223 research outputs found
Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA
The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Isolation of aDNA Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification) Support Protocol 1: Preparation of PTB-based mix Support Protocol 2: Preparation of binding buffer Basic Protocol 2: Preparation of genomic libraries Alternate Protocol 2: Preparation of genomic libraries with uracil removal Basic Protocol 3: Bioinformatic processing and authentication of aDNA
Testing A (Stringy) Model of Quantum Gravity
I discuss a specific model of space-time foam, inspired by the modern
non-perturbative approach to string theory (D-branes). The model views our
world as a three brane, intersecting with D-particles that represent stringy
quantum gravity effects, which can be real or virtual. In this picture, matter
is represented generically by (closed or open) strings on the D3 brane
propagating in such a background. Scattering of the (matter) strings off the
D-particles causes recoil of the latter, which in turn results in a distortion
of the surrounding space-time fluid and the formation of (microscopic, i.e.
Planckian size) horizons around the defects. As a mean-field result, the
dispersion relation of the various particle excitations is modified, leading to
non-trivial optical properties of the space time, for instance a non-trivial
refractive index for the case of photons or other massless probes. Such models
make falsifiable predictions, that may be tested experimentally in the
foreseeable future. I describe a few such tests, ranging from observations of
light from distant gamma-ray-bursters and ultra high energy cosmic rays, to
tests using gravity-wave interferometric devices and terrestrial particle
physics experients involving, for instance, neutral kaons.Comment: 25 pages LATEX, four figures incorporated, uses special proceedings
style. Invited talk at the third international conference on Dark Matter in
Astro and Particle Physics, DARK2000, Heidelberg, Germany, July 10-15 200
Corner contributions to holographic entanglement entropy
The entanglement entropy of three-dimensional conformal field theories
contains a universal contribution coming from corners in the entangling
surface. We study these contributions in a holographic framework and, in
particular, we consider the effects of higher curvature interactions in the
bulk gravity theory. We find that for all of our holographic models, the corner
contribution is only modified by an overall factor but the functional
dependence on the opening angle is not modified by the new gravitational
interactions. We also compare the dependence of the corner term on the new
gravitational couplings to that for a number of other physical quantities, and
we show that the ratio of the corner contribution over the central charge
appearing in the two-point function of the stress tensor is a universal
function for all of the holographic theories studied here. Comparing this
holographic result to the analogous functions for free CFT's, we find fairly
good agreement across the full range of the opening angle. However, there is a
precise match in the limit where the entangling surface becomes smooth, i.e.,
the angle approaches , and we conjecture the corresponding ratio is a
universal constant for all three-dimensional conformal field theories. In this
paper, we expand on the holographic calculations in our previous letter
arXiv:1505.04804, where this conjecture was first introduced.Comment: 62 pages, 6 figures, 1 table; v2: minor modifications to match
published version, typos fixe
Holographic c-theorems in arbitrary dimensions
We re-examine holographic versions of the c-theorem and entanglement entropy
in the context of higher curvature gravity and the AdS/CFT correspondence. We
select the gravity theories by tuning the gravitational couplings to eliminate
non-unitary operators in the boundary theory and demonstrate that all of these
theories obey a holographic c-theorem. In cases where the dual CFT is
even-dimensional, we show that the quantity that flows is the central charge
associated with the A-type trace anomaly. Here, unlike in conventional
holographic constructions with Einstein gravity, we are able to distinguish
this quantity from other central charges or the leading coefficient in the
entropy density of a thermal bath. In general, we are also able to identify
this quantity with the coefficient of a universal contribution to the
entanglement entropy in a particular construction. Our results suggest that
these coefficients appearing in entanglement entropy play the role of central
charges in odd-dimensional CFT's. We conjecture a new c-theorem on the space of
odd-dimensional field theories, which extends Cardy's proposal for even
dimensions. Beyond holography, we were able to show that for any
even-dimensional CFT, the universal coefficient appearing the entanglement
entropy which we calculate is precisely the A-type central charge.Comment: 62 pages, 4 figures, few typo's correcte
Potential Sensitivity of Gamma-Ray Burster Observations to Wave Dispersion in Vacuo
The recent confirmation that at least some gamma-ray bursters (GRBs) are
indeed at cosmological distances raises the possibility that observations of
these could provide interesting constraints on the fundamental laws of physics.
Here we demonstrate that the fine-scale time structure and hard spectra of GRB
emissions are very sensitive to the possible dispersion of electromagnetic
waves in vacuo with velocity differences \delta v \sim E/E_{\QG}, as
suggested in some approaches to quantum gravity. A simple estimate shows that
GRB measurements might be sensitive to a dispersion scale comparable
to the Planck energy scale GeV, sufficient to test some of
these theories, and we outline aspects of an observational programme that could
address this goal.Comment: LaTex. 9 pages. Version accepted for publication in Nature. (A few
changes to the reference list. Additional comments on the analyticity
properties of the dispersion law.
Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival
The large-conductance Ca2+-activated K+ (BK) channel and its β-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and to reveal putative BK functions, we undertook a systems analysis of BK and BK-Associated Proteins (BKAPS) in the chicken cochlea and compared these results to other species. We identified 110 putative partners from cytoplasmic and membrane/cytoskeletal fractions, using a combination of coimmunoprecipitation, 2-D gel, and LC-MS/MS. Partners included 14-3-3γ, valosin-containing protein (VCP), stathmin (STMN), cortactin (CTTN), and prohibitin (PHB), of which 16 partners were verified by reciprocal coimmunoprecipitation. Bioinformatics revealed binary partners, the resultant interactome, subcellular localization, and cellular processes. The interactome contained 193 proteins involved in 190 binary interactions in subcellular compartments such as the ER, mitochondria, and nucleus. Comparisons with mice showed shared hub proteins that included N-methyl-D-aspartate receptor (NMDAR) and ATP-synthase. Ortholog analyses across six species revealed conserved interactions involving apoptosis, Ca2+ binding, and trafficking, in chicks, mice, and humans. Functional studies using recombinant BK and RNAi in a heterologous expression system revealed that proteins important to cell death/survival, such as annexinA5, γ-actin, lamin, superoxide dismutase, and VCP, caused a decrease in BK expression. This revelation led to an examination of specific kinases and their effectors relevant to cell viability. Sequence analyses of the BK C-terminus across 10 species showed putative binding sites for 14-3-3, RAC-α serine/threonine-protein kinase 1 (Akt), glycogen synthase kinase-3β (GSK3β) and phosphoinositide-dependent kinase-1 (PDK1). Knockdown of 14-3-3 and Akt caused an increase in BK expression, whereas silencing of GSK3β and PDK1 had the opposite effect. This comparative systems approach suggests conservation in BK function across different species in addition to novel functions that may include the initiation of signals relevant to cell death/survival
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