A widely tunable few electron droplet

Quasi-static transport measurements are employed to characterize a few electron quantum dot electrostatically defined in a GaAs/AlGaAs heterostructure. The gate geometry allows observations on one and the same electron droplet within a wide range of coupling strengths to the leads. The weak coupling regime is described by discrete quantum states. At strong interaction with the leads Kondo phenomena are observed as a function of a magnetic field. By varying gate voltages the electron droplet can, in addition, be distorted into a double quantum dot with a strong interdot tunnel coupling while keeping track of the number of trapped electrons.Comment: 11 pages, 5 figure

Negative frequency tuning of a carbon nanotube nano-electromechanical resonator

A suspended, doubly clamped single wall carbon nanotube is characterized as driven nano-electromechanical resonator at cryogenic temperatures. Electronically, the carbon nanotube displays small bandgap behaviour with Coulomb blockade oscillations in electron conduction and transparent contacts in hole conduction. We observe the driven mechanical resonance in dc-transport, including multiple higher harmonic responses. The data shows a distinct negative frequency tuning at finite applied gate voltage, enabling us to electrostatically decrease the resonance frequency to 75% of its maximum value. This is consistently explained via electrostatic softening of the mechanical mode.Comment: 4 pages, 4 figures; submitted for the IWEPNM 2013 conference proceeding

Impact of boundary layer flow velocity on oxygen utilisation in coastal sediments

Small pressure gradients generated by boundary flow-topography interactions cause advective pore water flows in permeable sediments. Advective pore water exchange enhances the flux of solutes between the sediment and the overlying water, thus generating conditions for an increased utilisation of oxygen. We compared a less permeable (k = 5 x 10(-12) m(2)) with a permeable sediment (k = 5 x 10(-11) m(2)) typical for coastal and shelf sediments. Total oxygen utilisation (TOU) in incubated sediment cores was measured in 10 laboratory experiments using recirculating flow tanks (33 runs). TOU was a function of now velocity in permeable sediment where advective pore water now occurred. TOU increased with the increasing volume of sediment flushed with oxygenated water. We found that TOU increased by 91 +/- 23% in coarse sand when now increased from 3 to 14 cm s(-1) (38 mounds m(-2) height 10 to 30 mm, now measured 8 cm above the sediment). Addition of fresh algal material caused a stronger stimulation of TOU in the coarse sand than in the fine sand (4 additional flume runs). After the addition, intensive oxygen consumption reduced the oxygen penetration depth in the advectively flushed zone of the coarse sediment. However, counteracting this process, advective flow maintained an oxic sediment volume still larger than that in the less permeable sediment. Flow-enhanced oxygen utilisation is potentially effective in permeable beds of coastal and shelf regions, in contrast to the situation in cohesive sediments limited by predominantly diffusive oxygen supply

The oxygen-independent metabolism of cyclic monoterpenes in Castellaniella defragrans 65Phen

BACKGROUND: The facultatively anaerobic betaproteobacterium Castellaniella defragrans 65Phen utilizes acyclic, monocyclic and bicyclic monoterpenes as sole carbon source under oxic as well as anoxic conditions. A biotransformation pathway of the acyclic β-myrcene required linalool dehydratase-isomerase as initial enzyme acting on the hydrocarbon. An in-frame deletion mutant did not use myrcene, but was able to grow on monocyclic monoterpenes. The genome sequence and a comparative proteome analysis together with a random transposon mutagenesis were conducted to identify genes involved in the monocyclic monoterpene metabolism. Metabolites accumulating in cultures of transposon and in-frame deletion mutants disclosed the degradation pathway. RESULTS: Castellaniella defragrans 65Phen oxidizes the monocyclic monoterpene limonene at the primary methyl group forming perillyl alcohol. The genome of 3.95 Mb contained a 70 kb genome island coding for over 50 proteins involved in the monoterpene metabolism. This island showed higher homology to genes of another monoterpene-mineralizing betaproteobacterium, Thauera terpenica 58Eu(T), than to genomes of the family Alcaligenaceae, which harbors the genus Castellaniella. A collection of 72 transposon mutants unable to grow on limonene contained 17 inactivated genes, with 46 mutants located in the two genes ctmAB (cyclic terpene metabolism). CtmA and ctmB were annotated as FAD-dependent oxidoreductases and clustered together with ctmE, a 2Fe-2S ferredoxin gene, and ctmF, coding for a NADH:ferredoxin oxidoreductase. Transposon mutants of ctmA, B or E did not grow aerobically or anaerobically on limonene, but on perillyl alcohol. The next steps in the pathway are catalyzed by the geraniol dehydrogenase GeoA and the geranial dehydrogenase GeoB, yielding perillic acid. Two transposon mutants had inactivated genes of the monoterpene ring cleavage (mrc) pathway. 2-Methylcitrate synthase and 2-methylcitrate dehydratase were also essential for the monoterpene metabolism but not for growth on acetate. CONCLUSIONS: The genome of Castellaniella defragrans 65Phen is related to other genomes of Alcaligenaceae, but contains a genomic island with genes of the monoterpene metabolism. Castellaniella defragrans 65Phen degrades limonene via a limonene dehydrogenase and the oxidation of perillyl alcohol. The initial oxidation at the primary methyl group is independent of molecular oxygen

Targeted deep sequencing of flowering regulators in Brassica napus reveals extensive copy number variation

Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species. Target enrichment was performed using the Agilent SureSelect technology, followed by Illumina sequencing. A bait (probe) pool was developed based on results of a preliminary experiment with representatives from different B. napus morphotypes. A very high mean target coverage of ~670x allowed reliable calling of CNV, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) polymorphisms. No accession exhibited no CNV, and at least one homolog of every gene we investigated showed CNV in some accessions. Some CNV appear more often in specific morphotypes, indicating a role in diversification

Post-polyploidisation morphotype diversification associates with gene copy number variation

Genetic models for polyploid crop adaptation provide important information relevant for future breeding prospects. A well-suited model is Brassica napus, a recent allopolyploid closely related to Arabidopsis thaliana. Flowering time is a major adaptation trait determining life cycle synchronization with the environment. Here we unravel natural genetic variation in B. napus flowering time regulators and investigate associations with evolutionary diversification into different life cycle morphotypes. Deep sequencing of 35 flowering regulators was performed in 280 diverse B. napus genotypes. High sequencing depth enabled high-quality calling of single-nucleotide polymorphisms (SNPs), insertion-deletions (InDels) and copy number variants (CNVs). By combining these data with genotyping data from the Brassica 60 K Illumina® Infinium SNP array, we performed a genome-wide marker distribution analysis across the 4 ecogeographical morphotypes. Twelve haplotypes, including Bna.FLC.A10, Bna.VIN3.A02 and the Bna.FT promoter on C02_random, were diagnostic for the diversification of winter and spring types. The subspecies split between oilseed/kale (B. napus ssp. napus) and swedes/rutabagas (B. napus ssp. napobrassica) was defined by 13 haplotypes, including genomic rearrangements encompassing copies of Bna.FLC, Bna.PHYA and Bna.GA3ox1. De novo variation in copies of important flowering-time genes in B. napus arose during allopolyploidisation, enabling sub-functionalisation that allowed different morphotypes to appropriately fine-tune their lifecycle

Functional brain networks involved in gaze and emotional processing

Eye-gaze direction plays a fundamental role in the perception of facial features and particularly the processing of emotional facial expressions. Yet, the neural underpinnings of the integration of eye gaze and emotional facial cues are not well understood. The primary aim of this study was to delineate the functional networks that subserve the recognition of emotional expressions as a function of eye gaze. Participants were asked to identify happy, angry, or neutral faces, displayed with direct or averted gaze, while their neural responses were measured with fMRI. The results showed that recognition of happy expressions, irrespective of eye-gaze direction, engaged the critical nodes of the default mode network. Recognition of angry faces, on the other hand, was gaze-dependent, engaging the critical nodes of the salience network when presented with direct gaze, but fronto-parietal areas when presented with averted gaze. Functional connectivity analysis further showed gaze-dependent engagement of a large-scale network connected to bilateral amygdala during the recognition of angry expressions. This study provides important insights into the functional connectivity between the amygdala and other critical social-cognitive brain nodes, which are essential in processing of ambiguous, potentially threatening social signals. These findings have implications for psychiatric disorders, such as post-traumatic stress disorder, which are characterized by aberrant limbic connectivity

Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence

The identification of body fluids is an essential tool for clarifying the course of events at a criminal site. The analytical problem is the fact that the biological material has been very often exposed to detrimental exogenous influences. Thereby, the molecular substrates used for the identification of the traces may become degraded. So far, most protocols utilize cell specific proteins or RNAs. Instead of measuring these more sensitive compounds this paper describes the application of the differential DNA-methylation. As a result of two genome wide screenings with the Illumina HumanMethylation BeadChips 27 and 450k we identified 150 candidate loci revealing differential methylation with regard to the body fluids venous blood, menstrual blood, vaginal fluid, saliva and sperm. Among them we selected 9 loci as the most promising markers. For the final determination of the methylation degree we applied the SNuPE-method. Because the degree of methylation might be modified by various endogenous and exogenous factors, we tested each marker with approximately 100 samples of each target fluid in a validation study. The stability of the detection procedure is proved in various simulated forensic surroundings according to standardized conditions. We studied the potential influence of 12 relatively common tumors on the methylation of the 9 markers. For this purpose the target fluids of 34 patients have been analysed. Only the cervix carcinoma might have an remarkable effect because impairing the signal of both vaginal markers. Using the Illumina MiSeq device we tested the potential influence of cis acting sequence variants on the methylation degree of the 9 markers in the specific body fluid DNA of 50 individuals. For 4 marker loci we observed such an influence either by sole SNPs or haplotypes. The identification of each target fluid is possible in arbitrary mixtures with the remaining four body fluids. The sensitivity of the individual body fluid tests is in the same range as for the forensic STR-analysis. It is the first forensic body fluid protocol which considers the exogenic and endogenic parameters potentially interfering with the true results