A Comparison Between Stochastic and Deterministic Models of a Biological Oscillator

We look at the behavior of biological oscillators, specifically analyzing a genetic circuit that has oscillatory behavior. Implementing the system in deterministic and stochastic models, we compare the two models using various tests and analyze the effect of stochastic noise on these oscillations. We first investigate the effect of volume and find that at small system volumes, stochastic events cause the system to exhibit more sporadic oscillations and a longer period of oscillation. Next, we develop classification systems for discerning the boundary in the parameter space where the model begins to show oscillations. This is more challenging in the stochastic model, due to persistent fluctuations. We compare different methods of analysis of our deterministic and stochastic models and visualize the conditions which lead to oscillation in each model. We find that the parameter range of oscillation is larger in the stochastic model than in the deterministic model. Finally, we find an increased rate of mRNA production can create greater noise in a system and amplify the difference between a stochastic and deterministic system

HNRNPK maintains epidermal progenitor function through transcription of proliferation genes and degrading differentiation promoting mRNAs.

Maintenance of high-turnover tissues such as the epidermis requires a balance between stem cell proliferation and differentiation. The molecular mechanisms governing this process are an area of investigation. Here we show that HNRNPK, a multifunctional protein, is necessary to prevent premature differentiation and sustains the proliferative capacity of epidermal stem and progenitor cells. To prevent premature differentiation of progenitor cells, HNRNPK is necessary for DDX6 to bind a subset of mRNAs that code for transcription factors that promote differentiation. Upon binding, these mRNAs such as GRHL3, KLF4, and ZNF750 are degraded through the mRNA degradation pathway, which prevents premature differentiation. To sustain the proliferative capacity of the epidermis, HNRNPK is necessary for RNA Polymerase II binding to proliferation/self-renewal genes such as MYC, CYR61, FGFBP1, EGFR, and cyclins to promote their expression. Our study establishes a prominent role for HNRNPK in maintaining adult tissue self-renewal through both transcriptional and post-transcriptional mechanisms

Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used heuristic methods that analyze summaries of the multilocus sequence data to detect gene flow, which may suffer from low power. Here we use the full likelihood method implemented in the Bayesian program BPP to reanalyze these data. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 65%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. Our analyses highlight the importance of using adequate statistical methods to reach reliable biological conclusions concerning cross-species gene flow

Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HyDe to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program bpp to reanalyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HyDe, and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data

Heavy-quark contribution to the proton's magnetic moment

We study the contribution to the proton's magnetic moment from a heavy quark sea in quantum chromodynamics. The heavy quark is integrated out perturbatively to obtain an effective dimension-6 magnetic moment operator composed of three gluon fields. The leading contribution to the matrix element in the proton comes from a quadratically divergent term associated with a light-quark tensor operator. With an approximate knowledge of the proton's tensor charge, we conclude that a heavy sea-quark contribution to the proton's magnetic moment is positive in the asymptotic limit. We comment on the implication of this result for the physical strange quark.Comment: 4 pages, 2 figure

Three-Quark Light-Cone Amplitudes of The Proton And Quark-Orbital-Motion Dependent Observables

We study the three-quark light-cone amplitudes of the proton including quarks' transverse momenta. We classify these amplitudes using a newly-developed method in which light-cone wave functions are constructed from a class of light-cone matrix elements. We derive the constraints on the amplitudes from parity and time-reversal symmetries. We use the amplitudes to calculate the physical observables which vanish when the quark orbital angular momentum is absent. These include transverse-momentum dependent parton distributions $\Delta q_T(x, k_\perp)$, $q_T(x, k_\perp)$, $\delta q(x, k_\perp)$, and $\delta q_L(x,k_\perp)$, twist-three parton distributions $g_T(x)$ and $h_L(x)$, helicity-flip generalized parton distributions $E(x, \xi=0, Q^2)$ and its associates, and the Pauli form factor $F_2(Q^2)$.Comment: 20 pages, no figur

Imaging calcium microdomains within entire astrocyte territories and endfeet with GCaMPs expressed using adeno-associated viruses.

Intracellular Ca(2+) transients are considered a primary signal by which astrocytes interact with neurons and blood vessels. With existing commonly used methods, Ca(2+) has been studied only within astrocyte somata and thick branches, leaving the distal fine branchlets and endfeet that are most proximate to neuronal synapses and blood vessels largely unexplored. Here, using cytosolic and membrane-tethered forms of genetically encoded Ca(2+) indicators (GECIs; cyto-GCaMP3 and Lck-GCaMP3), we report well-characterized approaches that overcome these limitations. We used in vivo microinjections of adeno-associated viruses to express GECIs in astrocytes and studied Ca(2+) signals in acute hippocampal slices in vitro from adult mice (aged ∼P80) two weeks after infection. Our data reveal a sparkling panorama of unexpectedly numerous, frequent, equivalently scaled, and highly localized Ca(2+) microdomains within entire astrocyte territories in situ within acute hippocampal slices, consistent with the distribution of perisynaptic branchlets described using electron microscopy. Signals from endfeet were revealed with particular clarity. The tools and experimental approaches we describe in detail allow for the systematic study of Ca(2+) signals within entire astrocytes, including within fine perisynaptic branchlets and vessel-associated endfeet, permitting rigorous evaluation of how astrocytes contribute to brain function

An Analysis of the Next-to-Leading Order Corrections to the g_T(=g_1+g_2) Scaling Function

We present a general method for obtaining the quantum chromodynamical radiative corrections to the higher-twist (power-suppressed) contributions to inclusive deep-inelastic scattering in terms of light-cone correlation functions of the fundamental fields of quantum chromodynamics. Using this procedure, we calculate the previously unknown ${\cal O}(\alpha_s)$ corrections to the twist-three part of the spin scaling function $g_T(x_B,Q^2) (=g_1(x_B,Q^2)+g_2(x_B,Q^2))$ and the corresponding forward Compton amplitude $S_T(\nu,Q^2)$. Expanding our result about the unphysical point $x_B=\infty$, we arrive at an operator product expansion of the nonlocal product of two electromagnetic current operators involving twist-two and -three operators valid to ${\cal O}(\alpha_s)$ for forward matrix elements. We find that the Wandzura-Wilczek relation between $g_1(x_B,Q^2)$ and the twist-two part of $g_T(x_B,Q^2)$ is respected in both the singlet and non-singlet sectors at this order, and argue its validity to all orders. The large-$N_c$ limit does not appreciably simplify the twist-three Wilson coefficients.Comment: 41 pages, 9 figures, corrected minor erro

Exclusive production of lepton, quark and meson pairs in peripheral ultrarelativistic heavy ion collisions

We discuss exclusive production of lepton-antilepton, quark-antiquark, $\pi \pi$ and $\rho^0 \rho^0$ pairs in ultraperipheral, ultrarelativistic heavy-ion collisions. The cross sections for exclusive production of pairs of particles is calculated in Equivalent Photon Approximation (EPA). Realistic (Fourier transform of charge density) charge form factors of nuclei are used and the corresponding results are compared with the cross sections calculated with monopole form factor used in the literature. Absorption effects are discussed and quantified. The cross sections obtained with realistic form factors are significantly smaller than those obtained with the monopole form factors.Comment: 9 pages, 13 figures an invited talk at the international conference "Hadron Structure 2011", Slovakia, June 201