A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, and removing the majority of errors. Digital normalization substantially reduces the size of shotgun data sets and decreases the memory and time requirements for {\em de novo} sequence assembly, all without significantly impacting content of the generated contigs. We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification

A quantitative evaluation of metallic conduction in conjugated polymers

As the periodicity in crystalline materials creates the optimal condition for electronic delocalization, one might expect that in partially crystalline conjugated polymers delocalization is impeded by intergrain transport. However, for the best conducting polymers this presumption fails. Delocalization is obstructed by interchain rather than intergrain charge transfer and we propose a model of weakly coupled disordered chains to describe the physics near the metal-insulator transition. Our quantitative calculations match the outcome of recent broad-band optical experiments and provide a consistent explanation of metallic conduction in polymers.Comment: 4 pages incl. 3 figure

Improved labelling of DTPA- and DOTA-conjugated peptides and antibodies with 111In in HEPES and MES buffer

Contains fulltext : 108269.pdf (publisher's version ) (Open Access)ABSTRACT: BACKGROUND: In single photon emission computed tomography [SPECT], high specific activity of 111In-labelled tracers will allow administration of low amounts of tracer to prevent receptor saturation and/or side effects. To increase the specific activity, we studied the effect of the buffer used during the labelling procedure: NaAc, NH4Ac, HEPES and MES buffer. The effect of the ageing of the 111InCl3 stock and cadmium contamination, the decay product of 111In, was also examined in these buffers. METHODS: Escalating amounts of 111InCl3 were added to 1 mug of the diethylene triamine pentaacetic acid [DTPA]- and 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid [DOTA]-conjugated compounds (exendin-3, octreotide and anti-carbonic anhydrase IX [CAIX] antibody). Five volumes of 2-(N-morpholino)ethanesulfonic acid [MES], 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [HEPES], NH4Ac or NaAc (0.1 M, pH 5.5) were added. After 20 min at 20 degrees C (DTPA-conjugated compounds), at 95 degrees C (DOTA-exendin-3 and DOTA-octreotide) or at 45 degrees C (DOTA-anti-CAIX antibody), the labelling efficiency was determined by instant thin layer chromatography. The effect of the ageing of the 111InCl3 stock on the labelling efficiency of DTPA-exendin-3 as well as the effect of increasing concentrations of Cd2+ (the decay product of 111In) were also examined. RESULTS: Specific activities obtained for DTPA-octreotide and DOTA-anti-CAIX antibody were five times higher in MES and HEPES buffer. Radiolabelling of DTPA-exendin-3, DOTA-exendin-3 and DTPA-anti-CAIX antibody in MES and HEPES buffer resulted in twofold higher specific activities than that in NaAc and NH4Ac. Labelling of DTPA-exendin-3 decreased with 66% and 73% for NaAc and NH4Ac, respectively, at day 11 after the production date of 111InCl3, while for MES and HEPES, the maximal decrease in the specific activity was 10% and 4% at day 11, respectively. The presence of 1 pM Cd2+ in the labelling mixture of DTPA-exendin-3 in NaAc and NH4Ac markedly reduced the labelling efficiency, whereas Cd2+ concentrations up to 0.1 nM did not affect the labelling efficiency in MES and HEPES buffer. CONCLUSIONS: We showed improved labelling of DTPA- and DOTA-conjugated compounds with 111In in HEPES and MES buffer. The enhanced labelling efficiency appears to be due to the reduced competitive chelation of cadmium. The enhanced labelling efficiency will allow more sensitive imaging of the biomarkers with SPECT

68Ga-labelled exendin-3, a new agent for the detection of insulinomas with PET

Contains fulltext : 89596.pdf (publisher's version ) (Closed access)PURPOSE: Insulinomas are neuroendocrine tumours derived from pancreatic beta-cells. The glucagon-like peptide 1 receptor (GLP-1R) is expressed with a high incidence (>90%) and high density in insulinomas. Glucagon-like peptide 1 (GLP-1), the natural ligand of GLP-1R, is rapidly degraded in vivo. A more stable agonist of GLP-1R is exendin-3. We investigated imaging of insulinomas with DOTA-conjugated exendin-3 labelled with (68)Ga. METHODS: Targeting of insulinomas with [Lys(40)(DOTA)]exendin-3 labelled with either (111)In or (68)Ga was investigated in vitro using insulinoma tumour cells (INS-1). [Lys(40)((111)In-DTPA)]Exendin-3 was used as a reference in this study. In vivo targeting was investigated in BALB/c nude mice with subcutaneous INS-1 tumours. PET imaging was performed using a preclinical PET/CT scanner. RESULTS: In vitro exendin-3 specifically bound and was internalized by GLP-1R-positive cells. In BALB/c nude mice with subcutaneous INS-1 tumours a high uptake of [Lys(40)((111)In-DTPA)]exendin-3 in the tumour was observed (33.5 +/- 11.6%ID/g at 4 h after injection). Uptake was specific, as determined by coinjection of an excess of unlabelled [Lys(40)]exendin-3 (1.8 +/- 0.1%ID/g). The pancreas also exhibited high and specific uptake (11.3 +/- 1.0%ID/g). High uptake was also found in the kidneys (144 +/- 24%ID/g) and this uptake was not receptor-mediated. In this murine tumour model optimal targeting of the GLP-1R expressing tumour was obtained at exendin doses < or =0.1 microg. Remarkably, tumour uptake of (68)Ga-labelled [Lys(40)(DOTA)]exendin-3 was lower (8.9 +/- 3.1%ID/g) than tumour uptake of (111)In-labelled [Lys(40)(DTPA)]exendin-3 (25.4 +/- 7.2%ID/g). The subcutaneous tumours were clearly visualized by small-animal PET imaging after injection of 3 MBq of [Lys(40)((68)Ga-DOTA)]exendin-3. CONCLUSION: [Lys(40)((68)Ga-DOTA)]Exendin-3 specifically accumulates in insulinomas, although the uptake is lower than that of [Lys(40)((111)In-DTPA)]exendin-3. Therefore, [Lys(40)((68)Ga-DOTA)]exendin-3 is a promising tracer to visualize insulinomas with PET.01 juli 201

High-bias stability of monatomic chains

For the metals Au, Pt and Ir it is possible to form freely suspended monatomic chains between bulk electrodes. The atomic chains sustain very large current densities, but finally fail at high bias. We investigate the breaking mechanism, that involves current-induced heating of the atomic wires and electromigration forces. We find good agreement of the observations for Au based on models due to Todorov and coworkers. The high-bias breaking of atomic chains for Pt can also be described by the models, although here the parameters have not been obtained independently. In the limit of long chains the breaking voltage decreases inversely proportional to the length.Comment: 7 pages, 5 figure

Observation of Supershell Structure in Alkali Metal Nanowires

Nanowires are formed by indenting and subsequently retracting two pieces of sodium metal. Their cross-section gradually reduces upon retraction and the diameters can be obtained from the conductance. In previous work we have demonstrated that when one constructs a histogram of diameters from large numbers of indentation-retraction cycles, such histograms show a periodic pattern of stable nanowire diameters due to shell structure in the conductance modes. Here, we report the observation of a modulation of this periodic pattern, in agreement with predictions of a supershell structure.Comment: Phys. Rev. Lett., in prin

Evidence for saturation of channel transmission from conductance fluctuations in atomic-size point contacts

The conductance of atomic size contacts has a small, random, voltage dependent component analogous to conductance fluctuations observed in diffusive wires (UCF). A new effect is observed in gold contacts, consisting of a marked suppression of these fluctuations when the conductance of the contact is close to integer multiples of the conductance quantum. Using a model based on the Landauer-Buettiker formalism we interpret this effect as evidence that the conductance tends to be built up from fully transmitted (i.e., saturated) channels plus a single, which is partially transmitted.Comment: An error in Eq.(2) was corrected, where a square root was added to the factor (1-cos(gamma)). This results in a revised estimate for the mean free path of 5 nm, which is now fully consistent with the estimates from the series resistance and the thermopowe

Measurement of the conductance of a hydrogen molecule

Recent years have shown steady progress in research towards molecular electronics [1,2], where molecules have been investigated as switches [3-5], diodes [6], and electronic mixers [7]. In much of the previous work a Scanning Tunnelling Microscope was employed to address an individual molecule. As this arrangement does not provide long-term stability, more recently metal-molecule-metal links have been made using break junction devices [8-10]. However, it has been difficult to establish unambiguously that a single molecule forms the contact [11]. Here, we show that a single H2 molecule can form a stable bridge between Pt electrodes. In contrast to results for other organic molecules, the bridge has a nearly perfect conductance of one quantum unit, carried by a single channel. The H2-bridge provides a simple test system and a fundamental step towards understanding transport properties of single-molecule devices.Comment: 6 pages, 4 figure