Browsing by Subject "Temperature"
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Item Open Access A Quantitative Analysis of Growth and Size Regulation in Manduca sexta: The Physiological Basis of Variation in Size and Age at Metamorphosis.(PLoS One, 2015) Grunert, Laura W; Clarke, Jameson W; Ahuja, Chaarushi; Eswaran, Harish; Nijhout, H FrederikBody size and development time are important life history traits because they are often highly correlated with fitness. Although the developmental mechanisms that control growth have been well studied, the mechanisms that control how a species-characteristic body size is achieved remain poorly understood. In insects adult body size is determined by the number of larval molts, the size increment at each molt, and the mechanism that determines during which instar larval growth will stop. Adult insects do not grow, so the size at which a larva stops growing determines adult body size. Here we develop a quantitative understanding of the kinetics of growth throughout larval life of Manduca sexta, under different conditions of nutrition and temperature, and for genetic strains with different adult body sizes. We show that the generally accepted view that the size increment at each molt is constant (Dyar's Rule) is systematically violated: there is actually a progressive increase in the size increment from instar to instar that is independent of temperature. In addition, the mass-specific growth rate declines throughout the growth phase in a temperature-dependent manner. We show that growth within an instar follows a truncated Gompertz trajectory. The critical weight, which determines when in an instar a molt will occur, and the threshold size, which determines which instar is the last, are different in genetic strains with different adult body sizes. Under nutrient and temperature stress Manduca has a variable number of larval instars and we show that this is due to the fact that more molts at smaller increments are taken before threshold size is reached. We test whether the new insight into the kinetics of growth and size determination are sufficient to explain body size and development time through a mathematical model that incorporates our quantitative findings.Item Open Access A Time Series Regression Analysis of Future Climate(2012-04-23) Rudulph, JakeCurrent approaches to climate modeling, including environmental simulation, may not be able to generate actionable results for a few decades yet. Over the last 50 years, methods attempting to capture and predict states of the climate system have flourished and diversified. However, many such models are subject to errors and uncertainty arising from parameterization problems, the obligate characterization of poorly understood phenomena, and high capacity requirements stemming from the incredible computing power needed. As the window for meaningful actions towards altering the climate change trajectory closes, we should consider the use of simple methods that generally predict the conditions of the future climate. For my analysis, I developed a time-series regression analysis of land surface trends in precipitation and near-surface temperature. For each global 0.5º land surface grid, values for 1901-2009 baseline means were calculated, and 2050 values were predicted using time series regression models for each of four historical data subsets. Average predicted warming across the subsets range from 0.89 ºC to 5.8 ºC above the baseline, with high northern latitudes predicted to experience the most warming. Precipitation is predicted to follow the “wet getting wetter, dry getting dryer” paradigm, with average predicted changes across the subsets ranging from 3.2% to 26% above the baseline.Item Open Access Assessing the Injury Tolerance of the Human Spine(2017) Schmidt, Allison LindseyChronic and acute back injuries are widespread, affecting people in environments where they are exposed to vibration and repeated shock. These issues have been widely reported among personnel on aircraft and small watercraft; operators of heavy industrial or construction equipment may also experience morbidity associated with cyclic loading. To prevent these types of injuries, an improved understanding is needed of the spine’s tolerance to fatigue injury and of the factors that affect fatigue tolerance.
These types of vibration and shock exposures are addressed by international standards that propose limitations on the length and severity of the accelerations to which an individual is subjected. However, the current standard, ISO 2631-5:2004, provides an imprecise health hazard assessment. In this dissertation, a detailed technical critique is presented to examine the assumptions on which ISO 2631-5:2004 is based. An original analysis of existing data yields an age-based regression of the ultimate strength of lumbar spinal units and demonstrates sources of error in the strength regression in the standard. This dissertation also demonstrates that, contradicting earlier assumptions, the ultimate strength of the spine does not lie on a power-law S-N curve, and fatigue tolerance cannot be extrapolated from ultimate strength tests.
An alternative approach is presented for estimating the injury risk due to repeated loading. Drawing from existing data in the literature, a large dataset of in vitro fatigue tests of lumbar spinal segments was assembled. Using this fatigue data, a survival analysis approach was used to estimate the risk of failure based on several factors. Number of cycles, load amplitude, sex, and age all were significant predictors of bony failure in the spinal column. The parameter described by ISO 2631-5:2004 to quantify repeated loading exposure was modified, and an injury risk model was developed based on this modified parameter which relates risk of vertebral failure to repeated compressive loading. Notably, the effect of sex on fatigue tolerance persisted after normalizing by area, emphasizing the need for men and women to be addressed separately in the creation of injury risk predictions and occupational guidelines.
Posture has also been implicated in altering the injury mechanisms and tolerance to fatigue loading. However, few previous investigations in cyclic loading have addressed non-neutral postures. To assess the influence of dynamic flexion on the fatigue tolerance of the lumbar spine, a series of tests were conducted which combined a cyclic compressive force with a dynamic flexing motion. A study of 17 spinal segments from six young male cadavers was conducted, with tests ranging from 1000 to 500 000 cycles. Of the 17 specimens, 7 failed during testing. These failures were analyzed using a Cox Proportional Hazards model. As in compressive fatigue behavior, significant factors were the magnitude of the applied load and the age of the specimen. However, when the dynamically flexed specimens in these tests were compared to the specimens in the axial fatigue dataset, the flexion condition did not have a detectable effect on fatigue tolerance.
The Hybrid III dummy is a critical tool the assessment of such loading. Although the Hybrid III was originally designed for automotive frontal impact testing, these dummies have since been used to measure exposures and estimate injury risks of a wide variety of scenarios. These scenarios often involve using the dummy under non-standard temperatures or with little recovery interval between tests. Series of tests were conducted on the Hybrid III neck and lumbar components to assess the effects of rest duration intervals and a range of temperatures. Variations in rest duration intervals had little effect on the response of either component. However, both components were extremely sensitive to changes in temperature. For the 50th percentile male HIII neck, the stiffness fell by 18% between 25°C and 37.5°C; at 0°C, the stiffness more than doubled, increasing by 115%. Temperature variation had an even more pronounced effect on the HIII lumbar. Compared to room temperature, the lumbar stiffness at 37.5°C fell by 40%, and at 12.5°C, the stiffness more than doubled, increasing by 115%.
This dissertation has advanced the state of knowledge about the fatigue characteristics of the spine. An injury risk function has been developed that can serve as a tool for health hazard assessment in occupational standards. It has also contributed a fatigue dataset with dynamic flexion. This work will improve the scientific community’s ability to prevent repeated loading injuries. This dissertation has also demonstrated the immense sensitivity to temperature of the Hybrid III spinal components. This finding has major implications for the interpretation of previously published work using the Hybrid III, for the conduct of future research, and for future dummy design.
Item Open Access Boosting high-intensity focused ultrasound-induced anti-tumor immunity using a sparse-scan strategy that can more effectively promote dendritic cell maturation.(J Transl Med, 2010-01-27) Liu, Fang; Hu, Zhenlin; Qiu, Lei; Hui, Chun; Li, Chao; Zhong, Pei; Zhang, JunpingBACKGROUND: The conventional treatment protocol in high-intensity focused ultrasound (HIFU) therapy utilizes a dense-scan strategy to produce closely packed thermal lesions aiming at eradicating as much tumor mass as possible. However, this strategy is not most effective in terms of inducing a systemic anti-tumor immunity so that it cannot provide efficient micro-metastatic control and long-term tumor resistance. We have previously provided evidence that HIFU may enhance systemic anti-tumor immunity by in situ activation of dendritic cells (DCs) inside HIFU-treated tumor tissue. The present study was conducted to test the feasibility of a sparse-scan strategy to boost HIFU-induced anti-tumor immune response by more effectively promoting DC maturation. METHODS: An experimental HIFU system was set up to perform tumor ablation experiments in subcutaneous implanted MC-38 and B16 tumor with dense- or sparse-scan strategy to produce closely-packed or separated thermal lesions. DCs infiltration into HIFU-treated tumor tissues was detected by immunohistochemistry and flow cytometry. DCs maturation was evaluated by IL-12/IL-10 production and CD80/CD86 expression after co-culture with tumor cells treated with different HIFU. HIFU-induced anti-tumor immune response was evaluated by detecting growth-retarding effects on distant re-challenged tumor and tumor-specific IFN-gamma-secreting cells in HIFU-treated mice. RESULTS: HIFU exposure raised temperature up to 80 degrees centigrade at beam focus within 4 s in experimental tumors and led to formation of a well-defined thermal lesion. The infiltrated DCs were recruited to the periphery of lesion, where the peak temperature was only 55 degrees centigrade during HIFU exposure. Tumor cells heated to 55 degrees centigrade in 4-s HIFU exposure were more effective to stimulate co-cultured DCs to mature. Sparse-scan HIFU, which can reserve 55 degrees-heated tumor cells surrounding the separated lesions, elicited an enhanced anti-tumor immune response than dense-scan HIFU, while their suppressive effects on the treated primary tumor were maintained at the same level. Flow cytometry analysis showed that sparse-scan HIFU was more effective than dense-scan HIFU in enhancing DC infiltration into tumor tissues and promoting their maturation in situ. CONCLUSION: Optimizing scan strategy is a feasible way to boost HIFU-induced anti-tumor immunity by more effectively promoting DC maturation.Item Open Access Calibrating single-ended fiber-optic Raman spectra distributed temperature sensing data.(Sensors (Basel), 2011) Hausner, Mark B; Suárez, Francisco; Glander, Kenneth E; van de Giesen, Nick; Selker, John S; Tyler, Scott WHydrologic research is a very demanding application of fiber-optic distributed temperature sensing (DTS) in terms of precision, accuracy and calibration. The physics behind the most frequently used DTS instruments are considered as they apply to four calibration methods for single-ended DTS installations. The new methods presented are more accurate than the instrument-calibrated data, achieving accuracies on the order of tenths of a degree root mean square error (RMSE) and mean bias. Effects of localized non-uniformities that violate the assumptions of single-ended calibration data are explored and quantified. Experimental design considerations such as selection of integration times or selection of the length of the reference sections are discussed, and the impacts of these considerations on calibrated temperatures are explored in two case studies.Item Open Access Comparing the model-simulated global warming signal to observations using empirical estimates of unforced noise.(Sci Rep, 2015-04-21) ◦Brown, P.T., W. Li, E.C. Cordero, S.A. MaugetThe comparison of observed global mean surface air temperature (GMT) change to the mean change simulated by climate models has received much public and scientific attention. For a given global warming signal produced by a climate model ensemble, there exists an envelope of GMT values representing the range of possible unforced states of the climate system (the Envelope of Unforced Noise; EUN). Typically, the EUN is derived from climate models themselves, but climate models might not accurately simulate the correct characteristics of unforced GMT variability. Here, we simulate a new, empirical, EUN that is based on instrumental and reconstructed surface temperature records. We compare the forced GMT signal produced by climate models to observations while noting the range of GMT values provided by the empirical EUN. We find that the empirical EUN is wide enough so that the interdecadal variability in the rate of global warming over the 20(th) century does not necessarily require corresponding variability in the rate-of-increase of the forced signal. The empirical EUN also indicates that the reduced GMT warming over the past decade or so is still consistent with a middle emission scenario's forced signal, but is likely inconsistent with the steepest emission scenario's forced signal.Item Open Access Connecting differential responses of native and invasive riparian plants to climate change and environmental alteration.(Ecol Appl, 2015-04) Flanagan, Neal E; Richardson, Curtis J; Ho, MengchiClimate change is predicted to impact river systems in the southeastern United States through alterations of temperature, patterns of precipitation and hydrology. Future climate scenarios for the southeastern United States predict (1) surface water temperatures will warm in concert with air temperature, (2) storm flows will increase and base flows will decrease, and (3) the annual pattern of synchronization between hydroperiod and water temperature will be altered. These alterations are expected to disturb floodplain plant communities, making them more vulnerable to establishment of invasive species. The primary objective of this study is to evaluate whether native and invasive riparian plant assemblages respond differently to alterations of climate and land use. To study the response of riparian wetlands to watershed and climate alterations, we utilized an existing natural experiment imbedded in gradients of temperature and hydrology-found among dammed and undammed rivers. We evaluated a suite of environmental variables related to water temperature, hydrology, watershed disturbance, and edaphic conditions to identify the strongest predictors of native and invasive species abundances. We found that native species abundance is strongly influenced by climate-driven variables such as temperature and hydrology, while invasive species abundance is more strongly influenced by site-specific factors such as land use and soil nutrient availability. The patterns of synchronization between plant phenology, annual hydrographs, and annual water temperature cycles may be key factors sustaining the viability of native riparian plant communities. Our results demonstrate the need to understand the interactions between climate, land use, and nutrient management in maintaining the species diversity of riparian plant communities. Future climate change is likely to result in diminished competitiveness of native plant species, while the competitiveness of invasive species will increase due to anthropogenic watershed disturbance and accelerated nutrient and sediment export.Item Open Access Elevational ranges of birds on a tropical montane gradient lag behind warming temperatures.(PloS one, 2011-01) Forero-Medina, German; Terborgh, John; Socolar, S Jacob; Pimm, Stuart LBackground
Species may respond to a warming climate by moving to higher latitudes or elevations. Shifts in geographic ranges are common responses in temperate regions. For the tropics, latitudinal temperature gradients are shallow; the only escape for species may be to move to higher elevations. There are few data to suggest that they do. Yet, the greatest loss of species from climate disruption may be for tropical montane species.Methodology/principal findings
We repeat a historical transect in Peru and find an average upward shift of 49 m for 55 bird species over a 41 year interval. This shift is significantly upward, but also significantly smaller than the 152 m one expects from warming in the region. To estimate the expected shift in elevation we first determined the magnitude of warming in the locality from historical data. Then we used the temperature lapse rate to infer the required shift in altitude to compensate for warming. The range shifts in elevation were similar across different trophic guilds.Conclusions
Endothermy may provide birds with some flexibility to temperature changes and allow them to move less than expected. Instead of being directly dependent on temperature, birds may be responding to gradual changes in the nature of the habitat or availability of food resources, and presence of competitors. If so, this has important implications for estimates of mountaintop extinctions from climate change.Item Open Access Esterified Trehalose Analogues Protect Mammalian Cells from Heat Shock.(Chembiochem : a European journal of chemical biology, 2017-09) Bragg, Jack T; D'Ambrosio, Hannah K; Smith, Timothy J; Gorka, Caroline A; Khan, Faraz A; Rose, Joshua T; Rouff, Andrew J; Fu, Terence S; Bisnett, Brittany J; Boyce, Michael; Khetan, Sudhir; Paulick, Margot GTrehalose is a disaccharide produced by many organisms to better enable them to survive environmental stresses, including heat, cold, desiccation, and reactive oxygen species. Mammalian cells do not naturally biosynthesize trehalose; however, when introduced into mammalian cells, trehalose provides protection from damage associated with freezing and drying. One of the major difficulties in using trehalose as a cellular protectant for mammalian cells is the delivery of this disaccharide into the intracellular environment; mammalian cell membranes are impermeable to the hydrophilic sugar trehalose. A panel of cell-permeable trehalose analogues, in which the hydrophilic hydroxyl groups of trehalose are masked as esters, have been synthesized and the ability of these analogues to load trehalose into mammalian cells has been evaluated. Two of these analogues deliver millimolar concentrations of free trehalose into a variety of mammalian cells. Critically, Jurkat cells incubated with these analogues show improved survival after heat shock, relative to untreated Jurkat cells. The method reported herein thus paves the way for the use of esterified analogues of trehalose as a facile means to deliver high concentrations of trehalose into mammalian cells for use as a cellular protectant.Item Open Access Estimating the effects of vegetation and increased albedo on the urban heat island effect with spatial causal inference.(Scientific reports, 2024-01) Calhoun, Zachary D; Willard, Frank; Ge, Chenhao; Rodriguez, Claudia; Bergin, Mike; Carlson, DavidThe urban heat island effect causes increased heat stress in urban areas. Cool roofs and urban greening have been promoted as mitigation strategies to reduce this effect. However, evaluating their efficacy remains a challenge, as potential temperature reductions depend on local characteristics. Existing methods to characterize their efficacy, such as computational fluid dynamics and urban canopy models, are computationally burdensome and require a high degree of expertise to employ. We propose a data-driven approach to overcome these hurdles, inspired by recent innovations in spatial causal inference. This approach allows for estimates of hypothetical interventions to reduce the urban heat island effect. We demonstrate this approach by modeling evening temperature in Durham, North Carolina, using readily retrieved air temperature, land cover, and satellite data. Hypothetical interventions such as lining streets with trees, cool roofs, and changing parking lots to green space are estimated to decrease evening temperatures by a maximum of 0.7-0.9 [Formula: see text], with reduced effects on temperature as a function of distance from the intervention. Because of the ease of data access, this approach may be applied to other cities in the U.S. to help them come up with city-specific solutions for reducing urban heat stress.Item Open Access Estimation of in-canopy ammonia sources and sinks in a fertilized Zea mays field.(Environ Sci Technol, 2010-03-01) Bash, JO; Walker, JT; Katul, GG; Jones, MR; Nemitz, E; Robarg, WPAn analytical model was developed to describe in-canopy vertical distribution of ammonia (NH(3)) sources and sinks and vertical fluxes in a fertilized agricultural setting using measured in-canopy mean NH(3) concentration and wind speed profiles. This model was applied to quantify in-canopy air-surface exchange rates and above-canopy NH(3) fluxes in a fertilized corn (Zea mays) field. Modeled air-canopy NH(3) fluxes agreed well with independent above-canopy flux estimates. Based on the model results, the urea fertilized soil surface was a consistent source of NH(3) one month following the fertilizer application, whereas the vegetation canopy was typically a net NH(3) sink with the lower portion of the canopy being a constant sink. The model results suggested that the canopy was a sink for some 70% of the estimated soil NH(3) emissions. A logical conclusion is that parametrization of within-canopy processes in air quality models are necessary to explore the impact of agricultural field level management practices on regional air quality. Moreover, there are agronomic and environmental benefits to timing liquid fertilizer applications as close to canopy closure as possible. Finally, given the large within-canopy mean NH(3) concentration gradients in such agricultural settings, a discussion about the suitability of the proposed model is also presented.Item Open Access Functional stability of unliganded envelope glycoprotein spikes among isolates of human immunodeficiency virus type 1 (HIV-1).(PloS one, 2011-01) Agrawal, Nitish; Leaman, Daniel P; Rowcliffe, Eric; Kinkead, Heather; Nohria, Raman; Akagi, Junya; Bauer, Katherine; Du, Sean X; Whalen, Robert G; Burton, Dennis R; Zwick, Michael BThe HIV-1 envelope glycoprotein (Env) spike is challenging to study at the molecular level, due in part to its genetic variability, structural heterogeneity and lability. However, the extent of lability in Env function, particularly for primary isolates across clades, has not been explored. Here, we probe stability of function for variant Envs of a range of isolates from chronic and acute infection, and from clades A, B and C, all on a constant virus backbone. Stability is elucidated in terms of the sensitivity of isolate infectivity to destabilizing conditions. A heat-gradient assay was used to determine T(90) values, the temperature at which HIV-1 infectivity is decreased by 90% in 1 h, which ranged between ∼40 to 49°C (n = 34). For select Envs (n = 10), the half-lives of infectivity decay at 37°C were also determined and these correlated significantly with the T(90) (p = 0.029), though two 'outliers' were identified. Specificity in functional Env stability was also evident. For example, Env variant HIV-1(ADA) was found to be labile to heat, 37°C decay, and guanidinium hydrochloride but not to urea or extremes of pH, when compared to its thermostable counterpart, HIV-1(JR-CSF). Blue native PAGE analyses revealed that Env-dependent viral inactivation preceded complete dissociation of Env trimers. The viral membrane and membrane-proximal external region (MPER) of gp41 were also shown to be important for maintaining trimer stability at physiological temperature. Overall, our results indicate that primary HIV-1 Envs can have diverse sensitivities to functional inactivation in vitro, including at physiological temperature, and suggest that parameters of functional Env stability may be helpful in the study and optimization of native Env mimetics and vaccines.Item Open Access How Bees Deter Elephants: Beehive Trials with Forest Elephants (Loxodonta africana cyclotis) in Gabon.(PLoS One, 2016) Ngama, Steeve; Korte, Lisa; Bindelle, Jérôme; Vermeulen, Cédric; Poulsen, John RIn Gabon, like elsewhere in Africa, crops are often sources of conflict between humans and wildlife. Wildlife damage to crops can drastically reduce income, amplifying poverty and creating a negative perception of wild animal conservation among rural people. In this context, crop-raiding animals like elephants quickly become "problem animals". To deter elephants from raiding crops beehives have been successfully employed in East Africa; however, this method has not yet been tested in Central Africa. We experimentally examined whether the presence of Apis mellifera adansonii, the African honey bee species present in Central Africa, deters forest elephants (Loxodonta Africana cyclotis) from feeding on fruit trees. We show for the first time that the effectiveness of beehives as deterrents of elephants is related to bee activity. Empty hives and those housing colonies of low bee activity do not deter elephants all the time; but beehives with high bee activity do. Although elephant disturbance of hives does not impede honey production, there is a tradeoff between deterrence and the quantity of honey produced. To best achieve the dual goals of deterring elephants and producing honey colonies must maintain an optimum activity level of 40 to 60 bee movements per minute. Thus, beehives colonized by Apis mellifera adansonii bees can be effective elephant deterrents, but people must actively manage hives to maintain bee colonies at the optimum activity level.Item Open Access Identification of cyclosporin C from Amphichorda felina using a Cryptococcus neoformans differential temperature sensitivity assay.(Applied microbiology and biotechnology, 2018-03) Xu, Lijian; Li, Yan; Biggins, John B; Bowman, Brian R; Verdine, Gregory L; Gloer, James B; Alspaugh, J Andrew; Bills, Gerald FWe used a temperature differential assay with the opportunistic fungal pathogen Cryptococcus neoformans as a simple screening platform to detect small molecules with antifungal activity in natural product extracts. By screening of a collection extracts from two different strains of the coprophilous fungus, Amphichorda felina, we detected strong, temperature-dependent antifungal activity using a two-plate agar zone of inhibition assay at 25 and 37 °C. Bioassay-guided fractionation of the crude extract followed by liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance spectroscopy (NMR) identified cyclosporin C (CsC) as the main component of the crude extract responsible for growth inhibition of C. neoformans at 37 °C. The presence of CsC was confirmed by comparison with a commercial standard. We sequenced the genome of A. felina to identify and annotate the CsC biosynthetic gene cluster. The only previously characterized gene cluster for the biosynthesis of similar compounds is that of the related immunosuppressant drug cyclosporine A (CsA). The CsA and CsC gene clusters share a high degree of synteny and sequence similarity. Amino acid changes in the adenylation domain of the CsC nonribosomal peptide synthase's sixth module may be responsible for the substitution of L-threonine compared to L-α-aminobutyric acid in the CsA peptide core. This screening strategy promises to yield additional antifungal natural products with a focused spectrum of antimicrobial activity.Item Open Access Incubation temperature effects on hatchling performance in the loggerhead sea turtle (Caretta caretta).(PloS one, 2014-01) Fisher, Leah R; Godfrey, Matthew H; Owens, David WIncubation temperature has significant developmental effects on oviparous animals, including affecting sexual differentiation for several species. Incubation temperature also affects traits that can influence survival, a theory that is verified in this study for the Northwest Atlantic loggerhead sea turtle (Caretta caretta). We conducted controlled laboratory incubations and experiments to test for an effect of incubation temperature on performance of loggerhead hatchlings. Sixty-eight hatchlings were tested in 2011, and 31 in 2012, produced from eggs incubated at 11 different constant temperatures ranging from 27°C to 33°C. Following their emergence from the eggs, we tested righting response, crawling speed, and conducted a 24-hour long swim test. The results support previous studies on sea turtle hatchlings, with an effect of incubation temperature seen on survivorship, righting response time, crawling speed, change in crawl speed, and overall swim activity, and with hatchlings incubated at 27°C showing decreased locomotor abilities. No hatchlings survived to be tested in both years when incubated at 32°C and above. Differences in survivorship of hatchlings incubated at high temperatures are important in light of projected higher sand temperatures due to climate change, and could indicate increased mortality from incubation temperature effects.Item Open Access Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials.(J Chem Phys, 2013-02-28) Lu, Jianfeng; Vanden-Eijnden, EricReplica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently Plattner et al. [J. Chem. Phys. 135, 134111 (2011)] proposed a method to implement infinite swapping REMD in practice. Here we introduce a natural modification of this method that involves molecular dynamics simulations over a mixture potential. This modification is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also has implications for generalizations of REMD in which the swaps involve other parameters than the temperature.Item Open Access Initiation and Maintenance of Temperature-Dependent Sex Determination in the Red-Eared Slider Turtle(2020) Weber, CeriThe vertebrate gonad is an excellent model to study organogenesis due to its unique ability to form two distinct organs from a common bipotential primordium. No single factor is responsible for activation of ovary or testis development in all vertebrate species, but these developmental pathways tend to converge on the same cohort of genetic regulators. The structures of testes and ovaries are extremely similar across vertebrates, and this high level of conservation is also observed in the gene regulatory processes underlying their differentiation. In heterogametic species such as mice and chickens, genes on the sex chromosomes activate the genes that drive differentiation of the testis of ovary. However, not all vertebrate species have sex chromosomes, and it’s unknown how the many genetic and cellular processes that direct gonad development are activated in the absence of a clear genetic signal. Temperature-dependent sex determination (TSD) is one of the primary sex determination strategies found in reptiles and has repeatedly evolved in multiple reptilian lineages. During TSD, the fate of the gonad is driven by nest temperatures experienced during embryonic development. In the decades since TSD was first described, the molecular processes underlying this phenomenon have remained a mystery.
The Red-Eared Slider turtle, Trachemys scripta elegans (T. scripta), is a widely-studied model for temperature-dependent sex determination. When eggs are incubated at a constant 26˚C, 100% of embryos will develop testes. Incubating eggs at a constant 31˚C produces only embryos with ovaries. Prior work has focused the regulation of aromatase, which is crucial to estrogen synthesis, but it is expressed relatively late in the sex determination window. A transcriptome analysis of T. scripta gonads through sex determination revealed a group of early, male-biased genes, including the H3K27 demethylase Kdm6b. In many vertebrates, the epigenetic state of key sex determining genes appears to be critical in the activation of testis or ovary specific-signaling. We investigated whether KDM6B mediates the effect of temperature on gene expression in T. scripta and we found that it activates a conserved regulator of male sex development, DMRT1.
One of the few identified transcriptional regulators of Kdm6b, the transcription factor STAT3, is only phosphorylated at the warmer, female-producing temperature (FPT). We show that pSTAT3 binds the Kdm6b locus to repress transcription and inhibition of pSTAT3 is sufficient to induce female-to-male sex reversal. Using primary cells derived from T. scripta gonads, we found that a heat-mediated influx of calcium at FPT promotes phosphorylation of STAT3. From these data we propose the model that heat-mediated influx of calcium at FPT promotes activation of STAT3, a transcriptional repressor of the male pathway. Our model is the first proposed mechanism of temperature-dependent sex determination supported by direct experimental evidence.
It is unknown how the gonad interprets environmental signals and coordinates cell fates across the tissue. The embryonic gonad coelomic epithelium is a common feature of many vertebrate gonads, and its development is critical to placement of the germ cells in the appropriate stem cell niche, which is required for germ cell survival and maturation. Previous studies of testis morphogenesis in T. scripta show that invaginations of the coelomic epithelium move germ cells into the gonad medulla to form the seminiferous tubules. We show that these invaginations only occur below germ cells, express the conserved Steroli cell marker SOX9, and are sensitive to the hormone environment of the gonad. These data suggest that signals between the germ cell, somatic cells in the coelomic epithelium, and somatic cells of the primordial cords collectively participate in the morphogenetic changes underlying testis development in T. scripta.
Our findings provide a framework for future investigations into the mechanism underlying temperature-dependent sex determination by identifying the initial signaling events that regulate the epigenetic state of sex-specific genes and describing how cellular fates are maintained during the sex determination window. STAT3 signaling can be activated by many inputs and have numerous downstream impacts, only some of which have been experimentally tested, providing direction and future lines of investigation for the field. The data presented here has laid the groundwork for identifying how temperature-sex determination operates in the turtle and how pieces of this process may be conserved among many animal phyla.
Item Open Access Inkless microcontact printing on SAMs of Boc- and TBS-protected thiols.(Nano Lett, 2010-01) Shestopalov, Alexander A; Clark, Robert L; Toone, Eric JWe report a new inkless catalytic muCP technique that achieves accurate, fast, and complete pattern reproduction on SAMs of Boc- and TBS-protected thiols immobilized on gold using a polyurethane-acrylate stamp functionalized with covalently bound sulfonic acids. Pattern transfer is complete at room temperature just after one minute of contact and renders sub-200 nm size structures of chemically differentiated SAMs.Item Open Access Mass spectrometry-based thermal shift assay for protein-ligand binding analysis.(Anal Chem, 2010-07-01) West, GM; Thompson, JW; Soderblom, EJ; Dubois, LG; Moseley, MA; Fitzgerald, MCDescribed here is a mass spectrometry-based screening assay for the detection of protein-ligand binding interactions in multicomponent protein mixtures. The assay utilizes an oxidation labeling protocol that involves using hydrogen peroxide to selectively oxidize methionine residues in proteins in order to probe the solvent accessibility of these residues as a function of temperature. The extent to which methionine residues in a protein are oxidized after specified reaction times at a range of temperatures is determined in a MALDI analysis of the intact proteins and/or an LC-MS analysis of tryptic peptide fragments generated after the oxidation reaction is quenched. Ultimately, the mass spectral data is used to construct thermal denaturation curves for the detected proteins. In this proof-of-principle work, the protocol is applied to a four-protein model mixture comprised of ubiquitin, ribonuclease A (RNaseA), cyclophilin A (CypA), and bovine carbonic anhydrase II (BCAII). The new protocol's ability to detect protein-ligand binding interactions by comparing thermal denaturation data obtained in the absence and in the presence of ligand is demonstrated using cyclosporin A (CsA) as a test ligand. The known binding interaction between CsA and CypA was detected using both the MALDI- and LC-MS-based readouts described here.Item Open Access Morphing low-affinity ligands into high-avidity nanoparticles by thermally triggered self-assembly of a genetically encoded polymer.(ACS Nano, 2010-04-27) Simnick, Andrew J; Valencia, C Alexander; Liu, Rihe; Chilkoti, AshutoshMultivalency is the increase in avidity resulting from the simultaneous interaction of multiple ligands with multiple receptors. This phenomenon, seen in antibody-antigen and virus-cell membrane interactions, is useful in designing bioinspired materials for targeted delivery of drugs or imaging agents. While increased avidity offered by multivalent targeting is attractive, it can also promote nonspecific receptor interaction in nontarget tissues, reducing the effectiveness of multivalent targeting. Here, we present a thermal targeting strategy--dynamic affinity modulation (DAM)--using elastin-like polypeptide diblock copolymers (ELP(BC)s) that self-assemble from a low-affinity to high-avidity state by a tunable thermal "switch", thereby restricting activity to the desired site of action. We used an in vitro cell binding assay to investigate the effect of the thermally triggered self-assembly of these ELP(BC)s on their receptor-mediated binding and cellular uptake. The data presented herein show that (1) ligand presentation does not disrupt ELP(BC) self-assembly; (2) both multivalent ligand presentation and upregulated receptor expression are needed for receptor-mediated interaction; (3) increased size of the hydrophobic segment of the block copolymer promotes multivalent interaction with membrane receptors, potentially due to changes in the nanoscale architecture of the micelle; and (4) nanoscale presentation of the ligand is important, as presentation of the ligand by micrometer-sized aggregates of an ELP showed a low level of binding/uptake by receptor-positive cells compared to its presentation on the corona of a micelle. These data validate the concept of thermally triggered DAM and provide rational design parameters for future applications of this technology for targeted drug delivery.