First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA

<p>Abstract</p> <p>Background</p> <p>Proteins search along the DNA for targets, such as transcription initiation sequences, according to one-dimensional diffusion, which is interrupted by micro- and macro-hopping events and intersegmental transfers that occur under close packing conditions.</p> <p>Results</p> <p>A one-dimensional diffusion-reaction model in the form of difference-differential equations is proposed to analyze the nonequilibrium protein sliding kinetics along a segment of bacterial DNA. A renormalization approach is used to derive an expression for the mean first-passage time to arrive at sites downstream of the origin from the occupation probabilities given by the individual transport equations. Monte Carlo simulations are employed to assess the validity of the proposed approach, and all results are interpreted within the context of bacterial transcription.</p> <p>Conclusions</p> <p>Mean first-passage times decrease with increasing reaction rates, indicating that, on average, surviving proteins more rapidly locate downstream targets than their reaction-free counterparts, but at the price of increasing rarity. Two qualitatively different screening regimes are identified according to whether the search process operates under “small” or “large” values for the dissociation rate of the protein-DNA complex. Lower bounds are placed on the overall search time for varying reactive conditions. Good agreement with experimental estimates requires the reaction rate reside near the transition between both screening regimes, suggesting that biology balances a need for rapid searches against maximum exploration during each round of the sliding phase.</p

Similarity Attraction and Old School Values: African American Led Nonprofits and African American Youth

This article examines the role of similarity-attraction between African American-led nonprofits and the predominately African American youth they serve. Informed by interview data with executive directors, board members, volunteers, and students, this research captures how similarity-attraction operates in the context of three, well-established African American-led nonprofit organizations by utilizing an old-school values approach. The findings suggest that each of these programs provides a direct focus on African American history and positive role models. Further, these programs teach African American youth how to excel while being black, from people who know first-hand what that experience entails. Nonprofit program leaders become trusted sources of advice and, ultimately, build self-confidence in the youth they serve. Given the limited research that focuses on African American-led nonprofits, this research illuminates an important, understudied area in nonprofit studies

Transcriptional network growing models using motif-based preferential attachment

Understanding relationships between architectural properties of gene-regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics, as it can provide insights into, e.g., disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs – i.e., small-node subgraphs that occur more abundantly in GRNs than expected from chance alone. Because these transcriptional modules represent “building blocks” of complex networks and exhibit a wide range of functional and dynamical properties, they may contribute to the remarkable robustness and dynamical stability associated with the whole of GRNs. Here, we developed network-construction models to better understand this relationship, which produce randomized GRNs by using transcriptional motifs as the fundamental growth unit in contrast to other methods that construct similar networks on a node-by-node basis. Because this model produces networks with a prescribed lower bound on the number of choice transcriptional motifs (e.g., downlinks, feed-forward loops), its fidelity to the motif distributions observed in model organisms represents an improvement over existing methods, which we validated by contrasting their resultant motif and degree distributions against existing network-growth models and data from the model organism of the bacteriumEscherichia coli. These models may therefore serve as novel testbeds for further elucidating relationships between the topology of transcriptional motifs and network-wide dynamical properties

Band structure in classical field theory

Stability and instability bands in classical mechanics are well-studied in connection with systems such as described by the Mathieu equation. We examine whether such band structure can arise in classical field theory in the context of an embedded kink in 1+1 dimensions. The static embedded kink is unstable to perturbations but we show that if the kink is dynamic it can exhibit stability in certain parameter bands. Our results are relevant for estimating the lifetimes of various embedded defects and, in particular, loops of electroweak Z-string.Comment: 6 pages, 4 fig. Reference added, Fig. 3 updated with improved numerical code, minor comments added. Version to be published in Phys. Rev.

Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators.

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych.uic.edu in their daily work and guided the development, refinement and expansion of the system into a suite of tools intended for use by the wider scientific community

Pamphlet to Accompany Geologic Map GMC-34: Geologic Map of the O’Neill 1º x 2º Quadrangle, Nebraska, with Configuration Maps of Surfaces of Formations

This map is necessarily generalized. It is based primarily on data from 7.5’ surficial geologic quadrangle maps of the map area prepared by the authors principally from 1991 to 2000, from Voorhies (unpub. data, 1974), as well as data from test-hole drilling done across the quadrangle by the Conservation and Survey Division, University of Nebraska, and its cooperators over many years since the 1930s. For more detailed information, consult the geologic data files of the Conservation and Survey Division, School of Natural Resources, University of Nebraska-Lincoln. The quadrangle is mostly covered by vegetation and Holocene sediments. Limited good exposures of older sediments and bedrock occur usually in road cuts, in quarry and pit excavations, on valley sides, on stream and river cut banks, and in isolated erosional remnants on uplands. Users of this map should remember that the scale of the map is small and allows only a general picture of the geology of the quadrangle to be depicted. Users should check with the authors regarding specific sites and, if necessary, do field checks of these sites. As new data become available the authors intend to update the data sets used in preparation of this quadrangle text and maps and to issue refined versions, if necessary. The earliest geologic map that included part of the study area was published by Charles Lyell in 1845 (Diffendal, 1993). Other geologic maps at different scales that include all or parts of the map area are by Darton (1899, 1905), Condra (1908), Schulte (1952), Mendenhall (1953), Lampshire (1956), Burchett (1986), Weeks and Gutentag, (1981), Weeks and others (1988), Swinehart and others (1994), and Diffendal and Voorhies (1994). Geologic maps of adjacent areas in Nebraska and South Dakota include Burchett and others (1975), Burchett and others (1988), Diffendal (1991), and Souders (2000) for Nebraska and Stevenson and Carlson (1950, 1951), Baker and others (1952), Collins and French (1958), Schoon and Sevon (1958), Stevenson and others (1958), and Stevenson and others (1959) for parts of South Dakota. Detailed groundwater investigations and associated stratigraphic test drilling (of parts or all of the map area) were done by Darton (1905), Condra (1908), Reed (1944), Keech and Schreurs (1953, 1954), Cronin and Newport (1956), Reed (1957), Smith (1958), Newport (1959), Souders and Shaffer (1969), Souders (1976), Gutentag and Weeks (1980), Luckey and others (1981), Lawton and Hiergesell (1988), Weeks and others (1988), Pierce (1989), Rahn and David (1989), Burchett and Smith (1992), and Lackey and others (1995, 1998a, 1998b, 2000)

Statics and dynamics of single DNA molecules confined in nanochannels

The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics

The science of contemporary street protest: new efforts in the United States

Since the inauguration of Donald Trump, there has been substantial and ongoing protest against the Administration. Street demonstrations are some of the most visible forms of opposition to the Administration and its policies. This article reviews the two most central methods for studying street protest on a large scale: building comprehensive event databases and conducting field surveys of participants at demonstrations. After discussing the broader development of these methods, this article provides a detailed assessment of recent and ongoing projects studying the current wave of contention. Recommendations are offered to meet major challenges, including making data publicly available in near real time, increasing the validity and reliability of event data, expanding the scope of crowd surveys, and integrating ongoing projects in a meaningful way by building new research infrastructure