Co-orientation of replication and transcription preserves genome integrity.

In many bacteria, there is a genome-wide bias towards co-orientation of replication and transcription, with essential and/or highly-expressed genes further enriched co-directionally. We previously found that reversing this bias in the bacterium Bacillus subtilis slows replication elongation, and we proposed that this effect contributes to the evolutionary pressure selecting the transcription-replication co-orientation bias. This selection might have been based purely on selection for speedy replication; alternatively, the slowed replication might actually represent an average of individual replication-disruption events, each of which is counter-selected independently because genome integrity is selected. To differentiate these possibilities and define the precise forces driving this aspect of genome organization, we generated new strains with inversions either over approximately 1/4 of the chromosome or at ribosomal RNA (rRNA) operons. Applying mathematical analysis to genomic microarray snapshots, we found that replication rates vary dramatically within the inverted genome. Replication is moderately impeded throughout the inverted region, which results in a small but significant competitive disadvantage in minimal medium. Importantly, replication is strongly obstructed at inverted rRNA loci in rich medium. This obstruction results in disruption of DNA replication, activation of DNA damage responses, loss of genome integrity, and cell death. Our results strongly suggest that preservation of genome integrity drives the evolution of co-orientation of replication and transcription, a conserved feature of genome organization.

When the library is located in prime real estate: a case study on the loss of space from the Duke University Medical Center Library and Archives.

The Duke University Medical Center Library and Archives is located in the heart of the Duke Medicine campus, surrounded by Duke Hospital, ambulatory clinics, and numerous research facilities. Its location is considered prime real estate, given its adjacency to patient care, research, and educational activities. In 2005, the Duke University Library Space Planning Committee had recommended creating a learning center in the library that would support a variety of educational activities. However, the health system needed to convert the library's top floor into office space to make way for expansion of the hospital and cancer center. The library had only five months to plan the storage and consolidation of its journal and book collections, while working with the facilities design office and architect on the replacement of key user spaces on the top floor. Library staff worked together to develop plans for storing, weeding, and consolidating the collections and provided input into renovation plans for users spaces on its mezzanine level. The library lost 15,238 square feet (29%) of its net assignable square footage and a total of 16,897 (30%) gross square feet. This included 50% of the total space allotted to collections and over 15% of user spaces. The top-floor space now houses offices for Duke Medicine oncology faculty and staff. By storing a large portion of its collection off-site, the library was able to remove more stacks on the remaining stack level and convert them to user spaces, a long-term goal for the library. Additional space on the mezzanine level had to be converted to replace lost study and conference room spaces. While this project did not match the recommended space plans for the library, it underscored the need for the library to think creatively about the future of its facility and to work toward a more cohesive master plan.

Spaces of Order: An African Poetics of Space

“Spaces of Order” argues that the African novel should be studied as a revolutionary form characterized by aesthetic innovations that are not comprehensible in terms of the novel’s European archive of forms. It does this by mapping an African spatial order that undermines the spatial problematic at the formal and ideological core of the novel—the split between a private, subjective interior, and an abstract, impersonal outside. The project opens with an examination of spatial fragmentation as figured in the “endless forest” of Amos Tutuola’s The Palmwine Drinkard (1952). The second chapter studies Chinua Achebe’s Things Fall Apart (1958) as a fictional world built around a peculiar category of space, the “evil forest,” which constitutes an African principle of order and modality of power. Chapter three returns to Tutuola via Ben Okri’s The Famished Road (1991) and shows how the dispersal of fragmentary spaces of exclusion and terror within the colonial African city helps us conceive of political imaginaries outside the nation and other forms of liberal political communities. The fourth chapter shows Nnedi Okorafor—in her 2014 science-fiction novel Lagoon—rewriting Things Fall Apart as an alien-encounter narrative in which Africa is center-stage of a planetary, multi-species drama. Spaces of Order is a study of the African novel as a new logic of world making altogether.

Different stimuli, different spatial codes: a visual map and an auditory rate code for oculomotor space in the primate superior colliculus.

Maps are a mainstay of visual, somatosensory, and motor coding in many species. However, auditory maps of space have not been reported in the primate brain. Instead, recent studies have suggested that sound location may be encoded via broadly responsive neurons whose firing rates vary roughly proportionately with sound azimuth. Within frontal space, maps and such rate codes involve different response patterns at the level of individual neurons. Maps consist of neurons exhibiting circumscribed receptive fields, whereas rate codes involve open-ended response patterns that peak in the periphery. This coding format discrepancy therefore poses a potential problem for brain regions responsible for representing both visual and auditory information. Here, we investigated the coding of auditory space in the primate superior colliculus(SC), a structure known to contain visual and oculomotor maps for guiding saccades. We report that, for visual stimuli, neurons showed circumscribed receptive fields consistent with a map, but for auditory stimuli, they had open-ended response patterns consistent with a rate or level-of-activity code for location. The discrepant response patterns were not segregated into different neural populations but occurred in the same neurons. We show that a read-out algorithm in which the site and level of SC activity both contribute to the computation of stimulus location is successful at evaluating the discrepant visual and auditory codes, and can account for subtle but systematic differences in the accuracy of auditory compared to visual saccades. This suggests that a given population of neurons can use different codes to support appropriate multimodal behavior.

Discharge competence and pattern formation in peatlands: a meta-ecosystem model of the Everglades ridge-slough landscape.

Regular landscape patterning arises from spatially-dependent feedbacks, and can undergo catastrophic loss in response to changing landscape drivers. The central Everglades (Florida, USA) historically exhibited regular, linear, flow-parallel orientation of high-elevation sawgrass ridges and low-elevation sloughs that has degraded due to hydrologic modification. In this study, we use a meta-ecosystem approach to model a mechanism for the establishment, persistence, and loss of this landscape. The discharge competence (or self-organizing canal) hypothesis assumes non-linear relationships between peat accretion and water depth, and describes flow-dependent feedbacks of microtopography on water depth. Closed-form model solutions demonstrate that 1) this mechanism can produce spontaneous divergence of local elevation; 2) divergent and homogenous states can exhibit global bi-stability; and 3) feedbacks that produce divergence act anisotropically. Thus, discharge competence and non-linear peat accretion dynamics may explain the establishment, persistence, and loss of landscape pattern, even in the absence of other spatial feedbacks. Our model provides specific, testable predictions that may allow discrimination between the self-organizing canal hypotheses and competing explanations. The potential for global bi-stability suggested by our model suggests that hydrologic restoration may not re-initiate spontaneous pattern establishment, particularly where distinct soil elevation modes have been lost. As a result, we recommend that management efforts should prioritize maintenance of historic hydroperiods in areas of conserved pattern over restoration of hydrologic regimes in degraded regions. This study illustrates the value of simple meta-ecosystem models for investigation of spatial processes.

Improvement in visual search with practice: mapping learning-related changes in neurocognitive stages of processing.

Practice can improve performance on visual search tasks; the neural mechanisms underlying such improvements, however, are not clear. Response time typically shortens with practice, but which components of the stimulus-response processing chain facilitate this behavioral change? Improved search performance could result from enhancements in various cognitive processing stages, including (1) sensory processing, (2) attentional allocation, (3) target discrimination, (4) motor-response preparation, and/or (5) response execution. We measured event-related potentials (ERPs) as human participants completed a five-day visual-search protocol in which they reported the orientation of a color popout target within an array of ellipses. We assessed changes in behavioral performance and in ERP components associated with various stages of processing. After practice, response time decreased in all participants (while accuracy remained consistent), and electrophysiological measures revealed modulation of several ERP components. First, amplitudes of the early sensory-evoked N1 component at 150 ms increased bilaterally, indicating enhanced visual sensory processing of the array. Second, the negative-polarity posterior-contralateral component (N2pc, 170-250 ms) was earlier and larger, demonstrating enhanced attentional orienting. Third, the amplitude of the sustained posterior contralateral negativity component (SPCN, 300-400 ms) decreased, indicating facilitated target discrimination. Finally, faster motor-response preparation and execution were observed after practice, as indicated by latency changes in both the stimulus-locked and response-locked lateralized readiness potentials (LRPs). These electrophysiological results delineate the functional plasticity in key mechanisms underlying visual search with high temporal resolution and illustrate how practice influences various cognitive and neural processing stages leading to enhanced behavioral performance.

Orientation, Flow, and Clogging in a Two-Dimensional Hopper: Ellipses vs. Disks

Two-dimensional (2D) hopper flow of disks has been extensively studied. Here, we investigate hopper flow of ellipses with aspect ratio $\alpha = 2$, and we contrast that behavior to the flow of disks. We use a quasi-2D hopper containing photoelastic particles to obtain stress/force information. We simultaneously measure the particle motion and stress. We determine several properties, including discharge rates, jamming probabilities, and the number of particles in clogging arches. For both particle types, the size of the opening, $D$, relative to the size of particles, $\ell$ is an important dimensionless measure. The orientation of the ellipses plays an important role in flow rheology and clogging. The alignment of contacting ellipses enhances the probability of forming stable arches. This study offers insight for applications involving the flow of granular materials consisting of ellipsoidal shapes, and possibly other non-spherical shapes.