1,789 research outputs found
Toolbox approaches using molecular markers and 16S rRNA gene amplicon data sets for identification of fecal pollution in surface water
In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small
Real Time Global Tests of the ALICE High Level Trigger Data Transport Framework
The High Level Trigger (HLT) system of the ALICE experiment is an online
event filter and trigger system designed for input bandwidths of up to 25 GB/s
at event rates of up to 1 kHz. The system is designed as a scalable PC cluster,
implementing several hundred nodes. The transport of data in the system is
handled by an object-oriented data flow framework operating on the basis of the
publisher-subscriber principle, being designed fully pipelined with lowest
processing overhead and communication latency in the cluster. In this paper, we
report the latest measurements where this framework has been operated on five
different sites over a global north-south link extending more than 10,000 km,
processing a ``real-time'' data flow.Comment: 8 pages 4 figure
A mutate-and-map protocol for inferring base pairs in structured RNA
Chemical mapping is a widespread technique for structural analysis of nucleic
acids in which a molecule's reactivity to different probes is quantified at
single-nucleotide resolution and used to constrain structural modeling. This
experimental framework has been extensively revisited in the past decade with
new strategies for high-throughput read-outs, chemical modification, and rapid
data analysis. Recently, we have coupled the technique to high-throughput
mutagenesis. Point mutations of a base-paired nucleotide can lead to exposure
of not only that nucleotide but also its interaction partner. Carrying out the
mutation and mapping for the entire system gives an experimental approximation
of the molecules contact map. Here, we give our in-house protocol for this
mutate-and-map strategy, based on 96-well capillary electrophoresis, and we
provide practical tips on interpreting the data to infer nucleic acid
structure.Comment: 22 pages, 5 figure
Understanding the errors of SHAPE-directed RNA structure modeling
Single-nucleotide-resolution chemical mapping for structured RNA is being
rapidly advanced by new chemistries, faster readouts, and coupling to
computational algorithms. Recent tests have shown that selective 2'-hydroxyl
acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in
modeling the helices of RNA secondary structure. Here, we benchmark the method
using six molecules for which crystallographic data are available: tRNA(phe)
and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I
ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic
di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs
gave an overall false negative rate (FNR) of 17% and a false discovery rate
(FDR) of 21%, with at least one helix prediction error in five of the six
cases. Extensive variations of data processing, normalization, and modeling
parameters did not significantly mitigate modeling errors. Only one varation,
filtering out data collected with deoxyinosine triphosphate during primer
extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual
structure modeling errors are explained by the insufficient information content
of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping
analysis. Beyond these benchmark cases, bootstrapping suggests a low level of
confidence (<50%) in the majority of helices in a previously proposed
SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA
modeling is not always unambiguous, and helix-by-helix confidence estimates, as
described herein, may be critical for interpreting results from this powerful
methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011
Demonstration of Universal Parametric Entangling Gates on a Multi-Qubit Lattice
We show that parametric coupling techniques can be used to generate selective
entangling interactions for multi-qubit processors. By inducing coherent
population exchange between adjacent qubits under frequency modulation, we
implement a universal gateset for a linear array of four superconducting
qubits. An average process fidelity of is estimated for
three two-qubit gates via quantum process tomography. We establish the
suitability of these techniques for computation by preparing a four-qubit
maximally entangled state and comparing the estimated state fidelity against
the expected performance of the individual entangling gates. In addition, we
prepare an eight-qubit register in all possible bitstring permutations and
monitor the fidelity of a two-qubit gate across one pair of these qubits.
Across all such permutations, an average fidelity of
is observed. These results thus offer a path to a scalable architecture with
high selectivity and low crosstalk
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