358 research outputs found
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
© 2016 Rinke et al. High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100-1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics
Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia
The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit
Worldvolume Superalgebra Of BLG Theory With Nambu-Poisson Structure
Recently it was proposed that the Bagger-Lambert-Gustavsson theory with
Nambu-Poisson structure describes an M5-brane in a three-form flux background.
In this paper we investigate the superalgebra associated with this theory. We
derive the central charges corresponding to M5-brane solitons in 3-form
backgrounds. We also show that double dimensional reduction of the superalgebra
gives rise to the Poisson bracket terms of a non-commutative D4-brane
superalgebra. We provide interpretations of the D4-brane charges in terms of
spacetime intersections.Comment: 23 pages; references added, section 4 clarification
Boundary Conditions for Interacting Membranes
We investigate supersymmetric boundary conditions in both the Bagger-Lambert
and the ABJM theories of interacting membranes. We find boundary conditions
associated to the fivebrane, the ninebrane and the M-theory wave. For the ABJM
theory we are able to understand the enhancement of supersymmetry to produce
the (4,4) supersymmetry of the self-dual string. We also include supersymmetric
boundary conditions on the gauge fields that cancel the classical gauge anomaly
of the Chern-Simons terms.Comment: 36 pages, latex, v2 minor typos correcte
R-parity Conservation via the Stueckelberg Mechanism: LHC and Dark Matter Signals
We investigate the connection between the conservation of R-parity in
supersymmetry and the Stueckelberg mechanism for the mass generation of the B-L
vector gauge boson. It is shown that with universal boundary conditions for
soft terms of sfermions in each family at the high scale and with the
Stueckelberg mechanism for generating mass for the B-L gauge boson present in
the theory, electric charge conservation guarantees the conservation of
R-parity in the minimal B-L extended supersymmetric standard model. We also
discuss non-minimal extensions. This includes extensions where the gauge
symmetries arise with an additional U(1)_{B-L} x U(1)_X, where U(1)_X is a
hidden sector gauge group. In this case the presence of the additional U(1)_X
allows for a Z' gauge boson mass with B-L interactions to lie in the sub-TeV
region overcoming the multi-TeV LEP constraints. The possible tests of the
models at colliders and in dark matter experiments are analyzed including
signals of a low mass Z' resonance and the production of spin zero bosons and
their decays into two photons. In this model two types of dark matter
candidates emerge which are Majorana and Dirac particles. Predictions are made
for a possible simultaneous observation of new physics events in dark matter
experiments and at the LHC.Comment: 38 pages, 7 fig
Evaluation of the current knowledge limitations in breast cancer research: a gap analysis
BACKGROUND
A gap analysis was conducted to determine which areas of breast cancer research, if targeted by researchers and funding bodies, could produce the greatest impact on patients.
METHODS
Fifty-six Breast Cancer Campaign grant holders and prominent UK breast cancer researchers participated in a gap analysis of current breast cancer research. Before, during and following the meeting, groups in seven key research areas participated in cycles of presentation, literature review and discussion. Summary papers were prepared by each group and collated into this position paper highlighting the research gaps, with recommendations for action.
RESULTS
Gaps were identified in all seven themes. General barriers to progress were lack of financial and practical resources, and poor collaboration between disciplines. Critical gaps in each theme included: (1) genetics (knowledge of genetic changes, their effects and interactions); (2) initiation of breast cancer (how developmental signalling pathways cause ductal elongation and branching at the cellular level and influence stem cell dynamics, and how their disruption initiates tumour formation); (3) progression of breast cancer (deciphering the intracellular and extracellular regulators of early progression, tumour growth, angiogenesis and metastasis); (4) therapies and targets (understanding who develops advanced disease); (5) disease markers (incorporating intelligent trial design into all studies to ensure new treatments are tested in patient groups stratified using biomarkers); (6) prevention (strategies to prevent oestrogen-receptor negative tumours and the long-term effects of chemoprevention for oestrogen-receptor positive tumours); (7) psychosocial aspects of cancer (the use of appropriate psychosocial interventions, and the personal impact of all stages of the disease among patients from a range of ethnic and demographic backgrounds).
CONCLUSION
Through recommendations to address these gaps with future research, the long-term benefits to patients will include: better estimation of risk in families with breast cancer and strategies to reduce risk; better prediction of drug response and patient prognosis; improved tailoring of treatments to patient subgroups and development of new therapeutic approaches; earlier initiation of treatment; more effective use of resources for screening populations; and an enhanced experience for people with or at risk of breast cancer and their families. The challenge to funding bodies and researchers in all disciplines is to focus on these gaps and to drive advances in knowledge into improvements in patient care
The holographic principle
There is strong evidence that the area of any surface limits the information
content of adjacent spacetime regions, at 10^(69) bits per square meter. We
review the developments that have led to the recognition of this entropy bound,
placing special emphasis on the quantum properties of black holes. The
construction of light-sheets, which associate relevant spacetime regions to any
given surface, is discussed in detail. We explain how the bound is tested and
demonstrate its validity in a wide range of examples.
A universal relation between geometry and information is thus uncovered. It
has yet to be explained. The holographic principle asserts that its origin must
lie in the number of fundamental degrees of freedom involved in a unified
description of spacetime and matter. It must be manifest in an underlying
quantum theory of gravity. We survey some successes and challenges in
implementing the holographic principle.Comment: 52 pages, 10 figures, invited review for Rev. Mod. Phys; v2:
reference adde
Modalidades de pago de los servicios del Reino de Valencia a la Corona (1585-1604) Pagos directos, pagos delegados
Se analiza las relaciones entre la Hacienda Real y la Hacienda de la DiputaciĂłn del Reino deValencia en la satisfacciĂłn de los pagos de los gastos diversos contraĂdos por parte de la Corona. Una parte importante consistiĂł en operaciones de endoso, por las cuáles el rey trasladaba el pago de una deuda suya a su deudora, la Generalidad del Reino de Valencia, con criterios de eficiencia, para el pronto pago de los acreedores.The relations between the Royal Treasury and the Treasury the Generalitat of the Kingdom of Valencia are analyzed in the satisfaction of the payments of the various expenses incurred by the Cromw. An important part consisted of endorsement operations, for which the king transferred the payment of a debt to his debtor, the Generalitat of the Kingdom of Valencia, with efficiency criteria, for the prompt payment of creditors
The stellar halo of the Galaxy
Stellar halos may hold some of the best preserved fossils of the formation
history of galaxies. They are a natural product of the merging processes that
probably take place during the assembly of a galaxy, and hence may well be the
most ubiquitous component of galaxies, independently of their Hubble type. This
review focuses on our current understanding of the spatial structure, the
kinematics and chemistry of halo stars in the Milky Way. In recent years, we
have experienced a change in paradigm thanks to the discovery of large amounts
of substructure, especially in the outer halo. I discuss the implications of
the currently available observational constraints and fold them into several
possible formation scenarios. Unraveling the formation of the Galactic halo
will be possible in the near future through a combination of large wide field
photometric and spectroscopic surveys, and especially in the era of Gaia.Comment: 46 pages, 16 figures. References updated and some minor changes.
Full-resolution version available at
http://www.astro.rug.nl/~ahelmi/stellar-halo-review.pd
Assessing Biofuel Crop Invasiveness: A Case Study
BACKGROUND: There is widespread interest in biofuel crops as a solution to the world's energy needs, particularly in light of concerns over greenhouse-gas emissions. Despite reservations about their adverse environmental impacts, no attempt has been made to quantify actual, relative or potential invasiveness of terrestrial biofuel crops at an appropriate regional or international scale, and their planting continues to be largely unregulated. METHODOLOGY/PRINCIPAL FINDINGS: Using a widely accepted weed risk assessment system, we analyzed a comprehensive list of regionally suitable biofuel crops to show that seventy percent have a high risk of becoming invasive versus one-quarter of non-biofuel plant species and are two to four times more likely to establish wild populations locally or be invasive in Hawaii or in other locations with a similar climate. CONCLUSIONS/SIGNIFICANCE: Because of climatic and ecological similarities, predictions of biofuel crop invasiveness in Hawaii are applicable to other vulnerable island and subtropical ecosystems worldwide. We demonstrate the utility of an accessible and scientifically proven risk assessment protocol that allows users to predict if introduced species will become invasive in their region of interest. Other evidence supports the contention that propagule pressure created by extensive plantings will exacerbate invasions, a scenario expected with large-scale biofuel crop cultivation. Proactive measures, such as risk assessments, should be employed to predict invasion risks, which could then be mitigated via implementation of appropriate planting policies and adoption of the "polluter-pays" principle
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