Recurrent Herpetic Stromal Keratitis in Mice,a Model for Studying Human HSK

Herpetic eye disease, termed herpetic stromal keratitis (HSK), is a potentially blinding infection of the cornea that results in over 300,000 clinical visits each year for treatment. Between 1 and 2 percent of those patients with clinical disease will experience loss of vision of the infected cornea. The vast majority of these cases are the result of reactivation of a latent infection by herpes simplex type I virus and not due to acute disease. Interestingly, the acute infection is the model most often used to study this disease. However, it was felt that a recurrent model of HSK would be more reflective of what occurs during clinical disease. The recurrent animal models for HSK have employed both rabbits and mice. The advantage of rabbits is that they experience reactivation from latency absent any known stimulus. That said, it is difficult to explore the role that many immunological factors play in recurrent HSK because the rabbit model does not have the immunological and genetic resources that the mouse has. We chose to use the mouse model for recurrent HSK because it has the advantage of there being many resources available and also we know when reactivation will occur because reactivation is induced by exposure to UV-B light. Thus far, this model has allowed those laboratories using it to define several immunological factors that are important to this disease. It has also allowed us to test both therapeutic and vaccine efficacy.     

The Saccharomyces cerevisiae SCRaMbLE system and genome minimization

We have recently reported the first partially synthetic eukaryotic genome. Saccharomyces cerevisiae chromosomes synIXR and semi-synVIL are fully synthetic versions of the right arm of chromosome IX and the telomeric segment of the left arm of chromosome VI, respectively, and represent the beginning of the synthetic yeast genome project, Sc2.0, that progressively replaces native yeast DNA with synthetic sequences. We have designed synthetic chromosome sequences according to principles specifying a wild-type phenotype, highly stable genome, and maintenance of genetic flexibility. Although other synthetic genome projects exist, the Sc2.0 approach is unique in that we have implemented design specifications predicted to generate a wild-type phenotype until induction of "SCRaMbLE," an inducible evolution system that generates significant genetic diversity. Here we further explore the significance of Sc2.0 and show how SCRaMbLE can serve as a genome minimization tool.     

A humble man in tireless pursuit: Shu Chien, a 2010 national medal of science awardee

On his 70th birthday, Shu Chien's colleagues put together a 600-page book of letters, essays, and photographs as a tribute not only to his contributions to the field of bioengineering but also in honor of his character as a valued friend, research collaborator, and family member. Perhaps they thought that the book would commemorate the moment when Chien began to consider retirement. But in the last decade, he has added more than 140 publications to an already impressive list of 379. And he shows no sign of slowing down.     

No‐analog climates and shifting realized niches during the late quaternary: implications for 21st‐century predictions by species distribution models

Empirically derived species distributions models (SDMs) are increasingly relied upon to forecast species vulnerabilities to future climate change. However, many of the assumptions of SDMs may be violated when they are used to project species distributions across significant climate change events. In particular, SDM's in theory assume stable fundamental niches, but in practice, they assume stable realized niches. The assumption of a fixed realized niche relative to climate variables remains unlikely for various reasons, particularly if novel future climates open up currently unavailable portions of species’ fundamental niches. To demonstrate this effect, we compare the climate distributions for fossil‐pollen data from 21 to 15 ka bp (relying on paleoclimate simulations) when communities and climates with no modern analog were common across North America to observed modern pollen assemblages. We test how well SDMs are able to project 20th century pollen‐based taxon distributions with models calibrated using data from 21 to 15 ka. We find that taxa which were abundant in areas with no‐analog late glacial climates, such as Fraxinus, Ostrya/Carpinus and Ulmus, substantially shifted their realized niches from the late glacial period to present. SDMs for these taxa had low predictive accuracy when projected to modern climates despite demonstrating high predictive accuracy for late glacial pollen distributions. For other taxa, e.g. Quercus, Picea, Pinus strobus, had relatively stable realized niches and models for these taxa tended to have higher predictive accuracy when projected to present. Our findings reinforce the point that a realized niche at any one time often represents only a subset of the climate conditions in which a taxon can persist. Projections from SDMs into future climate conditions that are based solely on contemporary realized distributions are potentially misleading for assessing the vulnerability of species to future climate change.     

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

The three-dimensional structure of the ribosomal large subunit (LSU) reveals a single morphological element, although the 23S rRNA is contained in six secondary structure domains. Based upon maps of inter- and intra-domain interactions and proposed evolutionary pathways of development, we hypothesize that Domain III is a truly independent structural domain of the LSU. Domain III is primarily stabilized by intra-domain interactions, negligibly perturbed by inter-domain interactions, and is not penetrated by ribosomal proteins or other rRNA. We have probed the structure of Domain III rRNA alone and when contained within the intact 23S rRNA using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), in the absence and presence of magnesium. The combined results support the hypothesis that Domain III alone folds to a near-native state with secondary structure, intra-domain tertiary interactions, and inter-domain interactions that are independent of whether or not it is embedded in the intact 23S rRNA or within the LSU. The data presented support previous suggestions that Domain III was added relatively late in ribosomal evolution.     

Integrating stomach content and stable isotope analyses to elucidate the feeding habits of non-native sharptooth catfish <Emphasis Type="Italic">Clarias gariepinus</Emphasis>

Sharptooth catfish Clarias gariepinus was introduced into the Eastern Cape Province, South Africa, in 1976 and there are concerns about its possible negative impacts on native biota. This study investigated its trophic impact by examining its feeding habits. Stomach content and stable isotope analyses were compared from three localities—the Great Fish River, Sundays River and Glen Melville Dam. Stomach content analysis indicated a catholic diet dominated by fish particularly in all localities. Spatially, however, the diets revealed differences based on the dominance of macrophytes that were only present in the rivers, and aquatic invertebrates that appeared more diverse within the Great Fish River compared to other localities. By contrast, stable isotopes revealed a more generalised feeding pattern with no clear dominance of particular prey. Stable isotopes further showed that the catfish was a complex predator, with large catfish being top predators whereas smaller size groups appeared to feed lower in the food chain. An ontogenetic shift in diet was evident, with small fish predominantly consuming aquatic invertebrates and shifting towards fish with increasing size. High dietary overlap suggests the potential risk associated catfish feeding, especially the potential of piscivory by small catfish that are more likely to persist in shallow and marginal where endangered indigenous minnows occur. The alteration of environmental conditions, especially flow by inter-basin water transfer (IBWT) schemes, was inferred to have had a probable influence its invasion success. Occurrence of other invaders, which was facilitated by the IBWT together with the catfish, posits the risk of invasion meltdown within the study systems.     

Linaria dalmatica invades south-facing slopes and less grazed areas in grazing-tolerant mixed-grass prairie

Identifying environments where invasive plants are most invasive is key to understanding causes of invasion and developing effective management strategies. In mixed-grass prairie, invasive plants are often successful in relatively wet, nitrogen-rich areas, and areas protected from grazing. Dalmatian toadflax, a common invader of mixed-grass prairie, can also be favored by high water and nitrogen availability, but is thought to be relatively unpalatable to cattle, and therefore favored by grazing. We used spatially-adjusted model selection techniques to quantify relationships between toadflax cover (measured using very high-resolution aerial imagery), and relative snow deposition (estimated with a blowing snow model), slope, aspect, soil texture, and grazing intensity (estimated by proximity to water tanks). Toadflax was common throughout the 400 ha study site, occurring in 742 of 1,861 images. Toadflax cover was high on steeper slopes, particularly those with southern aspects. These two topographic variables were more effective in explaining toadflax distribution than modeled snow deposition, suggesting that factors other than snow deposition cause toadflax invasion on south-facing slopes. Toadflax cover was also high in areas further from water tanks, indicating that grazing may inhibit toadflax invasion. More broadly, this result suggests that grazing can reduce invasion of even relatively unpalatable species in ecosystems with long evolutionary histories of grazing.     

Fluorinated colloidal gold immunolabels for imaging select proteins in parallel with lipids using high-resolution secondary ion mass spectrometry

The local abundance of specific lipid species near a membrane protein is hypothesized to influence the protein's activity. The ability to simultaneously image the distributions of specific protein and lipid species in the cell membrane would facilitate testing these hypotheses. Recent advances in imaging the distribution of cell membrane lipids with mass spectrometry have created the desire for membrane protein probes that can be simultaneously imaged with isotope labeled lipids. Such probes would enable conclusive tests to determine whether specific proteins colocalize with particular lipid species. Here, we describe the development of fluorine-functionalized colloidal gold immunolabels that facilitate the detection and imaging of specific proteins in parallel with lipids in the plasma membrane using high-resolution SIMS performed with a NanoSIMS. First, we developed a method to functionalize colloidal gold nanoparticles with a partially fluorinated mixed monolayer that permitted NanoSIMS detection and rendered the functionalized nanoparticles dispersible in aqueous buffer. Then, to allow for selective protein labeling, we attached the fluorinated colloidal gold nanoparticles to the nonbinding portion of antibodies. By combining these functionalized immunolabels with metabolic incorporation of stable isotopes, we demonstrate that influenza hemagglutinin and cellular lipids can be imaged in parallel using NanoSIMS. These labels enable a general approach to simultaneously imaging specific proteins and lipids with high sensitivity and lateral resolution, which may be used to evaluate predictions of protein colocalization with specific lipid species.     

Genetic divergence, speciation and biogeography of Mustelus (sharks) in the central Indo-Pacific and Australasia

The shark genus Mustelus is speciose, commercially important and systematically troublesome. We use a molecular approach combining inter and intra-specific data to investigate Mustelus species in the central Indo-Pacific and Australasia. Our analysis supports two Mustelus clades, one comprising species with no white spots and a placental reproductive mode and a second clade of white spotted, aplacental species. Levels of genetic divergence are low, especially among species in the white spotted, aplacental clade and this should be taken into account when employing molecular data to delineate species. Our data support the hypothesis of a radiation following dispersal from a northern hemisphere ancestor. Molecular dating suggests that localised speciation in Australasia may have occurred during the Pleistocene. We propose that some of the difficulties associated with Mustelus systematics relate to a recent radiation, particularly in the Australasian region.