Showing 4061 - 4070 of 5713 Items
Efficient and rapid identification of Candida albicans allelic status using SNP-RFLP
Date: 2009-11-01
Creator: Anja Forche, Musetta Steinbach, Judith Berman
Access: Open access
- Candida albicans is the most prevalent opportunistic fungal pathogen in the clinical setting, causing a wide spectrum of diseases ranging from superficial mucosal lesions to life-threatening deep-tissue infections. Recent studies provide strong evidence that C. albicans possesses an arsenal of genetic mechanisms promoting genome plasticity and that it uses these mechanisms under conditions of nutritional or antifungal drug stress. Two microarray-based methods, single nucleotide polymorphism (SNP) and comparative genome hybridization arrays, have been developed to study genome changes in C. albicans. However, array technologies can be relatively expensive and are not available to every laboratory. In addition, they often generate more data than needed to analyze specific genomic loci or regions. Here, we have developed a set of SNP-restriction fragment length polymorphism (RFLP) (or PCR-RFLP) markers, two per chromosome arm, for C. albicans. These markers can be used to rapidly and accurately detect large-scale changes in the C. albicans genome including loss of heterozygosity (LOH) at single loci, across chromosome arms or across whole chromosomes. Furthermore, skewed SNP-RFLP allelic ratios are indicative of trisomy at heterozygous loci. While less comprehensive than array-based approaches, we propose SNP-RFLP as an inexpensive, rapid, and reliable method to screen strains of interest for possible genome changes. © 2009 Federation of European Microbiological Societies.
Cell Adhesion in Arabidopsis thaliana Access to this record is restricted to members of the Bowdoin community. Log in here to view.
Date: 2019-05-01
Creator: Natasha Ann Belsky
Access: Access restricted to the Bowdoin Community
Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss
Date: 2006-12-19
Creator: William R. Jackman, David W. Stock
Access: Open access
- It has been considered a "law" that a lost structure cannot reappear in evolution. The common explanation, that genes required for the development of the lost structure degrade by mutation, remains largely theoretical, however. Additionally, the extent to which this mechanism applies to systems of repeated parts, where individual modules are likely to exhibit few unique aspects of genetic control, is unclear. We investigated reversibility of evolution in one such system, the vertebrate dentition, using as a model loss of oral teeth in cypriniform fishes, which include the zebra fish. This evolutionary event, which occurred >50 million years ago, has not been reversed despite subsequent diversification of feeding modes and retention of pharyngeal teeth. We asked whether the cis-regulatory region of a gene whose expression loss parallels cypriniform tooth loss, Dlx2b, retains the capacity for expression in oral teeth. We first created a zebrafish reporter transgenic line that recapitulates endogenous dlx2b expression. We then showed that this zebrafish construct drives reporter expression in oral teeth of the related characiform Astyanax mexicanus. This result, along with our finding that Dlx genes are required for normal tooth development, suggests that changes in trans-acting regulators of these genes were responsible for loss of cypriniform oral teeth. Preservation of oral enhancer function unused for >50 million years could be the result of pleiotropic function in the pharyngeal dentition. If enhancers of other genes in the tooth developmental pathway are similarly preserved, teeth lost from specific regions may be relatively easy to reacquire in evolution. © 2006 by The National Academy of Sciences of the USA.
Effects of Alkalinity and Ocean Acidification on Clam Shell Development in Phippsburg, ME
Date: 2014-08-01
Creator: Bailey Moritz
Access: Open access
- With increased CO2 in the atmosphere from the burning of fossil fuels, more is absorbed into the surface ocean, causing a reaction that leads to lower pH. This process is known as ocean acidification, which has raised global concern. Over the past decade, the clam flat near Head Beach in Phippsburg has been reduced to approximately a sixth of its former productive area. The town of Phippsburg allots money every spring to seed the clam flat with juvenile soft-shell clams (Mya arenaria) in order to support the local clamming economy, but the clams are no longer growing in much of the mud flat. A possible explanation for this loss is acidification. In order to understand if ocean acidification is the cause, I collected water samples from the mud to test for alkalinity along a transect of 5 sites spanning productive and non-productive areas of the flat. Alkalinity is a measurement of the waters ability to buffer pH changes. Lower alkalinity could mean that clams would have more difficulty forming their calcium carbonate shells due to dissolution in low pH waters. Combined with the pH measurements gathered by my peer, Lloyd Anderson ‘16, we were able to calculate aragonite saturation state. Water with a saturation state below 1 is capable of dissolving calcium carbonate (aragonite) shells. A large portion of this research project was figuring out the best methodology to use for collecting data on the clam flat. The tested water needs to represent that which the clams are actually using while they are embedded in the mud. Additionally, juvenile clams only live in the upper centimeter or so of sediment. We followed methodologies used in past studies in Maine (Green et al 2013). Three pore water samples from each site were extracted and brought back to the lab to be filtered on 7 separate days throughout July. We began sampling 2 hours prior to low tide. I determined alkalinity using an automated titration system. Average alkalinity ranged from 2200-2500 μeq/kg. The results indicated that there was not a significant difference or pattern in alkalinity or saturation state between productive and unproductive areas of the clam flat (Fig. 1). Error bars in the figure represent variability at each site over the entire study period, while analytical reproducibility was ± 9.04 μeq/L. Large changes were observed merely from one day to another. Coastal ecosystems are complex and variations such as time of day, temperature, or productivity may have influences on the porewater characteristics (Duarte 2013). While ocean acidification does not appear to be the primary driving force behind the clams’ decline at this location, the saturation state was consistently quite low ( Final Report of research funded by the Rusack Coastal Studies Fellowship.
Salton Collection : Renaissance & Baroque Medals & Plaquettes (1969 Revision)
Date: 1969-01-01
Access: Open access
- "The present collection ... belongs to Mr. and Mrs. Mark Salton of New York." "One thousand five hundred copies of this catalogue have been printed ... Composition by the Anthosensen Press, Portland, Maine. Photography by John McKee. Design by Leonard Baskin. October MCMLXV"--Colophon This is a revised edition of the 1965 original publication.
Investigating the Effects of Climatic Change and Fire Dynamics on Peatland Carbon Accumulation in Coastal Labrador, Canada
Date: 2014-08-01
Creator: Anna Hall
Access: Open access
- High-latitude peatlands store a large stock of carbon in accumulated belowground biomass, estimated at 500 ± 100 Gt C (Yu 2012). For comparison, the atmospheric C pool is estimated at about 775 Gt (IPCC 2007) making the peatland carbon pool a potentially significant player in the global carbon cycle. Peatland carbon storage is controlled by a balance between plant productivity and decomposition, with plant matter produced during the summer months accumulating from year to year rather than fully decomposing. Peatlands are sensitive to changes in climatic regime and have the potential to shift from a net sink of atmospheric C to a net source of C with future disturbance by climate warming (Yu 2012).There are two major predictions as to how climate change could affect peatland C accumulation. Warmer temperatures could cause faster decomposition of plant biomass and lead to C release to the atmosphere and a positive feedback effect on climate change (Schuur et al. 2008). If this is the case, current warming trends suggest that peatlands could release up to 100 Gt C to the atmosphere by the year 2100 (Davidson and Janssens 2006). Alternatively, warmer summer temperatures and a longer growing season could lead to faster peat production and therefore CO2 drawdown from the atmosphere, somewhat mitigating the effects of climate change (Schuur et al. 2008). A detailed study of past C accumulation rates over a known historical warm period gives insight into how peatlands may respond to future climate warming. This project focuses on C accumulation in peatlands in Labrador, Canada, over the past 8,000 years. Because Canadian peatlands store approximately 150 Gt C, approximately 1/3 of the global peatland carbon pool, it is important to understand how the dynamics of these peatlands could be affected by present and future climate warming (Tarnocai 2006). However, the majority of research has focused on central Canada, leaving significant knowledge gaps surrounding coastal Eastern Canada (vanBellen et al. 2012). Particular emphasis in this study was given to the Holocene Thermal Maximum (HTM) which occurred from 4-6 thousand years ago in Labrador, when summer temperatures were 0.5 – 1°C warmer than at present (Kerwin et al. 2004). This study also attempts to determine the effect of fires on rates of C storage in these peatlands. Lightning-ignited peat fires have the potential to consume stored biomass and release significant CO2 to the atmosphere (Tarnocai 2006). Six peat cores (out of a total of 14 collected in Labrador in 2013) were used for this study. Throughout the following year, calibrated radiocarbon dates, bulk density, and percent carbon were used to calculate carbon accumulation rates. This summer, areal charcoal concentration (a measure of macroscopic charcoal used as a proxy for fire severity) was used to determine the influence of fires in this region. From 8,000 years ago to the present, rates of C accumulation averaged 23.1 ± 6.7 gC m-2 yr-1. Accumulation rates were highest during the HTM, averaging 29.6 ± 2.4 g C m-2 yr-1. Samples containing macroscopic charcoal had an average concentration of 0.62 mm2 cm-3 with a maximum concentration found of 3.51 mm2 cm-3. These consistently low charcoal concentrations indicate that fire was neither common nor severe in Labrador peatlands. While Kuhry (1994) and Payette et al. (2012) found that fires in Canada occurred twice as frequently during the HTM than at present, no trends in fire severity were found in these cores, and there was no evidence that fires had a significant influence on C accumulation. Therefore, the C accumulation trend we see in Labrador is not controlled by fire and is likely either a direct result of temperature variation or of vegetational and hydrological shifts caused by changes in climate. This work supports a growing body of evidence from high latitude peatlands suggesting that future warming conditions could lead to increased soil C sequestration. Final Report of research funded by the Freedman Coastal Studies Fellowship.
Time-Periodic Solutions of Driven-Damped Trimer Granular Crystals
Date: 2015-01-01
Creator: E. G. Charalampidis, F. Li, C. Chong, J. Yang, P. G., Kevrekidis
Access: Open access
- We consider time-periodic structures of granular crystals consisting of alternate chrome steel (S) and tungsten carbide (W) spherical particles where each unit cell follows the pattern of a 2: 1 trimer: S-W-S. The configuration at the left boundary is driven by a harmonic in-time actuation with given amplitude and frequency while the right one is a fixed wall. Similar to the case of a dimer chain, the combination of dissipation, driving of the boundary, and intrinsic nonlinearity leads to complex dynamics. For fixed driving frequencies in each of the spectral gaps, we find that the nonlinear surface modes and the states dictated by the linear drive collide in a saddle-node bifurcation as the driving amplitude is increased, beyond which the dynamics of the system becomes chaotic. While the bifurcation structure is similar for solutions within the first and second gap, those in the first gap appear to be less robust. We also conduct a continuation in driving frequency, where it is apparent that the nonlinearity of the system results in a complex bifurcation diagram, involving an intricate set of loops of branches, especially within the spectral gap. The theoretical findings are qualitatively corroborated by the experimental full-field visualization of the time-periodic structures.
Recent increases in global HFC-23 emissions
Date: 2010-01-01
Creator: S. A. Montzka, L. Kuijpers, M. O. Battle, M. Aydin, K. R., Verhulst, E. S. Saltzman, D. W. Fahey
Access: Open access
- Firn-air and ambient air measurements of CHF3 (HFC- 23) from three excursions to Antarctica between 2001 and 2009 are used to construct a consistent Southern Hemisphere (SH) atmospheric history. The results show atmospheric mixing ratios of HFC-23 continuing to increase through 2008. Mean global emissions derived from this data for 2006-2008 are 13.5 ± 2 Gg/yr (200 ± 30 × 1012gCO2- equivalent/yr, or MtCO2-eq./yr), ∼50% higher than the 8.7 ± 1 Gg/yr (130 ± 15 MtCO2-eq./yr) derived for the 1990s. HFC-23 emissions arise primarily from over-fluorination of chloroform during HCFC-22 production. The recent global emission increases are attributed to rapidly increasing HCFC-22 production in developing countries since reported HFC-23 emissions from developed countries decreased over this period. The emissions inferred here for developing countries during 2006-2008 averaged 11 ± 2 Gg/yr HFC-23 (160 ± 30 MtCO2-eq./yr) and are larger than the ∼6 Gg/yr of HFC-23 destroyed in United Nations Framework Convention on Climate Change Clean Development Mechanism projects during 2007 and 2008. © Copyright 2010 by the American Geophysical Union.
Institutions and democratic invention in 19th-century America: Evidence from "great inventors," 1790-1930
Date: 2004-05-01
Creator: B. Zorina Khan, Kenneth L. Sokoloff
Access: Open access