Art Advancing Science: Filmmaking Leads to Molecular Insights at the Nanoscale.

PubMed

Reilly, Charles; Ingber, Donald E

2017-12-26

Many have recognized the potential value of facilitating activities that span the art-science interface for the benefit of society; however, there are few examples that demonstrate how pursuit of an artistic agenda can lead to scientific insights. Here, we describe how we set out to produce an entertaining short film depicting the fertilization of the egg by sperm as a parody of a preview for another Star Wars movie to excite the public about science, but ended up developing a simulation tool for multiscale modeling. To produce an aesthetic that communicates mechanical continuity across spatial scales, we developed custom strategies that integrate physics-based animation software from the entertainment industry with molecular dynamics simulation tools, using experimental data from research publications. Using this approach, we were able to depict biological physicality across multiple spatial scales, from how sperm tails move to collective molecular behavior within the axoneme to how the molecular motor, dynein, produces force at the nanometer scale. The dynein simulations, which were validated by replicating results of past simulations and cryo-electron microscopic studies, also predicted a potential mechanism for how ATP hydrolysis drives dynein motion along the microtubule as well as how dynein changes its conformation when it goes through the power stroke. Thus, pursuit of an artistic work led to insights into biology at the nanoscale as well as the development of a highly generalizable modeling and simulation technology that has utility for nanoscience and any other area of scientific investigation that involves analysis of complex multiscale systems.

Molecular insight in the multifunctional activities of Withaferin A.

PubMed

Vanden Berghe, Wim; Sabbe, Linde; Kaileh, Mary; Haegeman, Guy; Heyninck, Karen

2012-11-15

Herbal medicine which involves the use of plants for their medicinal value, dates as far back as the origin of mankind and demonstrates an array of applications including cardiovascular protection and anti-cancer activities, via antioxidant, anti-inflammatory and metabolic activities. Even today the popularity of medicinal herbs is still growing like in traditional medicines such as the Indian medicine, Ayurveda. One of the Ayurvedic medicinal plants is Withania somnifera Dunal, of which the important constituents are the withanolides. Among them, Withaferin A is one of the most bioactive compounds, exerting anti-inflammatory, pro-apoptotic but also anti-invasive and anti-angiogenic effects. In the context of modern pharmacology, a better insight in the underlying mechanism of the broad range of bioactivities exerted by Withaferin A is compulsory. Therefore, a lot of effort was made to explore the intracellular effects of Withaferin A and to characterize its target proteins. This review provides a decisive insight on the molecular basis of the health-promoting potential of Withaferin A. Copyright © 2012 Elsevier Inc. All rights reserved.

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sidhu, Navdeep S.; University of Göttingen, Tammannstrasse 4, 37077 Göttingen; Schreiber, Kathrin

2014-05-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However,more » the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.« less

Palaeoclimatic insights into future climate challenges.

PubMed

Alley, Richard B

2003-09-15

Palaeoclimatic data document a sensitive climate system subject to large and perhaps difficult-to-predict abrupt changes. These data suggest that neither the sensitivity nor the variability of the climate are fully captured in some climate-change projections, such as the Intergovernmental Panel on Climate Change (IPCC) Summary for Policymakers. Because larger, faster and less-expected climate changes can cause more problems for economies and ecosystems, the palaeoclimatic data suggest the hypothesis that the future may be more challenging than anticipated in ongoing policy making. Large changes have occurred repeatedly with little net forcing. Increasing carbon dioxide concentration appears to have globalized deglacial warming, with climate sensitivity near the upper end of values from general circulation models (GCMs) used to project human-enhanced greenhouse warming; data from the warm Cretaceous period suggest a similarly high climate sensitivity to CO(2). Abrupt climate changes of the most recent glacial-interglacial cycle occurred during warm as well as cold times, linked especially to changing North Atlantic freshwater fluxes. GCMs typically project greenhouse-gas-induced North Atlantic freshening and circulation changes with notable but not extreme consequences; however, such models often underestimate the magnitude, speed or extent of past changes. Targeted research to assess model uncertainties would help to test these hypotheses.

Estimating the limits of adaptation from historical behaviour: Insights from the American Climate Prospectus

NASA Astrophysics Data System (ADS)

Jina, A.; Hsiang, S. M.; Kopp, R. E., III; Rasmussen, D.; Rising, J.

2014-12-01

The American Climate Prospectus (ACP), the technical analysis underlying the Risky Business project, quantitatively assessed the climate risks posed to the United States' economy in a number of economic sectors [1]. The main analysis presents projections of climate impacts with an assumption of "no adaptation". Yet, historically, when the climate imposed an economic cost upon society, adaptive responses were taken to minimise these costs. These adaptive behaviours, both autonomous and planned, can be expected to occur as climate impacts increase in the future. To understand the extent to which adaptation might decrease some of the worst impacts of climate change, we empirically estimate adaptive responses. We do this in three sectors considered in the analysis - crop yield, crime, and mortality - and estimate adaptive capacity in two steps. First, looking at changes in climate impacts through time, we identify a historical rate of adaptation. Second, spatial differences in climate impacts are then used to stratify regions into more adapted or less adapted based on climate averages. As these averages change across counties in the US, we allow each to become more adapted at the rate identified in step one. We are then able to estimate the residual damages, assuming that only the historical adaptive behaviours have taken place (fig 1). Importantly, we are unable to estimate any costs associated with these adaptations, nor are we able to estimate more novel (for example, new technological discoveries) or more disruptive (for example, migration) adaptive behaviours. However, an important insight is that historical adaptive behaviours may not be capable of reducing the worst impacts of climate change. The persistence of impacts in even the most exposed areas indicates that there are non-trivial costs associated with adaptation that will need to be met from other sources or through novel behavioural changes. References: [1] T. Houser et al. (2014), American Climate

Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

NASA Astrophysics Data System (ADS)

Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

2015-03-01

We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

Molecular electronics: insight from first-principles transport simulations.

PubMed

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2010-01-01

Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

Climate change induced transformations of agricultural systems: insights from a global model

NASA Astrophysics Data System (ADS)

Leclère, D.; Havlík, P.; Fuss, S.; Schmid, E.; Mosnier, A.; Walsh, B.; Valin, H.; Herrero, M.; Khabarov, N.; Obersteiner, M.

2014-12-01

Climate change might impact crop yields considerably and anticipated transformations of agricultural systems are needed in the coming decades to sustain affordable food provision. However, decision-making on transformational shifts in agricultural systems is plagued by uncertainties concerning the nature and geography of climate change, its impacts, and adequate responses. Locking agricultural systems into inadequate transformations costly to adjust is a significant risk and this acts as an incentive to delay action. It is crucial to gain insight into how much transformation is required from agricultural systems, how robust such strategies are, and how we can defuse the associated challenge for decision-making. While implementing a definition related to large changes in resource use into a global impact assessment modelling framework, we find transformational adaptations to be required of agricultural systems in most regions by 2050s in order to cope with climate change. However, these transformations widely differ across climate change scenarios: uncertainties in large-scale development of irrigation span in all continents from 2030s on, and affect two-thirds of regions by 2050s. Meanwhile, significant but uncertain reduction of major agricultural areas affects the Northern Hemisphere’s temperate latitudes, while increases to non-agricultural zones could be large but uncertain in one-third of regions. To help reducing the associated challenge for decision-making, we propose a methodology exploring which, when, where and why transformations could be required and uncertain, by means of scenario analysis.

Molecular genetics and genomics generate new insights into invertebrate pest invasions.

PubMed

Kirk, Heather; Dorn, Silvia; Mazzi, Dominique

2013-07-01

Invertebrate pest invasions and outbreaks are associated with high social, economic, and ecological costs, and their significance will intensify with an increasing pressure on agricultural productivity as a result of human population growth and climate change. New molecular genetic and genomic techniques are available and accessible, but have been grossly underutilized in studies of invertebrate pest invasions, despite that they are useful tools for applied pest management and for understanding fundamental features of pest invasions including pest population demographics and adaptation of pests to novel and/or changing environments. Here, we review current applications of molecular genetics and genomics in the study of invertebrate pest invasions and outbreaks, and we highlight shortcomings from the current body of research. We then discuss recent conceptual and methodological advances in the areas of molecular genetics/genomics and data analysis, and we highlight how these advances will further our understanding of the demographic, ecological, and evolutionary features of invertebrate pest invasions. We are now well equipped to use molecular data to understand invertebrate dispersal and adaptation, and this knowledge has valuable applications in agriculture at a time when these are critically required.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

PubMed

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus

PubMed Central

2010-01-01

Background The dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish Galaxias maculatus in Patagonia (~300 individuals from 36 locations). Results Contemporary populations of G. maculatus, east and west of the Andes in Patagonia, represent a single monophyletic lineage comprising several well supported groups. Mantel tests using control region data revealed a strong positive relationship when geographic distance was modeled according to a scenario of marine dispersal. (r = 0.69, P = 0.055). By contrast, direct distance between regions was poorly correlated with genetic distance (r = -0.05, P = 0.463). Hierarchical AMOVAs using mtDNA revealed that pooling samples according to historical (pre-LGM) oceanic drainage (Pacific vs. Atlantic) explained approximately four times more variance than pooling them into present-day drainage (15.6% vs. 3.7%). Further post-hoc AMOVA tests revealed additional genetic structure between populations east and west of the Chilean Coastal Cordillera (coastal vs. interior). Overall female effective population size appears to have remained relatively constant until roughly 0.5 Ma when population size rapidly increased several orders of magnitude [100× (60×-190×)] to reach contemporary levels. Maximum likelihood analysis of nuclear alleles revealed a poorly supported gene tree which was paraphyletic with respect to mitochondrial-defined haplogroups. Conclusions First diversifying in the central/north-west region of Patagonia, G. maculatus extended its range into Argentina via the southern coastal regions that join the Pacific and Atlantic oceans. More recent gene flow between northern populations involved the most

Ice formation on kaolinite: Insights from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sosso, Gabriele C.; Tribello, Gareth A.; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

2016-12-01

The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral.

Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations.

PubMed

Dehury, Budheswar; Maharana, Jitendra; Sahoo, Bikash Ranjan; Sahu, Jagajjit; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

2015-04-01

The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming

DOE PAGES

Chen, Hongmei; Yang, Ziming; Chu, Rosalie K.; ...

2018-03-23

Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. By using ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter (EDOM) in an anoxic warming incubation experiment (up to 122 days) with a tundra soil from Alaska (United States). EDOM was extracted with 10 mM NH 4HCO 3 from both the organic- and mineral-layer soils during incubation at both -2 and 8°C. Based on their O:C and H:C ratios, EDOM molecular formulas were qualitatively grouped into nine biochemical classesmore » of compounds, among which lignin-like compounds dominated both the organic and the mineral soils and were the most stable, whereas amino sugars, peptides, and carbohydrate-like compounds were the most biologically labile. These results corresponded with shifts in EDOM elemental composition in which the ratios of O:C and N:C decreased, while the average C content in EDOM, molecular mass, and aromaticity increased after 122 days of incubation. This research demonstrates that certain EDOM components, such as amino sugars, peptides, and carbohydrate-like compounds, are disproportionately more susceptible to microbial degradation than others in the soil, and these results should be considered in SOC degradation models to improve predictions of Arctic climate feedbacks.« less

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Hongmei; Yang, Ziming; Chu, Rosalie K.

Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. By using ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter (EDOM) in an anoxic warming incubation experiment (up to 122 days) with a tundra soil from Alaska (United States). EDOM was extracted with 10 mM NH 4HCO 3 from both the organic- and mineral-layer soils during incubation at both -2 and 8°C. Based on their O:C and H:C ratios, EDOM molecular formulas were qualitatively grouped into nine biochemical classesmore » of compounds, among which lignin-like compounds dominated both the organic and the mineral soils and were the most stable, whereas amino sugars, peptides, and carbohydrate-like compounds were the most biologically labile. These results corresponded with shifts in EDOM elemental composition in which the ratios of O:C and N:C decreased, while the average C content in EDOM, molecular mass, and aromaticity increased after 122 days of incubation. This research demonstrates that certain EDOM components, such as amino sugars, peptides, and carbohydrate-like compounds, are disproportionately more susceptible to microbial degradation than others in the soil, and these results should be considered in SOC degradation models to improve predictions of Arctic climate feedbacks.« less

Teaching climate change in undergraduate courses

NASA Astrophysics Data System (ADS)

Sadler, Michael

2013-04-01

Although anthropogenic climate change is generally accepted in the scientific community, there is considerable skepticism among the general population and, therefore, in undergraduate students of all majors. Students are often asked by their peers, family members, and others, whether they ``believe'' climate change is occurring and what should be done about it (if anything). I will present my experiences and recommendations for teaching the physics of climate change to both physics and non-science majors. For non-science majors, the basic approach is to try to develop an appreciation for the scientific method (particularly peer-reviewed research) in a course on energy and the environment. For physics majors, the pertinent material is normally covered in their undergraduate courses in modern physics and thermodynamics. Nevertheless, it helps to review the basics, e.g. introductory quantum mechanics (discrete energy levels of atomic systems), molecular spectroscopy, and blackbody radiation. I have done this in a separate elective topics course, titled ``Physics of Climate Change,'' to help the students see how their knowledge gives them insight into a topic that is very volatile (socially and politically).

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE PAGES

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.; ...

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doughty, Benjamin; Goverapet Srinivasan, Sriram; Bryantsev, Vyacheslav S.

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments,more » and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO 2 catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO 2 (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.« less

New insights for the hydrology of the Rhine based on the new generation climate models

NASA Astrophysics Data System (ADS)

Bouaziz, Laurène; Sperna Weiland, Frederiek; Beersma, Jules; Buiteveld, Hendrik

2014-05-01

Decision makers base their choices of adaptation strategies on climate change projections and their associated hydrological consequences. New insights of climate change gained under the new generation of climate models belonging to the IPCC 5th assessment report may influence (the planning of) adaption measures and/or future expectations. In this study, hydrological impacts of climate change as projected under the new generation of climate models for the Rhine were assessed. Hereto we downscaled 31 General Circulation Models (GCMs), which were developed as part of the Coupled Model Intercomparison Project Phase 5 (CMIP5), using an advanced Delta Change Method for the Rhine basin. Changes in mean monthly, maximum and minimum flows at Lobith were derived with the semi-distributed hydrological model HBV of the Rhine. The projected changes were compared to changes that were previously obtained in the trans-boundary project Rheinblick using eight CMIP3 GCMs and Regional Climate Models (RCMs) for emission scenario A1B. All eight selected CMIP3 models (scenario A1B) predicted for 2071-2100 a decrease in mean monthly flows between June and October. Similar decreases were found for some of the 31 CMIP5 models for Representative Concentration Pathways (RCPs) 4.5, 6.0 and 8.5. However, under each RCP, there were also models that projected an increase in mean flows between June and October and on average the decrease was smaller than for the eight CMIP3 models. For 2071-2100, also the mean annual minimum 7-days discharge decreased less in the CMIP5 model simulations than was projected in CMIP3. When assessing the response of mean monthly flows of the CMIP5 simulation with the CSIRO-Mk3-6-0 and HadGEM2-ES models with respect to initial conditions and RCPs, it was found that natural variability plays a dominant role in the near future (2021-2050), while changes in mean monthly flows are dominated by the radiative forcing in the far future (2071-2100). According to RCP 8.5 model

Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations.

PubMed

Saeedi, Marzieh; Lyubartsev, Alexander P; Jalili, Seifollah

2017-07-01

To provide insight into the molecular mechanisms of local anesthetic action, we have carried out an extensive investigation of two amide type local anesthetics, lidocaine and articaine in both charged and uncharged forms, interacting with DMPC lipid membrane. We have applied both standard molecular dynamics simulations and metadynamics simulations to provide a detailed description of the free energy landscape of anesthetics embedded in the lipid bilayer. The global minimum of the free energy surface (equilibrium position of anesthetics in the lipid membrane) occurred around 1nm of the bilayer center. The uncharged anesthetics show more affinity to bind to this region compared to the charged drugs. The binding free energy of uncharged lidocaine in the membrane (-30.3kJ/mol) is higher than uncharged articaine (-24.0kJ/mol), which is in good agreement with higher lipid solubility of lidocaine relative to the articaine. The octanol/water partition coefficient of uncharged drugs was also investigated using expanded ensemble simulations. In addition, complementary standard MD simulations were carried out to study the partitioning behavior of multiple anesthetics inside the lipid bilayer. The results obtained here are in line with previously reported simulations and suggest that the different forms of anesthetics induce different structural modifications in the lipid bilayer, which can provide new insights into their complex membrane translocation phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Life on thin ice: Insights from Uummannaq, Greenland for connecting climate science with Arctic communities

NASA Astrophysics Data System (ADS)

Baztan, Juan; Cordier, Mateo; Huctin, Jean-Michel; Zhu, Zhiwei; Vanderlinden, Jean-Paul

2017-09-01

What are the links between mainstream climate science and local community knowledge? This study takes the example of Greenland, considered one of the regions most impacted by climate change, and Inuit people, characterized as being highly adaptive to environmental change, to explore this question. The study is based on 10 years of anthropological participatory research in Uummannaq, Northwest Greenland, along with two fieldwork periods in October 2014 and April 2015, and a quantitative bibliometric analysis of the international literature on sea ice - a central subject of concern identified by Uummannaq community members during the fieldwork periods. Community members' perceptions of currently available scientific climate knowledge were also collected during the fieldwork. This was done to determine if community members consider available scientific knowledge salient and if it covers issues they consider relevant. The bibliometric analysis of the sea ice literature provided additional insight into the degree to which scientific knowledge about climate change provides information relevant for the community. Our results contribute to the ongoing debate on the missing connections between community worldviews, cultural values, livelihood needs, interests and climate science. Our results show that more scientific research efforts should consider local-level needs in order to produce local-scale knowledge that is more salient, credible and legitimate for communities experiencing climate change. In Uummannaq, as in many Inuit communities with similar conditions, more research should be done on sea ice thickness in winter and in areas through which local populations travel. This paper supports the growing evidence that whenever possible, climate change research should focus on environmental features that matter to communities, at temporal and spatial scales relevant to them, in order to foster community adaptations to change. We recommend such research be connected to and

Thermophysical Properties of Energetic Ionic Liquids/Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations

DTIC Science & Technology

2013-01-01

W L. Physical properties of concentrated nitric acid . UNT Digital Library. http://digital.library.unt.edu/ark:/67531/metadc56640/.) 23 M. Engelmann... Nitric Acid Mixtures: Insights from Molecular Dynamics Simulations 5a. CONTRACT NUMBER FA9300-11-C-3012 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...Rev. 8-98) Prescribed by ANSI Std. 239.18 1     Thermophysical  Properties  of  Energetic  Ionic  Liquids/ Nitric   Acid

Molecular-level insights into intrinsic peroxidase-like activity of nanocarbon oxides.

PubMed

Zhao, Ruisheng; Zhao, Xiang; Gao, Xingfa

2015-01-12

Nanocarbon oxides have been proved to possess great peroxidase-like activity, catalyzing the oxidation of many peroxidase substrates, such as 3,3',5,5'-tetramethylbenzidine (TMB) and o-phenylenediamine dihydrochloride (OPD), accompanied by a significant color change. This chromogenic reaction is widely used to detect glucose and occult blood. The chromogenic reaction was intensively investigated with density functional theory and molecular-level insights into the nature of peroxidase-like activity were gained. A radical mechanism was unraveled and the carboxyl groups of nanocarbon oxides were identified as the reactive sites. Aromatic domains connected with the carboxyl groups were critical to the peroxidase-like activity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular asymmetry in extraterrestrial chemistry: Insights from a pristine meteorite

NASA Astrophysics Data System (ADS)

Pizzarello, Sandra; Huang, Yongsong; Alexandre, Marcelo R.

2008-03-01

The nonracemic amino acids of meteorites provide the only natural example of molecular asymmetry measured so far outside the biosphere. Because extant life depends on chiral homogeneity for the structure and function of biopolymers, the study of these meteoritic compounds may offer insights into the establishment of prebiotic attributes in chemical evolution as well as the origin of terrestrial homochirality. However, all efforts to understand the origin, distribution, and scope of these amino acids' enantiomeric excesses (ee) have been frustrated by the ready exposure of meteorites to terrestrial contaminants and the ubiquitous homochirality of such contamination. We have analyzed the soluble organic composition of a carbonaceous meteorite from Antarctica that was collected and stored under controlled conditions, largely escaped terrestrial contamination and offers an exceptionally pristine sample of prebiotic material. Analyses of the meteorite diastereomeric amino acids alloisoleucine and isoleucine allowed us to show that their likely precursor molecules, the aldehydes, also carried a sizable molecular asymmetry of up to 14% in the asteroidal parent body. Aldehydes are widespread and abundant interstellar molecules; that they came to be present, survived, and evolved in the solar system carrying ee gives support to the idea that biomolecular traits such as chiral asymmetry could have been seeded in abiotic chemistry ahead of life.

Molecular asymmetry in extraterrestrial chemistry: Insights from a pristine meteorite.

PubMed

Pizzarello, Sandra; Huang, Yongsong; Alexandre, Marcelo R

2008-03-11

The nonracemic amino acids of meteorites provide the only natural example of molecular asymmetry measured so far outside the biosphere. Because extant life depends on chiral homogeneity for the structure and function of biopolymers, the study of these meteoritic compounds may offer insights into the establishment of prebiotic attributes in chemical evolution as well as the origin of terrestrial homochirality. However, all efforts to understand the origin, distribution, and scope of these amino acids' enantiomeric excesses (ee) have been frustrated by the ready exposure of meteorites to terrestrial contaminants and the ubiquitous homochirality of such contamination. We have analyzed the soluble organic composition of a carbonaceous meteorite from Antarctica that was collected and stored under controlled conditions, largely escaped terrestrial contamination and offers an exceptionally pristine sample of prebiotic material. Analyses of the meteorite diastereomeric amino acids alloisoleucine and isoleucine allowed us to show that their likely precursor molecules, the aldehydes, also carried a sizable molecular asymmetry of up to 14% in the asteroidal parent body. Aldehydes are widespread and abundant interstellar molecules; that they came to be present, survived, and evolved in the solar system carrying ee gives support to the idea that biomolecular traits such as chiral asymmetry could have been seeded in abiotic chemistry ahead of life.

Insights into Penultimate Interglacial-Glacial Climate Change on Vegetation History at Lake Van, Turkey

NASA Astrophysics Data System (ADS)

Pickarski, N.; Litt, T.

2017-12-01

-resolution record presents an improved insight into regional vegetation dynamics and climate variability in the eastern Mediterranean region.

Structured Ionomer Thin Films at Water Interface: Molecular Dynamics Simulation Insight

DOE PAGES

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; ...

2017-08-23

Controlling the structure and dynamics of thin films of ionizable polymers at water interfaces is critical to their many applications. As the chemical diversity within one polymer is increased, controlling the structure and dynamics of the polymer, which is a key to their use, becomes a challenge. Here molecular dynamics simulations (MD) are used to obtain molecular insight into the structure and dynamics of thin films of one such macromolecule at the interface with water. The polymer consists of an ABCBA topology with randomly sulfonated polystyrene (C), tethered symmetrically to flexible poly(ethylene- r-propylene) blocks (B), and end-capped by a poly(more » t-butylstyrene) block (A). The compositions of the interfacial and bulk regions of thin films of the ABCBA polymers are followed as a function of exposure time to water. We find that interfacial rearrangements take place where buried ionic segments migrate toward the water interface. The hydrophobic blocks collapse and rearrange to minimize their exposure to water. In conclusion, the water that initially drives interfacial reengagements breaks the ionic clusters within the film, forming a dynamic hydrophilic internal network within the hydrophobic segments.« less

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal.

PubMed

Shrivastava, Dipty; Nain, Vikrant; Sahi, Shakti; Verma, Anju; Sharma, Priyanka; Sharma, Prakash Chand; Kumar, Polumetla Ananda

2011-01-22

Resistance (R) protein recognizes molecular signature of pathogen infection and activates downstream hypersensitive response signalling in plants. R protein works as a molecular switch for pathogen defence signalling and represent one of the largest plant gene family. Hence, understanding molecular structure and function of R proteins has been of paramount importance for plant biologists. The present study is aimed at predicting structure of R proteins signalling domains (CC-NBS) by creating a homology model, refining and optimising the model by molecular dynamics simulation and comparing ADP and ATP binding. Based on sequence similarity with proteins of known structures, CC-NBS domains were initially modelled using CED- 4 (cell death abnormality protein) and APAF-1 (apoptotic protease activating factor) as multiple templates. The final CC-NBS structural model was built and optimized by molecular dynamic simulation for 5 nanoseconds (ns). Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy. Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch. Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.

New insights into the molecular characteristics behind the function of Renilla luciferase.

PubMed

Fanaei-Kahrani, Zahra; Ganjalikhany, Mohamad Reza; Rasa, Seyed Mohammad Mahdi; Emamzadeh, Rahman

2018-02-01

Renilla Luciferase (RLuc) is a blue light emitter protein which can be applied as a valuable tool in medical diagnosis. But due to lack of the crystal structure of RLuc-ligand complex, the functional motions and catalytic mechanism of this enzyme remain largely unknown. In the present study, the active site properties and the ligand-receptor interactions of the native RLuc and its red-shifted light emitting variant (Super RLuc 8) were investigated using molecular docking approach, molecular dynamics (MD) analysis, and MM-PBSA method. The detailed analysis of the main clusters led to identifying a lid-like structure and its functional motions. Furthermore, an induced-fit mechanism is proposed where ligand-binding induces conformational changes of the active site. Our findings give an insight into the deeper understanding of RLuc conformational changes during binding steps and ligand-receptor pattern. Moreover, our work broaden our understanding of how active site geometry is adjusted to support the catalytic activity and red-shifted light emission in Super RLuc 8. © 2017 Wiley Periodicals, Inc.

Milestone in the NTB phase investigation and beyond: direct insight into molecular self-assembly.

PubMed

Ivšić, Trpimir; Vinković, Marijana; Baumeister, Ute; Mikleušević, Ana; Lesac, Andreja

2014-12-14

Although liquid-crystalline materials are most widely exploited for flat-panel displays, their ability to self-organize into periodically ordered nanostructures gives rise to a broad variety of additional applications. The recently discovered low-temperature nematic phase (N(TB)) with unusual characteristics generated considerable attention within the scientific community: despite the fact that the molecules from which the phase is composed are not chiral, the helicoidal structure of the phase is strongly implicated. Here we report on combined experimental, computational and spectroscopic studies of the structural aspects influencing formation of the N(TB) phase as well as on the molecular organization within the phase. In an extensive DFT study, the structure-property prerequisite was traced to a "bent-propeller" shape of the molecule. We also demonstrate the first utilization of liquid state NMR for direct analysis of intermolecular interactions within thermotropic liquid-crystalline phases, providing new insight into molecular packing that can lead towards design of novel chiral functional materials. The synergy of experimental, computational and NMR studies suggests a syn-parallel helical molecular organization within the N(TB) phase.

Unveiling the molecular mechanism of brassinosteroids: Insights from structure-based molecular modeling studies.

PubMed

Lei, Beilei; Liu, Jiyuan; Yao, Xiaojun

2015-12-01

Brassinosteroid (BR) phytohormones play indispensable roles in plant growth and development. Brassinolide (BL) and 24-epibrassinolide (24-epiBL) are the most active ones among the BRs reported thus far. Unfortunately, the extremely low natural content and intricate synthesis process limit their popularization in agricultural production. Earlier reports to discover alternative compounds have resulted in molecules with nearly same scaffold structure and without diversity in chemical space. In the present study, receptors structure based BRs regulation mechanism was analyzed. First, we examined the detailed binding interactions and their dynamic stability between BL and its receptor BRI1 and co-receptor BAK1. Then, the binding modes and binding free energies for 24-epiBL and a series of representative BRs binding with BRI1 and BRI1-BAK1 were carried out by molecular docking, energy minimization and MM-PBSA free energy calculation. The obtained binding structures and energetic results provided vital insights into the structural factors affecting the activity from both receptors and BRs aspects. Subsequently, the obtained knowledge will serve as valuable guidance to build pharmacophore models for rational screening of new scaffold alternative BRs. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae).

PubMed

Jaramillo-Correa, Juan-Pablo; Rodríguez-Quilón, Isabel; Grivet, Delphine; Lepoittevin, Camille; Sebastiani, Federico; Heuertz, Myriam; Garnier-Géré, Pauline H; Alía, Ricardo; Plomion, Christophe; Vendramin, Giovanni G; González-Martínez, Santiago C

2015-03-01

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change. Copyright © 2015 by the Genetics Society of America.

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton, Pinaceae)

PubMed Central

Jaramillo-Correa, Juan-Pablo; Rodríguez-Quilón, Isabel; Grivet, Delphine; Lepoittevin, Camille; Sebastiani, Federico; Heuertz, Myriam; Garnier-Géré, Pauline H.; Alía, Ricardo; Plomion, Christophe; Vendramin, Giovanni G.; González-Martínez, Santiago C.

2015-01-01

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP–climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change. PMID:25549630

Molecular Insights Into a Dinoflagellate Bloom Imply Bacterial Cultivation

NASA Astrophysics Data System (ADS)

Gong, W.; Hall, N.; Schruth, D.; Paerl, H. W.; Marchetti, A.

2016-02-01

In coastal waters, an increase in frequency and intensity of algal blooms worldwide has recently been observed primarily due to eutrophication, with further increases predicted as a consequence of climate change. In many marine habitats most impacted by human activities, efforts have been made to prevent conditions that promote harmful algal blooms, or HABs, although progress is limited, due in part to our current lack of understanding of the environmental and cellular processes that promote and propagate these blooms. Comparative metatranscriptomics was used to investigate the underlying molecular mechanisms associated with a dinoflagellate bloom in a highly eutrophied estuarine system. Here we show that under bloom conditions, there is increased expression of metabolic pathways indicative of rapidly growing cells, including energy production, carbon metabolism, transporters and synthesis of nucleic acids and cellular membrane components. In addition, there is a prominence of highly expressed genes involved in synthesis of membrane-associated molecules, including those for the production of glycosaminoglycans (GAGs), which may serve roles in nutrient acquisition and/or cell surface adhesion. Biotin and thiamine synthesis genes also increased expression along with several cobalamin biosynthesis-associated genes that suggests processing of B12 intermediates by dinoflagellates. The patterns in gene expression observed are consistent with bloom-forming dinoflagellates eliciting a cellular response to facilitate interactions with their surrounding bacterial consortium, possibly in an effort to cultivate for enhancement of vitamin and nutrient exchanges and/or direct consumption. Our findings provide potential molecular targets for HAB detection and remediation efforts.

Extending Molecular Signatures of Climatic and Environmental Change to the Mesozoic

NASA Astrophysics Data System (ADS)

Brassell, S. C.

2007-12-01

The distributions, abundances and isotopic compositions of molecular constituents in sediments depend on their source organisms and the combination of environmental and climatic parameters that constrain or control their biosynthesis. Many such relationships are well documented and understood, thereby providing proxies of proven utility in paleoclimatic reconstructions. Thus, the temperature dependence in the extent of unsaturation in alkenones derived from prymnesiophyte algae, and in the proportion of ring structures in glycerol dibiphytanyl glycerol tetraethers (GDGTs) synthesized by crenarchaeota enables determination of sea surface paleotemperatures from sedimentary records. This molecular approach presumes temporal uniformity in the controlling factors on biosynthesis of these lipids, and their survival in the geological record, notwithstanding the challenge of establishing ancient calibrations for such proxies. Thus, alkenone records from marine sediments document cooling at the Eocene/Oligocene boundary but cannot assess changes in ocean temperatures during the Cretaceous, unlike GDGTs, which record fluctuations in ocean temperatures during the Early Cretaceous, and even survive in Jurassic strata. Other molecular measures offer less precise, yet informative, indications of climate. For example, the occurrence of sterol ethers in Valanginian sediments from the mid-Pacific suggests some cooling at that time, since these compounds are only known to occur elsewhere in cold waters or upwelling systems. Molecular compositions can also attest to levels of oxygenation in marine systems. In particular, the occurrence of 13C-depleted isorenieratane indicates the presence of photosynthetic green sulfur bacteria, and therefore anoxic conditions, albeit perhaps short-lived. Intermittent occurrences of isorenieratane often alternate with the appearance of 2-methylhopanoids, which provide separate distinct evidence for variations in oxygenation, linked to circumstances

A multi-layered governance framework for incorporating social science insights into adapting to the health impacts of climate change.

PubMed

Bowen, Kathryn J; Ebi, Kristie; Friel, Sharon; McMichael, Anthony J

2013-09-10

Addressing climate change and its associated effects is a multi-dimensional and ongoing challenge. This includes recognizing that climate change will affect the health and wellbeing of all populations over short and longer terms, albeit in varied ways and intensities. That recognition has drawn attention to the need to take adaptive actions to lessen adverse impacts over the next few decades from unavoidable climate change, particularly in developing country settings. A range of sectors is responsible for appropriate adaptive policies and measures to address the health risks of climate change, including health services, water and sanitation, trade, agriculture, disaster management, and development. To broaden the framing of governance and decision-making processes by using innovative methods and assessments to illustrate the multi-sectoral nature of health-related adaptation to climate change. This is a shift from sector-specific to multi-level systems encompassing sectors and actors, across temporal and spatial scales. A review and synthesis of the current knowledge in the areas of health and climate change adaptation governance and decision-making processes. A novel framework is presented that incorporates social science insights into the formulation and implementation of adaptation activities and policies to lessen the health risks posed by climate change. Clarification of the roles that different sectors, organizations, and individuals occupy in relation to the development of health-related adaptation strategies will facilitate the inclusion of health and wellbeing within multi-sector adaptation policies, thereby strengthening the overall set of responses to minimize the adverse health effects of climate change.

A multi-layered governance framework for incorporating social science insights into adapting to the health impacts of climate change

PubMed Central

Bowen, Kathryn J.; Ebi, Kristie; Friel, Sharon; McMichael, Anthony J.

2013-01-01

Background Addressing climate change and its associated effects is a multi-dimensional and ongoing challenge. This includes recognizing that climate change will affect the health and wellbeing of all populations over short and longer terms, albeit in varied ways and intensities. That recognition has drawn attention to the need to take adaptive actions to lessen adverse impacts over the next few decades from unavoidable climate change, particularly in developing country settings. A range of sectors is responsible for appropriate adaptive policies and measures to address the health risks of climate change, including health services, water and sanitation, trade, agriculture, disaster management, and development. Objectives To broaden the framing of governance and decision-making processes by using innovative methods and assessments to illustrate the multi-sectoral nature of health-related adaptation to climate change. This is a shift from sector-specific to multi-level systems encompassing sectors and actors, across temporal and spatial scales. Design A review and synthesis of the current knowledge in the areas of health and climate change adaptation governance and decision-making processes. Results A novel framework is presented that incorporates social science insights into the formulation and implementation of adaptation activities and policies to lessen the health risks posed by climate change. Conclusion Clarification of the roles that different sectors, organizations, and individuals occupy in relation to the development of health-related adaptation strategies will facilitate the inclusion of health and wellbeing within multi-sector adaptation policies, thereby strengthening the overall set of responses to minimize the adverse health effects of climate change. PMID:24028938

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase–Protein Interactions

PubMed Central

Zhang, Liqun; Bouguet-Bonnet, Sabine; Buck, Matthias

2014-01-01

Combinations of experimentally derived data from nuclear magnetic resonance spectroscopy and analyses of molecular dynamics trajectories increasingly allow us to obtain a detailed description of the molecular mechanisms by which proteins function in signal transduction. This chapter provides an introduction into these two methodologies, illustrated by example of a small GTPase–effector interaction. It is increasingly becoming clear that new insights are provided by the combination of experimental and computational methods. Understanding the structural and protein dynamical contributions to allostery will be useful for the engineering of new binding interfaces and protein functions, as well as for the design/in silico screening of chemical agents that can manipulate the function of small GTPase–protein interactions in diseases such as cancer. PMID:22052494

Structural insights into the molecular mechanisms of myasthenia gravis and their therapeutic implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noridomi, Kaori; Watanabe, Go; Hansen, Melissa N.

The nicotinic acetylcholine receptor (nAChR) is a major target of autoantibodies in myasthenia gravis (MG), an autoimmune disease that causes neuromuscular transmission dysfunction. Despite decades of research, the molecular mechanisms underlying MG have not been fully elucidated. Here, we present the crystal structure of the nAChR α1 subunit bound by the Fab fragment of mAb35, a reference monoclonal antibody that causes experimental MG and competes with ~65% of antibodies from MG patients. Our structures reveal for the first time the detailed molecular interactions between MG antibodies and a core region on nAChR α1. These structures suggest a major nAChR-binding mechanismmore » shared by a large number of MG antibodies and the possibility to treat MG by blocking this binding mechanism. Structure-based modeling also provides insights into antibody-mediated nAChR cross-linking known to cause receptor degradation. Our studies establish a structural basis for further mechanistic studies and therapeutic development of MG.« less

Assessing surface water flood risk and management strategies under future climate change: Insights from an Agent-Based Model.

PubMed

Jenkins, K; Surminski, S; Hall, J; Crick, F

2017-10-01

Climate change and increasing urbanization are projected to result in an increase in surface water flooding and consequential damages in the future. In this paper, we present insights from a novel Agent Based Model (ABM), applied to a London case study of surface water flood risk, designed to assess the interplay between different adaptation options; how risk reduction could be achieved by homeowners and government; and the role of flood insurance and the new flood insurance pool, Flood Re, in the context of climate change. The analysis highlights that while combined investment in property-level flood protection and sustainable urban drainage systems reduce surface water flood risk, the benefits can be outweighed by continued development in high risk areas and the effects of climate change. In our simulations, Flood Re is beneficial in its function to provide affordable insurance, even under climate change. However, the scheme does face increasing financial pressure due to rising surface water flood damages. If the intended transition to risk-based pricing is to take place then a determined and coordinated strategy will be needed to manage flood risk, which utilises insurance incentives, limits new development, and supports resilience measures. Our modelling approach and findings are highly relevant for the ongoing regulatory and political approval process for Flood Re as well as for wider discussions on the potential of insurance schemes to incentivise flood risk management and climate adaptation in the UK and internationally. Copyright © 2017 Elsevier B.V. All rights reserved.

Plant molecular responses to the elevated ambient temperatures expected under global climate change.

PubMed

Fei, Qionghui; Li, Jingjing; Luo, Yunhe; Ma, Kun; Niu, Bingtao; Mu, Changjun; Gao, Huanhuan; Li, Xiaofeng

2018-01-02

Environmental temperatures affect plant distribution, growth, and development. The Intergovernmental Panel on Climate Change (IPCC) predicts that global temperatures will rise by at least 1.5°C by the end of this century. Global temperature changes have already had a discernable impact on agriculture, phenology, and ecosystems. At the molecular level, extensive literature exists on the mechanism controlling plant responses to high temperature stress. However, few studies have focused on the molecular mechanisms behind plant responses to mild increases in ambient temperature. Previous research has found that moderately higher ambient temperatures can induce hypocotyl elongation and early flowering. Recent evidence demonstrates roles for the phytohormones auxin and ethylene in adaptive growth of plant roots to slightly higher ambient temperatures.

Late Oligocene to Late Miocene Antarctic Climate Reconstructions Using Molecular and Isotopic Biomarker Proxies

NASA Astrophysics Data System (ADS)

Duncan, B.; Mckay, R. M.; Bendle, J. A.; Naish, T.; Levy, R. H.; Ventura, G. T.; Moossen, H. M.; Krishnan, S.; Pagani, M.

2015-12-01

Major climate and environmental changes occurred during late Oligocene to the late Miocene when atmospheric CO2 ranged between 500 and 300ppm, indicating threshold response of Antarctic ice sheets and climate to relatively modest CO2 variations. This implies that the southern high latitudes are highly sensitive to feedbacks associated with changes in global ice sheet and sea-ice extent, as well as terrestrial and marine ecosystems. This study focuses on two key intervals during the evolution of the Antarctic Ice Sheet: (1) The Late Oligocene and the Oligocene/Miocene boundary, when the East Antarctic Ice Sheet expanded close to present day volume following an extended period of inferred warmth. (2) The Mid-Miocene Climate Optimum (MMCO ~17-15 Ma), a period of global warmth and moderately elevated CO2 (350->500 ppm) which was subsequently followed by rapid cooling at 14-13.5 Ma. Reconstructions of climate and ice sheet variability, and thus an understanding of the various feedbacks that occurred during these intervals, are hampered by a lack of temperature and hydroclimate proxy data from the southern high latitudes. We present proxy climate reconstructions using terrestrial and marine organic biomarkers that provide new insights into Antarctica's climate evolution, using Antarctic drill cores and outcrop samples from a range of depositional settings. Bacterial ether-lipids have been analysed to determine terrestrial mean annual temperatures and soil pH (via the methylation and cyclisation indexes of branched tetraethers - MBT and CBT, respectively). Tetraether-lipids of crenarchaeota found in marine sediments sampled from continental shelves around Antarctica have been used to derive sea surface temperatures using the TEX86 index. Compound specific stable isotopes on n-alkanes sourced from terrestrial plants have been analysed to investigate changes in the hydrological and carbon cycles.

Macroscale patterns in body size of intertidal crustaceans provide insights on climate change effects

PubMed Central

Dugan, Jenifer E.; Hubbard, David M.; Contreras, Heraldo; Duarte, Cristian; Acuña, Emilio; Schoeman, David S.

2017-01-01

Predicting responses of coastal ecosystems to altered sea surface temperatures (SST) associated with global climate change, requires knowledge of demographic responses of individual species. Body size is an excellent metric because it scales strongly with growth and fecundity for many ectotherms. These attributes can underpin demographic as well as community and ecosystem level processes, providing valuable insights for responses of vulnerable coastal ecosystems to changing climate. We investigated contemporary macroscale patterns in body size among widely distributed crustaceans that comprise the majority of intertidal abundance and biomass of sandy beach ecosystems of the eastern Pacific coasts of Chile and California, USA. We focused on ecologically important species representing different tidal zones, trophic guilds and developmental modes, including a high-shore macroalga-consuming talitrid amphipod (Orchestoidea tuberculata), two mid-shore scavenging cirolanid isopods (Excirolana braziliensis and E. hirsuticauda), and a low-shore suspension-feeding hippid crab (Emerita analoga) with an amphitropical distribution. Significant latitudinal patterns in body sizes were observed for all species in Chile (21° - 42°S), with similar but steeper patterns in Emerita analoga, in California (32°- 41°N). Sea surface temperature was a strong predictor of body size (-4% to -35% °C-1) in all species. Beach characteristics were subsidiary predictors of body size. Alterations in ocean temperatures of even a few degrees associated with global climate change are likely to affect body sizes of important intertidal ectotherms, with consequences for population demography, life history, community structure, trophic interactions, food-webs, and indirect effects such as ecosystem function. The consistency of results for body size and temperature across species with different life histories, feeding modes, ecological roles, and microhabitats inhabiting a single widespread coastal

Macroscale patterns in body size of intertidal crustaceans provide insights on climate change effects.

PubMed

Jaramillo, Eduardo; Dugan, Jenifer E; Hubbard, David M; Contreras, Heraldo; Duarte, Cristian; Acuña, Emilio; Schoeman, David S

2017-01-01

Predicting responses of coastal ecosystems to altered sea surface temperatures (SST) associated with global climate change, requires knowledge of demographic responses of individual species. Body size is an excellent metric because it scales strongly with growth and fecundity for many ectotherms. These attributes can underpin demographic as well as community and ecosystem level processes, providing valuable insights for responses of vulnerable coastal ecosystems to changing climate. We investigated contemporary macroscale patterns in body size among widely distributed crustaceans that comprise the majority of intertidal abundance and biomass of sandy beach ecosystems of the eastern Pacific coasts of Chile and California, USA. We focused on ecologically important species representing different tidal zones, trophic guilds and developmental modes, including a high-shore macroalga-consuming talitrid amphipod (Orchestoidea tuberculata), two mid-shore scavenging cirolanid isopods (Excirolana braziliensis and E. hirsuticauda), and a low-shore suspension-feeding hippid crab (Emerita analoga) with an amphitropical distribution. Significant latitudinal patterns in body sizes were observed for all species in Chile (21° - 42°S), with similar but steeper patterns in Emerita analoga, in California (32°- 41°N). Sea surface temperature was a strong predictor of body size (-4% to -35% °C-1) in all species. Beach characteristics were subsidiary predictors of body size. Alterations in ocean temperatures of even a few degrees associated with global climate change are likely to affect body sizes of important intertidal ectotherms, with consequences for population demography, life history, community structure, trophic interactions, food-webs, and indirect effects such as ecosystem function. The consistency of results for body size and temperature across species with different life histories, feeding modes, ecological roles, and microhabitats inhabiting a single widespread coastal

Sustainable management for rangelands in a variable climate: evidence and insights from northern Australia.

PubMed

O'Reagain, P J; Scanlan, J C

2013-03-01

Inter-annual rainfall variability is a major challenge to sustainable and productive grazing management on rangelands. In Australia, rainfall variability is particularly pronounced and failure to manage appropriately leads to major economic loss and environmental degradation. Recommended strategies to manage sustainably include stocking at long-term carrying capacity (LTCC) or varying stock numbers with forage availability. These strategies are conceptually simple but difficult to implement, given the scale and spatial heterogeneity of grazing properties and the uncertainty of the climate. This paper presents learnings and insights from northern Australia gained from research and modelling on managing for rainfall variability. A method to objectively estimate LTCC in large, heterogeneous paddocks is discussed, and guidelines and tools to tactically adjust stocking rates are presented. The possible use of seasonal climate forecasts (SCF) in management is also considered. Results from a 13-year grazing trial in Queensland show that constant stocking at LTCC was far more profitable and largely maintained land condition compared with heavy stocking (HSR). Variable stocking (VAR) with or without the use of SCF was marginally more profitable, but income variability was greater and land condition poorer than constant stocking at LTCC. Two commercial scale trials in the Northern Territory with breeder cows highlighted the practical difficulties of variable stocking and provided evidence that heavier pasture utilisation rates depress reproductive performance. Simulation modelling across a range of regions in northern Australia also showed a decline in resource condition and profitability under heavy stocking rates. Modelling further suggested that the relative value of variable v. constant stocking depends on stocking rate and land condition. Importantly, variable stocking may possibly allow slightly higher stocking rates without pasture degradation. Enterprise

Congruent climate-related genecological responses from molecular markers and quantitative traits for western white pine (Pinus monticola)

Treesearch

Bryce A. Richardson; Gerald E. Rehfeldt; Mee-Sook Kim

2009-01-01

Analyses of molecular and quantitative genetic data demonstrate the existence of congruent climate-related patterns in western white pine (Pinus monticola). Two independent studies allowed comparisons of amplified fragment length polymorphism (AFLP) markers with quantitative variation in adaptive traits. Principal component analyses...

Cushing's disease: current medical therapies and molecular insights guiding future therapies.

PubMed

Lau, Darryl; Rutledge, Caleb; Aghi, Manish K

2015-02-01

OBJECT Cushing's disease (CD) can lead to significant morbidity secondary to hormonal sequelae or mass effect from the pituitary tumor. A transsphenoidal approach to resection of the adrenocorticotropic hormone (ACTH)-secreting pituitary adenoma is the first-line treatment. However, in the setting in which patients are unable to undergo surgery, have acute hypercortisolism, or have recurrent disease, medical therapy can play an important role. The authors performed a systematic review to highlight the efficacy of medical treatment of CD and discuss novel molecular insights that could guide the development of future medical treatments of CD. METHODS A search on current medical therapies for CD was performed. After individual medical therapeutic agents for CD were identified, each agent underwent a formal systematic search. The phrase "(name of agent) and Cushing's" was used as a search term in PubMed for all years up to 2014. The abstract of each article was reviewed for studies that evaluated the efficacy of medical treatment of CD. Only studies that enrolled at least 20 patients were included in the review. RESULTS A total of 11 articles on 6 individual agents were included in this review. Specific medical therapies were categorized based on the level of action: pituitary directed (cabergoline and pasireotide), adrenal/steroidogenesis directed (ketoconazole, metyrapone, and mitotane), and end-tissue directed/cortisol receptors (mifepristone). The studies identified consisted of a mix of retrospective reviews and small clinical trials. Only pasireotide and mifepristone have undergone Phase III clinical trials, from which they garnered FDA approval for the treatment of patients with CD. Overall, agents targeting ACTH secretion and steroidogenesis were found to be quite effective in reducing urine free cortisol (UFC) to levels near normal. A significant reduction in UFC was observed in 45%-100% of patients and a majority of patients gained clinical improvement

When climate science became climate politics: British media representations of climate change in 1988.

PubMed

Jaspal, Rusi; Nerlich, Brigitte

2014-02-01

Climate change has become a pressing environmental concern for scientists, social commentators and politicians. Previous social science research has explored media representations of climate change in various temporal and geographical contexts. Through the lens of Social Representations Theory, this article provides a detailed qualitative thematic analysis of media representations of climate change in the 1988 British broadsheet press, given that this year constitutes an important juncture in this transition of climate change from the domain of science to that of the socio-political sphere. The following themes are outlined: (i) "Climate change: a multi-faceted threat"; (ii) "Collectivisation of threat"; (iii) "Climate change and the attribution of blame"; and (iv) "Speculative solutions to a complex socio-environmental problem." The article provides detailed empirical insights into the "starting-point" for present-day disputes concerning climate change and lays the theoretical foundations for tracking the continuities and discontinuities characterising social representations of climate change in the future.

Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis.

PubMed

Casas, Laura; Saborido-Rey, Fran; Ryu, Taewoo; Michell, Craig; Ravasi, Timothy; Irigoien, Xabier

2016-10-17

Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups-rather than just two contrasting conditions- and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.

Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

PubMed Central

Casas, Laura; Saborido-Rey, Fran; Ryu, Taewoo; Michell, Craig; Ravasi, Timothy; Irigoien, Xabier

2016-01-01

Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites. PMID:27748421

Communicating Climate Change in the Agricultural Sector: Insights from Surveys and Interviews with Agricultural Advisors in the Midwestern United States

NASA Astrophysics Data System (ADS)

Prokopy, L. S.; Carlton, S.; Dunn, M.

2014-12-01

Understanding U.S. agricultural stakeholder views about the existence of climate change and what influences these views is central to developing communication in support of adaptation and mitigation. It has been postulated in the literature that extreme weather events can shape people's climate change beliefs and adaptation attitudes. In this presentation, we use data from pre- and post-extreme event surveys and interviews to examine the effects of the 2012 Midwestern US drought on agricultural advisors' climate change beliefs, adaptation attitudes, and risk perceptions. We found that neither climate change beliefs nor attitudes toward adaptation changed significantly as a result of the drought. Risk perceptions did change, however, with advisors becoming more concerned about risks from drought and pests and less concerned about risks related to flooding and ponding. Qualitative interviews revealed that while advisors readily accept the occurrence of extreme weather as a risk, the irregularity and unpredictability of extreme events for specific localities limits day-to-day consideration in respect to prescribed management advice. Instead, advisors' attention is directed towards planning for short-term changes encompassing weather, pests, and the market, as well as planning for long-term trends related to water availability. These findings provide important insights for communicating climate change in this critical sector while illustrating the importance of social science research in planning and executing communication campaigns.

Insight into the binding interactions of CYP450 aromatase inhibitors with their target enzyme: a combined molecular docking and molecular dynamics study.

PubMed

Galeazzi, Roberta; Massaccesi, Luca

2012-03-01

CYP450 aromatase catalyzes the terminal and rate-determining step in estrogen synthesis, the aromatization of androgens, and its inhibition is an efficient approach to treating estrogen-dependent breast cancer. Insight into the molecular basis of the interaction at the catalytic site between CYP450 aromatase inhibitors and the enzyme itself is required in order to design new and more active compounds. Hence, a combined molecular docking-molecular dynamics study was carried out to obtain the structure of the lowest energy association complexes of aromatase with some third-generation aromatase inhibitors (AIs) and with other novel synthesized letrozole-derived compounds which showed high in vitro activity. The results obtained clearly demonstrate the role of the pharmacophore groups present in the azaheterocyclic inhibitors (NSAIs)-namely the triazolic ring and highly functionalized aromatic moieties carrying H-bond donor or acceptor groups. In particular, it was pointed out that all of them can contribute to inhibition activity by interacting with residues of the catalytic cleft, but the amino acids involved are different for each compound, even if they belong to the same class. Furthermore, the azaheterocyclic group strongly coordinates with the Fe(II) of heme cysteinate in the most active NSAI complexes, while it prefers to adopt another orientation in less active ones.

Methods of teaching the physics of climate change in undergraduate physics courses

NASA Astrophysics Data System (ADS)

Sadler, Michael

2015-04-01

Although anthropogenic climate change is generally accepted in the scientific community, there is considerable skepticism among the general population and, therefore, in undergraduate students of all majors. Students are often asked by their peers, family members, and others, whether they ``believe'' climate change is occurring and what should be done about it (if anything). I will present my experiences and recommendations for teaching the physics of climate change to both physics and non-science majors. For non-science majors, the basic approach is to try to develop an appreciation for the scientific method (particularly peer-reviewed research) in a course on energy and the environment. For physics majors, the pertinent material is normally covered in their undergraduate courses in modern physics and thermodynamics. Nevertheless, it helps to review the basics, e.g. introductory quantum mechanics (discrete energy levels of atomic systems), molecular spectroscopy, and blackbody radiation. I have done this in a separate elective topics course, titled ``Physics of Climate Change,'' to help the students see how their knowledge gives them insight into a topic that is very volatile (socially and politically).

Teaching Climate Social Science and Its Practices: A Two-Pronged Approach to Climate Literacy

NASA Astrophysics Data System (ADS)

Shwom, R.; Isenhour, C.; McCright, A.; Robinson, J.; Jordan, R.

2014-12-01

The Essential Principles of Climate Science Literacy states that a climate-literate individual can: "understand the essential principles of Earth's climate system, assess scientifically credible information about climate change, communicate about climate and climate change in a meaningful way, and make informed and responsible decisions with regard to actions that may affect climate." We argue that further integration of the social science dimensions of climate change will advance the climate literacy goals of communication and responsible actions. The underlying rationale for this argues: 1) teaching the habits of mind and scientific practices that have synergies across the social and natural sciences can strengthen students ability to understand and assess science in general and that 2) understanding the empirical research on the social, political, and economic processes (including climate science itself) that are part of the climate system is an important step for enabling effective action and communication. For example, while climate literacy has often identified the public's faulty mental models of climate processes as a partial explanation of complacency, emerging research suggests that the public's mental models of the social world are equally or more important in leading to informed and responsible climate decisions. Building student's ability to think across the social and natural sciences by understanding "how we know what we know" through the sciences and a scientific understanding of the social world allows us to achieve climate literacy goals more systematically and completely. To enable this integration we first identify the robust social science insights for the climate science literacy principles that involve social systems. We then briefly identify significant social science contributions to climate science literacy that do not clearly fit within the seven climate literacy principles but arguably could advance climate literacy goals. We conclude

Insights from Modeling the Integrated Climate, Biogeochemical Cycles, Human Activities and Their Interactions in the ACME Earth System Model

NASA Astrophysics Data System (ADS)

Leung, L. R.; Thornton, P. E.; Riley, W. J.; Calvin, K. V.

2017-12-01

Towards the goal of understanding the contributions from natural and managed systems to current and future greenhouse gas fluxes and carbon-climate and carbon-CO2 feedbacks, efforts have been underway to improve representations of the terrestrial, river, and human components of the ACME earth system model. Broadly, our efforts include implementation and comparison of approaches to represent the nutrient cycles and nutrient limitations on ecosystem production, extending the river transport model to represent sediment and riverine biogeochemistry, and coupling of human systems such as irrigation, reservoir operations, and energy and land use with the ACME land and river components. Numerical experiments have been designed to understand how terrestrial carbon, nitrogen, and phosphorus cycles regulate climate system feedbacks and the sensitivity of the feedbacks to different model treatments, examine key processes governing sediment and biogeochemistry in the rivers and their role in the carbon cycle, and exploring the impacts of human systems in perturbing the hydrological and carbon cycles and their interactions. This presentation will briefly introduce the ACME modeling approaches and discuss preliminary results and insights from numerical experiments that lay the foundation for improving understanding of the integrated climate-biogeochemistry-human system.

Climate controls over ecosystem metabolism: insights from a fifteen-year inductive artificial neural network synthesis for a subalpine forest.

PubMed

Albert, Loren P; Keenan, Trevor F; Burns, Sean P; Huxman, Travis E; Monson, Russell K

2017-05-01

Eddy covariance (EC) datasets have provided insight into climate determinants of net ecosystem productivity (NEP) and evapotranspiration (ET) in natural ecosystems for decades, but most EC studies were published in serial fashion such that one study's result became the following study's hypothesis. This approach reflects the hypothetico-deductive process by focusing on previously derived hypotheses. A synthesis of this type of sequential inference reiterates subjective biases and may amplify past assumptions about the role, and relative importance, of controls over ecosystem metabolism. Long-term EC datasets facilitate an alternative approach to synthesis: the use of inductive data-based analyses to re-examine past deductive studies of the same ecosystem. Here we examined the seasonal climate determinants of NEP and ET by analyzing a 15-year EC time-series from a subalpine forest using an ensemble of Artificial Neural Networks (ANNs) at the half-day (daytime/nighttime) time-step. We extracted relative rankings of climate drivers and driver-response relationships directly from the dataset with minimal a priori assumptions. The ANN analysis revealed temperature variables as primary climate drivers of NEP and daytime ET, when all seasons are considered, consistent with the assembly of past studies. New relations uncovered by the ANN approach include the role of soil moisture in driving daytime NEP during the snowmelt period, the nonlinear response of NEP to temperature across seasons, and the low relevance of summer rainfall for NEP or ET at the same daytime/nighttime time step. These new results offer a more complete perspective of climate-ecosystem interactions at this site than traditional deductive analyses alone.

The Psychology of Climate Change Communication - Insights from the Center for Research on Environmental Decisions (CRED) (Invited)

NASA Astrophysics Data System (ADS)

Marx, S.

2010-12-01

social goals in favor or self interest; early involvement of stakeholders through participatory processes can help identify key concerns and information needs which can then be addressed in a tailored approach; taking advantage of default effects can make it easier for people to choose environmentally and socially beneficial options. Using research into the reactions of groups as disparate as African farmers and conservative U.S. voters, we offer insights on how scientists, educators, journalists and others can effectively connect with wider audiences. The communication principles presented in this talk can be applied beyond climate change and to science communication in general.

Insight into the molecular genetics of myopia

PubMed Central

Li, Jiali

2017-01-01

Myopia is the most common cause of visual impairment worldwide. Genetic and environmental factors contribute to the development of myopia. Studies on the molecular genetics of myopia are well established and have implicated the important role of genetic factors. With linkage analysis, association studies, sequencing analysis, and experimental myopia studies, many of the loci and genes associated with myopia have been identified. Thus far, there has been no systemic review of the loci and genes related to non-syndromic and syndromic myopia based on the different approaches. Such a systemic review of the molecular genetics of myopia will provide clues to identify additional plausible genes for myopia and help us to understand the molecular mechanisms underlying myopia. This paper reviews recent genetic studies on myopia, summarizes all possible reported genes and loci related to myopia, and suggests implications for future studies on the molecular genetics of myopia. PMID:29386878

Insight into the molecular genetics of myopia.

PubMed

Li, Jiali; Zhang, Qingjiong

2017-01-01

Myopia is the most common cause of visual impairment worldwide. Genetic and environmental factors contribute to the development of myopia. Studies on the molecular genetics of myopia are well established and have implicated the important role of genetic factors. With linkage analysis, association studies, sequencing analysis, and experimental myopia studies, many of the loci and genes associated with myopia have been identified. Thus far, there has been no systemic review of the loci and genes related to non-syndromic and syndromic myopia based on the different approaches. Such a systemic review of the molecular genetics of myopia will provide clues to identify additional plausible genes for myopia and help us to understand the molecular mechanisms underlying myopia. This paper reviews recent genetic studies on myopia, summarizes all possible reported genes and loci related to myopia, and suggests implications for future studies on the molecular genetics of myopia.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

NASA Astrophysics Data System (ADS)

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-01

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

Insight into the Li2CO3-K2CO3 eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics.

PubMed

Corradini, Dario; Coudert, François-Xavier; Vuilleumier, Rodolphe

2016-03-14

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li2CO3-K2CO3 (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self-diffusion coefficients, viscosity, and ionic conductivity.

UV photodissociation of proline-containing peptide ions: insights from molecular dynamics.

PubMed

Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

2015-03-01

UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S(2) and S(3), lie close to 213 nm. Non-adiabatic MD simulation starting from S(2) and S(3) shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

NASA Astrophysics Data System (ADS)

Girod, Marion; Sanader, Zeljka; Vojkovic, Marin; Antoine, Rodolphe; MacAleese, Luke; Lemoine, Jérôme; Bonacic-Koutecky, Vlasta; Dugourd, Philippe

2015-03-01

UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of proline-containing peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S2 and S3, lie close to 213 nm. Non-adiabatic MD simulation starting from S2 and S3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

PubMed

Ocak, S; Sos, M L; Thomas, R K; Massion, P P

2009-08-01

During the last decade, high-throughput technologies including genomic, epigenomic, transcriptomic and proteomic have been applied to further our understanding of the molecular pathogenesis of this heterogeneous disease, and to develop strategies that aim to improve the management of patients with lung cancer. Ultimately, these approaches should lead to sensitive, specific and noninvasive methods for early diagnosis, and facilitate the prediction of response to therapy and outcome, as well as the identification of potential novel therapeutic targets. Genomic studies were the first to move this field forward by providing novel insights into the molecular biology of lung cancer and by generating candidate biomarkers of disease progression. Lung carcinogenesis is driven by genetic and epigenetic alterations that cause aberrant gene function; however, the challenge remains to pinpoint the key regulatory control mechanisms and to distinguish driver from passenger alterations that may have a small but additive effect on cancer development. Epigenetic regulation by DNA methylation and histone modifications modulate chromatin structure and, in turn, either activate or silence gene expression. Proteomic approaches critically complement these molecular studies, as the phenotype of a cancer cell is determined by proteins and cannot be predicted by genomics or transcriptomics alone. The present article focuses on the technological platforms available and some proposed clinical applications. We illustrate herein how the "-omics" have revolutionised our approach to lung cancer biology and hold promise for personalised management of lung cancer.

A Social Identity Analysis of Climate Change and Environmental Attitudes and Behaviors: Insights and Opportunities

PubMed Central

Fielding, Kelly S.; Hornsey, Matthew J.

2016-01-01

Environmental challenges are often marked by an intergroup dimension. Political conservatives and progressives are divided on their beliefs about climate change, farmers come into conflict with scientists and environmentalists over water allocation or species protection, and communities oppose big business and mining companies that threaten their local environment. These intergroup tensions are reminders of the powerful influence social contexts and group memberships can have on attitudes, beliefs, and actions relating to climate change and the environment more broadly. In this paper, we use social identity theory to help describe and explain these processes. We review literature showing, how conceiving of oneself in terms of a particular social identity influences our environmental attitudes and behaviors, how relations between groups can impact on environmental outcomes, and how the content of social identities can direct group members to act in more or less pro-environmental ways. We discuss the similarities and differences between the social identity approach to these phenomena and related theories, such as cultural cognition theory, the theory of planned behavior, and value-belief-norm theory. Importantly, we also advance social-identity based strategies to foster more sustainable environmental attitudes and behaviors. Although this theoretical approach can provide important insights and potential solutions, more research is needed to build the empirical base, especially in relation to testing social identity solutions. PMID:26903924

A Social Identity Analysis of Climate Change and Environmental Attitudes and Behaviors: Insights and Opportunities.

PubMed

Fielding, Kelly S; Hornsey, Matthew J

2016-01-01

Environmental challenges are often marked by an intergroup dimension. Political conservatives and progressives are divided on their beliefs about climate change, farmers come into conflict with scientists and environmentalists over water allocation or species protection, and communities oppose big business and mining companies that threaten their local environment. These intergroup tensions are reminders of the powerful influence social contexts and group memberships can have on attitudes, beliefs, and actions relating to climate change and the environment more broadly. In this paper, we use social identity theory to help describe and explain these processes. We review literature showing, how conceiving of oneself in terms of a particular social identity influences our environmental attitudes and behaviors, how relations between groups can impact on environmental outcomes, and how the content of social identities can direct group members to act in more or less pro-environmental ways. We discuss the similarities and differences between the social identity approach to these phenomena and related theories, such as cultural cognition theory, the theory of planned behavior, and value-belief-norm theory. Importantly, we also advance social-identity based strategies to foster more sustainable environmental attitudes and behaviors. Although this theoretical approach can provide important insights and potential solutions, more research is needed to build the empirical base, especially in relation to testing social identity solutions.

Calcium-Activated Cl- Channel: Insights on the Molecular Identity in Epithelial Tissues.

PubMed

Rottgen, Trey S; Nickerson, Andrew J; Rajendran, Vazhaikkurichi M

2018-05-10

Calcium-activated chloride secretion in epithelial tissues has been described for many years. However, the molecular identity of the channel responsible for the Ca 2+ -activated Cl − secretion in epithelial tissues has remained a mystery. More recently, TMEM16A has been identified as a new putative Ca 2+ -activated Cl − channel (CaCC). The primary goal of this article will be to review the characterization of TMEM16A, as it relates to the physical structure of the channel, as well as important residues that confer voltage and Ca 2+ -sensitivity of the channel. This review will also discuss the role of TMEM16A in epithelial physiology and potential associated-pathophysiology. This will include discussion of developed knockout models that have provided much needed insight on the functional localization of TMEM16A in several epithelial tissues. Finally, this review will examine the implications of the identification of TMEM16A as it pertains to potential novel therapies in several pathologies.

Endometriosis: translation of molecular insights to management.

PubMed

Langan, K L; Farrell, M E; Keyser, E A; Salyer, B A; Burney, R O

2014-09-01

Endometriosis is a debilitating gynecologic disorder causing pelvic pain and infertility and characterized by the implantation of endometrial tissue to extrauterine locations. Though aspects of the condition remain enigmatic, the molecular pathophysiology of endometriosis appears to be clarifying. Estrogen dependence of the disease is a sentinel endocrine feature and reduction of estrogen bioavailability is the therapeutic principle upon which traditional treatment and prevention approaches have been based. Endometriosis is a chronic inflammatory condition associated with lesional neoangiogenesis and attenuated progesterone action at the level of the endometrium. The elucidation of the molecular pathways mediating these observations has revealed new targets for directed medical and surgical treatment. This paper will review current approaches to the management of endometriosis in the context of the molecular pathophysiology.

Insights into molecular interactions between CaM and its inhibitors from molecular dynamics simulations and experimental data.

PubMed

González-Andrade, Martin; Rodríguez-Sotres, Rogelio; Madariaga-Mazón, Abraham; Rivera-Chávez, José; Mata, Rachel; Sosa-Peinado, Alejandro; Del Pozo-Yauner, Luis; Arias-Olguín, Imilla I

2016-01-01

In order to contribute to the structural basis for rational design of calmodulin (CaM) inhibitors, we analyzed the interaction of CaM with 14 classic antagonists and two compounds that do not affect CaM, using docking and molecular dynamics (MD) simulations, and the data were compared to available experimental data. The Ca(2+)-CaM-Ligands complexes were simulated 20 ns, with CaM starting in the "open" and "closed" conformations. The analysis of the MD simulations provided insight into the conformational changes undergone by CaM during its interaction with these ligands. These simulations were used to predict the binding free energies (ΔG) from contributions ΔH and ΔS, giving useful information about CaM ligand binding thermodynamics. The ΔG predicted for the CaM's inhibitors correlated well with available experimental data as the r(2) obtained was 0.76 and 0.82 for the group of xanthones. Additionally, valuable information is presented here: I) CaM has two preferred ligand binding sites in the open conformation known as site 1 and 4, II) CaM can bind ligands of diverse structural nature, III) the flexibility of CaM is reduced by the union of its ligands, leading to a reduction in the Ca(2+)-CaM entropy, IV) enthalpy dominates the molecular recognition process in the system Ca(2+)-CaM-Ligand, and V) the ligands making more extensive contact with the protein have higher affinity for Ca(2+)-CaM. Despite their limitations, docking and MD simulations in combination with experimental data continue to be excellent tools for research in pharmacology, toward a rational design of new drugs.

Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling.

PubMed

Lodola, Alessio; Mor, Marco; Sirirak, Jitnapa; Mulholland, Adrian J

2009-04-01

FAAH (fatty acid amide hydrolase) is a promising target for the treatment of several central nervous system and peripheral disorders. Combined QM/MM (quantum mechanics/molecular mechanics) calculations have elucidated the role of its unusual catalytic triad in the hydrolysis of oleamide and oleoylmethyl ester substrates, and have identified the productive inhibitor-binding orientation for the carbamoylating compound URB524. These are potentially crucial insights for designing new covalent inhibitors of this drug target.

Molecular profiling of permafrost soil organic carbon composition and degradation

NASA Astrophysics Data System (ADS)

Gu, B.; Mann, B.

2014-12-01

Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon (C) cycling, though the dynamics of these transformations remain unclear at the molecular level. This study reports the application of ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to profile molecular components of Arctic SOM collected from the surface water and the mineral horizon of a low-centered polygon soil at Barrow Environmental Observatory (BEO), Barrow, Alaska. Soil samples were subjected to anaerobic warming experiments for a period of 40 days, and the SOM was extracted before and after the incubation to determine the components of organic C that were degraded over the course of the study. A CHO index based on molecular composition data was utilized to codify SOM components according to their observed degradation potential. Carbohydrate- and lignin-like compounds in the water-soluble fraction (WSF) demonstrated a high degradation potential, while structures with similar stoichiometries in the base-soluble fraction (BSF) were not readily degraded. The WSF of SOM also shifted to a wider range of measured molecular masses including an increased prevalence of larger compounds, while the size distribution of compounds in the BSF changed little over the same period. Additionally, the molecular profiling data indicated an apparently ordered incorporation of organic nitrogen in the BSF immobilized as primary and secondary amines, possibly as components of N-heterocycles, which may provide insight into nitrogen immobilization or mobilization processes in SOM. Our study represents an important step forward for studying Arctic SOM with improved understanding of the molecular properties of soil organic C and the ability to represent SOM in climate models that will predict the impact of climate change on soil C and nutrient cycling.

Introduction to the special issue on molecular spectroscopy, atmospheric composition and climate change

NASA Astrophysics Data System (ADS)

Boudon, Vincent; Sears, Trevor; Coheur, Pierre-François

2018-06-01

Changes to the Earth's climate system resulting from modification of the atmosphere caused by both anthropogenic and natural effects are one of the great long-term threats to our society. In order to measure and understand the drivers of these changes, quantitative field measurements combined with precise and accurate laboratory data are needed. The Kyoto Protocol [1], signed in 1997, focused the scientific community on the need for data aimed at developing a better understanding of the physics and chemistry of molecular and aerosol species that lead to long-term climate change. The results have been impressive. Continuous and extensive concentration measurements are now being performed from the ground, e.g. the TCCON network, from balloons and airplanes and, of course, from space (e.g. ACE-Scisat, TANSO-GOSAT, IASI-Metop, OCO-2, Sentinel-5P, …). With the observing system now in place the concentration profiles of a suite of species, including greenhouse gases, aerosol precursors and others are measured with increasing precision over large areas of the Earth, leading to a much more complete understanding of the radiative forcing budget.

Hydroclimate variability in Scandinavia over the last millennium - insights from a climate model-proxy data comparison

NASA Astrophysics Data System (ADS)

Seftigen, Kristina; Goosse, Hugues; Klein, Francois; Chen, Deliang

2017-12-01

The integration of climate proxy information with general circulation model (GCM) results offers considerable potential for deriving greater understanding of the mechanisms underlying climate variability, as well as unique opportunities for out-of-sample evaluations of model performance. In this study, we combine insights from a new tree-ring hydroclimate reconstruction from Scandinavia with projections from a suite of forced transient simulations of the last millennium and historical intervals from the CMIP5 and PMIP3 archives. Model simulations and proxy reconstruction data are found to broadly agree on the modes of atmospheric variability that produce droughts-pluvials in the region. Despite these dynamical similarities, large differences between simulated and reconstructed hydroclimate time series remain. We find that the GCM-simulated multi-decadal and/or longer hydroclimate variability is systematically smaller than the proxy-based estimates, whereas the dominance of GCM-simulated high-frequency components of variability is not reflected in the proxy record. Furthermore, the paleoclimate evidence indicates in-phase coherencies between regional hydroclimate and temperature on decadal timescales, i.e., sustained wet periods have often been concurrent with warm periods and vice versa. The CMIP5-PMIP3 archive suggests, however, out-of-phase coherencies between the two variables in the last millennium. The lack of adequate understanding of mechanisms linking temperature and moisture supply on longer timescales has serious implications for attribution and prediction of regional hydroclimate changes. Our findings stress the need for further paleoclimate data-model intercomparison efforts to expand our understanding of the dynamics of hydroclimate variability and change, to enhance our ability to evaluate climate models, and to provide a more comprehensive view of future drought and pluvial risks.

Trichoderma for climate resilient agriculture.

PubMed

Kashyap, Prem Lal; Rai, Pallavi; Srivastava, Alok Kumar; Kumar, Sudheer

2017-08-01

Climate change is one of the biggest challenges of the twenty-first century for sustainable agricultural production. Several reports highlighted the need for better agricultural practices and use of eco-friendly methods for sustainable crop production under such situations. In this context, Trichoderma species could be a model fungus to sustain crop productivity. Currently, these are widely used as inoculants for biocontrol, biofertilization, and phytostimulation. They are reported to improve photosynthetic efficiency, enhance nutrient uptake and increase nitrogen use efficiency in crops. Moreover, they can be used to produce bio-energy, facilitate plants for adaptation and mitigate adverse effect of climate change. The technological advancement in high throughput DNA sequencing and biotechnology provided deep insight into the complex and diverse biotic interactions established in nature by Trichoderma spp. and efforts are being made to translate this knowledge to enhance crop growth, resistance to disease and tolerance to abiotic stresses under field conditions. The discovery of several traits and genes that are involved in the beneficial effects of Trichoderma spp. has resulted in better understanding of the performance of bioinoculants in the field, and will lead to more efficient use of these strains and possibly to their improvement by genetic modification. The present mini-review is an effort to elucidate the molecular basis of plant growth promotion and defence activation by Trichoderma spp. to garner broad perspectives regarding their functioning and applicability for climate resilient agriculture.

Insights into the immuno-molecular biology of Angiostrongylus vasorum through transcriptomics--prospects for new interventions.

PubMed

Ansell, Brendan R E; Schnyder, Manuela; Deplazes, Peter; Korhonen, Pasi K; Young, Neil D; Hall, Ross S; Mangiola, Stefano; Boag, Peter R; Hofmann, Andreas; Sternberg, Paul W; Jex, Aaron R; Gasser, Robin B

2013-12-01

Angiostrongylus vasorum is a metastrongyloid nematode of dogs and other canids of major clinical importance in many countries. In order to gain first insights into the molecular biology of this worm, we conducted the first large-scale exploration of its transcriptome, and predicted essential molecules linked to metabolic and biological processes as well as host immune responses. We also predicted and prioritized drug targets and drug candidates. Following Illumina sequencing (RNA-seq), 52.3 million sequence reads representing adult A. vasorum were assembled and annotated. The assembly yielded 20,033 contigs, which encoded proteins with 11,505 homologues in Caenorhabditis elegans, and additional 2252 homologues in various other parasitic helminths for which curated data sets were publicly available. Functional annotation was achieved for 11,752 (58.6%) proteins predicted for A. vasorum, including peptidases (4.5%) and peptidase inhibitors (1.6%), protein kinases (1.7%), G protein-coupled receptors (GPCRs) (1.5%) and phosphatases (1.2%). Contigs encoding excretory/secretory and immuno-modulatory proteins represented some of the most highly transcribed molecules, and encoded enzymes that digest haemoglobin were conserved between A. vasorum and other blood-feeding nematodes. Using an essentiality-based approach, drug targets, including neurotransmitter receptors, an important chemosensory ion channel and cysteine proteinase-3 were predicted in A. vasorum, as were associated small molecular inhibitors/activators. Future transcriptomic analyses of all developmental stages of A. vasorum should facilitate deep explorations of the molecular biology of this important parasitic nematode and support the sequencing of its genome. These advances will provide a foundation for exploring immuno-molecular aspects of angiostrongylosis and have the potential to underpin the discovery of new methods of intervention. © 2013.

The terrestrial hydro-climate of the Early Eocene: insights from the oxygen and clumped isotope composition of pedogenic siderite

NASA Astrophysics Data System (ADS)

van Dijk, J.; Fernandez, A.; Müller, I.; White, T. S.; Bernasconi, S. M.

2016-12-01

The Early Eocene (56 Ma) is the youngest period of Earth's history when CO2 concentrations in the atmosphere (600-1500 ppm) reached levels close to those predicted for future emission scenarios. Proxy-based climate reconstructions from this interval can therefore be used to gain insights on effects that anthropogenic emissions might have on the climate system. So far, Early Eocene climatic data is limited to the oceans, where proxies for temperature are abundant and relatively well understood. However, in order to get a complete picture of the Early Eocene climate, temperature and rainfall reconstructions on the continental paleo-surface are needed. Here, we present clumped and stable oxygen isotope measurements of siderite samples collected along a North-South transect in the North American Continent. These siderites formed in kaolinitic soils that developed globally under the extremely wet and warm conditions of the Early Eocene. They provide a record of both soil temperature and the δ18O composition of meteoric water, which can be used to unravel the regional paleo-precipitation rate. Both parameters were estimated using an elaborate in-house calibration constructed with synthetic siderite precipitated in the presence or absence of iron reducing bacteria. Measurements of δD on plant-derived N-alkanes present within the same soils align well with our δ18Owater data, confirming an Early Eocene meteoric water line similar to the present day. We provide an estimate of the meridional temperature gradient during the Early Eocene and offer constraints on the boundary conditions of the Earth's hydrologic cycle under high pCO2.

First insight into the molecular epidemiology of Mycobacterium tuberculosis in Santa Catarina, southern Brazil.

PubMed

Nogueira, Christiane Lourenço; Prim, Rodrigo Ivan; Senna, Simone Gonçalves; Rovaris, Darcita Büerger; Maurici, Rosemeri; Rossetti, Maria Lúcia; Couvin, David; Rastogi, Nalin; Bazzo, Maria Luiza

2016-03-01

Molecular epidemiology of Mycobacterium tuberculosis is useful for understanding disease transmission dynamics, and to establish strategic measures for TB control and prevention. The aim of this study was to analyze clinical, epidemiological and molecular characteristics of MTBC clinical isolates from Santa Catarina state, southern Brazil. During one-year period, 406 clinical isolates of MTBC were collected from Central Laboratory of Public Health and typed by spoligotyping. Demographic and clinical data were collected from the Brazilian National Mandatory Disease Reporting System. The majority of cases occurred in highest population densities regions and about 50% had some condition associated with TB. Among all isolates, 5.7% were MDR, which showed association with drug addiction. LAM was the most predominant lineage with 47.5%, followed by the T superfamily with 25.9% and Haarlem with 12.3%. The MST showed two major groups: the first was formed mainly by the LAM lineage and the second was mainly formed by the T and Haarlem lineages. Others lineages were distributed in peripheral positions. This study provides the first insight into the population structure of M. tuberculosis in SC State. Spoligotyping and other genotyping analyses are important to establish strategic measures for TB control and prevention. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular insights into the progression of crystalline silica-induced pulmonary toxicity in rats.

PubMed

Sellamuthu, Rajendran; Umbright, Christina; Roberts, Jenny R; Cumpston, Amy; McKinney, Walter; Chen, Bean T; Frazer, David; Li, Shengqiao; Kashon, Michael; Joseph, Pius

2013-04-01

Identification of molecular target(s) and mechanism(s) of silica-induced pulmonary toxicity is important for the intervention and/or prevention of diseases associated with exposure to silica. Rats were exposed to crystalline silica by inhalation (15 mg m(-3), 6 h per day, 5 days) and global gene expression profile was determined in the lungs by microarray analysis at 1, 2, 4, 8 and 16 weeks following termination of silica exposure. The number of significantly differentially expressed genes (>1.5-fold change and <0.01 false discovery rate P-value) detected in the lungs during the post-exposure time intervals analyzed exhibited a steady increase in parallel with the progression of silica-induced pulmonary toxicity noticed in the rats. Quantitative real-time PCR analysis of a representative set of 10 genes confirmed the microarray findings. The number of biological functions, canonical pathways and molecular networks significantly affected by silica exposure, as identified by the bioinformatics analysis of the significantly differentially expressed genes detected during the post-exposure time intervals, also exhibited a steady increase similar to the silica-induced pulmonary toxicity. Genes involved in oxidative stress, inflammation, respiratory diseases, cancer, and tissue remodeling and fibrosis were significantly differentially expressed in the rat lungs; however, unresolved inflammation was the single most significant biological response to pulmonary exposure to silica. Excessive mucus production, as implicated by significant overexpression of the pendrin coding gene, SLC26A4, was identified as a potential novel mechanism for silica-induced pulmonary toxicity. Collectively, the findings of our study provided insights into the molecular mechanisms underlying the progression of crystalline silica-induced pulmonary toxicity in the rat. Published 2012. This article is a US Government work and is in the public domain in the USA. Published 2012. This article is a US

Natural and molecular history of prolactinoma: insights from a Prlr-/- mouse model.

PubMed

Bernard, Valérie; Villa, Chiara; Auguste, Aurélie; Lamothe, Sophie; Guillou, Anne; Martin, Agnès; Caburet, Sandrine; Young, Jacques; Veitia, Reiner A; Binart, Nadine

2018-01-19

Lactotroph adenoma, also called prolactinoma, is the most common pituitary tumor but little is known about its pathogenesis. Mouse models of prolactinoma can be useful to better understand molecular mechanisms involved in abnormal lactotroph cell proliferation and secretion. We have previously developed a prolactin receptor deficient ( Prlr -/- ) mouse, which develops prolactinoma. The present study aims to explore the natural history of prolactinoma formation in Prlr -/- mice, using hormonal, radiological, histological and molecular analyses to uncover mechanisms involved in lactotroph adenoma development. Prlr -/- females develop large secreting prolactinomas from 12 months of age, with a penetrance of 100%, mimicking human aggressive densely granulated macroprolactinoma, which is a highly secreting subtype. Mean blood PRL measurements reach 14 902 ng/mL at 24 months in Prlr -/- females while PRL levels were below 15 ng/mL in control mice ( p < 0.01). By comparing pituitary microarray data of Prlr -/- mice and an estrogen-induced prolactinoma model in ACI rats, we pinpointed 218 concordantly differentially expressed (DE) genes involved in cell cycle, mitosis, cell adhesion molecules, dopaminergic synapse and estrogen signaling. Pathway/gene-set enrichment analyses suggest that the transcriptomic dysregulation in both models of prolactinoma might be mediated by a limited set of transcription factors (i.e., STAT5, STAT3, AhR, ESR1, BRD4, CEBPD, YAP, FOXO1) and kinases (i.e., JAK2, AKT1, BRAF, BMPR1A, CDK8, HUNK, ALK, FGFR1, ILK). Our experimental results and their bioinformatic analysis provide insights into early genomic changes in murine models of the most frequent human pituitary tumor.

Molecular insights into early stage aggregation of di-Fmoc-L-lysine in binary mixture of organic solvent and water

NASA Astrophysics Data System (ADS)

Huda, Md Masrul; Rai, Neeraj

Molecular gels are relatively new class of soft materials, which are formed by the supramolecular aggregation of low molecular weight gelators (LMWGs) in organic solvents and/or water. Hierarchical self-assembly of small gelator molecules lead to three-dimensional complex fibrillar networks, which restricts the flow of solvents and results in viscous solid like materials or gels. These gels have drawn significant attentions for their potential applications for drug delivery, tissue engineering, materials for sensors etc. As of now, self-assembly of gelator molecules into one-dimensional fibers is not well understood, although that is very important to design new gelators for desired applications. Here, we present molecular dynamics study that provides molecular level insight into early stage aggregation of selected gelator, di-Fmoc-L-lysine in binary mixture of organic solvent and water. We will present the role of different functional groups of gelator molecule such as aromatic ring, amide, and carboxylic group on aggregation. We will also present the effect of concentrations of gelator and solvent on self-assembly of gelators. This study has captured helical fiber growth and branching of fiber, which is in good agreement with experimental observations.

Criminality and climate change

NASA Astrophysics Data System (ADS)

White, Rob

2016-08-01

The impacts of climate change imply a reconceptualization of environment-related criminality. Criminology can offer insight into the definitions and dynamics of this behaviour, and outline potential areas of redress.

Theoretical Insight into Shocked Gases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leiding, Jeffery Allen

2016-09-29

I present the results of statistical mechanical calculations on shocked molecular gases. This work provides insight into the general behavior of shock Hugoniots of gas phase molecular targets with varying initial pressures. The dissociation behavior of the molecules is emphasized. Impedance matching calculations are performed to determine the maximum degree of dissociation accessible for a given flyer velocity as a function of initial gas pressure.

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling.

PubMed

Tan, Jianjun; Yuan, Hongling; Li, Chunhua; Zhang, Xiaoyi; Wang, Cunxin

2016-04-01

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular insights into melanoma brain metastases.

PubMed

Westphal, Dana; Glitza Oliva, Isabella C; Niessner, Heike

2017-06-01

Substantial proportions of patients with metastatic melanoma develop brain metastases during the course of their disease, often resulting in significant morbidity and death. Despite recent advances with BRAF/MEK and immune-checkpoint inhibitors in the treatment of patients who have melanoma with extracerebral metastases, patients who have melanoma brain metastases still have poor overall survival, highlighting the need for further therapy options. A deeper understanding of the molecular pathways involved in the development of melanoma brain metastases is required to develop more brain-specific therapies. Here, the authors summarize the currently known preclinical data and describe steps involved in the development of melanoma brain metastases. Only by knowing the molecular background is it possible to design new therapeutic agents that can be used to improve the outcome of patients with melanoma brain metastases. Cancer 2017;123:2163-75. © 2017 American Cancer Society. © 2017 American Cancer Society.

Whole-genome transcriptomic insights into protective molecular mechanisms in metabolically healthy obese African Americans.

PubMed

Gaye, Amadou; Doumatey, Ayo P; Davis, Sharon K; Rotimi, Charles N; Gibbons, Gary H

2018-01-01

Several clinical guidelines have been proposed to distinguish metabolically healthy obesity (MHO) from other subgroups of obesity but the molecular mechanisms by which MHO individuals remain metabolically healthy despite having a high fat mass are yet to be elucidated. We conducted the first whole blood transcriptomic study designed to identify specific sets of genes that might shed novel insights into the molecular mechanisms that protect or delay the occurrence of obesity-related co-morbidities in MHO. The study included 29 African-American obese individuals, 8 MHO and 21 metabolically abnormal obese (MAO). Unbiased transcriptome-wide network analysis was carried out to identify molecular modules of co-expressed genes that are collectively associated with MHO. Network analysis identified a group of 23 co-expressed genes, including ribosomal protein genes (RPs), which were significantly downregulated in MHO subjects. The three pathways enriched in the group of co-expressed genes are EIF2 signaling, regulation of eIF4 and p70S6K signaling, and mTOR signaling. The expression of ten of the RPs collectively predicted MHO status with an area under the curve of 0.81. Triglycerides/HDL (TG/HDL) ratio, an index of insulin resistance, was the best predictor of the expression of genes in the MHO group. The higher TG/HDL values observed in the MAO subjects may underlie the activation of endoplasmic reticulum (ER) and related-stress pathways that lead to a chronic inflammatory state. In summary, these findings suggest that controlling ER stress and/or ribosomal stress by downregulating RPs or controlling TG/HDL ratio may represent effective strategies to prevent or delay the occurrence of metabolic disorders in obese individuals.

Assessing Climate Risk on Agricultural Production: Insights Using Retrospective Analysis of Crop Insurance and Climatic Trends

NASA Astrophysics Data System (ADS)

Reyes, J. J.; Elias, E.; Eischens, A.; Shilts, M.; Rango, A.; Steele, R.

2017-12-01

The collaborative synthesis of existing datasets, such as long-term climate observations and farmers' crop insurance payments, can increase their overall collective value and societal application. The U.S. Department of Agriculture (USDA) Climate Hubs were created to develop and deliver science-based information and technologies to agricultural and natural resource managers to enable climate-informed decision-making. As part of this mission, Hubs work across USDA and other climate service agencies to synthesize existing information. The USDA Risk Management Agency (RMA) is responsible for overseeing the Federal crop insurance program which currently insures over $100 billion in crops annually. RMA hosts data describing the cause for loss (e.g. drought, wind, irrigation failure) and indemnity amount (i.e. total cost of loss) at multiple spatio-temporal scales (i.e. state, county, year, month). The objective of this paper is to link climate information with indemnities, and their associated cause of loss, to assess climate risk on agricultural production and provide regionally-relevant information to stakeholders to promote resilient working landscapes. We performed a retrospective trend analysis at the state-level for the American Southwest (SW). First, we assessed indemnity-only trends by cause of loss and crop type at varying temporal scales. Historical monthly weather data (i.e. precipitation and temperature) and long-term drought indices (e.g. Palmer Drought Severity Index) were then linked with indemnities and grouped by different causes of loss. Climatological ranks were used to integrate historical comparative intensity of acute and long-term climatic events. Heat and drought as causes of loss were most correlated with temperature and drought indicators, respectively. Across all SW states increasing indemnities were correlated with warmer conditions. Multiple statistical trend analyses suggest a framework is necessary to appropriately measure the biophysical

Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes.

PubMed

Meik, Jesse M; Streicher, Jeffrey W; Lawing, A Michelle; Flores-Villela, Oscar; Fujita, Matthew K

2015-01-01

Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus.

Characterization of hairless (Hr) and FGF5 genes provides insights into the molecular basis of hair loss in cetaceans

PubMed Central

2013-01-01

Background Hair is one of the main distinguishing characteristics of mammals and it has many important biological functions. Cetaceans originated from terrestrial mammals and they have evolved a series of adaptations to aquatic environments, which are of evolutionary significance. However, the molecular mechanisms underlying their aquatic adaptations have not been well explored. This study provided insights into the evolution of hair loss during the transition from land to water by investigating and comparing two essential regulators of hair follicle development and hair follicle cycling, i.e., the Hairless (Hr) and FGF5 genes, in representative cetaceans and their terrestrial relatives. Results The full open reading frame sequences of the Hr and FGF5 genes were characterized in seven cetaceans. The sequence characteristics and evolutionary analyses suggested the functional loss of the Hr gene in cetaceans, which supports the loss of hair during their full adaptation to aquatic habitats. By contrast, positive selection for the FGF5 gene was found in cetaceans where a series of positively selected amino acid residues were identified. Conclusions This is the first study to investigate the molecular basis of the hair loss in cetaceans. Our investigation of Hr and FGF5, two indispensable regulators of the hair cycle, provide some new insights into the molecular basis of hair loss in cetaceans. The results suggest that positive selection for the FGF5 gene might have promoted the termination of hair growth and early entry into the catagen stage of hair follicle cycling. Consequently, the hair follicle cycle was disrupted and the hair was lost completely due to the loss of the Hr gene function in cetaceans. This suggests that cetaceans have evolved an effective and complex mechanism for hair loss. PMID:23394579

Genomic basis for coral resilience to climate change.

PubMed

Barshis, Daniel J; Ladner, Jason T; Oliver, Thomas A; Seneca, François O; Traylor-Knowles, Nikki; Palumbi, Stephen R

2013-01-22

Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using Illumina sequencing) among conspecific thermally sensitive and thermally resilient corals to identify the molecular pathways contributing to coral resilience. Under simulated bleaching stress, sensitive and resilient corals change expression of hundreds of genes, but the resilient corals had higher expression under control conditions across 60 of these genes. These "frontloaded" transcripts were less up-regulated in resilient corals during heat stress and included thermal tolerance genes such as heat shock proteins and antioxidant enzymes, as well as a broad array of genes involved in apoptosis regulation, tumor suppression, innate immune response, and cell adhesion. We propose that constitutive frontloading enables an individual to maintain physiological resilience during frequently encountered environmental stress, an idea that has strong parallels in model systems such as yeast. Our study provides broad insight into the fundamental cellular processes responsible for enhanced stress tolerances that may enable some organisms to better persist into the future in an era of global climate change.

Insight to forcing of late Quaternary climate change from aeolian dust archives in eastern Australia

NASA Astrophysics Data System (ADS)

McGowan, H. A.; Marx, S.; Soderholm, J.; Denholm, J.; Petherick, L.

2010-12-01

The Australian continent is the largest source of dust in the Southern Hemisphere. Historical dust emissions records display inter-annual variability in response to the El Niño Southern Oscillation (ENSO) phenomenon and inter-decadal variability which has been linked to the Pacific Decadal Oscillation (PDO). These reflect change in hydrometeorology of the continents two major dust source regions, the Murray-Darling Basin and the Lake Eyre Basin. The historical records do not allow longer term variability of ENSO and the PDO and their influence on Australia to be quantified. Importantly, sub-Milankovitch centennial to multi-millennial scale climate cycles and their impacts are not represented in the historical records. In this paper we present summary results from the analysis of two aeolain dust records spanning 7 ka and 45 ka. These were developed from ombrotrophic mire and lacustrine sediment cores collected from the Australian Alps and southeast Queensland. Both sites are located in the southeast Australian dust transport pathway and provide rare insight to forcings of climate variability and its impacts on eastern Australia through the late Quaternary. Age controls for the cores were established using 14C and 210Pb dating [McGowan et al. 2008, 2010]. The cores were sliced into 2 to 5 mm segments with a sub-sample of each segment combusted at 450°C for 12 hrs to destroy organic material and allow recovery of mineral dust. Geochemical fingerprinting of the < 90 µm fraction of the dust was used to determine provenance and to account for contamination by fluvial and/or colluvial sediments [Marx et al. 2005]. Analysis of the dust records, proxy for hydrometeorology, identified tropical ocean teleconnections, variability of solar irradiance and change in ocean deep water circulation as the principal causes of inter-decadal to centennial scale climate cycles and change. Predictions of future climate must consider these forcings so that in water scarce regions of

New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability

NASA Astrophysics Data System (ADS)

Maurice, Pascal; Baud, Stéphanie; Bocharova, Olga V.; Bocharov, Eduard V.; Kuznetsov, Andrey S.; Kawecki, Charlotte; Bocquet, Olivier; Romier, Beatrice; Gorisse, Laetitia; Ghirardi, Maxime; Duca, Laurent; Blaise, Sébastien; Martiny, Laurent; Dauchez, Manuel; Efremov, Roman G.; Debelle, Laurent

2016-12-01

Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural and biochemical data cannot account for such membrane localization. By combining molecular biology and biochemical analyses with structural biophysics and computational approaches, we identified here two regions in human NEU1 - segments 139-159 (TM1) and 316-333 (TM2) - as potential transmembrane (TM) domains. In membrane mimicking environments, the corresponding peptides form stable α-helices and TM2 is suited for self-association. This was confirmed with full-size NEU1 by co-immunoprecipitations from membrane preparations and split-ubiquitin yeast two hybrids. The TM2 region was shown to be critical for dimerization since introduction of point mutations within TM2 leads to disruption of NEU1 dimerization and decrease of sialidase activity in membrane. In conclusion, these results bring new insights in the molecular organization of membrane-bound NEU1 and demonstrate, for the first time, the presence of two potential TM domains that may anchor NEU1 in the membrane, control its dimerization and sialidase activity.

Informing climate change adaptation with insights from famine early warning (Invited)

NASA Astrophysics Data System (ADS)

Funk, C. C.; Verdin, J. P.

2010-12-01

Famine early warning systems provide a unique viewpoint for understanding the implications of climate change on food security, identifying the locations and seasons where millions of food insecure people are dependent upon climate-sensitive agricultural systems. The Famine Early Warning Systems Network (FEWS NET) is a decision support system sponsored by the Office of Food for Peace of the U.S. Agency for International Development (USAID), which distributes over two billion dollars of food aid to more than 40 countries each year. FEWS NET identifies the times and places where food aid is required by the most climatically sensitive and consequently food insecure populations of the developing world. As result, FEWS NET has developed its own "climate service", implemented by USGS, NOAA, and NASA, to support its decision making processes. The foundation of this climate service is the monitoring of current growing conditions for early identification of agricultural drought that might impact food security. Since station networks are sparse in the countries monitored, FEWS NET has a tradition (dating back to 1985) of reliance on satellite remote sensing of vegetation and rainfall. In the last ten years, climate forecasts have become an additional tool for food security assessment, extending the early warning perspective to include expected agricultural outcomes for the season ahead. More recently, research has expanded to include detailed analyses of recent observed climate trends, combined with diagnostic ocean-atmosphere studies. These studies are then used to develop interpretations of GCM scenarios and their implications for future patterns of precipitation and temperature, revealing trends towards warmer/drier climate conditions and increases in the relative frequency of drought. In some regions, like Eastern Africa, such changes seem to be already occurring, with an associated increase in food insecurity. Sub-national analyses for Kenya, for example, point to the

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

PubMed Central

Flores-Villela, Oscar; Fujita, Matthew K.

2015-01-01

Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus. PMID:26107178

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

PubMed Central

Yu, Xiaozhen; Sigler, Sara C.; Hossain, Delwar; Wierdl, Monika; Gwaltney, Steven R.; Potter, Philip M.; Wadkins, Randy M.

2013-01-01

Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. In humans, substrates for these enzymes are far-ranging, and include the street drug heroin and the anticancer agent irinotecan. Hence, their ability to bind and metabolize substrates is of broad interest to biomedical science. In this study, we focused our attention on dynamic motions of a CE from B. subtilis (pnbCE), with emphasis on the question of what individual domains of the enzyme might contribute to its catalytic activity. We used a 10 ns all-atom molecular dynamics simulation, normal mode calculations, and enzyme kinetics to understand catalytic consequences of structural changes within this enzyme. Our results shed light on how molecular motions are coupled with catalysis. During molecular dynamics, we observed a distinct C-C bond rotation between two conformations of Glu310. Such a bond rotation would alternately facilitate and impede protonation of the active site His399 and act as a mechanism by which the enzyme alternates between its active and inactive conformation. Our normal mode results demonstrate that the distinct low-frequency motions of two loops in pnbCE, coil_5 and coil_21, are important in substrate conversion and seal the active site. Mutant CEs lacking these external loops show significantly reduced rates of substrate conversion, suggesting this sealing motion prevents escape of substrate. Overall, the results of our studies give new insight into the structure-function relationship of CEs and have implications for the entire family of α/β fold family of hydrolases, of which this CE is a member. PMID:22127613

Climate Variability and Wildfires: Insights from Global Earth System Models

NASA Astrophysics Data System (ADS)

Ward, D. S.; Shevliakova, E.; Malyshev, S.; Lamarque, J. F.; Wittenberg, A. T.

2016-12-01

Better understanding of the relationship between variability in global climate and emissions from wildfires is needed for predictions of fire activity on interannual to multi-decadal timescales. Here we investigate this relationship using the long, preindustrial control simulations and historical ensembles of two Earth System models; CESM1 and the NOAA/GFDL ESM2Mb. There is smaller interannual variability of global fires in both models than in present day inventories, especially in boreal regions where observed fires vary substantially from year to year. Patterns of fire response to climate oscillation indices, including the El Niño / Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO) and Atlantic Meridional Oscillation (AMO) are explored with the model results and compared to the response derived from satellite measurements and proxy observations. Increases in fire emissions in southeast Asia and boreal North America are associated with positive ENSO and PDO, while United States fires and Sahel fires decrease for the same climate conditions. Boreal fire emissions decrease in CESM1 for the warm phase of the AMO, while ESM2Mb did not produce a reliable AMO. CESM1 produces a weak negative trend in global fire emissions for the period 1920 to 2005, while ESM2Mb produces a positive trend over the same period. Both trends are statistically significant at a confidence level of 95% or greater given the variability derived from the respective preindustrial controls. In addition to climate variability impacts on fires, we also explore the impacts of fire emissions on climate variability and atmospheric chemistry. We analyze three long, free-evolving ESM2Mb simulations; one without fire emissions, one with constant year-over-year fire emissions based on a present day inventory, and one with interannually varying fire emissions coupled between the terrestrial and atmospheric components of the model, to gain a better understanding of the role of fire emissions in

Using Morphological, Molecular and Climatic Data to Delimitate Yews along the Hindu Kush-Himalaya and Adjacent Regions

PubMed Central

Poudel, Ram C.; Möller, Michael; Gao, Lian-Ming; Ahrends, Antje; Baral, Sushim R.; Liu, Jie; Thomas, Philip; Li, De-Zhu

2012-01-01

Background Despite the availability of several studies to clarify taxonomic problems on the highly threatened yews of the Hindu Kush-Himalaya (HKH) and adjacent regions, the total number of species and their exact distribution ranges remains controversial. We explored the use of comprehensive sets of morphological, molecular and climatic data to clarify taxonomy and distributions of yews in this region. Methodology/Principal Findings A total of 743 samples from 46 populations of wild yew and 47 representative herbarium specimens were analyzed. Principle component analyses on 27 morphological characters and 15 bioclimatic variables plus altitude and maximum parsimony analysis on molecular ITS and trnL-F sequences indicated the existence of three distinct species occurring in different ecological (climatic) and altitudinal gradients along the HKH and adjacent regions Taxus contorta from eastern Afghanistan to the eastern end of Central Nepal, T. wallichiana from the western end of Central Nepal to Northwest China, and the first report of the South China low to mid-elevation species T. mairei in Nepal, Bhutan, Northeast India, Myanmar and South Vietnam. Conclusion/Significance The detailed sampling and combination of different data sets allowed us to identify three clearly delineated species and their precise distribution ranges in the HKH and adjacent regions, which showed no overlap or no distinct hybrid zone. This might be due to differences in the ecological (climatic) requirements of the species. The analyses further provided the selection of diagnostic morphological characters for the identification of yews occurring in the HKH and adjacent regions. Our work demonstrates that extensive sampling combined with the analysis of diverse data sets can reliably address the taxonomy of morphologically challenging plant taxa. PMID:23056501

Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin

PubMed Central

Dai, Shao-Xing; Li, Wen-Xing

2016-01-01

Besides its anti-inflammatory, analgesic and anti-pyretic properties, aspirin is used for the prevention of cardiovascular disease and various types of cancer. The multiple activities of aspirin likely involve several molecular targets and pathways rather than a single target. Therefore, systematic identification of these targets of aspirin can help us understand the underlying mechanisms of the activities. In this study, we identified 23 putative targets of aspirin in the human proteome by using binding pocket similarity detecting tool combination with molecular docking, free energy calculation and pathway analysis. These targets have diverse folds and are derived from different protein family. However, they have similar aspirin-binding pockets. The binding free energy with aspirin for newly identified targets is comparable to that for the primary targets. Pathway analysis revealed that the targets were enriched in several pathways such as vascular endothelial growth factor (VEGF) signaling, Fc epsilon RI signaling and arachidonic acid metabolism, which are strongly involved in inflammation, cardiovascular disease and cancer. Therefore, the predicted target profile of aspirin suggests a new explanation for the disease prevention ability of aspirin. Our findings provide a new insight of aspirin and its efficacy of disease prevention in a systematic and global view. PMID:26989626

Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin.

PubMed

Dai, Shao-Xing; Li, Wen-Xing; Li, Gong-Hua; Huang, Jing-Fei

2016-01-01

Besides its anti-inflammatory, analgesic and anti-pyretic properties, aspirin is used for the prevention of cardiovascular disease and various types of cancer. The multiple activities of aspirin likely involve several molecular targets and pathways rather than a single target. Therefore, systematic identification of these targets of aspirin can help us understand the underlying mechanisms of the activities. In this study, we identified 23 putative targets of aspirin in the human proteome by using binding pocket similarity detecting tool combination with molecular docking, free energy calculation and pathway analysis. These targets have diverse folds and are derived from different protein family. However, they have similar aspirin-binding pockets. The binding free energy with aspirin for newly identified targets is comparable to that for the primary targets. Pathway analysis revealed that the targets were enriched in several pathways such as vascular endothelial growth factor (VEGF) signaling, Fc epsilon RI signaling and arachidonic acid metabolism, which are strongly involved in inflammation, cardiovascular disease and cancer. Therefore, the predicted target profile of aspirin suggests a new explanation for the disease prevention ability of aspirin. Our findings provide a new insight of aspirin and its efficacy of disease prevention in a systematic and global view.

Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors.

PubMed

Dineshram, Ramadoss; Chandramouli, Kondethimmanahalli; Ko, Ginger Wai Kuen; Zhang, Huoming; Qian, Pei-Yuan; Ravasi, Timothy; Thiyagarajan, Vengatesen

2016-06-01

The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs. © 2016 John Wiley & Sons Ltd.

Molecular-level insights into aging processes of skin elastin.

PubMed

Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang; Heyroth, Frank; Heinz, Andrea

2016-01-01

Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin fibers was characterized by scanning electron microscopy. Mass spectrometric analysis and label-free quantification allowed identifying differences in the cleavage patterns of the elastin samples after enzymatic digestion. Principal component analysis and hierarchical cluster analysis were used to visualize differences between the samples and to determine the contribution of extrinsic and intrinsic aging to the proteolytic susceptibility of elastin. Moreover, the release of potentially bioactive peptides was studied. Skin aging is associated with the decomposition of elastin fibers, which is more pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26. Photoaging makes the N-terminal and central parts of the tropoelastin molecules more susceptible towards enzymatic cleavage and, hence, accelerates the age-related degradation of elastin. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food

PubMed Central

Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

2015-01-01

Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are

An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food.

PubMed

Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

2015-01-01

Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are

The Structural Basis of IKs Ion-Channel Activation: Mechanistic Insights from Molecular Simulations.

PubMed

Ramasubramanian, Smiruthi; Rudy, Yoram

2018-06-05

Relating ion channel (iCh) structural dynamics to physiological function remains a challenge. Current experimental and computational techniques have limited ability to explore this relationship in atomistic detail over physiological timescales. A framework associating iCh structure to function is necessary for elucidating normal and disease mechanisms. We formulated a modeling schema that overcomes the limitations of current methods through applications of artificial intelligence machine learning. Using this approach, we studied molecular processes that underlie human IKs voltage-mediated gating. IKs malfunction underlies many debilitating and life-threatening diseases. Molecular components of IKs that underlie its electrophysiological function include KCNQ1 (a pore-forming tetramer) and KCNE1 (an auxiliary subunit). Simulations, using the IKs structure-function model, reproduced experimentally recorded saturation of gating-charge displacement at positive membrane voltages, two-step voltage sensor (VS) movement shown by fluorescence, iCh gating statistics, and current-voltage relationship. Mechanistic insights include the following: 1) pore energy profile determines iCh subconductance; 2) the entire protein structure, not limited to the pore, contributes to pore energy and channel subconductance; 3) interactions with KCNE1 result in two distinct VS movements, causing gating-charge saturation at positive membrane voltages and current activation delay; and 4) flexible coupling between VS and pore permits pore opening at lower VS positions, resulting in sequential gating. The new modeling approach is applicable to atomistic scale studies of other proteins on timescales of physiological function. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Variability of North African hydroclimate during the last two climatic cycles: New insights from dust flux and provenance

NASA Astrophysics Data System (ADS)

Skonieczny, C.; McGee, D.; Bory, A. J. M.; Winckler, G.; Bradtmiller, L.; Bout-Roumazeilles, V.; Perala-Dewey, J.; Delattre, M.; Kinsley, C. W.; Polissar, P. J.; Malaizé, B.

2016-12-01

Every year, several hundred teragrams of dust are emitted from the Sahara and Sahel regions. These mineral particles sensitively track variations in atmospheric circulation and continental aridity. Sediments of the Northeastern Tropical Atlantic Ocean (NETAO) are fed by this intense dust supply and comprise unique long-term archives of past Saharan/Sahelian dust emissions. Past modifications of dust characteristics in these sedimentary archives can provide unique insights into changes in environmental conditions in source areas (aridity, weathering), as well as changes in atmospheric transport (wind direction and strength). Here we document changes in sediment supply to the NETAO using marine sediment core MD03-2705 (18°05N; 21°09W; 3085m water depth). This record is strategically located under the influence of seasonal dust plumes, and marine sediments of this area have revealed that past dust inputs were sensitive to global climate changes over the late Quaternary. We will focus our study on the last two climatic cycles (0-240ka), a period orbitally characterized by changes in the amplitude of both precession (MIS6-5 vs. MIS1-2) and ice volume (MIS 7 vs. MIS5). We will present, for the first time in this area, a continuous high-resolution record of dust, opal, carbonate and organic matter fluxes using 230Th-normalization. The constant flux proxy 230Thxs provides flux data that are not substantially affected by lateral advection or age model errors. These fluxes data will be complemented by grain-size, clay mineralogical and geochemical (major elements) analysis. By pairing dust flux measurements with complementary proxy data reflecting changes in aridity, wind strength and dust source, this study will provide a robust, continuous record of the magnitude and pacing of the North African hydroclimate variability through the last two climatic cycles. In particular, this long-term study will offer the opportunity to compare the well-documented North African climate

Interactive Correlation Analysis and Visualization of Climate Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Kwan-Liu

The relationship between our ability to analyze and extract insights from visualization of climate model output and the capability of the available resources to make those visualizations has reached a crisis point. The large volume of data currently produced by climate models is overwhelming the current, decades-old visualization workflow. The traditional methods for visualizing climate output also have not kept pace with changes in the types of grids used, the number of variables involved, and the number of different simulations performed with a climate model or the feature-richness of high-resolution simulations. This project has developed new and faster methods formore » visualization in order to get the most knowledge out of the new generation of high-resolution climate models. While traditional climate images will continue to be useful, there is need for new approaches to visualization and analysis of climate data if we are to gain all the insights available in ultra-large data sets produced by high-resolution model output and ensemble integrations of climate models such as those produced for the Coupled Model Intercomparison Project. Towards that end, we have developed new visualization techniques for performing correlation analysis. We have also introduced highly scalable, parallel rendering methods for visualizing large-scale 3D data. This project was done jointly with climate scientists and visualization researchers at Argonne National Laboratory and NCAR.« less

Molecular characterization and evolutionary insights into potential sex-determination genes in the western orchard predatory mite Metaseiulus occidentalis (Chelicerata: Arachnida: Acari: Phytoseiidae).

PubMed

Pomerantz, Aaron F; Hoy, Marjorie A; Kawahara, Akito Y

2015-01-01

Little is known about the process of sex determination at the molecular level in species belonging to the subclass Acari, a taxon of arachnids that contains mites and ticks. The recent sequencing of the transcriptome and genome of the western orchard predatory mite Metaseiulus occidentalis allows investigation of molecular mechanisms underlying the biological processes of sex determination in this predator of phytophagous pest mites. We identified four doublesex-and-mab-3-related transcription factor (dmrt) genes, one transformer-2 gene, one intersex gene, and two fruitless-like genes in M. occidentalis. Phylogenetic analyses were conducted to infer the molecular relationships to sequences from species of arthropods, including insects, crustaceans, acarines, and a centipede, using available genomic data. Comparative analyses revealed high sequence identity within functional domains and confirmed that the architecture for certain sex-determination genes is conserved in arthropods. This study provides a framework for identifying potential target genes that could be implicated in the process of sex determination in M. occidentalis and provides insight into the conservation and change of the molecular components of sex determination in arthropods.

Molecular Insights into Division of Single Human Cancer Cells in On-Chip Transparent Microtubes

PubMed Central

2016-01-01

In vivo, mammalian cells proliferate within 3D environments consisting of numerous microcavities and channels, which contain a variety of chemical and physical cues. External environments often differ between normal and pathological states, such as the unique spatial constraints that metastasizing cancer cells experience as they circulate the vasculature through arterioles and narrow capillaries, where they can divide and acquire elongated cylindrical shapes. While metastatic tumors cause most cancer deaths, factors impacting early cancer cell proliferation inside the vasculature and those that can promote the formation of secondary tumors remain largely unknown. Prior studies investigating confined mitosis have mainly used 2D cell culture systems. Here, we mimic aspects of metastasizing tumor cells dividing inside blood capillaries by investigating single-cell divisions of living human cancer cells, trapped inside 3D rolled-up, transparent nanomembranes. We assess the molecular effects of tubular confinement on key mitotic features, using optical high- and super-resolution microscopy. Our experiments show that tubular confinement affects the morphology and dynamics of the mitotic spindle, chromosome arrangements, and the organization of the cell cortex. Moreover, we reveal that membrane blebbing and/or associated processes act as a potential genome-safety mechanism, limiting the extent of genomic instability caused by mitosis in confined circumstances, especially in tubular 3D microenvironments. Collectively, our study demonstrates the potential of rolled-up nanomembranes for gaining molecular insights into key cellular events occurring in tubular 3D microenvironments in vivo. PMID:27267364

Beyond equilibrium climate sensitivity

NASA Astrophysics Data System (ADS)

Knutti, Reto; Rugenstein, Maria A. A.; Hegerl, Gabriele C.

2017-10-01

Equilibrium climate sensitivity characterizes the Earth's long-term global temperature response to increased atmospheric CO2 concentration. It has reached almost iconic status as the single number that describes how severe climate change will be. The consensus on the 'likely' range for climate sensitivity of 1.5 °C to 4.5 °C today is the same as given by Jule Charney in 1979, but now it is based on quantitative evidence from across the climate system and throughout climate history. The quest to constrain climate sensitivity has revealed important insights into the timescales of the climate system response, natural variability and limitations in observations and climate models, but also concerns about the simple concepts underlying climate sensitivity and radiative forcing, which opens avenues to better understand and constrain the climate response to forcing. Estimates of the transient climate response are better constrained by observed warming and are more relevant for predicting warming over the next decades. Newer metrics relating global warming directly to the total emitted CO2 show that in order to keep warming to within 2 °C, future CO2 emissions have to remain strongly limited, irrespective of climate sensitivity being at the high or low end.

Molecular Insights into Metabotropic Glutamate Receptor Allosteric Modulation

PubMed Central

Gregory, Karen J.

2015-01-01

The metabotropic glutamate (mGlu) receptors are a group of eight family C G protein–coupled receptors that are expressed throughout the central nervous system (CNS) and periphery. Within the CNS the different subtypes are found in neurons, both pre- and/or postsynaptically, where they mediate modulatory roles and in glial cells. The mGlu receptor family provides attractive targets for numerous psychiatric and neurologic disorders, with the majority of discovery programs focused on targeting allosteric sites, with allosteric ligands now available for all mGlu receptor subtypes. However, the development of allosteric ligands remains challenging. Biased modulation, probe dependence, and molecular switches all contribute to the complex molecular pharmacology exhibited by mGlu receptor allosteric ligands. In recent years we have made significant progress in our understanding of this molecular complexity coupled with an increased understanding of the structural basis of mGlu allosteric modulation. PMID:25808929

Molecular Insights into Crimean-Congo Hemorrhagic Fever Virus

DOE PAGES

Zivcec, Marko; Scholte, Florine; Spiropoulou, Christina; ...

2016-04-21

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes high morbidity and mortality. Efficacy of vaccines and antivirals to treat human CCHFV infections remains limited and controversial. Research into pathology and underlying molecular mechanisms of CCHFV and other nairoviruses is limited. Significant progress has been made in our understanding of CCHFV replication and pathogenesis in the past decade. Here we review the most recent molecular advances in CCHFV-related research, and provide perspectives on future research.

Molecular Insights into Crimean-Congo Hemorrhagic Fever Virus.

PubMed

Zivcec, Marko; Scholte, Florine E M; Spiropoulou, Christina F; Spengler, Jessica R; Bergeron, Éric

2016-04-21

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes high morbidity and mortality. Efficacy of vaccines and antivirals to treat human CCHFV infections remains limited and controversial. Research into pathology and underlying molecular mechanisms of CCHFV and other nairoviruses is limited. Significant progress has been made in our understanding of CCHFV replication and pathogenesis in the past decade. Here we review the most recent molecular advances in CCHFV-related research, and provide perspectives on future research.

Molecular Insights into Crimean-Congo Hemorrhagic Fever Virus

PubMed Central

Zivcec, Marko; Scholte, Florine E. M.; Spiropoulou, Christina F.; Spengler, Jessica R.; Bergeron, Éric

2016-01-01

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes high morbidity and mortality. Efficacy of vaccines and antivirals to treat human CCHFV infections remains limited and controversial. Research into pathology and underlying molecular mechanisms of CCHFV and other nairoviruses is limited. Significant progress has been made in our understanding of CCHFV replication and pathogenesis in the past decade. Here we review the most recent molecular advances in CCHFV-related research, and provide perspectives on future research. PMID:27110812

Molecular Insights into Crimean-Congo Hemorrhagic Fever Virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zivcec, Marko; Scholte, Florine; Spiropoulou, Christina

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes high morbidity and mortality. Efficacy of vaccines and antivirals to treat human CCHFV infections remains limited and controversial. Research into pathology and underlying molecular mechanisms of CCHFV and other nairoviruses is limited. Significant progress has been made in our understanding of CCHFV replication and pathogenesis in the past decade. Here we review the most recent molecular advances in CCHFV-related research, and provide perspectives on future research.

New insights into the molecular epidemiology and population genetics of Schistosoma mansoni in Ugandan pre-school children and mothers.

PubMed

Betson, Martha; Sousa-Figueiredo, Jose C; Kabatereine, Narcis B; Stothard, J Russell

2013-01-01

Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission. However, they are currently excluded from control programmes. Molecular phylogenetic studies have provided insights into the evolutionary origins and transmission dynamics of S. mansoni, but there has been no research into schistosome molecular epidemiology in pre-school children. Here, we investigated the genetic diversity and population structure of S. mansoni in pre-school children and mothers living in lakeshore communities in Uganda and monitored for changes over time after praziquantel treatment. Parasites were sampled from children (<6 years) and mothers enrolled in the longitudinal Schistosomiasis Mothers and Infants Study at baseline and at 6-, 12- and 18-month follow-up surveys. 1347 parasites from 35 mothers and 45 children were genotyped by direct sequencing of the cytochrome c oxidase (cox1) gene. The cox1 region was highly diverse with over 230 unique sequences identified. Parasite populations were genetically differentiated between lakes and non-synonymous mutations were more diverse at Lake Victoria than Lake Albert. Surprisingly, parasite populations sampled from children showed a similar genetic diversity to those sampled from mothers, pointing towards a non-linear relationship between duration of exposure and accumulation of parasite diversity. The genetic diversity six months after praziquantel treatment was similar to pre-treatment diversity. Our results confirm the substantial genetic diversity of S. mansoni in East Africa and provide significant insights into transmission dynamics within young children and mothers, important information for schistosomiasis control programmes.

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

PubMed Central

2016-01-01

The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments. PMID:27228560

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

PubMed

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

2016-06-22

The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that, by improving (i) existing interatomic potentials and (ii) currently available enhanced sampling methods, the community can move toward accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments.

Hybrid Zones: Windows on Climate Change

PubMed Central

Larson, Erica L.; Harrison, Richard G.

2016-01-01

Defining the impacts of anthropogenic climate change on biodiversity and species distributions is currently a high priority. Niche models focus primarily on predicted changes in abiotic factors; however, species interactions and adaptive evolution will impact the ability of species to persist in the face of changing climate. Our review focuses on the use of hybrid zones to monitor species' responses to contemporary climate change. Monitoring hybrid zones provides insight into how range boundaries shift in response to climate change by illuminating the combined effects of species interactions and physiological sensitivity. At the same time, the semi-permeable nature of species boundaries allows us to document adaptive introgression of alleles associated with response to climate change. PMID:25982153

Risky Business and the American Climate Prospectus: Economic Risks of Climate Change in the United States"

NASA Astrophysics Data System (ADS)

Gordon, K.; Houser, T.; Kopp, R. E., III; Hsiang, S. M.; Larsen, K.; Jina, A.; Delgado, M.; Muir-Wood, R.; Rasmussen, D.; Rising, J.; Mastrandrea, M.; Wilson, P. S.

2014-12-01

The United States faces a range of economic risks from global climate change - from increased flooding and storm damage, to climate-driven changes in crop yields and labor productivity, to heat-related strains on energy and public health systems. The Risky Business Project commissioned a groundbreaking new analysis of these and other climate risks by region of the country and sector of the economy. The American Climate Prospectus (ACP) links state-of-the-art climate models with econometric research of human responses to climate variability and cutting edge private sector risk assessment tools, the ACP offers decision-makers a data driven assessment of the specific risks they face. We describe the challenge, methods, findings, and policy implications of the national risk analysis, with particular focus on methodological innovations and novel insights.

Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30

PubMed Central

Louet, Maxime; Labbé, Céline M.; Aono, Cassiano M.; Homem-de-Mello, Paula; Villoutreix, Bruno O.

2018-01-01

Cytochrome P450 2C9 (CYP2C9) metabolizes about 15% of clinically administrated drugs. The allelic variant CYP2C9*30 (A477T) is associated to diminished response to the antihypertensive effects of the prodrug losartan and affected metabolism of other drugs. Here, we investigated molecular mechanisms involved in the functional consequences of this amino-acid substitution. Molecular dynamics (MD) simulations performed for the active species of the enzyme (heme in the Compound I state), in the apo or substrate-bound state, and binding energy analyses gave insights into altered protein structure and dynamics involved in the defective drug metabolism of human CYP2C9.30. Our data revealed an increased rigidity of the key Substrate Recognition Sites SRS1 and SRS5 and shifting of the β turn 4 of SRS6 toward the helix F in CYP2C9.30. Channel and binding substrate dynamics analyses showed altered substrate channel access and active site accommodation. These conformational and dynamic changes are believed to be involved in the governing mechanism of the reduced catalytic activity. An ensemble of representative conformations of the WT and A477T mutant properly accommodating drug substrates were identified, those structures can be used for prediction of new CYP2C9 and CYP2C9.30 substrates and drug-drug interactions. PMID:29746595

Climate adaptation

NASA Astrophysics Data System (ADS)

Kinzig, Ann P.

2015-03-01

This paper is intended as a brief introduction to climate adaptation in a conference devoted otherwise to the physics of sustainable energy. Whereas mitigation involves measures to reduce the probability of a potential event, such as climate change, adaptation refers to actions that lessen the impact of climate change. Mitigation and adaptation differ in other ways as well. Adaptation does not necessarily have to be implemented immediately to be effective; it only needs to be in place before the threat arrives. Also, adaptation does not necessarily require global, coordinated action; many effective adaptation actions can be local. Some urban communities, because of land-use change and the urban heat-island effect, currently face changes similar to some expected under climate change, such as changes in water availability, heat-related morbidity, or changes in disease patterns. Concern over those impacts might motivate the implementation of measures that would also help in climate adaptation, despite skepticism among some policy makers about anthropogenic global warming. Studies of ancient civilizations in the southwestern US lends some insight into factors that may or may not be important to successful adaptation.

Inspiring your audience to action: insights from theory and practice

NASA Astrophysics Data System (ADS)

Wong, W.; Hekkers, J.; Mott, B.

2011-12-01

Findings from market research sponsored by The Ocean Project, along with many other recent studies, have revealed two troubling facts: 1. Despite increased efforts to grow climate and ocean literacy among the general public, American adult's knowledge of climate and ocean health has remained stagnant in the past decade; and 2. Knowledge and level of concern about climate change show little correlation, i.e. the people who are most concerned about climate change are not the ones who know most about the science of climate change, and vice versa. If knowledge does not lead to action among the general public, what implications does this have for those of us working for conservation? How can we motivate people to act for conservation? The Ocean Project's large-scale survey of American attitudes and values vis-à-vis ocean, climate change, and related conservation issues provides answers to many such burning questions. Our research findings reveal critical insights about what, who, and how we can communicate for maximum efficacy. In particular, youth and minorities emerged as important constituencies: not only are they more environmentally aware and/or socially conscious, they are important influencers who demonstrate greater propensity to modify their behaviors and/or engage in conservation advocacy. Our presentation will discuss the implications of these findings for strategic communication for conservation action as well as present case studies from the Monterey Bay Aquarium that support these research findings and provide insights from evaluation of two significantly different interpretive approaches to communicate about climate change-a live animal exhibit and a video-based, live-narrated auditorium program.

Molecular and Microscopic Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dohnalkova, Alice C.; Tfaily, Malak M.; Smith, A. Peyton

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is scarce. This study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix with limited nutrients. We utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of newly-formed SOM compounds, and considered implications regarding their degree of long-term persistence. The microbes in this controlled, nutrient-limitedmore » system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. Here, these findings provide insight into the formation of SOM products in ecosystems, and show that the plant- and microbially-derived material associated with mineral matrices may be important components in current soil carbon models.« less

Molecular and Microscopic Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

DOE PAGES

Dohnalkova, Alice C.; Tfaily, Malak M.; Smith, A. Peyton; ...

2017-08-26

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is scarce. This study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix with limited nutrients. We utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of newly-formed SOM compounds, and considered implications regarding their degree of long-term persistence. The microbes in this controlled, nutrient-limitedmore » system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. Here, these findings provide insight into the formation of SOM products in ecosystems, and show that the plant- and microbially-derived material associated with mineral matrices may be important components in current soil carbon models.« less

The Social Impact of Climate

NASA Astrophysics Data System (ADS)

Hsiang, S. M.

2013-12-01

Managing climate change requires that we understand the social value of climate-related decisions. Rational decision-making demands that we weigh the potential benefits of climate-related investments against their costs. To date, it has been challenging to quantify the relative social benefit of living under different climatic conditions, so policy debates tend to focus on investment costs without considering their benefits. Here I will discuss challenges and advances in the measurement of climate's impact on society. By linking data and methods across physical and social sciences, we are beginning to understand when, where, and how climatic conditions have a causal impact on human wellbeing. I will present examples from this burgeoning interdisciplinary field that quantify the effect of temperature on macroeconomic performance, the effects of climate on human conflict, and the long-term health and economic impact of tropical cyclones. Each of these examples provide new insight into previously unknown benefits of various climate management strategies. I conclude by describing new efforts to systematically gather and compare findings from across the research community to support informed and rational climate management decisions.

Conflict in a changing climate

NASA Astrophysics Data System (ADS)

Carleton, T.; Hsiang, S. M.; Burke, M.

2016-05-01

A growing body of research illuminates the role that changes in climate have had on violent conflict and social instability in the recent past. Across a diversity of contexts, high temperatures and irregular rainfall have been causally linked to a range of conflict outcomes. These findings can be paired with climate model output to generate projections of the impact future climate change may have on conflicts such as crime and civil war. However, there are large degrees of uncertainty in such projections, arising from (i) the statistical uncertainty involved in regression analysis, (ii) divergent climate model predictions, and (iii) the unknown ability of human societies to adapt to future climate change. In this article, we review the empirical evidence of the climate-conflict relationship, provide insight into the likely extent and feasibility of adaptation to climate change as it pertains to human conflict, and discuss new methods that can be used to provide projections that capture these three sources of uncertainty.

Global Climate Change: Valuable Insights from Concordant and Discordant Ice Core Histories

NASA Astrophysics Data System (ADS)

Mosley-Thompson, E.; Thompson, L. G.; Porter, S. E.; Goodwin, B. P.; Wilson, A. B.

2014-12-01

Earth's ice cover is responding to the ongoing large-scale warming driven in part by anthropogenic forces. The highest tropical and subtropical ice fields are dramatically shrinking and/or thinning and unique climate histories archived therein are now threatened, compromised or lost. Many ice fields in higher latitudes are also experiencing and recording climate system changes although these are often manifested in less evident and spectacular ways. The Antarctic Peninsula (AP) has experienced a rapid, widespread and dramatic warming over the last 60 years. Carefully selected ice fields in the AP allow reconstruction of long histories of key climatic variables. As more proxy climate records are recovered it is clear they reflect a combination of expected and unexpected responses to seemingly similar climate forcings. Recently acquired temperature and precipitation histories from the Bruce Plateau are examined within the context provided by other cores recently collected in the AP. Understanding the differences and similarities among these records provides a better understanding of the forces driving climate variability in the AP over the last century. The Arctic is also rapidly warming. The δ18O records from the Bona-Churchill and Mount Logan ice cores from southeast Alaska and southwest Yukon Territory, respectively, do not record this strong warming. The Aleutian Low strongly influences moisture transport to this geographically complex region, yet its interannual variability is preserved differently in these cores located just 110 km apart. Mount Logan is very sensitive to multi-decadal to multi-centennial climate shifts in the tropical Pacific while low frequency variability on Bona-Churchill is more strongly connected to Western Arctic sea ice extent. There is a natural tendency to focus more strongly on commonalities among records, particularly on regional scales. However, it is also important to investigate seemingly poorly correlated records, particularly

Climate program "stone soup": Assessing climate change vulnerabilities in the Aleutian and Bering Sea Islands of Alaska

NASA Astrophysics Data System (ADS)

Littell, J. S.; Poe, A.; van Pelt, T.

2015-12-01

Climate change is already affecting the Bering Sea and Aleutian Island region of Alaska. Past and present marine research across a broad spectrum of disciplines is shedding light on what sectors of the ecosystem and the human dimension will be most impacted. In a grassroots approach to extend existing research efforts, leveraging recently completed downscaled climate projections for the Bering Sea and Aleutian Islands region, we convened a team of 30 researchers-- with expertise ranging from anthropology to zooplankton to marine mammals-- to assess climate projections in the context of their expertise. This Aleutian-Bering Climate Vulnerability Assessment (ABCVA) began with researchers working in five teams to evaluate the vulnerabilities of key species and ecosystem services relative to projected changes in climate. Each team identified initial vulnerabilities for their focal species or services, and made recommendations for further research and information needs that would help managers and communities better understand the implications of the changing climate in this region. Those draft recommendations were shared during two focused, public sessions held within two hub communities for the Bering and Aleutian region: Unalaska and St. Paul. Qualitative insights about local concerns and observations relative to climate change were collected during these sessions, to be compared to the recommendations being made by the ABCVA team of researchers. Finally, we used a Structured Decision Making process to prioritize the recommendations of participating scientists, and integrate the insights shared during our community sessions. This work brought together residents, stakeholders, scientists, and natural resource managers to collaboratively identify priorities for addressing current and expected future impacts of climate change. Recommendations from this project will be incorporated into future research efforts of the Aleutian and Bering Sea Islands Landscape Conservation

Mechanistic insights into the effects of climate change on larval cod.

PubMed

Kristiansen, Trond; Stock, Charles; Drinkwater, Kenneth F; Curchitser, Enrique N

2014-05-01

Understanding the biophysical mechanisms that shape variability in fisheries recruitment is critical for estimating the effects of climate change on fisheries. In this study, we used an Earth System Model (ESM) and a mechanistic individual-based model (IBM) for larval fish to analyze how climate change may impact the growth and survival of larval cod in the North Atlantic. We focused our analysis on five regions that span the current geographical range of cod and are known to contain important spawning populations. Under the SRES A2 (high emissions) scenario, the ESM-projected surface ocean temperatures are expected to increase by >1 °C for 3 of the 5 regions, and stratification is expected to increase at all sites between 1950-1999 and 2050-2099. This enhanced stratification is projected to decrease large (>5 μm ESD) phytoplankton productivity and mesozooplankton biomass at all 5 sites. Higher temperatures are projected to increase larval metabolic costs, which combined with decreased food resources will reduce larval weight, increase the probability of larvae dying from starvation and increase larval exposure to visual and invertebrate predators at most sites. If current concentrations of piscivore and invertebrate predators are maintained, larval survival is projected to decrease at all five sites by 2050-2099. In contrast to past observed responses to climate variability in which warm anomalies led to better recruitment in cold-water stocks, our simulations indicated that reduced prey availability under climate change may cause a reduction in larval survival despite higher temperatures in these regions. In the lower prey environment projected under climate change, higher metabolic costs due to higher temperatures outweigh the advantages of higher growth potential, leading to negative effects on northern cod stocks. Our results provide an important first large-scale assessment of the impacts of climate change on larval cod in the North Atlantic. © 2013 John

Contrasting fire responses to climate and management: insights from two Australian ecosystems.

PubMed

King, Karen J; Cary, Geoffrey J; Bradstock, Ross A; Marsden-Smedley, Jonathan B

2013-04-01

This study explores effects of climate change and fuel management on unplanned fire activity in ecosystems representing contrasting extremes of the moisture availability spectrum (mesic and arid). Simulation modelling examined unplanned fire activity (fire incidence and area burned, and the area burned by large fires) for alternate climate scenarios and prescribed burning levels in: (i) a cool, moist temperate forest and wet moorland ecosystem in south-west Tasmania (mesic); and (ii) a spinifex and mulga ecosystem in central Australia (arid). Contemporary fire activity in these case study systems is limited, respectively, by fuel availability and fuel amount. For future climates, unplanned fire incidence and area burned increased in the mesic landscape, but decreased in the arid landscape in accordance with predictions based on these limiting factors. Area burned by large fires (greater than the 95th percentile of historical, unplanned fire size) increased with future climates in the mesic landscape. Simulated prescribed burning was more effective in reducing unplanned fire activity in the mesic landscape. However, the inhibitory effects of prescribed burning are predicted to be outweighed by climate change in the mesic landscape, whereas in the arid landscape prescribed burning reinforced a predicted decline in fire under climate change. The potentially contrasting direction of future changes to fire will have fundamentally different consequences for biodiversity in these contrasting ecosystems, and these will need to be accommodated through contrasting, innovative management solutions. © 2012 Blackwell Publishing Ltd.

Molecular Insight into the Slipperiness of Ice.

PubMed

Weber, Bart; Nagata, Yuki; Ketzetzi, Stefania; Tang, Fujie; Smit, Wilbert J; Bakker, Huib J; Backus, Ellen H G; Bonn, Mischa; Bonn, Daniel

2018-05-16

Measurements of the friction coefficient of steel-on-ice over a large temperature range reveal very high friction at low temperatures (-100 °C) and a steep decrease in the friction coefficient with increasing temperature. Very low friction is only found over the limited temperature range typical for ice skating. The strong decrease in the friction coefficient with increasing temperature exhibits Arrhenius behavior with an activation energy of E a ≈ 11.5 kJ mol -1 . Remarkably, molecular dynamics simulations of the ice-air interface reveal a very similar activation energy for the mobility of surface molecules. Weakly hydrogen-bonded surface molecules diffuse over the surface in a rolling motion, their number and mobility increasing with increasing temperature. This correlation between macroscopic friction and microscopic molecular mobility indicates that slippery ice arises from the high mobility of its surface molecules, making the ice surface smooth and the shearing of the weakly bonded surface molecules easy.

Insights into Meteoric 10Be Dynamics and Climate Stability along the Hawaiian Kohala Climosequence

NASA Astrophysics Data System (ADS)

Dixon, J. L.; Chadwick, O.

2017-12-01

We measure meteoric 10Be in soils across a well-studied climate gradient spanning Kohala, Hawaii to provide new understanding of the isotope behavior in soils and constraints on nuclide delivery rates to Earth's surface. Annual rainfall across the Kohala climogradient varies from 16 - 300 cm, with Hawaiian soils reflecting evolution over the past 150 ka, the nominal age of the volcanic parent material. We analyzed a sequence of nine soil profiles for meteoric 10Be and compared with previously measured data on soil chemistry and dust fluxes. In the Kohala system, soil inventories of 10Be span 40-300 x 109 atom/cm2 and generally increase linearly with rainfall, consistent with precipitation-driven fluxes and the high retention of 10Be in clay-rich soil horizons. However, nuclide inventories dramatically decrease for soils at rainfall >140 cm/y. The observed decrease corresponds with other strong changes in weathering intensity across the climate gradient, associated with previously studied and recognized pedogenic thresholds. These thresholds represent abrupt transitions in soil chemistry related to increased throughflow of soil solutions, decreases in base saturation and pH, and the destruction of phyllosilicates and replacement with amorphous oxyhydroxides. Meteoric-derived ages, based on 10Be-flux estimates and measured inventories are uniform for dry soils ( 60ka), but far less than the known substrate age (150ka), indicating that actual delivery rates are lower than predicted from current models in this region. Despite the offset in predicted and substrate ages, the consistency in pattern suggests that the rainfall gradient over the 150 thousand years of soil development has not deviated significantly from its present structure. Furthermore, based on clear 10Be losses in soils with high moisture availability, our results indicate meteoric 10Be may not be a robust tracer of soil age and movement in systems with high rainfall and weathering intensity and low soil

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

PubMed

Haldar, Susanta; Kührová, Petra; Banáš, Pavel; Spiwok, Vojtěch; Šponer, Jiří; Hobza, Pavel; Otyepka, Michal

2015-08-11

RNA hairpins capped by 5'-GNRA-3' or 5'-UNCG-3' tetraloops (TLs) are prominent RNA structural motifs. Despite their small size, a wealth of experimental data, and recent progress in theoretical simulations of their structural dynamics and folding, our understanding of the folding and unfolding processes of these small RNA elements is still limited. Theoretical description of the folding and unfolding processes requires robust sampling, which can be achieved by either an exhaustive time scale in standard molecular dynamics simulations or sophisticated enhanced sampling methods, using temperature acceleration or biasing potentials. Here, we study structural dynamics of 5'-GNRA-3' and 5'-UNCG-3' TLs by 15-μs-long standard simulations and a series of well-tempered metadynamics, attempting to accelerate sampling by bias in a few chosen collective variables (CVs). Both methods provide useful insights. The unfolding and refolding mechanisms of the GNRA TL observed by well-tempered metadynamics agree with the (reverse) folding mechanism suggested by recent replica exchange molecular dynamics simulations. The orientation of the glycosidic bond of the GL4 nucleobase is critical for the UUCG TL folding pathway, and our data strongly support the hypothesis that GL4-anti forms a kinetic trap along the folding pathway. Along with giving useful insight, our study also demonstrates that using only a few CVs apparently does not capture the full folding landscape of the RNA TLs. Despite using several sophisticated selections of the CVs, formation of the loop appears to remain a hidden variable, preventing a full convergence of the metadynamics. Finally, our data suggest that the unfolded state might be overstabilized by the force fields used.

Changing climate, changing forests: The impacts of climate change on forests of the northeastern United States and eastern Canada

Treesearch

Lindsey Rustad; John Campbell; Jeffrey S. Dukes; Thomas Huntington; Kathy Fallon Lambert; Jacqueline Mohan; Nicholas Rodenhouse

2012-01-01

Decades of study on climatic change and its direct and indirect effects on forest ecosystems provide important insights for forest science, management, and policy. A synthesis of recent research from the northeastern United States and eastern Canada shows that the climate of the region has become warmer and wetter over the past 100 years and that there are more extreme...

Divergent selection along climatic gradients in a rare central European endemic species, Saxifraga sponhemica

PubMed Central

Walisch, Tania J.; Colling, Guy; Bodenseh, Melanie; Matthies, Diethart

2015-01-01

Background and Aims The effects of habitat fragmentation on quantitative genetic variation in plant populations are still poorly known. Saxifraga sponhemica is a rare endemic of Central Europe with a disjunct distribution, and a stable and specialized habitat of treeless screes and cliffs. This study therefore used S. sponhemica as a model species to compare quantitative and molecular variation in order to explore (1) the relative importance of drift and selection in shaping the distribution of quantitative genetic variation along climatic gradients; (2) the relationship between plant fitness, quantitative genetic variation, molecular genetic variation and population size; and (3) the relationship between the differentiation of a trait among populations and its evolvability. Methods Genetic variation within and among 22 populations from the whole distribution area of S. sponhemica was studied using RAPD (random amplified polymorphic DNA) markers, and climatic variables were obtained for each site. Seeds were collected from each population and germinated, and seedlings were transplanted into a common garden for determination of variation in plant traits. Key Results In contrast to previous results from rare plant species, strong evidence was found for divergent selection. Most population trait means of S. sponhemica were significantly related to climate gradients, indicating adaptation. Quantitative genetic differentiation increased with geographical distance, even when neutral molecular divergence was controlled for, and QST exceeded FST for some traits. The evolvability of traits was negatively correlated with the degree of differentiation among populations (QST), i.e. traits under strong selection showed little genetic variation within populations. The evolutionary potential of a population was not related to its size, the performance of the population or its neutral genetic diversity. However, performance in the common garden was lower for plants from

Molecular insights into the binding of phosphoinositides to the TH domain region of TIPE proteins.

PubMed

Antony, Priya; Baby, Bincy; Vijayan, Ranjit

2016-11-01

Phosphatidylinositols and their phosphorylated derivatives, phosphoinositides, play a central role in regulating diverse cellular functions. These phospholipids have been shown to interact with the hydrophobic TH domain of the tumor necrosis factor (TNF)-α-induced protein 8 (TIPE) family of proteins. However, the precise mechanism of interaction of these lipids is unclear. Here we report the binding mode and interactions of these phospholipids in the TH domain, as elucidated using molecular docking and simulations. Results indicate that phosphoinositides bind to the TH domain in a similar way by inserting their lipid tails in the hydrophobic cavity. The exposed head group is stabilized by interactions with critical positively charged residues on the surface of these proteins. Further MD simulations confirmed the dynamic stability of these lipids in the TH domain. This computational analysis thus provides insight into the binding mode of phospholipids in the TH domain of the TIPE family of proteins. Graphical abstract A phosphoinositide (phosphatidylinositol 4-phosphate; PtdIns4P) docked to TIPE2.

Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change.

PubMed

Qian, Chaoju; Yin, Hengxia; Shi, Yong; Zhao, Jiecai; Yin, Chengliang; Luo, Wanyin; Dong, Zhibao; Chen, Guoxiong; Yan, Xia; Wang, Xiao-Ru; Ma, Xiao-Fei

2016-05-23

Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.

Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change

PubMed Central

Qian, Chaoju; Yin, Hengxia; Shi, Yong; Zhao, Jiecai; Yin, Chengliang; Luo, Wanyin; Dong, Zhibao; Chen, Guoxiong; Yan, Xia; Wang, Xiao-Ru; Ma, Xiao-Fei

2016-01-01

Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change. PMID:27210568

Translating Scientific Judgment, Technological Insight and Economic Theory Into Practical Policy Lessons: The Case of Climate Regulation in the United States

NASA Astrophysics Data System (ADS)

Mignone, B. K.

2008-12-01

Effective solutions to the climate change problem will require unprecedented cooperation across space, continuity across time and coordination between disciplines. One well-known methodology for synthesizing the lessons of physical science, energy engineering and economics is integrated assessment. Typically, integrated assessment models use scientific and technological relationships as physical constraints in a larger macroeconomic optimization that is designed to either balance the costs and benefits of climate change mitigation or find the least-cost path to an exogenously prescribed endpoint (e.g. atmospheric CO2 stabilization). The usefulness of these models depends to a large extent on the quality of the assumptions and the relevance of the outcome metrics chosen by the user. In this study, I show how a scientifically-based emissions reduction scenario can be combined with engineering-based assumptions about the energy system (e.g. estimates of the marginal cost premium of carbon-free technology) to yield insights about the price path of CO2 under a future regulatory regime. I then show how this outcome metric (carbon price) relates to key decisions about the design of a future cap-and-trade system and the way in which future carbon markets may be regulated.

Using Data from Climate Science to Teach Introductory Statistics

ERIC Educational Resources Information Center

Witt, Gary

2013-01-01

This paper shows how the application of simple statistical methods can reveal to students important insights from climate data. While the popular press is filled with contradictory opinions about climate science, teachers can encourage students to use introductory-level statistics to analyze data for themselves on this important issue in public…

Doliroside A from Dolichos falcata Klein suppressing amyloid β-protein 42 fibrillogenesis: An insight at molecular level.

PubMed

Li, Dongpu; Yu, Hongfei; Lin, Qinxiong; Liu, Yun

2017-01-01

A bioactive chemical constituent, doliroside A, from Chinese traditional herbal medicine Dolichos falcata Klein was isolated, purified and identified by 60% ethanol extraction, thin layer chromatography (TLC), high performance liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) spectroscopy. Molecular interaction mechanism between doliroside and amyloid β42 protein was evaluated by thioflavin T fluorescence (ThT), circular dichroism (CD), atomic force microscope (AFM), and differential scanning calorimeter (DSC) from the aspects of kinetics, secondary structure, morphology, and thermodynamics, respectively. Results show that the purity of doliroside A is 99.9% by HPLC, and its chemical structure is identified by 1H- and 13C-NMR. Doliroside A is observed to be concentration-dependent inhibiting the fibrillation of Aβ42 with the IC50 value of 26.57 ± 1.6 μM. CD and DSC results imply that doliroside A can bind to the nuclei and oligomers of Aβ42 to form a stable complex and suppress Aβ42 fibrillation. AFM images show that doliroside A, after bound to the nuclei and oligomers, redirect Aβ42 into off-pathway, amorphous oligomers. These findings not only provide a full insight into the molecular interaction mechanisms between Aβ42 and doliroside A, but also facilitate the development of new native anti-AD drug of doliroside A compound.

Microsecond molecular dynamics simulations provide insight into the ATP-competitive inhibitor-induced allosteric protection of Akt kinase phosphorylation.

PubMed

Mou, Linkai; Cui, Tongwei; Liu, Weiguang; Zhang, Hong; Cai, Zhanxiu; Lu, Shaoyong; Gao, Guojun

2017-05-01

Akt is a serine/threonine protein kinase, a critical mediator of growth factor-induced survival in key cellular pathways. Allosteric signaling between protein intramolecular domains requires long-range communication mediated by hotspot residues, often triggered by ligand binding. Here, based on extensive 3 μs explicit solvent molecular dynamics (MD) simulations of Akt1 kinase domain in the unbound (apo) and ATP-competitive inhibitor, GDC-0068-bound states, we propose a molecular mechanism for allosteric regulation of Akt1 kinase phosphorylation by GDC-0068 binding to the ATP-binding site. MD simulations revealed that the apo Akt1 is flexible with two disengaged N- and C-lobes, equilibrated between the open and closed conformations. GDC-0068 occupancy of the ATP-binding site shifts the conformational equilibrium of Akt1 from the open conformation toward the closed conformation and stabilizes the closed state. This effect enables allosteric signal propagation from the GDC-0068 to the phosphorylated T308 (pT308) in the activation loop and restrains phosphatase access to pT308, thereby protecting the pT308 in the GDC-0068-bound Akt1. Importantly, functional hotspots involved in the allosteric communication from the GDC-0068 to the pT308 are identified. Our analysis of GDC-0068-induced allosteric protection of Akt kinase phosphorylation yields important new insights into the molecular mechanism of allosteric regulation of Akt kinase activity. © 2016 John Wiley & Sons A/S.

Topographic Evolution and Climate Aridification during Continental Collision: Insights from Computer Simulations.

PubMed

Garcia-Castellanos, Daniel; Jiménez-Munt, Ivone

2015-01-01

How do the feedbacks between tectonics, sediment transport and climate work to shape the topographic evolution of the Earth? This question has been widely addressed via numerical models constrained with thermochronological and geomorphological data at scales ranging from local to orogenic. Here we present a novel numerical model that aims at reproducing the interaction between these processes at the continental scale. For this purpose, we combine in a single computer program: 1) a thin-sheet viscous model of continental deformation; 2) a stream-power surface-transport approach; 3) flexural isostasy allowing for the formation of large sedimentary foreland basins; and 4) an orographic precipitation model that reproduces basic climatic effects such as continentality and rain shadow. We quantify the feedbacks between these processes in a synthetic scenario inspired by the India-Asia collision and the growth of the Tibetan Plateau. We identify a feedback between erosion and crustal thickening leading locally to a <50% increase in deformation rates in places where orographic precipitation is concentrated. This climatically-enhanced deformation takes place preferentially at the upwind flank of the growing plateau, specially at the corners of the indenter (syntaxes). We hypothesize that this may provide clues for better understanding the mechanisms underlying the intriguing tectonic aneurisms documented in the Himalayas. At the continental scale, however, the overall distribution of topographic basins and ranges seems insensitive to climatic factors, despite these do have important, sometimes counterintuitive effects on the amount of sediments trapped within the continent. The dry climatic conditions that naturally develop in the interior of the continent, for example, trigger large intra-continental sediment trapping at basins similar to the Tarim Basin because they determine its endorheic/exorheic drainage. These complex climatic-drainage-tectonic interactions make the

Topographic Evolution and Climate Aridification during Continental Collision: Insights from Computer Simulations

PubMed Central

2015-01-01

How do the feedbacks between tectonics, sediment transport and climate work to shape the topographic evolution of the Earth? This question has been widely addressed via numerical models constrained with thermochronological and geomorphological data at scales ranging from local to orogenic. Here we present a novel numerical model that aims at reproducing the interaction between these processes at the continental scale. For this purpose, we combine in a single computer program: 1) a thin-sheet viscous model of continental deformation; 2) a stream-power surface-transport approach; 3) flexural isostasy allowing for the formation of large sedimentary foreland basins; and 4) an orographic precipitation model that reproduces basic climatic effects such as continentality and rain shadow. We quantify the feedbacks between these processes in a synthetic scenario inspired by the India-Asia collision and the growth of the Tibetan Plateau. We identify a feedback between erosion and crustal thickening leading locally to a <50% increase in deformation rates in places where orographic precipitation is concentrated. This climatically-enhanced deformation takes place preferentially at the upwind flank of the growing plateau, specially at the corners of the indenter (syntaxes). We hypothesize that this may provide clues for better understanding the mechanisms underlying the intriguing tectonic aneurisms documented in the Himalayas. At the continental scale, however, the overall distribution of topographic basins and ranges seems insensitive to climatic factors, despite these do have important, sometimes counterintuitive effects on the amount of sediments trapped within the continent. The dry climatic conditions that naturally develop in the interior of the continent, for example, trigger large intra-continental sediment trapping at basins similar to the Tarim Basin because they determine its endorheic/exorheic drainage. These complex climatic-drainage-tectonic interactions make the

The Data Platform for Climate Research and Action: Introducing Climate Watch

NASA Astrophysics Data System (ADS)

Hennig, R. J.; Ge, M.; Friedrich, J.; Lebling, K.; Carlock, G.; Arcipowska, A.; Mangan, E.; Biru, H.; Tankou, A.; Chaudhury, M.

2017-12-01

The Paris Agreement, adopted through Decision 1/CP.21, brings all nations together to take on ambitious efforts to combat climate change. Open access to climate data supporting climate research, advancing knowledge, and informing decision making is key to encourage and strengthen efforts of stakeholders at all levels to address and respond to effects of climate change. Climate Watch is a robust online data platform developed in response to the urgent needs of knowledge and tools to empower climate research and action, including those of researchers, policy makers, the private sector, civil society, and all other non-state actors. Building on the rapid growing technology of open data and information sharing, Climate Watch is equipped with extensive amount of climate data, informative visualizations, concise yet efficient user interface, and connection to resources users need to gather insightful information on national and global progress towards delivering on the objective of the Convention and the Paris Agreement. Climate Watch brings together hundreds of quantitative and qualitative indicators for easy explore, visualize, compare, download at global, national, and sectoral levels: Greenhouse gas (GHG) emissions for more than 190 countries over the1850-2014 time period, covering all seven Kyoto Gases following IPCC source/sink categories; Structured information on over 150 NDCs facilitating the clarity, understanding and transparency of countries' contributions to address climate change; Over 6500 identified linkages between climate actions in NDCs across the 169 targets of the sustainable development goals (SDG); Over 200 indicators describing low carbon pathways from models and scenarios by integrated assessment models (IAMs) and national sources; and Data on vulnerability and risk, policies, finance, and many more. Climate Watch platform is developed as part of the broader efforts within the World Resources Institute, the NDC Partnership, and in collaboration

Insight into the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} eutectic mixture from classical molecular dynamics: Thermodynamics, structure, and dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corradini, Dario; Vuilleumier, Rodolphe, E-mail: rodolphe.vuilleumier@ens.fr; Sorbonne Universités, UPMC Univ. Paris 06, PASTEUR, 75005 Paris

We use molecular dynamics simulations to study the thermodynamics, structure, and dynamics of the Li{sub 2}CO{sub 3}–K{sub 2}CO{sub 3} (62:38 mol. %) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations data as reference. This simple force field allows efficient molecular simulations of phenomena at long time scales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900–1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, wemore » present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture’s self-diffusion coefficients, viscosity, and ionic conductivity.« less

Insight into Nucleation Mechanisms of Tetrahedral Materials from Advanced Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Bi, Yuanfei

nucleation, which can be considered to be an entropically driven, kinetic process that proceeds via multiple pathways that have similar free energy profiles. Finally, inspired by our insight gained in studying gas hydrate nucleation, we proposed a novel synthesis route to obtain inert gas silicon clathrate, which has an attractive opto-electronic property for energy application, but remains as an experimental challenge for synthesis. We thoroughly examined this proposal through high-throughput computational studies that show the novel phases of silicon could form spontaneously from liquid silicon in the presence of noble gases under high pressure and high temperature. In particular, our results show that a medium size of noble gas, e.g., Ar, can trigger the nucleation and growth of inert-gas silicon clathrate, whereas a small noble gas such as He is able to induce the formation of an unconventional, inclusion-type compound Si2He. Our findings, along with the gained molecular insights, thus strongly suggest it is viable to experimentally synthesize novel silicon phases with noble gas through high pressure and high temperature. (Abstract shortened by ProQuest.).

Understanding and managing trust at the climate science-policy interface

NASA Astrophysics Data System (ADS)

Lacey, Justine; Howden, Mark; Cvitanovic, Christopher; Colvin, R. M.

2018-01-01

Climate change effects are accelerating, making the need for appropriate actions informed by sound climate knowledge ever more pressing. A strong climate science-policy relationship facilitates the effective integration of climate knowledge into local, national and global policy processes, increases society's responsiveness to a changing climate, and aligns research activity to policy needs. This complex science-policy relationship requires trust between climate science `producers' and `users', but our understanding of trust at this interface remains largely uncritical. To assist climate scientists and policymakers, this Perspective provides insights into how trust develops and operates at the interface of climate science and policy, and examines the extent to which trust can manage — or even create — risk at this interface.

Economics, ethics, and climate policy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howarth, R.B.; Monahan, P.A.

1992-11-01

Are the costs of greenhouse gas emissions abatement justified by the perceived benefits of sustained climate stability? Do people of the present generation have a moral right to impose climate risks on their descendants in generations to come? This report examines these questions in light of the emergent facts of climate science and their socioeconomic implications. We consider alternative normative criteria for social decision-making with particular emphasis on cost-benefit analysis and the principle of sustainable development. While each framework yields important insights, we argue that the gross uncertainties associated with climate change and the distribution of impacts between present andmore » future generations constrain the usefulness of cost-benefit criteria in evaluating climate policy. If one accepts the ethical proposition that it is morally wrong to impose catastrophic risks on unborn generations when reducing those risks would not noticeably diminish the quality of life of existing persons, a case can be made for concerted policy action to reduce greenhouse gas emissions.« less

Economics, ethics, and climate policy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howarth, R.B.; Monahan, P.A.

1992-11-01

Are the costs of greenhouse gas emissions abatement justified by the perceived benefits of sustained climate stability Do people of the present generation have a moral right to impose climate risks on their descendants in generations to come This report examines these questions in light of the emergent facts of climate science and their socioeconomic implications. We consider alternative normative criteria for social decision-making with particular emphasis on cost-benefit analysis and the principle of sustainable development. While each framework yields important insights, we argue that the gross uncertainties associated with climate change and the distribution of impacts between present andmore » future generations constrain the usefulness of cost-benefit criteria in evaluating climate policy. If one accepts the ethical proposition that it is morally wrong to impose catastrophic risks on unborn generations when reducing those risks would not noticeably diminish the quality of life of existing persons, a case can be made for concerted policy action to reduce greenhouse gas emissions.« less

Molecular Insight into Gut Microbiota and Rheumatoid Arthritis.

PubMed

Wu, Xiaohao; He, Bing; Liu, Jin; Feng, Hui; Ma, Yinghui; Li, Defang; Guo, Baosheng; Liang, Chao; Dang, Lei; Wang, Luyao; Tian, Jing; Zhu, Hailong; Xiao, Lianbo; Lu, Cheng; Lu, Aiping; Zhang, Ge

2016-03-22

Rheumatoid arthritis (RA) is a systemic, inflammatory, and autoimmune disorder. Gut microbiota play an important role in the etiology of RA. With the considerable progress made in next-generation sequencing techniques, the identified gut microbiota difference between RA patients and healthy individuals provides an updated overview of the association between gut microbiota and RA. We reviewed the reported correlation and underlying molecular mechanisms among gut microbiota, the immune system, and RA. It has become known that gut microbiota contribute to the pathogenesis of RA via multiple molecular mechanisms. The progressive understanding of the dynamic interaction between gut microbiota and their host will help in establishing a highly individualized management for each RA patient, and achieve a better efficacy in clinical practice, or even discovering new drugs for RA.

Country, climate change adaptation and colonisation: insights from an Indigenous adaptation planning process, Australia.

PubMed

Nursey-Bray, Melissa; Palmer, Robert

2018-03-01

Indigenous peoples are going to be disproportionately affected by climate change. Developing tailored, place based, and culturally appropriate solutions will be necessary. Yet finding cultural and institutional 'fit' within and between competing values-based climate and environmental management governance regimes remains an ongoing challenge. This paper reports on a collaborative research project with the Arabana people of central Australia, that resulted in the production of the first Indigenous community-based climate change adaptation strategy in Australia. We aimed to try and understand what conditions are needed to support Indigenous driven adaptation initiatives, if there are any cultural differences that need accounting for and how, once developed they be integrated into existing governance arrangements. Our analysis found that climate change adaptation is based on the centrality of the connection to 'country' (traditional land), it needs to be aligned with cultural values, and focus on the building of adaptive capacity. We find that the development of climate change adaptation initiatives cannot be divorced from the historical context of how the Arabana experienced and collectively remember colonisation. We argue that in developing culturally responsive climate governance for and with Indigenous peoples, that that the history of colonisation and the ongoing dominance of entrenched Western governance regimes needs acknowledging and redressing into contemporary environmental/climate management.

Sensitivity of crop cover to climate variability: insights from two Indian agro-ecoregions.

PubMed

Mondal, Pinki; Jain, Meha; DeFries, Ruth S; Galford, Gillian L; Small, Christopher

2015-01-15

Crop productivity in India varies greatly with inter-annual climate variability and is highly dependent on monsoon rainfall and temperature. The sensitivity of yields to future climate variability varies with crop type, access to irrigation and other biophysical and socio-economic factors. To better understand sensitivities to future climate, this study focuses on agro-ecological subregions in Central and Western India that span a range of crops, irrigation, biophysical conditions and socioeconomic characteristics. Climate variability is derived from remotely-sensed data products, Tropical Rainfall Measuring Mission (TRMM - precipitation) and Moderate Resolution Imaging Spectroradiometer (MODIS - temperature). We examined green-leaf phenologies as proxy for crop productivity using the MODIS Enhanced Vegetation Index (EVI) from 2000 to 2012. Using both monsoon and winter growing seasons, we assessed phenological sensitivity to inter-annual variability in precipitation and temperature patterns. Inter-annual EVI phenology anomalies ranged from -25% to 25%, with some highly anomalous values up to 200%. Monsoon crop phenology in the Central India site is highly sensitive to climate, especially the timing of the start and end of the monsoon and intensity of precipitation. In the Western India site, monsoon crop phenology is less sensitive to precipitation variability, yet shows considerable fluctuations in monsoon crop productivity across the years. Temperature is critically important for winter productivity across a range of crop and management types, such that irrigation might not provide a sufficient buffer against projected temperature increases. Better access to weather information and usage of climate-resilient crop types would play pivotal role in maintaining future productivity. Effective strategies to adapt to projected climate changes in the coming decades would also need to be tailored to regional biophysical and socio-economic conditions. Copyright © 2014

Mechanistic Insights into Molecular Targeting and Combined Modality Therapy for Aggressive, Localized Prostate Cancer

PubMed Central

Dal Pra, Alan; Locke, Jennifer A.; Borst, Gerben; Supiot, Stephane; Bristow, Robert G.

2016-01-01

Radiation therapy (RT) is one of the mainstay treatments for prostate cancer (PCa). The potentially curative approaches can provide satisfactory results for many patients with non-metastatic PCa; however, a considerable number of individuals may present disease recurrence and die from the disease. Exploiting the rich molecular biology of PCa will provide insights into how the most resistant tumor cells can be eradicated to improve treatment outcomes. Important for this biology-driven individualized treatment is a robust selection procedure. The development of predictive biomarkers for RT efficacy is therefore of utmost importance for a clinically exploitable strategy to achieve tumor-specific radiosensitization. This review highlights the current status and possible opportunities in the modulation of four key processes to enhance radiation response in PCa by targeting the: (1) androgen signaling pathway; (2) hypoxic tumor cells and regions; (3) DNA damage response (DDR) pathway; and (4) abnormal extra-/intracell signaling pathways. In addition, we discuss how and which patients should be selected for biomarker-based clinical trials exploiting and validating these targeted treatment strategies with precision RT to improve cure rates in non-indolent, localized PCa. PMID:26909338

Climate Change Education for Sustainability in Brazil: A Status Report

ERIC Educational Resources Information Center

Trajber, Rachel; Mochizuki, Yoko

2015-01-01

This article maps and explains Brazil's policies, strategies, plans and initiatives related to Climate Change Education (CCE), in the overall context of Environmental Education (EE) and Education for Sustainable Development (ESD). The case of Brazil offers useful insights on how to enhance climate response through education because of its unique…

800,000 Years of Arctic Climate Variability: Insights from Lake El'gygytgyn, Far East Russia

NASA Astrophysics Data System (ADS)

Castañeda, I. S.; Habicht, H.; Patterson, M. O.; Burns, S. J.; Deconto, R. M.; Brigham-Grette, J.

2017-12-01

The regional response of the high Arctic to past climate variability is little known prior to 100,000 years ago. In 2009, a 3.6 Ma sediment core was recovered from Lake El'gygytgyn (Russia), the largest and oldest unglaciated Arctic lake basin. These sediments offer a unique opportunity to examine Plio-Pleistocene high-latitude continental climate variability. Determining the magnitude of past Arctic temperature and precipitation variability is especially relevant to understanding the mechanisms and feedbacks contributing to arctic amplification. Here we present results of ongoing organic geochemical analyses of Lake El'gygytgyn sediments focusing on the past 800,000 years. We use the methylation and cyclization index of branched tetraethers (MBT'/CBT) to reconstruct past temperature (Weijers et al., 2007; Peterse et al., 2012; De Jonge et al., 2014) and ratios of plant leaf waxes to examine vegetation variability within the lake catchment. In addition, algal biomarkers and bulk carbon isotopes provide insights into past changes in primary productivity. Trends noted in the MBT'/CBT record are in close agreement with pollen-based temperature estimates throughout the entire core and reveal a strong response to interglacial-glacial variability as well as local summer insolation. Our temperature reconstructions indicate the terrestrial Arctic experienced both warm interglacials and mild glacial periods during the Mid-Pleistocene but transitioned to more extreme temperature fluctuations in the more recent part of the record. Plant leaf wax average chain lengths suggest that glacial intervals were marked by increased aridity, while interglacial periods were wetter at Lake El'gygytgyn. Time-series analysis of the organic geochemical temperature and vegetation reconstructions records revealed variability at precession and obliquity frequencies, respectively. We also find a signal of the Mid-Brunhes Event (MBE) recorded in numerous Lake El'gygytgyn proxy records. Pre- and

Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight.

PubMed

Shamsi, Anas; Ahmed, Azaj; Bano, Bilqees

2018-05-01

The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of complex between HSA and temsirolimus. Fluorescence quenching experiments clearly showed quenching in the fluorescence of HSA in the presence of temsirolimus confirming the complex formation and also confirmed that static mode of interaction is operative for this binding process. Binding constant values obtained through UV and fluorescence spectroscopy reveal strong interaction; temsirolimus binds to HSA at 298 K with a binding constant of 2.9 × 10 4  M -1 implying the strength of interaction. The negative Gibbs free energy obtained through Isothermal titration calorimetry as well as quenching experiments suggests that binding process is spontaneous. Molecular docking further provides an insight of various residues that are involved in this binding process; showing the binding energy to be -12.9 kcal/mol. CD spectroscopy was retorted to analyze changes in secondary structure of HSA; increased intensity in presence of temsirolimus showing changes in secondary structure of HSA induced by temsirolimus. This study is of importance as it provides an insight into the binding mechanism of an important antirenal cancer drug with an important carrier protein. Once temsirolimus binds to HSA, it changes conformation of HSA which in turn can alter the functionality of this important carrier protein and this altered functionality of HSA can be highlighted in variety of diseases.

Crystal Structures of Human and Staphylococcus aureus Pyruvate Carboxylase and Molecular Insights into the Carboxyltransfer Reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiang,S.; Tong, L.

2008-01-01

Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-Angstroms resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in themore » active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.« less

Molecular and Imaging Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

NASA Astrophysics Data System (ADS)

Dohnalkova, A.; Tfaily, M.; Smith, A. P.; Chu, R. K.; Crump, A.; Brislawn, C.; Varga, T.; Shi, Z.; Thomashow, L. S.; Harsh, J. B.; Balogh-Brunstad, Z.; Keller, C. K.

2017-12-01

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is limited. The objective of this study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix. We hypothesized that nutrient limitation would cause formation of microbially-produced C constituents that would contribute to SOM stabilization. We focused on the processes of rhizodeposition in the rhizosphere, and we utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of the microbial community and the newly-formed SOM compounds in the rhizosphere and the bulk soil. We considered implications regarding their degree of long-term stability. The microbes in this controlled, nutrient-limited system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. These findings provide insight into the various degrees of stability of microbial SOM products in ecosystems and evidence that the residual biogenic material associated with mineral matrices may be important components in current carbon cycle models.

Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight.

PubMed

Purohit, Rituraj

2014-01-01

KIT receptor is the prime target in gastrointestinal stromal tumor (GISTs) therapy. Second generation inhibitor, Sunitinib, binds to an inactivated conformation of KIT receptor and stabilizes it in order to prevent tumor formation. Here, we investigated the dynamic behavior of wild type and mutant D816H KIT receptor, and emphasized the extended A-loop (EAL) region (805-850) by conducting molecular dynamics simulation (∼100 ns). We analyzed different properties such as root mean square cutoff or deviation, root mean square fluctuation, radius of gyration, solvent-accessible surface area, hydrogen bonding network analysis, and essential dynamics. Apart from this, clustering and cross-correlation matrix approach was used to explore the conformational space of the wild type and mutant EAL region of KIT receptor. Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region. Moreover, flexible secondary elements, specially, coil and turns were dominated in EAL region of mutant KIT receptor during simulation. This phenomenon increased the movement of EAL region which in turn helped in shifting the equilibrium towards the active kinase conformation. Our atomic investigation of mutant KIT receptor which emphasized on EAL region provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor and would help to discover new therapeutics for KIT-based resistant tumor cells in GIST therapy.

National Security and the Threat of Climate Change

DTIC Science & Technology

2007-01-01

life by preventing the formation of shells and skeletons of some very numerous and important zoo- plankton [48]. Coral reefs are particularly...http://lwf.ncdc.noaa.gov/oa/climate/research/trends.html 48. James C. Orr, Scott Doney, et al. 2005. Anthropogenic Ocean Acidification Over the...National Oceanic and Atmospheric Administration provided many valuable insights into climate science and reviewed our draft report. Dr. Robert Frosch

Comparative transcriptome analysis reveals a global insight into molecular processes regulating citrate accumulation in sweet orange (Citrus sinensis).

PubMed

Lu, Xiaopeng; Cao, Xiongjun; Li, Feifei; Li, Jing; Xiong, Jiang; Long, Guiyou; Cao, Shangyin; Xie, Shenxi

2016-12-01

Citrate, the predominant organic acid in citrus, determines the taste of these fruits. However, little is known about the synergic molecular processes regulating citrate accumulation. Using 'Dahongtiancheng' (Citrus sinensis) and 'Bingtangcheng' (C. sinensis) with significant difference in citrate, the objectives of this study were to understand the global mechanisms of high-citrate accumulation in sweet orange. 'Dahongtiancheng' and 'Bingtangcheng' exhibit significantly different patterns in citrate accumulation throughout fruit development, with the largest differences observed at 50-70 days after full bloom (DAFB). Comparative transcriptome profiling was performed for the endocarps of both cultivars at 50 and 70 DAFB. Over 34.5 million clean reads per library were successfully mapped to the reference database and 670-2630 differentially expressed genes (DEGs) were found in four libraries. Among the genes, five transcription factors were ascertained to be the candidates regulating citrate accumulation. Functional assignments of the DEGs indicated that photosynthesis, the citrate cycle and amino acid metabolism were significantly altered in 'Dahongtiancheng'. Physiological and molecular analyses suggested that high photosynthetic efficiency and partial impairment of citrate catabolism were crucial for the high-citrate trait, and amino acid biosynthesis was one of the important directions for citrate flux. The results reveal a global insight into the gene expression changes in a high-citrate compared with a low-citrate sweet orange. High accumulating efficiency and impaired degradation of citrate may be associated with the high-citrate trait of 'Dahongtiancheng'. Findings in this study increase understanding of the molecular processes regulating citrate accumulation in sweet orange. © 2016 Scandinavian Plant Physiology Society.

New insights into the use of stable water isotopes at the northern Antarctic Peninsula as a tool for regional climate studies

NASA Astrophysics Data System (ADS)

Fernandoy, Francisco; Tetzner, Dieter; Meyer, Hanno; Gacitúa, Guisella; Hoffmann, Kirstin; Falk, Ulrike; Lambert, Fabrice; MacDonell, Shelley

2018-03-01

Due to recent atmospheric and oceanic warming, the Antarctic Peninsula is one of the most challenging regions of Antarctica to understand in terms of both local- and regional-scale climate signals. Steep topography and a lack of long-term and in situ meteorological observations complicate the extrapolation of existing climate models to the sub-regional scale. Therefore, new techniques must be developed to better understand processes operating in the region. Isotope signals are traditionally related mainly to atmospheric conditions, but a detailed analysis of individual components can give new insight into oceanic and atmospheric processes. This paper aims to use new isotopic records collected from snow and firn cores in conjunction with existing meteorological and oceanic datasets to determine changes at the climatic scale in the northern extent of the Antarctic Peninsula. In particular, a discernible effect of sea ice cover on local temperatures and the expression of climatic modes, especially the Southern Annular Mode (SAM), is demonstrated. In years with a large sea ice extension in winter (negative SAM anomaly), an inversion layer in the lower troposphere develops at the coastal zone. Therefore, an isotope-temperature relationship (δ-T) valid for all periods cannot be obtained, and instead the δ-T depends on the seasonal variability of oceanic conditions. Comparatively, transitional seasons (autumn and spring) have a consistent isotope-temperature gradient of +0.69 ‰ °C-1. As shown by firn core analysis, the near-surface temperature in the northern-most portion of the Antarctic Peninsula shows a decreasing trend (-0.33 °C year-1) between 2008 and 2014. In addition, the deuterium excess (dexcess) is demonstrated to be a reliable indicator of seasonal oceanic conditions, and therefore suitable to improve a firn age model based on seasonal dexcess variability. The annual accumulation rate in this region is highly variable, ranging between 1060 and 2470 kg m

Molecular Insights into Plant-Microbial Processes and Carbon Storage in Mangrove Ecosystems

NASA Astrophysics Data System (ADS)

Romero, I. C.; Ziegler, S. E.; Fogel, M.; Jacobson, M.; Fuhrman, J. A.; Capone, D. G.

2009-12-01

Mangrove forests, in tropical and subtropical coastal zones, are among the most productive ecosystems, representing a significant global carbon sink. We report new molecular insights into the functional relationship among microorganisms, mangrove trees and sediment geochemistry. The interactions among these elements were studied in peat-based mangrove sediments (Twin Cays, Belize) subjected to a long-term fertilization experiment with N and P, providing an analog for eutrophication. The composition and δ13C of bacterial PLFA showed that bacteria and mangrove trees had similar nutrient limitation patterns (N in the fringe mangrove zone, P in the interior zone), and that fertilization with N or P can affect bacterial metabolic processes and bacterial carbon uptake (from diverse mangrove sources including leaf litter, live and dead roots). PCR amplified nifH genes showed a high diversity (26% nifH novel clones) and a remarkable spatial and temporal variability in N-fixing microbial populations in the rhizosphere, varying primarily with the abundance of dead roots, PO4-3 and H2S concentrations in natural and fertilized environments. Our results indicate that eutrophication of mangrove ecosystems has the potential to alter microbial organic matter remineralization and carbon release with important implications for the coastal carbon budget. In addition, we will present preliminary data from a new study exploring the modern calibration of carbon and hydrogen isotopes of plant leaf waxes as a proxy recorder of past environmental change in mangrove ecosystems.

Molecular insights into the activity and mechanism of cyanide hydratase enzyme associated with cyanide biodegradation by Serratia marcescens.

PubMed

Kushwaha, Madhulika; Kumar, Virender; Mahajan, Rishi; Bhalla, Tek Chand; Chatterjee, Subhankar; Akhter, Yusuf

2018-05-09

The present study provides molecular insights into the activity and mechanism of cyanide hydratase enzyme associated with degradation of cyanide compounds, using Serratia marcescens RL2b as a model organism. Resting cells harvested after 20 h achieved complete degradation of 12 mmol l - 1 cyanide in approximately 10 h. High-performance liquid chromatography analysis of reaction samples revealed formation of formamide as the only end product, which confirmed the presence of cyanide hydratase activity in S. marcescens RL2b. Comparative structural analysis with the other nitrilase family proteins, which was carried out using a sequence of cyanide hydratase from a phylogenetically related strain S. marcescens WW4, also revealed subtle but significant differences in amino acid residues of the substrate-binding pocket and catalytic triad (Cys-Lys-Glu).

Postglacial Human resilience and susceptibility to abrupt climate change new insights from Star Carr

NASA Astrophysics Data System (ADS)

Blockley, Simon; Abrook, Ashley; Bayliss, Alex; Candy, Ian; Conneller, Chantal; Darvill, Chris; Deeprose, Laura; Kearney, Rebecca; Langdon, Pete; Langdon Langdon, Cath; Lincoln, Paul; Macleod, Alison; Matthews, Ian; Palmer, Adrian; Schreve, Danielle; Taylor, Barry; Milner, Nicky

2017-04-01

We know little about the lives of the early humans who lived during the early Postglacial period (the Lateglacial and Early Holocene), a time characterised by abrupt climate change after 16,000, which includes a series of abrupt climatic transitions linked to the reorganisation of the global environment after the glacial maximum and the last major global warming event at the onset of the Holocene. The hunter-gatherers who lived during the early Postglacial have been characterised as highly mobile, dispersed and living within small groups, and there is much debate as to how they adapted to climatic and environmental change: did they move in response to climatic transitions (and if so what was the climatic threshold), or instead adapt their lifeways to the new environmental conditions? A key area for examining these ideas is the British Isles as it sits on the Atlantic fringe of Northwest Europe with a climate that is highly responsive to the wider climate forcing experienced in the northern Hemisphere. Furthermore, in this period, Britain is directly linked to continental Europe due to lowered global sea levels allowing for the ease of human migration in and out of this region. In general the British record has been seen as being dominated by abandonment and reoccupation in the Postglacial during periods of climatic transition with hunter-gatherer mobility being closely linked to the prevailing environment. Recent discoveries at the Early Mesolithic site of Star Carr and surrounding area, linked to local and regional climate records, based on isotopic, chironomid and pollen proxy data and dated at high chronological resolution, offer a new picture. Postglacial human occupation of the area commences at the Pleistocene/Holocene transition but is short lived and appears to end close to the Pre-Boreal Oscillation, However, this is followed by a period where hunter-gatherers occupy Star Carr and settle and invest time and effort into building huts and large scale wooden

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

PubMed

Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo

2016-01-21

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.

Emerging insights into the molecular and cellular basis of glioblastoma

PubMed Central

Dunn, Gavin P.; Rinne, Mikael L.; Wykosky, Jill; Genovese, Giannicola; Quayle, Steven N.; Dunn, Ian F.; Agarwalla, Pankaj K.; Chheda, Milan G.; Campos, Benito; Wang, Alan; Brennan, Cameron; Ligon, Keith L.; Furnari, Frank; Cavenee, Webster K.; Depinho, Ronald A.; Chin, Lynda; Hahn, William C.

2012-01-01

Glioblastoma is both the most common and lethal primary malignant brain tumor. Extensive multiplatform genomic characterization has provided a higher-resolution picture of the molecular alterations underlying this disease. These studies provide the emerging view that “glioblastoma” represents several histologically similar yet molecularly heterogeneous diseases, which influences taxonomic classification systems, prognosis, and therapeutic decisions. PMID:22508724

Human T-cell lymphotropic virus type 1 subtype C molecular variants among indigenous australians: new insights into the molecular epidemiology of HTLV-1 in Australo-Melanesia.

PubMed

Cassar, Olivier; Einsiedel, Lloyd; Afonso, Philippe V; Gessain, Antoine

2013-01-01

HTLV-1 infection is endemic among people of Melanesian descent in Papua New Guinea, the Solomon Islands and Vanuatu. Molecular studies reveal that these Melanesian strains belong to the highly divergent HTLV-1c subtype. In Australia, HTLV-1 is also endemic among the Indigenous people of central Australia; however, the molecular epidemiology of HTLV-1 infection in this population remains poorly documented. Studying a series of 23 HTLV-1 strains from Indigenous residents of central Australia, we analyzed coding (gag, pol, env, tax) and non-coding (LTR) genomic proviral regions. Four complete HTLV-1 proviral sequences were also characterized. Phylogenetic analyses implemented with both Neighbor-Joining and Maximum Likelihood methods revealed that all proviral strains belong to the HTLV-1c subtype with a high genetic diversity, which varied with the geographic origin of the infected individuals. Two distinct Australians clades were found, the first including strains derived from most patients whose origins are in the North, and the second comprising a majority of those from the South of central Australia. Time divergence estimation suggests that the speciation of these two Australian clades probably occurred 9,120 years ago (38,000-4,500). The HTLV-1c subtype is endemic to central Australia where the Indigenous population is infected with diverse subtype c variants. At least two Australian clades exist, which cluster according to the geographic origin of the human hosts. These molecular variants are probably of very ancient origin. Further studies could provide new insights into the evolution and modes of dissemination of these retrovirus variants and the associated ancient migration events through which early human settlement of Australia and Melanesia was achieved.

Molecular mechanisms involved in convergent crop domestication.

PubMed

Lenser, Teresa; Theißen, Günter

2013-12-01

Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Linking Teleconnections and Iowa's Climate

NASA Astrophysics Data System (ADS)

Rowe, S. T.; Villarini, G.; Lavers, D. A.; Scoccimarro, E.

2013-12-01

In recent years Iowa and the U.S. Midwest has experienced both extreme drought and flood periods. With a drought in 2012 bounded by major floods in 2011 and 2013, the rapid progression from one extreme to the next is on the forefront of the public mind. Given that Iowa is a major agricultural state, extreme weather conditions can have severe socioeconomic consequences. In this research we investigate the large-scale climate processes that occurred concurrently and before a range of dry/wet and cold/hot periods to improve process understanding of these events. It is essential to understand the large-scale climate processes, as these can then provide valuable insight toward the development of long-term climate forecasts for Iowa. In this study monthly and seasonal surface temperature and precipitation over 1950-2012 across Iowa are used. Precipitation and surface temperature data are retrieved from the Parameter-elevation Regressions on Independent Slopes Model (PRISM) Climate Group at Oregon State University. The large-scale atmospheric fields are obtained from the National Center for Environmental Prediction (NCEP) / National Center for Atmospheric Research (NCAR) Reanalysis 1 Project. Precipitation is stratified according to wet, normal, and dry conditions, while temperature according to hot, average, and cold periods. Different stratification criteria based on the precipitation and temperature distributions are examined. Mean sea-level pressure and sea-surface temperature composite maps for the northern hemisphere are then produced for the wet/dry conditions, and cold/hot conditions. Further analyses include correlation, anomalies, and assessment of large-scale planetary wave activity, shedding light on the differences and similarities among the opposite weather conditions. The results of this work will highlight regional weather patterns that are related to the climate over Iowa, providing valuable insight into the mechanisms controlling the occurrence of

Towards a more molecular taxonomy of disease.

PubMed

Park, Jisoo; Hescott, Benjamin J; Slonim, Donna K

2017-07-27

Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we can infer disease relationships from molecular data alone may yield insights into how to ultimately construct more modern taxonomies that integrate both physiological and molecular information. We introduce a new technique we call Parent Promotion to infer hierarchical relationships between disease terms using disease-gene data. We compare this technique with both an established ontology inference method (CliXO) and a minimum weight spanning tree approach. Because there is no gold standard molecular disease taxonomy available, we compare our inferred hierarchies to both the Medical Subject Headings (MeSH) category C forest of diseases and to subnetworks of the Disease Ontology (DO). This comparison provides insights about the inference algorithms, choices of evaluation metrics, and the existing molecular content of various subnetworks of MeSH and the DO. Our results suggest that the Parent Promotion method performs well in most cases. Performance across MeSH trees is also correlated between inference methods. Specifically, inferred relationships are more consistent with those in smaller MeSH disease trees than larger ones, but there are some notable exceptions that may correlate with higher molecular content in MeSH. Our experiments provide insights about learning relationships between diseases from disease genes alone. Future work should explore the prospect of disease term discovery from molecular data and how best to integrate molecular data with anatomical and clinical knowledge. This study nonetheless suggests that disease gene information has the potential to form an important part of the foundation for future representations of the disease landscape.

Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain

PubMed Central

Poplawski, Amanda; Hu, Kaifeng; Lee, Woonghee; Natesan, Senthil; Peng, Danni; Carlson, Samuel; Shi, Xiaobing; Balaz, Stefan; Markley, John L.; Glass, Karen C.

2014-01-01

The monocytic leukemic zinc-finger (MOZ) histone acetyltransferase (HAT) acetylates free histones H3, H4, H2A, and H2B in vitro and is associated with up-regulation of gene transcription. The MOZ HAT functions as a quaternary complex with the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5), and hEaf6 subunits. BRPF1 links the MOZ catalytic subunit to the ING5 and hEaf6 subunits, thereby promoting MOZ HAT activity. Human BRPF1 contains multiple effector domains with known roles in gene transcription, and chromatin binding and remodeling. However, the biological function of the BRPF1 bromodomain remains unknown. Our findings reveal novel interactions of the BRPF1 bromodomain with multiple acetyllysine residues on the N-terminus of histones, and show it preferentially selects for H2AK5ac, H4K12ac and H3K14ac. We used chemical shift perturbation data from NMR titration experiments to map the BRPF1 bromodomain ligand binding pocket and identified key residues responsible for coordination of the post-translationally modified histones. Extensive molecular dynamics simulations were used to generate structural models of bromodomain-histone ligand complexes, to analyze H-bonding and other interactions, and to calculate the binding free energies. Our results outline the molecular mechanism driving binding specificity of the BRPF1 bromodomain for discrete acetyllysine residues on the N-terminal histone tails. Together these data provide insights on how histone recognition by the bromodomain directs the biological function of BRPF1, ultimately targeting the MOZ HAT complex to chromatin substrates. PMID:24333487

Climate Change: From Science to Practice.

PubMed

Wheeler, Nicola; Watts, Nick

2018-03-01

Climate change poses a significant threat to human health. Understanding how climate science can be translated into public health practice is an essential first step in enabling robust adaptation and improving resiliency to climate change. Recent research highlights the importance of iterative approaches to public health adaptation to climate change, enabling uncertainties of health impacts and barriers to adaptation to be accounted for. There are still significant barriers to adaptation, which are context-specific and thus present unique challenges to public health practice. The implementation of flexible adaptation approaches, using frameworks targeted for public health, is key to ensuring robust adaptation to climate change in public health practice. The BRACE framework provides an excellent approach for health adaptation to climate change. Combining this with the insights provided and by the adaptation pathways approach allows for more deliberate accounting of long-term uncertainties. The mainstreaming of climate change adaptation into public health practice and planning is important in facilitating this approach and overcoming the significant barriers to effective adaptation. Yet, the immediate and future limits to adaptation provide clear justification for urgent and accelerated efforts to mitigate climate change.

Climate-Induced Changes in the Chemical Characteristics of Natural Organic Matter at a Small Freshwater Wetland

NASA Astrophysics Data System (ADS)

Maurice, P. A.; Cabaniss, S. E.; Drummond, J.

2001-12-01

This study investigated the spatiotemporal variability in dissolved organic carbon concentration (DOC), natural organic matter (NOM) weight average molecular weight (Mw), and absorptivity at 280 nm (e280, an estimator of aromaticity) at McDonalds Branch, a first-order stream that is a fen wetland. When ground-water discharge to the stream was predominant, the DOC, the Mw, and the e280 were all relatively low. When soil porewater was more important, not only was the DOC higher, but also the Mw and e280. Hence, the contribution of soil pore water relative to ground water controlled not only the concentration but also the average physicochemical characteristics of the NOM. Results from this small watershed study provide insight into climatic effects on surface-water NOM characteristics in a small freshwater fen. Low-flow periods resulted in lower Mw, more aliphatic NOM derived primarily from ground-water discharge to the stream whereas higher flow periods resulted in a higher Mw(by 150-500 Da), more aromatic downstream surface-water NOM pool. Hence, during future summer drought periods, as suggested by climate-change models for much of North America, surface-water NOM likely will be lower molecular weight, more aliphatic, and more hydrophilic with lesser metal binding and HOC uptake abilities, along with decreased ability to attenuate UV radiation.

Migration out of 1930s Rural Eastern Oklahoma: Insights for Climate Change Research

ERIC Educational Resources Information Center

McLeman, Robert

2006-01-01

The question of how communities and individuals adapt to changing climatic conditions is of pressing concern to scientists and policymakers in light of the growing evidence that human activity has modified the Earth's climate. A number of authors have suggested that widespread changes in human settlement and migration patterns may occur in…

Coupled Ethical-Epistemic Analysis of Climate Change

NASA Astrophysics Data System (ADS)

Vezer, M.

2015-12-01

Are there inherent limitations to what we can know about how the climate will change in the years ahead? How can we use what is known about the future climate in a way that promotes ethical decision-making? These questions call for urgent attention because important policy decisions need to be made in order to prepare for climate change in North America and around the world. While the science of climate change is central to this line of inquiry, the fields of epistemology, moral, political and environmental philosophy may provide insights on how these issues should be addressed. Detailing the relationship between evidential and ethical dimensions of climate change, this research aims to improve our understanding of the interconnections among several lines of inquiry and to develop solutions to problems of decision-making under conditions of scientific uncertainty.

The Political Economy of Health Co-Benefits: Embedding Health in the Climate Change Agenda.

PubMed

Workman, Annabelle; Blashki, Grant; Bowen, Kathryn J; Karoly, David J; Wiseman, John

2018-04-04

A complex, whole-of-economy issue such as climate change demands an interdisciplinary, multi-sectoral response. However, evidence suggests that human health has remained elusive in its influence on the development of ambitious climate change mitigation policies for many national governments, despite a recognition that the combustion of fossil fuels results in pervasive short- and long-term health consequences. We use insights from literature on the political economy of health and climate change, the science–policy interface and power in policy-making, to identify additional barriers to the meaningful incorporation of health co-benefits into climate change mitigation policy development. Specifically, we identify four key interrelated areas where barriers may exist in relation to health co-benefits: discourse, efficiency, vested interests and structural challenges. With these insights in mind, we argue that the current politico-economic paradigm in which climate change is situated and the processes used to develop climate change mitigation policies do not adequately support accounting for health co-benefits. We present approaches for enhancing the role of health co-benefits in the development of climate change mitigation policies to ensure that health is embedded in the broader climate change agenda.

The Political Economy of Health Co-Benefits: Embedding Health in the Climate Change Agenda

PubMed Central

Workman, Annabelle; Blashki, Grant; Bowen, Kathryn J.; Karoly, David J.; Wiseman, John

2018-01-01

A complex, whole-of-economy issue such as climate change demands an interdisciplinary, multi-sectoral response. However, evidence suggests that human health has remained elusive in its influence on the development of ambitious climate change mitigation policies for many national governments, despite a recognition that the combustion of fossil fuels results in pervasive short- and long-term health consequences. We use insights from literature on the political economy of health and climate change, the science–policy interface and power in policy-making, to identify additional barriers to the meaningful incorporation of health co-benefits into climate change mitigation policy development. Specifically, we identify four key interrelated areas where barriers may exist in relation to health co-benefits: discourse, efficiency, vested interests and structural challenges. With these insights in mind, we argue that the current politico-economic paradigm in which climate change is situated and the processes used to develop climate change mitigation policies do not adequately support accounting for health co-benefits. We present approaches for enhancing the role of health co-benefits in the development of climate change mitigation policies to ensure that health is embedded in the broader climate change agenda. PMID:29617317

From Molecular Docking to 3D-Quantitative Structure-Activity Relationships (3D-QSAR): Insights into the Binding Mode of 5-Lipoxygenase Inhibitors.

PubMed

Eren, Gokcen; Macchiarulo, Antonio; Banoglu, Erden

2012-02-01

Pharmacological intervention with 5-Lipoxygenase (5-LO) is a promising strategy for treatment of inflammatory and allergic ailments, including asthma. With the aim of developing predictive models of 5-LO affinity and gaining insights into the molecular basis of ligand-target interaction, we herein describe QSAR studies of 59 diverse nonredox-competitive 5-LO inhibitors based on the use of molecular shape descriptors and docking experiments. These studies have successfully yielded a predictive model able to explain much of the variance in the activity of the training set compounds while predicting satisfactorily the 5-LO inhibitory activity of an external test set of compounds. The inspection of the selected variables in the QSAR equation unveils the importance of specific interactions which are observed from docking experiments. Collectively, these results may be used to design novel potent and selective nonredox 5-LO inhibitors. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding global climate change scenarios through bioclimate stratification

NASA Astrophysics Data System (ADS)

Soteriades, A. D.; Murray-Rust, D.; Trabucco, A.; Metzger, M. J.

2017-08-01

Despite progress in impact modelling, communicating and understanding the implications of climatic change projections is challenging due to inherent complexity and a cascade of uncertainty. In this letter, we present an alternative representation of global climate change projections based on shifts in 125 multivariate strata characterized by relatively homogeneous climate. These strata form climate analogues that help in the interpretation of climate change impacts. A Random Forests classifier was calculated and applied to 63 Coupled Model Intercomparison Project Phase 5 climate scenarios at 5 arcmin resolution. Results demonstrate how shifting bioclimate strata can summarize future environmental changes and form a middle ground, conveniently integrating current knowledge of climate change impact with the interpretation advantages of categorical data but with a level of detail that resembles a continuous surface at global and regional scales. Both the agreement in major change and differences between climate change projections are visually combined, facilitating the interpretation of complex uncertainty. By making the data and the classifier available we provide a climate service that helps facilitate communication and provide new insight into the consequences of climate change.

Vegetation zones in changing climate

NASA Astrophysics Data System (ADS)

Belda, Michal; Holtanova, Eva; Halenka, Tomas; Kalvova, Jaroslava

2017-04-01

Climate patterns analysis can be performed for individual climate variables separately or the data can be aggregated using e.g. some kind of climate classification. These classifications usually correspond to vegetation distribution in the sense that each climate type is dominated by one vegetation zone or eco-region. Thus, the Köppen-Trewartha classification provides integrated assessment of temperature and precipitation together with their annual cycle as well. This way climate classifications also can be used as a convenient tool for the assessment and validation of climate models and for the analysis of simulated future climate changes. The Köppen-Trewartha classification is applied on full CMIP5 family of more than 40 GCM simulations and CRU dataset for comparison. This evaluation provides insight on the GCM performance and errors for simulations of the 20th century climate. Common regions are identified, such as Australia or Amazonia, where many state-of-the-art models perform inadequately. Moreover, the analysis of the CMIP5 ensemble for future under RCP 4.5 and RCP 8.5 is performed to assess the climate change for future. There are significant changes for some types in most models e.g. increase of savanna and decrease of tundra for the future climate. For some types significant shifts in latitude can be seen when studying their geographical location in selected continental areas, e.g. toward higher latitudes for boreal climate. Quite significant uncertainty can be seen for some types. For Europe, EuroCORDEX results for both 0.11 and 0.44 degree resolution are validated using Köppen-Trewartha types in comparison to E-OBS based classification. ERA-Interim driven simulations are compared to both present conditions of CMIP5 models as well as their downscaling by EuroCORDEX RCMs. Finally, the climate change signal assessment is provided using the individual climate types. In addition to the changes assessed similarly as for GCMs analysis in terms of the area

Climate change studies and the human sciences

NASA Astrophysics Data System (ADS)

Holm, Poul; Winiwarter, Verena

2017-09-01

Policy makers have made repeated calls for integration of human and natural sciences in the field of climate change. Serious multidisciplinary attempts began already in the 1950s. Progress has certainly been made in understanding the role of humans in the planetary system. New perspectives have clarified policy advice, and three insights are singled out in the paper: the critique of historicism, the distinction between benign and wicked problems, and the cultural critique of the 'myths of nature'. Nevertheless, analysis of the IPCC Assessment Reports indicates that integration is skewed towards a particular dimension of human sciences (economics) and major insights from cultural theory and historical analysis have not made it into climate science. A number of relevant disciplines are almost absent in the composition of authorship. Nevertheless, selective assumptions and arguments are made about e.g. historical findings in key documents. In conclusion, we suggest to seek remedies for the lack of historical scholarship in the IPCC reports. More effort at science-policy exchange is needed, and an Integrated Platform to channel humanities and social science expertise for climate change research might be one promising way.

Advancing Climate Change and Impacts Science Through Climate Informatics

NASA Astrophysics Data System (ADS)

Lenhardt, W.; Pouchard, L. C.; King, A. W.; Branstetter, M. L.; Kao, S.; Wang, D.

2010-12-01

This poster will outline the work to date on developing a climate informatics capability at Oak Ridge National Laboratory (ORNL). The central proposition of this effort is that the application of informatics and information science to the domain of climate change science is an essential means to bridge the realm of high performance computing (HPC) and domain science. The goal is to facilitate knowledge capture and the creation of new scientific insights. For example, a climate informatics capability will help with the understanding and use of model results in domain sciences that were not originally in the scope. From there, HPC can also benefit from feedback as the new approaches may lead to better parameterization in the models. In this poster we will summarize the challenges associated with climate change science that can benefit from the systematic application of informatics and we will highlight our work to date in creating the climate informatics capability to address these types of challenges. We have identified three areas that are particularly challenging in the context of climate change science: 1) integrating model and observational data across different spatial and temporal scales, 2) model linkages, i.e. climate models linked to other models such as hydrologic models, and 3) model diagnostics. Each of these has a methodological component and an informatics component. Our project under way at ORNL seeks to develop new approaches and tools in the context of linking climate change and water issues. We are basing our work on the following four use cases: 1) Evaluation/test of CCSM4 biases in hydrology (precipitation, soil water, runoff, river discharge) over the Rio Grande Basin. User: climate modeler. 2) Investigation of projected changes in hydrology of Rio Grande Basin using the VIC (Variable Infiltration Capacity Macroscale) Hydrologic Model. User: watershed hydrologist/modeler. 3) Impact of climate change on agricultural productivity of the Rio Grande

Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study.

PubMed

Zhang, Ruiming; Shi, Xiangli; Sun, Yanhui; Zhang, Qingzhu; Wang, Wenxing

2018-05-17

The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl (2,3-DD-4,4'-DBPH) by Pandoraea pnomenusa strain B-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4'-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol -1 , respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4'-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB. Copyright © 2018. Published by Elsevier Ltd.

Thermodynamic Insights into Effects of Water Displacement and Rearrangement upon Ligand Modification using Molecular Dynamics Simulations.

PubMed

Wahl, Joel; Smiesko, Martin

2018-05-04

Computational methods, namely Molecular Dynamics Simulations (MD simulations) in combination with Inhomogeneous Fluid Solvation Theory (IFST) were used to retrospectively investigate various cases of ligand structure modifications that led to the displacement of binding site water molecules. Our findings are that the water displacement per se is energetically unfavorable in the discussed examples, and that it is merely the fine balance between change in protein-ligand interaction energy, ligand solvation free energies and binding site solvation free energies that determine if water displacement is favorable or not. We furthermore evaluated if we can reproduce experimental binding affinities by a computational approach combining changes in solvation free energies with changes in protein-ligand interaction energies and entropies. In two of the seven cases, this estimation led to large errors, implying that accurate predictions of relative binding free energies based on solvent thermodynamics is challenging. Still, MD simulations can provide insights into which water molecules can be targeted for displacement. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Risk communication, public engagement, and climate change: a role for emotions.

PubMed

Roeser, Sabine

2012-06-01

This article discusses the potential role that emotions might play in enticing a lifestyle that diminishes climate change. Climate change is an important challenge for society. There is a growing consensus that climate change is due to our behavior, but few people are willing to significantly adapt their lifestyle. Empirical studies show that people lack a sense of urgency: they experience climate change as a problem that affects people in distant places and in a far future. Several scholars have claimed that emotions might be a necessary tool in communication about climate change. This article sketches a theoretical framework that supports this hypothesis, drawing on insights from the ethics of risk and the philosophy of emotions. It has been shown by various scholars that emotions are important determinants in risk perception. However, emotions are generally considered to be irrational states and are hence excluded from communication and political decision making about risky technologies and climate change, or they are used instrumentally to create support for a position. However, the literature on the ethics of risk shows that the dominant, technocratic approach to risk misses the normative-ethical dimension that is inherent to decisions about acceptable risk. Emotion research shows that emotions are necessary for practical and moral decision making. These insights can be applied to communication about climate change. Emotions are necessary for understanding the moral impact of the risks of climate change, and they also paradigmatically provide for motivation. Emotions might be the missing link in effective communication about climate change. © 2012 Society for Risk Analysis.

Ecotypic differentiation under farmers' selection: Molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes.

PubMed

Delêtre, Marc; Soengas, Beatriz; Vidaurre, Prem Jai; Meneses, Rosa Isela; Delgado Vásquez, Octavio; Oré Balbín, Isabel; Santayana, Monica; Heider, Bettina; Sørensen, Marten

2017-06-01

Understanding the distribution of crop genetic diversity in relation to environmental factors can give insights into the eco-evolutionary processes involved in plant domestication. Yam beans ( Pachyrhizus Rich. ex DC.) are leguminous crops native to South and Central America that are grown for their tuberous roots but are seed-propagated. Using a landscape genetic approach, we examined correlations between environmental factors and phylogeographic patterns of genetic diversity in Pachyrhizus landrace populations. Molecular analyses based on chloroplast DNA sequencing and a new set of nuclear microsatellite markers revealed two distinct lineages, with strong genetic differentiation between Andean landraces (lineage A) and Amazonian landraces (lineage B). The comparison of different evolutionary scenarios for the diversification history of yam beans in the Andes using approximate Bayesian computation suggests that Pachyrhizus ahipa and Pachyrhizus tuberosus share a progenitor-derivative relationship, with environmental factors playing an important role in driving selection for divergent ecotypes. The new molecular data call for a revision of the taxonomy of Pachyrhizus but are congruent with paleoclimatic and archeological evidence, and suggest that selection for determinate growth was part of ecophysiological adaptations associated with the diversification of the P. tuberosus - P. ahipa complex during the Mid-Holocene.

Molecular insights into the novel aspects of diatom biology.

PubMed

Scala, S; Bowler, C

2001-10-01

Diatoms are unicellular photosynthetic eukaryotes that are thought to contribute as much as 25% of global primary productivity. In spite of their ecological importance in the worlds oceans, very little information is available at the molecular level about the novel aspects of their biology. Recent advances, such as the development of gene transfer protocols, are now allowing the genetic dissection of diatom biology. Notable examples are advances in understanding the genetic basis for the silica-based bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. The potentiation of current research will allow an evaluation of the use of diatoms to construct submicrometre-scale silicon structures for the nanotechnology industry and will reveal the molecular secrets underlying their ecological success.

Molecular insights into the role of white adipose tissue in metabolically unhealthy normal weight and metabolically healthy obese individuals.

PubMed

Badoud, Flavia; Perreault, Maude; Zulyniak, Michael A; Mutch, David M

2015-03-01

Obesity is a risk factor for the development of type 2 diabetes and cardiovascular disease. However, it is now recognized that a subset of individuals have reduced cardiometabolic risk despite being obese. Paradoxically, a subset of lean individuals is reported to have high risk for cardiometabolic complications. These distinct subgroups of individuals are referred to as metabolically unhealthy normal weight (MUNW) and metabolically healthy obese (MHO). Although the clinical relevance of these subgroups remains debated, evidence shows a critical role for white adipose tissue (WAT) function in the development of these phenotypes. The goal of this review is to provide an overview of our current state of knowledge regarding the molecular and metabolic characteristics of WAT associated with MUNW and MHO. In particular, we discuss the link between different WAT depots, immune cell infiltration, and adipokine production with MUNW and MHO. Furthermore, we also highlight recent molecular insights made with genomic technologies showing that processes such as oxidative phosphorylation, branched-chain amino acid catabolism, and fatty acid β-oxidation differ between these phenotypes. This review provides evidence that WAT function is closely linked with cardiometabolic risk independent of obesity and thus contributes to the development of MUNW and MHO. © FASEB.

Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function.

PubMed

Gupta, Payal; Dash, Prasanta K

2017-09-11

Secretory phospholipase A 2 (sPLA 2 ) are low molecular weight proteins (12-18 kDa) involved in a suite of plant cellular processes imparting growth and development. With myriad roles in physiological and biochemical processes in plants, detailed analysis of sPLA 2 in flax/linseed is meagre. The present work, first in flax, embodies cloning, expression, purification and molecular characterisation of two distinct sPLA 2 s (I and II) from flax. PLA 2 activity of the cloned sPLA 2 s were biochemically assayed authenticating them as bona fide phospholipase A 2 . Physiochemical properties of both the sPLA 2 s revealed they are thermostable proteins requiring di-valent cations for optimum activity.While, structural analysis of both the proteins revealed deviations in the amino acid sequence at C- & N-terminal regions; hydropathic study revealed LusPLA 2 I as a hydrophobic protein and LusPLA 2 II as a hydrophilic protein. Structural analysis of flax sPLA 2 s revealed that secondary structure of both the proteins are dominated by α-helix followed by random coils. Modular superimposition of LusPLA 2 isoforms with rice sPLA 2 confirmed monomeric structural preservation among plant phospholipase A 2 and provided insight into structure of folded flax sPLA 2 s.

Molecular Insights Into the Evolutionary Pathway of Vibrio cholerae O1 Atypical El Tor Variants

PubMed Central

Kim, Eun Jin; Lee, Dokyung; Moon, Se Hoon; Lee, Chan Hee; Kim, Sang Jun; Lee, Jae Hyun; Kim, Jae Ouk; Song, Manki; Das, Bhabatosh; Clemens, John D.; Pape, Jean William; Nair, G. Balakrish; Kim, Dong Wook

2014-01-01

Pandemic V. cholerae strains in the O1 serogroup have 2 biotypes: classical and El Tor. The classical biotype strains of the sixth pandemic, which encode the classical type cholera toxin (CT), have been replaced by El Tor biotype strains of the seventh pandemic. The prototype El Tor strains that produce biotype-specific cholera toxin are being replaced by atypical El Tor variants that harbor classical cholera toxin. Atypical El Tor strains are categorized into 2 groups, Wave 2 and Wave 3 strains, based on genomic variations and the CTX phage that they harbor. Whole-genome analysis of V. cholerae strains in the seventh cholera pandemic has demonstrated gradual changes in the genome of prototype and atypical El Tor strains, indicating that atypical strains arose from the prototype strains by replacing the CTX phages. We examined the molecular mechanisms that effected the emergence of El Tor strains with classical cholera toxin-carrying phage. We isolated an intermediary V. cholerae strain that carried two different CTX phages that encode El Tor and classical cholera toxin, respectively. We show here that the intermediary strain can be converted into various Wave 2 strains and can act as the source of the novel mosaic CTX phages. These results imply that the Wave 2 and Wave 3 strains may have been generated from such intermediary strains in nature. Prototype El Tor strains can become Wave 3 strains by excision of CTX-1 and re-equipping with the new CTX phages. Our data suggest that inter-chromosomal recombination between 2 types of CTX phages is possible when a host bacterial cell is infected by multiple CTX phages. Our study also provides molecular insights into population changes in V. cholerae in the absence of significant changes to the genome but by replacement of the CTX prophage that they harbor. PMID:25233006

Novel Insights into Cell Entry of Emerging Human Pathogenic Arenaviruses.

PubMed

Fedeli, Chiara; Moreno, Héctor; Kunz, Stefan

2018-06-22

Viral hemorrhagic fevers caused by emerging RNA viruses of the Arenavirus family are among the most devastating human diseases. Climate change, global trade, and increasing urbanization promote the emergence and re-emergence of these human pathogenic viruses. Emerging pathogenic arenaviruses are of zoonotic origin and reservoir-to-human transmission is crucial for spillover into human populations. Host cell attachment and entry are the first and most fundamental steps of every virus infection and represent major barriers for zoonotic transmission. During host cell invasion, viruses critically depend on cellular factors, including receptors, co-receptors, and regulatory proteins of endocytosis. An in-depth understanding of the complex interaction of a virus with cellular factors implicated in host cell entry is therefore crucial to predict the risk of zoonotic transmission, define the tissue tropism, and assess disease potential. Over the past years, investigation of the molecular and cellular mechanisms underlying host cell invasion of human pathogenic arenaviruses uncovered remarkable viral strategies and provided novel insights into viral adaptation and virus-host co-evolution that will be covered in the present review. Copyright © 2018. Published by Elsevier Ltd.

Climate change impacts on Swiss groundwater: insights from historical records

NASA Astrophysics Data System (ADS)

Figura, S.; Livingstone, D. M.; Kipfer, R.

2012-04-01

Knowledge of the impact of climate change on groundwater is limited mainly by a lack of relevant long-term data that would allow the effects of climatic forcing to be assessed empirically. With the aim of assessing the consequences of climate change on groundwater, we collected and statistically analysed historical groundwater data from Switzerland. While most existing studies have focused on the impact of climate change on groundwater quantity, we focus on groundwater quality. As measures of groundwater quality we chose groundwater temperature and oxygen concentration because of their importance for biogeochemical processes and for reasons of data availability. Our analyses show that in aquifers that are recharged by riverbank infiltration, groundwater temperature has increased by 1°C - 1.5°C over the last 30 years. By contrast, in aquifers that are recharged only by the percolation of precipitation, increases in groundwater temperature are slight or non-existent. A detailed analysis of groundwater temperatures measured in the pumping wells of five aquifers that are recharged by riverbank infiltration revealed that an abrupt temperature increase in the late 1980s, which was also detected in Swiss air temperature and river water temperatures and which is traceable ultimately to a change in the behaviour of the Arctic Oscillation, accounted for a large proportion of the total groundwater warming [1]. Oxygen concentrations were available for four of the five aquifers we investigated. In two of these aquifers the oxygen concentration underwent a strong decrease, in the third a slight decrease, and in the fourth a slight increase. Neither long-term trends in river water oxygen concentration nor altered hydraulic conditions seem to be responsible for the long-term trends in groundwater oxygen concentrations. However, the decreasing oxygen concentrations were accompanied by decreasing DOC concentrations in the groundwater, while DOC concentrations in the river water

Noachian Climate of Mars: Insights from Noachian Stratigraphy and Valley Networks System Formation Times

NASA Astrophysics Data System (ADS)

Head, J. W., III

2017-12-01

Noachian climate models have been proposed in order to account for 1) observed fluvial and lacustrine activity, 2) weathering processes producing phyllosilicates, and 3) an unusual impact record including three major impact basins and unusual degradation processes. We adopt a stratigraphic approach in order place these observations in a temporal context. Formation of the major impact basins Hellas, Isidis and Argyre in earlier Noachian profoundly influenced the uplands geology and appears to have occurred concurrently with major phyllosilicate and related surface occurrences/deposits; the immediate aftermath of these basins appears to have created a temporary hot and wet surface environment with significant effect on surface morphology and alteration processes. Formation of Late Noachian-Early Hesperian valley network systems (VNS) signaled the presence of warm/wet conditions generating several hypotheses for climates permissive of these conditions. We examined estimates for the time required to carve channels/deltas and total duration implied by plausible intermittencies. Synthesis of required timescales show that the total time to carve the VN does not exceed 106 years, < 0.25% of the total Noachian. What climate models can account for the VNS? 1) Warm and wet/semiarid/arid climate: Sustained background MAT >273 K, hydrological system vertically integrated, and rainfall occurs to recharge the aquifer. 2) Cold and Icy climate warmed by greenhouse gases or episodic stochastic events: Climate is sustained cold/icy, but greenhouse gases of unspecified nature/amount/duration elevate MAT by several tens of Kelvins, bringing the annual temperature range into the realm where peak seasonal temperatures (PST) exceed 273 K. In this climate environment, analogous to the Antarctic Dry Valleys, seasonal summer temperatures above 273 K are sufficient to melt snow/ice and form fluvial and lacustrine features, but MAT is well below 273 K (253 K); punctuated warming alternatives

Climate-driven tree mortality: insights from the pinon pine die-off in the United States

Treesearch

Jeffrey A. Hicke; Melanie J. B. Zeppel

2013-01-01

The global climate is changing, and a range of negative effects on plants has already been observed and will likely continue into the future. One of the most apparent consequences of climate change is widespread tree mortality (Fig. 1). Extensive tree die-offs resulting from recent climate change have been documented across a range of forest types on all forested...

Climate change & livestock health on the U.S. Northern Plains; Actionable economic insights & needs

USDA-ARS?s Scientific Manuscript database

Climate change will impact livestock health through numerous direct mechanisms and indirect drivers. Examples of direct mechanisms include climate-driven changes in the biology of pathogens, and the distribution of vectors. Indirect drivers may include changes in environmental factors, land-use, and...

The structure of biodiversity – insights from molecular phylogeography

PubMed Central

Hewitt, Godfrey M

2004-01-01

DNA techniques, analytical methods and palaeoclimatic studies are greatly advancing our knowledge of the global distribution of genetic diversity, and how it evolved. Such phylogeographic studies are reviewed from Arctic, Temperate and Tropical regions, seeking commonalities of cause in the resulting genetic patterns. The genetic diversity is differently patterned within and among regions and biomes, and is related to their histories of climatic changes. This has major implications for conservation science. PMID:15679920

Climate-driven thresholds for chemical weathering in postglacial soils of New Zealand

NASA Astrophysics Data System (ADS)

Dixon, Jean L.; Chadwick, Oliver A.; Vitousek, Peter M.

2016-09-01

Chemical weathering in soils dissolves and alters minerals, mobilizes metals, liberates nutrients to terrestrial and aquatic ecosystems, and may modulate Earth's climate over geologic time scales. Climate-weathering relationships are often considered fundamental controls on the evolution of Earth's surface and biogeochemical cycles. However, surprisingly little consensus has emerged on if and how climate controls chemical weathering, and models and data from published literature often give contrasting correlations and predictions for how weathering rates and climate variables such as temperature or moisture are related. Here we combine insights gained from the different approaches, methods, and theory of the soil science, biogeochemistry, and geomorphology communities to tackle the fundamental question of how rainfall influences soil chemical properties. We explore climate-driven variations in weathering and soil development in young, postglacial soils of New Zealand, measuring soil elemental geochemistry along a large precipitation gradient (400-4700 mm/yr) across the Waitaki basin on Te Waipounamu, the South Island. Our data show a strong climate imprint on chemical weathering in these young soils. This climate control is evidenced by rapid nonlinear changes along the gradient in total and exchangeable cations in soils and in the increased movement and redistribution of metals with rainfall. The nonlinear behavior provides insight into why climate-weathering relationships may be elusive in some landscapes. These weathering thresholds also have significant implications for how climate may influence landscape evolution and the release of rock-derived nutrients to ecosystems, as landscapes that transition to wetter climates across this threshold may weather and deplete rapidly.

New molecular insights into the pools and mechanisms of Arctic soil organic matter decomposition under warming

NASA Astrophysics Data System (ADS)

Gu, B.

2017-12-01

It is estimated that Arctic permafrost soils store approximately half of the global belowground organic carbon, which is susceptible to microbial decomposition under warming climate. Studies have shown that rates of soil organic carbon (SOC) decomposition are controlled not only by temperature but also SOC substrate quality or chemical composition. However, detailed molecular-scale characterization of SOC and its susceptibility to degradation are lacking, due to extremely complex nature of SOC. Here, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was utilized to determine compositional changes of SOC during a microcosm warming experiment using tundra soils that were collected from the Barrow Environmental Observatory in Alaska, USA. Soil microcosm incubation was conducted with both organic and mineral active layer soils at two temperatures (-2°C and 8°C) up to 122 days, and water-extractable SOC was analyzed. Results indicate that peptides, amino sugars, and carbohydrate-like compounds are among the most labile SOC compounds to be degraded, with nitrogen-containing compounds degrading at a much faster rate than those containing no nitrogen. Refractory SOC components are dominated by the lignin- or tannin-like compounds and, to a less extent, the aliphatic compounds. Additionally, elemental ratios of O:C, H:C, and N:C were found to decrease with incubation time, and SOC in the mineral soil exhibited lower O:C and N:C ratios than those of the organic-rich soil. A biodegradation index is proposed to facilitate the incorporation of mass spectrometry data into mechanistic models of SOC degradation and thus improved prediction model of climate feedbacks in the Arctic.

New molecular insights into the pools and mechanisms of Arctic soil organic matter decomposition under warming

NASA Astrophysics Data System (ADS)

Gilbert, A.; Yamada, K.; Julien, M.; Yoshida, N.; Remaud, G.; Robins, R.

2016-12-01

It is estimated that Arctic permafrost soils store approximately half of the global belowground organic carbon, which is susceptible to microbial decomposition under warming climate. Studies have shown that rates of soil organic carbon (SOC) decomposition are controlled not only by temperature but also SOC substrate quality or chemical composition. However, detailed molecular-scale characterization of SOC and its susceptibility to degradation are lacking, due to extremely complex nature of SOC. Here, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was utilized to determine compositional changes of SOC during a microcosm warming experiment using tundra soils that were collected from the Barrow Environmental Observatory in Alaska, USA. Soil microcosm incubation was conducted with both organic and mineral active layer soils at two temperatures (-2°C and 8°C) up to 122 days, and water-extractable SOC was analyzed. Results indicate that peptides, amino sugars, and carbohydrate-like compounds are among the most labile SOC compounds to be degraded, with nitrogen-containing compounds degrading at a much faster rate than those containing no nitrogen. Refractory SOC components are dominated by the lignin- or tannin-like compounds and, to a less extent, the aliphatic compounds. Additionally, elemental ratios of O:C, H:C, and N:C were found to decrease with incubation time, and SOC in the mineral soil exhibited lower O:C and N:C ratios than those of the organic-rich soil. A biodegradation index is proposed to facilitate the incorporation of mass spectrometry data into mechanistic models of SOC degradation and thus improved prediction model of climate feedbacks in the Arctic.

Distributed Generation to Support Development-Focused Climate Action

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cox, Sadie; Gagnon, Pieter; Stout, Sherry

2016-09-01

This paper explores the role of distributed generation, with a high renewable energy contribution, in supporting low emission climate-resilient development. The paper presents potential impacts on development (via energy access), greenhouse gas emission mitigation, and climate resilience directly associated with distributed generation, as well as specific actions that may enhance or increase the likelihood of climate and development benefits. This paper also seeks to provide practical and timely insights to support distributed generation policymaking and planning within the context of common climate and development goals as the distributed generation landscape rapidly evolves globally. Country-specific distributed generation policy and program examples,more » as well as analytical tools that can inform efforts internationally, are also highlighted throughout the paper.« less

Exploring molecular insights into the interaction mechanism of cholesterol derivatives with the Mce4A: A combined spectroscopic and molecular dynamic simulation studies.

PubMed

Khan, Shagufta; Khan, Faez Iqbal; Mohammad, Taj; Khan, Parvez; Hasan, Gulam Mustafa; Lobb, Kevin A; Islam, Asimul; Ahmad, Faizan; Imtaiyaz Hassan, Md

2018-05-01

Mammalian cell entry protein (Mce4A) is a member of MCE-family, and is being considered as a potential drug target of Mycobacterium tuberculosis infection because it is required for invasion and latent survival of pathogen by utilizing host's cholesterol. In the present study, we performed molecular docking followed by 100 ns MD simulation studies to understand the mechanism of interaction of Mce4A to the cholesterol derivatives and probucol. The selected ligands, cholesterol, 25-hydroxycholesterol, 5-cholesten-3β-ol-7-one and probucol bind to the predicted active site cavity of Mce4A, and complexes remain stable during entire simulation of 100 ns. In silico studies were further validated by fluorescence-binding studies to calculate actual binding affinity and number of binding site(s). The non-toxicity of all ligands was confirmed on human monocytic cell (THP1) by MTT assay. This work provides a deeper insight into the mechanism of interaction of Mce4A to cholesterol derivatives, which may be further exploited to design potential and specific inhibitors to ameliorate the Mycobacterium pathogenesis. Copyright © 2018 Elsevier B.V. All rights reserved.

Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae

PubMed Central

Lens, Frederic; Vos, Rutger A.; Charrier, Guillaume; van der Niet, Timo; Merckx, Vincent; Baas, Pieter; Aguirre Gutierrez, Jesus; Jacobs, Bart; Chacon Dória, Larissa; Smets, Erik; Delzon, Sylvain; Janssens, Steven B.

2016-01-01

Background and Aims Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related genera of Adoxaceae, Viburnum and Sambucus, and link the anatomical divergence with climatic and physiological insights. Methods After performing wood anatomical observations, we used a molecular phylogenetic framework to estimate divergence times for 127 Adoxaceae species. The conditions under which the genera diversified were estimated using ancestral area reconstruction and optimization of ancestral climates, and xylem-specific conductivity measurements were performed. Key Results Viburnum, characterized by scalariform vessel perforations (ancestral), diversified earlier than Sambucus, having simple perforations (derived). Ancestral climate reconstruction analyses point to cold temperate preference for Viburnum and warm temperate for Sambucus. This is reflected in the xylem-specific conductivity rates of the co-occurring species investigated, showing that Viburnum lantana has rates much lower than Sambucus nigra. Conclusions The lack of selective pressure for high conductive efficiency during early diversification of Viburnum and the potentially adaptive value of scalariform perforations in frost-prone cold temperate climates have led to retention of the ancestral vessel perforation type, while higher temperatures during early diversification of Sambucus have triggered the evolution of simple vessel perforations, allowing more efficient long-distance water transport. PMID:27498812

New Insights into the Organization, Recombination, Expression and Functional Mechanism of Low Molecular Weight Glutenin Subunit Genes in Bread Wheat

PubMed Central

Fan, Huajie; Sun, Jiazhu; Zhang, Zhongjuan; Qin, Huanju; Li, Bin; Hao, Shanting; Li, Zhensheng; Wang, Daowen; Zhang, Aimin; Ling, Hong-Qing

2010-01-01

The bread-making quality of wheat is strongly influenced by multiple low molecular weight glutenin subunit (LMW-GS) proteins expressed in the seeds. However, the organization, recombination and expression of LMW-GS genes and their functional mechanism in bread-making are not well understood. Here we report a systematic molecular analysis of LMW-GS genes located at the orthologous Glu-3 loci (Glu-A3, B3 and D3) of bread wheat using complementary approaches (genome wide characterization of gene members, expression profiling, proteomic analysis). Fourteen unique LMW-GS genes were identified for Xiaoyan 54 (with superior bread-making quality). Molecular mapping and recombination analyses revealed that the three Glu-3 loci of Xiaoyan 54 harbored dissimilar numbers of LMW-GS genes and covered different genetic distances. The number of expressed LMW-GS in the seeds was higher in Xiaoyan 54 than in Jing 411 (with relatively poor bread-making quality). This correlated with the finding of higher numbers of active LMW-GS genes at the A3 and D3 loci in Xiaoyan 54. Association analysis using recombinant inbred lines suggested that positive interactions, conferred by genetic combinations of the Glu-3 locus alleles with more numerous active LMW-GS genes, were generally important for the recombinant progenies to attain high Zeleny sedimentation value (ZSV), an important indicator of bread-making quality. A higher number of active LMW-GS genes tended to lead to a more elevated ZSV, although this tendency was influenced by genetic background. This work provides substantial new insights into the genomic organization and expression of LMW-GS genes, and molecular genetic evidence suggesting that these genes contribute quantitatively to bread-making quality in hexaploid wheat. Our analysis also indicates that selection for high numbers of active LMW-GS genes can be used for improvement of bread-making quality in wheat breeding. PMID:20975830

Multi objective climate change impact assessment using multi downscaled climate scenarios

NASA Astrophysics Data System (ADS)

Rana, Arun; Moradkhani, Hamid

2016-04-01

Global Climate Models (GCMs) are often used to downscale the climatic parameters on a regional and global scale. In the present study, we have analyzed the changes in precipitation and temperature for future scenario period of 2070-2099 with respect to historical period of 1970-2000 from a set of statistically downscaled GCM projections for Columbia River Basin (CRB). Analysis is performed using 2 different statistically downscaled climate projections namely the Bias Correction and Spatial Downscaling (BCSD) technique generated at Portland State University and the Multivariate Adaptive Constructed Analogs (MACA) technique, generated at University of Idaho, totaling to 40 different scenarios. Analysis is performed on spatial, temporal and frequency based parameters in the future period at a scale of 1/16th of degree for entire CRB region. Results have indicated in varied degree of spatial change pattern for the entire Columbia River Basin, especially western part of the basin. At temporal scales, winter precipitation has higher variability than summer and vice-versa for temperature. Frequency analysis provided insights into possible explanation to changes in precipitation.

Probability for Weather and Climate

NASA Astrophysics Data System (ADS)

Smith, L. A.

2013-12-01

Over the last 60 years, the availability of large-scale electronic computers has stimulated rapid and significant advances both in meteorology and in our understanding of the Earth System as a whole. The speed of these advances was due, in large part, to the sudden ability to explore nonlinear systems of equations. The computer allows the meteorologist to carry a physical argument to its conclusion; the time scales of weather phenomena then allow the refinement of physical theory, numerical approximation or both in light of new observations. Prior to this extension, as Charney noted, the practicing meteorologist could ignore the results of theory with good conscience. Today, neither the practicing meteorologist nor the practicing climatologist can do so, but to what extent, and in what contexts, should they place the insights of theory above quantitative simulation? And in what circumstances can one confidently estimate the probability of events in the world from model-based simulations? Despite solid advances of theory and insight made possible by the computer, the fidelity of our models of climate differs in kind from the fidelity of models of weather. While all prediction is extrapolation in time, weather resembles interpolation in state space, while climate change is fundamentally an extrapolation. The trichotomy of simulation, observation and theory which has proven essential in meteorology will remain incomplete in climate science. Operationally, the roles of probability, indeed the kinds of probability one has access too, are different in operational weather forecasting and climate services. Significant barriers to forming probability forecasts (which can be used rationally as probabilities) are identified. Monte Carlo ensembles can explore sensitivity, diversity, and (sometimes) the likely impact of measurement uncertainty and structural model error. The aims of different ensemble strategies, and fundamental differences in ensemble design to support of

"Molecular Clock" Analogs: A Relative Rates Exercise

ERIC Educational Resources Information Center

Wares, John P.

2008-01-01

Although molecular clock theory is a commonly discussed facet of evolutionary biology, undergraduates are rarely presented with the underlying information of how this theory is examined relative to empirical data. Here a simple contextual exercise is presented that not only provides insight into molecular clocks, but is also a useful exercise for…

A warm or a cold early Earth? New insights from a 3-D climate-carbon model

NASA Astrophysics Data System (ADS)

Charnay, Benjamin; Le Hir, Guillaume; Fluteau, Frédéric; Forget, François; Catling, David C.

2017-09-01

Oxygen isotopes in marine cherts have been used to infer hot oceans during the Archean with temperatures between 60 °C (333 K) and 80 °C (353 K). Such climates are challenging for the early Earth warmed by the faint young Sun. The interpretation of the data has therefore been controversial. 1D climate modeling inferred that such hot climates would require very high levels of CO2 (2-6 bars). Previous carbon cycle modeling concluded that such stable hot climates were impossible and that the carbon cycle should lead to cold climates during the Hadean and the Archean. Here, we revisit the climate and carbon cycle of the early Earth at 3.8 Ga using a 3D climate-carbon model. We find that CO2 partial pressures of around 1 bar could have produced hot climates given a low land fraction and cloud feedback effects. However, such high CO2 partial pressures should not have been stable because of the weathering of terrestrial and oceanic basalts, producing an efficient stabilizing feedback. Moreover, the weathering of impact ejecta during the Late Heavy Bombardment (LHB) would have strongly reduced the CO2 partial pressure leading to cold climates and potentially snowball Earth events after large impacts. Our results therefore favor cold or temperate climates with global mean temperatures between around 8 °C (281 K) and 30 °C (303 K) and with 0.1-0.36 bar of CO2 for the late Hadean and early Archean. Finally, our model suggests that the carbon cycle was efficient for preserving clement conditions on the early Earth without necessarily requiring any other greenhouse gas or warming process.

Novel Insights into the Molecular Interaction of a Panduratin A Derivative with the Non Structural Protein (NS3) of Dengue Serotypes: A Molecular Dynamics Study.

PubMed

Parida, Pratap; Yadav, Raj Narain Singh; Dehury, Budheswar; Ghosh, Debosree; Mahapatra, Namita; Mitra, Analava; Mohanta, Tapan Kumar

2017-01-01

The ligand PKP10 having substitution of Cl- at R2 and R3 positions of ring A of Panduratin A i.e., ((1R,2S,5S)-5-(2,3-dichlorophenyl)-3-methyl-2-(3-methylbut-2-nyl)cyclohex-3- enyl)(2,6-dihydroxy-4-methylphenyl)methanone hydrate) has been observed to block the Nuclear Receptor Binding Protein binding site of Non Structural protein 3 in all dengue serotypes. In continuation with our earlier study, we have reported sixty novel Panduratin A derivatives compounds where substitution was done in positions 2 and 3 position of the benzyl ring A of Panduratin A with various substituents. We selected ((1R,2S,5S)-5-(2,3-dichlorophenyl)-3-methyl-2-(3-methylbut-2-nyl)cyclohex-3- nyl) (2,6-dihydroxy-4-methylphenyl) methanone hydrate) (PKP10) for molecular dynamics (MD) simulations as it constantly produced lowest CDocker interaction energy of among all the sixty five derivatives. The CDocker interaction energy was predicted to be -140.804, -79.807, -78.217 and -84.073 Kcalmol-1 respectively against NS3 protein of dengue serotypes (DENV1-4). To understand the dynamics of the PKP10 with NS3 protein, each complex was subjected to molecular dynamics simulations of 50 ns in aqueous solution. MD (Molecular Dynamics) simulation study revealed that the binding of ligand PKP10 at the active site of NS3 induces a conformational change in all serotypes which was well supported by principal component analysis. To the best of our knowledge, this is first ever study which provided atomistic insights into the interaction of PKP10 with NS3 protein of dengue serotypes. The result from our study along with in vitro studies is expected to open up better avenues to develop inhibitors for dengue virus in the near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The essential interactions between understanding climate variability and climate change

NASA Astrophysics Data System (ADS)

Neelin, J. D.

2017-12-01

Global change is sometimes perceived as a field separate from other aspects of atmospheric and oceanic sciences. Despite the long history of communication between the scientific communities studying global change and those studying interannual variability and weather, increasing specialization and conflicting societal demands on the fields can put these interactions at risk. At the same time, current trajectories for greenhouse gas emissions imply substantial adaptation to climate change will be necessary. Instead of simply projecting effects to be avoided, the field is increasingly being asked to provide regional-level information for specific adaptation strategies—with associated requirements for increased precision on projections. For extreme events, challenges include validating models for rare events, especially for events that are unprecedented in the historical record. These factors will be illustrated with examples of information transfer to climate change from work on fundamental climate processes aimed originally at timescales from hours to interannual. Work to understand the effects that control probability distributions of moisture, temperature and precipitation in historical weather can yield new factors to examine for the changes in the extremes of these distributions under climate change. Surprisingly simple process models can give insights into the behavior of vastly more complex climate models. Observation systems and model ensembles aimed at weather and interannual variations prove valuable for global change and vice versa. Work on teleconnections in the climate system, such as the remote impacts of El Niño, is informing analysis of projected regional rainfall change over California. Young scientists need to prepare to work across the full spectrum of climate variability and change, and to communicate their findings, as they and our society head for future that is more interesting than optimal.

Sharing the cost of river basin adaptation portfolios to climate change: Insights from social justice and cooperative game theory

NASA Astrophysics Data System (ADS)

Girard, Corentin; Rinaudo, Jean-Daniel; Pulido-Velazquez, Manuel

2016-10-01

The adaptation of water resource systems to the potential impacts of climate change requires mixed portfolios of supply and demand adaptation measures. The issue is not only to select efficient, robust, and flexible adaptation portfolios but also to find equitable strategies of cost allocation among the stakeholders. Our work addresses such cost allocation problems by applying two different theoretical approaches: social justice and cooperative game theory in a real case study. First of all, a cost-effective portfolio of adaptation measures at the basin scale is selected using a least-cost optimization model. Cost allocation solutions are then defined based on economic rationality concepts from cooperative game theory (the Core). Second, interviews are conducted to characterize stakeholders' perceptions of social justice principles associated with the definition of alternatives cost allocation rules. The comparison of the cost allocation scenarios leads to contrasted insights in order to inform the decision-making process at the river basin scale and potentially reap the efficiency gains from cooperation in the design of river basin adaptation portfolios.

Educating with Resilience in Mind: Addressing Climate Change in Post-Sandy New York City

ERIC Educational Resources Information Center

Dubois, Bryce; E. Krasny, Marianne

2016-01-01

How educators adapt their programs following a climate related disturbance can provide insights into potential climate education practices. Therefore, we used semi-structured interviews to explore changes in environmental education practice in NYC following Hurricane Sandy. Educators adopted new language to reflect funding opportunities and…

Climate change and outdoor recreation participation in the Southern United States

Treesearch

J.M. Bowker; Ashley E. Askew; Neelam Poudyal; Stanley J. Zarnoch; Lynne Seymour; H. Ken Cordell

2014-01-01

In this chapter we begin to assess the potential effects of climate change on future outdoor recreation in the South, a region spanning 13 states from Virginia to Texas (Chapter 1). Our goal is to provide some useful insights about future natural resource-based recreation-an important nontimber product derived from southern forests-in the face of climate change. We...

Climate Change: Modeling the Human Response

NASA Astrophysics Data System (ADS)

Oppenheimer, M.; Hsiang, S. M.; Kopp, R. E.

2012-12-01

Integrated assessment models have historically relied on forward modeling including, where possible, process-based representations to project climate change impacts. Some recent impact studies incorporate the effects of human responses to initial physical impacts, such as adaptation in agricultural systems, migration in response to drought, and climate-related changes in worker productivity. Sometimes the human response ameliorates the initial physical impacts, sometimes it aggravates it, and sometimes it displaces it onto others. In these arenas, understanding of underlying socioeconomic mechanisms is extremely limited. Consequently, for some sectors where sufficient data has accumulated, empirically based statistical models of human responses to past climate variability and change have been used to infer response sensitivities which may apply under certain conditions to future impacts, allowing a broad extension of integrated assessment into the realm of human adaptation. We discuss the insights gained from and limitations of such modeling for benefit-cost analysis of climate change.

Nanopatterning by molecular polygons.

PubMed

Jester, Stefan-S; Sigmund, Eva; Höger, Sigurd

2011-07-27

Molecular polygons with three to six sides and binary mixtures thereof form long-range ordered patterns at the TCB/HOPG interface. This includes also the 2D crystallization of pentagons. The results provide an insight into how the symmetry of molecules is translated into periodic structures.

Molecular insights into the biology of Greater Sage-Grouse

USGS Publications Warehouse

Oyler-McCance, Sara J.; Quinn, Thomas W.

2011-01-01

Recent research on Greater Sage-Grouse (Centrocercus urophasianus) genetics has revealed some important findings. First, multiple paternity in broods is more prevalent than previously thought, and leks do not comprise kin groups. Second, the Greater Sage-Grouse is genetically distinct from the congeneric Gunnison sage-grouse (C. minimus). Third, the Lyon-Mono population in the Mono Basin, spanning the border between Nevada and California, has unique genetic characteristics. Fourth, the previous delineation of western (C. u. phaios) and eastern Greater Sage-Grouse (C. u. urophasianus) is not supported genetically. Fifth, two isolated populations in Washington show indications that genetic diversity has been lost due to population declines and isolation. This chapter examines the use of molecular genetics to understand the biology of Greater Sage-Grouse for the conservation and management of this species and put it into the context of avian ecology based on selected molecular studies.

Diversification of land plants: insights from a family-level phylogenetic analysis

PubMed Central

2011-01-01

Background Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. Results We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. Conclusions This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario. PMID:22103931

Diversification of land plants: insights from a family-level phylogenetic analysis.

PubMed

Fiz-Palacios, Omar; Schneider, Harald; Heinrichs, Jochen; Savolainen, Vincent

2011-11-21

Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.

Rapid climate change and the rate of adaptation: insight from experimental quantitative genetics.

PubMed

Shaw, Ruth G; Etterson, Julie R

2012-09-01

Evolution proceeds unceasingly in all biological populations. It is clear that climate-driven evolution has molded plants in deep time and within extant populations. However, it is less certain whether adaptive evolution can proceed sufficiently rapidly to maintain the fitness and demographic stability of populations subjected to exceptionally rapid contemporary climate change. Here, we consider this question, drawing on current evidence on the rate of plant range shifts and the potential for an adaptive evolutionary response. We emphasize advances in understanding based on theoretical studies that model interacting evolutionary processes, and we provide an overview of quantitative genetic approaches that can parameterize these models to provide more meaningful predictions of the dynamic interplay between genetics, demography and evolution. We outline further research that can clarify both the adaptive potential of plant populations as climate continues to change and the role played by ongoing adaptation in their persistence. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

PubMed Central

Perilla, Juan R; Schlicksup, Christopher John; Venkatakrishnan, Balasubramanian; Zlotnick, Adam; Schulten, Klaus

2018-01-01

The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid’s influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid’s triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids. PMID:29708495

Male sex determination: insights into molecular mechanisms

PubMed Central

McClelland, Kathryn; Bowles, Josephine; Koopman, Peter

2012-01-01

Disorders of sex development often arise from anomalies in the molecular or cellular networks that guide the differentiation of the embryonic gonad into either a testis or an ovary, two functionally distinct organs. The activation of the Y-linked gene Sry (sex-determining region Y) and its downstream target Sox9 (Sry box-containing gene 9) triggers testis differentiation by stimulating the differentiation of Sertoli cells, which then direct testis morphogenesis. Once engaged, a genetic pathway promotes the testis development while actively suppressing genes involved in ovarian development. This review focuses on the events of testis determination and the struggle to maintain male fate in the face of antagonistic pressure from the underlying female programme. PMID:22179516

Recent advances in understanding secondary organic aerosol: Implications for global climate forcing: Advances in Secondary Organic Aerosol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shrivastava, Manish; Cappa, Christopher D.; Fan, Jiwen

aerosol mass and number with knowledge of particle properties such as volatility and viscosity are crucial for improving understanding of non-linear SOA-related processes. For example, useful insights can be attained by combining bottom-up information related to the molecular speciation of gas- and particle-phase precursors with top-down insights on size evolution dynamics of SOA. Continuing efforts are also needed to rank the most influential processes affecting SOA lifecycle, so that these processes can be accurately represented in atmospheric chemistry-climate models.« less

Feeling bogged down about climate change mitigation? Insights from a new high resolution peatland-bog model validated at two Dutch monitoring sites.

NASA Astrophysics Data System (ADS)

Lippmann, Tanya; van Huissteden, Ko; Hendriks, Dimmie

2017-04-01

Increasing the global carbon sink is one of two options to mitigate CO2 and CH4 increases in the atmosphere (the other is emissions reductions at the source). Peatlands release carbon to the atmosphere when disturbed by natural or human causes and absorb carbon when vegetation and soil organic matter accumulate after rewetting or natural revegetation. However, rewetting of drained peatlands is frequently not considered as a climate mitigation strategy due to the enhanced methane emissions that accompany newly formed anaerobic peatland environments. We hypothesise that at most sites, this trend will be temporal but long-term, lasting for tens of years post re-wetting before stabilisation takes place. This study investigates the ability of rewetted peatland sites to act as either a source or sink for atmospheric methane and carbon dioxide under climate change. The hydrology of a peatland is fundamental to its functioning. Therefore, the use of a full water balance table has the potential to simulate greenhouse gas fluxes to a greater degree of certainty. MODFLOW is the internationally most widely used ground and surface water model and is freely available to the scientific community. This is the first time that a gridded peatland process based model has been constructed at a spatial resolution as high as 25m x 25m. This new high-resolution model allows for investigation into the complex biophysical and hydrological factors that are necessary to reliably estimate atmospheric greenhouse gas fluxes in a peatland ecosystem. We assess the model's skill against observations collected at two monitoring sites of differing soil properties and vegetation in the Netherlands. These results discuss site-specific suitability of peatland regeneration, useful for climate change mitigation activities. Aside from the insight into transient atmosphere-peatland carbon fluxes, this work is a stepping stone towards more robust model coupling and greater spatial coverage.

Molecular insights into human daily behavior

PubMed Central

Brown, Steven A.; Kunz, Dieter; Dumas, Amelie; Westermark, Pål O.; Vanselow, Katja; Tilmann-Wahnschaffe, Amely; Herzel, Hanspeter; Kramer, Achim

2008-01-01

Human beings exhibit wide variation in their timing of daily behavior. We and others have suggested previously that such differences might arise because of alterations in the period length of the endogenous human circadian oscillator. Using dermal fibroblast cells from skin biopsies of 28 subjects of early and late chronotype (11 “larks” and 17 “owls”), we have studied the circadian period lengths of these two groups, as well as their ability to phase-shift and entrain to environmental and chemical signals. We find not only period length differences between the two classes, but also significant changes in the amplitude and phase-shifting properties of the circadian oscillator among individuals with identical “normal” period lengths. Mathematical modeling shows that these alterations could also account for the extreme behavioral phenotypes of these subjects. We conclude that human chronotype may be influenced not only by the period length of the circadian oscillator, but also by cellular components that affect its amplitude and phase. In many instances, these changes can be studied at the molecular level in primary dermal cells. PMID:18227513

Molecular Modeling of Water Interfaces: From Molecular Spectroscopy to Thermodynamics.

PubMed

Nagata, Yuki; Ohto, Tatsuhiko; Backus, Ellen H G; Bonn, Mischa

2016-04-28

Understanding aqueous interfaces at the molecular level is not only fundamentally important, but also highly relevant for a variety of disciplines. For instance, electrode-water interfaces are relevant for electrochemistry, as are mineral-water interfaces for geochemistry and air-water interfaces for environmental chemistry; water-lipid interfaces constitute the boundaries of the cell membrane, and are thus relevant for biochemistry. One of the major challenges in these fields is to link macroscopic properties such as interfacial reactivity, solubility, and permeability as well as macroscopic thermodynamic and spectroscopic observables to the structure, structural changes, and dynamics of molecules at these interfaces. Simulations, by themselves, or in conjunction with appropriate experiments, can provide such molecular-level insights into aqueous interfaces. In this contribution, we review the current state-of-the-art of three levels of molecular dynamics (MD) simulation: ab initio, force field, and coarse-grained. We discuss the advantages, the potential, and the limitations of each approach for studying aqueous interfaces, by assessing computations of the sum-frequency generation spectra and surface tension. The comparison of experimental and simulation data provides information on the challenges of future MD simulations, such as improving the force field models and the van der Waals corrections in ab initio MD simulations. Once good agreement between experimental observables and simulation can be established, the simulation can be used to provide insights into the processes at a level of detail that is generally inaccessible to experiments. As an example we discuss the mechanism of the evaporation of water. We finish by presenting an outlook outlining four future challenges for molecular dynamics simulations of aqueous interfacial systems.

The relationship between team climate and interprofessional collaboration: Preliminary results of a mixed methods study.

PubMed

Agreli, Heloise F; Peduzzi, Marina; Bailey, Christopher

2017-03-01

Relational and organisational factors are key elements of interprofessional collaboration (IPC) and team climate. Few studies have explored the relationship between IPC and team climate. This article presents a study that aimed to explore IPC in primary healthcare teams and understand how the assessment of team climate may provide insights into IPC. A mixed methods study design was adopted. In Stage 1 of the study, team climate was assessed using the Team Climate Inventory with 159 professionals in 18 interprofessional teams based in São Paulo, Brazil. In Stage 2, data were collected through in-depth interviews with a sample of team members who participated in the first stage of the study. Results from Stage 1 provided an overview of factors relevant to teamwork, which in turn informed our exploration of the relationship between team climate and IPC. Preliminary findings from Stage 2 indicated that teams with a more positive team climate (in particular, greater participative safety) also reported more effective communication and mutual support. In conclusion, team climate provided insights into IPC, especially regarding aspects of communication and interaction in teams. Further research will provide a better understanding of differences and areas of overlap between team climate and IPC. It will potentially contribute for an innovative theoretical approach to explore interprofessional work in primary care settings.

Prehistoric Packrats Piled Up Clues to Climate Change

USGS Publications Warehouse

Cole, Kenneth L.

2008-01-01

Scientists from the U.S. Geological Survey and Northern Arizona University studying climate change in the Southwestern United States are getting a helping hand?or would that be paw??from prehistoric packrats. By hoarding parts of animals and plants, including seeds and leaves, in garbage piles or ?middens,? these bushy-tailed rodents preserved crucial ecological and environmental information about the past. From these middens, scientists are able to reconstruct plant communities and natural systems from as long ago as 50,000 years. The contents of middens allow scientists to understand how ecosystems responded to rapid, large-scale climate changes of the past. The insights gained from midden research could offer clues to future changes driven by rapid climate shifts.

Agro-ecological class stability decreases in response to climate change projections for the Pacific Northwest, USA

USDA-ARS?s Scientific Manuscript database

Climate change will impact bioclimatic drivers that regulate the geospatial distribution of dryland agro-ecological classes (AECs). Characterizing the geospatial relationship between present AECs and their bioclimatic controls will provide insights into potential future shifts in AECs as climate cha...

Natural genetic variation for morphological and molecular determinants of plant growth and yield.

PubMed

Nunes-Nesi, Adriano; Nascimento, Vitor de Laia; de Oliveira Silva, Franklin Magnum; Zsögön, Agustin; Araújo, Wagner L; Sulpice, Ronan

2016-05-01

The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation.

PubMed

Fu, Yankai; Yan, Tingxuan; Xu, Xia

2017-09-28

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

New Insights into the Phylogeny and Molecular Classification of Nicotinamide Mononucleotide Deamidases

PubMed Central

Sánchez-Carrón, Guiomar; Martínez-Moñino, Ana Belén; Sola-Carvajal, Agustín; Takami, Hideto; García-Carmona, Francisco; Sánchez-Ferrer, Álvaro

2013-01-01

Nicotinamide mononucleotide (NMN) deamidase is one of the key enzymes of the bacterial pyridine nucleotide cycle (PNC). It catalyzes the conversion of NMN to nicotinic acid mononucleotide, which is later converted to NAD+ by entering the Preiss-Handler pathway. However, very few biochemical data are available regarding this enzyme. This paper represents the first complete molecular characterization of a novel NMN deamidase from the halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiPncC). The enzyme was active over a broad pH range, with an optimum at pH 7.4, whilst maintaining 90 % activity at pH 10.0. Surprisingly, the enzyme was quite stable at such basic pH, maintaining 61 % activity after 21 days. As regard temperature, it had an optimum at 65 °C but its stability was better below 50 °C. OiPncC was a Michaelian enzyme towards its only substrate NMN, with a K m value of 0.18 mM and a kcat/K m of 2.1 mM-1 s-1. To further our understanding of these enzymes, a complete phylogenetic and structural analysis was carried out taking into account the two Pfam domains usually associated with them (MocF and CinA). This analysis sheds light on the evolution of NMN deamidases, and enables the classification of NMN deamidases into 12 different subgroups, pointing to a novel domain architecture never before described. Using a Logo representation, conserved blocks were determined, providing new insights on the crucial residues involved in the binding and catalysis of both CinA and MocF domains. The analysis of these conserved blocks within new protein sequences could permit the more efficient data curation of incoming NMN deamidases. PMID:24340054

Crop epigenetics and the molecular hardware of genotype × environment interactions.

PubMed

King, Graham J

2015-01-01

Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal

Crop epigenetics and the molecular hardware of genotype × environment interactions

PubMed Central

King, Graham J.

2015-01-01

Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal

Molecular insights into regulation of JAK2 in myeloproliferative neoplasms

PubMed Central

Hubbard, Stevan R.

2015-01-01

The critical role of Janus kinase-2 (JAK2) in regulation of myelopoiesis was established 2 decades ago, but identification of mutations in the pseudokinase domain of JAK2 in myeloproliferative neoplasms (MPNs) and in other hematologic malignancies highlighted the role of JAK2 in human disease. These findings have revolutionized the diagnostics of MPNs and led to development of novel JAK2 therapeutics. However, the molecular mechanisms by which mutations in the pseudokinase domain lead to hyperactivation of JAK2 and clinical disease have been unclear. Here, we describe recent advances in the molecular characterization of the JAK2 pseudokinase domain and how pathogenic mutations lead to constitutive activation of JAK2. PMID:25824690

For Me It Was When I Saw a Simple Chart: Former Climate Contrarians Recount What Changed Their Minds

NASA Astrophysics Data System (ADS)

Kirk, K. B.

2017-12-01

Efforts to advance climate policy in the US have been hindered by a sector of the public that is reluctant to accept the science of anthropogenic climate change. Climate educators, advocates, and policymakers seek to resolve this roadblock through educational efforts and strategic messaging, while social science research strives to understand the causes of resistance on climate change. A discussion on the social media platform, AskReddit, offered a surprising source of insight when a tantalizing question was posed, "Former climate deniers, what changed your mind?" Responses to the query offered a rare glimpse into the process of how people switched camps, outgrew their parents' values, had transformative experiences, or were worn down by mounting scientific evidence. The posts contained 66 examples of people who were initially uncertain or dismissive of climate change, but came to accept the mainstream science. The commenters provided insightful narratives describing the origins of their skeptical beliefs, the rationales for their changing opinions, and the events that caused them to reverse course. Analysis of the comments revealed the primary reasons that influenced people to change their minds. Those were: science and evidence (cited as a factor in 47% of the comments); stewardship for the Earth and concerns about pollution (29%); unusual weather events (21%); and the untrustworthiness of the messengers who claim that climate change is false (17%). Note that several commenters pointed to more than one factor that contributed to their evolving views. While neither the setting nor the sample size allow a robust scientific analysis, these anecdotal accounts offer useful insights on a vexing problem. Learning about the circumstances that lead people to update their thinking can help us improve efforts to communicate the science and policy around climate change. This work is the topic of an article at Yale Climate Connections, https

Migration in the context of vulnerability and adaptation to climate change: insights from analogues

PubMed Central

McLeman, Robert A.; Hunter, Lori M.

2011-01-01

Migration is one of the variety of ways by which human populations adapt to environmental changes. The study of migration in the context of anthropogenic climate change is often approached using the concept of vulnerability and its key functional elements: exposure, system sensitivity, and adaptive capacity. This article explores the interaction of climate change and vulnerability through review of case studies of dry-season migration in the West African Sahel, hurricane-related population displacements in the Caribbean basin, winter migration of ‘snowbirds’ to the US Sun-belt, and 1930s drought migration on the North American Great Plains. These examples are then used as analogues for identifying general causal, temporal, and spatial dimensions of climate migration, along with potential considerations for policy-making and future research needs. PMID:22022342

Managing the risks of extreme events and disasters to advance climate change adaptation. Special report of the Intergovernmental Panel on Climate Change (IPCC)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Field, C.B.; Barros, V.; Stocker, T.F.

2012-07-01

This Special Report on Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation (SREX) has been jointly coordinated by Working Groups I (WGI) and II (WGII) of the Intergovernmental Panel on Climate Change (IPCC). The report focuses on the relationship between climate change and extreme weather and climate events, the impacts of such events, and the strategies to manage the associated risks. This Special Report, in particular, contributes to frame the challenge of dealing with extreme weather and climate events as an issue in decision making under uncertainty, analyzing response in the context of risk management.more » The report consists of nine chapters, covering risk management; observed and projected changes in extreme weather and climate events; exposure and vulnerability to as well as losses resulting from such events; adaptation options from the local to the international scale; the role of sustainable development in modulating risks; and insights from specific case studies. (LN)« less

New Insights into the 8.2 ka Cold Event and Subsequent Climate Recovery in Central Europe Provided by a Precisely Dated Ostracod δ18O Record from Mondsee (Austria)

NASA Astrophysics Data System (ADS)

Lauterbach, S.; Andersen, N.; Brauer, A.; Erlenkeuser, H.; Danielopol, D. L.; Namiotko, T.; Huels, M.; Belmecheri, S.; Nantke, C.; Meyer, H.; Chapligin, B.; von Grafenstein, U.

2015-12-01

As evidenced by numerous palaeoclimate records worldwide, the Holocene warm period has been interrupted by several short, low-amplitude cold episodes. Among these, the so-called 8.2 ka cold event is the most prominent Holocene climate perturbation but despite extensive studies, knowledge about its synchrony in different areas and particularly about the dynamics of subsequent climate recovery is still limited. As this is of crucial importance for understanding the complex mechanisms that trigger rapid climate fluctuations and for testing the performance of climate models, new data on the 8.2 ka cold event are needed. Here we present a new sub-decadally resolved, precisely dated oxygen isotope (δ18O) record for the interval 7.7-8.7 ka BP obtained from benthic ostracods preserved in the varved lake sediments of Mondsee (Austria), providing new insights into climate development around the 8.2 ka cold event in Central Europe. The new high-resolution δ18O data set reveals the occurrence of a pronounced cold spell around 8.2 ka BP, whose amplitude (~1.0 ‰, equivalent to a 1.5-2.0 °C cooling), total duration (151 a) and absolute dating (8231-8080 a BP, i.e. calendar years before AD 1950) perfectly agree with results from other Northern Hemisphere palaeoclimate archives, e.g. the precisely dated Greenland ice cores. In addition, the Mondsee δ18O record also indicates a 75-year-long air temperature overshoot of ~0.7 °C directly after the 8.2 ka event (between 8080 and 8005 a BP), which is so far only poorly documented in the mid-latitudes. However, this observation is consistent with results from coupled climate models and high-latitude proxy records, thus likely reflecting a hemispheric-scale climate signal driven by enhanced resumption of the Atlantic meridional overturning circulation (AMOC), which apparently also caused synchronous migrations of atmospheric and oceanic front systems in the North Atlantic realm.

Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant.

PubMed

Alexander, Jake M

2013-09-22

A topic of great current interest is the capacity of populations to adapt genetically to rapidly changing climates, for example by evolving the timing of life-history events, but this is challenging to address experimentally. I use a plant invasion as a model system to tackle this question by combining molecular markers, a common garden experiment and climatic niche modelling. This approach reveals that non-native Lactuca serriola originates primarily from Europe, a climatic subset of its native range, with low rates of admixture from Asia. It has rapidly refilled its climatic niche in the new range, associated with the evolution of flowering phenology to produce clines along climate gradients that mirror those across the native range. Consequently, some non-native plants have evolved development times and grow under climates more extreme than those found in Europe, but not among populations from the native range as a whole. This suggests that many plant populations can adapt rapidly to changed climatic conditions that are already within the climatic niche space occupied by the species elsewhere in its range, but that evolution to conditions outside of this range is more difficult. These findings can also help to explain the prevalence of niche conservatism among non-native species.

Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

PubMed

Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

2018-04-13

To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

Expansion Under Climate Change: The Genetic Consequences.

PubMed

Garnier, Jimmy; Lewis, Mark A

2016-11-01

Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-diffusion model coupled to a heterogeneous environment that develops in time due to climate change. We decompose the resulting travelling wave solution into neutral genetic components to analyse the spatio-temporal dynamics of its genetic structure. Our analysis shows that range expansions and range shifts under slow climate change preserve genetic diversity. This is because slow climate change creates range boundaries that promote spatial mixing of genetic components. Mathematically, the mixing leads to so-called pushed travelling wave solutions. This mixing phenomenon is not seen in spatially homogeneous environments, where range expansion reduces genetic diversity through gene surfing arising from pulled travelling wave solutions. However, the preservation of diversity is diminished when climate change occurs too quickly. Using diversity indices, we show that fast expansions and range shifts erode genetic diversity more than slow range expansions and range shifts. Our study provides analytical insight into the dynamics of travelling wave solutions in heterogeneous environments.

The Climate of Inclusive Classrooms: The Pupil Perspective

ERIC Educational Resources Information Center

Tetler, Susan; Baltzer, Kirsten

2011-01-01

This paper offers insights into learning experiences in inclusive classrooms, gained by giving voices to pupils about their perceptions of themselves and their opinions on classroom climate. A positive response pattern is identified concerning academic and social dimensions of schools, while the overall picture concerning the dimension of…

Predicting phenology by integrating ecology, evolution and climate science

USGS Publications Warehouse

Pau, Stephanie; Wolkovich, Elizabeth M.; Cook, Benjamin I.; Davies, T. Jonathan; Kraft, Nathan J.B.; Bolmgren, Kjell; Betancourt, Julio L.; Cleland, Elsa E.

2011-01-01

Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology — the timing of life-history events. Phenology has well-demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species' reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.

A method for screening climate change-sensitive infectious diseases.

PubMed

Wang, Yunjing; Rao, Yuhan; Wu, Xiaoxu; Zhao, Hainan; Chen, Jin

2015-01-14

Climate change is a significant and emerging threat to human health, especially where infectious diseases are involved. Because of the complex interactions between climate variables and infectious disease components (i.e., pathogen, host and transmission environment), systematically and quantitatively screening for infectious diseases that are sensitive to climate change is still a challenge. To address this challenge, we propose a new statistical indicator, Relative Sensitivity, to identify the difference between the sensitivity of the infectious disease to climate variables for two different climate statuses (i.e., historical climate and present climate) in non-exposure and exposure groups. The case study in Anhui Province, China has demonstrated the effectiveness of this Relative Sensitivity indicator. The application results indicate significant sensitivity of many epidemic infectious diseases to climate change in the form of changing climatic variables, such as temperature, precipitation and absolute humidity. As novel evidence, this research shows that absolute humidity has a critical influence on many observed infectious diseases in Anhui Province, including dysentery, hand, foot and mouth disease, hepatitis A, hemorrhagic fever, typhoid fever, malaria, meningitis, influenza and schistosomiasis. Moreover, some infectious diseases are more sensitive to climate change in rural areas than in urban areas. This insight provides guidance for future health inputs that consider spatial variability in response to climate change.

Molecular Population Genetics

PubMed Central

Casillas, Sònia; Barbadilla, Antonio

2017-01-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. PMID:28270526

An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

ERIC Educational Resources Information Center

Uyulgan, Melis Arzu; Akkuzu, Nalan

2016-01-01

The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

Contemplating the Future: Building Student Resilience in Climate Change Education

NASA Astrophysics Data System (ADS)

Allison, E.

2015-12-01

Climate change research has largely focused on the biophysical, economic, and political aspects of the phenomenon, its projected impacts, and the possibilities for adaptation (Carey et al. 2014; Castree et al. 2014). In the classroom, too, climate change is generally presented as a scientific, technological, political, and economic challenge. However, defining climate change as physical challenge, divorced from its cultural causes and responses, forecloses some pathways of inquiry and limits the possibilities for adaptation (Adger et al. 2013). Recent perspectives by the environmental historian Mark Carey and colleagues (2014) and by the geographer Noel Castree and colleagues (2014) contend that ethnographic, narrative, social scientific, and humanistic insights are necessary additions to the climate change policy process and can contribute to deliberate, resilient responses to climate change. Among the humanistic insights needed are strategies and practices to maintain fortitude and persistence in the midst of dispiriting ecological trends. Students facing the "gloom and doom" of climate change data in environmental studies courses can experience negative states of mind such as denial, despair, burnout, and grief. Emerging research, however, demonstrates how contemplative practice can shift consciousness and promote resilience. Contemplative practices are those that consciously direct calm, focused attention. Such practices can build internal resilience, by promoting a greater sense of calm and well-being, decreasing stress, and sharpening focus and concentration. In addition, contemplative practices improve relationships with other people, through increasing compassion and flexibility in thinking. They also strengthen relationships with the surrounding world by increasing our ability to question, explore, and cope with rapid change and complexity. This presentation provides a context for incorporating contemplative practices, including mindfulness exercises

Modeling the effects of weather and climate change on malaria transmission.

PubMed

Parham, Paul Edward; Michael, Edwin

2010-05-01

In recent years, the impact of climate change on human health has attracted considerable attention; the effects on malaria have been of particular interest because of its disease burden and its transmission sensitivity to environmental conditions. We investigated and illustrated the role that dynamic process-based mathematical models can play in providing strategic insights into the effects of climate change on malaria transmission. We evaluated a relatively simple model that permitted valuable and novel insights into the simultaneous effects of rainfall and temperature on mosquito population dynamics, malaria invasion, persistence and local seasonal extinction, and the impact of seasonality on transmission. We illustrated how large-scale climate simulations and infectious disease systems may be modeled and analyzed and how these methods may be applied to predicting changes in the basic reproduction number of malaria across Tanzania. We found extinction to be more strongly dependent on rainfall than on temperature and identified a temperature window of around 32-33 degrees C where endemic transmission and the rate of spread in disease-free regions is optimized. This window was the same for Plasmodium falciparum and P. vivax, but mosquito density played a stronger role in driving the rate of malaria spread than did the Plasmodium species. The results improved our understanding of how temperature shifts affect the global distribution of at-risk regions, as well as how rapidly malaria outbreaks take off within vulnerable populations. Disease emergence, extinction, and transmission all depend strongly on climate. Mathematical models offer powerful tools for understanding geographic shifts in incidence as climate changes. Nonlinear dependences of transmission on climate necessitates consideration of both changing climate trends and variability across time scales of interest.

Signal to noise quantification of regional climate projections

NASA Astrophysics Data System (ADS)

Li, S.; Rupp, D. E.; Mote, P.

2016-12-01

One of the biggest challenges in interpreting climate model outputs for impacts studies and adaptation planning is understanding the sources of disagreement among models (which is often used imperfectly as a stand-in for system uncertainty). Internal variability is a primary source of uncertainty in climate projections, especially for precipitation, for which models disagree about even the sign of changes in large areas like the continental US. Taking advantage of a large initial-condition ensemble of regional climate simulations, this study quantifies the magnitude of changes forced by increasing greenhouse gas concentrations relative to internal variability. Results come from a large initial-condition ensemble of regional climate model simulations generated by weather@home, a citizen science computing platform, where the western United States climate was simulated for the recent past (1985-2014) and future (2030-2059) using a 25-km horizontal resolution regional climate model (HadRM3P) nested in global atmospheric model (HadAM3P). We quantify grid point level signal-to-noise not just in temperature and precipitation responses, but also the energy and moisture flux terms that are related to temperature and precipitation responses, to provide important insights regarding uncertainty in climate change projections at local and regional scales. These results will aid modelers in determining appropriate ensemble sizes for different climate variables and help users of climate model output with interpreting climate model projections.

Effect of Heat Stress on Reproduction in Dairy Cows: Insights into the Cellular and Molecular Responses of the Oocyte.

PubMed

Roth, Zvi

2017-02-08

Among the components of the female reproductive tract, the ovarian pool of follicles and their enclosed oocytes are highly sensitive to hyperthermia. Heat-induced alterations in small antral follicles can be expressed later as compromised maturation and developmental capacity of the ovulating oocyte. This review summarizes the most up-to-date information on the effects of heat stress on the oocyte with an emphasis on unclear points and open questions, some of which might involve new research directions, for instance, whether preantral follicles are heat resistant. The review focuses on the follicle-enclosed oocytes, provides new insights into the cellular and molecular responses of the oocyte to elevated temperature, points out the role of the follicle microenvironment, and discusses some mechanisms that might underlie oocyte impairment. Mechanisms include nuclear and cytoplasmic maturation, mitochondrial function, apoptotic pathways, and oxidative stress. Understanding the mechanism by which heat stress compromises fertility might enable development of new strategies to mitigate its effects.

Evolution in Australia's mesic biome under past and future climates: Insights from a phylogenetic study of the Australian Rock Orchids (Dendrobium speciosum complex, Orchidaceae).

PubMed

Simpson, Lalita; Clements, Mark A; Crayn, Darren M; Nargar, Katharina

2018-01-01

The Australian mesic biome spans c. 33° of latitude along Australia's east coast and ranges and is dissected by historical and contemporary biogeographical barriers. To investigate the impact of these barriers on evolutionary diversification and to predict the impact of future climate change on the distribution of species and genetic diversity within this biome, we inferred phylogenetic relationships within the Dendrobium speciosum complex (Orchidaceae) across its distribution and undertook environmental niche modelling (ENM) under past, contemporary and projected future climates. Neighbor Joining tree inference, NeighborNet and Structure analyses of Amplified Fragment Length Polymorphism (AFLP) profiles for D. speciosum sampled from across its distribution showed that the complex consists of two highly supported main groups that are geographically separated by the St. Lawrence gap, an area of dry sclerophyll forest and woodland. The presence of several highly admixed individuals identified by the Structure analysis provided evidence of genetic exchange between the two groups across this gap. Whereas previous treatments have recognised between one to eleven species, the molecular results support the taxonomic treatment of the complex as a single species with two subspecies. The ENM analysis supported the hypothesis that lineage divergence within the complex was driven by past climatic changes. The St. Lawrence gap represented a stronger biogeographic barrier for the D. speciosum complex during the cool and dry glacial climatic conditions of the Pleistocene than under today's interglacial conditions. Shallow genetic divergence was found within the two lineages, which mainly corresponded to three other biogeographic barriers: the Black Mountain Corridor, Glass House Mountains and the Hunter Valley. Our ENM analyses provide further support for the hypothesis that biogeographic barriers along Australia's east coast were somewhat permeable to genetic exchange due to

Molecular modeling of human neutral sphingomyelinase provides insight into its molecular interactions.

PubMed

Dinesh; Goswami, Angshumala; Suresh, Panneer Selvam; Thirunavukkarasu, Chinnasamy; Weiergräber, Oliver H; Kumar, Muthuvel Suresh

2011-01-01

The neutral sphingomyelinase (N-SMase) is considered a major candidate for mediating the stress-induced production of ceramide, and it plays an important role in cell-cycle arrest, apoptosis, inflammation, and eukaryotic stress responses. Recent studies have identified a small region at the very N-terminus of the 55 kDa tumour necrosis factor receptor (TNF-R55), designated the neutral sphingomyelinase activating domain (NSD) that is responsible for the TNF-induced activation of N-SMase. There is no direct association between TNF-R55 NSD and N-SMase; instead, a protein named factor associated with N-SMase activation (FAN) has been reported to couple the TNF-R55 NSD to N-SMase. Since the three-dimensional fold of N-SMase is still unknown, we have modeled the structure using the protein fold recognition and threading method. Moreover, we propose models for the TNF-R55 NSD as well as the FAN protein in order to study the structural basis of N-SMase activation and regulation. Protein-protein interaction studies suggest that FAN is crucially involved in mediating TNF-induced activation of the N-SMase pathway, which in turn regulates mitogenic and proinflammatory responses. Inhibition of N-SMase may lead to reduction of ceramide levels and hence may provide a novel therapeutic strategy for inflammation and autoimmune diseases. Molecular dynamics (MD) simulations were performed to check the stability of the predicted model and protein-protein complex; indeed, stable RMS deviations were obtained throughout the simulation. Furthermore, in silico docking of low molecular mass ligands into the active site of N-SMase suggests that His135, Glu48, Asp177, and Asn179 residues play crucial roles in this interaction. Based on our results, these ligands are proposed to be potent and selective N-SMase inhibitors, which may ultimately prove useful as lead compounds for drug development.

Molecular and cellular insights into Zika virus-related neuropathies.

PubMed

Zhou, Kai; Wang, Long; Yu, Di; Huang, Hesuyuan; Ji, Hong; Mo, Xuming

2017-06-01

Zika virus (ZIKV), a relatively elusive Aedes mosquito-transmitted flavivirus, had been brought into spotlight until recent widespread outbreaks accompanied by unexpectedly severe clinical neuropathies, including fetal microcephaly and Guillain-Barré syndrome (GBS) in the adult. In this review, we focus on the underlying cellular and molecular mechanisms by which vertically transmitted microorganisms reach the fetus and trigger neuropathies.

Effects of climate legacies on above- and belowground community assembly.

PubMed

Delgado-Baquerizo, Manuel; Eldridge, David J; Travers, Samantha K; Val, James; Oliver, Ian; Bissett, Andrew

2018-05-11

The role of climatic legacies in regulating community assembly of above- and belowground species in terrestrial ecosystems remains largely unexplored and poorly understood. Here, we report on two separate regional and continental empirical studies, including >500 locations, aiming to identify the relative importance of climatic legacies (climatic anomaly over the last 20,000 years) compared to current climates in predicting the relative abundance of ecological clusters formed by species strongly co-occurring within two independent above- and belowground networks. Climatic legacies explained a significant portion of the variation in the current community assembly of terrestrial ecosystems (up to 15.4%) that could not be accounted for by current climate, soil properties, and management. Changes in the relative abundance of ecological clusters linked to climatic legacies (e.g., past temperature) showed the potential to indirectly alter other clusters, suggesting cascading effects. Our work illustrates the role of climatic legacies in regulating ecosystem community assembly and provides further insights into possible winner and loser community assemblies under global change scenarios. © 2018 John Wiley & Sons Ltd.

Molecular Insights into the Local Anesthetic Receptor within Voltage-Gated Sodium Channels Using Hydroxylated Analogs of Mexiletine

PubMed Central

Desaphy, Jean-François; Dipalma, Antonella; Costanza, Teresa; Carbonara, Roberta; Dinardo, Maria Maddalena; Catalano, Alessia; Carocci, Alessia; Lentini, Giovanni; Franchini, Carlo; Camerino, Diana Conte

2011-01-01

, these results confirm our former hypothesis by showing that the presence of hydroxyl groups to the aryloxy moiety of mexiletine greatly reduced sodium channel block, and provide molecular insights into the intimate interaction of local anesthetics with their receptor. PMID:22403541

Application of computer-assisted molecular modeling for immunoassay of low molecular weight food contaminants: A review.

PubMed

Xu, Zhen-Lin; Shen, Yu-Dong; Beier, Ross C; Yang, Jin-Yi; Lei, Hong-Tao; Wang, Hong; Sun, Yuan-Ming

2009-08-11

Immunoassay for low molecular weight food contaminants, such as pesticides, veterinary drugs, and mycotoxins is now a well-established technique which meets the demand for a rapid, reliable, and cost-effective analytical method. However, due to limited understanding of the molecular structure of antibody binding sites and antigenic epitopes, as well as the intermolecular binding forces that come into play, the traditional 'trial and error' method used to develop antibodies still remains the method of choice. Therefore, development of enhanced immunochemical techniques for specific- and generic-assays, requires new approaches for antibody design that will improve affinity and specificity of the antibody in a more rapid and economic manner. Computer-assisted molecular modeling (CAMM) has been demonstrated to be a useful tool to help the immunochemist develop immunoassays. CAMM methods can be used to help direct improvements to important antibody features, and can provide insights into the effects of molecular structure on biological activity that are difficult or impossible to obtain in any other way. In this review, we briefly summarize applications of CAMM in immunoassay development, including assisting in hapten design, explaining cross-reactivity, modeling antibody-antigen interactions, and providing insights into the effects of the mouse body temperature on the three-dimensional conformation of a hapten during antibody production. The fundamentals and theory, programs and software, limitations, and prospects of CAMM in immunoassay development were also discussed.

Insight into the fundamental interactions between LEDGF binding site inhibitors and integrase combining docking and molecular dynamics simulations.

PubMed

De Luca, Laura; Morreale, Francesca; Chimirri, Alba

2012-12-21

In recent years, HIV-1 integrase (IN) has emerged as an attractive target for novel anti-AIDS agents. In particular, nonactive-site-binding IN inhibitors would display synergy with current strand-transfer-specific IN inhibitors and other antiretroviral drugs in clinical use. An effective allosteric inhibitory approach would be the disruption of protein-protein interaction (PPI) between IN and cellular cofactors, such as LEDGF/p75. To date, several small molecules have been reported to be inhibitors of the PPI between IN and LEDGF/p75. In this study, we investigated the most relevant interactions between five selected PPI inhibitors and IN comparing them to the naturally occurring IN-LEDGF/p75 complex. We calculated the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA). Total energy was decomposed on per residue contribution, and hydrogen bond occupancies were monitored throughout the simulations. Considering all these results we obtained a good correlation with experimental activity and useful insights for the development of new inhibitors.

Reduction of α,β-Unsaturated Ketones by Old Yellow Enzymes: Mechanistic Insights from Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Lonsdale, Richard; Reetz, Manfred T

2015-11-25

Enoate reductases catalyze the reduction of activated C═C bonds with high enantioselectivity. The oxidative half-reaction, which involves the addition of a hydride and a proton to opposite faces of the C═C bond, has been studied for the first time by hybrid quantum mechanics/molecular mechanics (QM/MM). The reduction of 2-cyclohexen-1-one by YqjM from Bacillus subtilis was selected as the model system. Two-dimensional QM/MM (B3LYP-D/OPLS2005) reaction pathways suggest that the hydride and proton are added as distinct steps, with the former step preceding the latter. Furthermore, we present interesting insights into the reactivity of this enzyme, including the weak binding of the substrate in the active site, the role of the two active site histidine residues for polarization of the substrate C═O bond, structural details of the transition states to hydride and proton transfer, and the role of Tyr196 as proton donor. The information presented here will be useful for the future design of enantioselective YqjM mutants for other substrates.

High-resolution climate monitoring on a mountain island: the Saguaro National Park pilot study

Treesearch

Michael A. Crimmins

2005-01-01

A pilot project to identify climate monitoring needs within Saguaro National Park began in fall 2003. Nine weather stations were deployed across the complex topography of the park to provide insight into the spatial and temporal patterns of climate within the park management unit. This project will provide a valuable baseline for park management and may highlight...

Nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass: Insights from molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kilymis, D. A.; Ispas, S., E-mail: simona.ispas-crouzet@umontpellier.fr; Delaye, J.-M.

2016-07-28

We have carried out classical molecular dynamics simulations in order to get insight into the atomistic mechanisms of the deformation during nanoindentation of the pristine and irradiated forms of a sodium borosilicate glass. In terms of the glass hardness, we have found that the primary factor affecting the decrease of hardness after irradiation is depolymerization rather than free volume, and we argue that this is a general trend applicable to other borosilicate glasses with similar compositions. We have analyzed the changes of the short- and medium-range structures under deformation and found that the creation of oxygen triclusters is an importantmore » mechanism in order to describe the deformation of highly polymerized borosilicate glasses and is essential in the understanding of the folding of large rings under stress. We have equally found that the less polymerized glasses present a higher amount of relative densification, while the analysis of bond-breaking during the nanoindentation has showed that shear flow is more likely to appear around sodium atoms. The results provided in this study can be proven to be useful in the interpretation of experimental results.« less

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CRISPR-Cas adaptation: insights into the mechanism of action.

PubMed

Amitai, Gil; Sorek, Rotem

2016-02-01

Since the first demonstration that CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against phages and plasmids, numerous studies have yielded key insights into the molecular mechanisms governing how these systems attack and degrade foreign DNA. However, the molecular mechanisms underlying the adaptation stage, in which new immunological memory is formed, have until recently represented a major unresolved question. In this Progress article, we discuss recent discoveries that have shown both how foreign DNA is identified by the CRISPR-Cas adaptation machinery and the molecular basis for its integration into the chromosome to form an immunological memory. Furthermore, we describe the roles of each of the specific CRISPR-Cas components that are involved in memory formation, and consider current models for their evolutionary origin.

Evolution of the Climate Continuum from the Mid-Miocene Climatic Optimum to the Present

NASA Astrophysics Data System (ADS)

Aswasereelert, W.; Meyers, S. R.; Hinnov, L. A.; Kelly, D.

2011-12-01

The recognition of orbital rhythms in paleoclimate data has led to a rich understanding of climate evolution during the Neogene and Quaternary. In contrast, changes in stochastic variability associated with the transition from unipolar to bipolar glaciation have received less attention, although the stochastic component likely preserves key insights about climate. In this study, we seek to evaluate the dominance and character of stochastic climate energy since the Middle Miocene Climatic Optimum (~17 Ma). These analyses extend a previous study that suggested diagnostic stochastic responses associated with Northern Hemisphere ice sheet development during the Plio-Pleistocene (Meyers and Hinnov, 2010). A critical and challenging step necessary to conduct the work is the conversion of depth data to time data. We investigate climate proxy datasets using multiple time scale hypotheses, including depth-derived time scales, sedimentologic/geochemical "tuning", minimal orbital tuning, and comprehensive orbital tuning. To extract the stochastic component of climate, and also explore potential relationships between the orbital parameters and paleoclimate response, a number of approaches rooted in Thomson's (1982) multi-taper spectral method (MTM) are applied. Importantly, the MTM technique is capable of separating the spectral "continuum" - a measure of stochastic variability - from the deterministic periodic orbital signals (spectral "lines") preserved in proxy data. Time series analysis of the proxy records using different chronologic approaches allows us to evaluate the sensitivity of our conclusion about stochastic and deterministic orbital processes during the Middle Miocene to present. Moreover, comparison of individual records permits examination of the spatial dependence of the identified climate responses. Meyers, S.R., and Hinnov, L.A. (2010), Northern Hemisphere glaciation and the evolution of Plio-Pleistocene climate noise: Paleoceanography, 25, PA3207, doi:10

Molecular Diagnostics of Fusion and Laboratory Plasmas

NASA Astrophysics Data System (ADS)

Fantz, U.

2005-05-01

The presence of molecules in the cold scrape-off layer of fusion experiments and industrial plasmas requires an understanding of the molecular dynamics in these low temperature plasmas. Suitable diagnostic methods can provide an insight in molecular processes in the plasma volume as well as for plasma surface interactions. A very simple but powerful technique is the molecular emission spectroscopy. Spectra are obtained easily, whereas interpretation might be very complex and relies on the availability of atomic and molecular data. Examples are given for hydrogen plasmas and plasmas with hydrocarbons which both are of importance in industrial applications as well as in fusion experiments.

New insights into the molecular mechanism of intestinal fatty acid absorption

PubMed Central

Wang, Tony Y.; Liu, Min; Portincasa, Piero; Wang, David Q.-H.

2013-01-01

Background Dietary fat is the most important energy source of all the nutrients. Fatty acids, stored as triacylglycerols in the body, are an important reservoir of stored energy and derive primarily from animal fats and vegetable oils. Design Although the molecular mechanisms for the transport of water-insoluble amphipathic fatty acids across cell membranes have been debated for many years, it is now believed that the dominant means for intestinal fatty acid uptake is via membrane-associated fatty acid-binding proteins, i.e., fatty acid transporters on the apical membrane of enterocytes. Results These findings indicate that intestinal fatty acid absorption is a multistep process that is regulated by multiple genes at the enterocyte level, and intestinal fatty acid absorption efficiency could be determined by factors influencing intraluminal fatty acid molecules across the brush border membrane of enterocytes. To facilitate research on intestinal, hepatic and plasma triacylglycerol metabolism, it is imperative to establish standard protocols for precisely and accurately measuring the efficiency of intestinal fatty acid absorption in humans and animal models. In this review, we will discuss the chemical structure and nomenclature of fatty acids and summarize recent progress in investigating the molecular mechanisms underlying the intestinal absorption of fatty acids, with a particular emphasis on the physical-chemistry of intestinal lipids and the molecular physiology of intestinal fatty acid transporters. Conclusions A better understanding of the molecular mechanism of intestinal fatty acid absorption should lead to novel approaches to the treatment and the prevention of fatty acid-related metabolic diseases that are prevalent worldwide. PMID:24102389

Climate change, urbanization, and optimal long-term floodplain protection

NASA Astrophysics Data System (ADS)

Zhu, Tingju; Lund, Jay R.; Jenkins, Marion W.; Marques, Guilherme F.; Ritzema, Randall S.

2007-06-01

This paper examines levee-protected floodplains and economic aspects of adaptation to increasing long-term flood risk due to urbanization and climate change. The lower American River floodplain in the Sacramento, California, metropolitan area is used as an illustration to explore the course of optimal floodplain protection decisions over long periods. A dynamic programming model is developed and suggests economically desirable adaptations for floodplain levee systems given simultaneous changes in flood climate and urban land values. Economic engineering optimization analyses of several climate change and urbanization scenarios are made. Sensitivity analyses consider assumptions about future values of floodplain land and damageable property along with the discount rate. Methodological insights and policy lessons are drawn from modeling results, reflecting the joint effects and relationships that climate, economic costs, and regional economic growth can have on floodplain levee planning decisions.

Cardiac Channel Molecular Autopsy: Insights From 173 Consecutive Cases of Autopsy-Negative Sudden Unexplained Death Referred for Postmortem Genetic Testing

PubMed Central

Tester, David J.; Medeiros-Domingo, Argelia; Will, Melissa L.; Haglund, Carla M.; Ackerman, Michael J.

2012-01-01

Objective To perform long QT syndrome and catecholaminergic polymorphic ventricular tachycardia cardiac channel postmortem genetic testing (molecular autopsy) for a large cohort of cases of autopsy-negative sudden unexplained death (SUD). Methods From September 1, 1998, through October 31, 2010, 173 cases of SUD (106 males; mean ± SD age, 18.4±12.9 years; age range, 1-69 years; 89% white) were referred by medical examiners or coroners for a cardiac channel molecular autopsy. Using polymerase chain reaction, denaturing high-performance liquid chromatography, and DNA sequencing, a comprehensive mutational analysis of the long QT syndrome susceptibility genes (KCNQ1, KCNH2, SCN5A, KCNE1, and KCNE2) and a targeted analysis of the catecholaminergic polymorphic ventricular tachycardia type 1–associated gene (RYR2) were conducted. Results Overall, 45 putative pathogenic mutations absent in 400 to 700 controls were identified in 45 autopsy-negative SUD cases (26.0%). Females had a higher yield (26/67 [38.8%]) than males (19/106 [17.9%]; P<.005). Among SUD cases with exercise-induced death, the yield trended higher among the 1- to 10-year-olds (8/12 [66.7%]) compared with the 11- to 20-year-olds (4/27 [14.8%]; P=.002). In contrast, for those who died during a period of sleep, the 11- to 20-year-olds had a higher yield (9/25 [36.0%]) than the 1- to 10-year-olds (1/24 [4.2%]; P=.01). Conclusion Cardiac channel molecular autopsy should be considered in the evaluation of autopsy-negative SUD. Several interesting genotype-phenotype observations may provide insight into the expected yields of postmortem genetic testing for SUD and assist in selecting cases with the greatest potential for mutation discovery and directing genetic testing efforts. PMID:22677073

Computational Modelling of Dapsone Interaction With Dihydropteroate Synthase in Mycobacterium leprae; Insights Into Molecular Basis of Dapsone Resistance in Leprosy.

PubMed

Chaitanya V, Sundeep; Das, Madhusmita; Bhat, Pritesh; Ebenezer, Mannam

2015-10-01

The molecular basis for determination of resistance to anti-leprosy drugs is the presence of point mutations within the genes of Mycobacterium leprae (M. leprae) that encode active drug targets. The downstream structural and functional implications of these point mutations on drug targets were scarcely studied. In this study, we utilized computational tools to develop native and mutant protein models for 5 point mutations at codon positions 53 and 55 in 6-hydroxymethyl-7, 8-dihydropteroate synthase (DHPS) of M. leprae, an active target for dapsone encoded by folp1 gene, that confer resistance to dapsone. Molecular docking was performed to identify variations in dapsone interaction with mutant DHPS in terms of hydrogen bonding, hydrophobic interactions, and energy changes. Schrodinger Suite 2014-3 was used to build homology models and in performing molecular docking. An increase in volume of the binding cavities of mutant structures was noted when compared to native form indicating a weakening in interaction (60.7 Å(3) in native vs. 233.6 Å(3) in Thr53Ala, 659.9 Å(3) in Thr53Ile, 400 Å(3) for Thr53Val, 385 Å(3) for Pro55Arg, and 210 Å(3) for Pro55Leu). This was also reflected by changes in hydrogen bonds and decrease in hydrophobic interactions in the mutant models. The total binding energy (ΔG) decreased significantly in mutant forms when compared to the native form (-51.92 Kcal/mol for native vs. -35.64, -35.24, -46.47, -47.69, and -41.36 Kcal/mol for mutations Thr53Ala, Thr53Ile, Thr53Val, Pro55Arg, and Pro55Leu, respectively. In brief, this analysis provided structural and mechanistic insights to the degree of dapsone resistance contributed by each of these DHPS mutants in leprosy. © 2015 Wiley Periodicals, Inc.

A Method for Screening Climate Change-Sensitive Infectious Diseases

PubMed Central

Wang, Yunjing; Rao, Yuhan; Wu, Xiaoxu; Zhao, Hainan; Chen, Jin

2015-01-01

Climate change is a significant and emerging threat to human health, especially where infectious diseases are involved. Because of the complex interactions between climate variables and infectious disease components (i.e., pathogen, host and transmission environment), systematically and quantitatively screening for infectious diseases that are sensitive to climate change is still a challenge. To address this challenge, we propose a new statistical indicator, Relative Sensitivity, to identify the difference between the sensitivity of the infectious disease to climate variables for two different climate statuses (i.e., historical climate and present climate) in non-exposure and exposure groups. The case study in Anhui Province, China has demonstrated the effectiveness of this Relative Sensitivity indicator. The application results indicate significant sensitivity of many epidemic infectious diseases to climate change in the form of changing climatic variables, such as temperature, precipitation and absolute humidity. As novel evidence, this research shows that absolute humidity has a critical influence on many observed infectious diseases in Anhui Province, including dysentery, hand, foot and mouth disease, hepatitis A, hemorrhagic fever, typhoid fever, malaria, meningitis, influenza and schistosomiasis. Moreover, some infectious diseases are more sensitive to climate change in rural areas than in urban areas. This insight provides guidance for future health inputs that consider spatial variability in response to climate change. PMID:25594780

Precambrian Surface Temperatures and Molecular Phylogeny

NASA Astrophysics Data System (ADS)

Schwartzman, David; Lineweaver, Charles H.

2004-06-01

The timing of emergence of major organismal groups is consistent with the climatic temperature being equal to their upper temperature limit of growth (T_{max}), implying a temperature constraint on the evolution of each group, with the climatic temperature inferred from the oxygen isotope record of marine cherts. Support for this constraint comes from the correlation of T_{max} with the rRNA molecular phylogenetic distance from the last common ancestor (LCA) for both thermophilic Archaea and Bacteria. In particular, this correlation for hyperthermophilic Archaea suggests a climatic temperature of about 120°C at the time of the LCA, likely in the Hadean.

Computer-Based Molecular Modelling: Finnish School Teachers' Experiences and Views

ERIC Educational Resources Information Center

Aksela, Maija; Lundell, Jan

2008-01-01

Modern computer-based molecular modelling opens up new possibilities for chemistry teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based molecular modelling in teaching chemistry, into the different working and teaching methods used, and their opinions about necessary…

Recent insights into the molecular mechanisms of the NLRP3 inflammasome activation

PubMed Central

Próchnicki, Tomasz; Mangan, Matthew S.; Latz, Eicke

2016-01-01

Inflammasomes are high-molecular-weight protein complexes that are formed in the cytosolic compartment in response to danger- or pathogen-associated molecular patterns. These complexes enable activation of an inflammatory protease caspase-1, leading to a cell death process called pyroptosis and to proteolytic cleavage and release of pro-inflammatory cytokines interleukin (IL)-1β and IL-18. Along with caspase-1, inflammasome components include an adaptor protein, ASC, and a sensor protein, which triggers the inflammasome assembly in response to a danger signal. The inflammasome sensor proteins are pattern recognition receptors belonging either to the NOD-like receptor (NLR) or to the AIM2-like receptor family. While the molecular agonists that induce inflammasome formation by AIM2 and by several other NLRs have been identified, it is not well understood how the NLR family member NLRP3 is activated. Given that NLRP3 activation is relevant to a range of human pathological conditions, significant attempts are being made to elucidate the molecular mechanism of this process. In this review, we summarize the current knowledge on the molecular events that lead to activation of the NLRP3 inflammasome in response to a range of K + efflux-inducing danger signals. We also comment on the reported involvement of cytosolic Ca 2+ fluxes on NLRP3 activation. We outline the recent advances in research on the physiological and pharmacological mechanisms of regulation of NLRP3 responses, and we point to several open questions regarding the current model of NLRP3 activation. PMID:27508077

Biological invasions, climate change and genomics

PubMed Central

Chown, Steven L; Hodgins, Kathryn A; Griffin, Philippa C; Oakeshott, John G; Byrne, Margaret; Hoffmann, Ary A

2015-01-01

The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species’ geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved. PMID:25667601

Multidisciplinary approaches to climate change questions

USGS Publications Warehouse

Middleton, Beth A.; LePage, Ben A.

2011-01-01

Multidisciplinary approaches are required to address the complex environmental problems of our time. Solutions to climate change problems are good examples of situations requiring complex syntheses of ideas from a vast set of disciplines including science, engineering, social science, and the humanities. Unfortunately, most ecologists have narrow training, and are not equipped to bring their environmental skills to the table with interdisciplinary teams to help solve multidisciplinary problems. To address this problem, new graduate training programs and workshops sponsored by various organizations are providing opportunities for scientists and others to learn to work together in multidisciplinary teams. Two examples of training in multidisciplinary thinking include those organized by the Santa Fe Institute and Dahlem Workshops. In addition, many interdisciplinary programs have had successes in providing insight into climate change problems including the International Panel on Climate Change, the Joint North American Carbon Program, the National Academy of Science Research Grand Challenges Initiatives, and the National Academy of Science. These programs and initiatives have had some notable success in outlining some of the problems and solutions to climate change. Scientists who can offer their specialized expertise to interdisciplinary teams will be more successful in helping to solve the complex problems related to climate change.

Molecular insight into the counteraction of trehalose on urea-induced protein denaturation using molecular dynamics simulation.

PubMed

Zhang, Na; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

2012-06-21

Considerable experimental evidence indicates that trehalose can counteract the denaturing effects of urea on proteins. However, its molecular mechanism remains unknown due to the limitations of current experimental techniques. Herein, molecular dynamics simulations were performed to investigate the counteracting effects of trehalose against urea-induced denaturation of chymotrypsin inhibitor 2. The simulations indicate that the protein unfolds in 8 mol/L urea, but at the same condition the protein retains its native structure in the ternary solution of 8 mol/L urea and 1 mol/L trehalose. It is confirmed that the preferential exclusion of trehalose from the protein surface is the origin of its counteracting effects. It is found that trehalose binds urea via hydrogen bonds, so urea molecules are also expelled from the protein surface along with the preferential exclusion of trehalose. The exclusion of urea from the protein surface leads to the alleviation of the Lennard-Jones interactions between urea and the hydrophobic side chains of the protein in the ternary solution. In contrast, the electrostatic interactions between urea and the protein change little in the presence of trehalose because the decrease in the electrostatic interactions between urea and the protein backbone is canceled by the increase in the electrostatic interactions between urea and the charged side chains of the protein. The results have provided molecular explanations for the counteraction of urea-induced protein denaturation by trehalose.

Molecular Population Genetics.

PubMed

Casillas, Sònia; Barbadilla, Antonio

2017-03-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

Economic development, climate and values: making policy.

PubMed

Stern, Nicholas

2015-08-07

The two defining challenges of this century are overcoming poverty and managing the risks of climate change. Over the past 10 years, we have learned much about how to tackle them together from ideas on economic development and public policy. My own work in these areas over four decades as an academic and as a policy adviser in universities and international financial institutions has focused on how the investment environment and the empowerment of people can change lives and livelihoods. The application of insights from economic development and public policy to climate change requires rigorous analysis of issues such as discounting, modelling the risks of unmanaged climate change, climate policy targets and estimates of the costs of mitigation. The latest research and results show that the case for avoiding the risks of dangerous climate change through the transition to low-carbon economic development and growth is still stronger than when the Stern Review was published. This is partly because of evidence that some of the impacts of climate change are happening more quickly than originally expected, and because of remarkable advances in technologies, such as solar power. Nevertheless, significant hurdles remain in securing the international cooperation required to avoid dangerous climate change, not least because of disagreements and misunderstandings about key issues, such as ethics and equity. © 2015 The Author(s).

Economic development, climate and values: making policy

PubMed Central

Stern, Nicholas

2015-01-01

The two defining challenges of this century are overcoming poverty and managing the risks of climate change. Over the past 10 years, we have learned much about how to tackle them together from ideas on economic development and public policy. My own work in these areas over four decades as an academic and as a policy adviser in universities and international financial institutions has focused on how the investment environment and the empowerment of people can change lives and livelihoods. The application of insights from economic development and public policy to climate change requires rigorous analysis of issues such as discounting, modelling the risks of unmanaged climate change, climate policy targets and estimates of the costs of mitigation. The latest research and results show that the case for avoiding the risks of dangerous climate change through the transition to low-carbon economic development and growth is still stronger than when the Stern Review was published. This is partly because of evidence that some of the impacts of climate change are happening more quickly than originally expected, and because of remarkable advances in technologies, such as solar power. Nevertheless, significant hurdles remain in securing the international cooperation required to avoid dangerous climate change, not least because of disagreements and misunderstandings about key issues, such as ethics and equity. PMID:26203007

Do it well and do it right: The impact of service climate and ethical climate on business performance and the boundary conditions.

PubMed

Jiang, Kaifeng; Hu, Jia; Hong, Ying; Liao, Hui; Liu, Songbo

2016-11-01

Prior research has demonstrated that service climate can enhance unit performance by guiding employees' service behavior to satisfy customers. Extending this literature, we identified ethical climate toward customers as another indispensable organizational climate in service contexts and examined how and when service climate operates in conjunction with ethical climate to enhance business performance of service units. Based on data collected in 2 phases over 6 months from multiple sources of 196 movie theaters, we found that service climate and ethical climate had disparate impacts on business performance, operationalized as an index of customer attendance rate and operating income per labor hour, by enhancing service behavior and reducing unethical behavior, respectively. Furthermore, we found that service behavior and unethical behavior interacted to affect business performance, in such a way that service behavior was more positively related to business performance when unethical behavior was low than when it was high. This interactive effect between service and unethical behaviors was further strengthened by high market turbulence and competitive intensity. These findings provide new insight into theoretical development of service management and offer practical implications about how to maximize business performance of service units by managing organizational climates and employee behaviors synergistically. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

New insights into the molecular mechanism of intestinal fatty acid absorption.

PubMed

Wang, Tony Y; Liu, Min; Portincasa, Piero; Wang, David Q-H

2013-11-01

Dietary fat is one of the most important energy sources of all the nutrients. Fatty acids, stored as triacylglycerols (also called triglycerides) in the body, are an important reservoir of stored energy and derived primarily from animal fats and vegetable oils. Although the molecular mechanisms for the transport of water-insoluble amphipathic fatty acids across cell membranes have been debated for many years, it is now believed that the dominant means for intestinal fatty acid uptake is via membrane-associated fatty acid-binding proteins, that is, fatty acid transporters on the apical membrane of enterocytes. These findings indicate that intestinal fatty acid absorption is a multistep process that is regulated by multiple genes at the enterocyte level, and intestinal fatty acid absorption efficiency could be determined by factors influencing intraluminal fatty acid molecules across the brush border membrane of enterocytes. To facilitate research on intestinal, hepatic and plasma triacylglycerol metabolism, it is imperative to establish standard protocols for precisely and accurately measuring the efficiency of intestinal fatty acid absorption in humans and animal models. In this review, we will discuss the chemical structure and nomenclature of fatty acids and summarize recent progress in investigating the molecular mechanisms underlying the intestinal absorption of fatty acids, with a particular emphasis on the physical chemistry of intestinal lipids and the molecular physiology of intestinal fatty acid transporters. A better understanding of the molecular mechanism of intestinal fatty acid absorption should lead to novel approaches to the treatment and the prevention of fatty acid-related metabolic diseases that are prevalent worldwide. © 2013 Stichting European Society for Clinical Investigation Journal Foundation. Published by John Wiley & Sons Ltd.

Using climate models to estimate the quality of global observational data sets.

PubMed

Massonnet, François; Bellprat, Omar; Guemas, Virginie; Doblas-Reyes, Francisco J

2016-10-28

Observational estimates of the climate system are essential to monitoring and understanding ongoing climate change and to assessing the quality of climate models used to produce near- and long-term climate information. This study poses the dual and unconventional question: Can climate models be used to assess the quality of observational references? We show that this question not only rests on solid theoretical grounds but also offers insightful applications in practice. By comparing four observational products of sea surface temperature with a large multimodel climate forecast ensemble, we find compelling evidence that models systematically score better against the most recent, advanced, but also most independent product. These results call for generalized procedures of model-observation comparison and provide guidance for a more objective observational data set selection. Copyright © 2016, American Association for the Advancement of Science.

Structural insights into simocyclinone as an antibiotic, effector ligand and substrate

PubMed Central

Buttner, Mark J; Schäfer, Martin; Lawson, David M

2017-01-01

Abstract Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins. PMID:29126195

Structural insights into simocyclinone as an antibiotic, effector ligand and substrate.

PubMed

Buttner, Mark J; Schäfer, Martin; Lawson, David M; Maxwell, Anthony

2018-01-01

Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins. © FEMS 2017.

Understanding scale dependency of climatic processes with diarrheal disease

NASA Astrophysics Data System (ADS)

Nasr Azadani, F.; Jutla, A.; Akanda, A. S. S.; Colwell, R. R.

2015-12-01

The issue of scales in linking climatic processes with diarrheal diseases is perhaps one of the most challenging aspect to develop any predictive algorithm for outbreaks and to understand impacts of changing climate. Majority of diarrheal diseases have shown to be strongly associated with climate modulated environmental processes where pathogens survive. Using cholera as an example of characteristic diarrheal diseases, this study will provide methodological insights on dominant scale variability in climatic processes that are linked with trigger and transmission of disease. Cholera based epidemiological models use human to human interaction as a main transmission mechanism, however, environmental conditions for creating seasonality in outbreaks is not explicitly modeled. For example, existing models cannot create seasonality, unless some of the model parameters are a-priori chosen to vary seasonally. A systems based feedback approach will be presented to understand role of climatic processes on trigger and transmission disease. In order to investigate effect of changing climate on cholera, a downscaling approach using support vector machine will be used. Our preliminary results using three climate models, ECHAM5, GFDL, and HADCM show that varying modalities in future cholera outbreaks.

An Analysis of the Climate Data Initiative's Data Collection

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Bugbee, K.

2015-12-01

The Climate Data Initiative (CDI) is a broad multi-agency effort of the U.S. government that seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate-change preparedness. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. To date, the CDI has curated seven themes, or topics, relevant to climate change resiliency. These themes include Coastal Flooding, Food Resilience, Water, Ecosystem Vulnerability, Human Health, Energy Infrastructure, and Transportation. Each theme was curated by subject matter experts who selected datasets relevant to the topic at hand. An analysis of the entire Climate Data Initiative data collection and the data curated for each theme offers insights into which datasets are considered most relevant in addressing climate resiliency. Other aspects of the data collection will be examined including which datasets were the most visited or popular and which datasets were the most sought after for curation by the theme teams. Results from the analysis of the CDI collection will be presented in this talk.

Development and Application of Future Climate Scenarios for Natural Resource Management in Southwestern Colorado

NASA Astrophysics Data System (ADS)

Rangwala, I.; Rondeau, R.; Wyborn, C.; Clifford, K. R.; Travis, W.

2015-12-01

Locally relevant projections of climate change provide critical insights for natural resource managers seeking to adapt their management activities to climate change in the context of uncertainty. To provide such information, we developed climate scenarios, in form of narratives and quantitative information, of future climate change and its impacts in southwestern Colorado. This information was intended to provide detailed insights into the range of changes that natural resource managers may face in the future. The scenarios were developed in an iterative process through interactions among the ecologists, social and climate scientists. In our scenario development process, climate uncertainty is acknowledged by having multiple scenarios, where each scenario is regarded as a storyline with equal likelihood as another scenario. We quantified changes in several decision relevant climate and ecological responses based on our best available understanding and provided a tight storyline for each scenario to facilitate (a) a more augmented use of scientific information in a decision-making process, (b) differential responses from stakeholders across the different scenarios, and (c) identification of strategies that could work across these multiple scenarios. Here, we discuss the process of selecting the scenarios, quantifying climate and ecological responses, and the criteria for building the narrative for each scenario. We also discuss the process by which these scenarios get used, and provide an assessment of their effectiveness and users' feedbacks that could inform the future development of these tools and processes. This research involvement and collaboration occurred, in part, as a result of the PACE Fellowship Program that is associated with NOAA Climate Program Office and the U.S. CLIVAR community.

Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

DOE PAGES

Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; ...

2016-02-04

Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the graftedmore » PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.« less

Nanoarchitectonics of molecular aggregates: science and technology.

PubMed

Ramanathan, Muruganathan; Hong, Kunlun; Ji, Qingmin; Yonamine, Yusuke; Hill, Jonathan P; Ariga, Katsuhiko

2014-01-01

The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review, we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

Nanoarchitectonics of Molecular Aggregates: Science and Technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin

2014-01-01

The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

A Mouse Ependymoma Model Provides Molecular Insights into Tumor Formation.

PubMed

Pajtler, Kristian W; Pfister, Stefan M

2018-06-26

Ozawa et al. present a murine tumor model resembling the most frequent molecular group of human supratentorial ependymoma, ST-EPN-RELA. Their model shows RELA-fusion-based de novo ependymoma tumorigenesis in the forebrain derived from neural stem cells. Copyright © 2018. Published by Elsevier Inc.

Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: insight into the regulation of muscle contraction.

PubMed

Varughese, Jayson F; Chalovich, Joseph M; Li, Yumin

2010-10-01

Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and cardiac (cTn) troponin. The interactions and correlated motions among the three components of the troponin complex were analyzed using both Molecular Mechanics-Generalized Born Surface Area (MMGBSA) and cross-correlation techniques. The TnTH2 helix was strongly positively correlated with the two long helices of TnI. The C domain of TnC was positively correlated with TnI and TnT. The N domain of TnC was negatively correlated with TnI and TnT in cTn, but not in sTn. The two C-domain calcium-binding sites of TnC were dynamically correlated. The two regulatory N-domain calcium-binding sites of TnC were dynamically correlated, even though the calcium-binding site I is dysfunctional. The strong interaction residue pairs and the strong dynamically correlated residues pairs among the three components of troponin complexes were identified. These correlated motions are consistent with the idea that there is a high degree of cooperativity among the components of the regulatory complex in response to Ca(2+) and other effectors. This approach may give insight into the mechanism by which mutations of troponin cause disease. It is interesting that some observed disease causing mutations fall within regions of troponin that are strongly correlated or interacted.

Development and nationwide scale-up of Climate Matters, a localized climate change education program delivered by TV weathercasters.

NASA Astrophysics Data System (ADS)

Cullen, H. M.; Maibach, E.

2016-12-01

its development and national scale-up, and conclude with insights for how to develop climate communication initiatives for other professional communities of practice in the U.S. and other countries.

Insights into molecular structure and digestion rate of oat starch.

PubMed

Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

2017-04-01

The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Insights into the transmembrane helix associations of kit ligand by molecular dynamics simulation and TOXCAT.

PubMed

Chai, Mengya; Liu, Bo; Sun, Fude; Wei, Peng; Chen, Peng; Xu, Lida; Luo, Shi-Zhong

2017-07-01

Kit ligand (KITL) plays important roles in cell proliferation, differentiation, and survival via interaction with its receptor Kit. The previous studies demonstrated that KITL formed a noncovalent homodimer through transmembrane (TM) domain; however, the undergoing mechanism of transmembrane association that determines KITL TM dimerization is still not clear. Herein, molecular dynamics (MD) simulation strategy and TOXCAT assay were combined to characterize the dimerization interface and structure of KITL TM in details. KITL TM formed a more energetically favorable noncovalent dimer through a conserved SxxxGxxxG motif in the MD simulation. Furthermore, the TOXCAT results demonstrated that KITL TM self-associated strongly in the bilayer membrane environment. Mutating any one of the small residues Ser11, Gly15 or Gly19 to Ile disrupted KITL TM dimerization dramatically, which further validated our MD simulation results. In addition, our results showed that Tyr22 could help to stabilize the TM interactions via interacting with the phosphoric group in the bilayer membrane. Pro7 did not induce helix kinks or swivel angles in KITL TM, but it was related with the pitch of the turn around this residue so as to affect the dimer formation. Combining the results of computer modeling and experimental mutagenesis studies on the KITL TM provide new insights for the transmembrane helix association of KITL dimerization. Proteins 2017; 85:1362-1370. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Helicases as molecular motors: An insight

NASA Astrophysics Data System (ADS)

Tuteja, Narendra; Tuteja, Renu

2006-12-01

Helicases are one of the smallest motors of biological system, which harness the chemical free energy of ATP hydrolysis to catalyze the opening of energetically stable duplex nucleic acids and thereby are involved in almost all aspect of nucleic acid metabolism including replication, repair, recombination, transcription, translation, and ribosome biogenesis. Basically, they break the hydrogen bonding between the duplex helix and translocate unidirectionally along the bound strand. Mostly all the helicases contain some conserved signature motifs, which act as an engine to power the unwinding. After the discovery of the first prokaryotic DNA helicase from Escherichia coli bacteria in 1976 and the first eukaryotic one from the lily plant in 1978, many more (>100) have been isolated. All the helicases share some common properties, including nucleic acid binding, NTP hydrolysis and unwinding of the duplex. Many helicases have been crystallized and their structures have revealed an underlying common structural fold for their function. The defects in helicases gene have also been reported to be responsible for variety of human genetic disorders, which can lead to cancer, premature aging or mental retardation. Recently, a new role of a helicase in abiotic stress signaling in plant has been discovered. Overall, helicases act as essential molecular tools for cellular machinery and help in maintaining the integrity of genome. Here an overview of helicases has been covered which includes history, biochemical assay, properties, classification, role in human disease and mechanism of unwinding and translocation.

Climate adaption and post-fire restoration of a foundational perennial in cold desert: Insights from intraspecific variation in response to weather

USGS Publications Warehouse

Brabec, Martha M.; Germino, Matthew; Richardson, Bryce A.

2017-01-01

responses among subspecies/cytotypes were not as strong and did not relate to survival patterns. 5.Synthesis and applications. Low temperature responses are a key axis defining climate adaptation in young sagebrush seedlings and vary more with cytotype than with subspecies, which contrasts with the traditional emphases on (i) water limitations to explain establishment in these deserts, and (ii) subspecies in selecting restoration seedings. These important and novel insights on climate adaptation are critical for seed selection and parameterizing seed transfer zones, and were made possible by incorporating weather data with survival statistics. The survival/weather statistics used here could be applied to any restoration planting or seeding to help elucidate factors contributing to success and enable adaptive management.

Smallholder agriculture in India and adaptation to current and future climate variability and climate change

NASA Astrophysics Data System (ADS)

Murari, K. K.; Jayaraman, T.

2014-12-01

of climate variability on smallholder agriculture in the present can therefore provide important insights into the nature of its vulnerability to future climate change.

Climate and topography explain range sizes of terrestrial vertebrates

NASA Astrophysics Data System (ADS)

Li, Yiming; Li, Xianping; Sandel, Brody; Blank, David; Liu, Zetian; Liu, Xuan; Yan, Shaofei

2016-05-01

Identifying the factors that influence range sizes of species provides important insight into the distribution of biodiversity, and is crucial for predicting shifts in species ranges in response to climate change. Current climate (for example, climate variability and climate extremes), long-term climate change, evolutionary age, topographic heterogeneity, land area and species traits such as physiological thermal limits, dispersal ability, annual fecundity and body size have been shown to influence range size. Yet, few studies have examined the generality of each of these factors among different taxa, or have simultaneously evaluated the strength of relationships between range size and these factors at a global scale. We quantify contributions of these factors to range sizes of terrestrial vertebrates (mammals, birds and reptiles) at a global scale. We found that large-ranged species experience greater monthly extremes of maximum or minimum temperature within their ranges, or occur in areas with higher long-term climate velocity and lower topographic heterogeneity or lower precipitation seasonality. Flight ability, body mass and continent width are important only for particular taxa. Our results highlight the importance of climate and topographic context in driving range size variation. The results suggest that small-range species may be vulnerable to climate change and should be the focus of conservation efforts.

Holocene Glacier Fluctuations in the Peruvian Andes Indicate Northern Climate Linkages

NASA Astrophysics Data System (ADS)

Licciardi, Joseph M.; Schaefer, Joerg M.; Taggart, Jean R.; Lund, David C.

2009-09-01

The role of the tropics in triggering, transmitting, and amplifying interhemispheric climate signals remains a key debate in paleoclimatology. Tropical glacier fluctuations provide important insight on regional paleoclimatic trends and forcings, but robust chronologies are scarce. Here, we report precise moraine ages from the Cordillera Vilcabamba (13°20‧S) of southern Peru that indicate prominent glacial events and associated climatic shifts in the outer tropics during the early Holocene and late in the “Little Ice Age” period. Our glacier chronologies differ from the New Zealand record but are broadly correlative with well-dated glacial records in Europe, suggesting climate linkages between the tropics and the North Atlantic region.

First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

PubMed

Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

2015-02-01

Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.

Vegetation and climate variability in tropical and subtropical South America during the late Quaternary

NASA Astrophysics Data System (ADS)

Behling, H.

2013-05-01

Detailed palynological studies from different ecosystems in tropical and subtropical South America reflect interesting vegetation and climate dynamics, in particular during glacial and late glacial times. Records from ecosystems such as the Amazon rainforest, savanna, Caatinga, Atlantic rainforest, Araucaria forest and grasslands provide interesting insight of past climate variability. The influence of events such as Dansgaard-Oeschger, Heinnrich stadials, changes in the thermohaline circulation (THC) will be discussed. In particular the Younger Dryas (YD) period shows at different places distinct vegetational changes, revealing unexpected past climatic conditions.

Climate Change Impacts and Responses: Societal Indicators for the National Climate Assessment

NASA Technical Reports Server (NTRS)

Kenney, Melissa A.; Chen, Robert S.; Maldonado, Julie; Quattrochi, Dale

2011-01-01

The Climate Change Impacts and Responses: Societal Indicators for the National Climate Assessment workshop, sponsored by the National Aeronautics and Space Administration (NASA) for the National Climate Assessment (NCA), was held on April 28-29, 2011 at The Madison Hotel in Washington, DC. A group of 56 experts (see list in Appendix B) convened to share their experiences. Participants brought to bear a wide range of disciplinary expertise in the social and natural sciences, sector experience, and knowledge about developing and implementing indicators for a range of purposes. Participants included representatives from federal and state government, non-governmental organizations, tribes, universities, and communities. The purpose of the workshop was to assist the NCA in developing a strategic framework for climate-related physical, ecological, and socioeconomic indicators that can be easily communicated with the U.S. population and that will support monitoring, assessment, prediction, evaluation, and decision-making. The NCA indicators are envisioned as a relatively small number of policy-relevant integrated indicators designed to provide a consistent, objective, and transparent overview of major variations in climate impacts, vulnerabilities, adaptation, and mitigation activities across sectors, regions, and timeframes. The workshop participants were asked to provide input on a number of topics, including: (1) categories of societal indicators for the NCA; (2) alternative approaches to constructing indicators and the better approaches for NCA to consider; (3) specific requirements and criteria for implementing the indicators; and (4) sources of data for and creators of such indicators. Socioeconomic indicators could include demographic, cultural, behavioral, economic, public health, and policy components relevant to impacts, vulnerabilities, and adaptation to climate change as well as both proactive and reactive responses to climate change. Participants provided

Communication: Molecular-level insights into asymmetric triblock copolymers: Network and phase development

NASA Astrophysics Data System (ADS)

Tallury, Syamal S.; Mineart, Kenneth P.; Woloszczuk, Sebastian; Williams, David N.; Thompson, Russell B.; Pasquinelli, Melissa A.; Banaszak, Michal; Spontak, Richard J.

2014-09-01

Molecularly asymmetric triblock copolymers progressively grown from a parent diblock copolymer can be used to elucidate the phase and property transformation from diblock to network-forming triblock copolymer. In this study, we use several theoretical formalisms and simulation methods to examine the molecular-level characteristics accompanying this transformation, and show that reported macroscopic-level transitions correspond to the onset of an equilibrium network. Midblock conformational fractions and copolymer morphologies are provided as functions of copolymer composition and temperature.

Molecular diagnostics of neurodegenerative disorders.

PubMed

Agrawal, Megha; Biswas, Abhijit

2015-01-01

Molecular diagnostics provide a powerful method to detect and diagnose various neurological diseases such as Alzheimer's and Parkinson's disease. The confirmation of such diagnosis allows early detection and subsequent medical counseling that help specific patients to undergo clinically important drug trials. This provides a medical pathway to have better insight of neurogenesis and eventual cure of the neurodegenerative diseases. In this short review, we present recent advances in molecular diagnostics especially biomarkers and imaging spectroscopy for neurological diseases. We describe advances made in Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD), and finally present a perspective on the future directions to provide a framework for further developments and refinements of molecular diagnostics to combat neurodegenerative disorders.

Animal Models of Depression: Molecular Perspectives

PubMed Central

Krishnan, Vaishnav; Nestler, Eric J.

2012-01-01

Much of the current understanding about the pathogenesis of altered mood, impaired concentration and neurovegetative symptoms in major depression has come from animal models. However, because of the unique and complex features of human depression, the generation of valid and insightful depression models has been less straightforward than modeling other disabling diseases like cancer or autoimmune conditions. Today’s popular depression models creatively merge ethologically valid behavioral assays with the latest technological advances in molecular biology and automated video-tracking. This chapter reviews depression assays involving acute stress (e.g., forced swim test), models consisting of prolonged physical or social stress (e.g., social defeat), models of secondary depression, genetic models, and experiments designed to elucidate the mechanisms of antidepressant action. These paradigms are critically evaluated in relation to their ease, validity and replicability, the molecular insights that they have provided, and their capacity to offer the next generation of therapeutics for depression. PMID:21225412

Molecular and genetic insights into an infantile epileptic encephalopathy - CDKL5 disorder.

PubMed

Zhou, Ailing; Han, Song; Zhou, Zhaolan Joe

2017-02-01

The discovery that mutations in cyclin-dependent kinase-like 5 ( CDKL5 ) gene are associated with infantile epileptic encephalopathy has stimulated world-wide research effort to understand the molecular and genetic basis of CDKL5 disorder. Given the large number of literature published thus far, this review aims to summarize current genetic studies, draw a consensus on proposed molecular functions, and point to gaps of knowledge in CDKL5 research. A systematic review process was conducted using the PubMed search engine focusing on CDKL5 studies in the recent ten years. We analyzed these publications and summarized the findings into four sections: genetic studies, CDKL5 expression patterns, molecular functions, and animal models. We also discussed challenges and future directions in each section. On the clinical side, CDKL5 disorder is characterized by early onset epileptic seizures, intellectual disability, and stereotypical behaviors. On the research side, a series of molecular and genetic studies in human patients, cell cultures and animal models have established the causality of CDKL5 to the infantile epileptic encephalopathy, and pointed to a key role for CDKL5 in regulating neuronal function in the brain. Mouse models of CDKL5 disorder have also been developed, and notably, manifest behavioral phenotypes, mimicking numerous clinical symptoms of CDKL5 disorder and advancing CDKL5 research to the preclinical stage. Given what we have learned thus far, future identification of robust, quantitative, and sensitive outcome measures would be the key in animal model studies, particularly in heterozygous females. In the meantime, molecular and cellular studies of CDKL5 should focus on mechanism-based investigation and aim to uncover druggable targets that offer the potential to rescue or ameliorate CDKL5 disorder-related phenotypes.

Molecular investigation of active binding site of isoniazid (INH) and insight into resistance mechanism of S315T-MtKatG in Mycobacterium tuberculosis.

PubMed

Srivastava, Gaurava; Tripathi, Shubhandra; Kumar, Akhil; Sharma, Ashok

2017-07-01

Multi drug resistant tuberculosis is a major threat for mankind. Resistance against Isoniazid (INH), targeting MtKatG protein, is one of the most commonly occurring resistances in MDR TB strains. S315T-MtKatG mutation is widely reported for INH resistance. Despite having knowledge about the mechanism of INH, exact binding site of INH to MtKatG is still uncertain and proposed to have three presumable binding sites (site-1, site-2, and site-3). In the current study docking, molecular dynamics simulation, binding free energy estimation, principal component analysis and free energy landscape analysis were performed to get molecular level details of INH binding site on MtKatG, and to probe the effect of S315T mutation on INH binding. Molecular docking and MD analysis suggested site-1 as active binding site of INH, where the effects of S315T mutation were observed on both access tunnel as well as molecular interaction between INH and its neighboring residues. MMPBSA also supported site-1 as potential binding site with lowest binding energy of -44.201 kJ/mol. Moreover, PCA and FEL revealed that S315T mutation not only reduces the dimension of heme access tunnel but also showed that extra methyl group at 315 position altered heme cavity, enforcing heme group distantly from INH, and thus preventing INH activation. The present study not only investigated the active binding site of INH but also provides a new insight about the conformational changes in the binding site of S315T-MtKatG. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of Pectin Molecular Weight Changes on the Structure, Dynamics, and Polysaccharide Interactions of Primary Cell Walls of Arabidopsis thaliana: Insights from Solid-State NMR.

PubMed

Phyo, Pyae; Wang, Tuo; Xiao, Chaowen; Anderson, Charles T; Hong, Mei

2017-09-11

Significant cellulose-pectin interactions in plant cell walls have been reported recently based on 2D 13 C solid-state NMR spectra of intact cell walls, but how these interactions affect cell growth has not been probed. Here, we characterize two Arabidopsis thaliana lines with altered expression of the POLYGALACTURONASE INVOLVED IN EXPANSION1 (PGX1) gene, which encodes a polygalacturonase that cleaves homogalacturonan (HG). PGX1 AT plants overexpress PGX1, have HG with lower molecular weight, and grow larger, whereas pgx1-2 knockout plants have HG with higher molecular weight and grow smaller. Quantitative 13 C solid-state NMR spectra show that PGX1 AT cell walls have lower galacturonic acid and xylose contents and higher HG methyl esterification than controls, whereas high molecular weight pgx1-2 walls have similar galacturonic acid content and methyl esterification as controls. 1 H-transferred 13 C INEPT spectra indicate that the interfibrillar HG backbones are more aggregated whereas the RG-I side chains are more dispersed in PGX1 AT cell walls than in pgx1-2 walls. In contrast, the pectins that are close to cellulose become more mobile and have weaker cross peaks with cellulose in PGX1 AT walls than in pgx1-2 walls. Together, these results show that polygalacturonase-mediated plant growth is accompanied by increased esterification and decreased cross-linking of HG, increased aggregation of interfibrillar HG, and weaker HG-cellulose interactions. These structural and dynamical differences give molecular insights into how pectins influence wall dynamics during cell growth.

Molecular Taxonomy Provides New Insights into Anopheles Species of the Neotropical Arribalzagia Series

PubMed Central

Gómez, Giovan F.; Bickersmith, Sara A.; González, Ranulfo; Conn, Jan E.; Correa, Margarita M.

2015-01-01

Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs). Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors. PMID:25774795

Improving the effectiveness of communication about climate science: Insights from the "Global Warming's Six Americas" audience segmentation research project

NASA Astrophysics Data System (ADS)

Maibach, E.; Roser-Renouf, C.

2011-12-01

That the climate science community has not been entirely effective in sharing what it knows about climate change with the broader public - and with policy makers and organizations that should be considering climate change when making decisions - is obvious. Our research shows that a large majority of the American public trusts scientists (76%) and science-based agencies (e.g., 76% trust NOAA) as sources of information about climate change. Yet, despite the widespread agreement in the climate science community that the climate is changing as a result of human activity, only 64% of the public understand that the world's average temperature has been increasing (and only about half of them are sure), less than half (47%) understand that the warming is caused mostly by human activity, and only 39% understand that most scientists think global warming is happening (in fact, only 13% understand that the large majority of climate scientists think global warming is happening). Less obvious is what the climate science community should do to become more effective in sharing what it knows. In this paper, we will use evidence from our "Global Warming's Six Americas" audience segmentation research project to suggest ways that individual climate scientists -- and perhaps more importantly, ways in which climate science agencies and professional societies -- can enhance the effectiveness of their communication efforts. We will conclude by challenging members of the climate science community to identify and convey "simple, clear messages, repeated often, by a variety of trusted sources" - an approach to communication repeatedly shown to be effective by the public health community.

Climatic Factors Drive Population Divergence and Demography: Insights Based on the Phylogeography of a Riparian Plant Species Endemic to the Hengduan Mountains and Adjacent Regions.

PubMed

Wang, Zhi-Wei; Chen, Shao-Tian; Nie, Ze-Long; Zhang, Jian-Wen; Zhou, Zhuo; Deng, Tao; Sun, Hang

2015-01-01

Quaternary climatic factors have played a significant role in population divergence and demography. Here we investigated the phylogeography of Osteomeles schwerinae, a dominant riparian plant species of the hot/warm-dry river valleys of the Hengduan Mountains (HDM), Qinling Mountains (QLM) and Yunnan-Guizhou Plateau (YGP). Three chloroplast DNA (cpDNA) regions (trnD-trnT, psbD-trnT, petL-psbE), one single copy nuclear gene (glyceraldehyde 3-phosphate dehydrogenase; G3pdh), and climatic data during the Last Interglacial (LIG; c. 120-140 ka), Last Glacial Maximum (LGM; c. 21 ka), and Current (c. 1950-2000) periods were used in this study. Six cpDNA haplotypes and 15 nuclear DNA (nDNA) haplotypes were identified in the 40 populations of O. schwerinae. Spatial Analysis of Molecular Variance, median-joining networks, and Bayesian phylogenetic trees based on the cpDNA and nDNA datasets, all suggested population divergence between the QLM and HDM-YGP regions. Our climatic analysis identified significant heterogeneity of the climatic factors in the QLM and HDM-YGP regions during the aforementioned three periods. The divergence times based on cpDNA and nDNA haplotypes were estimated to be 466.4-159.4 ka and 315.8-160.3 ka, respectively, which coincide with the time of the weakening of the Asian monsoons in these regions. In addition, unimodal pairwise mismatch distribution curves, expansion times, and Ecological Niche Modeling suggested a history of population expansion (rather than contraction) during the last glaciation. Interestingly, the expansion times were found being well consistent with the intensification of the Asian monsoons during this period. We inferred that the divergence between the two main lineages is probably caused by disruption of more continuous distribution because of weakening of monsoons/less precipitation, whilst subsequent intensification of the Asian monsoons during the last glaciation facilitated the expansion of O. schwerinae populations.

Insights into the sequence parameters for halophilic adaptation.

PubMed

Nath, Abhigyan

2016-03-01

The sequence parameters for halophilic adaptation are still not fully understood. To understand the molecular basis of protein hypersaline adaptation, a detailed analysis is carried out, and investigated the likely association of protein sequence attributes to halophilic adaptation. A two-stage strategy is implemented, where in the first stage a supervised machine learning classifier is build, giving an overall accuracy of 86 % on stratified tenfold cross validation and 90 % on blind testing set, which are better than the previously reported results. The second stage consists of statistical analysis of sequence features and possible extraction of halophilic molecular signatures. The results of this study showed that, halophilic proteins are characterized by lower average charge, lower K content, and lower S content. A statistically significant preference/avoidance list of sequence parameters is also reported giving insights into the molecular basis of halophilic adaptation. D, Q, E, H, P, T, V are significantly preferred while N, C, I, K, M, F, S are significantly avoided. Among amino acid physicochemical groups, small, polar, charged, acidic and hydrophilic groups are preferred over other groups. The halophilic proteins also showed a preference for higher average flexibility, higher average polarity and avoidance for higher average positive charge, average bulkiness and average hydrophobicity. Some interesting trends observed in dipeptide counts are also reported. Further a systematic statistical comparison is undertaken for gaining insights into the sequence feature distribution in different residue structural states. The current analysis may facilitate the understanding of the mechanism of halophilic adaptation clearer, which can be further used for rational design of halophilic proteins.

Environmental gradients and grassland trait variation: Insight into the effects of climate change

NASA Astrophysics Data System (ADS)

Tardella, Federico M.; Piermarteri, Karina; Malatesta, Luca; Catorci, Andrea

2016-10-01

The research aim was to understand how variation of temperature and water availability drives trait assemblage of seminatural grasslands in sub-Mediterranean climate, where climate change is expected to intensify summer aridity. In the central Italy, we recorded species abundance and elevation, slope aspect and angle in 129 plots. The traits we analysed were life span, growth form, clonality, belowground organs, leaf traits, plant height, seed mass, and palatability. We used Ellenberg's indicators as a proxy to assess air temperature and soil moisture gradients. From productive to harsh conditions, we observed a shift from tolerance to avoidance strategies, and a change in resource allocation strategies to face competition and stress or that maximize exploitation of patchily distributed soil resource niches. In addition, we found that the increase of temperature and water scarcity leads to the establishment of regeneration strategies that enable plants to cope with the unpredictability of changes in stress intensity and duration. Since the dry habitats of higher elevations are also constrained by winter cold stress, we argue that, within the sub-Mediterranean bioclimate, climate change will likely lead to a variation in dominance inside plant communities rather than a shift upwards of species ranges. At higher elevations, drought-adaptive traits might become more abundant on south-facing slopes that are less stressed by winter low temperatures; traits related to productive conditions and cold stress would be replaced on north-facing slopes by those adapted to overcome both the drought and the cold stresses.

Feasible Electricity Infrastructure Pathways in the Context of Climate-Water Change Constraints

NASA Astrophysics Data System (ADS)

Miara, A.; Vorosmarty, C. J.; Macknick, J.; Cohen, S. M.; Tidwell, V. C.; Newmark, R. L.; Fekete, B. M.; Corsi, F.; Sun, Y.; Proussevitch, A. A.; Glidden, S.

2017-12-01

The carbon and water intensity of US electricity generation has recently decreased due to the natural gas revolution and deployment of renewable technologies. Yet, power plants that require water for cooling still provide 80% of electricity generation and projected climate-water conditions may limit their power output and affect reliability. Understanding the connections and tradeoffs across water, electricity and climate systems is timely, as the nation tries to mitigate and adapt to a changing climate. Electricity expansion models are used to provide insight on power sector pathways given certain policy goals and economic conditions, but do not typically account for productivity limitations due to physical climate-water constraints. Here, we account for such constraints by coupling an electricity expansion model (Regional Energy Deployment System - ReEDS) with the combined Water Balance and Thermoelectric Power and Thermal Pollution Models (WBM-TP2M), which calculate the available capacity at power plants as a function of hydrologic flows, climate conditions, power plant technology and environmental regulations. To fully capture and incorporate climate-water impacts into ReEDS, a specific rule-set was designed for the temporal and spatial downscaling and up-scaling of ReEDS results into WBM-TP2M inputs and visa versa - required to achieve a modeling `loop' that will enable convergence on a feasible solution in the context of economic and geophysical constraints and opportunities. This novel modeling approach is the next phase of research for understanding electricity system vulnerabilities and adaptation measures using energy-water-climate modeling, which to-date has been limited by a focus on individual generators without analyzing power generation as a collective regional system. This study considers four energy policy/economic pathways under future climate-water resource conditions, designed under the National Energy Water System assessment framework. Results

Molecular evolution of the CPP-like gene family in plants: insights from comparative genomics of Arabidopsis and rice.

PubMed

Yang, Zefeng; Gu, Shiliang; Wang, Xuefeng; Li, Wenjuan; Tang, Zaixiang; Xu, Chenwu

2008-09-01

CPP-like genes are members of a small family which features the existence of two similar Cys-rich domains termed CXC domains in their protein products and are distributed widely in plants and animals but do not exist in yeast. The members of this family in plants play an important role in development of reproductive tissue and control of cell division. To gain insights into how CPP-like genes evolved in plants, we conducted a comparative phylogenetic and molecular evolutionary analysis of the CPP-like gene family in Arabidopsis and rice. The results of phylogeny revealed that both gene loss and species-specific expansion contributed to the evolution of this family in Arabidopsis and rice. Both intron gain and intron loss were observed through intron/exon structure analysis for duplicated genes. Our results also suggested that positive selection was a major force during the evolution of CPP-like genes in plants, and most amino acid residues under positive selection were disproportionately located in the region outside the CXC domains. Further analysis revealed that two CXC domains and sequences connecting them might have coevolved during the long evolutionary period.

Genotypic variation in traits linked to climate and aboveground productivity in a widespread C₄ grass: evidence for a functional trait syndrome.

PubMed

Aspinwall, Michael J; Lowry, David B; Taylor, Samuel H; Juenger, Thomas E; Hawkes, Christine V; Johnson, Mari-Vaughn V; Kiniry, James R; Fay, Philip A

2013-09-01

Examining intraspecific variation in growth and function in relation to climate may provide insight into physiological evolution and adaptation, and is important for predicting species responses to climate change. Under common garden conditions, we grew nine genotypes of the C₄ species Panicum virgatum originating from different temperature and precipitation environments. We hypothesized that genotype productivity, morphology and physiological traits would be correlated with climate of origin, and a suite of adaptive traits would show high broad-sense heritability (H(2)). Genotype productivity and flowering time increased and decreased, respectively, with home-climate temperature, and home-climate temperature was correlated with genotypic differences in a syndrome of morphological and physiological traits. Genotype leaf and tiller size, leaf lamina thickness, leaf mass per area (LMA) and C : N ratios increased with home-climate temperature, whereas leaf nitrogen per unit mass (Nm ) and chlorophyll (Chl) decreased with home-climate temperature. Trait variation was largely explained by genotypic differences (H(2) = 0.33-0.85). Our results provide new insight into the role of climate in driving functional trait coordination, local adaptation and genetic divergence within species. These results emphasize the importance of considering intraspecific variation in future climate change scenarios. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Bromine soil/sediment enrichment in tidal salt marshes as a potential indicator of climate changes driven by solar activity: New insights from W coast Portuguese estuaries.

PubMed

Moreno, J; Fatela, F; Leorri, E; Moreno, F; Freitas, M C; Valente, T; Araújo, M F; Gómez-Navarro, J J; Guise, L; Blake, W H

2017-02-15

This paper aims at providing insight about bromine (Br) cycle in four Portuguese estuaries: Minho, Lima (in the NW coast) and Sado, Mira (in the SW coast). The focus is on their tidal marsh environments, quite distinct with regard to key biophysicochemical attributes. Regardless of the primary bromide (Br - ) common natural source, i.e., seawater, the NW marshes present relatively higher surface soil/sediment Br concentrations than the ones from SW coast. This happens in close connection with organic matter (OM) content, and is controlled by their main climatic contexts. Yet, the anthropogenic impact on Br concentrations cannot be discarded. Regarding [Br] spatial patterns across the marshes, the results show a general increase from tidal flat toward high marsh. Maxima [Br] occur in the upper driftline zone, at transition from highest low marsh to high marsh, recognized as a privileged setting for OM accumulation. Based on the discovery of OM ubiquitous bromination in marine and transitional environments, it is assumed that this Br occurs mainly as organobromine. Analysis of two dated sediment cores indicates that, despite having the same age (AD ~1300), the Caminha salt marsh (Minho estuary) evidences higher Br enrichment than the Casa Branca salt marsh (Mira estuary). This is related to a greater Br storage ability, which is linked to OM build-up and rate dynamics under different climate scenarios. Both cores evidence a fairly similar temporal Br enrichment pattern, and may be interpreted in light of the sun-climate coupling. Thereby, most of the well-known Grand Solar Minima during the Little Ice Age appear to have left an imprint on these marshes, supported by higher [Br] in soils/sediments. Besides climate changes driven by solar activity and impacting marsh Br biogeodynamics, those Br enrichment peaks might also reflect inputs of enhanced volcanic activity covarying with Grand Solar Minima. Copyright © 2016 Elsevier B.V. All rights reserved.

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

Storm track response to climate change: Insights from simulations using an idealized dry GCM.

NASA Astrophysics Data System (ADS)

Mbengue, Cheikh; Schneider, Tapio

2013-04-01

The midlatitude storm tracks, where the most intense extratropical cyclones are found, are an important fixture in the general circulation. They are instrumental in balancing the Earth's heat, momentum, and moisture budgets and are responsible for the weather and climatic patterns over large regions of the Earth's surface. As a result, the midlatitude storm tracks are the subject of a considerable amount of scientific research to understand their response to global warming. This has produced the robust result showing that the storm tracks migrate poleward with global warming. However, the dynamical mechanisms responsible for this migration remain unclear. Our work seeks to broaden understanding of the dynamical mechanisms responsible for storm track migration. Competing mechanisms present in the comprehensive climate models often used to study storm track dynamics make it difficult to determine the primary mechanisms responsible for storm track migration. We are thus prompted to study storm track dynamics from a simplified and idealized framework, which enables the decoupling of mean temperature effects from the effects of static stability and of tropical from extratropical effects. Using a statistically zonally symmetric, dry general circulation model (GCM), we conduct a series of numerical simulations to help understand the storm track response to global mean temperatures and to the tropical convective static stability, which we can vary independently. We define storm tracks as regions of zonally and temporally averaged maxima of barotropic eddy kinetic energy (EKE). This storm track definition also allows us to use previously found scalings between the magnitude of bulk measures of mean available potential energy (MAPE) and EKE, to decompose MAPE, and to obtain some mechanistic understanding of the storm track response in our simulations. These simulations provide several insights, which enable us to extend upon existing theories on the mechanisms driving the

Climate sensitivity, sea level and atmospheric carbon dioxide

PubMed Central

Hansen, James; Sato, Makiko; Russell, Gary; Kharecha, Pushker

2013-01-01

Cenozoic temperature, sea level and CO2 covariations provide insights into climate sensitivity to external forcings and sea-level sensitivity to climate change. Climate sensitivity depends on the initial climate state, but potentially can be accurately inferred from precise palaeoclimate data. Pleistocene climate oscillations yield a fast-feedback climate sensitivity of 3±1°C for a 4 W m−2 CO2 forcing if Holocene warming relative to the Last Glacial Maximum (LGM) is used as calibration, but the error (uncertainty) is substantial and partly subjective because of poorly defined LGM global temperature and possible human influences in the Holocene. Glacial-to-interglacial climate change leading to the prior (Eemian) interglacial is less ambiguous and implies a sensitivity in the upper part of the above range, i.e. 3–4°C for a 4 W m−2 CO2 forcing. Slow feedbacks, especially change of ice sheet size and atmospheric CO2, amplify the total Earth system sensitivity by an amount that depends on the time scale considered. Ice sheet response time is poorly defined, but we show that the slow response and hysteresis in prevailing ice sheet models are exaggerated. We use a global model, simplified to essential processes, to investigate state dependence of climate sensitivity, finding an increased sensitivity towards warmer climates, as low cloud cover is diminished and increased water vapour elevates the tropopause. Burning all fossil fuels, we conclude, would make most of the planet uninhabitable by humans, thus calling into question strategies that emphasize adaptation to climate change. PMID:24043864

Climate Sensitivity, Sea Level, and Atmospheric Carbon Dioxide

NASA Technical Reports Server (NTRS)

Hansen, James; Sato, Makiko; Russell, Gary; Kharecha, Pushker

2013-01-01

Cenozoic temperature, sea level and CO2 covariations provide insights into climate sensitivity to external forcings and sea-level sensitivity to climate change. Climate sensitivity depends on the initial climate state, but potentially can be accurately inferred from precise palaeoclimate data. Pleistocene climate oscillations yield a fast-feedback climate sensitivity of 3+/-1deg C for a 4 W/sq m CO2 forcing if Holocene warming relative to the Last Glacial Maximum (LGM) is used as calibration, but the error (uncertainty) is substantial and partly subjective because of poorly defined LGM global temperature and possible human influences in the Holocene. Glacial-to-interglacial climate change leading to the prior (Eemian) interglacial is less ambiguous and implies a sensitivity in the upper part of the above range, i.e. 3-4deg C for a 4 W/sq m CO2 forcing. Slow feedbacks, especially change of ice sheet size and atmospheric CO2, amplify the total Earth system sensitivity by an amount that depends on the time scale considered. Ice sheet response time is poorly defined, but we show that the slow response and hysteresis in prevailing ice sheet models are exaggerated. We use a global model, simplified to essential processes, to investigate state dependence of climate sensitivity, finding an increased sensitivity towards warmer climates, as low cloud cover is diminished and increased water vapour elevates the tropopause. Burning all fossil fuels, we conclude, would make most of the planet uninhabitable by humans, thus calling into question strategies that emphasize adaptation to climate change.

Climate sensitivity, sea level and atmospheric carbon dioxide.

PubMed

Hansen, James; Sato, Makiko; Russell, Gary; Kharecha, Pushker

2013-10-28

Cenozoic temperature, sea level and CO2 covariations provide insights into climate sensitivity to external forcings and sea-level sensitivity to climate change. Climate sensitivity depends on the initial climate state, but potentially can be accurately inferred from precise palaeoclimate data. Pleistocene climate oscillations yield a fast-feedback climate sensitivity of 3±1(°)C for a 4 W m(-2) CO2 forcing if Holocene warming relative to the Last Glacial Maximum (LGM) is used as calibration, but the error (uncertainty) is substantial and partly subjective because of poorly defined LGM global temperature and possible human influences in the Holocene. Glacial-to-interglacial climate change leading to the prior (Eemian) interglacial is less ambiguous and implies a sensitivity in the upper part of the above range, i.e. 3-4(°)C for a 4 W m(-2) CO2 forcing. Slow feedbacks, especially change of ice sheet size and atmospheric CO2, amplify the total Earth system sensitivity by an amount that depends on the time scale considered. Ice sheet response time is poorly defined, but we show that the slow response and hysteresis in prevailing ice sheet models are exaggerated. We use a global model, simplified to essential processes, to investigate state dependence of climate sensitivity, finding an increased sensitivity towards warmer climates, as low cloud cover is diminished and increased water vapour elevates the tropopause. Burning all fossil fuels, we conclude, would make most of the planet uninhabitable by humans, thus calling into question strategies that emphasize adaptation to climate change.

Bioethics and the Framing of Climate Change's Health Risks.

PubMed

Valles, Sean A

2015-06-01

Cheryl Cox Macpherson recently argued, in an article for this journal, that 'Climate Change is a Bioethics Problem'. This article elaborates on that position, particularly highlighting bioethicists' potential ability to help reframe the current climate change discourse to give more attention to its health risks. This reframing process is especially important because of the looming problem of climate change skepticism. Recent empirical evidence from science framing experiments indicates that the public reacts especially positively to climate change messages framed in public health terms, and bioethicists are particularly well positioned to contribute their expertise to the process of carefully developing and communicating such messages. Additionally, as climate framing research and practice continue, it will be important for bioethicists to contribute to the creation of that project's nascent ethical standards. The discourse surrounding antibiotic resistance is posited as an example that can lend insight into how communicating a public health-framed message, including the participation of bioethicists, can help to override public skepticism about the findings of politically contentious scientific fields. © 2014 John Wiley & Sons Ltd.

Carbon dioxide-dependent regulation of NF-κB family members RelB and p100 gives molecular insight into CO2-dependent immune regulation.

PubMed

Keogh, Ciara E; Scholz, Carsten C; Rodriguez, Javier; Selfridge, Andrew C; von Kriegsheim, Alexander; Cummins, Eoin P

2017-07-07

CO 2 is a physiological gas normally produced in the body during aerobic respiration. Hypercapnia (elevated blood pCO 2 >≈50 mm Hg) is a feature of several lung pathologies, e.g. chronic obstructive pulmonary disease. Hypercapnia is associated with increased susceptibility to bacterial infections and suppression of inflammatory signaling. The NF-κB pathway has been implicated in these effects; however, the molecular mechanisms underpinning cellular sensitivity of the NF-κB pathway to CO 2 are not fully elucidated. Here, we identify several novel CO 2 -dependent changes in the NF-κB pathway. NF-κB family members p100 and RelB translocate to the nucleus in response to CO 2 A cohort of RelB protein-protein interactions ( e.g. with Raf-1 and IκBα) are altered by CO 2 exposure, although others are maintained ( e.g. with p100). RelB is processed by CO 2 in a manner dependent on a key C-terminal domain located in its transactivation domain. Loss of the RelB transactivation domain alters NF-κB-dependent transcriptional activity, and loss of p100 alters sensitivity of RelB to CO 2 Thus, we provide molecular insight into the CO 2 sensitivity of the NF-κB pathway and implicate altered RelB/p100-dependent signaling in the CO 2 -dependent regulation of inflammatory signaling. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure-informed insights for NLR functioning in plant immunity.

PubMed

Sukarta, Octavina C A; Slootweg, Erik J; Goverse, Aska

2016-08-01

To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermodynamics and kinetics of molecular motors.

PubMed

Astumian, R Dean

2010-06-02

Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics.

PubMed

Abhinand, P A; Shaikh, Faraz; Bhakat, Soumendranath; Radadiya, Ashish; Bhaskar, L V K S; Shah, Anamik; Ragunath, P K

2016-01-01

Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural tube defects and cardiovascular disease. Experimental studies have shown that the mutation does not affect the kinetic properties of MTHFR, but inactivates the protein by increasing flavin adenine dinucleotide (FAD) loss. The lack of completely solved crystal structure of MTHFR is an impediment in understanding the structural perturbations caused by the Ala222Val mutation; computational modeling provides a suitable alternative. The three-dimensional structure of human MTHFR protein was obtained through homology modeling, by taking the MTHFR structures from Escherichia coli and Thermus thermophilus as templates. Subsequently, the modeled structure was docked with FAD using Glide, which revealed a very good binding affinity, authenticated by a Glide XP score of -10.3983 (kcal mol(-1)). The MTHFR was mutated by changing Alanine 222 to Valine. The wild-type MTHFR-FAD complex and the Ala222Val mutant MTHFR-FAD complex were subjected to molecular dynamics simulation over 50 ns period. The average difference in backbone root mean square deviation (RMSD) between wild and mutant variant was found to be ~.11 Å. The greater degree of fluctuations in the mutant protein translates to increased conformational stability as a result of mutation. The FAD-binding ability of the mutant MTHFR was also found to be significantly lowered as a result of decreased protein grip caused by increased conformational flexibility. The study provides insights into the Ala222Val mutation of human MTHFR that induces major conformational changes in the tertiary structure, causing a significant reduction in the FAD-binding affinity.

Molecular Insights of p47phox Phosphorylation Dynamics in the Regulation of NADPH Oxidase Activation and Superoxide Production*

PubMed Central

Meijles, Daniel N.; Fan, Lampson M.; Howlin, Brendan J.; Li, Jian-Mei

2014-01-01

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox−/− coronary microvascular cells. Compared with wild-type p47phox cDNA transfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2⨪ production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells. PMID:24970888

Perceptions of climate-related risk among water sector professionals in Africa-Insights from the 2016 African Water Association Congress.

PubMed

Connolly, Katherine; Mbutu, Mwaura; Bartram, Jamie; Fuente, David

2018-06-01

The ability of water and wastewater utilities to provide safe and reliable water and sanitation services now and in the future will be determined, in part, by their resilience to climate change. Investment in infrastructure, planning, and operational practices that increase resilience are affected, in turn, by how water sector professionals perceive the risks posed to utilities by climate change and its related impacts. We surveyed water sector professionals at the 2016 African Water Association's Congress in Nairobi, Kenya to assess their perceptions of climate-specific and general risks that may disrupt utility service. We find that water sector professionals are most concerned about climate-specific and general risks that affect utility water supplies (quantity), followed by adequacy of utility infrastructure. We also find that professionals tend to rank climate-specific risks as less concerning than general risks facing utilities. Furthermore, non-utility professionals are more concerned about climate-specific risks and climate change in general than utility professionals. These findings highlight the multiple, competing risks utilities face and the need for adaptation strategies that simultaneously address climate-specific and general concerns of utilities. Copyright © 2018 Elsevier GmbH. All rights reserved.

Interannual to multidecadal climate forcings on groundwater resources of the U.S. West Coast

USGS Publications Warehouse

Velasco, Elzie M.; Gurdak, Jason J.; Dickinson, Jesse; Ferré, T.P.A.; Corona, Claudia

2017-01-01

Study regionThe U.S. West Coast, including the Pacific Northwest and California Coastal Basins aquifer systems.Study focusGroundwater response to interannual to multidecadal climate variability has important implications for security within the water–energy–food nexus. Here we use Singular Spectrum Analysis to quantify the teleconnections between AMO, PDO, ENSO, and PNA and precipitation and groundwater level fluctuations. The computer program DAMP was used to provide insight on the influence of soil texture, depth to water, and mean and period of a surface infiltration flux on the damping of climate signals in the vadose zone.New hydrological insights for the regionWe find that PDO, ENSO, and PNA have significant influence on precipitation and groundwater fluctuations across a north-south gradient of the West Coast, but the lower frequency climate modes (PDO) have a greater influence on hydrologic patterns than higher frequency climate modes (ENSO and PNA). Low frequency signals tend to be preserved better in groundwater fluctuations than high frequency signals, which is a function of the degree of damping of surface variable fluxes related to soil texture, depth to water, mean and period of the infiltration flux. The teleconnection patterns that exist in surface hydrologic processes are not necessarily the same as those preserved in subsurface processes, which are affected by damping of some climate variability signals within infiltrating water.

Climate and local abundance in freshwater fishes

PubMed Central

Knouft, Jason H.; Anthony, Melissa M.

2016-01-01

Identifying factors regulating variation in numbers of individuals among populations across a species' distribution is a fundamental goal in ecology. A common prediction, often referred to as the abundant-centre hypothesis, suggests that abundance is highest near the centre of a species' range. However, because of the primary focus on the geographical position of a population, this framework provides little insight into the environmental factors regulating local abundance. While range-wide variation in population abundance associated with environmental conditions has been investigated in terrestrial species, the relationship between climate and local abundance in freshwater taxa across species' distributions is not well understood. We used GIS-based temperature and precipitation data to determine the relationships between climatic conditions and range-wide variation in local abundance for 19 species of North American freshwater fishes. Climate predicted a portion of the variation in local abundance among populations for 18 species. In addition, the relationship between climatic conditions and local abundance varied among species, which is expected as lineages partition the environment across geographical space. The influence of local habitat quality on species persistence is well documented; however, our results also indicate the importance of climate in regulating population sizes across a species geographical range, even in aquatic taxa. PMID:27429769

Teaching About Climate Change in Medical Education: An Opportunity

PubMed Central

Maxwell, Janie; Blashki, Grant

2016-01-01

Climate change threatens many of the gains in development and health over the last century. However, it could also be a catalyst for a necessary societal transformation to a sustainable and healthy future. Doctors have a crucial role in climate change mitigation and health system adaptation to prepare for emergent health threats and a carbon-constrained future. This paper argues that climate change should be integrated into medical education for three reasons: first, to prepare students for clinical practice in a climate-changing world; secondly, to promote public health and eco-health literacy; and finally, to deepen existing learning and strengthen graduate attributes. This paper builds on existing literature and the authors’ experience to outline potential learning objectives, teaching methods and assessment tasks. In the wake of recent progress at the United Nations climate change conference, COP-21, it is hoped that this paper will assist universities to integrate teaching about climate change into medical education. Significance for public health There is a strong case for teaching about climate change in medical education. Anthropogenic climate change is accepted by scientists, governments and health authorities internationally. Given the dire implications for human health, climate change is of fundamental relevance to future doctors. Integrating climate change into medical education offers an opportunity for future doctors to develop skills and insights essential for clinical practice and a public health role in a climate-changing world. This echoes a broader call for improved public health literacy among medical graduates. This paper provides medical schools with a rationale and an outline for teaching on climate change. PMID:27190980

Teaching About Climate Change in Medical Education: An Opportunity.

PubMed

Maxwell, Janie; Blashki, Grant

2016-04-26

Climate change threatens many of the gains in development and health over the last century. However, it could also be a catalyst for a necessary societal transformation to a sustainable and healthy future. Doctors have a crucial role in climate change mitigation and health system adaptation to prepare for emergent health threats and a carbon-constrained future. This paper argues that climate change should be integrated into medical education for three reasons: first, to prepare students for clinical practice in a climate-changing world; secondly, to promote public health and eco-health literacy; and finally, to deepen existing learning and strengthen graduate attributes. This paper builds on existing literature and the authors' experience to outline potential learning objectives, teaching methods and assessment tasks. In the wake of recent progress at the United Nations climate change conference, COP-21, it is hoped that this paper will assist universities to integrate teaching about climate change into medical education. Significance for public healthThere is a strong case for teaching about climate change in medical education. Anthropogenic climate change is accepted by scientists, governments and health authorities internationally. Given the dire implications for human health, climate change is of fundamental relevance to future doctors. Integrating climate change into medical education offers an opportunity for future doctors to develop skills and insights essential for clinical practice and a public health role in a climate-changing world. This echoes a broader call for improved public health literacy among medical graduates. This paper provides medical schools with a rationale and an outline for teaching on climate change.

Acadia National Park Climate Change Scenario Planning Workshop summary

USGS Publications Warehouse

Star, Jonathan; Fisichelli, Nicholas; Bryan, Alexander; Babson, Amanda; Cole-Will, Rebecca; Miller-Rushing, Abraham J.

2016-01-01

This report summarizes outcomes from a two-day scenario planning workshop for Acadia National Park, Maine (ACAD). The primary objective of the workshop was to help ACAD senior leadership make management and planning decisions based on up-to-date climate science and assessments of future uncertainty. The workshop was also designed as a training program, helping build participants' capabilities to develop and use scenarios. The details of the workshop are given in later sections. The climate scenarios presented here are based on published global climate model output. The scenario implications for resources and management decisions are based on expert knowledge distilled through scientist-manager interaction during workgroup break-out sessions at the workshop. Thus, the descriptions below are from these small-group discussions in a workshop setting and should not be taken as vetted research statements of responses to the climate scenarios, but rather as insights and examinations of possible futures (Martin et al. 2011, McBride et al. 2012).

Molecular complexes in close and far away

PubMed Central

Klemperer, William; Vaida, Veronica

2006-01-01

In this review, gas-phase chemistry of interstellar media and some planetary atmospheres is extended to include molecular complexes. Although the composition, density, and temperature of the environments discussed are very different, molecular complexes have recently been considered as potential contributors to chemistry. The complexes reviewed include strongly bound aggregates of molecules with ions, intermediate-strength hydrogen bonded complexes (primarily hydrates), and weakly bonded van der Waals molecules. In low-density, low-temperature environments characteristic of giant molecular clouds, molecular synthesis, known to involve gas-phase ion-molecule reactions and chemistry at the surface of dust and ice grains is extended here to involve molecular ionic clusters. At the high density and high temperatures found on planetary atmospheres, molecular complexes contribute to both atmospheric chemistry and climate. Using the observational, laboratory, and theoretical database, the role of molecular complexes in close and far away is discussed. PMID:16740667

Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

PubMed

Muto, Yutaka; Yokoyama, Shigeyuki

2012-01-01

'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

Spatio-Temporal Pattern Analysis for Regional Climate Change Using Mathematical Morphology

NASA Astrophysics Data System (ADS)

Das, M.; Ghosh, S. K.

2015-07-01

Of late, significant changes in climate with their grave consequences have posed great challenges on humankind. Thus, the detection and assessment of climatic changes on a regional scale is gaining importance, since it helps to adopt adequate mitigation and adaptation measures. In this paper, we have presented a novel approach for detecting spatio-temporal pattern of regional climate change by exploiting the theory of mathematical morphology. At first, the various climatic zones in the region have been identified by using multifractal cross-correlation analysis (MF-DXA) of different climate variables of interest. Then, the directional granulometry with four different structuring elements has been studied to detect the temporal changes in spatial distribution of the identified climatic zones in the region and further insights have been drawn with respect to morphological uncertainty index and Hurst exponent. The approach has been evaluated with the daily time series data of land surface temperature (LST) and precipitation rate, collected from Microsoft Research - Fetch Climate Explorer, to analyze the spatio-temporal climatic pattern-change in the Eastern and North-Eastern regions of India throughout four quarters of the 20th century.

Decoding the spatial signatures of multi-scale climate variability - a climate network perspective

NASA Astrophysics Data System (ADS)

Donner, R. V.; Jajcay, N.; Wiedermann, M.; Ekhtiari, N.; Palus, M.

2017-12-01

During the last years, the application of complex networks as a versatile tool for analyzing complex spatio-temporal data has gained increasing interest. Establishing this approach as a new paradigm in climatology has already provided valuable insights into key spatio-temporal climate variability patterns across scales, including novel perspectives on the dynamics of the El Nino Southern Oscillation or the emergence of extreme precipitation patterns in monsoonal regions. In this work, we report first attempts to employ network analysis for disentangling multi-scale climate variability. Specifically, we introduce the concept of scale-specific climate networks, which comprises a sequence of networks representing the statistical association structure between variations at distinct time scales. For this purpose, we consider global surface air temperature reanalysis data and subject the corresponding time series at each grid point to a complex-valued continuous wavelet transform. From this time-scale decomposition, we obtain three types of signals per grid point and scale - amplitude, phase and reconstructed signal, the statistical similarity of which is then represented by three complex networks associated with each scale. We provide a detailed analysis of the resulting connectivity patterns reflecting the spatial organization of climate variability at each chosen time-scale. Global network characteristics like transitivity or network entropy are shown to provide a new view on the (global average) relevance of different time scales in climate dynamics. Beyond expected trends originating from the increasing smoothness of fluctuations at longer scales, network-based statistics reveal different degrees of fragmentation of spatial co-variability patterns at different scales and zonal shifts among the key players of climate variability from tropically to extra-tropically dominated patterns when moving from inter-annual to decadal scales and beyond. The obtained results

How to build a molecular shock absorber.

PubMed

McGough, A

1999-12-02

Newly determined structures of the alpha-helical repeats that make up the key 'rod' domains of spectrin and alpha-actinin - which serve as spacers between their actin-binding domains - have provided important insights into how these proteins function as molecular shock absorbers in cells.

Modelling climate change and malaria transmission.

PubMed

Parham, Paul E; Michael, Edwin

2010-01-01

The impact of climate change on human health has received increasing attention in recent years, with potential impacts due to vector-borne diseases only now beginning to be understood. As the most severe vector-borne disease, with one million deaths globally in 2006, malaria is thought most likely to be affected by changes in climate variables due to the sensitivity of its transmission dynamics to environmental conditions. While considerable research has been carried out using statistical models to better assess the relationship between changes in environmental variables and malaria incidence, less progress has been made on developing process-based climate-driven mathematical models with greater explanatory power. Here, we develop a simple model of malaria transmission linked to climate which permits useful insights into the sensitivity of disease transmission to changes in rainfall and temperature variables. Both the impact of changes in the mean values of these key external variables and importantly temporal variation in these values are explored. We show that the development and analysis of such dynamic climate-driven transmission models will be crucial to understanding the rate at which P. falciparum and P. vivax may either infect, expand into or go extinct in populations as local environmental conditions change. Malaria becomes endemic in a population when the basic reproduction number R0 is greater than unity and we identify an optimum climate-driven transmission window for the disease, thus providing a useful indicator for determing how transmission risk may change as climate changes. Overall, our results indicate that considerable work is required to better understand ways in which global malaria incidence and distribution may alter with climate change. In particular, we show that the roles of seasonality, stochasticity and variability in environmental variables, as well as ultimately anthropogenic effects, require further study. The work presented here

Climate change impacts on food system

NASA Astrophysics Data System (ADS)

Zhang, X.; Cai, X.; Zhu, T.

2014-12-01

Food system includes biophysical factors (climate, land and water), human environments (production technologies and food consumption, distribution and marketing), as well as the dynamic interactions within them. Climate change affects agriculture and food systems in various ways. Agricultural production can be influenced directly by climatic factors such as mean temperature rising, change in rainfall patterns, and more frequent extreme events. Eventually, climate change could cause shift of arable land, alteration of water availability, abnormal fluctuation of food prices, and increase of people at risk of malnutrition. This work aims to evaluate how climate change would affect agricultural production biophysically and how these effects would propagate to social factors at the global level. In order to model the complex interactions between the natural and social components, a Global Optimization model of Agricultural Land and Water resources (GOALW) is applied to the analysis. GOALW includes various demands of human society (food, feed, other), explicit production module, and irrigation water availability constraint. The objective of GOALW is to maximize global social welfare (consumers' surplus and producers' surplus).Crop-wise irrigation water use in different regions around the world are determined by the model; marginal value of water (MVW) can be obtained from the model, which implies how much additional welfare benefit could be gained with one unit increase in local water availability. Using GOALW, we will analyze two questions in this presentation: 1) how climate change will alter irrigation requirements and how the social system would buffer that by price/demand adjustment; 2) how will the MVW be affected by climate change and what are the controlling factors. These results facilitate meaningful insights for investment and adaptation strategies in sustaining world's food security under climate change.

Structural insight of DNA topoisomerases I from camptothecin-producing plants revealed by molecular dynamics simulations.

PubMed

Sirikantaramas, Supaart; Meeprasert, Arthitaya; Rungrotmongkol, Thanyada; Fuji, Hideyoshi; Hoshino, Tyuji; Sudo, Hiroshi; Yamazaki, Mami; Saito, Kazuki

2015-05-01

DNA topoisomerase I (Top1) catalyzes changes in DNA topology by cleaving and rejoining one strand of the double stranded (ds)DNA. Eukaryotic Top1s are the cellular target of the plant-derived anticancer indole alkaloid camptothecin (CPT), which reversibly stabilizes the Top1-dsDNA complex. However, CPT-producing plants, including Camptotheca acuminata, Ophiorrhiza pumila and Ophiorrhiza liukiuensis, are highly resistant to CPT because they possess point-mutated Top1. Here, the adaptive convergent evolution is reported between CPT production ability and mutations in their Top1, as a universal resistance mechanism found in all tested CPT-producing plants. This includes Nothapodytes nimmoniana, one of the major sources of CPT. To obtain a structural insight of the resistance mechanism, molecular dynamics simulations of CPT- resistant and -sensitive plant Top1s complexed with dsDNA and topotecan (a CPT derivative) were performed, these being compared to that for the CPT-sensitive human Top1. As a result, two mutations, Val617Gly and Asp710Gly, were identified in O. pumila Top1 and C. acuminata Top1, respectively. The substitutions at these two positions, surprisingly, are the same as those found in a CPT derivative-resistant human colon adenocarcinoma cell line. The results also demonstrated an increased linker flexibility of the CPT-resistant Top1, providing an additional explanation for the resistance mechanism found in CPT-producing plants. These mutations could reflect the long evolutionary adaptation of CPT-producing plant Top1s to confer a higher degree of resistance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Communicating climate change and health in the media.

PubMed

Depoux, Anneliese; Hémono, Mathieu; Puig-Malet, Sophie; Pédron, Romain; Flahault, Antoine

2017-01-01

The translation of science from research to real-world change is a central goal of public health. Communication has an essential role to play in provoking a response to climate change. It must first raise awareness, make people feel involved and ultimately motivate them to take action. The goal of this research is to understand how the information related to this issue is being addressed and disseminated to different audiences-public citizens, politicians and key climate change stakeholders. Initial results show that the scientific voice struggles to globally highlight this issue to a general audience and that messages that address the topic do not meet the challenges, going from a dramatic framing to a basic adaptation framing. Communication experts can help inform scientists and policy makers on how to best share information about climate change in an engaging and motivating way. This study gives an insight about the key role of the media and communications in addressing themes relating to climate change and transmitting information to the public in order to take action.

A modern pollen-climate dataset from the Darjeeling area, eastern Himalaya: Assessing its potential for past climate reconstruction

NASA Astrophysics Data System (ADS)

Ghosh, Ruby; Bruch, Angela A.; Portmann, Felix; Bera, Subir; Paruya, Dipak Kumar; Morthekai, P.; Ali, Sheikh Nawaz

2017-10-01

Relying on the ability of pollen assemblages to differentiate among elevationally stratified vegetation zones, we assess the potential of a modern pollen-climate dataset from the Darjeeling area, eastern Himalaya, in past climate reconstructions. The dataset includes 73 surface samples from 25 sites collected from a c. 130-3600 m a.s.l. elevation gradient along a horizontal distance of c. 150 km and 124 terrestrial pollen taxa, which are analysed with respect to various climatic and environmental variables such as mean annual temperature (MAT), mean annual precipitation (MAP), mean temperature of coldest quarter (MTCQ), mean temperature of warmest quarter (MTWQ), mean precipitation of driest quarter (MPDQ), mean precipitation of wettest quarter (MPWQ), AET (actual evapotranspiration) and MI (moisture index). To check the reliability of the modern pollen-climate relationships different ordination methods are employed and subsequently tested with Huisman-Olff-Fresco (HOF) models. A series of pollen-climate parameter transfer functions using weighted-averaging regression and calibration partial least squares (WA-PLS) models are developed to reconstruct past climate changes from modern pollen data, and have been cross-validated. Results indicate that three of the environmental variables i.e., MTCQ, MPDQ and MI have strong potential for past climate reconstruction based on the available surface pollen dataset. The potential of the present modern pollen-climate relationship for regional quantitative paleoclimate reconstruction is further tested on a Late Quaternary fossil pollen profile from the Darjeeling foothill region with previously reconstructed and quantified climate. The good agreement with existing data allows for new insights in the hydroclimatic conditions during the Last glacial maxima (LGM) with (winter) temperature being the dominant controlling factor for glacial changes during the LGM in the eastern Himalaya.

Mapping reversible photoswitching of molecular-resistance fluctuations during the conformational transformation of azobenzene-terminated molecular switches.

PubMed

Cho, Duckhyung; Yang, Myungjae; Shin, Narae; Hong, Seunghun

2018-06-07

We report a direct mapping and analysis of electrical noise in azobenzene-terminated molecular monolayers, revealing reversible photoswitching of the molecular-resistance fluctuations in the layers. In this work, a conducting atomic force microscope combined with a homemade spectrum analyzer was used to image electrical current and noise at patterned self-assembled monolayers (SAMs) of azobenzene-terminated molecular wires on a gold substrate. We analyzed the current and noise imaging data to obtain maps of molecular resistances and amount of mean-square fluctuations in the resistances of the regions of trans-azobenzene and a cis/trans-azobenzene mixture. We revealed that the fluctuations in the molecular resistances in the SAMs were enhanced after the trans-to-cis isomerization, while the resistances were reduced. This result could be attributed to enhanced disorders in the molecular arrangements in the cis-SAMs. Furthermore, we observed that the changes in the resistance fluctuations were reversible with respect to repeated trans-to-cis and cis-to-trans isomerizations, indicating that the effects originated from reversible photoswitching of the molecular structures rather than irreversible damages of the molecules. These findings provide valuable insights into the electrical fluctuations in photoswitchable molecules, which could be utilized in further studies on molecular switches and molecular electronics in general. © 2018 IOP Publishing Ltd.

Molecular contributions to conservation

USGS Publications Warehouse

Haig, Susan M.

1998-01-01

Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective population size, population-specific markers, etc. PCR (polymerase chain reaction) amplification of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.

Comparative transcriptome analysis provides insights into molecular mechanisms for parthenocarpic fruit development in eggplant (Solanum melongena L.).

PubMed

Chen, Xia; Zhang, Min; Tan, Jie; Huang, Shuping; Wang, Chunli; Zhang, Hongyuan; Tan, Taiming

2017-01-01

Genetic control of parthenocarpy, a desirable trait in edible fruit with hard seeds, has been extensively studied. However, the molecular mechanism of parthenocarpic fruit development in eggplant (Solanum melongena L.) is still unclear. To provide insights into eggplant parthenocarpy, the transcriptomic profiles of a natural parthenocarpic (PP05) and two non-parthenocarpic (PnP05 and GnP05) eggplant lines were analyzed using RNA-sequencing (RNA-seq) technology. These sequences were assembled into 38925 unigenes, of which 22683 had an annotated function and 3419 were predicted as novel genes or from alternative splicing. 4864 and 1592 unigenes that were identified as DEGs between comparison groups PP05 vs PnP05 and PP05 vs GnP05, respectively. 506 common DEGs were found contained in both comparison groups, including 258 up-regulated and 248 down-regulated genes. Functional enrichment analyses identified many common or specific biological processes and gene set potentially associated with plant development. The most pronounced findings are that differentially regulated genes potentially-related with auxin signaling between parthenocarpic and non-parthenocarpic eggplants, e.g. calcium-binding protein PBP1 and transcription factor E2FB, which mediate the auxin distribution and auxin-dependent cell division, respectively, are up-regulated in the PP05; whereas homologs of GH3.1 and AUX/IAA, which are involved in inactivation of IAA and interference of auxin signaling, respectively, are down-regulated in PP05. Furthermore, gibberellin and cytokinin signaling genes and genes related to flower development were found differentially regulated between these eggplant lines. The present study provides comprehensive transcriptomic profiles of eggplants with or without parthenocarpic capacity. The information will deepen our understanding of the molecular mechanisms of eggplant parthenocarpy. The DEGs, especially these filtered from PP05 vs PnP05 + GnP05, will be valuable for

Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rastogi, Monisha; Vaish, Rahul, E-mail: rahul@iitmandi.ac.in; Materials Research Centre, Indian Institute of Science, Bangalore 560 012

2015-05-15

The present work aims to investigate the phase transition, dispersion and diffusion behavior of nanocomposites of carbon nanotube (CNT) and straight chain alkanes. These materials are potential candidates for organic phase change materials(PCMs) and have attracted flurry of research recently. Accurate experimental evaluation of the mass, thermal and transport properties of such composites is both difficult as well as economically taxing. Additionally it is crucial to understand the factors that results in modification or enhancement of their characteristic at atomic or molecular level. Classical molecular dynamics approach has been extended to elucidate the same. Bulk atomistic models have been generatedmore » and subjected to rigorous multistage equilibration. To reaffirm the approach, both canonical and constant-temperature, constant- pressure ensembles were employed to simulate the models under consideration. Explicit determination of kinetic, potential, non-bond and total energy assisted in understanding the enhanced thermal and transport property of the nanocomposites from molecular point of view. Crucial parameters including mean square displacement and simulated self diffusion coefficient precisely define the balance of the thermodynamic and hydrodynamic interactions. Radial distribution function also reflected the density variation, strength and mobility of the nanocomposites. It is expected that CNT functionalization could improve the dispersion within n-alkane matrix. This would further ameliorate the mass and thermal properties of the composite. Additionally, the determined density was in good agreement with experimental data. Thus, molecular dynamics can be utilized as a high throughput technique for theoretical investigation of nanocomposites PCMs.« less

Efficient and Flexible Climate Analysis with Python in a Cloud-Based Distributed Computing Framework

NASA Astrophysics Data System (ADS)

Gannon, C.

2017-12-01

As climate models become progressively more advanced, and spatial resolution further improved through various downscaling projects, climate projections at a local level are increasingly insightful and valuable. However, the raw size of climate datasets presents numerous hurdles for analysts wishing to develop customized climate risk metrics or perform site-specific statistical analysis. Four Twenty Seven, a climate risk consultancy, has implemented a Python-based distributed framework to analyze large climate datasets in the cloud. With the freedom afforded by efficiently processing these datasets, we are able to customize and continually develop new climate risk metrics using the most up-to-date data. Here we outline our process for using Python packages such as XArray and Dask to evaluate netCDF files in a distributed framework, StarCluster to operate in a cluster-computing environment, cloud computing services to access publicly hosted datasets, and how this setup is particularly valuable for generating climate change indicators and performing localized statistical analysis.

New insights into molecular diagnostic pathology of primary liver cancer: Advances and challenges.

PubMed

Cong, Wen-Ming; Wu, Meng-Chao

2015-11-01

Primary liver cancer (PLC) is one of the most common malignancies worldwide with increasing incidence and accounts for the third leading cause of cancer-related mortality. Traditional morphopathology primarily emphasizes qualitative diagnosis of PLC, which is not sufficient to resolve the major concern of increasing the long-term treatment efficacy of PLC in clinical management for the modern era. Since the beginning of the 21st century, molecular pathology has played an active role in the investigation of the evaluation of the metastatic potential of PLC, detection of drug targets, prediction of recurrence risks, analysis of clonal origins, evaluation of the malignancy trend of precancerous lesions, and determination of clinical prognosis. As a result, many new progresses have been obtained, and new strategies of molecular-pathological diagnosis have been formed. Moreover, the new types of pathobiological diagnosis indicator systems for PLC have been preliminarily established. These achievements provide valuable molecular pathology-based guide for clinical formulation of individualized therapy programs for PLC. This review article briefly summarizes some relevant progresses of molecular-pathological diagnosis of PLC from the perspective of clinical translational application other than basic experimental studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Implementation and new insights in molecular diagnostics for HIV infection.

PubMed

Tsang, Hin-Fung; Chan, Lawrence Wing-Chi; Tong, Jennifer Chiu-Hung; Wong, Heong-Ting; Lai, Christopher Koon-Chi; Au, Thomas Chi-Chuen; Chan, Amanda Kit-Ching; Ng, Lawrence Po-Wah; Cho, William Chi-Shing; Wong, Sze-Chuen Cesar

2018-05-01

Acquired immunodeficiency syndrome (AIDS) is a kind of acquired disease that breaks down the immune system. Human immunodeficiency virus (HIV) is the causative agent of AIDS. By the end of 2016, there were 36.7 million people living with HIV worldwide. Early diagnosis can alert infected individuals to risk behaviors in order to control HIV transmission. Infected individuals are also benefited from proper treatment and management upon early diagnosis. Thanks to the public awareness of the disease, the annual increase of new HIV infections has been slowly declining over the past decades. The advent of molecular diagnostics has allowed early detection and better management of HIV infected patients. Areas covered: In this review, the authors summarized and discussed the current and future technologies in molecular diagnosis as well as the biomarkers developed for HIV infection. Expert Commentary: A simple and rapid detection of viral load is important for patients and doctors to monitor HIV progression and antiretroviral treatment efficiency. In the near future, it is expected that new technologies such as digital PCR and CRISPR-based technology will play more important role in HIV detection and patient management.

Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations.

PubMed

Liao, Chenyi; Esai Selvan, Myvizhi; Zhao, Jun; Slimovitch, Jonathan L; Schneebeli, Severin T; Shelley, Mee; Shelley, John C; Li, Jianing

2015-08-20

Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed—for the first time in atomistic detail—that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety.

Profound Climatic Effects on Two East Asian Black-Throated Tits (Ave: Aegithalidae), Revealed by Ecological Niche Models and Phylogeographic Analysis

PubMed Central

Wang, Wenjuan; Lin, Congtian; Gao, Bin; Yang, Xiaojun; Zhang, Zhengwang; Lei, Fumin

2011-01-01

Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory. PMID:22195047

Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations.

PubMed

Ballu, Srilata; Itteboina, Ramesh; Sivan, Sree Kanth; Manga, Vijjulatha

2018-02-01

Filamentous temperature-sensitive protein Z (FtsZ) is a protein encoded by the FtsZ gene that assembles into a Z-ring at the future site of the septum of bacterial cell division. Structurally, FtsZ is a homolog of eukaryotic tubulin but has low sequence similarity; this makes it possible to obtain FtsZ inhibitors without affecting the eukaryotic cell division. Computational studies were performed on a series of substituted 3-arylalkoxybenzamide derivatives reported as inhibitors of FtsZ activity in Staphylococcus aureus. Quantitative structure-activity relationship models (QSAR) models generated showed good statistical reliability, which is evident from r 2 ncv and r 2 loo values. The predictive ability of these models was determined and an acceptable predictive correlation (r 2 Pred ) values were obtained. Finally, we performed molecular dynamics simulations in order to examine the stability of protein-ligand interactions. This facilitated us to compare free binding energies of cocrystal ligand and newly designed molecule B1. The good concordance between the docking results and comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) contour maps afforded obliging clues for the rational modification of molecules to design more potent FtsZ inhibitors.

Climate and demography in early prehistory: using calibrated (14)C dates as population proxies.

PubMed

Riede, Felix

2009-04-01

Although difficult to estimate for prehistoric hunter-gatherer populations, demographic variables-population size, density, and the connectedness of demes-are critical for a better understanding of the processes of material culture change, especially in deep prehistory. Demography is the middle-range link between climatic changes and both biological and cultural evolutionary trajectories of human populations. Much of human material culture functions as a buffer against climatic changes, and the study of prehistoric population dynamics, estimated through changing frequencies of calibrated radiocarbon dates, therefore affords insights into how effectively such buffers operated and when they failed. In reviewing a number of case studies (Mesolithic Ireland, the origin of the Bromme culture, and the earliest late glacial human recolonization of southern Scandinavia), I suggest that a greater awareness of demographic processes, and in particular of demographic declines, provides many fresh insights into what structured the archaeological record. I argue that we cannot sideline climatic and environmental factors or extreme geophysical events in our reconstructions of prehistoric culture change. The implications of accepting demographic variability as a departure point for evaluating the archaeological record are discussed.

Climate change: The 2015 Paris Agreement thresholds and Mediterranean basin ecosystems.

PubMed

Guiot, Joel; Cramer, Wolfgang

2016-10-28

The United Nations Framework Convention on Climate Change Paris Agreement of December 2015 aims to maintain the global average warming well below 2°C above the preindustrial level. In the Mediterranean basin, recent pollen-based reconstructions of climate and ecosystem variability over the past 10,000 years provide insights regarding the implications of warming thresholds for biodiversity and land-use potential. We compare scenarios of climate-driven future change in land ecosystems with reconstructed ecosystem dynamics during the past 10,000 years. Only a 1.5°C warming scenario permits ecosystems to remain within the Holocene variability. At or above 2°C of warming, climatic change will generate Mediterranean land ecosystem changes that are unmatched in the Holocene, a period characterized by recurring precipitation deficits rather than temperature anomalies. Copyright © 2016, American Association for the Advancement of Science.

Library of molecular associations: curating the complex molecular basis of liver diseases.

PubMed

Buchkremer, Stefan; Hendel, Jasmin; Krupp, Markus; Weinmann, Arndt; Schlamp, Kai; Maass, Thorsten; Staib, Frank; Galle, Peter R; Teufel, Andreas

2010-03-20

Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.

Climate change, humidity, and mortality in the United States

PubMed Central

Barreca, Alan I.

2014-01-01

This paper estimates the effects of humidity and temperature on mortality rates in the United States (c. 1973–2002) in order to provide an insight into the potential health impacts of climate change. I find that humidity, like temperature, is an important determinant of mortality. Coupled with Hadley CM3 climate-change predictions, I project that mortality rates are likely to change little on the aggregate for the United States. However, distributional impacts matter: mortality rates are likely to decline in cold and dry areas, but increase in hot and humid areas. Further, accounting for humidity has important implications for evaluating these distributional effects. PMID:25328254

Prolactin and teleost ionocytes: new insights into cellular and molecular targets of prolactin in vertebrate epithelia

USGS Publications Warehouse

Breves, Jason P.; McCormick, Stephen D.; Karlstrom, Rolf O.

2014-01-01

The peptide hormone prolactin is a functionally versatile hormone produced by the vertebrate pituitary. Comparative studies over the last six decades have revealed that a conserved function for prolactin across vertebrates is the regulation of ion and water transport in a variety of tissues including those responsible for whole-organism ion homeostasis. In teleost fishes, prolactin was identified as the “freshwater-adapting hormone”, promoting ion-conserving and water-secreting processes by acting on the gill, kidney, gut and urinary bladder. In mammals, prolactin is known to regulate renal, intestinal, mammary and amniotic epithelia, with dysfunction linked to hypogonadism, infertility, and metabolic disorders. Until recently, our understanding of the cellular mechanisms of prolactin action in fishes has been hampered by a paucity of molecular tools to define and study ionocytes, specialized cells that control active ion transport across branchial and epidermal epithelia. Here we review work in teleost models indicating that prolactin regulates ion balance through action on ion transporters, tight-junction proteins, and water channels in ionocytes, and discuss recent advances in our understanding of ionocyte function in the genetically and embryonically accessible zebrafish (Danio rerio). Given the high degree of evolutionary conservation in endocrine and osmoregulatory systems, these studies in teleost models are contributing novel mechanistic insight into how prolactin participates in the development, function, and dysfunction of osmoregulatory systems across the vertebrate lineage.

Developments in Molecular Recognition and Sensing at Interfaces

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

2007-01-01

In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association

DOE PAGES

Rawle, Rachel A.; Hamerly, Timothy; Tripet, Brian P.; ...

2017-06-04

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized usingmore » interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.« less

Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association.

PubMed

Rawle, Rachel A; Hamerly, Timothy; Tripet, Brian P; Giannone, Richard J; Wurch, Louie; Hettich, Robert L; Podar, Mircea; Copié, Valerie; Bothner, Brian

2017-09-01

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis-N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. This multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis-N. equitans association. Our study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies. Copyright © 2017 Elsevier B.V. All rights reserved.

What actually confers adaptive capacity? Insights from agro-climatic vulnerability of Australian wheat.

PubMed

Bryan, Brett A; Huai, Jianjun; Connor, Jeff; Gao, Lei; King, Darran; Kandulu, John; Zhao, Gang

2015-01-01

Vulnerability assessments have often invoked sustainable livelihoods theory to support the quantification of adaptive capacity based on the availability of capital--social, human, physical, natural, and financial. However, the assumption that increased availability of these capitals confers greater adaptive capacity remains largely untested. We quantified the relationship between commonly used capital indicators and an empirical index of adaptive capacity (ACI) in the context of vulnerability of Australian wheat production to climate variability and change. We calculated ACI by comparing actual yields from farm survey data to climate-driven expected yields estimated by a crop model for 12 regions in Australia's wheat-sheep zone from 1991-2010. We then compiled data for 24 typical indicators used in vulnerability analyses, spanning the five capitals. We analyzed the ACI and used regression techniques to identify related capital indicators. Between regions, mean ACI was not significantly different but variance over time was. ACI was higher in dry years and lower in wet years suggesting that farm adaptive strategies are geared towards mitigating losses rather than capitalizing on opportunity. Only six of the 24 capital indicators were significantly related to adaptive capacity in a way predicted by theory. Another four indicators were significantly related to adaptive capacity but of the opposite sign, countering our theory-driven expectation. We conclude that the deductive, theory-based use of capitals to define adaptive capacity and vulnerability should be more circumspect. Assessments need to be more evidence-based, first testing the relevance and influence of capital metrics on adaptive capacity for the specific system of interest. This will more effectively direct policy and targeting of investment to mitigate agro-climatic vulnerability.

New insights into thermal growing conditions of Portuguese grapevine varieties under changing climates

NASA Astrophysics Data System (ADS)

Santos, João A.; Costa, Ricardo; Fraga, Helder

2018-03-01

New decision support tools for Portuguese viticulture are urging under a climate change context. In the present study, heat and chilling accumulation conditions of a collection of 44 grapevine cultivars currently grown in Portugal are assessed at very high spatial resolution ( 1 km) and for 1981-2015. Two bioclimatic indices that incorporate non-linear plant-temperature relationships are selected for this purpose: growing degree hours—GDH (February-October) and chilling portions—CP (October-February). The current thermal growing conditions of each variety are examined and three clusters of grapevine cultivars are identified based on their GDH medians, thus assembling varieties with close heat accumulation requirements and providing more physiologically consistent information when compared to previous studies, as non-linear plant-temperature relationships are herein taken into account. These new clusters are also a complement to previous bioclimatic zoning. Ensemble mean projections under two anthropogenic-driven scenarios (RCP4.5 and RCP8.5, 2041-2070), from four EURO-CORDEX simulations, reveal a widespread increase of GDH and decrease of CP, but with spatial heterogeneities. The spatial variability of these indices throughout Portugal is projected to decrease (strongest increases of GDH in the coolest regions of the northeast) and to increase (strongest decreases of CP in the warmest regions of the south and west), respectively. The typical heat accumulation conditions of each cluster are projected to gradually shift north-eastwards and to higher-elevation areas, whereas insufficient chilling may represent a new challenge in warmer future climates. An unprecedented level of detail for a large collection of grapevine varieties in Portugal is provided, thus promoting a better planning of climate change adaptation measures.

What Actually Confers Adaptive Capacity? Insights from Agro-Climatic Vulnerability of Australian Wheat

PubMed Central

Bryan, Brett A.; Huai, Jianjun; Connor, Jeff; Gao, Lei; King, Darran; Kandulu, John; Zhao, Gang

2015-01-01

Vulnerability assessments have often invoked sustainable livelihoods theory to support the quantification of adaptive capacity based on the availability of capital—social, human, physical, natural, and financial. However, the assumption that increased availability of these capitals confers greater adaptive capacity remains largely untested. We quantified the relationship between commonly used capital indicators and an empirical index of adaptive capacity (ACI) in the context of vulnerability of Australian wheat production to climate variability and change. We calculated ACI by comparing actual yields from farm survey data to climate-driven expected yields estimated by a crop model for 12 regions in Australia’s wheat-sheep zone from 1991–2010. We then compiled data for 24 typical indicators used in vulnerability analyses, spanning the five capitals. We analyzed the ACI and used regression techniques to identify related capital indicators. Between regions, mean ACI was not significantly different but variance over time was. ACI was higher in dry years and lower in wet years suggesting that farm adaptive strategies are geared towards mitigating losses rather than capitalizing on opportunity. Only six of the 24 capital indicators were significantly related to adaptive capacity in a way predicted by theory. Another four indicators were significantly related to adaptive capacity but of the opposite sign, countering our theory-driven expectation. We conclude that the deductive, theory-based use of capitals to define adaptive capacity and vulnerability should be more circumspect. Assessments need to be more evidence-based, first testing the relevance and influence of capital metrics on adaptive capacity for the specific system of interest. This will more effectively direct policy and targeting of investment to mitigate agro-climatic vulnerability. PMID:25668192

Retroperitoneal Liposarcoma: Current Insights in Diagnosis and Treatment

PubMed Central

Matthyssens, Lucas E.; Creytens, David; Ceelen, Wim P.

2015-01-01

Retroperitoneal liposarcoma (RLS) is a rare, biologically heterogeneous tumor that present considerable challenges due to its size and deep location. As a consequence, the majority of patients with high-grade RLS will develop locally recurrent disease following surgery, and this constitutes the cause of death in most patients. Here, we review current insights and controversies regarding histology, molecular biology, extent of surgery, (neo)adjuvant treatment, and systemic treatment including novel targeted agents in RLS. PMID:25713799

Molecular insight in gastric cancer induction: an overview of cancer stemness genes.

PubMed

Akhavan-Niaki, Haleh; Samadani, Ali Akbar

2014-04-01

Gastric cancer is one of the most outgoing human cancers in the world. Two main functional types were described: Intestinal adenocarcinoma and diffuse one. The most important purpose of this review is to analyze and investigate the main genetic factors involved in tumorogenesis of stomach and the molecular mechanism of their expression regulation alongside with the importance of cancer stem cells and their relationship with gastric cancer. It is evident that proper diagnosis of molecular case of cancer may lead to absolute treatment and at least reduction in the disease severity. However, stemness factors such as Sox2, Oct3/4, and Nanog were related with induced pluripotent stem cells, proposing a correlation between these stemness factors and cancer stem cells. Moreover, aberrant induction by Helicobacter pylori of the intestinal-specific homeobox transcription factors, CDX1 and CDX2, also plays an important role in this modification. There are some genes which are directly activated by CDX1 in gastric cancer and distinguished stemness-related reprogramming factors like SALL4 and KLF5. Correspondingly, we also aimed to present the main important epigenetic changes such as DNA methylation, histone modification, and chromatin modeling of stemness genes in disease development. Remarkably, a better understanding of molecular bases of cancer may lead to novel diagnostic, therapeutic, and preventive approaches by some genetic and epigenetic changes such as gene amplifications, gene silencing by DNA methylation, losses of imprinting, LOH, and mutations. Consequently, genome-wide searches of gene expression are widely important for surveying the proper mechanisms of cancer emergence and development. Conspicuously, this review explains an outline of the molecular mechanism and new approaches in gastric cancer.

Aminoglycosides: Molecular Insights on the Recognition of RNA and Aminoglycoside Mimics

PubMed Central

Chittapragada, Maruthi; Roberts, Sarah; Ham, Young Wan

2009-01-01

RNA is increasingly recognized for its significant functions in biological systems and has recently become an important molecular target for therapeutics development. Aminoglycosides, a large class of clinically significant antibiotics, exert their biological functions by binding to prokaryotic ribosomal RNA (rRNA) and interfering with protein translation, resulting in bacterial cell death. They are also known to bind to viral mRNAs such as HIV-1 RRE and TAR. Consequently, aminoglycosides are accepted as the single most important model in understanding the principles that govern small molecule-RNA recognition, which is essential for the development of novel antibacterial, antiviral or even anti-oncogenic agents. This review outlines the chemical structures and mechanisms of molecular recognition and antibacterial activity of aminoglycosides and various aminoglycoside mimics that have recently been devised to improve biological efficacy, binding affinity and selectivity, or to circumvent bacterial resistance. PMID:19812740

Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology.

PubMed

Coskuner-Weber, Orkid; Uversky, Vladimir N

2018-01-24

Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.

Incorporating climate-system and carbon-cycle uncertainties in integrated assessments of climate change. (Invited)

NASA Astrophysics Data System (ADS)

Rogelj, J.; McCollum, D. L.; Reisinger, A.; Knutti, R.; Riahi, K.; Meinshausen, M.

2013-12-01

The field of integrated assessment draws from a large body of knowledge across a range of disciplines to gain robust insights about possible interactions, trade-offs, and synergies. Integrated assessment of climate change, for example, uses knowledge from the fields of energy system science, economics, geophysics, demography, climate change impacts, and many others. Each of these fields comes with its associated caveats and uncertainties, which should be taken into account when assessing any results. The geophysical system and its associated uncertainties are often represented by models of reduced complexity in integrated assessment modelling frameworks. Such models include simple representations of the carbon-cycle and climate system, and are often based on the global energy balance equation. A prominent example of such model is the 'Model for the Assessment of Greenhouse Gas Induced Climate Change', MAGICC. Here we show how a model like MAGICC can be used for the representation of geophysical uncertainties. Its strengths, weaknesses, and limitations are discussed and illustrated by means of an analysis which attempts to integrate socio-economic and geophysical uncertainties. These uncertainties in the geophysical response of the Earth system to greenhouse gases remains key for estimating the cost of greenhouse gas emission mitigation scenarios. We look at uncertainties in four dimensions: geophysical, technological, social and political. Our results indicate that while geophysical uncertainties are an important factor influencing projections of mitigation costs, political choices that delay mitigation by one or two decades a much more pronounced effect.

Mars Climate History: Insights From Impact Crater Wall Slope Statistics

NASA Astrophysics Data System (ADS)

Kreslavsky, Mikhail A.; Head, James W.

2018-02-01

We use the global distribution of the steepest slopes on crater walls derived from Mars Orbiter Laser Altimeter profile data to assess the magnitudes of degradational processes with latitude, altitude, and time. We independently confirm that Amazonian polar/high-latitude crater slope modification is substantial, but that craters in the low latitudes have essentially escaped significant slope modification since the Early Hesperian. We find that the total amount of crater wall degradation in the Late Noachian is very small in comparison to the circumpolar regions in the Late Amazonian, an observation that we interpret to mean that the Late Noachian climate was not characterized by persistent and continuous warm and wet conditions. A confirmed elevational zonality in degradation in the Early Hesperian is interpreted to mean that the atmosphere was denser than today.

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations.

PubMed

Capoferri, Luigi; Leth, Rasmus; ter Haar, Ernst; Mohanty, Arun K; Grootenhuis, Peter D J; Vottero, Eduardo; Commandeur, Jan N M; Vermeulen, Nico P E; Jørgensen, Flemming Steen; Olsen, Lars; Geerke, Daan P

2016-03-01

Cytochrome P450 BM3 (CYP102A1) mutant M11 is able to metabolize a wide range of drugs and drug-like compounds. Among these, M11 was recently found to be able to catalyze formation of human metabolites of mefenamic acid and other nonsteroidal anti-inflammatory drugs (NSAIDs). Interestingly, single active-site mutations such as V87I were reported to invert regioselectivity in NSAID hydroxylation. In this work, we combine crystallography and molecular simulation to study the effect of single mutations on binding and regioselective metabolism of mefenamic acid by M11 mutants. The heme domain of the protein mutant M11 was expressed, purified, and crystallized, and its X-ray structure was used as template for modeling. A multistep approach was used that combines molecular docking, molecular dynamics (MD) simulation, and binding free-energy calculations to address protein flexibility. In this way, preferred binding modes that are consistent with oxidation at the experimentally observed sites of metabolism (SOMs) were identified. Whereas docking could not be used to retrospectively predict experimental trends in regioselectivity, we were able to rank binding modes in line with the preferred SOMs of mefenamic acid by M11 and its mutants by including protein flexibility and dynamics in free-energy computation. In addition, we could obtain structural insights into the change in regioselectivity of mefenamic acid hydroxylation due to single active-site mutations. Our findings confirm that use of MD and binding free-energy calculation is useful for studying biocatalysis in those cases in which enzyme binding is a critical event in determining the selective metabolism of a substrate. © 2016 Wiley Periodicals, Inc.

Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

PubMed

Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

2018-03-06

Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

Deriving meaningful climate-effects data from social media

NASA Astrophysics Data System (ADS)

Fuka, M. Z.; Fuka, D. R.

2011-12-01

This paper presents our research on extracting meaningful climate indicator data from unsolicited observations ("tweets") made by Twitter users regarding their physical surroundings and events occurring around them. Our goal is to establish whether the existing understanding of climate indicator data collected by more traditional means could be usefully supplemented by information derived from the potentially rich but also statistically diffuse data resource represented by social media. To this end, we've initiated an ongoing effort to collect and analyze Twitter observations made on a wide variety of climate-related phenological, biological, epidemiological and meteorological phenomena. We report on our acquisition methodology and discuss in particular our rationale for selecting keywords, phrases and filters for our searches. The iterative process of assembling an inventory of hundreds of climate-related search terms has in and of itself yielded interesting and sometimes surprising insights on what is and isn't noticed and commented on via social media with respect to climate indicator phenomenology. We report some of the highlights of those analyses along with significant findings from the data acquisition to date. In conclusion, we discuss our preliminary assessment of the approach, how it can be generalized and extended for social media other than Twitter, and how the resulting data could be used to serve climate science objectives.

Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient

PubMed Central

Westberg, Erik; Ohali, Shachar; Shevelevich, Anatoly; Fine, Pinchas; Barazani, Oz

2013-01-01

steep climatic gradient. In addition to molecular marker data, we made use of phenotypic evaluation from common garden experiments, and a broad GIS based environmental data with edaphic information gathered in the field. This study, among others, lead to the identification of an outlier locus with an association to trichome formation and herbivore defense, and its ecological adaptive value is discussed. PMID:24567822

Methods for extracting climate indicator data from social media.

NASA Astrophysics Data System (ADS)

Fuka, M. Z.; Fuka, D. R.

2011-12-01

This paper shows how we've used the R software suite to extract climate indicator data from Twitter. In the course of this research we've collected extensive data sets of unsolicited observations ("tweets") for hundreds of climate-related phenological, biological, epidemiological and meteorological effects. R has proved itself in our work as a useful tool for manipulating those large data sets. Our experience from this effort has yielded a variety of insights on using R to extract geophysics-specific information from publicly accessible social media sources. We illustrate our methodology by mapping tweeted US armadillo sightings to explore the impact of climate variability on the extent of the animal's range. This example usefully demonstrates R's technical capabilities in collecting, time-stamping, geolocating, analyzing, visualizing and otherwise processing climate-related data derived from unsolicited social media postings. We also "mash-up" the data sets with those acquired by more traditional means, for example, temperature and precipitation data across the armadillo's US range. Our data-handling practice is extendable to social sharing services other than Twitter, providing the environmental modeling community an opportunity to access largely untapped resources of non-traditional climate indicator data to better understand the effects of climate change at local, regional and global scales.

Country-Specific Effects of Climate Variability on Human Migration

PubMed Central

Gray, Clark; Wise, Erika

2016-01-01

Involuntary human migration is among the social outcomes of greatest concern in the current era of global climate change. Responding to this concern, a growing number of studies have investigated the consequences of short to medium-term climate variability for human migration using demographic and econometric approaches. These studies have provided important insights, but at the same time have been significantly limited by lack of expertise in the use of climate data, access to cross-national data on migration, and attention to model specification. To address these limitations, we link data on internal and international migration over a 6-year period from 9,812 origin households in Kenya, Uganda, Nigeria, Burkina Faso and Senegal to high-resolution gridded climate data from both station and satellite sources. Analyses of these data using several plausible specifications reveal that climate variability has country-specific effects on migration: Migration tends to increase with temperature anomalies in Uganda, tends to decrease with temperature anomalies in Kenya and Burkina Faso, and shows no consistent relationship with temperature in Nigeria and Senegal. Consistent with previous studies, precipitation shows weak and inconsistent relationships with migration across countries. These results challenge generalizing narratives that foresee a consistent migratory response to climate change across the globe. PMID:27092012

Country-Specific Effects of Climate Variability on Human Migration.

PubMed

Gray, Clark; Wise, Erika

2016-04-01

Involuntary human migration is among the social outcomes of greatest concern in the current era of global climate change. Responding to this concern, a growing number of studies have investigated the consequences of short to medium-term climate variability for human migration using demographic and econometric approaches. These studies have provided important insights, but at the same time have been significantly limited by lack of expertise in the use of climate data, access to cross-national data on migration, and attention to model specification. To address these limitations, we link data on internal and international migration over a 6-year period from 9,812 origin households in Kenya, Uganda, Nigeria, Burkina Faso and Senegal to high-resolution gridded climate data from both station and satellite sources. Analyses of these data using several plausible specifications reveal that climate variability has country-specific effects on migration: Migration tends to increase with temperature anomalies in Uganda, tends to decrease with temperature anomalies in Kenya and Burkina Faso, and shows no consistent relationship with temperature in Nigeria and Senegal. Consistent with previous studies, precipitation shows weak and inconsistent relationships with migration across countries. These results challenge generalizing narratives that foresee a consistent migratory response to climate change across the globe.

A mechanistic insight into the amyloidogenic structure of hIAPP peptide revealed from sequence analysis and molecular dynamics simulation.

PubMed

Chakraborty, Sandipan; Chatterjee, Barnali; Basu, Soumalee

2012-07-01

A collective approach of sequence analysis, phylogenetic tree and in silico prediction of amyloidogenecity using bioinformatics tools have been used to correlate the observed species-specific variations in IAPP sequences with the amyloid forming propensity. Observed substitution patterns indicate that probable changes in local hydrophobicity are instrumental in altering the aggregation propensity of the peptide. In particular, residues at 17th, 22nd and 23rd positions of the IAPP peptide are found to be crucial for amyloid formation. Proline25 primarily dictates the observed non-amyloidogenecity in rodents. Furthermore, extensive molecular dynamics simulation of 0.24 μs have been carried out with human IAPP (hIAPP) fragment 19-27, the portion showing maximum sequence variation across different species, to understand the native folding characteristic of this region. Principal component analysis in combination with free energy landscape analysis illustrates a four residue turn spanning from residue 22 to 25. The results provide a structural insight into the intramolecular β-sheet structure of amylin which probably is the template for nucleation of fibril formation and growth, a pathogenic feature of type II diabetes. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantifying impacts of historical climate change in American River basin

NASA Astrophysics Data System (ADS)

Sultana, R.

2017-12-01

There is a near consensus among scientists that climate has been changing for the last few decades in different parts of the world. Some regions are already experiencing the impacts of these changes. Warmer climate can alter the hydrology and water resources around the globe. Historical data shows the temperature has been rising in California and affecting California's water resource by reducing snowfall and snowmelt runoff during spring season. In this study, Soil and Water Assessment Tool (SWAT) model is used to simulate the historical climate in American River basin, a mountainous watershed in California. The results show that warmer climate in the recent decades (1995-2014) have already have affected streamflow characteristics of the watershed. Compared to the 1965-1974, the mean annual streamflow has decreased more than 6% and the peak streamflow has shifted from May to April. Understanding the changes will assist the water resource managers with valuable insight on the effectiveness of mitigation strategies considered as of now.

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.

PubMed

Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

2016-10-01

Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Molecular-Scale Electronics: From Concept to Function.

PubMed

Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

2016-04-13

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

Collaboration pathway(s) using new tools for optimizing operational climate monitoring from space

NASA Astrophysics Data System (ADS)

Helmuth, Douglas B.; Selva, Daniel; Dwyer, Morgan M.

2014-10-01

Consistently collecting the earth's climate signatures remains a priority for world governments and international scientific organizations. Architecting a solution requires transforming scientific missions into an optimized robust `operational' constellation that addresses the needs of decision makers, scientific investigators and global users for trusted data. The application of new tools offers pathways for global architecture collaboration. Recent (2014) rulebased decision engine modeling runs that targeted optimizing the intended NPOESS architecture, becomes a surrogate for global operational climate monitoring architecture(s). This rule-based systems tools provide valuable insight for Global climate architectures, through the comparison and evaluation of alternatives considered and the exhaustive range of trade space explored. A representative optimization of Global ECV's (essential climate variables) climate monitoring architecture(s) is explored and described in some detail with thoughts on appropriate rule-based valuations. The optimization tools(s) suggest and support global collaboration pathways and hopefully elicit responses from the audience and climate science shareholders.

Embracing and resisting climate identities in the Australian press: Sceptics, scientists and politics

PubMed Central

Jaspal, Rusi; Nerlich, Brigitte; van Vuuren, Kitty

2015-01-01

This article charts the development of a label that appeared early on in Australian debates on climate change, namely ‘greenhouse sceptics’. We explore who uses the label, for what purposes and with which effects, and how this label may contribute to the development of social representations in the climate debate. Our findings show that over the last 25 years, ‘greenhouse sceptic’ has been used by journalists and climate scientists to negativize those criticizing mainstream climate science, but that it has also been used, even embraced, by Australian climate sceptics to label themselves in order to construct a positive identity modelled on celebrity sceptics in the United States. We found that the label was grounded in religious metaphors that frame mainstream science as a catastrophist and alarmist religious cult. Overall, this article provides detailed insights into the genealogy of climate scepticism in a particular cultural and historical context. PMID:25957297

Plant developmental responses to climate change.

PubMed

Gray, Sharon B; Brady, Siobhan M

2016-11-01

Climate change is multi-faceted, and includes changing concentrations of greenhouse gases in the atmosphere, rising temperatures, changes in precipitation patterns, and increasing frequency of extreme weather events. Here, we focus on the effects of rising atmospheric CO 2 concentrations, rising temperature, and drought stress and their interaction on plant developmental processes in leaves, roots, and in reproductive structures. While in some cases these responses are conserved across species, such as decreased root elongation, perturbation of root growth angle and reduced seed yield in response to drought, or an increase in root biomass in shallow soil in response to elevated CO 2 , most responses are variable within and between species and are dependent on developmental stage. These variable responses include species-specific thresholds that arrest development of reproductive structures, reduce root growth rate and the rate of leaf initiation and expansion in response to elevated temperature. Leaf developmental responses to elevated CO 2 vary by cell type and by species. Variability also exists between C 3 and C 4 species in response to elevated CO 2 , especially in terms of growth and seed yield stimulation. At the molecular level, significantly less is understood regarding conservation and variability in molecular mechanisms underlying these traits. Abscisic acid-mediated changes in cell wall expansion likely underlie reductions in growth rate in response to drought, and changes in known regulators of flowering time likely underlie altered reproductive transitions in response to elevated temperature and CO 2 . Genes that underlie most other organ or tissue-level responses have largely only been identified in a single species in response to a single stress and their level of conservation is unknown. We conclude that there is a need for further research regarding the molecular mechanisms of plant developmental responses to climate change factors in general, and

Molecular mechanisms of floral mimicry in orchids.

PubMed

Schlüter, Philipp M; Schiestl, Florian P

2008-05-01

Deceptive plants do not produce floral rewards, but attract pollinators by mimicking signals of other organisms, such as food plants or female insects. Such floral mimicry is particularly common in orchids, in which flower morphology, coloration and odour play key roles in deceiving pollinators. A better understanding of the molecular bases for these traits should provide new insights into the occurrence, mechanisms and evolutionary consequences of floral mimicry. It should also reveal the molecular bases of pollinator-attracting signals, in addition to providing strategies for manipulating insect behaviour in general. Here, we review data on the molecular bases for traits involved in floral mimicry, and we describe methodological advances helpful for the functional evaluation of key genes.

Phylogeographic insights into cryptic glacial refugia.

PubMed

Provan, Jim; Bennett, K D

2008-10-01

The glacial episodes of the Quaternary (2.6 million years ago-present) were a major factor in shaping the present-day distributions of extant flora and fauna, with expansions and contractions of the ice sheets rendering large areas uninhabitable for most species. Fossil records suggest that many species survived glacial maxima by retreating to refugia, usually at lower latitudes. Recently, phylogeographic studies have given support to the existence of previously unknown, or cryptic, refugia. Here we summarise many of these insights into the glacial histories of species in cryptic refugia gained through phylogeographic approaches. Understanding such refugia might be important as the Earth heads into another period of climate change, in terms of predicting the effects on species distribution and survival.

Molecular insights into the heterogeneous crystal growth of si methane hydrate.

PubMed

Vatamanu, Jenel; Kusalik, Peter G

2006-08-17

In this paper we report a successful molecular simulation study exploring the heterogeneous crystal growth of sI methane hydrate along its [001] crystallographic face. The molecular modeling of the crystal growth of methane hydrate has proven in the past to be very challenging, and a reasonable framework to overcome the difficulties related to the simulation of such systems is presented. Both the microscopic mechanisms of heterogeneous crystal growth as well as interfacial properties of methane hydrate are probed. In the presence of the appropriate crystal template, a strong tendency for water molecules to organize into cages around methane at the growing interface is observed; the interface also demonstrates a strong affinity for methane molecules. The maximum growth rate measured for a hydrate crystal is about 4 times higher than the value previously determined for ice I in a similar framework (Gulam Razul, M. S.; Hendry, J. G.; Kusalik, P. G. J. Chem. Phys. 2005, 123, 204722).

Advancements in the use of speleothems as climate archives

NASA Astrophysics Data System (ADS)

Wong, Corinne I.; Breecker, Daniel O.

2015-11-01

Speleothems have become a cornerstone of the approach to better understanding Earth's climatic teleconnections due to their precise absolute chronologies, their continuous or semicontinuous deposition and their global terrestrial distribution. We review the last decade of speleothem-related research, building off a similar review by McDermott (2004), in three themes - i) investigation of global teleconnections using speleothem-based climate reconstructions, ii) refinement of climate interpretations from speleothem proxies through cave monitoring, and iii) novel, technical methods of speleothem-based climate reconstructions. Speleothem records have enabled critical insight into the response of global hydroclimate to large climate changes. This includes the relevant forcings and sequence of climatic responses involved in glacial terminations and recognition of a global monsoon response to climate changes on orbital and millennial time scales. We review advancements in understanding of the processes that control speleothem δ13C values and introduce the idea of a direct atmospheric pCO2 influence. We discuss progress in understanding kinetic isotope fractionation, which, with further advances, may help quantify paleoclimate changes despite non-equilibrium formation of speleothems. This feeds into the potential of proxy system modeling to consider climatic, hydrological and biogeochemical processes with the objective of quantitatively interpreting speleothem proxies. Finally, we provide an overview of emerging speleothem proxies and novel approaches using existing proxies. Most recently, technical advancements made in the measurement of fluid inclusions are now yielding reliable determinations of paleotemperatures.

Molecular and genetic insights into an infantile epileptic encephalopathy – CDKL5 disorder

PubMed Central

Zhou, Ailing; Han, Song

2017-01-01

Background The discovery that mutations in cyclin-dependent kinase-like 5 (CDKL5) gene are associated with infantile epileptic encephalopathy has stimulated world-wide research effort to understand the molecular and genetic basis of CDKL5 disorder. Given the large number of literature published thus far, this review aims to summarize current genetic studies, draw a consensus on proposed molecular functions, and point to gaps of knowledge in CDKL5 research. Methods A systematic review process was conducted using the PubMed search engine focusing on CDKL5 studies in the recent ten years. We analyzed these publications and summarized the findings into four sections: genetic studies, CDKL5 expression patterns, molecular functions, and animal models. We also discussed challenges and future directions in each section. Results On the clinical side, CDKL5 disorder is characterized by early onset epileptic seizures, intellectual disability, and stereotypical behaviors. On the research side, a series of molecular and genetic studies in human patients, cell cultures and animal models have established the causality of CDKL5 to the infantile epileptic encephalopathy, and pointed to a key role for CDKL5 in regulating neuronal function in the brain. Mouse models of CDKL5 disorder have also been developed, and notably, manifest behavioral phenotypes, mimicking numerous clinical symptoms of CDKL5 disorder and advancing CDKL5 research to the preclinical stage. Conclusions Given what we have learned thus far, future identification of robust, quantitative, and sensitive outcome measures would be the key in animal model studies, particularly in heterozygous females. In the meantime, molecular and cellular studies of CDKL5 should focus on mechanism-based investigation and aim to uncover druggable targets that offer the potential to rescue or ameliorate CDKL5 disorder-related phenotypes. PMID:28580010

Engaging informal audiences in learning about and responding to climate change through a portfolio of innovative approaches

NASA Astrophysics Data System (ADS)

Pfirman, S. L.; Brunacini, J.; Orlove, B. S.; Bachrach, E.; Hamilton, L.

2017-12-01

Informal learners have many different backgrounds, experiences, and perspectives. How can informal educators effectively reach such diverse audiences, meeting people where they are with regard to climate change? The Polar Learning and Responding: PoLAR Climate Change Education Partnership, supported by NSF, employs surveys, resource development, and research to develop innovative, evidence-based approaches that engage lifelong learners. General-public surveys on climate change yield insights on the knowledge and perceptions that informal learners bring to the table. That helps guide the creation of new tools for effective communication. For example, many people are unsure what causes sea level to rise. The Polar Explorer: Sea Level app uses a data and question-based approach guiding people through interactive maps to learn about melting land ice. In addition, people also tend to believe that climate impacts will happen in the future. Polar Voices podcasts feature Arctic Indigenous communities sharing first-hand experiences with climate change. Prior knowledge can be harnessed to enhance learning. Arctic SMARTIC engages people in role-playing negotiations with others to create a marine management plan. Climate game jams provide collaborative, creative spaces where participants learn as they interact with others. In each case participants, with all their knowledge and experience, are brought into group problem-solving. Understanding whom people trust for climate-change information offers insights that help them become climate communicators. Even those who are concerned about climate often do not discuss it with family and friends (Maibach et al. 2016), yet our research shows that family and friends are second only to scientists as trusted sources of climate information (Hamilton 2016). Fun and novel educational tools such as the EcoChains card game and the EcoKoin social networking app serve as conversation starters.

Recent molecular insights into rickettsial pathogenesis and immunity

PubMed Central

Sahni, Sanjeev K; Narra, Hema P; Sahni, Abha; Walker, David H

2013-01-01

Human infections with arthropod-borne Rickettsia species remain a major global health issue, causing significant morbidity and mortality. Epidemic typhus due to Rickettsia prowazekii has an established reputation as the ‘scourge of armies’, and as a major determinant of significant ‘historical turning points’. No suitable vaccines for human use are currently available to prevent rickettsial diseases. The unique lifestyle features of rickettsiae include obligate intracellular parasitism, intracytoplasmic niche within the host cell, predilection for infection of microvascular endothelium in mammalian hosts, association with arthropods and the tendency for genomic reduction. The fundamental research in the field of Rickettsiology has witnessed significant recent progress in the areas of pathogen adhesion/invasion and host immune responses, as well as the genomics, proteomics, metabolomics, phylogenetics, motility and molecular manipulation of important rickettsial pathogens. The focus of this review article is to capture a snapshot of the latest developments pertaining to the mechanisms of rickettsial pathogenesis and immunity. PMID:24059918

Molecular insights into primary hyperoxaluria type 1 pathogenesis.

PubMed

Cellini, Barbara; Oppici, Elisa; Paiardini, Alessandro; Montioli, Riccardo

2012-01-01

Primary hyperoxaluria type 1 (PH1) is a rare autosomal recessive disorder of glyoxylate metabolism caused by the deficiency of liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. The PH1 pathogenesis is mostly due to single point mutations (more than 150 so far identified) on the AGXT gene, and is characterized by a marked heterogeneity in terms of genotype, enzymatic and clinical phenotypes. This article presents an up to date review of selected aspects of the biochemical properties of the two allelic forms of AGT and of some PH1-causing variants. These recent discoveries highlight the effects at the protein level of the pathogenic mutations, and, together with previous cell biology and clinical data, (i) improve the understanding of the molecular basis of PH1 pathogenesis, and (ii) help to delineate perspectives for predicting the response to pyridoxine treatment or for suggesting new strategies for PH1 patients bearing the analyzed mutations.

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

PubMed Central

Liu, Qixin; Cai, Zhiyong

2014-01-01

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Mechanistic and quantitative insight into cell surface targeted molecular imaging agent design.

PubMed

Zhang, Liang; Bhatnagar, Sumit; Deschenes, Emily; Thurber, Greg M

2016-05-05

Molecular imaging agent design involves simultaneously optimizing multiple probe properties. While several desired characteristics are straightforward, including high affinity and low non-specific background signal, in practice there are quantitative trade-offs between these properties. These include plasma clearance, where fast clearance lowers background signal but can reduce target uptake, and binding, where high affinity compounds sometimes suffer from lower stability or increased non-specific interactions. Further complicating probe development, many of the optimal parameters vary depending on both target tissue and imaging agent properties, making empirical approaches or previous experience difficult to translate. Here, we focus on low molecular weight compounds targeting extracellular receptors, which have some of the highest contrast values for imaging agents. We use a mechanistic approach to provide a quantitative framework for weighing trade-offs between molecules. Our results show that specific target uptake is well-described by quantitative simulations for a variety of targeting agents, whereas non-specific background signal is more difficult to predict. Two in vitro experimental methods for estimating background signal in vivo are compared - non-specific cellular uptake and plasma protein binding. Together, these data provide a quantitative method to guide probe design and focus animal work for more cost-effective and time-efficient development of molecular imaging agents.

Recent clinical and molecular insights into emerging artemisinin resistance in Plasmodium falciparum

PubMed Central

O’Brien, Connor; Henrich, Philipp P.; Passi, Neha; Fidock, David A.

2012-01-01

Purpose of review Artemisinin-based combination therapies (ACTs) have been deployed globally with remarkable success for more than 10 years without having lost their malaria treatment efficacy. However, recent reports from the Thai–Cambodian border reveal evidence of emerging resistance to artemisinins. The latest published clinical and molecular findings are summarized herein. Recent findings Clinical studies have identified delayed parasite clearance time as the most robust marker of artemisinin resistance. Resistance has only been documented from Southeast Asia and has been observed in isolates that show no significant decrease in drug susceptibility in vitro. Genetic investigations have yet to uncover robust molecular markers. In-vitro studies have identified parasite quiescence or dormancy mechanisms that protect early ‘ring-stage’ intra-erythrocytic parasites against short-term artemisinin exposure. This might be achieved by reducing the rate of hemoglobin degradation, important for artemisinin bioactivation. Summary Should ACTs fail, no suitable alternatives exist as first-line treatments of P. falciparum malaria. Intensified efforts are essential to monitor the spread of resistance, define therapeutic and operational strategies to counter its impact, and understand its molecular basis. Success in these areas is critical to ensuring that recent gains in reducing the burden of malaria are not lost. PMID:22001944

Adaptation to climate change? Moving coast redwood seedlings northward and inland

Treesearch

Christa M. Dagley; John-Pascal Berrill; Forrest T. Johnson; Lucy P. Kerhoulas

2017-01-01

Insight into genetic variation in trees may provide opportunities to select for genotypes that are better adapted to new locations and future climate conditions. We established a field test at two sites in Humboldt County, California to study the performance of coast redwood (Sequoia sempervirens (D. Don) Endl.) under assisted migration. Both test...

The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms

PubMed Central

de Storme, Nico; Geelen, Danny

2014-01-01

In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved. PMID:23731015

Clinical and Mechanistic Insights into the Genetics of Cardiomyopathy

PubMed Central

Burke, Michael A.; Cook, Stuart A.; Seidman, Jonathan G.; Seidman, Christine E.

2018-01-01

Over the last quarter-century, there has been tremendous progress in genetics research that has defined molecular causes for cardiomyopathies. More than a thousand mutations have been identified in many genes with varying ontologies, therein indicating the diverse molecules and pathways that cause hypertrophic, dilated, restrictive, and arrhythmogenic cardiomyopathies. Translation of this research to the clinic via genetic testing can precisely group affected patients according to molecular etiology, and identify individuals without evidence of disease who are at high risk for developing cardiomyopathy. These advances provide insights into the earliest manifestations of cardiomyopathy and help to define the molecular pathophysiological basis for cardiac remodeling. Although these efforts remain incomplete, new genomic technologies and analytic strategies provide unparalleled opportunities to fully explore the genetic architecture of cardiomyopathies. Such data hold the promise that mutation-specific pathophysiology will uncover novel therapeutic targets, and herald the beginning of precision therapy for cardiomyopathy patients. PMID:28007147

Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design

NASA Astrophysics Data System (ADS)

Sheng, Chunquan; Ji, Haitao; Miao, Zhenyuan; Che, Xiaoyin; Yao, Jianzhong; Wang, Wenya; Dong, Guoqiang; Guo, Wei; Lü, Jiaguo; Zhang, Wannian

2009-06-01

Myristoyl-CoA:protein N-myristoyltransferase (NMT) is a cytosolic monomeric enzyme that catalyzes the transfer of the myristoyl group from myristoyl-CoA to the N-terminal glycine of a number of eukaryotic cellular and viral proteins. Recent experimental data suggest NMT from parasites could be a promising new target for the design of novel antiparasitic agents with new mode of action. However, the active site topology and inhibitor specificity of these enzymes remain unclear. In this study, three-dimensional models of NMT from Plasmodium falciparum (PfNMT), Leishmania major (LmNMT) and Trypanosoma brucei (TbNMT) were constructed on the basis of the crystal structures of fungal NMTs using homology modeling method. The models were further refined by energy minimization and molecular dynamics simulations. The active sites of PfNMT, LmNMT and TbNMT were characterized by multiple copy simultaneous search (MCSS). MCSS functional maps reveal that PfNMT, LmNMT and TbNMT share a similar active site topology, which is defined by two hydrophobic pockets, a hydrogen-bonding (HB) pocket, a negatively-charged HB pocket and a positively-charged HB pocket. Flexible docking approaches were then employed to dock known inhibitors into the active site of PfNMT. The binding mode, structure-activity relationships and selectivity of inhibitors were investigated in detail. From the results of molecular modeling, the active site architecture and certain key residues responsible for inhibitor binding were identified, which provided insights for the design of novel inhibitors of parasitic NMTs.

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

PubMed

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, M N V Prasad

2016-10-01

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Model confirmation in climate economics

PubMed Central

Millner, Antony; McDermott, Thomas K. J.

2016-01-01

Benefit–cost integrated assessment models (BC-IAMs) inform climate policy debates by quantifying the trade-offs between alternative greenhouse gas abatement options. They achieve this by coupling simplified models of the climate system to models of the global economy and the costs and benefits of climate policy. Although these models have provided valuable qualitative insights into the sensitivity of policy trade-offs to different ethical and empirical assumptions, they are increasingly being used to inform the selection of policies in the real world. To the extent that BC-IAMs are used as inputs to policy selection, our confidence in their quantitative outputs must depend on the empirical validity of their modeling assumptions. We have a degree of confidence in climate models both because they have been tested on historical data in hindcasting experiments and because the physical principles they are based on have been empirically confirmed in closely related applications. By contrast, the economic components of BC-IAMs often rely on untestable scenarios, or on structural models that are comparatively untested on relevant time scales. Where possible, an approach to model confirmation similar to that used in climate science could help to build confidence in the economic components of BC-IAMs, or focus attention on which components might need refinement for policy applications. We illustrate the potential benefits of model confirmation exercises by performing a long-run hindcasting experiment with one of the leading BC-IAMs. We show that its model of long-run economic growth—one of its most important economic components—had questionable predictive power over the 20th century. PMID:27432964

Utility of AIRS Retrievals for Climate Studies

NASA Technical Reports Server (NTRS)

Molnar, Guyla I.; Susskind, Joel

2007-01-01

Satellites provide an ideal platform to study the Earth-atmosphere system on practically all spatial and temporal scales. Thus, one may expect that their rapidly growing datasets could provide crucial insights not only for short-term weather processes/predictions but into ongoing and future climate change processes as well. Though Earth-observing satellites have been around for decades, extracting climatically reliable information from their widely varying datasets faces rather formidable challenges. AIRS/AMSU is a state of the art infrared/microwave sounding system that was launched on the EOS Aqua platform on May 4, 2002, and has been providing operational quality measurements since September 2002. In addition to temperature and atmospheric constituent profiles, outgoing longwave radiation and basic cloud parameters are also derived from the AIRS/AMSU observations. However, so far the AIRS products have not been rigorously evaluated and/or validated on a large scale. Here we present preliminary assessments of monthly and 8-day mean AIRS "Version 4.0" retrieved products (available to the public through the DAAC at NASA/GSFC) to assess their utility for climate studies. First we present "consistency checks" by evaluating the time series of means, and "anomalies" (relative to the first 4 full years' worth of AIRS "climate statistics") of several climatically important retrieved parameters. Finally, we also present preliminary results regarding interrelationships of some of these geophysical variables, to assess to what extent they are consistent with the known physics of climate variability/change. In particular, we find at least one observed relationship which contradicts current general circulation climate (GCM) model results: the global water vapor climate feedback which is expected to be strongly positive is deduced to be slightly negative (shades of the "Lindzen effect"?). Though the current AIRS climatology covers only -4.5 years, it will hopefully extend much

The climate change and energy security nexus

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, Marcus Dubois; Gulledge, Jay

2013-01-01

The study of the impacts of climate change on national and interna-tional security has grown as a research field, particularly in the last five years. Within this broad field, academic scholarship has concentrated primarily on whether climate change is, or may become, a driver of violent conflict. This relationship remains highly contested. However, national security policy and many non-governmental organizations have identified climate change as a threat multiplier in conflict situations. The U.S. Department of Defense and the United Kingdom's Ministry of Defense have incorporated these findings into strategic planning documents such as the Quadrennial Defense Review and the Strategicmore » Defence and Security Review. In contrast to the climate-conflict nexus, our analysis found that academic scholarship on the climate change and energy security nexus is small and more disciplinarily focused. In fact, a search of social science litera-ture found few sources, with a significant percentage of these works attribut-able to a single journal. Assuming that policymakers are more likely to rely on broader social science literature than technical or scientific journals, this leaves a limited foundation. This then begged the question: what are these sources? We identified a body of grey literature on the nexus of climate change and energy security of a greater size than the body of peer-reviewed social science literature. We reviewed fifty-eight recent reports, issue briefs, and transcripts to better understand the nexus of climate change and energy security, as well as to gain insight about the questions policymakers need answered by those undertaking the research. In this article, we describe the nature of the sources reviewed, highlight possible climate change and energy security linkages found within those sources, identify emerging risks, and offer conclusions that can guide further research.« less

The adaptation of polar fishes to climatic changes: Structure, function and phylogeny of haemoglobin.

PubMed

Verde, Cinzia; Giordano, Daniela; di Prisco, Guido

2008-01-01

In the Antarctic, fishes of dominant suborder Notothenioidei have evolved in a unique thermal scenario. Phylogenetically related taxa of the suborder live in a wide range of latitudes, in Antarctic, sub-Antarctic and temperate oceans. Consequently, they offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history. The evolutionary perspective has also been pursued by comparative studies of some features of the heme protein devoted to O(2) transport in fish living in the other polar region, the Arctic. The two polar regions differ by age and isolation. Fish living in each habitat have undergone regional constraints and fit into different evolutionary histories. The aim of this contribution is to survey the current knowledge of molecular structure, functional features, phylogeny and adaptations of the haemoglobins of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes), in search of insights into the convergent processes evolved in response to cooling. Current climate change may disturb adaptation, calling for strategies aimed at neutralising threats to biodiversity.

DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations.

PubMed

Boehm, Belinda J; Whidborne, Charles; Button, Alexander L; Pukala, Tara L; Huang, David M

2018-05-23

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes. The ability of molecular simulations in explicit solvent to accurately capture triplex thermodynamics is verified for the first time, with the free energy to dissociate a 15-base antiparallel purine triplex-forming oligomer (TFO) from the duplex found to be slightly higher than reported experimentally. The presence of netropsin in the minor groove destabilises the triplex as expected, reducing the dissociation free energy by approximately 50%. Netropsin binding is associated with localised narrowing of the minor groove near netropsin, an effect that has previously been under contention. This leads to localised widening of the major groove, weakening hydrogen bonds between the TFO and duplex. Consequently, destabilisation is found to be highly localised, occurring only when netropsin is bound directly opposite the TFO. The simulations also suggest that near saturation of the minor groove with ligand is required for complete triplex dissociation. A structural analysis of the DNA triplexes that can form with the FRDA-related duplex sequence indicates that the triplex with a parallel homopyrimidine TFO is likely to be more stable than the antiparallel homopurine-TFO triplex, which may have implications for disease onset and treatment.

Insights into H2 formation in space from ab initio molecular dynamics

PubMed Central

Casolo, Simone; Tantardini, Gian Franco; Martinazzo, Rocco

2013-01-01

Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley–Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley–Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account. PMID:23572584

Mandate for the Nursing Profession to Address Climate Change Through Nursing Education.

PubMed

Leffers, Jeanne; Levy, Ruth McDermott; Nicholas, Patrice K; Sweeney, Casey F

2017-11-01

The adverse health effects from climate change demand action from the nursing profession. This article examines the calls to action, the status of climate change in nursing education, and challenges and recommendations for nursing education related to climate change and human health. Discussion paper. The integration of climate change into nursing education is essential so that knowledge, skills, and insights critical for clinical practice in our climate-changing world are incorporated in curricula, practice, research, and policy. Our Ecological Planetary Health Model offers a framework for nursing to integrate relevant climate change education into nursing curricula and professional nursing education. Nursing education can offer a leadership role to address the mitigation, adaptation, and resilience strategies for climate change. An ecological framework is valuable for nursing education regarding climate change through its consideration of political, cultural, economic, and environmental interrelationships on human health and the health of the planet. Knowledge of climate change is important for integration into basic and advanced nursing education, as well as professional education for nurses to address adverse health impacts, climate change responses policy, and advocacy roles. For current and future nurses to provide care within a climate-changing environment, nursing education has a mandate to integrate knowledge about climate change issues across all levels of nursing education. Competence in nursing practice follows from knowledge and skill acquisition gained from integration of climate change content into nursing education. © 2017 Sigma Theta Tau International.

Combined terrestrial and marine biomarker records from an Icelandic fjord: insights into Holocene climate drivers and marine/ terrestrial responses

NASA Astrophysics Data System (ADS)

Moossen, H. M.; Seki, O.; Quillmann, U.; Andrews, J. T.; Bendle, J. A.

2012-12-01

Holocene climate change has affected human cultures throughout at least the last 4000 years (D'Andrea et al., 2011). Today, studying Holocene climate variability is important, both to constrain the influence of climate change on ancient cultures and to place contemporary climate change in a historic context. Organic geochemical biomarkers are an ideal tool to study how climatic changes have affected terrestrial and marine ecosystems, as a host of different biomarker based climate proxies have emerged over recent years. Applying the available biomarker proxies on sediment cores from fjordic environments facilitates the study of how climate has affected terrestrial and marine ecosystems, and how these ecosystems have interacted. Ìsafjardardjúp fjord in Northwest Iceland is an ideal location to study North Atlantic Holocene climate change because the area is very sensitive to changes in the oceanic and atmospheric current systems (Hurrell, 1995; Quillmann et al., 2010). In this study we present high resolution (1 sample/30 calibrated years) terrestrial and marine biomarker records from a 38 m sediment core from Ìsafjardardjúp fjord covering the Holocene. We reconstruct sea surface temperature variations using the alkenone derived UK'37 proxy. Air temperature changes are reconstructed using the GDGT derived MBT/CBT palaeothermometer. We use the average chain length (ACL) variability of n-alkanes derived from terrestrial higher plant leaf waxes to reconstruct changing precipitation regimes. The relationship between ACL and precipitation is confirmed by comparing it with the δD signature of the C29 n-alkane and soil pH changes inferred by the CBT proxy. The combined sea surface and air temperature and precipitation records indicate that different climate changing drivers were dominant at different stages of the Holocene. Sea surface temperatures were strongly influenced by the melting of the remaining glaciers from the last glacial maximum throughout the early

Environmental Forensics: Molecular Insight into Oil Spill Weathering Helps Advance High Magnetic Field FT-ICR Mass Spectrometry

NASA Astrophysics Data System (ADS)

McKenna, Amy

2013-03-01

events in the FT-ICR experiment. For example, the high density of peaks at each nominal mass unit provides unprecedented insight into how excitation conditions affect ion motion during detection. Aggregated oil (i.e., tar balls, tar mats) that reached the surface exhibits a more than two-fold increase in the total number of detected species, with an increased number of oxygenated species. Principal component analysis (PCA) applied to two possible source oils (contained within the same ship) and weathered samples provide the first application of FT-ICR MS for source identification. Molecular formulae from parent and weathered oil indicate that the lightest petroleum fractions (saturated hydrocarbons) are the most readily oxidized components, and can serve as a template to determine chemical transformations that occur throughout the water column. The ability to differentiate and catalogue compositional changes that occur to oil after its release into the environment relies heavily on gains achieved in nearly all steps in the FT-ICR mass spectral experiment required to accommodate larger ion populations inherent to heavily weathered crude oil. Here, we present the requirement for FT-ICR MS for comprehensive oil spill characterization, and highlight advances made to FT-ICR MS experimental conditions developed from petroleum characterization. Work supported by DMR-06-54118, NSF CHE-10-49753 (RAPID), BP/The Gulf of Mexico Research Initiative, and the State of Florida

Climate change and elevated extinction rates of reptiles from Mediterranean Islands.

PubMed

Foufopoulos, Johannes; Kilpatrick, A Marm; Ives, Anthony R

2011-01-01

Recent climate change has caused the distributions of many species to shift poleward, yet few empirical studies have addressed which species will be vulnerable to longer-term climate changes. To investigate past consequences of climate change, we calculated the population extinction rates of 35 reptile species from 87 Greek land-bridge islands in the Mediterranean that occurred over the past 16,000 years. Population extinction rates were higher for those species that today have more northern distributions. We further found that northern species requiring cool, mesic habitats had less available suitable habitat among islands, implicating loss of suitable habitat in their elevated extinction rates. These extinctions occurred in the context of increasing habitat fragmentation, with islands shrinking and separating as sea levels rose. Thus, the circumstances faced by reptiles on the islands are similar to challenges for numerous species today that must cope with a changing climate while living in an increasingly human-fragmented landscape. Our island-biogeographical approach to investigating historical population extinctions gives insight into the long-term patterns of species responses to climate change.

Analyzing the Response of Climate Perturbations to (Tropical) Cyclones using the WRF Model

NASA Astrophysics Data System (ADS)

Tewari, M.; Mittal, R.; Radhakrishnan, C.; Cipriani, J.; Watson, C.

2015-12-01

An analysis of global climate models shows considerable changes in the intensity and characteristics of future, warm climate cyclones. At regional scales, deviations in cyclone characteristics are often derived using idealized perturbations in the humidity, temperature and surface conditions. In this work, a more realistic approach is adopted by applying climate perturbations from the Community Climate System Model (CCSM4) to ERA-interim data to generate the initial and boundary conditions for future climate simulations. The climate signal perturbations are generated from the differences in 21 years of mean data from CCSM4 with representative concentration pathways (RCP8.5) for the periods: (a) 2070-2090 (future climate), (b) 2025-2045 (near-future climate) and (c) 1985-2005 (current climate). Four individual cyclone cases are simulated with and without climate perturbations using the Weather Research and Forecasting model with a nested configuration. Each cyclone is characterized by variations in intensity, landfall location, precipitation and societal damage. To calculate societal damage, we use the recently introduced Cyclone Damage Potential (CDP) index evolved from the Willis Hurricane Index (WHI). As CDP has been developed for general societal applications, this work should provide useful insights for resilience analyses and industry (e.g., re-insurance).

EFFECTS OF CLIMATE CHANGE ON LABILE AND STRUCTURAL CARBON IN DOUGLAS-FIR NEEDLES AS ESTIMATED BY DELTA 13C AND C AREA MEASUREMENTS

EPA Science Inventory

Isotopic measurements may provide new insights into levels in leaves of labile and structural carbon (C) under climate change. In a 4-year climate change experiment using Pseudotsuga menziesii (Douglas-fir) seedlings and a 2x2 factorial design in enclosed chambers (n=3), atmosph...

Cluster-based analysis of multi-model climate ensembles

NASA Astrophysics Data System (ADS)

Hyde, Richard; Hossaini, Ryan; Leeson, Amber A.

2018-06-01

Clustering - the automated grouping of similar data - can provide powerful and unique insight into large and complex data sets, in a fast and computationally efficient manner. While clustering has been used in a variety of fields (from medical image processing to economics), its application within atmospheric science has been fairly limited to date, and the potential benefits of the application of advanced clustering techniques to climate data (both model output and observations) has yet to be fully realised. In this paper, we explore the specific application of clustering to a multi-model climate ensemble. We hypothesise that clustering techniques can provide (a) a flexible, data-driven method of testing model-observation agreement and (b) a mechanism with which to identify model development priorities. We focus our analysis on chemistry-climate model (CCM) output of tropospheric ozone - an important greenhouse gas - from the recent Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP). Tropospheric column ozone from the ACCMIP ensemble was clustered using the Data Density based Clustering (DDC) algorithm. We find that a multi-model mean (MMM) calculated using members of the most-populous cluster identified at each location offers a reduction of up to ˜ 20 % in the global absolute mean bias between the MMM and an observed satellite-based tropospheric ozone climatology, with respect to a simple, all-model MMM. On a spatial basis, the bias is reduced at ˜ 62 % of all locations, with the largest bias reductions occurring in the Northern Hemisphere - where ozone concentrations are relatively large. However, the bias is unchanged at 9 % of all locations and increases at 29 %, particularly in the Southern Hemisphere. The latter demonstrates that although cluster-based subsampling acts to remove outlier model data, such data may in fact be closer to observed values in some locations. We further demonstrate that clustering can provide a viable and

Comparative proteomics lends insight into genotype-specific pathogenicity.

PubMed

Guarnieri, Michael T

2013-09-01

Comparative proteomic analyses have emerged as a powerful tool for the identification of unique biomarkers and mechanisms of pathogenesis. In this issue of Proteomics, Murugaiyan et al. utilize difference gel electrophoresis (DIGE) to examine differential protein expression between nonpathogenic and pathogenic genotypes of Prototheca zopfii, a causative agent in bovine enteritis and mastitis. Their findings provide insights into molecular mechanisms of infection and evolutionary adaptation of pathogenic genotypes, demonstrating the power of comparative proteomic analyses. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Repeated short climatic change affects the epidermal differentiation program and leads to matrix remodeling in a human organotypic skin model.

PubMed

Boutrand, Laetitia-Barbollat; Thépot, Amélie; Muther, Charlotte; Boher, Aurélie; Robic, Julie; Guéré, Christelle; Vié, Katell; Damour, Odile; Lamartine, Jérôme

2017-01-01

Human skin is subject to frequent changes in ambient temperature and humidity and needs to cope with these environmental modifications. To decipher the molecular response of human skin to repeated climatic change, a versatile model of skin equivalent subject to "hot-wet" (40°C, 80% relative humidity [RH]) or "cold-dry" (10°C, 40% RH) climatic stress repeated daily was used. To obtain an exhaustive view of the molecular mechanisms elicited by climatic change, large-scale gene expression DNA microarray analysis was performed and modulated function was determined by bioinformatic annotation. This analysis revealed several functions, including epidermal differentiation and extracellular matrix, impacted by repeated variations in climatic conditions. Some of these molecular changes were confirmed by histological examination and protein expression. Both treatments (hot-wet and cold-dry) reduced the expression of genes encoding collagens, laminin, and proteoglycans, suggesting a profound remodeling of the extracellular matrix. Strong induction of the entire family of late cornified envelope genes after cold-dry exposure, confirmed at protein level, was also observed. These changes correlated with an increase in epidermal differentiation markers such as corneodesmosin and a thickening of the stratum corneum, indicating possible implementation of defense mechanisms against dehydration. This study for the first time reveals the complex pattern of molecular response allowing adaption of human skin to repeated change in its climatic environment.

A 50,000 year insect record from Rancho La Brea, Southern California: Insights into past climate and fossil deposition

NASA Astrophysics Data System (ADS)

Holden, Anna R.; Southon, John R.; Will, Kipling; Kirby, Matthew E.; Aalbu, Rolf L.; Markey, Molly J.

2017-07-01

Rigorously studied and dated Late Quaternary paleoenvironmental reconstructions from Ranch La Brea (RLB) and the Los Angeles Basin are scarce. Here, we use data from AMS radiocarbon dated insect fragments to infer local climates over the past 50,000 years. Our results indicate: 1) Quaternary insect remains can be located with great accuracy in radiocarbon time, and 2) well-dated and documented climate indicator beetle species are sensitive proxies for environmental change in the Los Angeles Basin. A total of 182 extant RLB ground and darkling beetle species (Coleoptera: Carabidae, Tenebrionidae) were radiocarbon dated. The resulting radiocarbon dates form a semi-continuous range from ∼50 to 28, 16-7.5, and 4 kcal yrs BP to the present. Associated insect climate ranges indicate past conditions consistent with, or very similar to, the current Los Angeles Basin Mediterranean climate. Importantly, these insect data suggest higher temperatures and aridity than inferred previously from other RLB proxies. Furthermore, wider-than-assumed dating spreads for some deposits emphasize the lack of biostratigraphy for RLB, and challenge inferences based on limited sets of radiocarbon dates and assumptions about stratigraphic integrity. Our results demonstrate the necessity to independently radiocarbon date each taxon. The insect paleoclimate interpretations were compared to regional pollen data, primarily from various southern Californian sites including Lake Elsinore and Santa Barbara Basin. These comparisons reveal an important difference in climate interpretations for the last Glacial: the RLB insect data suggest climate similar to the current one, while the regional pollen data have been interpreted as indicating a climate wetter than present.

The predictive validity of safety climate.

PubMed

Johnson, Stephen E

2007-01-01

Safety professionals have increasingly turned their attention to social science for insight into the causation of industrial accidents. One social construct, safety climate, has been examined by several researchers [Cooper, M. D., & Phillips, R. A. (2004). Exploratory analysis of the safety climate and safety behavior relationship. Journal of Safety Research, 35(5), 497-512; Gillen, M., Baltz, D., Gassel, M., Kirsch, L., & Vacarro, D. (2002). Perceived safety climate, job Demands, and coworker support among union and nonunion injured construction workers. Journal of Safety Research, 33(1), 33-51; Neal, A., & Griffin, M. A. (2002). Safety climate and safety behaviour. Australian Journal of Management, 27, 66-76; Zohar, D. (2000). A group-level model of safety climate: Testing the effect of group climate on microaccidents in manufacturing jobs. Journal of Applied Psychology, 85(4), 587-596; Zohar, D., & Luria, G. (2005). A multilevel model of safety climate: Cross-level relationships between organization and group-level climates. Journal of Applied Psychology, 90(4), 616-628] who have documented its importance as a factor explaining the variation of safety-related outcomes (e.g., behavior, accidents). Researchers have developed instruments for measuring safety climate and have established some degree of psychometric reliability and validity. The problem, however, is that predictive validity has not been firmly established, which reduces the credibility of safety climate as a meaningful social construct. The research described in this article addresses this problem and provides additional support for safety climate as a viable construct and as a predictive indicator of safety-related outcomes. This study used 292 employees at three locations of a heavy manufacturing organization to complete the 16 item Zohar Safety Climate Questionnaire (ZSCQ) [Zohar, D., & Luria, G. (2005). A multilevel model of safety climate: Cross-level relationships between organization and group

Results of the 2004 Marine Corps Climate Surveys (MCCS): Management Report

DTIC Science & Technology

2006-11-01

of Different Racial/Ethnic Backgrounds Socialize Together During Command Functions...organizational climate of the Marine Corps, equal opportunity and related issues such as sexual harassment and gender discrimination. Responses to the Marine...type of survey, the Marine Corps is able to gain insights into trends occurring in the equal opportunity and sexual harassment areas. The Marine

Local oceanographic variability influences the performance of juvenile abalone under climate change.

PubMed

Boch, C A; Micheli, F; AlNajjar, M; Monismith, S G; Beers, J M; Bonilla, J C; Espinoza, A M; Vazquez-Vera, L; Woodson, C B

2018-04-03

Climate change is causing warming, deoxygenation, and acidification of the global ocean. However, manifestation of climate change may vary at local scales due to oceanographic conditions. Variation in stressors, such as high temperature and low oxygen, at local scales may lead to variable biological responses and spatial refuges from climate impacts. We conducted outplant experiments at two locations separated by ~2.5 km and two sites at each location separated by ~200 m in the nearshore of Isla Natividad, Mexico to assess how local ocean conditions (warming and hypoxia) may affect juvenile abalone performance. Here, we show that abalone growth and mortality mapped to variability in stress exposure across sites and locations. These insights indicate that management decisions aimed at maintaining and recovering valuable marine species in the face of climate change need to be informed by local variability in environmental conditions.

Unpuzzling American Climate: New World Experience and the Foundations of a New Science.

PubMed

White, Sam

2015-09-01

In the early exploration and colonization of the Americas, Europeans encountered unfamiliar climates that challenged received ideas from classical geography. This experience drove innovative efforts to understand and explain patterns of weather and seasons in the New World. A close examination of three climatic puzzles (the habitability of the tropics, debates on the likelihood of a Northwest Passage, and the unexpectedly harsh weather in the first North American colonies) illustrates how sixteenth- and seventeenth-century observers made three intellectual breakthroughs: conceiving of climates as a distinct subject of inquiry, crossing the hitherto-separated disciplines of geography and meteorology, and developing new theories regarding the influence of prevailing winds on patterns of weather and seasons. While unquantified and unsystematic, these novel approaches promoted a new understanding of climates critical to the emergence of climate science. This study offers new insights into the foundations of climatology and the role of the New World in early modern science.

Insights on drought and long-term climatic trends: Retrospective analyses of crop insurance data

USDA-ARS?s Scientific Manuscript database

A modern trend among federal agencies, funding streams, and research projects involves the synthesis of existing data to increase the overall collective value and meaning of such knowledge. The creation of the U.S. Department of Agriculture (USDA) Climate Hubs follows this line of thought with infor...

The Green Sahara: Climate Change, Hydrologic History and Human Occupation

NASA Technical Reports Server (NTRS)

Blom, Ronald G.; Farr, Tom G.; Feynmann, Joan; Ruzmaikin, Alexander; Paillou, Philippe

2009-01-01

Archaeology can provide insight into interactions of climate change and human activities in sensitive areas such as the Sahara, to the benefit of both disciplines. Such analyses can help set bounds on climate change projections, perhaps identify elements of tipping points, and provide constraints on models. The opportunity exists to more precisely constrain the relationship of natural solar and climate interactions, improving understanding of present and future anthropogenic forcing. We are beginning to explore the relationship of human occupation of the Sahara and long-term solar irradiance variations synergetic with changes in atmospheric-ocean circulation patterns. Archaeological and climate records for the last 12 K years are gaining adequate precision to make such comparisons possible. We employ a range of climate records taken over the globe (e.g. Antarctica, Greenland, Cariaco Basin, West African Ocean cores, records from caves) to identify the timing and spatial patterns affecting Saharan climate to compare with archaeological records. We see correlation in changing ocean temperature patterns approx. contemporaneous with drying of the Sahara approx. 6K years BP. The role of radar images and other remote sensing in this work includes providing a geographically comprehensive geomorphic overview of this key area. Such coverage is becoming available from the Japanese PALSAR radar system, which can guide field work to collect archaeological and climatic data to further constrain the climate change chronology and link to models. Our initial remote sensing efforts concentrate on the Gilf Kebir area of Egypt.

Preventing iron(ii) precipitation in aqueous systems using polyacrylic acid: some molecular insights.

PubMed

Artola, Pierre-Arnaud; Rousseau, Bernard; Clavaguéra, Carine; Roy, Marion; You, Dominique; Plancque, Gabriel

2018-06-22

We present molecular dynamics simulations of aqueous iron(ii) systems in the presence of polyacrylic acid (PAA) under the extreme conditions that take place in the secondary coolant circuit of a nuclear power plant. The aim of this work is to understand how the oligomer can prevent iron(ii) deposits, and to provide molecular interpretation. We show how, to this end, not only the complexant ability is necessary, but also the chain length compared to iron(ii) concentration. When the chain is long enough, a hyper-complexation phenomenon occurs that can explain the specific capacity of the polymer to prevent iron(ii) precipitation.

A complex relationship between calving glaciers and climate

USGS Publications Warehouse

Post, A.; O'Neel, S.; Motyka, R.J.; Streveler, G.

2011-01-01

Many terrestrial glaciers are sensitive indicators of past and present climate change as atmospheric temperature and snowfall modulate glacier volume. However, climate interpretations based on glacier behavior require careful selection of representative glaciers, as was recently pointed out for surging and debris-covered glaciers, whose behavior often defies regional glacier response to climate [Yde and Paasche, 2010]. Tidewater calving glaciers (TWGs)mountain glaciers whose termini reach the sea and are generally grounded on the seaflooralso fall into the category of non-representative glaciers because the regional-scale asynchronous behavior of these glaciers clouds their complex relationship with climate. TWGs span the globe; they can be found both fringing ice sheets and in high-latitude regions of each hemisphere. TWGs are known to exhibit cyclic behavior, characterized by slow advance and rapid, unstable retreat, largely independent of short-term climate forcing. This so-called TWG cycle, first described by Post [1975], provides a solid foundation upon which modern investigations of TWG stability are built. Scientific understanding has developed rapidly as a result of the initial recognition of their asynchronous cyclicity, rendering greater insight into the hierarchy of processes controlling regional behavior. This has improved the descriptions of the strong dynamic feedbacks present during retreat, the role of the ocean in TWG dynamics, and the similarities and differences between TWG and ice sheet outlet glaciers that can often support floating tongues.

Role of internal motions and molecular geometry on the NMR relaxation of hydrocarbons

NASA Astrophysics Data System (ADS)

Singer, P. M.; Asthagiri, D.; Chen, Z.; Valiya Parambathu, A.; Hirasaki, G. J.; Chapman, W. G.

2018-04-01

The role of internal motions and molecular geometry on 1H NMR relaxation rates in liquid-state hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for intramolecular and intermolecular 1H-1H dipole-dipole interactions. The effects of molecular geometry and internal motions on the functional form of the autocorrelation functions are studied by comparing symmetric molecules such as neopentane and benzene to corresponding straight-chain alkanes n-pentane and n-hexane, respectively. Comparison of rigid versus flexible molecules shows that internal motions cause the intramolecular and intermolecular correlation-times to get significantly shorter, and the corresponding relaxation rates to get significantly smaller, especially for longer-chain n-alkanes. Site-by-site simulations of 1H's across the chains indicate significant variations in correlation times and relaxation rates across the molecule, and comparison with measurements reveals insights into cross-relaxation effects. Furthermore, the simulations reveal new insights into the relative strength of intramolecular versus intermolecular relaxation as a function of internal motions, as a function of molecular geometry, and on a site-by-site basis across the chain.

Lipid Interaction Sites on Channels, Transporters and Receptors: Recent Insights from Molecular Dynamics Simulations

PubMed Central

Hedger, George; Sansom, Mark S. P.

2017-01-01

Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterisation of these sites is of importance for our understanding of the molecular basis of membrane protein function and stability, and may facilitate the design of lipid-like drug molecules. Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics. We describe recent notable biomolecular simulation studies which have identified lipid interaction sites on a range of different membrane proteins. The sites identified in these simulation studies agree well with those identified by complementary experimental techniques. This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins. PMID:26946244

Public Engagement on Climate Change

NASA Astrophysics Data System (ADS)

Curry, J.

2011-12-01

Climate change communication is complicated by complexity of the scientific problem, multiple perspectives on the magnitude of the risk from climate change, often acrimonious disputes between scientists, high stakes policy options, and overall politicization of the issue. Efforts to increase science literacy as a route towards persuasion around the need for a policy like cap and trade have failed, because the difficulty that a scientist has in attempting to make sense of the social and political complexity is very similar to the complexity facing the general public as they try to make sense of climate science itself. In this talk I argue for a shift from scientists and their institutions as information disseminators to that of public engagement and enablers of public participation. The goal of engagement is not just to inform, but to enable, motivate and educate the public regarding the technical, political, and social dimensions of climate change. Engagement is a two-way process where experts and decision-makers seek input and learn from the public about preferences, needs, insights, and ideas relative to climate change impacts, vulnerabilities, solutions and policy options. Effective public engagement requires that scientists detach themselves from trying to control what the public does with the acquired knowledge and motivation. The goal should not be to "sell" the public on particular climate change solutions, since such advocacy threatens public trust in scientists and their institutions. Conduits for public engagement include the civic engagement approach in the context of community meetings, and perhaps more significantly, the blogosphere. Since 2006, I have been an active participant in the climate blogosphere, focused on engaging with people that are skeptical of AGW. A year ago, I started my own blog Climate Etc. at judithcurry.com. The demographic that I have focused my communication/engagement activities are the technically educated and scientifically

Solar variability, coupling between atmospheric layers and climate change.