Pyrococcus horikoshii RadA Intein Site Selection

Inteins are protein segments interrupting polypeptides with the unique ability to excise from the host protein and link flanking protein fragments (exteins) to form a functional protein. Many of these proteins are involved in crucial processes such as DNA replication, DNA recombination, and DNA repair. The functionality of these elements in nature and applications in biotechnology necessitates the study of inteins. Pyrococcus horikoshii (Pho) provides an array of inteins to study, with a total of nine different proteins possessing inteins. Among the nine total inteins, the DNA repair and recombination protein RadA gained interest due to the speed and efficiency of splicing when flanked by non-native exteins. Curiously, RadA splices poorly within the native exteins in the absence of catalysts due to intein-extein interactions. Single-stranded DNA (ssDNA), which binds to RadA on the c-extein, vastly improves the speed and accuracy of splicing. ssDNA is not only a substrate of the RadA protein but also a signal indicating DNA damage and the need for recombinase activity. Given the observation that intein-extein interactions form to block splicing, we wondered how alternative intein insertion sites within the host protein would influence splicing. Observation and comparison of splicing speed and efficiency in natural and variant RadA proteins may help us further understand the phenomena of intein splicing, explain intein-extein relationships, and give insight on practical applications

Synoptic evolution of midwestern U.S. extreme dew point events

Eight Midwestern extremely high dew point events were examined with respect to their synoptic characteristics and evolution. Individual and composite analyses of events suggest that there exists three predominant features associated with extreme dew point events. In nearly all cases, the evolution of the synoptic environment includes the development and propagation of low pressure from the high plains through the upper Great Lakes. The low pressure increases and backs the surface winds acting to advect low-level moisture from eastern Nebraska, Iowa, Missouri eastward into Illinois and Indiana. The progression of the low pressure and attendant frontal boundaries also acts to modulate the length of the extreme low-level dew point event. Healthy crops and sufficient soil moisture content throughout this large agricultural region were also evident during the periods of extreme low-level moisture. Finally, the vertical thermal profile of the atmosphere during extreme dew point events supports previous findings and highlights the importance of restricted low-level mixing as instrumental in allowing near-surface moisture to become trapped and increased

Climatology of cloud-to-ground lightning in Georgia, USA, 1992-2003

A 12-year climatology of lightning cloud-to-ground flash activity for Georgia revealed the existence of three primary regions of high lightning activity: the area surrounding the Atlanta Metropolitan Statistical Area, east-central Georgia along the fall line, and along the Atlantic coast. Over 8.2 million ground flashes were identified during the climatology. July was the most active lightning month and December was the least active. Annual, seasonal, and diurnal distributions of cloud-to-ground flashes were also examined. These patterns illustrated the interacting effects of land cover, topography, and convective instability in enhancing lightning activity throughout Georgia. A synoptic analysis of the ten highest lightning days during the summer and winter revealed the importance of frontal boundaries in organizing convection and high lightning activity during both seasons. The prominence of convective instability during the summer and strong dynamical forcing in the winter was also found to lead to outbreaks of high lightning activity

Climatological Radar Delineation of Urban Convection for Atlanta, Georgia

The distribution of warm season (June through August) thunderstorm activity surrounding Atlanta, Georgia from 1997 to 2006 was determined utilizing composite reflectivity data obtained from the network of National Weather Service radars. The radar data, at 2 km and 5 min spatial and temporal resolutions, allows for high resolution analyses of urban convective trends when grid averaged over a 10-year period. Maxima of medium- to high-reflectivity episodes were identified to the north of and within downtown Atlanta and immediately east of the primary urban expansion of the central business district (CBD). Additional enhanced, high-reflectivity areas are found in southern Fulton and Clayton counties, located south of downtown Atlanta. These regions are also collocated with high-density urban expansion south of the Atlanta CBD. The research presented is the most comprehensive spatial and temporal analysis of grid averaged composite reflectivity data for urban convection conducted to date

Nonmeteorological Influences on Severe Thunderstorm Warning Issuance: A Geographically Weighted Regression-Based Analysis of County Warning Area Boundaries, Land Cover, and Demographic Variables

Studies have shown that the spatial distribution of severe thunderstorm warnings demonstrates variation beyond what can be attributed to weather and climate alone. Investigating spatial patterns of these variations can provide insight into nonmeteorological factors that might lead forecasters to issue warnings. Geographically weighted regression was performed on a set of demographic and land cover descriptors to ascertain their relationships with National Weather Service (NWS) severe thunderstorm warning polygons issued by 36 NWS forecast offices in the central and southeastern United States from 2008 to 2015. County warning area (CWA) boundaries and cities were predominant sources of variability in warning counts. Global explained variance in verified and unverified severe thunderstorm warnings ranged from 67% to 81% for population, median income, and percent imperviousness across the study area, which supports the spatial influence of these variables on warning issuance. Local regression coefficients indicated that verified and unverified warning counts increased disproportionately in larger cities relative to the global trend, particularly for NWS weather forecast office locations. However, local explained variance tended to be lower in cities, possibly due to greater complexity of social and economic factors shaping warning issuance. Impacts of thunderstorm type and anthropogenic modification of existing storms should also be considered when interpreting the results of this study

Connectivity in coastal systems: Barrier island vegetation influences upland migration in a changing climate

Due to their position at the land–sea interface, barrier islands are vulnerable to both oceanic and atmospheric climate change-related drivers. In response to relative sea-level rise, barrier islands tend to migrate landward via overwash processes which deposit sediment onto the backbarrier marsh, thus maintaining elevation above sea level. In this paper, we assess the importance of interior upland vegetation and sediment transport (from upland to marsh) on the movement of the marsh–upland boundary in a transgressive barrier system along the mid-Atlantic Coast. We hypothesize that recent woody expansion is altering the rate of marsh to upland conversion. Using Landsat imagery over a 32 year time period (1984–2016), we quantify transitions between land cover (bare, grassland, woody vegetation, and marsh) and the marsh–upland boundary. We find that the Virginia Barrier Islands have both gains and losses in backbarrier marsh and upland, with 19% net loss from the system during the timeframe of the study and increased variance in marsh to upland conversion. This is consistent with recent work indicating a shift toward increasing rates of landward barrier island migration. Despite a net loss of upland area, macroclimatic winter warming resulted in 41% increase in woody vegetation in protected, low-elevation areas, introducing new ecological scenarios that increase resistance to sediment movement from upland to marsh. Our analysis demonstrates how the interplay between elevation and interior island vegetative cover influences landward migration of the boundary between upland and marsh (a previously underappreciated indicator that an island is migrating), and thus, the importance of including ecological processes in the island interior into coastal modeling of barrier island migration and sediment movement across the barrier landscape

Considering river structure and stability in the light of evolution: Feedbacks between riparian vegetation and hydrogeomorphology

River ecological functioning can be conceptualized according to a four-dimensional framework, based on the responses of aquatic and riparian communities to hydrogeomorphic constraints along the longitudinal, transverse, vertical and temporal dimensions of rivers. Contemporary riparian vegetation responds to river dynamics at ecological timescales, but riparian vegetation, in one form or another, has existed on Earth since at least the Middle Ordovician (c. 450 Ma) and has been a significant controlling factor on river geomorphology since the late Silurian (c. 420 Ma). On such evolutionary timescales, plant adaptations to the fluvial environment and the subsequent effects of these adaptations on aspects of fluvial sediment and landform dynamics resulted in the emergence, from the Silurian to the Carboniferous, of a variety of contrasted fluvial biogeomorphic types where water flow, morphodynamics and vegetation interacted to different degrees. Here we identify several of these types and describe the consequences for biogeomorphic structure and stability (i.e. resistance and resilience), along the four river dimensions, of feedbacks between riparian plants and hydrogeomorphic processes on contrasting ecological and evolutionary timescales.This is the author's accepted manuscript and will be under embargo until the 18th of September 2015. The final version is available from Wiley at onlinelibrary.wiley.com/doi/10.1002/esp.3643/abstrac

Perspectives on synoptic climate classification and its role in interdisciplinary research

Synoptic climatology has a long history of research where weather data are aggregated and composited to gain a better understanding of atmospheric effects on non-atmospheric variables. This has resulted in an applied scientific discipline that yields methods and tools designed for applications across disciplinary boundaries. The spatial synoptic classification (SSC) is an example of such a tool that helps researcher bridge methodological gaps between disciplines, especially those studying weather effects on human health. The SSC has been applied in several multi-discipline projects, and it appears that there is ample opportunity for growth into new topical areas. Likewise, there is opportunity for the SSC network to be expanded across the globe, especially into mid-latitude locations in the southern hemisphere. There is some question of the utility of the SSC in tropical locations, but such decisions must be based on the actual weather data from individual locations. Despite all of the strengths and potential uses of the SSC, there are some research problems, some locations, and some datasets for which it is not suitable. Nevertheless, the success of the SSC as a cross-disciplinary method is noteworthy because it has become a catalyst for collaboration

Setting the agenda for social science research on the human microbiome

The human microbiome is an important emergent area of cross, multi and transdisciplinary study. The complexity of this topic leads to conflicting narratives and regulatory challenges. It raises questions about the benefits of its commercialisation and drives debates about alternative models for engaging with its publics, patients and other potential beneficiaries. The social sciences and the humanities have begun to explore the microbiome as an object of empirical study and as an opportunity for theoretical innovation. They can play an important role in facilitating the development of research that is socially relevant, that incorporates cultural norms and expectations around microbes and that investigates how social and biological lives intersect. This is a propitious moment to establish lines of collaboration in the study of the microbiome that incorporate the concerns and capabilities of the social sciences and the humanities together with those of the natural sciences and relevant stakeholders outside academia. This paper presents an agenda for the engagement of the social sciences with microbiome research and its implications for public policy and social change. Our methods were informed by existing multidisciplinary science-policy agenda-setting exercises. We recruited 36 academics and stakeholders and asked them to produce a list of important questions about the microbiome that were in need of further social science research. We refined this initial list into an agenda of 32 questions and organised them into eight themes that both complement and extend existing research trajectories. This agenda was further developed through a structured workshop where 21 of our participants refined the agenda and reflected on the challenges and the limitations of the exercise itself. The agenda identifies the need for research that addresses the implications of the human microbiome for human health, public health, public and private sector research and notions of self and identity. It also suggests new lines of research sensitive to the complexity and heterogeneity of human–microbiome relations, and how these intersect with questions of environmental governance, social and spatial inequality and public engagement with science