Effects of the built environment on childhood obesity: The case of urban recreational trails and crime

We study the effects of urban environment on childhood obesity by concentrating on the effects of walking trails and crime close to children's homes on their BMI and obesity status. We use a unique dataset, which combines information on recreational trails in Indianapolis with data on violent crimes and anthropomorphic and diagnostic data from children's clinic visits between 1996 and 2005. We find that having a trail near a home reduces children's weight. However, the effect depends on the amount of nearby violent crimes. Significant reductions occur only in low crime areas and trails could have opposite effects on weight in high crime areas. These effects are primarily among boys, older children, and children who live in higher income neighborhoods. Evaluated at the mean length of trails this effect for older children in no crime areas would be a reduction of 2 lb of the body weight. Falsification tests using planned trails instead of existing trails, show that trails are more likely to be located in areas with heavier children, suggesting that our results on effects of trails represent a lower bound.     

Program Code Generator for Cardiac Electrophysiology Simulation with Automatic PDE Boundary Condition Handling

Clinical and experimental studies involving human hearts can have certain limitations. Methods such as computer simulations can be an important alternative or supplemental tool. Physiological simulation at the tissue or organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and distributed parameters, such as those used in pharmacokinetics simulation, add to the complexity of the PDE solution. These factors can tailor PDE solutions and their corresponding program code to specific problems. Boundary condition and parameter changes in the customized code are usually prone to errors and time-consuming. We propose a general approach for handling PDEs and boundary conditions in computational models using a replacement scheme for discretization. This study is an extension of a program generator that we introduced in a previous publication. The program generator can generate code for multi-cell simulations of cardiac electrophysiology. Improvements to the system allow it to handle simultaneous equations in the biological function model as well as implicit PDE numerical schemes. The replacement scheme involves substituting all partial differential terms with numerical solution equations. Once the model and boundary equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to generate the program code. The resulting program code are in Java or C programming language. To validate the automatic handling of boundary conditions in the program code generator, we generated simulation code using the FHN, Luo-Rudy 1, and Hund-Rudy cell models and run cell-to-cell coupling and action potential propagation simulations. One of the simulations is based on a published experiment and simulation results are compared with the experimental data. We conclude that the proposed program code generator can be used to generate code for physiological simulations and provides a tool for studying cardiac electrophysiology.     

Development of a molecular diagnostic system to discriminate Dreissena polymorpha (zebra mussel) and Dreissena bugensis (quagga mussel)

A 3-primer PCR system was developed to discriminate invasive zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussel. The system is based on: 1) universal primers that amplifies a region of the nuclear 28s rDNA gene from both species and 2) a species-specific primer complementary to either zebra or quagga mussel. The species-specific primers bind to sequences between the binding sites for the universal primers resulting in the amplification of two products from the target species and one product from the nontarget species. Therefore, nontarget products are positive amplification controls. The 3-primer system accurately discriminated zebra and quagga mussels from seven geographically distinct populations.     

High-speed multicolor microscopy of repeating dynamic processes

Images of multiply labeled fluorescent samples provide unique insights into the localization of molecules, cells, and tissues. The ability to image multiple channels simultaneously at high speed without cross talk is limited to a few colors and requires dedicated multichannel or multispectral detection procedures. Simpler microscopes, in which each color is imaged sequentially, produce a much lower frame rate. Here, we describe a technique to image, at high frame rate, multiply labeled samples that have a repeating motion. We capture images in a single channel at a time over one full occurrence of the motion then repeat acquisition for other channels over subsequent occurrences. We finally build a high-speed multichannel image sequence by combining the images after applying a normalized mutual information-based time registration procedure. We show that this technique is amenable to image the beating heart of a double-labeled embryonic quail in three channels (brightfield, yellow, and mCherry fluorescent proteins) using a fluorescence wide-field microscope equipped with a single monochrome camera and without fast channel switching optics. We experimentally evaluate the accuracy of our method on image series from a two-channel confocal microscope.     

Polar bear (Ursus maritimus) cub mortality at a den site in northern Alaska

In March 2009, we documented the death of one member of a triplet polar bear (Ursus maritimus) litter at its den site in the southern Beaufort Sea (SBS) of Alaska. We used a self-contained video camera unit to document activity between den emergence and departure. All three cubs showed low activity levels relative to other cubs observed, and one died within one week of den emergence. Necropsy confirmed that the dead cub had a low body weight and was malnourished. Capture later confirmed that the two surviving cubs were also undersized. Polar bear cub survival is influenced by many factors including litter size and sea ice conditions. Triplet litters are often smaller and suffer higher mortality rates than singletons and twins. This cub was not only a triplet but also born following 2 years of record minimum sea ice extent, both of which may have played a role in this cub’s demise.     

More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis

All plants in natural ecosystems are thought to be symbioticwith mycorrhizal and/or endophytic fungi. Collectively, thesefungi express different symbiotic lifestyles ranging from parasitismto mutualism. Analysis of Colletotrichum species indicates thatindividual isolates can express either parasitic or mutualisticlifestyles depending on the host genotype colonized. The endophytecolonization pattern and lifestyle expression indicate thatplants can be discerned as either disease, non-disease, or non-hosts.Fitness benefits conferred by fungi expressing mutualistic lifestylesinclude biotic and abiotic stress tolerance, growth enhancement,and increased reproductive success. Analysis of plant–endophyteassociations in high stress habitats revealed that at leastsome fungal endophytes confer habitat-specific stress toleranceto host plants. Without the habitat-adapted fungal endophytes,the plants are unable to survive in their native habitats. Moreover,the endophytes have a broad host range encompassing both monocotsand eudicots, and confer habitat-specific stress tolerance toboth plant groups. Key words: Colletotrichum, fungal endophytes, stress tolerance, symbiosis, symbiotic lifestyle Received 19 June 2007; Revised 25 November 2007 Accepted 30 November 2007     

Breeding synchrony and extrapair paternity in a species with alternative reproductive strategies

Breeding synchrony may affect the tradeoff between pursuing multiple mates and avoiding paternity loss, translating into differences in the rate of extrapair paternity (EPP). However, diverse empirical relationships between breeding synchrony and EPP remain challenging to explain. We examined whether the relationship between breeding synchrony and EPP varied with male morph, age, body size, or breeding density in the white‐throated sparrow Zonotrichia albicollis. In this species, males of two genetically determined morphs pursue alternative mating strategies. Breeding synchrony positively correlated with EPP within polygamous white morph males, which have high rates of EPP and cuckoldry, but was unrelated to EPP within tan morph males, which prioritize mate guarding and paternal care. As previously reported, males that gained EPP were primarily white males. Males gained EPP more often than expected by chance during their mate's fertile period and on neighboring territories. Since extrapair copulation appears primarily male‐driven in this species, these results indicate that white males focus extra‐pair mating effort during periods of high synchrony and during their mates’ fertile periods, even at the expense of paternity loss within their own nests. Breeding density, male age, and male size did not modify the relationship between breeding synchrony and EPP. However, older white males had higher cuckoldry rates, perhaps reflecting declines in performance associated with senescence. Results suggest that, even within species, mating strategy may modify how breeding synchrony affects rates of EPP, with positive relationships manifest only within subsets of individuals that pursue a strategy of polygyny at the expense of paternity loss.     

Multispectral fingerprinting for improved in vivo cell dynamics analysis

Background  

Tracing cell dynamics in the embryo becomes tremendously difficult when cell trajectories cross in space and time and tissue density obscure individual cell borders. Here, we used the chick neural crest (NC) as a model to test multicolor cell labeling and multispectral confocal imaging strategies to overcome these roadblocks.     

Identification of emergent motion compartments in the amniote embryo

The tissue scale deformations (≥1mm) required to form an amniote embryo are poorly understood. Here, we studied ∼400 μm-sized explant units from gastrulating quail embryos. The explants deformed in a reproducible manner when grown using a novel vitelline membrane-based culture method. Time-lapse recordings of latent embryonic motion patterns were analyzed after disk-shaped tissue explants were excised from three specific regions near the primitive streak: 1) anterolateral epiblast, 2) posterolateral epiblast, and 3) the avian organizer (Hensen''s node). The explants were cultured for 8 hours—an interval equivalent to gastrulation. Both the anterolateral and the posterolateral epiblastic explants engaged in concentric radial/centrifugal tissue expansion. In sharp contrast, Hensen''s node explants displayed Cartesian-like, elongated, bipolar deformations—a pattern reminiscent of axis elongation. Time-lapse analysis of explant tissue motion patterns indicated that both cellular motility and extracellular matrix fiber (tissue) remodeling take place during the observed morphogenetic deformations. As expected, treatment of tissue explants with a selective Rho-Kinase (p160ROCK) signaling inhibitor, Y27632, completely arrested all morphogenetic movements. Microsurgical experiments revealed that lateral epiblastic tissue was dispensable for the generation of an elongated midline axis— provided that an intact organizer (node) is present. Our computational analyses suggest the possibility of delineating tissue-scale morphogenetic movements at anatomically discrete locations in the embryo. Further, tissue deformation patterns, as well as the mechanical state of the tissue, require normal actomyosin function. We conclude that amniote embryos contain tissue-scale, regionalized morphogenetic motion generators, which can be assessed using our novel computational time-lapse imaging approach. These data and future studies—using explants excised from overlapping anatomical positions—will contribute to understanding the emergent tissue flow that shapes the amniote embryo.