytokine milieu in the lung that ameliorated both inflammation and airway hyperresponsiveness in experimental allergic asthma. These findings provide novel insights into the functional role of IL-2 signaling in experimental asthma and suggest that blockade of the IL-2R beta-chain might be useful for therapy of allergic asthma in humans.     

Chemical profiles of mated and virgin queens, egg-laying intermorphs and workers of the ant Crematogaster smithi

Many colonies of the North American ant Crematogaster smithi contain a “third female caste” in addition to queens and workers. These “intermorphs” are morphological intermediate of queens and workers and have well-developed ovaries but lack a spermatheca for the storage of sperm. They are specialised for laying large numbers of unfertilised, viable eggs, most of which serve as food for larvae and adults, though a few may eventually develop into males. Based on the assumption that cuticular hydrocarbons (CHCs) in social insects honestly signal the reproductive status of an individual we investigated the CHC of mated mature queens, virgin queens, intermorphs and workers. We expected intermorphs to show chemical profiles intermediate between those of mated queens and non-reproductive workers. A discriminant analysis of the chemical profiles reliably separated queens, virgin queens, and workers, but failed to distinguish between queens and intermorphs even though workers were apparently capable of doing so.     

Protein-sphingolipid interactions within cellular membranes

Each intracellular organelle critically depends on maintaining its specific lipid composition that in turn contributes to the biophysical properties of the membrane. With our knowledge increasing about the organization of membranes with defined microdomains of different lipid compositions, questions arise regarding the molecular mechanisms that underlie the targeting to/segregation from microdomains of a given protein. In addition to specific lipid-transmembrane segment interactions as a basis for partitioning, the presence in a given microdomain may alter the conformation of proteins and, thus, the activity and availability for regulatory modifications. However, for most proteins, the specific lipid environment of transmembrane segments as well as its relevance to protein function and overall membrane organization are largely unknown. To help fill this gap, we have synthesized a novel photoactive sphingolipid precursor that, together with a precursor for phosphoglycerolipids and with photo-cholesterol, was investigated in vivo with regard to specific protein transmembrane span-lipid interactions. As a proof of principle, we show specific labeling of the ceramide transporter with the sphingolipid probe and describe specific in vivo interactions of lipids with caveolin-1, phosphatidylinositol transfer protein beta, and the mature form of nicastrin. This novel photolabile sphingolipid probe allows the detection of protein-sphingolipid interactions within the membrane bilayer of living cells.     

Crystal structures of the choline/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states

The ATP-binding cassette transporter ChoVWX is one of several choline import systems operating in Sinorhizobium meliloti. Here fluorescence-based ligand binding assays were used to quantitate substrate binding by the periplasmic ligand-binding protein ChoX. These data confirmed that ChoX recognizes choline and acetylcholine with high and medium affinity, respectively. We also report the crystal structures of ChoX in complex with either choline or acetylcholine. These structural investigations revealed an architecture of the ChoX binding pocket and mode of substrate binding similar to that reported previously for several compatible solute-binding proteins. Additionally the ChoX-acetylcholine complex permitted a detailed structural comparison with the carbamylcholine-binding site of the acetylcholine-binding protein from the mollusc Lymnaea stagnalis. In addition to the two liganded structures of ChoX, we were also able to solve the crystal structure of ChoX in a closed, substrate-free conformation that revealed an architecture of the ligand-binding site that is superimposable to the closed, ligand-bound form of ChoX. This structure is only the second of its kind and raises the important question of how ATP-binding cassette transporters are capable of distinguishing liganded and unliganded-closed states of the binding protein.     

Tetracyclines and Tetracycline Resistance in Agricultural Soils: Microcosm and Field Studies

The influence of the use of antibiotics on the prevalence of resistance genes in the environment is still poorly understood. We studied the diversity of tetracycline and sulfonamide resistance genes as influenced by fertilization with pig manure in soil microcosms and at two field locations. Manure contained a high diversity of resistance genes, regardless of whether it stemmed from a farm operation with low or regular use of antibiotics. In the microcosm soils, the influence of fertilization with manure was clearly shown by an increase in the number of resistance genes in the soil after manuring. Spiking of the tetracycline compounds to the microcosms had only little additional impact on the diversity of resistance genes. Overall, the tetracycline resistance genes tet(T), tet(W), and tet(Z) were ubiquitous in soil and pig slurries, whereas tet(Y), tet(S), tet(C), tet(Q), and tet(H) were introduced to the microcosm soil by manuring. The diversity of tetracycline and sulfonamide [sul(1), sul(2), and sul(3)] resistance genes on a Swiss pasture was very high even before slurry amendment, although manure from intensive farming had not been applied in the previous years. The additional effect of manuring was small, with the tetracycline and sulfonamide resistance diversity staying at high levels for the complete growth season. At an agricultural field site in Germany, the diversity of tetracycline and sulfonamide resistance genes was considerably lower, possibly reflecting regional differences in gene diversity. This study shows that there is a considerable pool of resistance genes in soils. Although it is not possible to conclude whether this diversity is caused by the global spread of resistance genes after 50 years of tetracycline use or is due to the natural background in soil resistance genes, it highlights a role that environmental reservoirs might play in resistance gene capture.