Showing 1231 - 1240 of 5831 Items
Complete mitochondrial genomes of the human follicle mites Demodex brevis and D. folliculorum: Novel gene arrangement, truncated tRNA genes, and ancient divergence between species
Date: 2014-12-16
Creator: Michael F. Palopoli, Samuel Minot, Dorothy Pei, Alicia Satterly, Julie, Endrizzi
Access: Open access
- Background: Follicle mites of the genus Demodex are found on a wide diversity of mammals, including humans. surprisingly little is known, however, about the evolution of this association. Additional sequence information promises to facilitate studies of Demodex variation within and between host species. Here we report the complete mitochondrial genome sequences of two species of Demodex known to live on humans-Demodex brevis and D. folliculorum-which are the first such genomes available for any member of the genus. We analyzed these sequences to gain insight into the evolution of mitochondrial genomes within the Acariformes. We also used relaxed molecular clock analyses, based on alignments of mitochondrial proteins, to estimate the time of divergence between these two species. Results: Both Demodex genomes shared a novel gene order that differs substantially from the ancestral chelicerate pattern, with transfer RNA (tRNA) genes apparently having moved much more often than other genes. Mitochondrial tRNA genes of both species were unusually short, with most of them unable to encode tRNAs that could fold into the canonical cloverleaf structure. indeed, several examples lacked both D- and T-arms. Finally, the high level of sequence divergence observed between these species suggests that these two lineages last shared a common ancestor no more recently than about 87 mya. Conclusions: Among Acariformes, rearrangements involving tRNA genes tend to occur much more often than those involving other genes. The truncated tRNA genes observed in both Demodex species would seem to require the evolution of extensive tRNA editing capabilities and/or coevolved interacting factors. The molecular machinery necessary for these unusual tRNAs to function might provide an avenue for developing treatments of skin disorders caused by Demodex. The deep divergence time estimated between these two species sets a lower bound on the time that Demodex have been coevolving with their mammalian hosts, and supports the hypothesis that there was an early split within the genus Demodex into species that dwell in different skin microhabitats.
An Assessment of pH and the Effects of Ocean Acidification in a Phippsburg, ME Clam Flat
Date: 2014-08-01
Creator: Lloyd Anderson
Access: Open access
- Increased atmospheric CO2 due to the combustion of fossil fuels and subsequent oceanic uptake has led to a phenomenon known as ocean acidification: CO2 gas dissolved in the ocean lowers surface ocean pH and acidifies ocean waters, a process which has raised global concern. The purpose of my research was to investigate why a particular clam flat in Phippsburg, ME is not as productive as it used to be. This clam flat, located on “The Branch” in Phippsburg adjacent to Head Beach, has decreased to approximately a sixth of its former productivity in just over a decade. A possible explanation for this drop in clam bed productivity is acidification. I worked in a partnership with Bailey Moritz ’16, with the goal to measure indicators of ocean acidification in the clam flat and see if there was a difference in those indicators between productive and unproductive areas of the flat. Bailey’s focus was alkalinity, a quantification of the buffering capacity of seawater, where my specific research focus was on the effective collection of pH measurements. We were ultimately able to combine our alkalinity and pH measurements to calculate saturation state, an indicator of the susceptibility of clam shells to dissolution. I measured pH, a direct indicator of water acidity, from the top centimeter of the mudflat, the region where clam spat (juvenile clams) are seeded. The first few weeks of my fellowship time I spent researching the most accurate and precise way to measure pH in the field, and ultimately decided to measure pH on site using glass electrode probes. Sites 1 and 2 were located in a productive region of the flat, sites 4 and 5 were located in an unproductive region, and site 3 was located on the boundary between the two zones. Average pH values within the clam flat ranged from 6.9-7.5, and there was no significant difference in pH between productive and unproductive sites across the flat (Figure 1). The wide variations in pH across this clam flat could potentially be attributed to daily shifts in temperature, freshwater input, and biological productivity in the sediments. Low average pH values seen across all sites contribute to a low saturation state across the flat: our average calculated saturation state was 0.47, lower than similar data measured by Green et al. on a clam flat in South Portland in 2013, where average saturation state was 0.9. Our data indicate that the soft-shell clams at the productive sites in this particular Phippsburg clam flat are managing to survive in undersaturated (saturation state < 1) conditions. Since saturation state was low across both productive and unproductive sites, ocean acidification seems not to be the cause for the clams’ decline. However, other factors such as dissolved oxygen or sediment type may have combined with low saturation states to create a difference in productivity across the flat. In further research I would be interested to see how average pH at these same sites varies over a year-long period, which would give a better representation of the environment that the soft-shell clams are exposed to through yearly cycles. Final Report of research funded by the Rusack Coastal Studies Fellowship.
GIS analysis of historical cod fisheries in the Gulf of Maine
Date: 2014-08-01
Creator: Nora Hefner
Access: Open access
- Gulf of Maine cod fisheries, once essential to Maine’s economy and culture, are currently in a state of collapse. Following a long decline throughout the 1800s and two collapses in the 1900s – one in the middle of the century and one in the 1990s, cod populations along the coast exist now as small fractions of their former bounty. Though the connection was largely forgotten in the twentieth century, fishermen in the nineteenth century attributed the decline of the cod fishery to the loss of alewives, an anadromous river herring upon which cod prey. Alewives have been cut off from their spawning and nursery habitat along much of the Gulf of Maine due to the damming of rivers that empty into the Gulf. My research is a part of an ongoing study that aims to establish the historical relationship between cod and other gadoid groundfish fisheries, their ecosystems, and anadromous alewives using spatial data from geographic information systems (GIS). GIS maps were created with the positions of 466 historical Gulf of Maine cod fishing grounds, identified using a database developed by fisheries scientist Ted Ames (whose work is largely responsible for fisheries scientists’ renewed interest in the groundfish-alewife connection). The spatial database generated from these data will be analyzed using a logistical regression to identify characteristics of fishing grounds that define them as fishing grounds, as well as characteristics that determine the relative quality of individual fishing grounds. The Ames database contains data in two main categories: biophysical (ecosystem characteristics) and socioeconomic (infrastructure). The focus of my research was on generating two specific data sets from historical literature, government reports, and experts in the field, and on mapping that data using GIS software (see Figure 1). The first was a list of rivers that supported annual alewife runs before the mid-twentieth century cod groundfish fishery collapse. Using GIS software, I mapped the locations at which these rivers enter the ocean, creating spatial data that show the point at which cod in the Gulf and alewives in the rivers would meet. The second data set was a list of ports and harbors that supported the groundfish industry, also before the mid-twentieth century collapse. These locations were mapped as the areas from which fishing boats would set out in pursuit of groundfish, again creating a set of spatial data points. Both of these data sets were added to the existing spatial database. My data and Ames’ data will be used to calculate distances between individual groundfish fishing grounds and historic alewife runs and between fishing grounds and ports and harbors. Statistical analyses will determine both whether those two factors have any significant relationship with fishing ground quality and the nature of their effects, if any. Ultimately, the results of these analyses will contribute to an increasingly detailed picture of the Gulf of Maine as it existed – physically, ecologically, and economically – when it still supported astoundingly large populations of cod and other groundfish. With a better idea of what the system looked like when it worked properly, we can make a more informed and focused attempt to rebuild it. This research provided me with opportunities to develop practical skills like use of GIS software, contacting and collaborating with scientists, researchers, and government agencies in my field, and data management. I also gained a greater understanding of and appreciation for the complexity and challenge of trying to bring research from the science level to management policy and action. Final Report of research funded by the Cooke Environmental Research Fellowship
Bio-optical discrimination of diatoms from other phytoplankton in the surface ocean: Evaluation and refinement of a model for the Northwest Atlantic
Date: 2018-11-01
Creator: Sasha J. Kramer, Collin S. Roesler, Heidi M. Sosik
Access: Open access
- Diatoms dominate global silica production and export production in the ocean; they form the base of productive food webs and fisheries. Thus, a remote sensing algorithm to identify diatoms has great potential to describe ecological and biogeochemical trends and fluctuations in the surface ocean. Despite the importance of detecting diatoms from remote sensing and the demand for reliable methods of diatom identification, there has not been a systematic evaluation of algorithms that are being applied to this end. The efficacy of these models remains difficult to constrain in part due to limited datasets for validation. In this study, we test a bio-optical algorithm developed by Sathyendranath et al. (2004) to identify diatom dominance from the relationship between ratios of remote sensing reflectance and chlorophyll concentration. We evaluate and refine the original model with data collected at the Martha's Vineyard Coastal Observatory (MVCO), a near-shore location on the New England shelf. We then validated the refined model with data collected in Harpswell Sound, Maine, a site with greater optical complexity than MVCO. At both sites, despite relatively large changes in diatom fraction (0.8–82% of chlorophyll concentration), the magnitude of variability in optical properties due to the dominance or non-dominance of diatoms is less than the variability induced by other absorbing and scattering constituents of the water. While the original model performance was improved through successive re-parameterizations and re-formulations of the absorption and backscattering coefficients, we show that even a model originally parameterized for the Northwest Atlantic and re-parameterized for sites such as MVCO and Harpswell Sound performs poorly in discriminating diatom-dominance from optical properties.
Natural and experimental evolution of sexual conflict within Caenorhabditis nematodes
Date: 2015-05-22
Creator: Michael F. Palopoli, Colin Peden, Caitlin Woo, Ken Akiha, Megan, Ary, Lori Cruze, Jennifer L. Anderson, Patrick C. Phillips
Access: Open access
- Background: Although males and females need one another in order to reproduce, they often have different reproductive interests, which can lead to conflict between the sexes. The intensity and frequency of male-male competition for fertilization opportunities is thought to be an important contributor to this conflict. The nematode genus Caenorhabditis provides an opportunity to test this hypothesis because the frequency of males varies widely among species with different mating systems. Results: We find evidence that there is strong inter- and intra-sexual conflict within C. remanei, a dioecious species composed of equal frequencies of males and females. In particular, some C. remanei males greatly reduce female lifespan following mating, and their sperm have a strong competitive advantage over the sperm of other males. In contrast, our results suggest that both types of conflict have been greatly reduced within C. elegans, which is an androdioecious species that is composed of self-fertilizing hermaphrodites and rare males. Using experimental evolution in mutant C. elegans populations in which sperm production is blocked in hermaphrodites (effectively converting them to females), we find that the consequences of sexual conflict observed within C. remanei evolve rapidly within C. elegans populations experiencing high levels of male-male competition. Conclusions: Together, these complementary data sets support the hypothesis that the intensity of intersexual conflict varies with the intensity of competition among males, and that male-induced collateral damage to mates can evolve very rapidly within populations.
Post-coring entrapment of modern air in some shallow ice cores collected near the firn-ice transition: Evidence from CFC-12 measurements in Antarctic firn air and ice cores
Date: 2010-06-18
Creator: M. Aydin, S. A. Montzka, M. O. Battle, M. B. Williams, W. J., De Bruyn, J. H. Butler, K. R. Verhulst, C. Tatum, B. K. Gun, D. A. Plotkin, B. D. Hall, E. S. Saltzman
Access: Open access
- In this study, we report measurements of CFC-12 (CCl2F2) in firn air and in air extracted from shallow ice cores from three Antarctic sites. The firn air data are consistent with the known atmospheric history of CFC-12. In contrast, some of the ice core samples collected near the firn-ice transition exhibit anomalously high CFC-12 levels. Together, the ice core and firn air data provide evidence for the presence of modern air entrapped in the shallow ice core samples that likely contained open pores at the time of collection. We propose that this is due to closure of the open pores after drilling, entrapping modern air and resulting in elevated CFC-12 mixing ratios. Our results reveal that open porosity can exist below the maximum depth at which firn air samples can be collected, particularly at sites with lower accumulation rates. CFC-12 measurements demonstrate that post-drilling closure of open pores can lead to a change in the composition of bubble air in shallow ice cores through purely physical processes. The results have implications for investigations involving trace gas composition of bubbles in shallow ice cores collected near the firn-ice transition. © Author(s) 2010.
JUST A BIG MISUNDERSTANDING? BIAS AND BAYESIAN AFFECTIVE POLARIZATION
Date: 2020-02-01
Creator: Daniel F. Stone
Access: Open access
- I present a model of affective polarization—growth in hostility over time between two parties—via quasi-Bayesian inference. In the model, two agents repeatedly choose actions. Each choice is based on a balance of concerns for private interests and the social good. More weight is put on private interests when an agent's character is intrinsically more self-serving and when the other agent is believed to be more self-serving. Each agent Bayesian updates about the other's character, and dislikes the other more when she is perceived as more self-serving. I characterize the effects on growth in dislike of three biases: a prior bias against the other agent's character, the false consensus bias, and limited strategic thinking. Prior bias against the other's character remains constant or declines over time, and actions do not diverge. The other two biases cause actions to become more extreme over time and repeatedly be “worse” than expected, causing mutual growth in dislike, that is, affective polarization. The magnitude of dislike can become arbitrarily large—even when both players are arbitrarily “good” (unselfish). The results imply that seemingly irrelevant cognitive biases can be an important cause of the devolution of relationships, in politics and beyond, and that subtlety and unawareness of bias can be key factors driving the degree of polarization.
Homotypic and heterotypic continuity of fine-grained temperament during infancy, toddlerhood, and early childhood
Date: 2008-07-01
Creator: Samuel P. Putnam, Mary K. Rothbart, Maria A. Gartstein
Access: Open access
- Longitudinal continuity was investigated for fine-grained and factor-level aspects of temperament measured with the Infant Behaviour Questionnaire-Revised (IBQ-R), Early Childhood Behaviour Questionnaire (ECBQ), and Children's Behaviour Questionnaire (CBQ). Considerable homotypic continuity was found. Convergent and discriminant validity of the measures was supported, as all fine-grained dimensions exhibited stability across adjacent measurement periods, and all scales found on both the ECBQ and CBQ were most highly correlated with their equivalent scales. At the factor level, Surgency and Negative Affect factors were stable across all time points, and Effortful Control/Regulatory Capacity was stable across adjacent time periods. High-Intensity Pleasure, Activity Level, and Impulsivity contributed strongly to continuity of Surgency, and Sadness, Frustration, and Falling Reactivity played strong roles in the continuity of Negative Affect. Heterotypic continuity was also found. High levels of Infant Surgency predicted high toddler Effortful Control, whereas high toddler Surgency predicted low Effortful Control in preschoolers. Infant Surgency dimensions especially predicted Toddler Attention Shifting and Low-Intensity Pleasure, and toddler Activity Level was most closely associated with later deficits in Effortful Control. Inverse relations were also obtained between Negative Affect and Effortful Control, with substantial negative connections between toddler Negative Affect and preschool Attention Focusing and Inhibitory Control. Copyright © 2008 John Wiley & Sons, Ltd.
Wave transmission in time- and space-variant helicoidal phononic crystals
Date: 2014-11-04
Creator: F. Li, C. Chong, J. Yang, P. G. Kevrekidis, C., Daraio
Access: Open access
- We present a dynamically tunable mechanism of wave transmission in one-dimensional helicoidal phononic crystals in a shape similar to DNA structures. These helicoidal architectures allow slanted nonlinear contact among cylindrical constituents, and the relative torsional movements can dynamically tune the contact stiffness between neighboring cylinders. This results in cross-talking between in-plane torsional and out-of-plane longitudinal waves. We numerically demonstrate their versatile wave mixing and controllable dispersion behavior in both wavenumber and frequency domains. Based on this principle, a suggestion toward an acoustic configuration bearing parallels to a transistor is further proposed, in which longitudinal waves can be switched on and off through torsional waves.