Memory and Modularity in Cell-Fate Decision Making

Genetically identical cells sharing an environment can display markedly different phenotypes. It is often unclear how much of this variation derives from chance, external signals, or attempts by individual cells to exert autonomous phenotypic programs. By observing thousands of cells for hundreds of consecutive generations under constant conditions, we dissect the stochastic decision between a solitary, motile state and a chained, sessile state in Bacillus subtilis. The motile state is memoryless, exhibiting no autonomous control over the time spent in the state, whereas chaining is tightly timed. Timing enforces coordination among related cells in the multicellular state. Further, we show that the three-protein regulatory circuit governing the decision is modular, as initiation and maintenance of chaining are genetically separable functions. As stimulation of the same initiating pathway triggers biofilm formation, we argue that autonomous timing allows a trial commitment to multicellularity that external signals could extend

Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution.

We designed an epi-illumination SPIM system that uses a single objective and has a sample interface identical to that of an inverted fluorescence microscope with no additional reflection elements. It achieves subcellular resolution and single-molecule sensitivity, and is compatible with common biological sample holders, including multi-well plates. We demonstrated multicolor fast volumetric imaging, single-molecule localization microscopy, parallel imaging of 16 cell lines and parallel recording of cellular responses to perturbations

Systematics within the Zopheridae Complex (Coleoptera: Tenebrionoidea).

The Ironclad Beetles, Cylindrical Bark Beetles, and Monommatid Beetles are a cosmopolitan family with over 1,700 species worldwide. Now constituting members from three previous families (Zopheridae, Monommatidae, Colydiidae), Zopheridae represent a wide array of morphological diversity and variability. Larvae of most members are fungivores/detritovores, while some are suspected of boring into sound wood. Adults are predaceous or fungivores, and some zopherids have been linked to the spread of fungal disease. Morphologically, adults are hard to separate from other tenebrionoid families. Zopherids can be distinguished by 9-11 segmented antennae with a usually abrupt, 1-3 segmented club, antennal insertions concealed from above, closed mesocoxal cavities, 4-4-4 or 5-5-4 tarsal formula, heteromeroid trochanters, and a tenebrionoid aedeagus. Systematically, the constitution and classification of Zopheridae is not yet settled, and the monophyly of the group with respect to other members of the Tenebrionoidea is in question. The research that follows attemps to rectify the classification of this taxonomically challenging group by investigating the relationships within and among zopherid members, as well as provide useful tools for the identification of these difficult little brown beetles. In Chapter 1, I present IroncladID: A Tool for Diagnosing Ironclad and Cylindrical Bark Beetles (Coleoptera: Zopheridae) of North America north of Mexico. This is an interactive electronic key designed to aid in the identification of adult Ironclad and Cylindrical Bark Beetles. A web interface was constructed to house a number of resources for the diagonsis of zopherid beetles including a specially-built Lucid interactive key (available from http://coleopterasystematics.com/ironcladid/index.html). Appendices A—F are located in the Appendices section of this document. Appendix F contains the USDA Announcement for IroncladID and is available as a supplementary file via LoboVault. See PDF titled Appendix_F_USDA_Announcement\u27. In Chapter 2, I present an Illustrated Catalogue and Type Designations of the New Zealand Zopheridae (Coleoptera: Tenebrionoidea). This comprehensive catalogue to the New Zealand members of the family Zopheridae was produced in an effort to stabilize the nomenclature preceding extensive revisionary taxonomy within the group. A checklist of the 17 New Zealand zopherid genera and an account for each of the 189 species (by current combination) is provided. Appendix G contains the figures 1—421 for Chapter 2 and is available as a supplementary file via LoboVault. See PDF titled \u27Appendix_G_Figures_Chapter2\u27. In Chapter 3, I present a Phylogenetic Analysis of the Ironclad and Cylindrical Bark Beetles of the World (Coleoptera: Tenebrionoidea: Zopheridae). I inferred the first molecular phylogenetic hypothesis for Zopheridae. Portions of three genes (28S rDNA, cytochrome c oxidase I and histone III) were analyzed. One hundred eighty three zopherid species were included, representing 2/2 subfamilies, 15/15 tribes, and more than half of the currently recognized genera. Twelve outgroup taxa from eight other families of Tenebrionoidea were included. Parsimony and partitioned Bayesian analyses were performed on the combined data set. In both phylogenetic analyses, Zopheridae was not recovered as monophyletic. The subfamily Zopherinae was not recovered as monophyletic in both analyses, and the subfamily Corticariinae was recovered as monophyletic only in the Bayesian analysis. Appendix H contains the figures 1a—2d for Chapter 3 and is available as a supplementary file via LoboVault. See PDF titled \u27Appendix_H_Figures_Chapter3\u27. In Chapter 4, I present Novel Microscopy Techniques Reveal Multiple Evolutionary Origins of Metal Incorporation into Mandibles of the Megadiverse Beetles (Coleoptera). A broad survey of presence/absence of mandibular metals across the order Coleoptera was conducted. To test for phylogenetic signal and evolutionary correlation between presence/absence of metals and adult mandibular use, we constructed a phylogeny under a Bayesian framework from a subsampling of a pre-existing dataset (Hunt et al. 2007), performed discrete statistical analyses on character evolution via BayesTraits Discrete (Pagel et al. 2004), and performed ancestral state reconstructions under both Parsimony and Bayesian frameworks via Mesquite (Maddison and Maddison 2011) and BayesTraits Multistate (Pagel et al. 2004). Resultant patterns of metal incorporation were strongly correlated with adult mandibular use and appear to have originated several times throughout Coleoptera. Additionally, the location and types of cuticular metals are demonstrated to be potentially valuable characters for taxonomic diagnoses. Appendix I contains the figures 1—17 for Chapter 4 and is available as a supplementary file via LoboVault. See PDF titled \u27Appendix_I_Figures_Chapter4\u27. Appendix J contains the supplementary ESEM-EDS mandibular scans and is available as a supplementary file via LoboVault. See PDF titled \u27Appendix_J_EDS_Chapter4\u27

The Influence Of Habitat Complexity, Prey Quality, And Predator Avoidance On Sea Otter Resource Selection In Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 2011The differential selection of habitat by animals is one of the fundamental relationships that enable species to coexist. Habitat selection may be among various discrete categories (e.g., mudflat, boulder field, or meadow) or among a continuous array of characteristics such as vegetation percent cover, benthic substrate size, substrate rugosity, distance to prey resources, or distance to suitable escape terrain from predation. Sea otters are particularly suitable for resource selection studies because they are capable of selecting a wide variety habitat types in response to prey availability, competition, and predation. In Alaska, sea otters associate with a range of habitats types including continuous bedrock reefs in the western Aleutians to heterogeneous fjord systems in Kackemak Bay, Lower Cook Inlet. Sea otters inhabiting the western Aleutians exhibit highly restricted habitat selection patterns characteristic of declining populations. In contrast, sea otters inhabiting Kachemak Bay exhibit selective use of a broad range of habitat types. Many factors contribute to the selective use of habitats by animals, including habitat suitability, prey quality, and predation risk. This thesis was designed to test factors contributing to sea otter resource selection in an area undergoing population increase versus an area experiencing high predation pressure. The contribution of prey size, abundance, biomass, potential energy density are considered in addition to physical habitat characteristics such as grain size, rugosity, depth, structural habitat complexity, and exposure to prevailing weather. Findings suggest that foraging sea otters differentially select habitat and prey resources based on prey accessibility and not on prey abundance or potential prey energy density. Findings further suggest that sea otter foraging site selection is based on habitat complexity in areas with increasing populations, but in areas with high predation pressure, proximity to suitable escape terrain appears to be more important than prey quality or benthic habitat complexity

Corals of the genus Porites are a locally abundant component of the epibiont community on mangrove prop roots at Calabash Caye, Turneffe Atoll, Belize

Mangroves are generally regarded as inhospitable for corals, but recent reports suggest they provide ecological refuge for some species. We surveyed diverse mangrove habitats on Turneffe Atoll, Belize, documenting 127 colonies of Porites divaricata (Thin Finger Coral) along 1858 m of mangrove prop roots at Calabash Caye and a much more diverse coral assemblage at Crooked Creek. At Calabash, corals were highly clumped, and varied widely in size and morphology, including large well-arborized colonies, encrusting forms with few branches, and new recruits with no branches, suggesting an age-structuredpopulation exhibiting extensive morphological plasticity. The data described here contributeto an emerging picture of mangroves as potentially critical habitat for many Caribbeancoral species.Accepted manuscrip

Herschel observations of EXtraordinary Sources: Analysis of the full Herschel/HIFI molecular line survey of Sagittarius B2(N)

A sensitive broadband molecular line survey of the Sagittarius B2(N) star-forming region has been obtained with the HIFI instrument on the Herschel Space Observatory, offering the first high-spectral resolution look at this well-studied source in a wavelength region largely inaccessible from the ground (625-157 um). From the roughly 8,000 spectral features in the survey, a total of 72 isotopologues arising from 44 different molecules have been identified, ranging from light hydrides to complex organics, and arising from a variety of environments from cold and diffuse to hot and dense gas. We present an LTE model to the spectral signatures of each molecule, constraining the source sizes for hot core species with complementary SMA interferometric observations, and assuming that molecules with related functional group composition are cospatial. For each molecule, a single model is given to fit all of the emission and absorption features of that species across the entire 480-1910 GHz spectral range, accounting for multiple temperature and velocity components when needed to describe the spectrum. As with other HIFI surveys toward massive star forming regions, methanol is found to contribute more integrated line intensity to the spectrum than any other species. We discuss the molecular abundances derived for the hot core, where the local thermodynamic equilibrium approximation is generally found to describe the spectrum well, in comparison to abundances derived for the same molecules in the Orion KL region from a similar HIFI survey.Comment: Accepted to ApJ. 64 pages, 14 figures. Truncated abstrac

Forming reproducible non-lithographic nanocontacts to assess the effect of contact compressive strain in nanomaterials

The application of electrical nanoprobes to measure and characterize nanomaterials has become widely spread. However, the formation of quality electrical contacts using metallic probes on nanostructures has not been directly assessed. We investigate here the electrical behaviour of non-lithographically formed contacts to ZnO nanowires (NWs) and develop a method to reproducibly form Ohmic contacts for accurate electrical measurement of the nanostructures. The contacting method used in this work relies on an electrical feedback mechanism to determine the point of contact to the individual NWs, ensuring minimal compressive strain at the contact. This developed method is compared with the standard tip deflection contacting technique and shows a significant improvement in reproducibility. The effect of excessive compressive strain at the contact was investigated, with a change from rectifying to ohmic I–V behaviour observed as compressive strain at the contact was increased, leading to irreversible changes to the electrical properties of the NW. This work provides an ideal method for forming reproducible non-lithographic nanocontacts to a multitude of nanomaterials

Accessible biometrics: a frustrated total internal reflection approach to imaging fingerprints

Fingerprints are widely used as a means of identifying persons of interest because of the highly individual nature of the spatial distribution and types of features (or minuta) found on the surface of a finger. This individuality has led to their wide application in the comparison of fingerprints found at crime scenes with those taken from known offenders and suspects in custody. However, despite recent advances in machine vision technology and image processing techniques, fingerprint evidence is still widely being collected using outdated practices involving ink and paper – a process that can be both time consuming and expensive. Reduction of forensic service budgets increasingly requires that evidence be gathered and processed more rapidly and efficiently. However, many of the existing digital fingerprint acquisition devices have proven too expensive to roll out on a large scale. As a result new, low-cost imaging technologies are required to increase the quality and throughput of the processing of fingerprint evidence. Here we describe an inexpensive approach to digital fingerprint acquisition that is based upon frustrated total internal reflection imaging. The quality and resolution of the images produced are shown to be as good as those currently acquired using ink and paper based methods. The same imaging technique is also shown to be capable of imaging powdered fingerprints that have been lifted from a crime scene using adhesive tape or gel lifters

Characteristics of outdoor falls among older people: A qualitative study

Background Falls are a major threat to older people’s health and wellbeing. Approximately half of falls occur in outdoor environments but little is known about the circumstances in which they occur. We conducted a qualitative study to explore older people’s experiences of outdoor falls to develop understanding of how they may be prevented. Methods We conducted nine focus groups across the UK (England, Wales, and Scotland). Our sample was from urban and rural settings and different environmental landscapes. Participants were aged 65+ and had at least one outdoor fall in the past year. We analysed the data using framework and content analyses. Results Forty-four adults aged 65 – 92 took part and reported their experience of 88 outdoor falls. Outdoor falls occurred in a variety of contexts, though reports suggested the following scenarios may have been more frequent: when crossing a road, in a familiar area, when bystanders were around, and with an unreported or unknown attribution. Most frequently, falls resulted in either minor or moderate injury, feeling embarrassed at the time of the fall, and anxiety about falling again. Ten falls resulted in fracture, but no strong pattern emerged in regard to the contexts of these falls. Anxiety about falling again appeared more prevalent among those that fell in urban settings and who made more visits into their neighbourhood in a typical week. Conclusions This exploratory study has highlighted several aspects of the outdoor environment that may represent risk factors for outdoor falls and associated fear of falling. Health professionals are recommended to consider outdoor environments as well as the home setting when working to prevent falls and increase mobility among older people