Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.Comment: Includes supporting informatio

Detection in Soil of a Deletion in an Engineered DNA Sequence by Using DNA Probes

Two Pseudomonas strains were engineered to contain the nptII gene and plasmid vector sequences in their chromosomes. After incubation of these strains in nonsterile soil, total bacterial DNA was isolated and analyzed by Southern blot hybridization with the nptII gene and the plasmid vector as probes. In addition to the expected bands of hybridization, a new band corresponding to the loss of vector sequences from the chromosome while retaining the nptII gene was observed for one of the strains. The more stressful conditions encountered in soil appeared to increase the frequency of loss of the vector sequences from this strain

Detailed Spatially Distributed Geothermal Heat-flow Data for Modeling of Basal Temperatures and Meltwater Production Beneath the Fennoscandian Ice Sheet

Accurate modeling of ice sheets requires proper information on boundary conditions, including the geothermal heat flow (or heat-flow density (HFD)). Traditionally, one uniform HFD value is adopted for the entire modeled domain. We have calculated a distributed, high-resolution HFD dataset for an approximate core area (Sweden and Finland) of the Scandinavian ice sheet, and imbedded this within lower-resolution data published for surrounding regions. Within the Last Glacial Maximum ice margin, HFD varies with a factor of as much as 2.8 (HFD values ranging between 30 and 83mWm–2), with an average of 49mWm–2. This average value is 17% higher than 42mWm–2, a common uniform value used in ice-sheet modeling studies of Fennoscandia. Using this new distributed dataset on HFD, instead of a traditional uniform value of 42mWm–2, yields a 1.4 times larger total basal meltwater production for the last glacial cycle. Furthermore, using the new dataset in high-resolution modeling results in increased spatial thermal gradients at the bed. This enhances and introduces new local and regional effects on basal ice temperatures and melt rates. We observed significant strengthening of local ‘ice streaming’, which in one case correlates to an ice-flow event previously interpreted from geomorphology. Regional to local variations in geothermal heat flow need to be considered for proper identification and treatment of thermal and hydraulic bed conditions, most likely also when studying Laurentide, Greenland and Antarctic ice sheets

Exploiting symmetries in SDP-relaxations for polynomial optimization

In this paper we study various approaches for exploiting symmetries in polynomial optimization problems within the framework of semi definite programming relaxations. Our special focus is on constrained problems especially when the symmetric group is acting on the variables. In particular, we investigate the concept of block decomposition within the framework of constrained polynomial optimization problems, show how the degree principle for the symmetric group can be computationally exploited and also propose some methods to efficiently compute in the geometric quotient.Comment: (v3) Minor revision. To appear in Math. of Operations Researc

A cubic-time algorithm for computing the trinet distance between level-1 networks

In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have efficiently computable metrics with which to systematically compare such networks. Through developing an optimal algorithm to enumerate all trinets displayed by a level-1 network (a type of network that is slightly more general than an evolutionary tree), here we propose a cubic-time algorithm to compute the trinet distance between two level-1 networks. Employing simulations, we also present a comparison between the trinet metric and the so-called Robinson-Foulds phylogenetic network metric restricted to level-1 networks. The algorithms described in this paper have been implemented in JAVA and are freely available at (https://www.uea.ac.uk/computing/TriLoNet

IPM measurements in the Tevatron

Two Ionization Profile Monitors (IPMs) were installed in the Tevatron in 2006. The detectors are capable of resolving single bunches turn-by-turn. This paper presents recent improvements to the system hardware and its use for beam monitoring. In particular, the correction of beam size oscillations observed at injection is discussed

Genome-wide profiling of Populus small RNAs

<p>Abstract</p> <p>Background</p> <p>Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced <it>Populus trichocarpa </it>using a concatenation strategy in combination with 454 sequencing.</p> <p>Results</p> <p>The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of <it>NBS-LRR </it>genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and <it>NBS-LRR </it>disease resistance genes, classes of genes that have been significantly expanded in <it>Populus</it>. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).</p> <p>Conclusions</p> <p>The short RNA population of <it>P. trichocarpa </it>is at least as complex as that of <it>Arabidopsis thaliana</it>. We provide a first genome-wide view of short RNA production for <it>P. trichocarpa </it>and identify new, non-conserved miRNAs.</p