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Sample records for climate molecular insights

  1. 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

  2. Vitamin D and Adipogenesis: New Molecular Insights

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The focus of the current review is to highlight some new insights into the molecular mechanism by which vitamin D, a potentially nutritionally modulated factor, influences adipogenesis. Recent studies, predominantly using the mouse 3T3-L1 pre-adipocyte cell culture model, have shown that the role of...

  3. Molecular insights into intracellular RNA localization

    PubMed Central

    Blower, Michael D.

    2013-01-01

    Localization of mRNAs to specific destinations within a cell or an embryo is important for local control of protein expression. mRNA localization is well-known to function in very large and polarized cells such as neurons, and to facilitate embryonic patterning during early development. However, recent genome-wide studies have revealed that mRNA localization is more widely utilized than previously thought to control gene expression. Not only can transcripts be localized asymmetrically within the cytoplasm, they are often also localized to symmetrically-distributed organelles. Recent genetic, cytological, and biochemical studies have begun to provide molecular insight into how cells select RNAs for transport, move them to specific destinations, and control their translation. This review will summarize recent insights into the mechanisms and function of RNA localization with a specific emphasis on molecular insights into each step in the mRNA localization process. PMID:23351709

  4. Monoamine transporters: insights from molecular dynamics simulations

    PubMed Central

    Grouleff, Julie; Ladefoged, Lucy Kate; Koldsø, Heidi; Schiøtt, Birgit

    2015-01-01

    The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson’s disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na+ symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors. PMID:26528185

  5. Molecular Epidemiology of Tuberculosis: Current Insights

    PubMed Central

    Mathema, Barun; Kurepina, Natalia E.; Bifani, Pablo J.; Kreiswirth, Barry N.

    2006-01-01

    Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB. PMID:17041139

  6. Haemophilia A and haemophilia B: molecular insights

    PubMed Central

    Bowen, D J

    2002-01-01

    This review focuses on selected areas that should interest both the scientist and the clinician alike: polymorphisms within the factor VIII and factor IX genes, their linkage, and their ethnic variation; a general assessment of mutations within both genes and a detailed inspection of the molecular pathology of certain mutations to illustrate the diverse cause–effect relations that exist; a summary of current knowledge on molecular aspects of inhibitor production; and an introduction to the new areas of factor VIII and factor IX catabolism. An appendix defining various terms encountered in the molecular genetics of the haemophilias is included, together with an appendix providing accession numbers and locus identification links for accessing gene and sequence information in the international nucleic acid databases. PMID:11836440

  7. Haemophilia A and haemophilia B: molecular insights

    PubMed Central

    Bowen, D J

    2002-01-01

    This review focuses on selected areas that should interest both the scientist and the clinician alike: polymorphisms within the factor VIII and factor IX genes, their linkage, and their ethnic variation; a general assessment of mutations within both genes and a detailed inspection of the molecular pathology of certain mutations to illustrate the diverse cause–effect relations that exist; a summary of current knowledge on molecular aspects of inhibitor production; and an introduction to the new areas of factor VIII and factor IX catabolism. An appendix defining various terms encountered in the molecular genetics of the haemophilias is included, together with an appendix providing accession numbers and locus identification links for accessing gene and sequence information in the international nucleic acid databases. PMID:11950963

  8. Combining Global Climate Model Outputs and Insights from Downscaling for Australian Climate Projections

    NASA Astrophysics Data System (ADS)

    Grose, M. R.; Timbal, B.; Katzfey, J. J.; Moise, A. F.; Eksrtrom, M.; Whetton, P.

    2013-12-01

    Dynamical and statistical downscaling of global climate model (GCM) outputs has the potential to provide valuable insights when making regional climate projections. It may reveal regional detail in the projected climate change signal through higher resolution and accounting for local influences such as topography and coastlines. However, climate change adaptation research and planning desires a coherent view of possible future climate that accounts for the various sources of uncertainty and at a relevant spatial scale. This means there is value in combining the most useful insights from all available downscaling with a more comprehensive set of designed global climate model (GCM) projections (e.g. the CMIP5 archive), and this is done for the next set of national climate projections products in Australia. There are several practical considerations in this process that affect the process, primarily because downscaling is done using various disparate methods for a limited set of models and scenarios. There is no objective framework to combine different sets of ad hoc downscaling simulations with a set of GCMs, so some degree of expert judgment is used. We emphasize cases where there is the most apparent ';added value' and report these insights in complement, and in some cases in preference to, GCM projections. Confidence in such insights first requires understanding of what input data is used from the host model, what biases are reduced and what new biases are potentially introduced. We then seek an understanding of how the climate change signal differs from that of the host model, and an attribution of the cause of this difference. Several case studies within Australia are discussed.

  9. 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.

  10. Hydropower licensing and climate change: Insights from cooperative game theory

    NASA Astrophysics Data System (ADS)

    Madani, Kaveh

    2011-02-01

    Cooperative game theory solutions can provide useful insights into how parties may use water and environmental resources and share any benefits of cooperation. Here, a method based on Nash and Nash-Harsanyi bargaining solutions is developed to explore the Federal Energy Regulatory Commission (FERC) relicensing process, in which owners of non-federal hydropower projects in the United States have to negotiate their allowable operations, with other interest groups (mainly environmental). Linkage of games to expand the feasible solution range and the "strategic loss" concept are discussed and a FERC relicensing bargaining model is developed for studying the bargaining stage (third stage) of the relicensing process. Based on the suggested solution method, how the lack of incentive for cooperation results in long delay in FERC relicensing in practice is explained. Further, potential effects of climate change on the FERC relicensing are presented and how climate change may provide an incentive for cooperation among the parties to hasten the relicensing is discussed. An "adaptive FERC license" framework is proposed, based on cooperative game theory, to improve the performance and adaptability of the system to future changes with no cost to the FERC, in face of uncertainty about future hydrological and ecological conditions.

  11. Molecular dynamics insights into human aquaporin 2 water channel.

    PubMed

    Binesh, A R; Kamali, R

    2015-12-01

    In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney. PMID:26489820

  12. Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations

    PubMed Central

    Elmore, Donald E.

    2012-01-01

    Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides. PMID:23022591

  13. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  14. New insight into the molecular control of bacterial functional amyloids

    PubMed Central

    Taylor, Jonathan D.; Matthews, Steve J.

    2015-01-01

    Amyloid protein structure has been discovered in a variety of functional or pathogenic contexts. What distinguishes the former from the latter is that functional amyloid systems possess dedicated molecular control systems that determine the timing, location, and structure of the fibers. Failure to guide this process can result in cytotoxicity, as observed in several pathologies like Alzheimer's and Parkinson's Disease. Many gram-negative bacteria produce an extracellular amyloid fiber known as curli via a multi-component secretion system. During this process, aggregation-prone, semi-folded curli subunits have to cross the periplasm and outer-membrane and self-assemble into surface-attached fibers. Two recent breakthroughs have provided molecular details regarding periplasmic chaperoning and subunit secretion. This review offers a combined perspective on these first mechanistic insights into the curli system. PMID:25905048

  15. Managing U.S. climate risk through mitigation: Insights from the American Climate Prospectus

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    The American Climate Prospectus (ACP), the technical analysis underlying the Risky Business project, quantitatively assessed the economic risks posed to the United States by six categories of climate change impacts: crop yield, energy demand, coastal storm damage, criminal activity, labor productivity, and mortality [1]. At a national level, measured by impact on gross domestic product, increased mortality and decreased labor productivity pose the large risks, followed by increased energy demand and coastal damages. Changes in crop yield and crime have smaller impacts. The ACP was not intended to conduct a benefit-cost analysis of climate change mitigation. It assessed the economic consequences of future impacts on an economy with a structure equivalent to that of the current economy, not accounting for socio-economic development and adaptation, and did not assess the cost of mitigation. One of its primary goals was to inform adaptation decisions that are conventionally considered 'endogenous' in economic analyses of climate change. Nonetheless, its results provide insight into the potential of mitigation to manage climate risk. Differences between RCP 8.5 (moderately-high business-as-usual emissions), RCP 4.5 (moderate mitigation) and RCP 2.6 (extremely strong mitigation) are not apparent until mid-century and become significant only late in the century. For all impacts except coastal damages, mitigation significantly reduces uncertainty in late-century impact estimates. Nationally, mitigation significantly and monotonically reduces median projected labor productivity losses and violent crime. Switching from RCP 8.5 to RCP 4.5 also significantly reduces median projections of mortality and energy demand, but the domestic value to the U.S. of further mitigation to RCP 2.6 is less clear. The marginal benefits decline in part because some regions of the country (especially the Northwest) may experience increased crop yields, reduced mortality, and reduced energy

  16. High Cholesterol Deteriorates Bone Health: New Insights into Molecular Mechanisms

    PubMed Central

    Mandal, Chandi C.

    2015-01-01

    Many epidemiological studies show a positive connection between cardiovascular diseases and risk of osteoporosis, suggesting a role of hyperlipidemia and/or hypercholesterolemia in regulating osteoporosis. The majority of the studies indicated a correlation between high cholesterol and high LDL-cholesterol level with low bone mineral density, a strong predictor of osteoporosis. Similarly, bone metastasis is a serious complication of cancer for patients. Several epidemiological and basic studies have established that high cholesterol is associated with increased cancer risk. Moreover, osteoporotic bone environment predisposes the cancer cells for metastatic growth in the bone microenvironment. This review focuses on how cholesterol and cholesterol-lowering drugs (statins) regulate the functions of bone residential osteoblast and osteoclast cells to augment or to prevent bone deterioration. Moreover, this study provides an insight into molecular mechanisms of cholesterol-mediated bone deterioration. It also proposes a potential mechanism by which cellular cholesterol boosts cancer-induced bone metastasis. PMID:26557105

  17. Recent insights into the molecular genetics of dementia

    PubMed Central

    Rademakers, Rosa; Rovelet-Lecrux, Anne

    2010-01-01

    Our understanding of the molecular genetic basis of two common neurodegenerative dementias, Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD) has greatly advanced in recent years. Progranulin mutations were identified as a major cause of FTLD and a potential susceptibility factor for other forms of dementia. In addition, through copy-number analyses of previously identified disease genes and the study of microRNA regulation in dementia, new evidence emerged to support the view that subtle variability in the expression of known disease proteins may increase the risk for sporadic forms of dementia. Finally, in late-onset AD populations, the first genome-wide association studies were performed and novel potential AD susceptibility genes reported. These exciting findings provide novel insights into the disease mechanisms underlying dementia and hold promise for the development of potential treatments. PMID:19640594

  18. Molecular insights into the terminal energy acceptor in cyanobacterial phycobilisome.

    PubMed

    Gao, Xiang; Wei, Tian-Di; Zhang, Nan; Xie, Bin-Bin; Su, Hai-Nan; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Wang, Zhi-Xin; Wu, Jia-Wei; Zhang, Yu-Zhong

    2012-09-01

    The linker protein L(CM) (ApcE) is postulated as the major component of the phycobilisome terminal energy acceptor (TEA) transferring excitation energy from the phycobilisome to photosystem II. L(CM) is the only phycobilin-attached linker protein in the cyanobacterial phycobilisome through auto-chromophorylation. However, the underlying mechanism for the auto-chromophorylation of L(CM) and the detailed molecular architecture of TEA is still unclear. Here, we demonstrate that the N-terminal phycobiliprotein-like domain of L(CM) (Pfam00502, LP502) can specifically recognize phycocyanobilin (PCB) by itself. Biochemical assays indicated that PCB binds into the same pocket in LP502 as that in the allophycocyanin α-subunit and that Ser152 and Asp155 play a vital role in LP502 auto-chromophorylation. By carefully conducting computational simulations, we arrived at a rational model of the PCB-LP502 complex structure that was supported by extensive mutational studies. In the PCB-LP502 complex, PCB binds into a deep pocket of LP502 with a distorted conformation, and Ser152 and Asp155 form several hydrogen bonds to PCB fixing the PCB Ring A and Ring D. Finally, based on our results, the dipoles and dipole-dipole interactions in TEA are analysed and a molecular structure for TEA is proposed, which gives new insights into the energy transformation mechanism of cyanobacterial phycobilisome. PMID:22758351

  19. 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. PMID:18310323

  20. Molecular insight into conformational transmission of human P-glycoprotein

    NASA Astrophysics Data System (ADS)

    Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

    2013-12-01

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp.

  1. Molecular insight into conformational transmission of human P-glycoprotein

    SciTech Connect

    Chang, Shan-Yan; Liu, Fu-Feng E-mail: ysun@tju.edu.cn; Dong, Xiao-Yan; Sun, Yan E-mail: ysun@tju.edu.cn

    2013-12-14

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp.

  2. Molecular Determinants of Magnesium Homeostasis: Insights from Human Disease

    PubMed Central

    Alexander, R. Todd; Hoenderop, Joost G.; Bindels, René J.

    2016-01-01

    The past decade has witnessed multiple advances in our understanding of magnesium (Mg2+) homeostasis. The discovery that mutations in claudin-16/paracellin-1 or claudin-19 are responsible for familial hypomagnesemia with hypercalciuria and nephrocalcinosis provided insight into the molecular mechanisms governing paracellular transport of Mg2+. Our understanding of the transcellular movement of Mg2+ was similarly enhanced by the realization that defects in transient receptor potential melastatin 6 (TRPM6) cause hypomagnesemia with secondary hypocalcemia. This channel regulates the apical entry of Mg2+ into epithelia. In so doing, TRPM6 alters whole-body Mg2+ homeostasis by controlling urinary excretion. Consequently, investigation into the regulation of TRPM6 has increased. Acid-base status, 17β estradiol, and the immunosuppressive agents FK506 and cyclosporine affect plasma Mg2+ levels by altering TRPM6 expression. A mutation in epithelial growth factor is responsible for isolated autosomal recessive hypomagnesemia, and epithelial growth factor activates TRPM6. A defect in the γ-subunit of the Na,K-ATPase causes isolated dominant hypomagnesemia by altering TRPM6 activity through a decrease in the driving force for apical Mg2+ influx. We anticipate that the next decade will provide further detail into the control of the gatekeeper TRPM6 and, therefore, overall whole-body Mg2+ balance. PMID:18562569

  3. Molecular Insights into the Biosynthesis of the F420 Coenzyme

    SciTech Connect

    Forouhar,F.; Abashidze, M.; Xu, H.; Grochowski, L.; Seetharaman, J.; Hussain, M.; Kuzin, A.; Chen, Y.; Zhou, W.; et al

    2008-01-01

    Coenzyme F420, a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F420-0 (F420 without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F420-producing organisms, and weak sequence homologs are also found in non-F420-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and Pi or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F420 coenzyme. Large structural differences in the active site region of the non-F420-producing CofD homologs suggest that they catalyze a different biochemical reaction.

  4. Molecular Characterization of the Endoplasmic Reticulum: insights from proteomic studies

    PubMed Central

    Chen, Xuequn; Karnovsky, Alla; Sans, Maria Dolors; Andrews, Philip C.; Williams, John A.

    2012-01-01

    The endoplasmic reticulum (ER) is a multifunctional intracellular organelle responsible for the synthesis, processing and trafficking of a wide variety of proteins essential for cell growth and survival. Thesefore, comprehensive characterization of the ER proteome is of great importance to the understanding of its functions and has been actively pursued in the past decade by scientists in the proteomics field. This review summarizes major proteomic studies published in the past decade that focused on the ER proteome. We evaluate the data sets obtained from two different organs, liver and pancreas each of which contains a primary cell type (hepatocyte and acinar cell) with specialized functions. We also discuss how the nature of the proteins uncovered is related to the methods of organelle purification, organelle purity and the techniques used for protein separation prior to mass spectrometry. In addition, this review also puts emphasis on the biological insights gained from these studies regarding to the molecular functions of the endoplasmic reticulum including protein synthesis and translocation, protein folding and quality control, ER-associated degradation and ER stress, ER export and membrane trafficking, calcium homeostasis, and detoxification and drug metabolism. PMID:21080494

  5. Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor

    PubMed Central

    Chantreau, Vanessa; Taddese, Bruck; Munier, Mathilde; Gourdin, Louis; Henrion, Daniel; Rodien, Patrice; Chabbert, Marie

    2015-01-01

    The thyrotropin receptor (TSHR) is a G protein-coupled receptor (GPCR) that is member of the leucine-rich repeat subfamily (LGR). In the absence of crystal structure, the success of rational design of ligands targeting the receptor internal cavity depends on the quality of the TSHR models built. In this subfamily, transmembrane helices (TM) 2 and 5 are characterized by the absence of proline compared to most receptors, raising the question of the structural conformation of these helices. To gain insight into the structural properties of these helices, we carried out bioinformatics and experimental studies. Evolutionary analysis of the LGR family revealed a deletion in TM5 but provided no information on TM2. Wild type residues at positions 2.58, 2.59 or 2.60 in TM2 and/or at position 5.50 in TM5 were substituted to proline. Depending on the position of the proline substitution, different effects were observed on membrane expression, glycosylation, constitutive cAMP activity and responses to thyrotropin. Only proline substitution at position 2.59 maintained complex glycosylation and high membrane expression, supporting occurrence of a bulged TM2. The TSHR transmembrane domain was modeled by homology with the orexin 2 receptor, using a protocol that forced the deletion of one residue in the TM5 bulge of the template. The stability of the model was assessed by molecular dynamics simulations. TM5 straightened during the equilibration phase and was stable for the remainder of the simulations. Our data support a structural model of the TSHR transmembrane domain with a bulged TM2 and a straight TM5 that is specific of glycoprotein hormone receptors. PMID:26545118

  6. New Molecular Insights of Insulin in Diabetic Cardiomyopathy.

    PubMed

    Westermeier, Francisco; Riquelme, Jaime A; Pavez, Mario; Garrido, Valeria; Díaz, Ariel; Verdejo, Hugo E; Castro, Pablo F; García, Lorena; Lavandero, Sergio

    2016-01-01

    Type 2 diabetes mellitus (T2DM) is a highly prevalent disease worldwide. Cardiovascular disorders generated as a consequence of T2DM are a major cause of death related to this disease. Diabetic cardiomyopathy (DCM) is characterized by the morphological, functional and metabolic changes in the heart produced as a complication of T2DM. This cardiac disorder is characterized by constant high blood glucose and lipids levels which eventually generate oxidative stress, defective calcium handling, altered mitochondrial function, inflammation and fibrosis. In this context, insulin is of paramount importance for cardiac contractility, growth and metabolism and therefore, an impaired insulin signaling plays a critical role in the DCM development. However, the exact pathophysiological mechanisms leading to DCM are still a matter of study. Despite the numerous questions raised in the study of DCM, there have also been important findings, such as the role of micro-RNAs (miRNAs), which can not only have the potential of being important biomarkers, but also therapeutic targets. Furthermore, exosomes also arise as an interesting variable to consider, since they represent an important inter-cellular communication mechanism and therefore, they may explain many aspects of the pathophysiology of DCM and their study may lead to the development of therapeutic agents capable of improving insulin signaling. In addition, adenosine and adenosine receptors (ARs) may also play an important role in DCM. Moreover, the possible cross-talk between insulin and ARs may provide new strategies to reverse its defective signaling in the diabetic heart. This review focuses on DCM, the role of insulin in this pathology and the discussion of new molecular insights which may help to understand its underlying mechanisms and generate possible new therapeutic strategies. PMID:27148064

  7. New Molecular Insights of Insulin in Diabetic Cardiomyopathy

    PubMed Central

    Westermeier, Francisco; Riquelme, Jaime A.; Pavez, Mario; Garrido, Valeria; Díaz, Ariel; Verdejo, Hugo E.; Castro, Pablo F.; García, Lorena; Lavandero, Sergio

    2016-01-01

    Type 2 diabetes mellitus (T2DM) is a highly prevalent disease worldwide. Cardiovascular disorders generated as a consequence of T2DM are a major cause of death related to this disease. Diabetic cardiomyopathy (DCM) is characterized by the morphological, functional and metabolic changes in the heart produced as a complication of T2DM. This cardiac disorder is characterized by constant high blood glucose and lipids levels which eventually generate oxidative stress, defective calcium handling, altered mitochondrial function, inflammation and fibrosis. In this context, insulin is of paramount importance for cardiac contractility, growth and metabolism and therefore, an impaired insulin signaling plays a critical role in the DCM development. However, the exact pathophysiological mechanisms leading to DCM are still a matter of study. Despite the numerous questions raised in the study of DCM, there have also been important findings, such as the role of micro-RNAs (miRNAs), which can not only have the potential of being important biomarkers, but also therapeutic targets. Furthermore, exosomes also arise as an interesting variable to consider, since they represent an important inter-cellular communication mechanism and therefore, they may explain many aspects of the pathophysiology of DCM and their study may lead to the development of therapeutic agents capable of improving insulin signaling. In addition, adenosine and adenosine receptors (ARs) may also play an important role in DCM. Moreover, the possible cross-talk between insulin and ARs may provide new strategies to reverse its defective signaling in the diabetic heart. This review focuses on DCM, the role of insulin in this pathology and the discussion of new molecular insights which may help to understand its underlying mechanisms and generate possible new therapeutic strategies. PMID:27148064

  8. Proteomic Insight into the Molecular Function of the Vitreous

    PubMed Central

    Skeie, Jessica M.; Roybal, C. Nathaniel; Mahajan, Vinit B.

    2015-01-01

    The human vitreous contains primarily water, but also contains proteins which have yet to be fully characterized. To gain insight into the four vitreous substructures and their potential functions, we isolated and analyzed the vitreous protein profiles of three non-diseased human eyes. The four analyzed substructures were the anterior hyaloid, the vitreous cortex, the vitreous core, and the vitreous base. Proteins were separated by multidimensional liquid chromatography and identified by tandem mass spectrometry. Bioinformatics tools then extracted the expression profiles, signaling pathways, and interactomes unique to each tissue. From each substructure, a mean of 2,062 unique proteins were identified, with many being differentially expressed in a specific substructure: 278 proteins were unique to the anterior hyaloid, 322 to the vitreous cortex, 128 to the vitreous base, and 136 to the vitreous core. When the identified proteins were organized according to relevant functional pathways and networks, key patterns appeared. The blood coagulation pathway and extracellular matrix turnover networks were highly represented. Oxidative stress regulation and energy metabolism proteins were distributed throughout the vitreous. Immune functions were represented by high levels of immunoglobulin, the complement pathway, damage-associated molecular patterns (DAMPs), and evolutionarily conserved antimicrobial proteins. The majority of vitreous proteins detected were intracellular proteins, some of which originate from the retina, including rhodopsin (RHO), phosphodiesterase 6 (PDE6), and glial fibrillary acidic protein (GFAP). This comprehensive analysis uncovers a picture of the vitreous as a biologically active tissue, where proteins localize to distinct substructures to protect the intraocular tissues from infection, oxidative stress, and energy disequilibrium. It also reveals the retina as a potential source of inflammatory mediators. The vitreous proteome catalogues the

  9. 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

  10. Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide.

    PubMed

    Li, Chun-Yang; Wei, Tian-Di; Zhang, Sheng-Hui; Chen, Xiu-Lan; Gao, Xiang; Wang, Peng; Xie, Bin-Bin; Su, Hai-Nan; Qin, Qi-Long; Zhang, Xi-Ying; Yu, Juan; Zhang, Hong-Hai; Zhou, Bai-Cheng; Yang, Gui-Peng; Zhang, Yu-Zhong

    2014-01-21

    The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn(2+) ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction. PMID:24395783

  11. Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide

    PubMed Central

    Li, Chun-Yang; Wei, Tian-Di; Zhang, Sheng-Hui; Chen, Xiu-Lan; Gao, Xiang; Wang, Peng; Xie, Bin-Bin; Su, Hai-Nan; Qin, Qi-Long; Zhang, Xi-Ying; Yu, Juan; Zhang, Hong-Hai; Zhou, Bai-Cheng; Yang, Gui-Peng; Zhang, Yu-Zhong

    2014-01-01

    The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn2+ ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between “open” and “closed” states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction. PMID:24395783

  12. Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide

    NASA Astrophysics Data System (ADS)

    Li, Chun-Yang; Wei, Tian-Di; Zhang, Sheng-Hui; Chen, Xiu-Lan; Gao, Xiang; Wang, Peng; Xie, Bin-Bin; Su, Hai-Nan; Qin, Qi-Long; Zhang, Xi-Ying; Yu, Juan; Zhang, Hong-Hai; Zhou, Bai-Cheng; Yang, Gui-Peng; Zhang, Yu-Zhong

    2014-01-01

    The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn2+ ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substrate-binding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.

  13. 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

  14. 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

  15. The PICS Climate Insights 101 Courses: A Visual Approach to Learning About Climate Science, Mitigation and Adaptation

    NASA Astrophysics Data System (ADS)

    Pedersen, T. F.; Zwiers, F. W.; Breen, C.; Murdock, T. Q.

    2014-12-01

    The Pacific Institute for Climate Solutions (PICS) has now made available online three free, peer-reviewed, unique animated short courses in a series entitled "Climate Insights 101" that respectively address basic climate science, carbon-emissions mitigation approaches and opportunities, and adaptation. The courses are suitable for students of all ages, and use professionally narrated animations designed to hold a viewer's attention. Multiple issues are covered, including complex concerns like the construction of general circulation models, carbon pricing schemes in various countries, and adaptation approaches in the face of extreme weather events. Clips will be shown in the presentation. The first course (Climate Science Basics) has now been seen by over two hundred thousand individuals in over 80 countries, despite being offered in English only. Each course takes about two hours to work through, and in recognizing that that duration might pose an attention barrier to some students, PICS selected a number of short clips from the climate-science course and posted them as independent snippets on YouTube. A companion series of YouTube videos entitled, "Clear The Air", was created to confront the major global-warming denier myths. But a major challenge remains: despite numerous efforts to promote the availability of the free courses and the shorter YouTube pieces, they have yet to become widely known. Strategies to overcome that constraint will be discussed.

  16. Molecular Insights into Crimean-Congo Hemorrhagic Fever Virus

    DOE PAGESBeta

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

  17. Insights from past millennia into climatic impacts on human health and survival.

    PubMed

    McMichael, Anthony J

    2012-03-27

    Climate change poses threats to human health, safety, and survival via weather extremes and climatic impacts on food yields, fresh water, infectious diseases, conflict, and displacement. Paradoxically, these risks to health are neither widely nor fully recognized. Historical experiences of diverse societies experiencing climatic changes, spanning multicentury to single-year duration, provide insights into population health vulnerability--even though most climatic changes were considerably less than those anticipated this century and beyond. Historical experience indicates the following. (i) Long-term climate changes have often destabilized civilizations, typically via food shortages, consequent hunger, disease, and unrest. (ii) Medium-term climatic adversity has frequently caused similar health, social, and sometimes political consequences. (iii) Infectious disease epidemics have often occurred in association with briefer episodes of temperature shifts, food shortages, impoverishment, and social disruption. (iv) Societies have often learnt to cope (despite hardship for some groups) with recurring shorter-term (decadal to multiyear) regional climatic cycles (e.g., El Niño Southern Oscillation)--except when extreme phases occur. (v) The drought-famine-starvation nexus has been the main, recurring, serious threat to health. Warming this century is not only likely to greatly exceed the Holocene's natural multidecadal temperature fluctuations but to occur faster. Along with greater climatic variability, models project an increased geographic range and severity of droughts. Modern societies, although larger, better resourced, and more interconnected than past societies, are less flexible, more infrastructure-dependent, densely populated, and hence are vulnerable. Adverse historical climate-related health experiences underscore the case for abating human-induced climate change. PMID:22315419

  18. Insights from past millennia into climatic impacts on human health and survival

    PubMed Central

    McMichael, Anthony J.

    2012-01-01

    Climate change poses threats to human health, safety, and survival via weather extremes and climatic impacts on food yields, fresh water, infectious diseases, conflict, and displacement. Paradoxically, these risks to health are neither widely nor fully recognized. Historical experiences of diverse societies experiencing climatic changes, spanning multicentury to single-year duration, provide insights into population health vulnerability—even though most climatic changes were considerably less than those anticipated this century and beyond. Historical experience indicates the following. (i) Long-term climate changes have often destabilized civilizations, typically via food shortages, consequent hunger, disease, and unrest. (ii) Medium-term climatic adversity has frequently caused similar health, social, and sometimes political consequences. (iii) Infectious disease epidemics have often occurred in association with briefer episodes of temperature shifts, food shortages, impoverishment, and social disruption. (iv) Societies have often learnt to cope (despite hardship for some groups) with recurring shorter-term (decadal to multiyear) regional climatic cycles (e.g., El Niño Southern Oscillation)—except when extreme phases occur. (v) The drought–famine–starvation nexus has been the main, recurring, serious threat to health. Warming this century is not only likely to greatly exceed the Holocene's natural multidecadal temperature fluctuations but to occur faster. Along with greater climatic variability, models project an increased geographic range and severity of droughts. Modern societies, although larger, better resourced, and more interconnected than past societies, are less flexible, more infrastructure-dependent, densely populated, and hence are vulnerable. Adverse historical climate-related health experiences underscore the case for abating human-induced climate change. PMID:22315419

  19. Exploring soil organic matter-mineral interactions: mechanistic insights at the nanometer and molecular length scales

    NASA Astrophysics Data System (ADS)

    Newcomb, C.; Qafoku, N. P.; Grate, J. W.; Hufschmid, R.; Browning, N.; De Yoreo, J. J.

    2015-12-01

    With elevated levels of carbon dioxide in the atmosphere due to anthropogenic emissions and disruption to the carbon cycle, the effects of climate change are being accelerated. Approximately 80% of Earth's terrestrial organic carbon is stored in soil, and the residence time of this carbon can range from hours to millenia. Understanding the dynamics of this carbon pool in the carbon cycle is crucial to both predicting climate and sustaining ecosystem services. Soil organic carbon is known to be strongly associated with high surface area clay minerals. The nature of these interactions is not well understood primarily due to the heterogeneity of soil, as much of the current knowledge relies on experiments that take a top-down approach using bulk experimental measurements. Our work seeks to probe physical, chemical, and molecular-level interactions at the organic-mineral interface using a bottom-up approach that establishes a model system where complexity can be built in systematically. By performing in situ techniques such as dynamic force spectroscopy, a technique where organic molecules can be brought into contact with mineral surfaces in a controlled manner using an atomic force microscope, we demonstrate the ability to mechanistically probe the energy landscape of individual organic molecules with mineral surfaces. We demonstrate the ability to measure the binding energies of soil-inspired organic functional groups (including carboxylic acid, amine, methyl, and phosphate) with clay and mineral surfaces as a function of solution chemistry. This effort can provide researchers with both guiding principles about carbon dynamics at the sub-nanometer length scale and insights into early aggregation events, where organic-mineral interactions play a significant role.

  20. 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

  1. 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

  2. New insights into the molecular mechanisms of general anaesthetics

    PubMed Central

    Chau, P-L

    2010-01-01

    This paper provides new insights of how general anaesthetic research should be carried out in the future by an analysis of what we know, what we do not know and what we would like to know. I describe previous hypotheses on the mechanism of action of general anaesthetics (GAs) involving membranes and protein receptors. I provide the reasons why the GABA type A receptor, the NMDA receptor and the glycine receptor are strong candidates for the sites of action of GAs. I follow with a review on attempts to provide a mechanism of action, and how future research should be conducted with the help of physical and chemical methods. PMID:20735416

  3. 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. PMID:26362600

  4. Chalcone Scaffold in Anticancer Armamentarium: A Molecular Insight

    PubMed Central

    Manna, Kuntal

    2016-01-01

    Cancer is an inevitable matter of concern in the medicinal chemistry era. Chalcone is the well exploited scaffold in the anticancer domain. The molecular mechanism of chalcone at cellular level was explored in past decades. This mini review provides the most recent updates on anticancer potential of chalcones. PMID:26880913

  5. New Insights into Molecular Ehrlichia chaffeensis-Host Interactions

    PubMed Central

    Wakeel, Abdul; Zhu, Bing; Yu, Xue-jie; McBride, Jere W.

    2010-01-01

    Ehrlichia chaffeensis is an obligately intracellular bacterium that exhibits tropism for mononuclear phagocytes and survives by reprogramming the host cell. Here we review new information regarding the newly characterized effector molecules and the complex network of molecular host-pathogen interactions that the organism exploits enabling it to thrive and persist intracellularly. PMID:20116446

  6. Molecular Insight into Gut Microbiota and Rheumatoid Arthritis

    PubMed Central

    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

    2016-01-01

    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. PMID:27011180

  7. Polycystic liver diseases: advanced insights into the molecular mechanisms

    PubMed Central

    Perugorria, Maria J.; Masyuk, Tatyana V.; Marin, Jose J.; Marzioni, Marco; Bujanda, Luis; LaRusso, Nicholas F.; Banales, Jesus M.

    2015-01-01

    Polycystic liver diseases are genetic disorders characterized by progressive bile duct dilatation and/or cyst development. The large volume of hepatic cysts causes different symptoms and complications such as abdominal distension, local pressure with back pain, hypertension, gastro-oesophageal reflux and dyspnea as well as bleeding, infection and rupture of the cysts. Current therapeutic strategies are based on surgical procedures and pharmacological management, which partially prevent or ameliorate the disease. However, as these treatments only show short-term and/or modest beneficial effects, liver transplantation is the only definitive therapy. Therefore, interest in understanding the molecular mechanisms involved in disease pathogenesis is increasing so that new targets for therapy can be identified. In this Review, the genetic mechanisms underlying polycystic liver diseases and the most relevant molecular pathways of hepatic cystogenesis are discussed. Moreover, the main clinical and preclinical studies are highlighted and future directions in basic as well as clinical research are indicated. PMID:25266109

  8. 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

  9. New Insights Into Molecular Mechanisms of Diabetic Kidney Disease

    PubMed Central

    Badal, Shawn S.; Danesh, Farhad R.

    2014-01-01

    Diabetic kidney disease remains a major microvascular complication of diabetes and the most common cause of chronic kidney failure requiring dialysis in the United States. Medical advances over the past century have substantially improved the management of diabetes mellitus and thereby have increased patient survival. However, current standards of care reduce but do not eliminate the risk of diabetic kidney disease, and further studies are warranted to define new strategies for reducing the risk of diabetic kidney disease. In this review, we highlight some of the novel and established molecular mechanisms that contribute to the development of the disease and its outcomes. In particular, we discuss recent advances in our understanding of the molecular mechanisms implicated in the pathogenesis and progression of diabetic kidney disease, with special emphasis on the mitochondrial oxidative stress and microRNA targets. Additionally, candidate genes associated with susceptibility to diabetic kidney disease and alterations in various cytokines, chemokines, and growth factors are addressed briefly. PMID:24461730

  10. Interaction of peptides with cell membranes: insights from molecular modeling

    NASA Astrophysics Data System (ADS)

    Li, Zhen-lu; Ding, Hong-ming; Ma, Yu-qiang

    2016-03-01

    The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.

  11. New insights into the molecular mechanisms of action of bisphosphonates.

    PubMed

    Rogers, Michael J

    2003-01-01

    Bisphosphonates are currently the most important and effective class of anti-resorptive drugs available, but the exact molecular mechanisms by which they inhibit osteoclast-mediated bone resorption have only recently been identified. Due to the targeting of bisphosphonates to bone mineral and the ability of osteoclasts to release bone-bound bisphosphonate, a direct effect on mature osteoclasts appears to be the most important route of action. As a result of recent discoveries concerning their molecular mechanism of action, bisphosphonates can be grouped into two classes. The simple bisphosphonates that closely resemble PPi (such as clodronate, etidronate and tiludronate) can be metabolically incorporated into non-hydrolysable analogues of ATP that accumulate intracellularly in osteoclasts, resulting in induction of osteoclast apoptosis. By contrast, the more potent, nitrogen-containing bisphosphonates (such as pamidronate, alendronate, risedronate, ibandronate and zoledronate) appear to act as analogues of isoprenoid diphosphate lipids, thereby inhibiting FPP synthase, an enzyme in the mevalonate pathway. Inhibition of this enzyme in osteoclasts prevents the biosynthesis of isoprenoid lipids (FPP and GGPP) that are essential for the post-translational farnesylation and geranylgeranylation of small GTPase signalling proteins. Loss of bone-resorptive activity and osteoclast apoptosis is due primarily to loss of geranylgeranylated small GTPases. Identification of FPP synthase as the target of nitrogen-containing bisphosphonates has also helped explain the molecular basis for the adverse effects of these agents in the GI tract and on the immune system. PMID:14529538

  12. From quantifying historical LULCC impacts to optimizing land management for climate mitigation: Insights from climate modelling

    NASA Astrophysics Data System (ADS)

    Davin, E.; Lejeune, Q.; Seneviratne, S. I.

    2015-12-01

    Human activities have profoundly transformed the land surface through land use/land cover change (LULCC). The consequence of this transformation is twofold: First, the conversion from natural to anthropogenic systems exert a direct forcing on climate (through both biogeochemical and biogeophysical processes); Second the transformed ecosystems may modify land-atmosphere feedback mechanisms thus modulating the response to climate change or to specific weather events. The first point will be illustrated by reviewing recent modelling results, including LUCID and CMIP5 model intercomparisons, to shed some light on the relative importance of LULCC versus other climate forcings. Given the importance of LULCC impacts at the regional scale, some recent efforts to improve the representation of land processes in regional climate models [1] as well as a regional assessment of the impact of amazonian deforestation [2] will be presented. The second point will be discussed through two examples. First, the fact that LULCC may modulate certain modes of variability will be illustrated based on model experiments highlighting the regional interplay between ENSO variability and amazonian deforestation. Second, we will show that peak temperatures during heat waves can be strongly influenced locally by the type of land cover or land management practices. In particular no-till farming, by increasing surface albedo, can lead to a substantial attenuation of hot temperatures during heat waves, in part due to a more efficient radiative cooling effect during cloud-free conditions [3]. References:[1] Davin, E.L. and S.I. Seneviratne (2012), Role of land surface processes and diffuse/direct radiation partitioning in simulating the European climate, Biogeosciences, 9, 1695-1707, doi:10.5194/bg-9-1695-2012.[2] Lejeune, Q., E.L. Davin, B. Guillod and S.I. Seneviratne (2015), Influence of Amazonian deforestation on the future evolution of regional surface fluxes, circulation, surface temperature and

  13. Buckling of microtubules: An insight by molecular and continuum mechanics

    SciTech Connect

    Zhang, Jin; Meguid, S. A.

    2014-10-27

    The molecular structural mechanics method has been extended to investigate the buckling of microtubules (MTs) with various configurations. The results indicate that for relative short MTs the shear deformation effect, rather than the nonlocal effect, is mainly responsible for the limitation of their widely used Euler beam description and the observed length-dependence of their bending stiffness. In addition, the configuration effect of MTs is also studied and considered as an explanation for the large scattering of the critical buckling force and bending stiffness observed in existing experiments. This configuration effect is also found to mainly originate from the geometry of the MTs and is mainly determined by the protofilament number.

  14. New insights on molecular mechanisms of renal aging.

    PubMed

    Schmitt, R; Melk, A

    2012-11-01

    Long-term transplant outcome is importantly influenced by the age of the organ donor. The mechanisms how age carries out its pathophysiological impact on graft survival are still not understood. One major contributing factor for the observed poor performance of old donor kidneys seems in particular the age-related loss in renal regenerative capacity. In this review, we will summarize recent findings about the molecular basis of renal aging with specific focus on the potential role of somatic cellular senescence and mitochondrial aging in renal transplant outcome. PMID:22882799

  15. New insights into nucleation, life cycle and climate impact of contrail cirrus

    NASA Astrophysics Data System (ADS)

    Voigt, C.

    2015-12-01

    Current growth rates in aviation demand a profound scientific data base in order to accurately assess the aviation impact on climate. A major contribution results from contrail cirrus and their radiative forcing is suggested to outbalance aviation CO2 and NOx effects. Direct observations of contrail cirrus throughout their life cycle are scarce and prone to substantial ambiguities currently limiting our understanding of the climate impact by aviation. Here, we give new insights into the nucleation, growth, life cycle and climate impact from contrail cirrus based on results from suite of aircraft experiments. NASA's ACCESSII mission focusses on aircraft emissions and initial stages of contrail formation. Nascent contrails were detected at cruise altitudes near 100 m distance to the engine exit. Contrail growth to 10-min contrail age is investigated during DLR's CONCERT campaigns. Finally, the objective of ML-CIRRUS with the HALO research aircraft is to study the life cycle and climate impact of contrail cirrus with a novel in-situ/remote sensing payload. The contrail measurements are related to previous observations and discussed in the context of recent developments in contrail modeling. Highlights include the quantification of the effects of aircraft type, engine technology and alternative fuels on contrail microphysics and climate.

  16. 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. PMID:26208115

  17. Analyses of genetic ancestry enable key insights for molecular ecology.

    PubMed

    Gompert, Zachariah; Buerkle, C Alex

    2013-11-01

    Gene flow and recombination in admixed populations produce genomes that are mosaic combinations of chromosome segments inherited from different source populations, that is, chromosome segments with different genetic ancestries. The statistical problem of estimating genetic ancestry from DNA sequence data has been widely studied, and analyses of genetic ancestry have facilitated research in molecular ecology and ecological genetics. In this review, we describe and compare different model-based statistical methods used to infer genetic ancestry. We describe the conceptual and mathematical structure of these models and highlight some of their key differences and shared features. We then discuss recent empirical studies that use estimates of genetic ancestry to analyse population histories, the nature and genetic basis of species boundaries, and the genetic architecture of traits. These diverse studies demonstrate the breadth of applications that rely on genetic ancestry estimates and typify the genomics-enabled research that is becoming increasingly common in molecular ecology. We conclude by identifying key research areas where future studies might further advance this field. PMID:24103088

  18. Molecular insights into the premature aging disease progeria.

    PubMed

    Vidak, Sandra; Foisner, Roland

    2016-04-01

    Hutchinson-Gilford progeria syndrome (HGPS) is an extremely rare premature aging disease presenting many features resembling the normal aging process. HGPS patients die before the age of 20 years due to cardiovascular problems and heart failure. HGPS is linked to mutations in the LMNA gene encoding the intermediate filament protein lamin A. Lamin A is a major component of the nuclear lamina, a scaffold structure at the nuclear envelope that defines mechanochemical properties of the nucleus and is involved in chromatin organization and epigenetic regulation. Lamin A is also present in the nuclear interior where it fulfills lamina-independent functions in cell signaling and gene regulation. The most common LMNA mutation linked to HGPS leads to mis-splicing of the LMNA mRNA and produces a mutant lamin A protein called progerin that tightly associates with the inner nuclear membrane and affects the dynamic properties of lamins. Progerin expression impairs many important cellular processes providing insight into potential disease mechanisms. These include changes in mechanosignaling, altered chromatin organization and impaired genome stability, and changes in signaling pathways, leading to impaired regulation of adult stem cells, defective extracellular matrix production and premature cell senescence. In this review, we discuss these pathways and their potential contribution to the disease pathologies as well as therapeutic approaches used in preclinical and clinical tests. PMID:26847180

  19. Molecular Insights into Poly(ADP-ribose) Recognition and Processing

    PubMed Central

    Žaja, Roko; Mikoč, Andreja; Barkauskaite, Eva; Ahel, Ivan

    2012-01-01

    Poly(ADP-ribosyl)ation is a post-translational protein modification involved in the regulation of important cellular functions including DNA repair, transcription, mitosis and apoptosis. The amount of poly(ADP-ribosyl)ation (PAR) in cells reflects the balance of synthesis, mediated by the PARP protein family, and degradation, which is catalyzed by a glycohydrolase, PARG. Many of the proteins mediating PAR metabolism possess specialised high affinity PAR-binding modules that allow the efficient sensing or processing of the PAR signal. The identification of four such PAR-binding modules and the characterization of a number of proteins utilising these elements during the last decade has provided important insights into how PAR regulates different cellular activities. The macrodomain represents a unique PAR-binding module which is, in some instances, known to possess enzymatic activity on ADP-ribose derivatives (in addition to PAR-binding). The most recently discovered example for this is the PARG protein, and several available PARG structures have provided an understanding into how the PARG macrodomain evolved into a major enzyme that maintains PAR homeostasis in living cells. PMID:24970154

  20. Molecular and isotopic insights into methane oxidation in Lake Kivu

    NASA Astrophysics Data System (ADS)

    Zigah, P. K.; Wehrli, B.; Schubert, C. J.

    2013-12-01

    Lake Kivu is a meromictic lake in the East African Rift Valley, located between the Republic of Rwanda and the Democratic Republic of Congo. The hypolimnion is permanently stratified and contain an unusually high amount of dissolved methane (CH4; ~ 60 km3) and carbon dioxide (CO2; ~300 km3) at standard temperature and pressure. While microbial-mediated methane oxidation is an important sink of methane in the lake, little is known about the distribution of microbes involved in the methane oxidation. To provide insights into methanotrophy in the lake, we analyzed depth profile of CH4, δ13C-CH4 and δ13C-DIC, δ13C-POC and the biomarkers of methanotrophic archaea and bacteria and their stable carbon isotopic composition from suspended particulate matter isolated from the lake water column. Our preliminary data show enhanced methane oxidation in oxic-anoxic transition zone in the water column. Depth distribution of diagnostic methanotrophic archaeal biomarkers such as archaeol and hydroxyarchaeol suggest archaea might be involved in anaerobic methane oxidation. Phospholipid fatty acids and diplopterol distribution and carbon isotopic signatures indicate bacteria-mediated anaerobic (and aerobic) methane oxidation in the lake.

  1. Molecular Insights into the Pathogenesis of IgA Nephropathy.

    PubMed

    Robert, Thomas; Berthelot, Laureline; Cambier, Alexandra; Rondeau, Eric; Monteiro, Renato C

    2015-12-01

    Immunoglobulin IgA nephropathy (IgAN) is the leading form of primary glomerulonephritis associated with end-stage renal failure, requiring either dialysis or renal transplantation. Microscopic hematuria and proteinuria are the most common presentations, and mesangial cell proliferation with IgA deposition are found in renal biopsies. There is growing evidence that IgAN is an immune complex (IC)-mediated disease. To date, three key molecules have been implicated in IC formation, correlating with disease progression/recurrence after transplantation: galactose-deficient IgA1 (Gd-IgA1), IgG anti-Gd-IgA1 antibodies, and soluble CD89 (an Fc receptor for IgA). This review examines recent data on the role of these molecular players in IgAN. Understanding these factors is essential because such knowledge could lead to improved strategies for the future management of patients with IgAN. PMID:26614735

  2. Brothers and Sisters: Molecular insights into arterial-venous heterogeneity

    PubMed Central

    Aitsebaomo, Julius; Portbury, Andrea L; Schisler, Jonathan C; Patterson, Cam

    2009-01-01

    The molecular differences between arteries and veins are genetically predetermined and are evident even before the first embryonic heart beat. Although ephrinB2 and EphB4 are expressed in cells that will ultimately differentiate into arteries and veins respectively, many other genes have been shown to play a significant role in cell fate determination. The expression patterns of ephrinB2 and EphB4 are restricted to arterial-venous boundaries, and Eph/ephrin signaling provides repulsive cues at arterial-venous boundaries that are thought to prevent intermixing of arterial- and venous-fated cells. However, the maintenance of arterial-venous fate is susceptible to some degree of plasticity. Thus, in response to signals from the ambient microenvironment and shear stress, there is flow-mediated intercalation of the arteries and veins that ultimately leads to the formation of a functional, closed-loop circulation. In addition, cells in the blood vessels of each organ undergo epigenetic, morphologic and functional adaptive changes that are specific to the proximate function of their cognate organ(s). These adaptive changes result in an inter-organ and intra-organ vessel heterogeneity that manifest clinically in a disparate response of different organs to identical risk factors and injury in the same animal. In this review, we will focus on the molecular and physiologic factors influencing arterial-venous heterogeneity between and within different organ(s). We will explore arterial-venous differences in selected organs as well as their respective endothelial cell architectural organization that results in their inter- and intra-organ heterogeneity. PMID:18948631

  3. Striped gold nanoparticles: New insights from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Velachi, Vasumathi; Bhandary, Debdip; Singh, Jayant K.; Cordeiro, M. Natália D. S.

    2016-06-01

    Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199-3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols' arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper, we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl's chain length, the length difference between the thiol mixtures, and solvent properties.

  4. Immunologic Function and Molecular Insight of Recombinant Interleukin-18.

    PubMed

    Saetang, Jirakrit; Puseenam, Aekkachai; Roongsawang, Niran; Voravuthikunchai, Supayang Piyawan; Sangkhathat, Surasak; Tipmanee, Varomyalin

    2016-01-01

    In recent years, cytokine-mediated therapy has emerged as further advance alternative in cancer therapy. Interleukin-18 (IL-18) has exhibited interesting anti-cancer properties especially when combined with IL-12. We engineered IL-18 in order to improve its activity using single point mutagenesis. IL-18 mutants were constructed according to binding residues and polarity which we tried to increase polarity in M33Q and M60Q, enhanced cationicity in E6K, and flexibility in T63A. All IL-18 proteins were expressed in Pichia pastoris, purified, and then measured the activity by treating with the NK-92MI cell line to evaluate interferon-γ (IFN-γ) stimulation. The E6K and T63A mutant forms showed higher activity with respect to native proteins at the concentration of 200 ng mL-1 by inducing the expression of IFN-γ, about factors of 9 and 4, respectively. Meanwhile, M33Q and M60Q had no significant activity to induce IFN-γ. Interestingly, the combination of E6K and T63A mutations could synergize the induction activity of IL-18 to be 16 times at 200 ng mL-1. Furthermore, molecular dynamics studies have elucidated the effect due to mutation on conformation of the binding site of IL-18. The results turn out that E6K provides structural perseverance against mutation, while M33Q and M60Q promote vivid overall change in protein conformation, especially at the binding site. For T63A, mutation yields small difference in structure but clearly increases structural flexibility. However, a small structural change was observed when T63A was combined with E6K. Our research resulted in a novel version of IL-18 which could be a new key candidate for cytokine-mediated therapy. PMID:27483370

  5. Molecular insights into seed dispersal mutualisms driving plant population recruitment

    NASA Astrophysics Data System (ADS)

    García, Cristina; Grivet, Delphine

    2011-11-01

    Most plant species require mutualistic interactions with animals to fulfil their demographic cycle. In this regard frugivory (i.e., the intake of fruits by animals) enhances natural regeneration by mobilizing a large amount of seeds from source trees to deposition sites across the landscape. By doing so, frugivores move propagules, and the genotypes they harbour creating the spatial, ecological, and genetic environment under which subsequent recruitment proceeds. Recruitment patterns can be envisioned as the result of two density- and distance-dependent processes: seed dispersal and seed/seedling survival (the Janzen-Connell model). Population genetic studies add another layer of complexity for understanding the fate of dispersed propagules: the genetic relatedness among neighbouring seeds within a seed clump, a major outcome of frugivore activity, modifies their chances of germinating and surviving. Yet, we virtually ignore how the spatial distribution of maternal progenies and recruitment patterns relate with each other in frugivore-generated seed rains. Here we focus on the critical role of frugivore-mediated seed dispersal in shaping the spatial distribution of maternal progenies in the seed rain. We first examine which genetic mechanisms underlying recruitment are influenced by the spatial distribution of maternal progenies. Next, we examine those studies depicting the spatial distribution of maternal progenies in a frugivore-generated seed rain. In doing so, we briefly review the most suitable analytical approaches applied to track the contribution of fruiting trees to the seed rain based on molecular data. Then we look more specifically at the role of distinct frugivore guilds in determining maternal genetic correlations and their expected consequences for recruitment patterns. Finally we posit some general conclusions and suggest future research directions that would provide a more comprehensive understanding of the ecological and evolutionary consequences

  6. Molecular signatures of ovarian diseases: Insights from network medicine perspective.

    PubMed

    Kori, Medi; Gov, Esra; Arga, Kazim Yalcin

    2016-08-01

    Dysfunctions and disorders in the ovary lead to a host of diseases including ovarian cancer, ovarian endometriosis, and polycystic ovarian syndrome (PCOS). Understanding the molecular mechanisms behind ovarian diseases is a great challenge. In the present study, we performed a meta-analysis of transcriptome data for ovarian cancer, ovarian endometriosis, and PCOS, and integrated the information gained from statistical analysis with genome-scale biological networks (protein-protein interaction, transcriptional regulatory, and metabolic). Comparative and integrative analyses yielded reporter biomolecules (genes, proteins, metabolites, transcription factors, and micro-RNAs), and unique or common signatures at protein, metabolism, and transcription regulation levels, which might be beneficial to uncovering the underlying biological mechanisms behind the diseases. These signatures were mostly associated with formation or initiation of cancer development, and pointed out the potential tendency of PCOS and endometriosis to tumorigenesis. Molecules and pathways related to MAPK signaling, cell cycle, and apoptosis were the mutual determinants in the pathogenesis of all three diseases. To our knowledge, this is the first report that screens these diseases from a network medicine perspective. This study provides signatures which could be considered as potential therapeutic targets and/or as medical prognostic biomarkers in further experimental and clinical studies. Abbreviations DAVID: Database for Annotation, Visualization and Integrated Discovery; DEGs: differentially expressed genes; GEO: Gene Expression Omnibus; KEGG: Kyoto Encyclopedia of Genes and Genomes; LIMMA: Linear Models for Microarray Data; MBRole: Metabolite Biological Role; miRNA: micro-RNA; PCOS: polycystic ovarian syndrome; PPI: protein-protein interaction; RMA: Robust Multi-Array Average; TF: transcription factor. PMID:27341345

  7. Molecular Ecological Insights into Neotropical Bird-Tick Interactions.

    PubMed

    Miller, Matthew J; Esser, Helen J; Loaiza, Jose R; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the dynamics of

  8. Immunologic Function and Molecular Insight of Recombinant Interleukin-18

    PubMed Central

    Saetang, Jirakrit; Puseenam, Aekkachai; Roongsawang, Niran; Voravuthikunchai, Supayang Piyawan; Sangkhathat, Surasak

    2016-01-01

    In recent years, cytokine-mediated therapy has emerged as further advance alternative in cancer therapy. Interleukin-18 (IL-18) has exhibited interesting anti-cancer properties especially when combined with IL-12. We engineered IL-18 in order to improve its activity using single point mutagenesis. IL-18 mutants were constructed according to binding residues and polarity which we tried to increase polarity in M33Q and M60Q, enhanced cationicity in E6K, and flexibility in T63A. All IL-18 proteins were expressed in Pichia pastoris, purified, and then measured the activity by treating with the NK-92MI cell line to evaluate interferon-γ (IFN-γ) stimulation. The E6K and T63A mutant forms showed higher activity with respect to native proteins at the concentration of 200 ng mL-1 by inducing the expression of IFN-γ, about factors of 9 and 4, respectively. Meanwhile, M33Q and M60Q had no significant activity to induce IFN-γ. Interestingly, the combination of E6K and T63A mutations could synergize the induction activity of IL-18 to be 16 times at 200 ng mL-1. Furthermore, molecular dynamics studies have elucidated the effect due to mutation on conformation of the binding site of IL-18. The results turn out that E6K provides structural perseverance against mutation, while M33Q and M60Q promote vivid overall change in protein conformation, especially at the binding site. For T63A, mutation yields small difference in structure but clearly increases structural flexibility. However, a small structural change was observed when T63A was combined with E6K. Our research resulted in a novel version of IL-18 which could be a new key candidate for cytokine-mediated therapy. PMID:27483370

  9. [New insights into the molecular mechanisms of lymphangiogenesis and pathophysiology].

    PubMed

    Hirakawa, Satoshi

    2012-01-01

    Lymphatic vessels play crucial roles in transporting tissue fluid and macromolecules, and in promoting tissue immune response. Recent studies have identified new lymphatic vessel growth in pathological conditions such as cancer progression. In fact, our experimental animal models revealed that tumors can induce lymphangiogenesis not only in primary sites, but in their draining lymph nodes (LNs), even before tumors get metastasized. In fact, lymphangiogenesis in draining lymph nodes leads to increased cancer spread to distant LNs and beyond. Importantly, we very recently identified that nodal lymphangiogenesis occurs in human skin cancers, and plays a significant role in promoting distant metastases resulting in reduced patient survival. Therefore, lymphangiogenesis could be a novel indicator and therapeutic target for the prevention of cancer metastasis. Recent advances in clarifying the functional role of lymphatic vessels began with the molecular identification of genes which are specifically expressed by the lymphatic endothelial cells. Lymphatic vessels arise from veins. Prox1, a homeobox transcription factor, specifies the lymphatic identity from venous endothelial cells. Thus, Prox1 is a master regulator of lymphatic vessel development. Vascular endothelial growth factor-C and its specific receptor VEGFR-3 compose an essential signal pathway for lymphatic vessel growth in physiological and pathological conditions. Furthermore, podoplanin, another transmembrane protein in lymphatic vessels is required for their separation from veins by activating CLEC2, the specific ligand in platelets, leading to thrombus formation between veins and lymphatic vessels. Moreover, recent progress in nano-scale technologies enabled to visualize lymphatic vessels and quantitate their transport, leading to new approaches for nano-based medicine. PMID:22293702

  10. Molecular Ecological Insights into Neotropical Bird–Tick Interactions

    PubMed Central

    Esser, Helen J.; Loaiza, Jose R.; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds’ role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually–sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical–Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically–identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly–discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the

  11. Molecular Responses to Climate and Resource Availability: Emerging Evidence from Systems Biology Research in Populus.

    SciTech Connect

    Wullschleger, Stan D; Weston, David; Davis, John M

    2009-01-01

    The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefitted greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which tree biologists can now explore the genome-wide effects of temperature, water and nutrient limitations on processes that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a number of examples whereby a systems approach, one that focuses on transcriptomic, proteomic, and metabolomic analyses is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment.

  12. New insights into the properties of contrail cirrus and their impact on climate from airborne experiments

    NASA Astrophysics Data System (ADS)

    Voigt, Christiane; Schumann, Ulrich; Minikin, Andreas; Schlager, Hans; Anderson, Bruce

    2016-04-01

    Current growth rates in aviation demand a profound scientific data base of contrail cirrus properties in order to accurately assess their climate impact. In particular, the differentiation of contrail cirrus in natural cirrus fields is challenging. Direct observations of contrail cirrus throughout their life cycle are scarce and therefore limit our understanding of the climate effects from contrail cirrus. Here, we give new insights into the growth, life-cycle and climate impact from contrail cirrus based on results from suite of aircraft experiments. NASA's ACCESSII mission focused on the detection of aircraft emissions and initial contrail stages. Nascent contrails were detected at cruise altitudes at 100 m distance to the engine exit. Contrail growth to 10-min contrail age was investigated during DLR's CONCERT campaigns. Finally, the objective of the ML-CIRRUS experiment was to study the life cycle and climate impact of contrail cirrus. The contrail measurements are related to previous observations and discussed in the context of recent developments in contrail modeling. Highlights include the quantification of the effects of aircraft type on contrail microphysics, the analysis of ice particle shapes and the quantitative distinction of contrail cirrus and natural cirrus.

  13. 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.

  14. Polymer Nanocomposites: Insights from Theory and Molecular Simulations

    NASA Astrophysics Data System (ADS)

    Pani, Rakhee

    Advantages of polymer nanocomposites have attracted great industrial attention due to their multifunctionality and innovative technological properties. Addition of small amount of nanoparticle (nanospheres, nanotubes, nanorods, nanoplatelets, or sheets) to polymer matrix cause dramatic improvement in structural and functional properties, which is difficult to attain from those of individual components. The interaction between polymer and nanoparticle create bulk materials dominated by solid state physics at the nanoscale. Furthermore, morphology of nanocomposites depends on structural arrangements of nanoparticles. Thus, for achievement of optimized functionality like electrical, optical, mechanical and thermal properties control over the dispersion of the nanoparticle is essential. However, properties of polymer nanocomposites depend on morphology control and nature of interfacial interactions. In order to control the morphology it is necessary to understand how the processing conditions, shape and size of nanoparticle influence the structure of composite. Molecular simulations can help us to predict the parameters that control the structural changes and we could design polymer nanocomposite entailing their end-use. In this work, we addressed the following research questions: (1) the dependence of nanoparticle ligand corona structure on solvent quality and (2) the role of interfacial energy and interactions on the dispersion of molecules and nanoparticles. Specifically, this research assessed the effect of solvent interactions on the structure of nanoparticles on the example of redox core encapsulating dendrimer and ligand functionalized gold nanoparticles, role of chemical interaction on solubility of glucose in ionic liquids, diffusion of fullerene nanoparticles in polymer matrix and influence of solubility parameters on the compatibility of gold nanoparticles with diblock copolymers. Computational methods allow quantifying the structure and flexibility of the

  15. Plasticity of oxidative metabolism in variable climates: molecular mechanisms.

    PubMed

    Seebacher, Frank; Brand, Martin D; Else, Paul L; Guderley, Helga; Hulbert, Anthony J; Moyes, Christopher D

    2010-01-01

    Converting food to chemical energy (ATP) that is usable by cells is a principal requirement to sustain life. The rate of ATP production has to be sufficient for housekeeping functions, such as protein synthesis and maintaining membrane potentials, as well as for growth and locomotion. Energy metabolism is temperature sensitive, and animals respond to environmental variability at different temporal levels, from within-individual to evolutionary timescales. Here we review principal molecular mechanisms that underlie control of oxidative ATP production in response to climate variability. Nuclear transcription factors and coactivators control expression of mitochondrial proteins and abundance of mitochondria. Fatty acid and phospholipid concentrations of membranes influence the activity of membrane-bound proteins as well as the passive leak of protons across the mitochondrial membrane. Passive proton leak as well as protein-mediated proton leak across the inner mitochondrial membrane determine the efficacy of ATP production but are also instrumental in endothermic heat production and as a defense against reactive oxygen species. Both transcriptional mechanisms and membrane composition interact with environmental temperature and diet, and this interaction between diet and temperature in determining mitochondrial function links the two major environmental variables that are affected by changing climates. The limits to metabolic plasticity could be set by the production of reactive oxygen species leading to cellular damage, limits to substrate availability in mitochondria, and a disproportionally large increase in proton leak over ATP production. PMID:20586603

  16. New insight into biodegradation of polylactide (PLA)/clay nanocomposites using molecular ecological techniques.

    PubMed

    Sangwan, Parveen; Way, Cameron; Wu, Dong-Yang

    2009-07-01

    Novel molecular ecological techniques were used to study changes in microbial community structure and population during degradation of polylactide (PLA)/organically modified layered silicates (OMLS) nanocomposites. Cloned gene sequences belonging to members of the phyla Actinobacteria and Ascomycota comprized the most dominant groups of microorganisms during biodegradation of PLA/OMLS nanocomposites. Due to their numerical abundance, members of these microbial groups are likely to play an important role during biodegradation process. This paper presents new insights into the biodegradability of PLA/OMLS nanocomposites and highlights the importance of using novel molecular ecological techniques for in situ identification of new microorganisms involved in biodegradation of polymeric materials. PMID:19148900

  17. 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. PMID:26903924

  18. 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

  19. 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

    2011-01-01

    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. PMID:21383919

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

    PubMed Central

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

    2011-01-01

    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. PMID:21383919

  1. 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

  2. Response of the benthic methane cycle to climate variability: insights from reaction-transport simulations

    NASA Astrophysics Data System (ADS)

    Regnier, P.; Dale, A.; Arndt, S.; Tsandev, I.; Ridgwell, A.

    2012-04-01

    Methanogenesis by microorganisms within anoxic sediments is a very slow process of CH4 production. Yet, over thousands or millions of years methanogenesis has resulted in vast CH4 accumulation, either dissolved in the interstitial water, in the form of gas bubbles, or condensed as gas hydrates (Buffett and Archer, 2004). On a global scale, sediments are thus the largest methane reservoir on Earth (Buffett and Archer, 2004), and they may exert a significant influence on the carbon cycle and Earth climate. For instance, CH4 release due to destabilization of gas hydrates has resulted in significant increases in atmospheric CH4 concentration during Earth's history (e.g. Dickens, 2003). Geochemical and microbiological evidence, together with mass balance calculations, nonetheless suggest that currently, up to 90% of the methane produced globally in marine sediments is consumed in situ before reaching the seafloor by the biogeochemical process of anaerobic oxidation of methane (AOM). Yet, the extent to which the efficiency of this methane sink could be affected by climate change remains essentially unknown. This contribution reviews how recent model developments, including improved representations of the physical, chemical and biological components of the benthic system, have led to novel insights into the transient response of the benthic methane cycle at the centennial timescale. Reactive-transport model simulations combined with high resolution data are used to quantify present-day rates of methanogenesis and methanotrophy in shelf sediments where free methane gas is widespread. Results reveal that in passive sediments AOM is currently a very efficient subsurface barrier against both the aqueous and gaseous methane flux migrating towards the seafloor. Numerical experiments are then carried out to forecast the evolution of the methane cycle over the next century, triggered by changes in climate. Simulations predict that the gaseous methane inventory will increase, but

  3. Ultrathin Molecular-Layer-by-Layer Polyamide Membranes: Insights from Atomistic Molecular Simulations.

    PubMed

    Liyana-Arachchi, Thilanga P; Sturnfield, James F; Colina, Coray M

    2016-09-01

    In this study, we present an atomistic simulation study of several physicochemical properties of polyamide (PA) membranes formed from interfacial polymerization or from a molecular-layer-by-layer (mLbL) on a silicon wafer. These membranes are composed of meta-phenylenediamine (MPD) and benzene-1,3,5-tricarboxylic acid chloride (TMC) for potential reverse osmosis (RO) applications. The mLbL membrane generation procedure and the force field models were validated, by comparison with available experimental data, for hydrated density, membrane swelling, and pore size distributions of PA membranes formed by interfacial polymerization. Physicochemical properties such as density, free volume, thickness, the degree of cross-linking, atomic compositions, and average molecular orientation (which is relevant for the mLbL membranes) are compared for these different processes. The mLbL membranes are investigated systematically with respect to TMC monomer growth rate per substrate surface area, MPD/TMC ratio, and the number of mLbL deposition cycles. Atomistic simulations show that the mLbL deposition generates membranes with a constant film growth if both the TMC monomer growth rate and MPD/TMC monomer ratio are kept constant. The film growth rate increases with TMC monomer growth rate or MPD/TMC ratio. Furthermore, it was found on one hand that the mLbL membrane density and free volume varies significantly with respect to the TMC monomer growth rate, while on the other hand the degree of cross-linking and the atomic composition varies considerably with the MPD/TMC ratio. Additionally, it was found that both TMC and MPD orient at a tilted angle with respect to the substrate surface, where their angular distribution and average angle orientation depend on both the TMC growth rate and the number of deposition cycles. This study illustrates that molecular simulations can play a crucial role in the understanding of structural properties that can empower the design of the next

  4. Molecular Insights into the Enigmatic Metabolic Regulator, SnRK1.

    PubMed

    Emanuelle, Shane; Doblin, Monika S; Stapleton, David I; Bacic, Antony; Gooley, Paul R

    2016-04-01

    Sucrose non-fermenting-1 (SNF1)-related kinase 1 (SnRK1) lies at the heart of metabolic homeostasis in plants and is crucial for normal development and response to stress. Evolutionarily related to SNF1 in yeast and AMP-activated kinase (AMPK) in mammals, SnRK1 acts protectively to maintain homeostasis in the face of fluctuations in energy status. Despite a conserved function, the structure and regulation of the plant kinase differ considerably from its relatively well-understood opisthokont orthologues. In this review, we highlight the known plant-specific modes of regulation involving SnRK1 together with new insights based on a 3D molecular model of the kinase. We also summarise how these differences from other orthologues may be specific adaptations to plant metabolism, and offer insights into possible avenues of future inquiry into this enigmatic enzyme. PMID:26642889

  5. Dynamic conformational ensembles regulate casein kinase-1 isoforms: Insights from molecular dynamics and molecular docking studies.

    PubMed

    Singh, Surya Pratap; Gupta, Dwijendra K

    2016-04-01

    Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of two isoforms (CK1-α/ε) has been shown to activate the carcinogenic pathway which involves the stabilization of of cytoplasmic β-catenin. Development of anticancer therapeutics is very laborious task and depends upon the structural and conformational details of the target. This study focuses on, how the structural dynamics and conformational changes of two CK1 isoforms are synchronized in carcinogenic pathway. The conformational dynamics in kinases is the responsible for their action as has been supported by the molecular docking experiments. PMID:26788877

  6. β-Cyclodextrin at the Water/1-Bromobutane Interface: Molecular Insight into Reverse Phase Transfer Catalysis.

    PubMed

    Elk, Jackson Chief; Benjamin, Ilan

    2015-05-12

    Molecular insight into the role of β-cyclodextrin (βCD) as a phase transfer catalyst at the liquid/liquid interface is obtained by molecular dynamics simulations of the structure and dynamics of βCD adsorbed at the interface between water and 1-bromobutane. In particular, we consider the structure and dynamics of the water and bromobutane molecules inside the βCD cavity and compare them with the behavior when βCD is dissolved in bulk water. βCD is preferentially oriented at the interface, with the cavity opening along the interface normal. While in bulk water the cavity includes 6-8 water molecules that are relatively mobile with short residence time, at the interface the cavity is mostly dehydrated and includes a single bromobutane molecule. This inclusion complex is stable in bulk water. The implication of this behavior for reverse phase transfer catalysis is discussed. PMID:25909764

  7. Alluvial fan response to climatic change: Insights from numerical modeling (Invited)

    NASA Astrophysics Data System (ADS)

    Pelletier, J. D.

    2009-12-01

    Alluvial fans in the western U.S. exhibit a regionally correlative sequence of Plio-Quaternary deposits. Cosmogenic and U-series dating has greatly improved the age control on these deposits and their associated terraces and generally strengthened the case for aggradation during humid-to-arid transitions. Still, the linkages between climate change, upland basin response, and alluvial fan response are not well constrained. Fans may fill and cut as a result of autogenetic processes/internal adjustments, changes in regional temperature (which controls snowmelt-induced flooding), changes in the frequency-size distribution of rainfall events, and/or changes in upslope vegetation. Here I describe the results of a numerical modeling study designed to better constrain the relationships between different end-member forcing mechanisms and the geologic record of alluvial fan deposits and terraces. The model solves the evolution of the fan topography using Exner's equation (conservation of mass) coupled with a nonlinear, threshold-controlled transport relation for sand and gravel. Bank retreat is modeled using an advection equation with a rate proportional to bank shear stress. I begin by considering the building of a fan under conditions of constant water and sediment supply. This simple system exhibits all of the complexity of fans developed under experimental conditions, and it provides insights into the mechanisms that control avulsions and it provides a baseline estimate for the within-fan relief that can result from autogenetic processes. Relationships between the magnitude and period of variations in the sediment-to-water ratio and the geomorphic response of fans are then discussed. I also consider the response of a coupled drainage basin-fan system to changes in climate, including the hydrologic and vegetation response of upland hillslopes. Fans can aggrade or incise in response to the same climatic event depending on the relief of the upstream drainage basin, which

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

    SciTech Connect

    Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph Steinfeld, Robert

    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, 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.

  9. Molecular self-assembly on two-dimensional atomic crystals: insights from molecular dynamics simulations.

    PubMed

    Zhao, Yinghe; Wu, Qisheng; Chen, Qian; Wang, Jinlan

    2015-11-19

    van der Waals (vdW) epitaxy of ultrathin organic films on two-dimensional (2D) atomic crystals has become a sovereign area because of their unique advantages in organic electronic devices. However, the dynamic mechanism of the self-assembly remains elusive. Here, we visualize the nanoscale self-assembly of organic molecules on graphene and boron nitride monolayer from a disordered state to a 2D lattice via molecular dynamics simulation for the first time. It is revealed that the assembly toward 2D ordered structures is essentially the minimization of the molecule-molecule interaction, that is, the vdW interaction in nonpolar systems and the vdW and Coulomb interactions in polar systems that are the decisive factors for the formation of the 2D ordering. The role of the substrate is mainly governing the array orientation of the adsorbates. The mechanisms unveiled here are generally applicable to a broad class of organic thin films via vdW epitaxy. PMID:26523464

  10. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations

    SciTech Connect

    Wang, Jing-Fang; Chou, Kuo-Chen

    2009-12-18

    Rab5a is currently a most interesting target because it is responsible for regulating the early endosome fusion in endocytosis and possibly the budding process. We utilized longtime-scale molecular dynamics simulations to investigate the internal motion of the wild-type Rab5a and its A30P mutant. It was observed that, after binding with GTP, the global flexibility of the two proteins is increasing, while the local flexibility in their sensitive sites (P-loop, switch I and II regions) is decreasing. Also, the mutation of Ala30 to Pro30 can cause notable flexibility variations in the sensitive sites. However, this kind of variations is dramatically reduced after binding with GTP. Such a remarkable feature is mainly caused by the water network rearrangements in the sensitive sites. These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association.

  11. New mechanistic insight in the thermal helix inversion of second-generation molecular motors.

    PubMed

    Klok, Martin; Walko, Martin; Geertsema, Edzard M; Ruangsupapichat, Nopporn; Kistemaker, Jos C M; Meetsma, Auke; Feringa, Ben L

    2008-01-01

    The introduction of dibenzocyclohepten-5-ylidene as part of a unidirectional light-driven molecular motor allows a more complete picture of the pathway of thermal helix inversion to be developed. The most stable conformation is similar to that found in related motors in that it has, overall, an anti-folded structure with the substituent at the stereogenic centre adopting an axial orientation. Photochemical cis/trans isomerisation at -40 degrees C results in the formation of an isomer in a syn-folded conformation with the methyl group in an axial orientation. This contrasts with previous studies on related molecular rotary motors. The conformation of the higher energy intermediate typically observed for this class of compound is the anti-folded conformation, in which the methyl group is in an equatorial orientation. This conformation is available through an energetically uphill upper half ring inversion of the observed photochemical product. However, this pathway competes with a second process that leads to the more stable anti-folded conformation in which the methyl group is oriented axially. It has been shown that the conformations and pathways available for second-generation molecular motors can be described by using similar overall geometries. Differences in the metastable high-energy species are attributable to the relative energy and position on the reaction coordinate of the transition states. Kinetic studies on these new molecular motors thus provide important insights into the conformational dynamics of the rotation cycle. PMID:18979464

  12. Reactivity and Selectivity of Heterogenized Homogeneous Catalysts: Insights from Molecular Simulations

    NASA Astrophysics Data System (ADS)

    Malek, Kourosh; van Santen, Rutger A.

    Immobilized metal complexes on nanoporous materials have recently been proposed as a novel class of heterogeneous enantioselective catalyst for epoxidation of unfunctionalized olefins as well as hydrogenation, alkylation, and nitroaldol reactions. The porous hosted materials affect catalytic performance due to a cooperative interaction among the nanoporous solid, immobilizing linker, and metal complex asymmetry. The effects of mesoporous materials and immobilizing agents on chiral catalysis are not well understood, however, the catalysts confined in nanopores show comparable or even higher conversions and enantioselectivity compared to their homogeneous counterparts. This chapter highlights major scientific problems for fundamental understanding and design of heterogenized homogeneous catalysts. It describes in detail the pivotal role of a sound framework in physical theory and molecular modeling in systematic efforts towards better materials and catalytic performance optimization. The common threads of the various topics addressed is the wide range of scales that has to be considered in establishing relations between structure, physicochemical properties, and catalytic performance. Physical theory and modeling employ a variety of methods, encompassing ab-initio calculations, molecular simulations, and the continuum model of transport and reaction in nanoporous materials. We particularly describe how molecular simulations can be used to investigate the origin of enantioselectivity of an anchored metal complex in nanoporous materials. These studies provide new insights into the steric effects that relate to choices of substrate and linker and to the interplay with mesopore confinement. We also bring detailed example of employing molecular simulations to unravel the catalytic properties of metallomacrocyclics for the electrochemical reduction of molecular oxygen in aqueous media. We rationalize the importance of immobilization and show how it relates to the steric

  13. Insight into the Functionality of Microbial Exopolysaccharides by NMR Spectroscopy and Molecular Modeling

    PubMed Central

    Larsen, Flemming H.; Engelsen, Søren B.

    2015-01-01

    Microbial polysaccharides represent an important class of microbial polymers with diverse functions such as biofilm formation, thickening, and gelling properties as well as health-promoting properties. The broad range of exopolysaccharide (EPS) functionalities has sparked a renewed interest in this class of molecules. Chemical, enzymatic as well as genetic modifications by metabolic engineering can be used to create large numbers of analogous EPS variants with respect to EPS functionality. While this top–down approach is effective in finding new candidates for desired functionality, there seems to be a lack of the corresponding bottom–up approach. The molecular mechanisms of the desired functionalities can be established from Nuclear Magnetic Resonance (NMR) and molecular models and it is proposed that these models can be fed back into the biotechnology by using a quantitative structure–property approach. In this way it will be possible to tailor specific functionality within a given design space. This perspective will include two well-known commercial microbial EPS examples namely gellan and diutan and show how even a limited use of multiphase NMR and molecular modeling can increase the insight into their different properties, which are based on only minor structural differences. PMID:26696983

  14. Insights into carbon nanotube and graphene formation mechanisms from molecular simulations: a review

    NASA Astrophysics Data System (ADS)

    Page, A. J.; Ding, F.; Irle, S.; Morokuma, K.

    2015-02-01

    The discovery of carbon nanotubes (CNTs) and graphene over the last two decades has heralded a new era in physics, chemistry and nanotechnology. During this time, intense efforts have been made towards understanding the atomic-scale mechanisms by which these remarkable nanostructures grow. Molecular simulations have made significant contributions in this regard; indeed, they are responsible for many of the key discoveries and advancements towards this goal. Here we review molecular simulations of CNT and graphene growth, and in doing so we highlight the many invaluable insights gained from molecular simulations into these complex nanoscale self-assembly processes. This review highlights an often-overlooked aspect of CNT and graphene formation—that the two processes, although seldom discussed in the same terms, are in fact remarkably similar. Both can be viewed as a 0D → 1D → 2D transformation, which converts carbon atoms (0D) to polyyne chains (1D) to a complete sp2-carbon network (2D). The difference in the final structure (CNT or graphene) is determined only by the curvature of the catalyst and the strength of the carbon-metal interaction. We conclude our review by summarizing the present shortcomings of CNT/graphene growth simulations, and future challenges to this important area.

  15. The mineralocorticoid receptor: insights into its molecular and (patho)physiological biology.

    PubMed

    Viengchareun, Say; Le Menuet, Damien; Martinerie, Laetitia; Munier, Mathilde; Pascual-Le Tallec, Laurent; Lombès, Marc

    2007-01-01

    The last decade has witnessed tremendous progress in the understanding of the mineralocorticoid receptor (MR), its molecular mechanism of action, and its implications for physiology and pathophysiology. After the initial cloning of MR, and identification of its gene structure and promoters, it now appears as a major actor in protein-protein interaction networks. The role of transcriptional coregulators and the determinants of mineralocorticoid selectivity have been elucidated. Targeted oncogenesis and transgenic mouse models have identified unexpected sites of MR expression and novel roles for MR in non-epithelial tissues. These experimental approaches have contributed to the generation of new cell lines for the characterization of aldosterone signaling pathways, and have also facilitated a better understanding of MR physiology in the heart, vasculature, brain and adipose tissues. This review describes the structure, molecular mechanism of action and transcriptional regulation mediated by MR, emphasizing the most recent developments at the cellular and molecular level. Finally, through insights obtained from mouse models and human disease, its role in physiology and pathophysiology will be reviewed. Future investigations of MR biology should lead to new therapeutic strategies, modulating cell-specific actions in the management of cardiovascular disease, neuroprotection, mineralocorticoid resistance, and metabolic disorders. PMID:18174920

  16. The mineralocorticoid receptor: insights into its molecular and (patho)physiological biology

    PubMed Central

    Viengchareun, Say; Le Menuet, Damien; Martinerie, Laetitia; Munier, Mathilde; Pascual-Le Tallec, Laurent; Lombès, Marc

    2007-01-01

    The last decade has witnessed tremendous progress in the understanding of the mineralocorticoid receptor (MR), its molecular mechanism of action, and its implications for physiology and pathophysiology. After the initial cloning of MR, and identification of its gene structure and promoters, it now appears as a major actor in protein-protein interaction networks. The role of transcriptional coregulators and the determinants of mineralocorticoid selectivity have been elucidated. Targeted oncogenesis and transgenic mouse models have identified unexpected sites of MR expression and novel roles for MR in non-epithelial tissues. These experimental approaches have contributed to the generation of new cell lines for the characterization of aldosterone signaling pathways, and have also facilitated a better understanding of MR physiology in the heart, vasculature, brain and adipose tissues. This review describes the structure, molecular mechanism of action and transcriptional regulation mediated by MR, emphasizing the most recent developments at the cellular and molecular level. Finally, through insights obtained from mouse models and human disease, its role in physiology and pathophysiology will be reviewed. Future investigations of MR biology should lead to new therapeutic strategies, modulating cell-specific actions in the management of cardiovascular disease, neuroprotection, mineralocorticoid resistance, and metabolic disorders. PMID:18174920

  17. 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. PMID:25346366

  18. Insights into carbon nanotube and graphene formation mechanisms from molecular simulations: a review.

    PubMed

    Page, A J; Ding, F; Irle, S; Morokuma, K

    2015-02-01

    The discovery of carbon nanotubes (CNTs) and graphene over the last two decades has heralded a new era in physics, chemistry and nanotechnology. During this time, intense efforts have been made towards understanding the atomic-scale mechanisms by which these remarkable nanostructures grow. Molecular simulations have made significant contributions in this regard; indeed, they are responsible for many of the key discoveries and advancements towards this goal. Here we review molecular simulations of CNT and graphene growth, and in doing so we highlight the many invaluable insights gained from molecular simulations into these complex nanoscale self-assembly processes. This review highlights an often-overlooked aspect of CNT and graphene formation-that the two processes, although seldom discussed in the same terms, are in fact remarkably similar. Both can be viewed as a 0D → 1D → 2D transformation, which converts carbon atoms (0D) to polyyne chains (1D) to a complete sp(2)-carbon network (2D). The difference in the final structure (CNT or graphene) is determined only by the curvature of the catalyst and the strength of the carbon-metal interaction. We conclude our review by summarizing the present shortcomings of CNT/graphene growth simulations, and future challenges to this important area. PMID:25746411

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

    PubMed Central

    Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

    2014-01-01

    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, 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. PMID:24816101

  20. Estimating evapotranspiration under warmer climates: Insights from a semiarid riparian system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper presents an approach to quantify evapotranspiration under changing climates, using field observations, theoretical evaporation models and meteorological predictions from global climate models. We analyzed evaporation and meteorological data from three riparian sites located in a semiarid ...

  1. An insight into the molecular characteristics of hepatitis C virus for clinicians

    PubMed Central

    Du, Lingyao; Tang, Hong

    2016-01-01

    Hepatitis C virus (HCV) consists of envelope proteins, core proteins, and genome RNA. The structural genes and non-structural genes in the open reading frame of its genome encode functional proteins essential to viral life cycles, ranging from virus attachment to progeny virus secretion. After infection, the host cells suffer damage from virus-induced oxidative stress, steatosis, and activation of proto-oncogenes. Every process during the viral life cycle can be considered as targets for direct acting antivirals. However, protective immunity cannot be easily acquired for the volatility in HCV antigenic epitopes. Understanding its molecular characteristics, especially pathogenesis and targets the drugs act on, not only helps professionals to make optimal therapeutic decisions, but also helps clinicians who do not specialize in infectious diseases/hepatology to provide better management for patients. This review serves to provide an insight for clinicians and this might provide a possible solution for any possible collision. PMID:27146609

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

    SciTech Connect

    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 the 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.

  3. Protein Fibrillar Nanopolymers: Molecular-Level Insights into Their Structural, Physical and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Trusova, Valeriya M.

    2015-09-01

    Amyloid fibrils represent a generic class of mechanically strong and stable biomaterials with extremely advantageous properties. Although amyloids were initially associated only with severe neurological disorders, the role of these structures nowadays is shifting from health debilitating to highly beneficial both in biomedical and technological aspects. Intensive involvement of fibrillar assemblies into the wide range of pathogenic and functional processes strongly necessitate the molecular level characterization of the structural, physical and elastic features of protein nanofibrils. In the present contribution, we made an attempt to highlight the up-to-date progress in the understanding of amyloid properties from the polymer physics standpoint. The fundamental insights into protein fibril behavior are essential not only for development of therapeutic strategies to combat the protein misfolding disorders but also for rational and precise design of novel biodegradable protein-based nanopolymers.

  4. 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

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

    PubMed

    Xi, Wang; Schmidt, Christine K; Sanchez, Samuel; Gracias, David H; Carazo-Salas, Rafael E; Butler, Richard; Lawrence, Nicola; Jackson, Stephen P; Schmidt, Oliver G

    2016-06-28

    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

  6. 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

  7. Molecular Insights into Aqueous NaCl Electrolytes Confined within Vertically-oriented Graphenes.

    PubMed

    Bo, Zheng; Yang, Huachao; Zhang, Shuo; Yang, Jinyuan; Yan, Jianhua; Cen, Kefa

    2015-01-01

    Vertically-oriented graphenes (VGs) are promising active materials for electric double layer capacitors (EDLCs) due to their unique morphological and structural features. This study, for the first time, reports the molecular dynamics (MD) simulations on aqueous NaCl electrolytes confined within VG channels with different surface charge densities and channel widths. Simulation results show that the accessibility of ions and the structure of EDLCs are determined by the ion type/size, surface charging, and VG channel width. For relatively narrow VG channels with the same width, the threshold charge density (to compensate the energy penalty for shedding hydration shell) and the dehydration rate of Cl(-) ions are larger than those of Na(+) ions. To achieve the highest ion concentration coefficient, the effective VG channel width should be between the crystal and hydration diameters of the ions. The results are further quantified and elucidated by calculating the electrolyte density profiles. The molecular insights obtained in the current work are useful in guiding the design and fabrication of VGs for advancing their EDLC applications. PMID:26424365

  8. Molecular Insights into Aqueous NaCl Electrolytes Confined within Vertically-oriented Graphenes

    PubMed Central

    Bo, Zheng; Yang, Huachao; Zhang, Shuo; Yang, Jinyuan; Yan, Jianhua; Cen, Kefa

    2015-01-01

    Vertically-oriented graphenes (VGs) are promising active materials for electric double layer capacitors (EDLCs) due to their unique morphological and structural features. This study, for the first time, reports the molecular dynamics (MD) simulations on aqueous NaCl electrolytes confined within VG channels with different surface charge densities and channel widths. Simulation results show that the accessibility of ions and the structure of EDLCs are determined by the ion type/size, surface charging, and VG channel width. For relatively narrow VG channels with the same width, the threshold charge density (to compensate the energy penalty for shedding hydration shell) and the dehydration rate of Cl− ions are larger than those of Na+ ions. To achieve the highest ion concentration coefficient, the effective VG channel width should be between the crystal and hydration diameters of the ions. The results are further quantified and elucidated by calculating the electrolyte density profiles. The molecular insights obtained in the current work are useful in guiding the design and fabrication of VGs for advancing their EDLC applications. PMID:26424365

  9. 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. PMID:26989626

  10. Molecular and evolutionary insights into the structural organization of cation chloride cotransporters

    PubMed Central

    Hartmann, Anna-Maria; Nothwang, Hans Gerd

    2015-01-01

    Cation chloride cotransporters (CCC) play an essential role for neuronal chloride homeostasis. K+-Cl− cotransporter (KCC2), is the principal Cl−-extruder, whereas Na+-K+-Cl− cotransporter (NKCC1), is the major Cl−-uptake mechanism in many neurons. As a consequence, the action of the inhibitory neurotransmitters gamma-aminobutyric acid (GABA) and glycine strongly depend on the activity of these two transporters. Knowledge of the mechanisms involved in ion transport and regulation is thus of great importance to better understand normal and disturbed brain function. Although no overall 3-dimensional crystal structures are yet available, recent molecular and phylogenetic studies and modeling have provided new and exciting insights into structure-function relationships of CCC. Here, we will summarize our current knowledge of the gross structural organization of the proteins, their functional domains, ion binding and translocation sites, and the established role of individual amino acids (aa). A major focus will be laid on the delineation of shared and distinct organizational principles between KCC2 and NKCC1. Exploiting the richness of recently generated genome data across the tree of life, we will also explore the molecular evolution of these features. PMID:25653592

  11. 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

  12. 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. PMID:26980497

  13. Selective Monocationic Inhibitors of Neuronal Nitric Oxide Synthase. Binding Mode Insights from Molecular Dynamics Simulations

    PubMed Central

    Huang, He; Ji, Haitao; Li, Huiying; Jing, Qing; Labby, Kristin Jansen; Martásek, Pavel; Roman, Linda J.; Poulos, Thomas L.; Silverman, Richard B.

    2012-01-01

    The reduction of pathophysiologic levels of nitric oxide through inhibition of neuronal nitric oxide synthase (nNOS) has the potential to be therapeutically beneficial in various neurodegenerative diseases. We have developed a series of pyrrolidine-based nNOS inhibitors that exhibit excellent potencies and isoform selectivities (J. Am. Chem. Soc. 2010, 132, 5437). However, there are still important challenges, such as how to decrease the multiple positive charges derived from basic amino groups, which contribute to poor bioavailability, without losing potency and/or selectivity. Here we present an interdisciplinary study combining molecular docking, crystallography, molecular dynamics simulations, synthesis, and enzymology to explore potential pharmacophoric features of nNOS inhibitors and to design potent and selective monocationic nNOS inhibitors. The simulation results indicate that different hydrogen bond patterns, electrostatic interactions, hydrophobic interactions, and a water molecule bridge are key factors for stabilizing ligands and controlling ligand orientation. We find that a heteroatom in the aromatic head or linker chain of the ligand provides additional stability and blocks the substrate binding pocket. Finally, the computational insights are experimentally validated with double-headed pyridine analogs. The compounds reported here are among the most potent and selective monocationic pyrrolidine-based nNOS inhibitors reported to date, and 10 shows improved membrane permeability. PMID:22731813

  14. 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

  15. 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.

  16. 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

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

    PubMed Central

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

    2015-01-01

    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. PMID:22431001

  18. 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

  19. 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

  20. Molecular fossils in modern genomes provide physiological and geochemical insights to the ancient earth (Invited)

    NASA Astrophysics Data System (ADS)

    Dupont, C.; Caetano-Anolles, G.

    2010-12-01

    The genomes of extant organisms are ultimately derived from ancient life, thus theoretically contain insight to ancient physiology, ecology, and environments. In particular, metalloenzymes may be particularly insightful. The fundamental chemistry of trace elements dictates the molecular speciation and reactivity both within cells and the environment at large. Using protein structure and comparative genomics, we elucidate several major influences this chemistry has had upon biology. All of life exhibits the same proteome size-dependent scaling for the number of metal-binding proteins within a proteome. This fundamental evolutionary constant shows that the selection of one element occurs at the exclusion of another, with the eschewal of Fe for Zn and Ca being a defining feature of eukaryotic pro- teomes. Early life lacked both the structures required to control intracellular metal concentrations and the metal-binding proteins that catalyze electron transport and redox transformations. The development of protein structures for metal homeostasis coincided with the emergence of metal-specific structures, which predomi- nantly bound metals abundant in the Archean ocean. Potentially, this promoted the diversification of emerging lineages of Archaea and Bacteria through the establishment of biogeochemical cycles. In contrast, structures binding Cu and Zn evolved much later, pro- viding further evidence that environmental availability influenced the selection of the elements. The late evolving Zn-binding proteins are fundamental to eukaryotic cellular biology, and Zn bioavailabil- ity may have been a limiting factor in eukaryotic evolution. The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods.

  1. Boron Isotope Based CO2 Reconstructions and Insights into the Sensitivity of the Climate System to CO2-forcing

    NASA Astrophysics Data System (ADS)

    Foster, G. L.

    2014-12-01

    system to CO2 change. This study provides new insights into the possibility of "hidden" feedbacks and the likelihood of a state dependency to climate sensitivity. [1] Rohling, E.J., et al., 2012. Nature, 491: 683-691. [2] Stainforth, D.A. et al., 2005. Nature, 433(7024): 403-406.

  2. 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.

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

    SciTech Connect

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

    2015-03-14

    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.

  4. 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…

  5. 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

  6. Temperature decomposition of paired site observations reveals new insights in climate models' capability to simulate the impact of LUC.

    NASA Astrophysics Data System (ADS)

    Vanden Broucke, Sam; Luyssaert, Sebastiaan; Davin, Edouard; Janssens, Ivan; Van Lipzig, Nicole

    2015-04-01

    The biogeophysical impact of land use change (LUC) has been shown to be a significant contributor to climate change. In this study, we present a new methodology for evaluating the impact of LUC in climate models. For this, we use observational data from paired eddy covariance flux towers, representing a LUC from forest to open land (deforestation). Two model simulations with a regional climate model (COSMO-CLM2) are performed which differ only in prescribed land use for site pair locations. The model is evaluated by comparing the observed and simulated difference in surface temperature (Ts) between open land and forests, an evaluation which is performed separately for summer/winter and daytime/ nighttime. Next, we identify the biogeophysical mechanisms responsible for Ts differences by applying a Ts decomposition method to both observations and model simulations, allowing us us to determine which LUC related biogeophysical mechanisms were well represented in COSMO-CLM2, and which were not. Results show that the model is able to simulate the increase in albedo and associated daytime surface cooling following deforestation reasonably well. Also well simulated is the overall decrease in sensible heat flux and associated daytime surface warming and nighttime surface cooling. However, it appears the model is missing one crucial impact of deforestation on the surface energy budget: a reduction in nighttime downwelling longwave radiation. As a result, the magnitude of nighttime cooling following deforestation is underestimated by 4 K. These new insights support a wider application of the methodology (to other climate models).

  7. Climate forcing and Neanderthal extinction in Southern Iberia: insights from a multiproxy marine record

    NASA Astrophysics Data System (ADS)

    Jiménez-Espejo, Francisco J.; Martínez-Ruiz, Francisca; Finlayson, Clive; Paytan, Adina; Sakamoto, Tatsuhiko; Ortega-Huertas, Miguel; Finlayson, Geraldine; Iijima, Koichi; Gallego-Torres, David; Fa, Darren

    2007-04-01

    Paleoclimate records from the western Mediterranean have been used to further understand the role of climatic changes in the replacement of archaic human populations inhabiting South Iberia. Marine sediments from the Balearic basin (ODP Site 975) was analysed at high resolution to obtain both geochemical and mineralogical data. These data were compared with climate records from nearby areas. Baexcces was used to characterize marine productivity and then related to climatic variability. Since variations in productivity were the consequence of climatic oscillations, climate/productivity events have been established. Sedimentary regime, primary marine productivity and oxygen conditions at the time of population replacement were reconstructed by means of a multiproxy approach. Climatic/oceanographic variations correlate well with Homo spatial and occupational patterns in Southern Iberia. It was found that low ventilation (U/Th), high river supply (Mg/Al), low aridity (Zr/Al) and low values of Baexcess coefficient of variation, may be linked with Neanderthal hospitable conditions. We attempt to support recent findings which claim that Neanderthals populations continued to inhabit southern Iberia between 30 and ˜28 ky cal BP and that this persistence was due to the specific characteristics of South Iberian climatic refugia. Comparisons of our data with other marine and continental records appear to indicate that conditions in South Iberia were highly inhospitable at ˜24 ky cal BP. Thus, it is proposed that the final disappearance of Neanderthals in this region could be linked with these extreme conditions.

  8. Topographic Signature of Climate Change- insights into climatic controls on landscape evolution under permafrost and non-permafrost environments

    NASA Astrophysics Data System (ADS)

    Gangodagamage, C.; Rowland, J. C.; Wilson, C. J.; Brumby, S.; Prancevic, J. P.; Crosby, B. T.; Marsh, P.; Altmann, G.

    2012-12-01

    Climate gradient across the deglaciated North American continental landscape has been a major control on the trajectory of landscape evolution following the Last Glacial Maximum (LGM) (~19-25 ka BP). Following deglaciation, landscapes in the Arctic and subarctic regions have been subject to climatic conditions favoring the development and/or preservation of permafrost. In more southerly latitudes, warmer conditions have favored non-permafrost conditions. A comparison of formerly glaciated landscapes in both permafrost and non-permafrost settings offers a unique natural experiment to explore the influence of climate on landscape evolution. Additionally, by comparing formerly glaciated terrains under both permafrost and non-permafrost conditions to landscapes never having undergone glaciation it may be possible to identify unique signatures of glaciation on hillslope morphology and processes. After glaciers retreated, newly exposed landscapes were exposed to both fluvial and hillslope mass wasting processes, the relative balance and influence of these processes on landscape evolution varied depending on Holocene climatic conditions (permafrost versus non-permaforst environments). Using analysis of high resolution Digital Elevation Model (DEM ~ 1m) data we show that the topographic denudation on these landscapes over the past Holocene has imprinted a unique climatic signature. Major differences are observed in landscape regimes and regime transitions. These differences are quantified mainly by introducing a new index, Normalized Directed Distance for Relief (NDDR), that treats the landscape relief differences and successfully identify the climate induced landscape responses. Previously glaciated permafrost landscapes are primarily characterized by narrow divergent hilltops (NDDR < 0.3), longer convergent flow paths (~500-1000 m) in hillslopes, and abrupt hillslope to fluvial transitions (< 100 m). Previously glaciated non-permafrost landscapes characterized by

  9. Stability and activity of mesophilic subtilisin E and its thermophilic homolog: Insights from molecular dynamics simulations

    SciTech Connect

    Colombo, G.; Merz, K.M. Jr.

    1999-07-28

    This report examines the origin of the high-temperature (250 K) behavior of a thermophilic mutant enzyme (labeled at 5-3H5; see Zhao and Arnold Prot. Eng. 1999, 12, 47--53) derived from subtilisin E by eight amino acid substitutions. Through the use of molecular dynamics (MD) simulations, the authors have provided molecular-level insights into how point mutations can affect protein structure and dynamics. From simulations the authors observed a reduced rmsd in several key regions, an increased overall flexibility, an increase in the number of hydrogen bonds, and an increase in the number of stabilizing interactions in the thermophilic system. It was shown that it is not a necessary requirement that thermophilic enzymes be less flexible than their mesophilic counterparts at low temperatures. However, thermophilic enzymes must retain their three-dimensional structures and flexibility at high temperatures in order to retain activity. Furthermore, the authors have been able to point out the effects of some of the single substitutions. Even if it is not possible yet to give general rules for rational protein design, the authors are able to make some predictions on how a protein should be stabilized in order to be thermophilic. In particular, the authors suggest that a promising strategy toward speeding up the design of thermally stable proteins would be to identify fluxional regions within a protein through the use of MD simulations (or suitable experiments). Presumably these regions allow for autocatalytic reactions to occur and are also involved in allowing water to gain access to the interior of the protein and initiate protein unfolding. These fluxional regions could also adversely affect the positioning of the catalytic machinery, thereby decreasing catalytic efficiency. Thus, once these locations have been identified, focused directed evolution studies could be designed that stabilize these fluxional regions.

  10. 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

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

    PubMed

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

    2014-04-17

    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, as well as 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 that 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 hydrogen 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 into how histone recognition by the bromodomain directs the biological function of BRPF1, ultimately targeting the MOZ HAT complex to chromatin substrates. PMID:24333487

  12. 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

  13. New Insights into Molecular Mechanisms of Immune Complex-Induced Injury in Lung.

    PubMed

    Ward, Peter A; Fattahi, Fatemeh; Bosmann, Markus

    2016-01-01

    While the phlogistic activities of IgM or IgG immune complexes (ICs) have been well established as complement-activating agents and seem likely to play important roles in humans with vasculitis, certain types of glomerulonephritis as well as in a variety of autoimmune diseases, the predominant clinical strategies have involved the use of immunosuppressive or anti-inflammatory drugs. Over the past decade, new insights into molecular events developing during IC models in rodents have identified new phlogistic products that may be candidates for therapeutic blockade. Extracellular histones, located in the web-like structures of neutrophil extracellular traps, are released from complement-activated polymorphonuclear neutrophils (PMNs) downstream of IC deposition. Extracellular histones appear to be a new class of highly tissue-damaging products derived from complement-activated PMNs. Histones have also been discovered in cell-free broncho-alveolar lavage fluids from humans with acute respiratory distress syndrome (ARDS). Recent studies emphasize that in the setting of ARDS-like reactions in rodents, extracellular histones are released and are exceedingly proinflammatory, tissue damaging, and prothrombotic. Such studies suggest that in humans with ARDS, extracellular histones may represent therapeutic targets for blockade. PMID:27014266

  14. Atractaspis aterrima toxins: the first insight into the molecular evolution of venom in side-stabbers.

    PubMed

    Terrat, Yves; Sunagar, Kartik; Fry, Bryan G; Jackson, Timothy N W; Scheib, Holger; Fourmy, Rudy; Verdenaud, Marion; Blanchet, Guillaume; Antunes, Agostinho; Ducancel, Frederic

    2013-11-01

    Although snake venoms have been the subject of intense research, primarily because of their tremendous potential as a bioresource for design and development of therapeutic compounds, some specific groups of snakes, such as the genus Atractaspis, have been completely neglected. To date only limited number of toxins, such as sarafotoxins have been well characterized from this lineage. In order to investigate the molecular diversity of venom from Atractaspis aterrima-the slender burrowing asp, we utilized a high-throughput transcriptomic approach completed with an original bioinformatics analysis pipeline. Surprisingly, we found that Sarafotoxins do not constitute the major ingredient of the transcriptomic cocktail; rather a large number of previously well-characterized snake venom-components were identified. Notably, we recovered a large diversity of three-finger toxins (3FTxs), which were found to have evolved under the significant influence of positive selection. From the normalized and non-normalized transcriptome libraries, we were able to evaluate the relative abundance of the different toxin groups, uncover rare transcripts, and gain new insight into the transcriptomic machinery. In addition to previously characterized toxin families, we were able to detect numerous highly-transcribed compounds that possess all the key features of venom-components and may constitute new classes of toxins. PMID:24169588

  15. New Insights into Molecular Mechanisms of Immune Complex-Induced Injury in Lung

    PubMed Central

    Ward, Peter A.; Fattahi, Fatemeh; Bosmann, Markus

    2016-01-01

    While the phlogistic activities of IgM or IgG immune complexes (ICs) have been well established as complement-activating agents and seem likely to play important roles in humans with vasculitis, certain types of glomerulonephritis as well as in a variety of autoimmune diseases, the predominant clinical strategies have involved the use of immunosuppressive or anti-inflammatory drugs. Over the past decade, new insights into molecular events developing during IC models in rodents have identified new phlogistic products that may be candidates for therapeutic blockade. Extracellular histones, located in the web-like structures of neutrophil extracellular traps, are released from complement-activated polymorphonuclear neutrophils (PMNs) downstream of IC deposition. Extracellular histones appear to be a new class of highly tissue-damaging products derived from complement-activated PMNs. Histones have also been discovered in cell-free broncho-alveolar lavage fluids from humans with acute respiratory distress syndrome (ARDS). Recent studies emphasize that in the setting of ARDS-like reactions in rodents, extracellular histones are released and are exceedingly proinflammatory, tissue damaging, and prothrombotic. Such studies suggest that in humans with ARDS, extracellular histones may represent therapeutic targets for blockade. PMID:27014266

  16. 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

  17. Molecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b

    PubMed Central

    Wang, Meimei; Soyano, Takashi; Machida, Satoru; Yang, Jun-Yi; Jung, Choonkyun; Chua, Nam-Hai; Yuan, Y. Adam

    2011-01-01

    The Agrobacterium Ti plasmid (T-DNA) 6b proteins interact with many different host proteins implicated in plant cell proliferation. Here, we show that Arabidopsis plants overexpressing 6b display microRNA (miRNA) deficiency by directly targeting SERRATE and AGO1 via a specific loop fragment (residues 40–55). In addition, we report the crystal structures of Agrobacterium tumefaciens AK6b at 2.1 Å, Agrobacterium vitis AB6b at 1.65 Å, and Arabidopsis ADP ribosylation factor (ARF) at 1.8 Å. The 6b structure adopts an ADP-ribosylating toxin fold closely related to cholera toxin. In vitro ADP ribosylation analysis demonstrates that 6b represents a new toxin family, with Tyr 66, Thr 93, and Tyr 153 as the ADP ribosylation catalytic residues in the presence of Arabidopsis ARF and GTP. Our work provides molecular insights, suggesting that 6b regulates plant cell growth by the disturbance of the miRNA pathway through its ADP ribosylation activity. PMID:21156810

  18. Unraveling the actions of AMP-activated protein kinase in metabolic diseases: Systemic to molecular insights.

    PubMed

    Weikel, Karen A; Ruderman, Neil B; Cacicedo, José M

    2016-05-01

    AMP-activated protein kinase (AMPK) plays a critical role both in sensing and regulating cellular energy state. In experimental animals, its activation has been shown to reduce the risk of obesity and diabetes-related co-morbidities such as insulin resistance, the metabolic syndrome and atherosclerotic cardiovascular disease. However, in humans, AMPK activation alone often does not completely resolve these conditions. Thus, an improved understanding of AMPK action and regulation in metabolic and other diseases is needed. Herein, we provide a brief description of the enzymatic regulation of AMPK and review its role in maintaining energy homeostasis. We then discuss tissue-specific actions of AMPK that become distorted during such conditions as obesity, type 2 diabetes and certain cancers. Finally, we explore recent findings regarding the interactions of AMPK with mammalian target of rapamycin complex 1 and the lysosome and discuss how changes in these relationships during overnutrition may lead to AMPK dysfunction. A more thorough understanding of AMPK's molecular interactions during diseases of overnutrition may provide key insights for the development of AMPK-based combinatorial treatments for metabolic disease. PMID:27085772

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

    PubMed

    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

  20. Insights into Medium-chain Acyl-CoA Dehydrogenase Structure by Molecular Dynamics Simulations.

    PubMed

    Bonito, Cátia A; Leandro, Paula; Ventura, Fátima V; Guedes, Rita C

    2016-08-01

    The medium-chain acyl-CoA dehydrogenase (MCAD) is a mitochondrial enzyme that catalyzes the first step of mitochondrial fatty acid β-oxidation (mFAO) pathway. Its deficiency is the most common genetic disorder of mFAO. Many of the MCAD disease-causing variants, including the most common p.K304E variant, show loss of function due to protein misfolding. Herein, we used molecular dynamics simulations to provide insights into the structural stability and dynamic behavior of MCAD wild-type (MCADwt) and validate a structure that would allow reliable new studies on its variants. Our results revealed that in both proteins the flavin adenine dinucleotide (FAD) has an important structural role on the tetramer stability and also in maintaining the volume of the enzyme catalytic pockets. We confirmed that the presence of substrate changes the dynamics of the catalytic pockets and increases FAD affinity. A comparison between the porcine MCADwt (pMCADwt) and human MCADwt (hMCADwt) structures revealed that both proteins are essentially similar and that the reversion of the double mutant E376G/T255E of hMCAD enzyme does not affect the structure of the protein neither its behavior in simulation. Our validated hMCADwt structure is crucial for complementing and accelerating the experimental studies aiming for the discovery and development of potential stabilizers of MCAD variants as candidates for the treatment of MCAD deficiency (MCADD). PMID:26992026

  1. Atractaspis aterrima Toxins: The First Insight into the Molecular Evolution of Venom in Side-Stabbers

    PubMed Central

    Terrat, Yves; Sunagar, Kartik; Fry, Bryan G.; Jackson, Timothy N. W.; Scheib, Holger; Fourmy, Rudy; Verdenaud, Marion; Blanchet, Guillaume; Antunes, Agostinho; Ducancel, Frederic

    2013-01-01

    Although snake venoms have been the subject of intense research, primarily because of their tremendous potential as a bioresource for design and development of therapeutic compounds, some specific groups of snakes, such as the genus Atractaspis, have been completely neglected. To date only limited number of toxins, such as sarafotoxins have been well characterized from this lineage. In order to investigate the molecular diversity of venom from Atractaspis aterrima—the slender burrowing asp, we utilized a high-throughput transcriptomic approach completed with an original bioinformatics analysis pipeline. Surprisingly, we found that Sarafotoxins do not constitute the major ingredient of the transcriptomic cocktail; rather a large number of previously well-characterized snake venom-components were identified. Notably, we recovered a large diversity of three-finger toxins (3FTxs), which were found to have evolved under the significant influence of positive selection. From the normalized and non-normalized transcriptome libraries, we were able to evaluate the relative abundance of the different toxin groups, uncover rare transcripts, and gain new insight into the transcriptomic machinery. In addition to previously characterized toxin families, we were able to detect numerous highly-transcribed compounds that possess all the key features of venom-components and may constitute new classes of toxins. PMID:24169588

  2. 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.

  3. Prolactin and teleost ionocytes: new insights into cellular and molecular targets of prolactin in vertebrate epithelia

    PubMed Central

    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. PMID:24434597

  4. 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.

  5. Molecular Insights into Pediatric Brain Tumors Have the Potential to Transform Therapy

    PubMed Central

    Gajjar, Amar; Pfister, Stefan M.; Taylor, Michael D.; Gilbertson, Richard J.

    2014-01-01

    High-throughput genomic technologies have shed light on the biologic heterogeneity of several pediatric brain tumors. The biology of the four common pediatric brain tumors—namely medulloblastoma, ependymoma, high-grade glioma including diffuse intrinsic pontine glioma and low-grade glioma are highlighted in this CCR Focus article. The discovery that medulloblastoma consists of 4 different subgroups namely WNT, SHH, Group 3 and Group 4, each with distinct clinical and molecular features, has impacted the treatment of children with medulloblastoma. Prospective studies have documented the efficacy of SMO inhibitors in a subgroup of patients with SHH medulloblastoma. Efforts are ongoing to develop specific therapies for each of the subgroups of medulloblastoma. Similar efforts are being pursued for ependymoma, high grade glioma and diffuse intrinsic pontine glioma where the disease outcome for the latter two tumors has not changed over the past 3 decades despite several prospective clinical trials. Developing and testing targeted therapies based on this new understanding remains a major challenge to the pediatric neuro-oncology community. The focus of this review is to summarize the rapidly evolving understanding of the common pediatric brain tumors based on genome wide analysis. These novel insights will add impetus to translating these laboratory based discoveries to newer therapies for children diagnosed with these tumors. PMID:25398846

  6. Prolactin and teleost ionocytes: new insights into cellular and molecular targets of prolactin in vertebrate epithelia.

    PubMed

    Breves, Jason P; McCormick, Stephen D; Karlstrom, Rolf O

    2014-07-01

    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. PMID:24434597

  7. Interactions of acidic pharmaceuticals with human serum albumin: insights into the molecular toxicity of emerging pollutants.

    PubMed

    Chen, Jiabin; Zhou, Xuefei; Zhang, Yalei; Qian, Yajie; Gao, Haiping

    2012-10-01

    Acidic pharmaceuticals such as diclofenac (DCF), clofibric acid (CA) and ketoprofen (KTP) have been detected frequently in environmental media. In order to reveal the toxicity of such emerging pollutants, their interactions with human serum albumin (HSA) were investigated by capillary electrophoresis, molecular spectrometry, and equilibrium dialysis. The binding constants and sites of these acidic pharmaceuticals with HSA were obtained. The thermodynamic parameters, e.g. enthalpy change and entropy change of these interactions were calculated to characterize that all the reactions resulted from hydrophobic and electrostatic interactions. The static quenching of the fluorescence of HSA was observed when interacted with acidic pharmaceuticals, indicating acidic pharmaceuticals bound to Tryptophan residue of HSA. The 3D fluorescence and circular dichroism confirmed that the secondary conformation of HSA changed after the interactions with the pharmaceuticals. At physiological condition, only 0.12 mM acidic pharmaceuticals reduced the binding of vitamin B(2) to HSA by 37, 30 and 21% for DCF, KTP and CA, respectively. This work provides an insight into non-covalent interactions between emerging contaminants and biomolecule, and is helpful for clarifying the toxic mechanism of such emerging contaminants. PMID:22307229

  8. Cellular and molecular mechanisms of negligible senescence: insight from the sea urchin

    PubMed Central

    Bodnar, Andrea G.

    2015-01-01

    Sea urchins exhibit a very different life history from humans and short-lived model animals and therefore provide the opportunity to gain new insight into the complex process of aging. Sea urchins grow indeterminately, regenerate damaged appendages, and reproduce throughout their lifespan. Some species show no increase in mortality rate at advanced ages. Nevertheless, different species of sea urchins have very different reported lifespans ranging from 4 to more than 100 years, thus providing a unique model to investigate the molecular, cellular, and physiological mechanisms underlying both lifespan determination and negligible senescence. Studies to date have demonstrated maintenance of telomeres, maintenance of antioxidant and proteasome enzyme activities, and little accumulation of oxidative cellular damage with age in tissues of sea urchin species with different lifespans. Gene expression studies indicate that key cellular pathways involved in energy metabolism, protein homeostasis, and tissue regeneration are maintained with age. Taken together, these studies suggest that long-term maintenance of mechanisms that sustain tissue homeostasis and regenerative capacity is essential for indeterminate growth and negligible senescence, and a better understanding of these processes may suggest effective strategies to mitigate the degenerative decline in human tissues with age. PMID:26136616

  9. 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.

  10. Parasite zoonoses and climate change: molecular tools for tracking shifting boundaries.

    PubMed

    Polley, Lydden; Thompson, R C Andrew

    2009-06-01

    For human, domestic animal and wildlife health, key effects of directional climate change include the risk of the altered occurrence of infectious diseases. Many parasite zoonoses have high potential for vulnerability to the new climate, in part because their free-living life-cycle stages and ectothermic hosts are directly exposed to climatic conditions. For these zoonoses, climate change can shift boundaries for ecosystem components and processes integral to parasite transmission and persistence, and these shifts can impact host health. Vulnerable boundaries include those for spatial distributions, host-parasite assemblages, demographic rates, life-cycle phenologies, associations within ecosystems, virulence, and patterns of infection and disease. This review describes these boundary shifts and how molecular techniques can be applied to defining the new boundaries. PMID:19428303

  11. 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. PMID:24680541

  12. Modelled Insights into Climate Dynamics of the Cretaceous and Paleogene Greenhouse

    NASA Astrophysics Data System (ADS)

    Lunt, D. J.; Loptson, C.; Farnsworth, A.; Markwick, P. J.

    2013-12-01

    Although the current paradigm is that CO2 is the primary driver of large-scale Earth System change through the Cretaceous and Paleogene, the relative importance of changing palaeogeography on climate dynamics through this greenhouse period is yet to be fully explored. In particular, the opening and closing of key ocean gateways, orogenesis, and continentality, could have a key role in determining not only the timing of key transitions (e.g. Eocene-Oligocene glaciation), but could also contribute directly to the large-scale trends. Here, we present a new series of climate model simulations, built upon state-of-the-art palaeogeographic maps (~20 in total covering the Cretaceous and Paleogene). The suite of simulations allows us to consider key questions related to climate dynamics through this time period: (1) What is the role of changing palaeogeography (including gateways) in mediating ocean circulation, through changing gateways and continental configuration? (2) What is the contribution of changing palaeogeography to climate, and climate sensitivity? Through considering the relationship between the local and regional scale, we explore the dangers of drawing global conclusions from local data, and highlight key areas where new palaeodata could be targeted to inform the above questions and better evaluate the models.

  13. 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

  14. 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. PMID

  15. 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

  16. 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

  17. 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

  18. Structural and molecular insights into novel surface-exposed mucus adhesins from Lactobacillus reuteri human strains.

    PubMed

    Etzold, Sabrina; MacKenzie, Donald A; Jeffers, Faye; Walshaw, John; Roos, Stefan; Hemmings, Andrew M; Juge, Nathalie

    2014-05-01

    The mucus layer covering the gastrointestinal tract is the first point of contact of the intestinal microbiota with the host. Cell surface macromolecules are critical for adherence of commensal bacteria to mucus but structural information is scarce. Here we report the first molecular and structural characterization of a novel cell-surface protein, Lar_0958 from Lactobacillus reuteri JCM 1112(T) , mediating adhesion of L. reuteri human strains to mucus. Lar_0958 is a modular protein of 133 kDa containing six repeat domains, an N-terminal signal sequence and a C-terminal anchoring motif (LPXTG). Lar_0958 homologues are expressed on the cell-surface of L. reuteri human strains, as shown by flow-cytometry and immunogold microscopy. Adhesion of human L. reuteri strains to mucus in vitro was significantly reduced in the presence of an anti-Lar_0958 antibody and Lar_0958 contribution to adhesion was further confirmed using a L. reuteri ATCC PTA 6475 lar_0958 KO mutant (6475-KO). The X-ray crystal structure of a single Lar_0958 repeat, determined at 1.5 Å resolution, revealed a divergent immunoglobulin (Ig)-like β-sandwich fold, sharing structural homology with the Ig-like inter-repeat domain of internalins of the food borne pathogen Listeria monocytogenes. These findings provide unique structural insights into cell-surface protein repeats involved in adhesion of Gram-positive bacteria to the intestine. PMID:24593252

  19. Dispersing perylene diimide/SWCNT hybrids: structural insights at the molecular level and fabricating advanced materials.

    PubMed

    Tsarfati, Yael; Strauss, Volker; Kuhri, Susanne; Krieg, Elisha; Weissman, Haim; Shimoni, Eyal; Baram, Jonathan; Guldi, Dirk M; Rybtchinski, Boris

    2015-06-17

    The unique properties of carbon nanotubes (CNT) are advantageous for emerging applications. Yet, the CNT insolubility hampers their potential. Approaches based on covalent and noncovalent methodologies have been tested to realize stable dispersions of CNTs. Noncovalent approaches are of particular interest as they preserve the CNT's structures and properties. We report on hybrids, in which perylene diimide (PDI) amphiphiles are noncovalently immobilized onto single wall carbon nanotubes (SWCNT). The resulting hybrids were dispersed and exfoliated both in water and organic solvents in the presence of two different PDI derivatives, PP2b and PP3a. The dispersions were investigated using cryogenic transmission electron microscopy (cryo-TEM), providing unique structural insights into the exfoliation. A helical arrangement of PP2b assemblies on SWCNTs dominates in aqueous dispersions, while a single layer of PP2b and PP3a was found on SWCNTs in organic dispersions. The dispersions were probed by steady-state and time-resolved spectroscopies, revealing appreciable charge redistribution in the ground state, and an efficient electron transfer from SWCNTs to PDIs in the excited state. We also fabricated hybrid materials from the PP2b/SWCNT dispersions. A supramolecular membrane was prepared from aqueous dispersions and used for size-selective separation of gold nanoparticles. Hybrid buckypaper films were prepared from the organic dispersions. In the latter, high conductivity results from enhanced electronic communication and favorable morphology within the hybrid material. Our findings shed light onto SWCNT/dispersant molecular interactions, and introduce a versatile approach toward universal solution processing of SWCNT-based materials. PMID:25977989

  20. New insights into the molecular mechanisms of biomembrane structural changes and interactions by optical biosensor technology.

    PubMed

    Lee, Tzong-Hsien; Hirst, Daniel J; Aguilar, Marie-Isabel

    2015-09-01

    Biomolecular-membrane interactions play a critical role in the regulation of many important biological processes such as protein trafficking, cellular signalling and ion channel formation. Peptide/protein-membrane interactions can also destabilise and damage the membrane which can lead to cell death. Characterisation of the molecular details of these binding-mediated membrane destabilisation processes is therefore central to understanding cellular events such as antimicrobial action, membrane-mediated amyloid aggregation, and apoptotic protein induced mitochondrial membrane permeabilisation. Optical biosensors have provided a unique approach to characterising membrane interactions allowing quantitation of binding events and new insight into the kinetic mechanism of these interactions. One of the most commonly used optical biosensor technologies is surface plasmon resonance (SPR) and there have been an increasing number of studies reporting the use of this technique for investigating biophysical analysis of membrane-mediated events. More recently, a number of new optical biosensors based on waveguide techniques have been developed, allowing membrane structure changes to be measured simultaneously with mass binding measurements. These techniques include dual polarisation interferometry (DPI), plasmon waveguide resonance spectroscopy (PWR) and optical waveguide light mode spectroscopy (OWLS). These techniques have expanded the application of optical biosensors to allow the analysis of membrane structure changes during peptide and protein binding. This review provides a theoretical and practical overview of the application of biosensor technology with a specific focus on DPI, PWR and OWLS to study biomembrane-mediated events and the mechanism of biomembrane disruption. This article is part of a Special Issue entitled: Lipid-protein interactions. PMID:26009270

  1. New insights on Arctic Quaternary climate variability from palaeo-records and numerical modelling

    NASA Astrophysics Data System (ADS)

    Jakobsson, Martin; Long, Antony; Ingólfsson, Ólafur; Kjær, Kurt H.; Spielhagen, Robert F.

    2010-12-01

    Terrestrial and marine geological archives in the Arctic contain information on environmental change through Quaternary interglacial-glacial cycles. The Arctic Palaeoclimate and its Extremes (APEX) scientific network aims to better understand the magnitude and frequency of past Arctic climate variability, with focus on the "extreme" versus the "normal" conditions of the climate system. One important motivation for studying the amplitude of past natural environmental changes in the Arctic is to better understand the role of this region in a global perspective and provide base-line conditions against which to explore potential future changes in Arctic climate under scenarios of global warming. In this review we identify several areas that are distinct to the present programme and highlight some recent advances presented in this special issue concerning Arctic palaeo-records and natural variability, including spatial and temporal variability of the Greenland Ice Sheet, Arctic Ocean sediment stratigraphy, past ice shelves and marginal marine ice sheets, and the Cenozoic history of Arctic Ocean sea ice in general and Holocene oscillations in sea ice concentrations in particular. The combined sea ice data suggest that the seasonal Arctic sea ice cover was strongly reduced during most of the early Holocene and there appear to have been periods of ice free summers in the central Arctic Ocean. This has important consequences for our understanding of the recent trend of declining sea ice, and calls for further research on causal links between Arctic climate and sea ice.

  2. Genetic response to climatic change: insights from ancient DNA and phylochronology.

    PubMed

    Hadly, Elizabeth A; Ramakrishnan, Uma; Chan, Yvonne L; van Tuinen, Marcel; O'Keefe, Kim; Spaeth, Paula A; Conroy, Chris J

    2004-10-01

    Understanding how climatic change impacts biological diversity is critical to conservation. Yet despite demonstrated effects of climatic perturbation on geographic ranges and population persistence, surprisingly little is known of the genetic response of species. Even less is known over ecologically long time scales pertinent to understanding the interplay between microevolution and environmental change. Here, we present a study of population variation by directly tracking genetic change and population size in two geographically widespread mammal species (Microtus montanus and Thomomys talpoides) during late-Holocene climatic change. We use ancient DNA to compare two independent estimates of population size (ecological and genetic) and corroborate our results with gene diversity and serial coalescent simulations. Our data and analyses indicate that, with population size decreasing at times of climatic change, some species will exhibit declining gene diversity as expected from simple population genetic models, whereas others will not. While our results could be consistent with selection, independent lines of evidence implicate differences in gene flow, which depends on the life history strategy of species. PMID:15361933

  3. 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. PMID:25549630

  4. 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

  5. The simulated climate of the Last Glacial Maximum and the insights into the global carbon cycle

    NASA Astrophysics Data System (ADS)

    Matear, R. J.; Lenton, A.; Etheridge, D.; Phipps, S. J.

    2015-03-01

    Global climate models (GCMs) provide an important tool for simulating the earth's climate. Here we present a GCM simulation of the climate of the Last Glacial Maximum (LGM), which was obtained by setting atmospheric greenhouse gas concentrations and the earth's orbital parameters to the values which prevailed at 21 000 years before present (BP). During the LGM, we simulate a significant cooling of the ocean and a dramatic expansion of the sea-ice extent. This behaviour agrees with reconstructions from paleoclimate archives. In the ocean, the LGM simulation produces a significant redistribution of dissolved oxygen and carbon. The oxygen levels rise and the volume of anoxic water declines by more than 50%, which is consistent with paleoclimate reconstructions of denitrification. The simulated LGM climate also stores more carbon in the deep ocean (below 2000 m), but with a reduced atmospheric CO2 level the total carbon stored in the ocean declines by 600 Pg C. The LGM ocean circulation preconditions the ocean to store carbon in the deep; however, the ocean circulation and sea-ice changes are insufficient alone to increase the total carbon stored in the ocean and modifications to the ocean biogeochemical cycles are required. With modifications to organic and inorganic carbon export and organic carbon remineralization one can increase ocean carbon storage (240 Pg C) to a level that is sufficient to explain the reduction in atmospheric and land carbon during the LGM (520 ± 400 Pg C). With the modified biogeochemical cycling in the ocean, the simulated aragonite lysocline depth and dissolved oxygen become more consistent with paleo-reconstructions.

  6. Enhanced insights into late Quaternary African hydroclimate dynamics using a water-isotope enabled climate model

    NASA Astrophysics Data System (ADS)

    Singarayer, Joy; Holloway, Max

    2016-04-01

    The climate of intertropical Africa is strongly governed by the dynamics of the tropical rainbelt, which is often associated with the Intertropical Convergence Zone (ITCZ). On millennial time-scales the primary drivers of variation in the rainbelt include orbital configuration changes to insolation seasonality and high-latitude forcing (e.g. Heinrich events). The spatial pattern of precipitation variability in tropical and subtropical Africa over the late Quaternary is complex and has long been debated. Stable water isotopes from inland lakes and off-shore ocean core records have provided longitudinal records, variously interpreted as changes to precipitation intensity or changes to moisture source location due to atmospheric circulation changes (or a combination of several factors). In this preliminary study we have used a global climate model, HadCM3, in which water isotopes are interactively coupled to produce snapshots at 1000-year intervals covering the last deglaciation (21kyr to pre-industrial). In conjunction with a comparison to available palaeodata, this enables us to better elucidate the connections between precipitation and other climate factors with changes to the water isotope signature, as well as how this varies regionally and through time.

  7. Role of Livelihood Capital in Reducing Climatic Vulnerability: Insights of Australian Wheat from 1990-2010.

    PubMed

    Huai, Jianjun

    2016-01-01

    In many agricultural countries, development of rural livelihood through increasing capital is a major regional policy to adapt to climate change. However, the role of livelihood capital in reducing climatic vulnerability is uncertain. This study assesses vulnerability and identifies the effects of common capital indicators on it, using Australian wheat as an example. We calculate exposure (a climate index) and sensitivity (a wheat failure index) to measure vulnerability and classify the resilient and sensitive cases, and express adaptive capacity through financial, human, natural, physical, and social capital indicators for 12 regions in the Australian wheat-sheep production zone from 1991-2010. We identify relationships between 12 indicators of five types of capital and vulnerability with t-tests and six logistic models considering the capital indicator itself, its first-order lag and its square as dependent variables to test the hypothesis that a high level of each capital metric results in low vulnerability. Through differing adaptive capacities between resilient and sensitive groups, we found that only four of the 12 (e.g., the access to finance, cash income level, total crop gross revenues, and family share of farm income) relate to vulnerability, which challenges the hypothesis that increasing capital reduces vulnerability. We conclude that further empirical reexaminations are required to test the relationships between capital measures and vulnerability under the sustainable livelihood framework (SLF). PMID:27022910

  8. Role of Livelihood Capital in Reducing Climatic Vulnerability: Insights of Australian Wheat from 1990–2010

    PubMed Central

    Huai, Jianjun

    2016-01-01

    In many agricultural countries, development of rural livelihood through increasing capital is a major regional policy to adapt to climate change. However, the role of livelihood capital in reducing climatic vulnerability is uncertain. This study assesses vulnerability and identifies the effects of common capital indicators on it, using Australian wheat as an example. We calculate exposure (a climate index) and sensitivity (a wheat failure index) to measure vulnerability and classify the resilient and sensitive cases, and express adaptive capacity through financial, human, natural, physical, and social capital indicators for 12 regions in the Australian wheat–sheep production zone from 1991–2010. We identify relationships between 12 indicators of five types of capital and vulnerability with t-tests and six logistic models considering the capital indicator itself, its first-order lag and its square as dependent variables to test the hypothesis that a high level of each capital metric results in low vulnerability. Through differing adaptive capacities between resilient and sensitive groups, we found that only four of the 12 (e.g., the access to finance, cash income level, total crop gross revenues, and family share of farm income) relate to vulnerability, which challenges the hypothesis that increasing capital reduces vulnerability. We conclude that further empirical reexaminations are required to test the relationships between capital measures and vulnerability under the sustainable livelihood framework (SLF). PMID:27022910

  9. New insights into the molecular-level control of silica mineralization by diatoms

    NASA Astrophysics Data System (ADS)

    Wallace, A. F.; Dove, P. M.

    2007-12-01

    microscopy with elements of modern materials chemistry, to directly measure the rate of amorphous silica nucleation on COOH, NH3+, and COOH / NH3+-terminated surfaces under controlled solution conditions. Our results provide new insights into the molecular-level control of silica mineralization in diatoms. We show that differences between substrate-specific nucleation rates are controlled largely by kinetic factors rather than thermodynamic drivers, and that amine-terminated surfaces are not capable of triggering the onset of silica deposition without the synergistic activity of neighboring negatively charged species on the surface or in solution (e.g. carboxyl or phosphoryl groups). In light of this result we conclude that sites on the organic matrix that have phosphate and amine moieties in close proximity serve not only as contact points between the constituent macromolecules in the matrix, but also as initial sites of silica deposition.

  10. 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.

  11. 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

  12. KZai 02 pollen record, an insight into West African monsoon fluctuations during the Last Climatic Cycle

    NASA Astrophysics Data System (ADS)

    Dalibard, M.; Popescu, S.; Maley, J.; Suc, J.

    2012-12-01

    Climate of the circum-Atlantic intertropical zone is driven by the ocean/atmosphere dynamics in response to variations of yearly insolation. These latitudes correspond to the convergence of the Hadley cells expressed on earth surface by intense trade winds and in lower troposphere by the African easterly jet making the edges of the intertropical zone relatively dry, while humidity is concentrated near the Equator. This phenomenon generates a precipitation front, known as the InterTropical Convergence Zone (ITCZ), the oscillations of which regulate the latitudinal vegetation distribution. Pollen record of core KZai 02 (Guinea Gulf) allows high resolution reconstruction of variations of past ecosystems over Central Africa during the Last Climatic Cycle. Plant taxa recorded in pollen analyses have been clustered according to their ecological requirements and African phytogeography. Fluctuations of these groups inform on precipitation intensity and their distribution during the last 130 ka. During Glacials, an open vegetation made of Cyperaceae marshes developed in the central Zaire/Congo Basin, surrounded by savannah on borders and afromontane forests on reliefs. Composition and distribution of vegetation indicate a decrease in monsoon activity and the strengthening of the precipitation front in the center of the basin. Interglacial phases are characterized by rain forest expansion over Central Africa in response to a precipitation enhancement associated with a northward shift of the rainfall front. Replacement of afromontane forest and marsh ecosystems by savannah then lowland pioneering, warm-temperate and rain forests characterized glacial/interglacial transitions. This succession suggests the increasing influence of at least two climatic parameters: the water availability and temperature and/or CO2 fluctuation. Spectral analysis applied to vegetation groups evidences the forcing of insolation, mainly driven by precession, on the West African monsoon system. Sub

  13. π-Hydrogen Bonding of Aromatics on the Surface of Aerosols: Insights from Ab Initio and Molecular Dynamics Simulation.

    PubMed

    Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei

    2016-07-14

    Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics. PMID:27280740

  14. 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. PMID:26990129

  15. Insights into Low-frequency Climate Dynamics from a Surface Temperature Reconstruction Spanning the Last 2,000 Years

    NASA Astrophysics Data System (ADS)

    Wang, J.; Emile-Geay, J.; McKay, N.; Guillot, D.

    2015-12-01

    Reconstructions of surface temperature over the past 2000 years extend our knowledge of temperature changes beyond the instrumental era, and thus allows for the characterization of climate variability on multidecadal to centennial timescales. This lends insight into our understanding and quantification of the influence of exogenous and endogenous global climate variability. In this study, we do so via a set of global temperature reconstructions based on the latest incarnation of the PAGES 2k global multi-proxy database (http://www.pages-igbp.org/ini/wg/2k-network/data/phase-2-data-status). Two climate field reconstruction (CFR) methods are employed: Gaussian graphical models embedded within the regularized EM algorithm (GraphEM, Guillot et al., 2015) and Canonical Correlation Analysis (CCA, Smerdon et al., 2010). We find a globally warm Medieval period, which was colder than the late twentieth-century by 0.5 C. With a probability of 87%, the 1961 - 1990 period was the warmest 40-year period in the past 2000 years in most regions, especially in the high latitudes of the Northern Hemisphere. We show that surface temperature has a robust large-scale cooling pattern shortly after a volcanic eruption; in particular, over the North Atlantic Ocean, the cooling can persist up to 3 years after an eruption. An El Niño-like response (~0.2 C) is also found in 2 and 3 years after an eruption. Solar irradiance forcing is found to be an important modulator of multidecadal climate variability, with the strongest solar response (0.25 C) in high latitude North America. These key features are echoed in multiple GCM simulations of the last millennium, though we find notable differences, in particular regarding the timing of the post-volcanic ENSO response, and the magnitude of the temperature response to solar irradiance forcing. The results suggest that there is no fundamental discrepancy between simulated and reconstructed climates of the last millennium, and thus lend credibility

  16. New Biogeographic insight into Bauhinia s.l. (Leguminosae): integration from fossil records and molecular analyses

    PubMed Central

    2014-01-01

    Background Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical intercontinental disjunction among the Asian, African, and American continents. Geographic distribution patterns are better recognized when fossil records and molecular sequences are combined in the analyses. Here, we describe a new macrofossil species of Bauhinia from the Upper Miocene Xiaolongtan Formation in Wenshan County, Southeast Yunnan, China, and elucidate the biogeographic significance through the analyses of molecules and fossils. Results Morphometric analysis demonstrates that the leaf shapes of B. acuminata, B. championii, B. chalcophylla, B. purpurea, and B. podopetala closely resemble the leaf shapes of the new finding fossil. Phylogenetic relationships among the Bauhinia species were reconstructed using maximum parsimony and Bayesian inference, which inferred that species in Bauhinia species are well-resolved into three main groups. Divergence times were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method under a relaxed clock, and inferred that the stem diversification time of Bauhinia was ca. 62.7 Ma. The Asian lineage first diverged at ca. 59.8 Ma, followed by divergence of the Africa lineage starting during the late Eocene, whereas that of the neotropical lineage starting during the middle Miocene. Conclusions Hypotheses relying on vicariance or continental history to explain pantropical disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. We suggest that Bauhinia originated in the middle Paleocene in Laurasia, probably in Asia, implying a possible Tethys Seaway origin or an “Out of Tropical Asia”, and dispersal of legumes. Its present pantropical disjunction resulted from disruption of the boreotropical flora by climatic cooling after the Paleocene-Eocene Thermal

  17. The role of observational reference data for climate downscaling: Insights from the VALUE COST Action

    NASA Astrophysics Data System (ADS)

    Kotlarski, Sven; Gutiérrez, José M.; Boberg, Fredrik; Bosshard, Thomas; Cardoso, Rita M.; Herrera, Sixto; Maraun, Douglas; Mezghani, Abdelkader; Pagé, Christian; Räty, Olle; Stepanek, Petr; Soares, Pedro M. M.; Szabo, Peter

    2016-04-01

    VALUE is an open European network to validate and compare downscaling methods for climate change research (http://www.value-cost.eu). A key deliverable of VALUE is the development of a systematic validation framework to enable the assessment and comparison of downscaling methods. Such assessments can be expected to crucially depend on the existence of accurate and reliable observational reference data. In dynamical downscaling, observational data can influence model development itself and, later on, model evaluation, parameter calibration and added value assessment. In empirical-statistical downscaling, observations serve as predictand data and directly influence model calibration with corresponding effects on downscaled climate change projections. We here present a comprehensive assessment of the influence of uncertainties in observational reference data and of scale-related issues on several of the above-mentioned aspects. First, temperature and precipitation characteristics as simulated by a set of reanalysis-driven EURO-CORDEX RCM experiments are validated against three different gridded reference data products, namely (1) the EOBS dataset (2) the recently developed EURO4M-MESAN regional re-analysis, and (3) several national high-resolution and quality-controlled gridded datasets that recently became available. The analysis reveals a considerable influence of the choice of the reference data on the evaluation results, especially for precipitation. It is also illustrated how differences between the reference data sets influence the ranking of RCMs according to a comprehensive set of performance measures.

  18. Unraveling the molecular effects of mutation L270P on Wiskkot-Aldrich syndrome protein: insights from molecular dynamics approach.

    PubMed

    Palaniappan, Chandrasekaran; Rao, Sethumadhavan; Ramalingam, Rajasekaran

    2016-09-01

    Missense mutation L270P disrupts the auto-inhibited state of "Wiskkot-Aldrich syndrome protein" (WASP), thereby constitutively activating the mutant structure, a key event for pathogenesis of X-linked neutropenia (XLN). In this study, we comprehensively deciphered the molecular feature of activated mutant structure by all atom molecular dynamics (MD) approach. MD analysis revealed that mutant structure exposed a wide variation in the spatial environment of atoms, resulting in enhanced residue flexibility. The increased flexibility of residues favored to decrease the number of intra-molecular hydrogen bonding interactions in mutant structure. The reduction of hydrogen bonds in the mutant structure resulted to disrupt the local folding of secondary structural elements that eventually affect the proper folding of mutants. The unfolded state of mutant structure established more number of inter-molecular hydrogen bonding interaction at interface level due to the conformational variability, thus mediated high binding affinity with its interacting partner, Cdc42. PMID:26457828

  19. Vulnerability of the northern Mongolian steppe to climate change: insights from flower production and phenology.

    PubMed

    Liancourt, Pierre; Spence, Laura A; Boldgiv, Bazartseren; Lkhagva, Ariuntsetseg; Helliker, Brent R; Casper, Brenda B; Petraitis, Peter S

    2012-04-01

    The semiarid, northern Mongolian steppe, which still supports pastoral nomads who have used the steppe for millennia, has experienced an average 1.7 degrees C temperature rise over the past 40 years. Continuing climate change is likely to affect flowering phenology and flower numbers with potentially important consequences for plant community composition, ecosystem services, and herder livelihoods. Over the growing seasons of 2009 and 2010, we examined flowering responses to climate manipulation using open-top passive warming chambers (OTCs) at two locations on a south-facing slope: one on the moister, cooler lower slope and the other on the drier, warmer upper slope, where a watering treatment was added in a factorial design with warming. Canonical analysis of principal coordinates (CAP) revealed that OTCs reduced flower production and delayed peak flowering in graminoids as a whole but only affected forbs on the upper slope, where peak flowering was also delayed. OTCs affected flowering phenology in seven of eight species, which were examined individually, either by altering the time of peak flowering and/or the onset and/or cessation of flowering, as revealed by survival analysis. In 2010, which was the drier year, OTCs reduced flower production in two grasses but increased production in an annual forb found only on the upper slope. The particular effects of OTCs on phenology, and whether they caused an extension or contraction of the flowering season, differed among species, and often depended on year, or slope, or watering treatment; however, a relatively strong pattern emerged for 2010 when four species showed a contraction of the flowering season in OTCs. Watering increased flower production in two species in 2010, but slope location more often affected flowering phenology than did watering. Our results show the importance of taking landscape-scale variation into account in climate change studies and also contrasted with those of several studies set in cold

  20. Molecular-Level Insights into Photocatalysis from Scanning Probe Microscopy Studies on TiO2(110)

    SciTech Connect

    Henderson, Michael A.; Lyubinetsky, Igor

    2013-06-12

    The field of heterogeneous photocatalysis has grown considerably in the decades since Fujishima and Honda's ground-breaking publications of photoelectrochemistry on TiO2. Numerous review articles continue to point to both progress made in the use of heterogeneous materials (such as TiO2) to perform photoconversion processes, and the many opportunities and challenges in heterogeneous photocatalysis research such as solar energy conversion and environmental remediation. The past decade has also seen an increase in the use of molecular-level approaches applied to model single crystal surfaces in an effort to obtain new insights into photocatalytic phenomena. In particular, scanning probe techniques (SPM) have enabled researchers to take a ‘nanoscale’ approach to photocatalysis that includes interrogation of the reactivities of specific sites and adsorbates on a model photocatalyst surface. The rutile TiO2(110) surface has become the prototypical oxide single crystal surface for fundamental studies of many interfacial phenomena. In particular, TiO2(110) has become an excellent model surface for probing photochemical and photocatalytic reactions at the molecular level. A variety of experimental approaches have emerged as being ideally suited for studying photochemical reactions on TiO2(110), including desorption-oriented approaches and electronic spectroscopies, but perhaps the most promising techniques for evaluating site-specific properties are those of SPM. In this review, we highlight the growing use of SPM techniques in providing molecular-level insights into surface photochemistry on the model photocatalyst surface of rutile TiO2(110). Our objective is to both illustrate the unique knowledge that scanning probe techniques have already provided the field of photocatalysis, and also to motivate a new generation of effort into the use of such approaches to obtain new insights into the molecular level details of photochemical events occurring at interfaces

  1. Global warming and changes in risk of concurrent climate extremes: Insights from the 2014 California drought

    NASA Astrophysics Data System (ADS)

    AghaKouchak, Amir; Cheng, Linyin; Mazdiyasni, Omid; Farahmand, Alireza

    2014-12-01

    Global warming and the associated rise in extreme temperatures substantially increase the chance of concurrent droughts and heat waves. The 2014 California drought is an archetype of an event characterized by not only low precipitation but also extreme high temperatures. From the raging wildfires, to record low storage levels and snowpack conditions, the impacts of this event can be felt throughout California. Wintertime water shortages worry decision-makers the most because it is the season to build up water supplies for the rest of the year. Here we show that the traditional univariate risk assessment methods based on precipitation condition may substantially underestimate the risk of extreme events such as the 2014 California drought because of ignoring the effects of temperature. We argue that a multivariate viewpoint is necessary for assessing risk of extreme events, especially in a warming climate. This study discusses a methodology for assessing the risk of concurrent extremes such as droughts and extreme temperatures.

  2. Climate control on ancestral population dynamics: insight from Patagonian fish phylogeography.

    PubMed

    Ruzzante, Daniel E; Walde, Sandra J; Gosse, John C; Cussac, Victor E; Habit, Evelyn; Zemlak, Tyler S; Adams, Emily D M

    2008-05-01

    Changes in lake and stream habitats during the growth and retreat of Pleistocene glaciers repeatedly altered the spatial distributions and population sizes of the aquatic fauna of the southern Andes. Here, we use variation in mtDNA control region sequences to infer the temporal dynamics of two species of southern Andean fish during the past few million years. At least five important climate events were associated with major demographic changes: (i) the widespread glaciations of the mid-Pliocene (c. 3.5 Ma); (ii) the largest Patagonian glaciation (1.1 Ma); (iii) the coldest Pleistocene glaciation as indicated by stacked marine delta(18)O (c. 0.7 Ma); (iv) the last southern Patagonian glaciation to reach the Atlantic coast (180 ka); and (v) the last glacial maximum (LGM, 23-25,000 years ago). The colder-water inhabitant, Galaxias platei, underwent a strong bottleneck during the LGM and its haplotype diversity coalesces c. 0.7 Ma. In contrast, the more warm-adapted and widely distributed Percichthys trucha showed continuous growth through the last two glacial cycles but went through an important bottleneck c. 180,000 years ago, at which time populations east of the Andes may have been eliminated. Haplotype diversity of the most divergent P. trucha populations, found west of the Andes, coalesces c. 3.2 Ma. The demographic timelines obtained for the two species thus illustrate the continent-wide response of aquatic life in Patagonia to climate change during the Pleistocene, but also show how differing ecological traits and distributions led to distinctive responses. PMID:18363661

  3. New Insights on Hydro-Climate Feedback Processes over the Tropical Ocean from TRMM

    NASA Technical Reports Server (NTRS)

    Lau, William K. M.; Wu, H. T.; Li, Xiaofan; Sui, C. H.

    2002-01-01

    In this paper, we study hydro-climate feedback processes over the tropical oceans, by examining the relationships among large scale circulation and Tropical Rainfall Measuring Mission Microwave Imager-Sea Surface Temperature (TMI-SST), and a range of TRMM rain products including rain rate, cloud liquid water, precipitable water, cloud types and areal coverage, and precipitation efficiency. Results show that for a warm event (1998), the 28C threshold of convective precipitation is quite well defined over the tropical oceans. However, for a cold event (1999), the SST threshold is less well defined, especially over the central and eastern Pacific cold tongue, where stratiform rain occurs at much lower than 28 C. Precipitation rates and cloud liquid water are found to be more closely related to the large scale vertical motion than to the underlying SST. While total columnar water vapor is more strongly dependent on SST. For a large domain, over the eastern Pacific, we find that the areal extent of the cloudy region tends to shrink as the SST increases. Examination of the relationship between cloud liquid water and rain rate suggests that the residence time of cloud liquid water tends to be shorter, associated with higher precipitation efficiency in a warmer climate. It is hypothesized that the reduction in cloudy area may be influenced both by the shift in large scale cloud patterns in response to changes in large scale forcings, and possible increase in the cloud liquid water conversion to rain water in a warmer environment. Results of numerical experiments with the Goddard cloud resolving model to test the hypothesis will be discussed.

  4. Oldest isotopically characterized fish otoliths provide insight to Jurassic continental climate of Europe

    NASA Astrophysics Data System (ADS)

    Patterson, William P.

    1999-03-01

    Large, shallow, epeiric seas and adjacent lagoons such as those described herein likely played a significant role in moderating Jurassic coastal and continental climate. Jurassic (Bathonian) ocean surface temperatures in Scotland have been calculated from δ18O(CaCO3) values of a suite of the oldest well-preserved fish otoliths analyzed to date. Otolith δ18O values range from -4.7‰ to -1.9‰ (Vienna Peedee belemnite, VPDB), while δ13C(CaCO3) values vary from -5.4‰ to +1.5‰ (VPDB), representing the oldest stable isotopic record of paleodiet, paleoecology, and fish migration to date. Using a global ocean δ18O(H2O) value of -1.0‰ (Vienna standard mean ocean water, VSMOW) for an ice-free Jurassic, fish species that migrated from estuarine to open marine water record time-averaged temperatures of 23 °C. Estuarine fish, assuming a similar temperature, record variation in δ18O(H2O) values from -3.7‰ to -2.0‰ (VSMOW). That significant mixing of fresh water and seawater occurred in the Jurassic in Scotland is in general agreement with data presented by others (molluscan fauna, lithostratigraphy, paleogeography, and paleocirculation models). The δ18O values and temperatures derived in this study correspond to the meteorologic and hydrologic parameters of a mid-latitude maritime climate with low seasonality, a mean temperature of 23 °C, and abundant precipitation and humidity. The δ18O(H2O) values calculated from estuarine fish indicate that rainfall must have a δ18O(H2O) value lower than -3.7‰ (VSMOW). Values of δ18O and δ13C suggest an environment hydrologically similar to that observed in the Everglades of south Florida or the estuaries of south Texas, both notable fish nurseries today. However, sea-surface temperatures were lower than those of modern Florida or Texas as evidenced by reduced evaporative enrichment of δ18O(H2O) values.

  5. Insights from the Molecular Dynamics Simulation of Cellobiohydrolase Cel6A Molecular Structural Model from Aspergillus fumigatus NITDGPKA3.

    PubMed

    Dodda, Subba Reddy; Sarkar, Nibedita; Aikat, Kaustav; Krishnaraj, Navanietha R; Bhattacharjee, Sanchari; Bagchi, Angshuman; Mukhopadhyay, Sudit S

    2016-01-01

    Global demand for bioethanol is increasing tremendously as it could help to replace the conventional fossil fuel and at the same time supporting the bioremediation of huge volume of cellulosic wastes generated from different sources. Ideal genetic engineering approaches are essential to improve the efficacy of the bioethanol production processes for real time applications. A locally isolated fungal strain Aspergillus fumigatus NITDGPKA3 was used in our laboratory for the hydrolysis of lignocellulose with good cellulolytic activity when compared with other contemporary fungal strains. An attempt is made to sequence the cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, model its structure to predict its catalytic activity towards improving the protein by genetic engineering approaches. Herein, the structure of the sequenced Cellobiohydrolases (CBHs) of A. fumigatus NITDGPKA3, modelled by homology modelling and its validation is reported. Further the catalytic activity of the modelled CBH enzyme was assessed by molecular docking analysis. Phylogenetic analysis showed that CBH from A. fumigatus NITDGPKA3 belongs to the Glycohydro 6 (Cel6A) super family. Molecular modeling and molecular dynamics simulation suggest the structural and functional mechanism of the enzyme. The structures of both the cellulose binding (CBD) and catalytic domain (CD) have been compared with most widely studied CBH of Trichoderma reesei. The molecular docking with cellulose suggests that Gln 248, Pro 287, Val236, Asn284, and Ala288 are the main amino acids involved in the hydrolysis of the β, 1-4, glycosidic bonds of cellulose. PMID:27109185

  6. Late Triassic tropical climate of Pangea: Carbon isotopic and other insights into the rise of dinosaurs

    NASA Astrophysics Data System (ADS)

    Whiteside, J. H.; Lindström, S.; Irmis, R. B.; Glasspool, I.; Schaller, M. F.; Dunlavey, M.; Nesbitt, S. J.; Smith, N. D.; Turner, A. H.

    2015-12-01

    The rarity and species-poor nature of early dinosaurs and their relatives at low paleolatitudes persisted for 30 million years after their origin and 10-15 million years after they became abundant and speciose at higher latitudes. New environmental reconstructions from stable carbon isotope ratios of preserved organic matter (δ13Corg), atmospheric pCO2 data based on the δ13C of soil carbonate, palynological, and wildfire data from charcoal from early dinosaur-bearing strata at low paleolatitudes in western North America show that variations in δ13Corg and palynomorph ecotypes are tightly correlated, displaying large and high-frequency excursions. These variations occurred within an environment characterized by elevated and increasing atmospheric pCO2, pervasive wildfires, and rapidly fluctuating extreme climatic conditions. Whereas pseudosuchian archosaur-dominated communities were able to persist in these same regions until the end-Triassic, the large-bodied, fast-growing tachymetabolic dinosaurian herbivores were not. We hypothesize that the greater resources required by the herbivores made it difficult from them to adapt to the unstable conditions at low paleolatitudes in the Late Triassic.

  7. Baffin Island snow extent sensitivity: Insights from a regional climate model

    NASA Astrophysics Data System (ADS)

    Berdahl, Mira; Robock, Alan

    2013-05-01

    Recent modeling efforts suggest that the Little Ice Age (LIA) onset could be explained by a series of four large decadally-spaced volcanic eruptions. At that time, glaciers on Baffin Island advanced and did not retreat until the past century, perhaps due to Arctic and North Atlantic Ocean sea ice feedbacks. To try to determine what parameters sustain snow cover, we investigate the relative impacts of changes in radiation and advection on minimum summer snow extent over Baffin Island. We used the Weather Research and Forecasting (WRF) model to run eight 6 month long (April-September), 10 km resolution simulations, in which we varied boundary condition temperatures, solar radiation, and sea ice cover. Although the Control Run underestimated cloud cover and thus produced an exaggerated diurnal 2 m temperature cycle, the relative changes of snow extent show that WRF accurately simulates snow expansion into the same regions as during the LIA. With an average temperature decrease from current temperatures by -3.9 ± 1.1 K, it only requires one season for the model to lower the snowline by comparable elevation changes seen during the descent into the LIA. WRF's maximum snow line sensitivity is 7 K/km, within the range of the typically assumed lapse rate of 5-7 K/km in the Canadian Arctic. Thus, if a shift in the Arctic climate greatly expanded sea ice coverage following large volcanic eruptions, this would have been enough to perpetuate an ice sheet on Baffin Island throughout the LIA.

  8. Insight into glacier climate interaction: reconstruction of the mass balance field using ice extent data

    NASA Astrophysics Data System (ADS)

    Visnjevic, Vjeran; Herman, Frédéric; Licul, Aleksandar

    2016-04-01

    With the end of the Last Glacial Maximum (LGM), about 20 000 years ago, ended the most recent long-lasting cold phase in Earth's history. We recently developed a model that describes large-scale erosion and its response to climate and dynamical changes with the application to the Alps for the LGM period. Here we will present an inverse approach we have recently developed to infer the LGM mass balance from known ice extent data, focusing on a glacier or ice cap. The ice flow model is developed using the shallow ice approximation and the developed codes are accelerated using GPUs capabilities. The mass balance field is the constrained variable defined by the balance rate β and the equilibrium line altitude (ELA), where c is the cutoff value: b = max(βṡ(S(z) - ELA), c) We show that such a mass balance can be constrained from the observed past ice extent and ice thickness. We are also investigating several different geostatistical methods to constrain spatially variable mass balance, and derive uncertainties on each of the mass balance parameters.

  9. Using Variation Theory with Metacognitive Monitoring to Develop Insights into How Students Learn from Molecular Visualizations

    ERIC Educational Resources Information Center

    Kelly, Resa M.

    2014-01-01

    Molecular visualizations have been widely endorsed by many chemical educators as an efficient way to convey the dynamic and atomic-level details of chemistry events. Research indicates that students who use molecular visualizations are able to incorporate most of the intended features of the animations into their explanations. However, studies…

  10. Molecular cooperativity in the dynamics of glass-forming systems: A new insight

    NASA Astrophysics Data System (ADS)

    Hong, L.; Gujrati, P. D.; Novikov, V. N.; Sokolov, A. P.

    2009-11-01

    The mechanism behind the steep slowing down of molecular motions upon approaching the glass transition remains a great puzzle. Most of the theories relate this mechanism to the cooperativity in molecular motion. In this work, we estimate the length scale of molecular cooperativity ξ for many glass-forming systems from the collective vibrations (the so-called boson peak). The obtained values agree well with the dynamic heterogeneity length scale estimated using four-dimensional NMR. We demonstrate that ξ directly correlates to the dependence of the structural relaxation on volume. This dependence presents only one part of the mechanism of slowing down the structural relaxation. Our analysis reveals that another part, the purely thermal variation in the structural relaxation (at constant volume), does not have a direct correlation with molecular cooperativity. These results call for a conceptually new approach to the analysis of the mechanism of the glass transition and to the role of molecular cooperativity.

  11. Atomic-Scale Insight into Tautomeric Recognition, Separation, and Interconversion of Guanine Molecular Networks on Au(111).

    PubMed

    Zhang, Chi; Xie, Lei; Wang, Likun; Kong, Huihui; Tan, Qinggang; Xu, Wei

    2015-09-16

    Although tautomerization may directly affect the chemical or biological properties of molecules, real-space investigation on the tautomeric behaviors of organic molecules in a larger area of molecular networks has been scarcely reported. In this paper, we choose guanine (G) molecule as a model system. From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have successfully achieved the tautomeric recognition, separation, and interconversion of G molecular networks (formed by two tautomeric forms G/9H and G/7H) with the aid of NaCl on the Au(111) surface in ultrahigh vacuum (UHV) conditions. Our results may serve as a prototypical system to provide important insights into tautomerization related issues, which should be intriguing to biochemistry, pharmaceutics, and other related fields. PMID:26322860

  12. Historical Arctic Logbooks Provide Insights into Past Diets and Climatic Responses of Cod.

    PubMed

    Townhill, Bryony L; Maxwell, David; Engelhard, Georg H; Simpson, Stephen D; Pinnegar, John K

    2015-01-01

    Gadus morhua (Atlantic cod) stocks in the Barents Sea are currently at levels not seen since the 1950s. Causes for the population increase last century, and understanding of whether such large numbers will be maintained in the future, are unclear. To explore this, we digitised and interrogated historical cod catch and diet datasets from the Barents Sea. Seventeen years of catch data and 12 years of prey data spanning 1930-1959 cover unexplored spatial and temporal ranges, and importantly capture the end of a previous warm period, when temperatures were similar to those currently being experienced. This study aimed to evaluate cod catch per unit effort and prey frequency in relation to spatial, temporal and environmental variables. There was substantial spatio-temporal heterogeneity in catches through the time series. The highest catches were generally in the 1930s and 1940s, although at some localities more cod were recorded late in the 1950s. Generalized Additive Models showed that environmental, spatial and temporal variables are all valuable descriptors of cod catches, with the highest occurring from 15-45°E longitude and 73-77°N latitude, at bottom temperatures between 2 and 4°C and at depths between 150 and 250 m. Cod diets were highly variable during the study period, with frequent changes in the relative frequencies of different prey species, particularly Mallotus villosus (capelin). Environmental variables were particularly good at describing the importance of capelin and Clupea harengus (herring) in the diet. These new analyses support existing knowledge about how the ecology of the region is controlled by climatic variability. When viewed in combination with more recent data, these historical relationships will be valuable in forecasting the future of Barents Sea fisheries, and in understanding how environments and ecosystems may respond. PMID:26331271

  13. Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.

    PubMed

    Kaniewska, Paulina; Chan, Chon-Kit Kenneth; Kline, David; Ling, Edmund Yew Siang; Rosic, Nedeljka; Edwards, David; Hoegh-Guldberg, Ove; Dove, Sophie

    2015-01-01

    Tropical reef-building coral stress levels will intensify with the predicted rising atmospheric CO2 resulting in ocean temperature and acidification increase. Most studies to date have focused on the destabilization of coral-dinoflagellate symbioses due to warming oceans, or declining calcification due to ocean acidification. In our study, pH and temperature conditions consistent with the end-of-century scenarios of the Intergovernmental Panel on Climate Change (IPCC) caused major changes in photosynthesis and respiration, in addition to decreased calcification rates in the coral Acropora millepora. Population density of symbiotic dinoflagellates (Symbiodinium) under high levels of ocean acidification and temperature (Representative Concentration Pathway, RCP8.5) decreased to half of that found under present day conditions, with photosynthetic and respiratory rates also being reduced by 40%. These physiological changes were accompanied by evidence for gene regulation of calcium and bicarbonate transporters along with components of the organic matrix. Metatranscriptomic RNA-Seq data analyses showed an overall down regulation of metabolic transcripts, and an increased abundance of transcripts involved in circadian clock control, controlling the damage of oxidative stress, calcium signaling/homeostasis, cytoskeletal interactions, transcription regulation, DNA repair, Wnt signaling and apoptosis/immunity/ toxins. We suggest that increased maintenance costs under ocean acidification and warming, and diversion of cellular ATP to pH homeostasis, oxidative stress response, UPR and DNA repair, along with metabolic suppression, may underpin why Acroporid species tend not to thrive under future environmental stress. Our study highlights the potential increased energy demand when the coral holobiont is exposed to high levels of ocean warming and acidification. PMID:26510159

  14. Historical Arctic Logbooks Provide Insights into Past Diets and Climatic Responses of Cod

    PubMed Central

    Townhill, Bryony L.; Maxwell, David; Engelhard, Georg H.; Simpson, Stephen D.; Pinnegar, John K.

    2015-01-01

    Gadus morhua (Atlantic cod) stocks in the Barents Sea are currently at levels not seen since the 1950s. Causes for the population increase last century, and understanding of whether such large numbers will be maintained in the future, are unclear. To explore this, we digitised and interrogated historical cod catch and diet datasets from the Barents Sea. Seventeen years of catch data and 12 years of prey data spanning 1930–1959 cover unexplored spatial and temporal ranges, and importantly capture the end of a previous warm period, when temperatures were similar to those currently being experienced. This study aimed to evaluate cod catch per unit effort and prey frequency in relation to spatial, temporal and environmental variables. There was substantial spatio-temporal heterogeneity in catches through the time series. The highest catches were generally in the 1930s and 1940s, although at some localities more cod were recorded late in the 1950s. Generalized Additive Models showed that environmental, spatial and temporal variables are all valuable descriptors of cod catches, with the highest occurring from 15–45°E longitude and 73–77°N latitude, at bottom temperatures between 2 and 4°C and at depths between 150 and 250 m. Cod diets were highly variable during the study period, with frequent changes in the relative frequencies of different prey species, particularly Mallotus villosus (capelin). Environmental variables were particularly good at describing the importance of capelin and Clupea harengus (herring) in the diet. These new analyses support existing knowledge about how the ecology of the region is controlled by climatic variability. When viewed in combination with more recent data, these historical relationships will be valuable in forecasting the future of Barents Sea fisheries, and in understanding how environments and ecosystems may respond. PMID:26331271

  15. Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change

    PubMed Central

    Kaniewska, Paulina; Chan, Chon-Kit Kenneth; Kline, David; Ling, Edmund Yew Siang; Rosic, Nedeljka; Edwards, David; Hoegh-Guldberg, Ove; Dove, Sophie

    2015-01-01

    Tropical reef-building coral stress levels will intensify with the predicted rising atmospheric CO2 resulting in ocean temperature and acidification increase. Most studies to date have focused on the destabilization of coral-dinoflagellate symbioses due to warming oceans, or declining calcification due to ocean acidification. In our study, pH and temperature conditions consistent with the end-of-century scenarios of the Intergovernmental Panel on Climate Change (IPCC) caused major changes in photosynthesis and respiration, in addition to decreased calcification rates in the coral Acropora millepora. Population density of symbiotic dinoflagellates (Symbiodinium) under high levels of ocean acidification and temperature (Representative Concentration Pathway, RCP8.5) decreased to half of that found under present day conditions, with photosynthetic and respiratory rates also being reduced by 40%. These physiological changes were accompanied by evidence for gene regulation of calcium and bicarbonate transporters along with components of the organic matrix. Metatranscriptomic RNA-Seq data analyses showed an overall down regulation of metabolic transcripts, and an increased abundance of transcripts involved in circadian clock control, controlling the damage of oxidative stress, calcium signaling/homeostasis, cytoskeletal interactions, transcription regulation, DNA repair, Wnt signaling and apoptosis/immunity/ toxins. We suggest that increased maintenance costs under ocean acidification and warming, and diversion of cellular ATP to pH homeostasis, oxidative stress response, UPR and DNA repair, along with metabolic suppression, may underpin why Acroporid species tend not to thrive under future environmental stress. Our study highlights the potential increased energy demand when the coral holobiont is exposed to high levels of ocean warming and acidification. PMID:26510159

  16. Understanding impacts of climatic extremes on diarrheal disease epidemics: Insights from mechanistic disease propagation models

    NASA Astrophysics Data System (ADS)

    Jutla, A.; Akanda, A. S.; Colwell, R. R.

    2013-12-01

    increased climatic variability, such as acceleration of hydrological cycle, hydroclimatic hazards, etc on diarrheal disease outbreaks.

  17. Climate impacts on human settlement and agricultural activities in northern Norway: new insights from biogeochemistry

    NASA Astrophysics Data System (ADS)

    D'anjou, R. M.; Bradley, R. S.; Balascio, N. L.; Finkelstein, D. B.

    2012-12-01

    Disentangling the effects of climate change and anthropogenic activities on the environment is a major challenge in paleoenvironmental research. Here, we used fecal sterols and other biogeochemical compounds in lake sediments from northern Norway to identify both natural and anthropogenic signals of environmental change during the late Holocene. The area was first occupied by humans and their grazing animals at ~2,250±75 cal yr BP. The arrival of humans is indicated by an abrupt increase in coprostanol (and its epimer epicoprostanol) in the sediments, and an associated increase in 5β-stigmastanol (and 5β-epistigmastanol), which resulted from human and animal feces washing into the lake. Human settlement was accompanied by an abrupt increase in landscape fires (indicated by the rise in pyrolytic polycyclic aromatic hydrocarbons, PAHs) and a decline in woodland (registered by a change in n-alkane chain lengths from leaf waxes), accelerating a process that began earlier in the Holocene. Human activity and associated landscape changes in the region over the last two millennia were mainly driven by summer temperatures, as indicated by independent tree-ring reconstructions, though there were periods when socio-economic factors played an equally important role. This is the first time that fecal sterols in lake sediments have been used to provide a record of human occupancy through time. This approach may be useful in many archeological studies, both to confirm the presence of humans and grazing animals, and to distinguish between anthropogenic and natural factors that have influenced the environment in the past.

  18. The microtubule-associated molecular pathways may be genetically disrupted in patients with Bipolar Disorder. Insights from the molecular cascades.

    PubMed

    Drago, Antonio; Crisafulli, Concetta; Sidoti, Antonina; Calabrò, Marco; Serretti, Alessandro

    2016-01-15

    Bipolar Disorder is a severe disease characterized by pathological mood swings from major depressive episodes to manic ones and vice versa. The biological underpinnings of Bipolar Disorder have yet to be defined. As a consequence, pharmacological treatments are suboptimal. In the present paper we test the hypothesis that the molecular pathways involved with the direct targets of lithium, hold significantly more genetic variations associated with BD. A molecular pathway approach finds its rationale in the polygenic nature of the disease. The pathways were tested in a sample of ∼ 7,000 patients and controls. Data are available from the public NIMH database. The definition of the pathways was conducted according to the National Cancer Institute (http://pid.nci.nih.gov/). As a result, 3 out of the 18 tested pathways related to lithium action resisted the permutation analysis and were found to be associated with BD. These pathways were related to Reelin, Integrins and Aurora. A pool of genes selected from the ones linked with the above pathways was further investigated in order to identify the fine molecular mechanics shared by our significant pathways and also their link with lithium mechanism of action. The data obtained point out to a possible involvement of microtubule-related mechanics. PMID:26551401

  19. Isotopic ratios of rainfall in eastern Africa: insights into reconstructing past climate from terrestrial archives

    NASA Astrophysics Data System (ADS)

    Levin, N. E.; Cerling, T. E.; Brown, F. H.; Quade, J.; Harris, J. M.

    2010-12-01

    The timing and intensity of rainfall dominate climate variability in eastern Africa on seasonal, interannual, and precessional timescales. Today, rainfall in eastern Africa is coupled to the position of the Intertropical Convergence Zone and the Congo Air Boundary; major wet and dry intervals during the late Pleistocene and Holocene are viewed with respect to the movement of these convergence zones. Oxygen and hydrogen isotopic ratios of rainfall in eastern Africa today reflect rainfall amount, moisture source and position relative to convergence zones, such that rainfall sourced in the Indian Ocean yields δ18O and δD values that are lower than δ18O and δD values of rainfall from interior sources (e.g., Congo Basin, Sud). An interior, recycled moisture source is likely responsible for the high δ18O and δD values of meteoric waters in Ethiopia today relative to other regions in East Africa. Here we propose that the connections between isotopic composition and moisture source in rainfall today can be used as a template for identifying shifts in moisture source and the position of convergence zones in the past. The isotopic composition of meteoric water is recorded in a variety of terrestrial materials such as soil and spring carbonates, bioapatites, mollusks and plant waxes, which have the potential to document the seasonality, intensity and source of rainfall. Soil carbonates and bioapatite from Pliocene and Pleistocene rift sediments in Kenya and Ethiopia indicate a >4‰ increase in δ18O values of rainfall since 2.0 Ma. In the Turkana Basin of northern Kenya, this record indicates more intense rainfall from the southeasterly monsoon prior to 2.0 Ma. In the Awash Basin of northeastern Ethiopia, low δ18O values in Plio-Pleistocene carbonates and bioapatite likely reflect the input of Indian Ocean moisture, which does not contribute substantial amounts of rainfall to the Awash Basin today. A northwestward shift of the Congo Air Boundary and an intensified

  20. Climatic vs. Seismic Controlled Rockglacier Advances in Northern Tien Shan - Insights from Lichenometry

    NASA Astrophysics Data System (ADS)

    Rosenwinkel, S.; Korup, O.; Landgraf, A.; Dzhumabaeva, A.

    2014-12-01

    patterns vary between the different locations and support the notion that the analyzed Tien Shan rockglaciers do not record climate-driven advances exclusively. We conclude by highlighting a number of constraints that may limit the use of lichenometry for dating rockglacier advances, and scope for future research on seismic triggers.

  1. Climate- vs. Earthquake-induced Rock-Glacier Advances in the Tien Shan: Insights from Lichenometry

    NASA Astrophysics Data System (ADS)

    Rosenwinkel, Swenja; Landgraf, Angela; Korup, Oliver; Sorg, Annina

    2014-05-01

    that Tien Shan rock glaciers do not record a consistent palaeoclimatic signal. We discuss whether distinct peaks of comparable lichen sizes and associated distributions of surface velocities for a given rock-glacier lobe result from rapid climate-driven advances or high lateral material input provided by seismically-induced slope instability instead. We compare our field data to advance-rate estimates from ground surveys and remote sensing (1 to >10 m/a), and dendrogeomorphic constraints obtained from trees growing on the rock glaciers. We conclude by highlighting a number of constraints that may limit the use of lichenometry for dating rock-glacier advances, and scope for future research on seismic triggers.

  2. Molecular taxonomy provides new insights into anopheles species of the neotropical arribalzagia series.

    PubMed

    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

  3. 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

  4. Acinar Cell Carcinoma of the Pancreas: Overview of Clinicopathologic Features and Insights into the Molecular Pathology

    PubMed Central

    La Rosa, Stefano; Sessa, Fausto; Capella, Carlo

    2015-01-01

    Acinar cell carcinomas (ACCs) of the pancreas are rare pancreatic neoplasms accounting for about 1–2% of pancreatic tumors in adults and about 15% in pediatric subjects. They show different clinical symptoms at presentation, different morphological features, different outcomes, and different molecular alterations. This heterogeneous clinicopathological spectrum may give rise to difficulties in the clinical and pathological diagnosis with consequential therapeutic and prognostic implications. The molecular mechanisms involved in the onset and progression of ACCs are still not completely understood, although in recent years, several attempts have been made to clarify the molecular mechanisms involved in ACC biology. In this paper, we will review the main clinicopathological and molecular features of pancreatic ACCs of both adult and pediatric subjects to give the reader a comprehensive overview of this rare tumor type. PMID:26137463

  5. Molecular recognition of malachite green by hemoglobin and their specific interactions: insights from in silico docking and molecular spectroscopy.

    PubMed

    Peng, Wei; Ding, Fei; Peng, Yu-Kui; Sun, Ying

    2014-01-01

    Malachite green is an organic compound that can be widely used as a dyestuff for various materials; it has also emerged as a controversial agent in aquaculture. Since malachite green is proven to be carcinogenic and mutagenic, it may become a hazard to public health. For this reason, it is urgently required to analyze this controversial dye in more detail. In our current research, the interaction between malachite green and hemoglobin under physiological conditions was investigated by the methods of molecular modeling, fluorescence spectroscopy, circular dichroism (CD) as well as hydrophobic ANS displacement experiments. From the molecular docking, the central cavity of hemoglobin was assigned to possess high-affinity for malachite green, this result was corroborated by time-resolved fluorescence and hydrophobic ANS probe results. The recognition mechanism was found to be of static type, or rather the hemoglobin-malachite green complex formation occurred via noncovalent interactions such as π-π interactions, hydrogen bonds and hydrophobic interactions with an association constant of 10(4) M(-1). Moreover, the results also show that the spatial structure of the biopolymer was changed in the presence of malachite green with a decrease of the α-helix and increase of the β-sheet, turn and random coil suggesting protein damage, as derived from far-UV CD and three-dimensional fluorescence. Results of this work will help to further comprehend the molecular recognition of malachite green by the receptor protein and the possible toxicological profiles of other compounds, which are the metabolites and ramifications of malachite green. PMID:24226412

  6. Electronic structure of covalently linked zinc bacteriochlorin molecular arrays: insights into molecular design for NIR light harvesting.

    PubMed

    Shrestha, Kushal; González-Delgado, Jessica M; Blew, James H; Jakubikova, Elena

    2014-10-23

    Pigment-based molecular arrays, especially those based on porphyrins, have been extensively studied as viable components of artificial light harvesting devices. Unlike porphyrins, bacteriochlorins absorb strongly in the NIR, yet little is known of the applicability of covalently linked bacteriochlorin-based arrays in this arena. To lay the foundation for future studies of excited state properties of such arrays, we present a systematic study of the ground state electronic structure of zinc bacteriochlorin (ZnBC) molecular arrays with various linkers and linker attachment sites (meso vs β) employing density functional theory in combination with the energy-based fragmentation (EBF) method, and the EBF with molecular orbitals (EBF-MO) method. We find that the level of steric hindrance between the ZnBC and the linker is directly correlated with the amount of ground sate electronic interactions between the ZnBCs. Low steric hindrance between the ZnBC and the linker found in alkyne-linked arrays results in strongly interacting arrays that are characterized by a decrease in the HOMO-LUMO energy gaps, large orbital energy dispersion in the frontier region, and low ZnBC-linker rotational barriers. In contrast, sterically hindered linkers, such as aryl-based linkers, result in weakly interacting arrays characterized by increased orbital energy degeneracy in the frontier region and high ZnBC-linker rotational barriers. For all linkers studied, the level of steric hindrance decreases when the ZnBCs are linked at the β position. Hence, ZnBC arrays that exhibit strong, weak, or intermediate ground-state electronic interactions can be realized by adjusting the level of steric hindrance with a judicious choice of the linker type and linker attachment site. Such tuning may be essential for design of light harvesting arrays with desired spectral properties. PMID:25237715

  7. Crater palaeolakes in the Tibesti mountains (Central Sahara, North Chad) - New insights into past Saharan climates

    NASA Astrophysics Data System (ADS)

    Kröpelin, Stefan; Dinies, Michèle; Sylvestre, Florence; Hoelzmann, Philipp

    2016-04-01

    For the first time continuous lacustrine sections were sampled from the volcanic Tibesti Mountains (Chad): In the 900 m deep crater of Trou au Natron at Pic Toussidé (3,315 m a.s.l.) and from the 800 m deep Era Kohor, the major sub-caldera of Emi Koussi (3,445 m a.s.l.). The remnant diatomites on their slopes are located 360 m (Trou au Natron) and 125 m (Era Kohor) above the present day bottom of the calderas. These sediments from highly continental positions in the central Sahara are keys for the reconstruction of the last climatic cycles (Kröpelin et al. 2015). We report first results from sedimentary-geochemical (total organic and total inorganic carbon contents; total nitrogen; major elements; mineralogy) and palynological analyses for palaeo-environmental interpretations. The diatomites from the Trou au Natron comprise 330 cm of mostly calcitic sediments with relatively low organic carbon (<2.5 %) and strongly varying aragonite and gypsum contents. Major elements (Ca, Fe, K, Mg, Mn, Na, P, S, Sr), elemental ratios (Sr/Ca, Mg/Ca, Fe/Mn) and the mineralogy are used to interpret the lake's salinity, productivity and ecological conditions. Trilete spores are preserved throughout the sequence, probably reflecting local moss/fern stands. Regional pollen rain-e.g. grasses and wormwood-is scarcely represented. Golden algae dominate in the lower section. The results of the first palynological samples suggest a small sedimentation basin. Two 14C-dated charcoals out of the upper part of the section indicate mid-Holocene ages and a linear extrapolation based on a sediment accumulation rate of 1.4mma-1 would lead to tentative dates of ~8650 cal a BP for basal lacustrine sediments and ~4450 cal a BP for the cessation of this lacustrine sequence. The diatomites from the Era Kohor reflect a suite of sections that in total sum up to 145 cm of mostly silica-based sediments with very low carbon contents (< 2% TC). Calcite dominated sediments are only present in the topmost 15

  8. Molecular interactions of UvrB protein and DNA from Helicobacter pylori: Insight into a molecular modeling approach.

    PubMed

    Bavi, Rohit; Kumar, Raj; Rampogu, Shailima; Son, Minky; Park, Chanin; Baek, Ayoung; Kim, Hyong-Ha; Suh, Jung-Keun; Park, Seok Ju; Lee, Keun Woo

    2016-08-01

    Helicobacter pylori (H. pylori) persevere in the human stomach, an environment in which they encounter many DNA-damaging conditions, including gastric acidity. The pathogenicity of H. pylori is enhanced by its well-developed DNA repair mechanism, thought of as 'machinery,' such as nucleotide excision repair (NER). NER involves multi-enzymatic excinuclease proteins (UvrABC endonuclease), which repair damaged DNA in a sequential manner. UvrB is the central component in prokaryotic NER, essential for damage recognition. Therefore, molecular modeling studies of UvrB protein from H. pylori are carried out with homology modeling and molecular dynamics (MD) simulations. The results reveal that the predicted structure is bound to a DNA hairpin with 3-bp stem, an 11-nucleotide loop, and 3-nt 3' overhang. In addition, a mutation of the Y96A variant indicates reduction in the binding affinity for DNA. Free-energy calculations demonstrate the stability of the complex and help identify key residues in various interactions based on residue decomposition analysis. Stability comparative studies between wild type and mutant protein-DNA complexes indicate that the former is relatively more stable than the mutant form. This predicted model could also be useful in designing new inhibitors for UvrB protein, as well as preventing the pathogenesis of H. pylori. PMID:27315565

  9. Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations.

    PubMed

    Hedger, George; Sansom, Mark S P

    2016-10-01

    Lipid molecules are able to selectively interact with specific sites on integral membrane proteins, and modulate their structure and function. Identification and characterization of these sites are 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. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26946244

  10. Coarse-grained modelling of triglyceride crystallisation: a molecular insight into tripalmitin tristearin binary mixtures by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pizzirusso, Antonio; Brasiello, Antonio; De Nicola, Antonio; Marangoni, Alejandro G.; Milano, Giuseppe

    2015-12-01

    The first simulation study of the crystallisation of a binary mixture of triglycerides using molecular dynamics simulations is reported. Coarse-grained models of tristearin (SSS) and tripalmitin (PPP) molecules have been considered. The models have been preliminarily tested in the crystallisation of pure SSS and PPP systems. Two different quenching procedures have been tested and their performances have been analysed. The structures obtained from the crystallisation procedures show a high orientation order and a high content of molecules in the tuning fork conformation, comparable with the crystalline α phase. The behaviour of melting temperatures for the α phase of the mixture SSS/PPP obtained from the simulations is in qualitative agreement with the behaviour that was experimentally determined.

  11. Energy frameworks: insights into interaction anisotropy and the mechanical properties of molecular crystals.

    PubMed

    Turner, Michael J; Thomas, Sajesh P; Shi, Ming W; Jayatilaka, Dylan; Spackman, Mark A

    2015-03-01

    We present an approach to understanding crystal packing via 'energy frameworks', that combines efficient calculation of accurate intermolecular interaction energies with a novel graphical representation of their magnitude. In this manner intriguing questions, such as why some crystals bend with an applied force while others break, and why one polymorph of a drug exhibits exceptional tabletability compared to others, can be addressed in terms of the anisotropy of the topology of pairwise intermolecular interaction energies. This approach is applied to a sample of organic molecular crystals with known bending, shearing and brittle behaviour, to illustrate its use in rationalising their mechanical behaviour at a molecular level. PMID:25525647

  12. Molecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4' benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations.

    PubMed

    Kumar, Akhil; Srivastava, Swati; Tripathi, Shubhandra; Singh, Sandeep Kumar; Srikrishna, Saripella; Sharma, Ashok

    2016-06-01

    Aggregation of amyloid peptide (Aβ) has been shown to be directly related to progression of Alzheimer's disease (AD). Aβ is neurotoxic and its deposition and aggregation ultimately lead to cell death. In our previous work, we reported flavonoid derivative (compound 1) showing promising result in transgenic AD model of Drosophila. Compound 1 showed prevention of Aβ-induced neurotoxicity and neuroprotective efficacy in Drosophila system. However, mechanism of action of compound 1 and its effect on the amyloid is not known. We therefore performed molecular docking and atomistic, explicit-solvent molecular dynamics simulations to investigate the process of Aβ interaction, inhibition, and destabilizing mechanism. Results showed different preferred binding sites of compound 1 and good affinity toward the target. Through the course of 35 ns molecular dynamics simulation, conformations_5 of compound 1 intercalates into the hydrophobic core near the salt bridge and showed major structural changes as compared to other conformations. Compound 1 showed interference with the salt bridge and thus reducing the inter strand hydrogen bound network. This minimizes the side chain interaction between the chains A-B leading to disorder in oligomer. Contact map analysis of amino acid residues between chains A and B also showed lesser interaction with adjacent amino acids in the presence of compound 1 (conformations_5). The study provides an insight into how compound 1 interferes and disorders the Aβ peptide. These findings will further help to design better inhibitors for aggregation of the amyloid oligomer. PMID:26208790

  13. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme—Catalase

    PubMed Central

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  14. Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

    SciTech Connect

    Rastogi, Monisha; Vaish, Rahul

    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 generated 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.

  15. Structure and Function: Insights into Bioinorganic Systems from Molecular Mechanics Calculations

    NASA Astrophysics Data System (ADS)

    Marques, Helder M.; Egan, Timothy J.; de Villiers, Katherine A.

    The use of empirical force field methods for modeling important systems in bioinorganic chemistry, including the cobalt corrins (derivatives of vitamin B12) and the iron porphyrins, is described. Particular attention is given to the use of molecular dynamics and simulated annealing calculations in exploring the solution structures of corrin, and those of likely complexes between the ferriprotoporphyrin-IX and the arylmethanol antimalarials.

  16. Molecular dynamics insight to phase transition in n-alkanes with carbon nanofillers

    NASA Astrophysics Data System (ADS)

    Rastogi, Monisha; Vaish, Rahul

    2015-05-01

    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 generated 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.

  17. 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. PMID:26276723

  18. Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes

    PubMed Central

    Barglow, Katherine T.; Saikatendu, Kumar S.; Bracey, Michael H.; Huey, Ruth; Morris, Garrett M.; Olson, Arthur J.; Stevens, Raymond C.; Cravatt, Benjamin F.

    2009-01-01

    Nitrilases are a large and diverse family of non-peptidic C-N hydrolases. The mammalian genome encodes eight nitrilase enzymes, several of which remain poorly characterized. Prominent among these are nitrilase-1 (Nit1) and nitrilase-2 (Nit2), which, despite having been shown to exert effects on cell growth and possibly serving as tumor suppressor genes, are without known substrates or selective inhibitors. In previous studies, we identified several nitrilases, including Nit1 and Nit2, as targets for dipeptide-chloroacetamide activity-based proteomics probes. Here, we have used these probes, in combination with high-resolution crystallography and molecular modeling, to systematically map the active site of Nit2 and identify residues involved in molecular recognition. We report the 1.4 Å crystal structure of mouse Nit2, and use this structure to identify residues that discriminate probe-labeling between the Nit1 and Nit2 enzymes. Interestingly, some of these residues are conserved across all vertebrate Nit2 enzymes and, conversely, not found in any vertebrate Nit1 enzymes, suggesting that they are key discriminators of molecular recognition between these otherwise highly homologous enzymes. Our findings thus point to a limited set of active site residues that establish distinct patterns of molecular recognition among nitrilases and provide chemical probes to selectively perturb the function of these enzymes in biological systems. PMID:19053248

  19. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme-Catalase.

    PubMed

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme-catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals' forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  20. 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

  1. Recent insights into the molecular mechanisms of the NLRP3 inflammasome activation.

    PubMed

    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

  2. Molecular insights into the microbial formation of marine dissolved organic matter: recalcitrant or labile?

    NASA Astrophysics Data System (ADS)

    Koch, B. P.; Kattner, G.; Witt, M.; Passow, U.

    2014-02-01

    The degradation of marine dissolved organic matter (DOM) is an important control variable in the global carbon cycle and dependent on the DOM composition. For our understanding of the kinetics of organic matter cycling in the ocean, it is therefore crucial to achieve a mechanistic and molecular understanding of its transformation processes. A long-term microbial experiment was performed to follow the production of non-labile DOM by marine bacteria. Two different glucose concentrations and dissolved algal exudates were used as substrates. We monitored the bacterial abundance, concentrations of dissolved and particulate organic carbon (DOC, POC), nutrients, amino acids, and transparent exopolymer particles (TEP) for two years. Ultrahigh resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) allowed the molecular characterization of extracted DOM after 70 days and after ∼2 years of incubation. Although glucose was quickly degraded, a DOC background was generated in glucose incubations. Only 20% of the organic carbon from algal exudate was degraded within the 2 years of incubation. TEP, which are released by micro-organisms, were produced during glucose degradation but decreased within less than three weeks back to half of the maximum concentration and were below detection in all treatments after 2 years. The molecular analysis demonstrated that DOM generated during glucose degradation differed appreciably from DOM produced during the degradation of the algal exudates. Our results led to several conclusions: (i) Higher substrate levels result in a higher level of non-labile DOC which is an important prerequisite for carbon sequestration in the ocean; (ii) TEP are generated by bacteria but are also degraded rapidly, thus limiting their potential contribution to carbon sequestration; (iii) The molecular signatures of DOM derived from algal exudates or glucose after 70 days of incubation differed strongly from refractory DOM. After 2 years

  3. DNA molecular wire-based nanoelectronics: New insight and high frequency AC electrical characterization

    NASA Astrophysics Data System (ADS)

    Wibowo, Denni Ari

    While recent research in electron-transport mechanism on a double strands DNA seems to converge into a consensus, experiments in direct electrical measurements on a long DNA molecules still lead to a conflicting result. This research investigates experimentally the attachment of DNA molecular wire to high aspect ratio three-dimensional (3D) metal electrode and the effect of temperature to its AC electrical conductivity. The 3-D microelectrode was built on a silicone oxide substrate using patterned thick layers of negative tone photoresist covered by sputtered gold on the top surface. Attachment of lambda-DNA to the microelectrode was demonstrated using oligonucleotide-DNA phosphate backbone ligation and thiol-gold covalent bonding. Electrical characterizations based on I-V and AC impedance analysis of several repeatable data points of attachment with varying lambda-DNA concentration (500 ng/microL to 0.0625 ng/microL) showed measurable and significant conductivity of lambda-DNA molecular wires. Further study was carried out by measuring I-V and impedance while ramping up the temperature to reach complete denaturation (~1100C) resulting in no current transduction. Subsequent re-annealing of the DNA through incubation in TM buffer at annealing temperature (~900C) resulted in recovery of electrical conduction, providing a strong proof that DNA molecular wire is the one generate the electrical conductivity. lambda-DNA molecular wires reported to have differing impedance response at two temperature regions: impedance increases (conductivity decrease) between 40C -- 400C, and then decreases from 400C until DNA completely denatured (~1100C). The increase conductivity after 400C is an experimental support the long distance electron transport mechanism referred as "thermal hopping" mechanism. We believe that this research represents a significant departure from previous studies and makes unique contributions through (i) modification of DNA attachment methods has increase

  4. Molecular Structure of Aggregated Amyloid-β: Insights from Solid-State Nuclear Magnetic Resonance.

    PubMed

    Tycko, Robert

    2016-01-01

    Amyloid-β (Aβ) peptides aggregate to form polymorphic amyloid fibrils and a variety of intermediate assemblies, including oligomers and protofibrils, both in vitro and in human brain tissue. Since the beginning of the 21st century, considerable progress has been made to characterize the molecular structures of Aβ aggregates. Full molecular structural models based primarily on data from measurements using solid-state nuclear magnetic resonance (ssNMR) have been developed for several in vitro Aβ fibrils and one metastable protofibril. Partial structural characterization of other aggregation intermediates has been achieved. One full structural model for fibrils derived from brain tissue has also been reported. Future work is likely to focus on additional structures from brain tissue and on further clarification of nonfibrillar Aβ aggregates. PMID:27481836

  5. Coexistence of spinodal instability and thermal nucleation in thin-film rupture: insights from molecular levels.

    PubMed

    Nguyen, Trung Dac; Fuentes-Cabrera, Miguel; Fowlkes, Jason D; Rack, Philip D

    2014-03-01

    Despite extensive investigation using hydrodynamic models and experiments over the past decades, there remain open questions regarding the origin of the initial rupture of thin liquid films. One of the reasons that makes it difficult to identify the rupture origin is the coexistence of two dewetting mechanisms, namely, thermal nucleation and spinodal instability, as observed in many experimental studies. Using a coarse-grained model and large-scale molecular dynamics simulations, we are able to characterize the very early stage of dewetting in nanometer-thick liquid-metal films wetting a solid substrate. We observe the features characteristic of both spinodal instability and thermal nucleation in the spontaneously dewetting films and show that these two macroscopic mechanisms share a common origin at molecular levels. PMID:24730848

  6. Coexistence of spinodal instability and thermal nucleation in thin-film rupture: Insights from molecular levels

    NASA Astrophysics Data System (ADS)

    Nguyen, Trung Dac; Fuentes-Cabrera, Miguel; Fowlkes, Jason D.; Rack, Philip D.

    2014-03-01

    Despite extensive investigation using hydrodynamic models and experiments over the past decades, there remain open questions regarding the origin of the initial rupture of thin liquid films. One of the reasons that makes it difficult to identify the rupture origin is the coexistence of two dewetting mechanisms, namely, thermal nucleation and spinodal instability, as observed in many experimental studies. Using a coarse-grained model and large-scale molecular dynamics simulations, we are able to characterize the very early stage of dewetting in nanometer-thick liquid-metal films wetting a solid substrate. We observe the features characteristic of both spinodal instability and thermal nucleation in the spontaneously dewetting films and show that these two macroscopic mechanisms share a common origin at molecular levels.

  7. 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

  8. Hypoglycosylation of dystroglycan due to T192M mutation: a molecular insight behind the fact.

    PubMed

    Bhattacharya, Simanti; Das, Amit; Ghosh, Semanti; Dasgupta, Rakhi; Bagchi, Angshuman

    2014-03-01

    Abnormal glycosylation of dystroglycan (DG), a transmembrane glycoprotein, results in a group of diseases known as dystroglycanopathy. A severe dystroglycanopathy known as the limb girdle disease MDDGC9 [OMIM: 613818] occurs as a result of hypoglycosylation of alpha subunit of DG. Reasons behind this has been traced back to a point mutation (T192M) in DG that leads to weakening of interactions of DG protein with laminin and subsequent loss of signal flow through the DG protein. In this work we have tried to analyze the molecular details of the interactions between DG and laminin1 in order to propose a mechanism about the onset of the disease MDDGC9. We have observed noticeable changes between the modeled structures of wild type and mutant DG proteins. We also have employed molecular docking techniques to study and compare the binding interactions between laminin1 and both the wild type and mutant DG proteins. The docking simulations have revealed that the mutant DG has weaker interactions with laminin1 as compared to the wild type DG. Till date there are no previous reports that deal with the elucidation of the interactions of DG with laminin1 from the molecular level. Our study is therefore the first of its kind which analyzes the differences in binding patterns of laminin1 with both the wild type and mutant DG proteins. Our work would therefore facilitate analysis of the molecular mechanism of the disease MDDGC9. Future work based on our results may be useful for the development of suitable drugs against this disease. PMID:24361964

  9. 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

  10. Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei

    PubMed Central

    Gao, Yi; Zhang, Xiaojun; Wei, Jiankai; Sun, Xiaoqing; Yuan, Jianbo; Li, Fuhua; Xiang, Jianhai

    2015-01-01

    Molting is one of the most important biological processes in shrimp growth and development. All shrimp undergo cyclic molting periodically to shed and replace their exoskeletons. This process is essential for growth, metamorphosis, and reproduction in shrimp. However, the molecular mechanisms underlying shrimp molting remain poorly understood. In this study, we investigated global expression changes in the transcriptomes of the Pacific white shrimp, Litopenaeus vannamei, the most commonly cultured shrimp species worldwide. The transcriptome of whole L. vannamei was investigated by RNA-sequencing (RNA-seq) throughout the molting cycle, including the inter-molt (C), pre-molt (D0, D1, D2, D3, D4), and post-molt (P1 and P2) stages, and 93,756 unigenes were identified. Among these genes, we identified 5,117 genes differentially expressed (log2ratio ≥1 and FDR ≤0.001) in adjacent molt stages. The results were compared against the National Center for Biotechnology Information (NCBI) non-redundant protein/nucleotide sequence database, Swiss-Prot, PFAM database, the Gene Ontology database, and the Kyoto Encyclopedia of Genes and Genomes database in order to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. The expression patterns for genes involved in several molecular events critical for molting, such as hormone regulation, triggering events, implementation phases, skelemin, immune responses were characterized and considered as mechanisms underlying molting in L. vannamei. Comparisons with transcriptomic analyses in other arthropods were also performed. The characterization of major transcriptional changes in genes involved in the molting cycle provides candidates for future investigation of the molecular mechanisms. The data generated in this study will serve as an important transcriptomic resource for the shrimp research community to facilitate gene and genome annotation and to characterize key molecular processes

  11. Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

    DOE PAGESBeta

    Vlcek, Lukas; Chialvo, Ariel A.

    2016-01-03

    The importance of single-ion hydration thermodynamic properties for understanding the driving forces of aqueous electrolyte processes, along with the impossibility of their direct experimental measurement, have prompted a large number of experimental, theoretical, and computational studies aimed at separating the cation and anion contributions. Here we provide an overview of historical approaches based on extrathermodynamic assumptions and more recent computational studies of single-ion hydration in order to evaluate the approximations involved in these methods, quantify their accuracy, reliability, and limitations in the light of the latest developments. Finally, we also offer new insights into the factors that influence the accuracymore » of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.« less

  12. Insight on Tricalcium Silicate Hydration and Dissolution Mechanism from Molecular Simulations.

    PubMed

    Manzano, Hegoi; Durgun, Engin; López-Arbeloa, Iñigo; Grossman, Jeffrey C

    2015-07-15

    Hydration of mineral surfaces, a critical process for many technological applications, encompasses multiple coupled chemical reactions and topological changes, challenging both experimental characterization and computational modeling. In this work, we used reactive force field simulations to understand the surface properties, hydration, and dissolution of a model mineral, tricalcium silicate. We show that the computed static quantities, i.e., surface energies and water adsorption energies, do not provide useful insight into predict mineral hydration because they do not account for major structural changes at the interface when dynamic effects are included. Upon hydration, hydrogen atoms from dissociated water molecules penetrate into the crystal, forming a disordered calcium silicate hydrate layer that is similar for most of the surfaces despite wide-ranging static properties. Furthermore, the dynamic picture of hydration reveals the hidden role of surface topology, which can lead to unexpected water tessellation that stabilizes the surface against dissolution. PMID:26107551

  13. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations.

    PubMed

    Oakes, V; Furini, S; Domene, C

    2016-01-01

    The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs. PMID:27586285

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

    DOE PAGESBeta

    Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; Grest, Gary S.

    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

  15. Mechanistic and quantitative insight into cell surface targeted molecular imaging agent design

    PubMed Central

    Zhang, Liang; Bhatnagar, Sumit; Deschenes, Emily; Thurber, Greg M.

    2016-01-01

    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. PMID:27147293

  16. Mechanistic and quantitative insight into cell surface targeted molecular imaging agent design

    NASA Astrophysics Data System (ADS)

    Zhang, Liang; Bhatnagar, Sumit; Deschenes, Emily; Thurber, Greg M.

    2016-05-01

    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.

  17. Cellular and molecular drivers of differential organ growth: insights from the limbs of Monodelphis domestica.

    PubMed

    Dowling, Anna; Doroba, Carolyn; Maier, Jennifer A; Cohen, Lorna; VandeBerg, John; Sears, Karen E

    2016-06-01

    A fundamental question in biology is "how is growth differentially regulated during development to produce organs of particular sizes?" We used a new model system for the study of differential organ growth, the limbs of the opossum (Monodelphis domestica), to investigate the cellular and molecular basis of differential organ growth in mammals. Opossum forelimbs grow much faster than hindlimbs, making opossum limbs an exceptional system with which to study differential growth. We first used the great differences in opossum forelimb and hindlimb growth to identify cellular processes and molecular signals that underlie differential limb growth. We then used organ culture and pharmacological addition of FGF ligands and inhibitors to test the role of the Fgf/Mitogen-activated protein kinases (MAPK) signaling pathway in driving these cellular processes. We found that molecular signals from within the limb drive differences in cell proliferation that contribute to the differential growth of the forelimb and hindlimbs of opossums. We also found that alterations in the Fgf/MAPK pathway can generate differences in cell proliferation that mirror those observed between wild-type forelimb and hindlimbs of opossums and that manipulation of Fgf/MAPK signaling affects downstream focal adhesion-extracellular matrix (FA-ECM) and Wnt signaling in opossum limbs. Taken together, these findings suggest that evolutionary changes in the Fgf/MAPK pathway could help drive the observed differences in cell behaviors and growth in opossum forelimb and hindlimbs. PMID:27194412

  18. Stress-induced neutral lipid biosynthesis in microalgae - Molecular, cellular and physiological insights.

    PubMed

    Zienkiewicz, Krzysztof; Du, Zhi-Yan; Ma, Wei; Vollheyde, Katharina; Benning, Christoph

    2016-09-01

    Photosynthetic microalgae have promise as biofuel feedstock. Under certain conditions, they produce substantial amounts of neutral lipids, mainly in the form of triacylglycerols (TAGs), which can be converted to fuels. Much of our current knowledge on the genetic and molecular basis of algal neutral lipid metabolism derives mainly from studies of plants, i.e. seed tissues, and to a lesser extent from direct studies of algal lipid metabolism. Thus, the knowledge of TAG synthesis and the cellular trafficking of TAG precursors in algal cells is to a large extent based on genome predictions, and most aspects of TAG metabolism have yet to be experimentally verified. The biofuel prospects of microalgae have raised the interest in mechanistic studies of algal TAG biosynthesis in recent years and resulted in an increasing number of publications on lipid metabolism in microalgae. In this review we summarize the current findings on genetic, molecular and physiological studies of TAG accumulation in microalgae. Special emphasis is on the functional analysis of key genes involved in TAG synthesis, molecular mechanisms of regulation of TAG biosynthesis, as well as on possible mechanisms of lipid droplet formation in microalgal cells. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner. PMID:26883557

  19. Molecular dynamics simulations provide insights into the substrate specificity of FAOX family members.

    PubMed

    Rigoldi, Federica; Spero, Ludovica; Dalle Vedove, Andrea; Redaelli, Alberto; Parisini, Emilio; Gautieri, Alfonso

    2016-07-19

    Enzymatic assays based on Fructosyl Amino Acid Oxidases (FAOX) represent a potential, rapid and economical strategy to measure glycated hemoglobin (HbA1c), which is in turn a reliable method to monitor the insurgence and the development of diabetes mellitus. However, the engineering of naturally occurring FAOX to specifically recognize fructosyl-valine (the glycated N-terminal residue of HbA1c) has been hindered by the paucity of information on the tridimensional structures and catalytic residues of the different FAOX that exist in nature, and in general on the molecular mechanisms that regulate specificity in this class of enzymes. In this study, we use molecular dynamics simulations and advanced modeling techniques to investigate five different relevant wild-type FAOX (Amadoriase I, Amadoriase II, PnFPOX, FPOX-E and N1-1-FAOD) in order to elucidate the molecular mechanisms that drive their specificity towards polar and nonpolar substrates. Specifically, we compare these five different FAOX in terms of overall folding, ligand entry tunnels, ligand binding residues and ligand binding energies. Our work will contribute to future enzyme structure modifications aimed at the rational design of novel biosensors for the monitoring of blood glucose levels. PMID:27327839

  20. Molecular insights into the microbial formation of marine dissolved organic matter: recalcitrant or labile?

    NASA Astrophysics Data System (ADS)

    Koch, B. P.; Kattner, G.; Witt, M.; Passow, U.

    2014-08-01

    The degradation of marine dissolved organic matter (DOM) is an important control variable in the global carbon cycle. For our understanding of the kinetics of organic matter cycling in the ocean, it is crucial to achieve a mechanistic and molecular understanding of its transformation processes. A long-term microbial experiment was performed to follow the production of non-labile DOM by marine bacteria. Two different glucose concentrations and dissolved algal exudates were used as substrates. We monitored the bacterial abundance, concentrations of dissolved and particulate organic carbon (DOC, POC), nutrients, amino acids and transparent exopolymer particles (TEP) for 2 years. The molecular characterization of extracted DOM was performed by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) after 70 days and after ∼2 years of incubation. Although glucose quickly degraded, a non-labile DOC background (5-9% of the initial DOC) was generated in the glucose incubations. Only 20% of the organic carbon from the algal exudate degraded within the 2 years of incubation. The degradation rates for the non-labile DOC background in the different treatments varied between 1 and 11 μmol DOC L-1 year-1. Transparent exopolymer particles, which are released by microorganisms, were produced during glucose degradation but decreased back to half of the maximum concentration within less than 3 weeks (degradation rate: 25 μg xanthan gum equivalents L-1 d-1) and were below detection in all treatments after 2 years. Additional glucose was added after 2 years to test whether labile substrate can promote the degradation of background DOC (co-metabolism; priming effect). A priming effect was not observed but the glucose addition led to a slight increase of background DOC. The molecular analysis demonstrated that DOM generated during glucose degradation differed appreciably from DOM transformed during the degradation of the algal exudates. Our

  1. Molecular insights on pathogenic effects of mutations causing phosphoglycerate kinase deficiency.

    PubMed

    Chiarelli, Laurent R; Morera, Simone M; Bianchi, Paola; Fermo, Elisa; Zanella, Alberto; Galizzi, Alessandro; Valentini, Giovanna

    2012-01-01

    Phosphoglycerate kinase (PGK) catalyzes an important ATP-generating step in glycolysis. PGK1 deficiency is an uncommon X-linked inherited disorder, generally characterized by various combinations of non-spherocytic hemolytic anemia, neurological dysfunctions, and myopathies. Patients rarely exhibit all three clinical features. To provide a molecular framework to the different pathological manifestations, all known mutations were reviewed and 16 mutant enzymes, obtained as recombinant forms, were functionally and structurally characterized. Most mutations heavily affect thermal stability and to a different extent catalytic efficiency, in line with the remarkably low PGK activity clinically observed in the patients. Mutations grossly impairing protein stability, but moderately affecting kinetic properties (p.I47N, p.L89P, p.C316R, p.S320N, and p.A354P) present the most homogeneous correlation with the clinical phenotype. Patients carrying these mutations display hemolytic anemia and neurological disorders, and,except for p.A354P variant, no myopaty. Variants highly perturbed in both catalytic efficiency (p.G158V, p.D164V, p.K191del, D285V, p.D315N, and p.T378P) and heat stability (all, but p.T378P) result to be mainly associated with myopathy alone. Finally, mutations faintly affecting molecular properties (p.R206P, p.E252A, p.I253T, p.V266M, and p.D268N) correlate with a wide spectrum of clinical symptoms. These are the first studies that correlate the clinical symptoms with the molecular properties of the mutant enzymes. All findings indicate that the different clinical manifestations associated with PGK1 deficiency chiefly depend on the distinctive type of perturbations caused by mutations in the PGK1 gene, highlighting the need for determination of the molecular properties of PGK variants to assist in prognosis and genetic counseling. However, the clinical symptoms can not be understood only on the bases of molecular properties of the mutant enzyme. Different

  2. Insights from the molecular characterization of mercury stress proteins identified by proteomics in E.coli nissle 1917.

    PubMed

    Seshapani, Panthangi; Rayalu, Daddam Jayasimha; Kumar, Vadde Kiran; Sekhar, Kathera Chandra; Kumari, Jasti Pramoda

    2013-01-01

    Differently expressed proteins in probiotic Escherichia coli nissle 1917 under mercury stress identified by using a proteomic approach. We applied to separate proteins by using two-dimensional gel electrophoresis and proteins were identified using MALDI-TOF-MS using PMF, by mascot database search using the NCBI database. we identified six proteins after exposure to mercury stress with respect to different functional classes. It is useful to understand the molecular insights into mercury stress in probiotic E. coli. Next we describe a structure generated by homology modelling and functional domain identification; it is interesting to study the impact of stress on protein structures. MS characterization and computational methods together provide the opportunity to examine the impact of stress arising from mercury. The role of these proteins in metal tolerance and structure relation is discussed. To the best of our knowledge, proteomics of E. coli nissle 1917 overview of mercury stress has been reported for the first time. PMID:23847405

  3. 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. PMID:26897548

  4. New Insights into the Molecular Epidemiology and Population Genetics of Schistosoma mansoni in Ugandan Pre-school Children and Mothers

    PubMed Central

    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. PMID:24349589

  5. New Insights into Fluvial Carbon Responses to Future Forest Management and Climate Change Obtained from Multi-Scale Modelling of Biogeochemical Processes

    NASA Astrophysics Data System (ADS)

    Oni, S. K.; Tiwari, T.; Futter, M. N.; Agren, A.; Teutschbein, C.; Ledesma, J.; Schelker, J.; Laudon, H.

    2014-12-01

    The boreal ecozone covers 2x107 km2 of the northern circumpolar region and includes 29% of the world's forests. The boreal consists of mosaic of forest/wetland landscape elements and stores about 500 Gt3 carbon (C) with a delicate sink-source C balance. Dissolved organic carbon (DOC) is the main form of C exported from boreal landscapes and is fundamental to global C cycling. This northern ecosystem is vulnerable to global climate change, and increasing demands for forest products threaten its surface water resources. So far, there have been no attempts to assess the combined impacts of climate change and forest management on the future DOC fluxes from boreal surface waters. While differences in model assumptions may have negligible effects on present day simulations, these differences could be amplified when projecting the future climate and land use change conditions. Here we use an ensemble of regional climate models and multi-scale models of biogeochemical processes to gain insights into uncertainties associated with climate change and forest management on C and runoff dynamics in boreal landscape. While there are significant uncertainties associated with model projections, our results show that climate change will be the main driver of long term DOC dynamics in meso- to large boreal catchments in the future. However, forestry intensifies hydrological processes and can lead to large DOC fluxes at the headwater scales.

  6. Tetramethoxybenzene is a Good Building Block for Molecular Wires: Insights from Photoinduced Electron Transfer.

    PubMed

    Heinz, Luisa G; Yushchenko, Oleksandr; Neuburger, Markus; Vauthey, Eric; Wenger, Oliver S

    2015-06-01

    Two donor bridge-acceptor molecules with terminal triarylamine and Ru(bpy)3(2+) (bpy = 2,2'-bipyridine) redox partners were synthesized and investigated by cyclic voltammetry, optical absorption, luminescence, and transient absorption spectroscopy. The two dyads differ only by the central bridging unit, which was tetramethoxybenzene (tmb) in one case and unsubstituted phenylene (ph) in the other case. Photoirradiation of the Ru(bpy)3(2+) complex of the two dyads triggers intramolecular electron transfer from the triarylamine to the (3)MLCT-excited metal complex, and this process occurs with time constants of 1.5 and 6.8 ns for the tmb- and ph-bridged dyads, respectively. Thermal electron transfer in the reverse direction then leads to disappearance of the photoproduct with a time constant of 10 ns in both dyads. The faster rate of photoinduced charge transfer in the tmb-bridged dyad can be understood in the framework of a hole-tunneling model in which the electron-rich tmb bridge imposes a more shallow barrier than the less electron-rich ph spacer. Until now tmb-based molecular wires have received very little attention, and alkoxy substituents have been mostly used for improving the solubility of oligo-p-phenylene vinylene (OPV) and oligo-p-phenylene ethynylene (OPE) wires. Our study illustrates how four alkoxy-substituents on a phenylene backbone can have a significant influence on the charge-transfer properties of a molecular wire, and this is relevant in the greater context of a future molecular electronics technology. PMID:25974891

  7. Promote potential applications of nanoparticles as respiratory drug carrier: insights from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lin, Xubo; Bai, Tingting; Zuo, Yi Y.; Gu, Ning

    2014-02-01

    Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs with different hydrophobicity and sizes on a dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface. Four different NPs were considered, including hydrophilic and hydrophobic NPs, each with two diameters of 3 nm and 5 nm (the sizes are comparable to that of generation 3 and 5 PAMAM dendrimers, which have been widely used for nanoscale drug carrier systems). Our simulations showed that hydrophilic NPs can readily penetrate into the aqueous phase with little or no disturbance on the DPPC monolayer. However, hydrophobic NPs tend to induce large structural disruptions, thus inhibiting the normal phase transition of the DPPC monolayer upon film compression. Our simulations also showed that this inhibitory effect of hydrophobic NPs can be mitigated through PEGylation. Our results provide useful guidelines for molecular design of NPs as carrier systems for pulmonary drug delivery.Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs

  8. Mitochondrial DNA disease—molecular insights and potential routes to a cure

    SciTech Connect

    Russell, Oliver; Turnbull, Doug

    2014-07-01

    Mitochondrial DNA diseases are common neurological conditions caused by mutations in the mitochondrial genome or nuclear genes responsible for its maintenance. Current treatments for these disorders are focussed on the management of the symptoms, rather than the correction of biochemical defects caused by the mutation. This review focuses on the molecular effects of mutations, the symptoms they cause and current work focusing on the development of targeted treatments for mitochondrial DNA disease. - Highlights: • We discuss several common disease causing mtDNA mutations. • We highlight recent work linking pathogenicity to deletion size and heteroplasmy. • We discuss recent advances in the development of targeted mtDNA disease treatments.

  9. Inhibitory effects of daidzein and genistein on trypsin: Insights from spectroscopic and molecular docking studies.

    PubMed

    Zeng, Hua-Jin; Wang, Ya-Ping; Yang, Ran; You, Jing; Qu, Ling-Bo

    2016-08-01

    In this work, the inhibitory effect of two isoflavonoids including daidzein and genistein on trypsin and their binding mechanism were determined by spectroscopic and molecular docking approaches. The results indicated that both daidzein and genistein reversibly inhibited trypsin in a competitive manner with IC50 values of 68.01×10(-6)molL(-1) and 64.70×10(-6)molL(-1) and Ki values of 62.12×10(-6)molL(-1) and 59.83×10(-6)molL(-1), respectively. They could spontaneously bind with trypsin mainly through hydrophobic force and electrostatic interactions with a single binding site. Analysis of circular dichrosim spectra and molecular docking revealed that both isoflavonoids bound directly into the catalytic cavity and the microenvironment and secondary structure of trypsin were changed in this process, which caused the inhibition of trypsin activity. All these experimental results and theoretical data in this work would be help in understanding the mechanism of inhibitory effects of daidzein and genistein against trypsin and the potential of isoflavonoid to relieve symptoms of pancreatitis. PMID:27109756

  10. Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy

    PubMed Central

    Martínez-Aguilar, Juan; Clifton-Bligh, Roderick; Molloy, Mark P.

    2016-01-01

    Around 5% of the general population have palpable thyroid nodules. Although most thyroid tumours are benign, thyroid cancer represents the most common malignancy of the endocrine system, comprising mainly follicular and papillary thyroid carcinomas. Previous studies have shed some light on the molecular pathogenesis of thyroid cancer but there have not been any comprehensive mass spectrometry-based proteomic studies of large scale to reveal protein expression differences between thyroid tumours and the molecular alterations associated with tumour malignancy. We applied data-independent acquisition mass spectrometry which enabled quantitative expression analysis of over 1,600 proteins from 32 specimens to compare normal thyroid tissue with the three most common tumours of the thyroid gland: follicular adenoma, follicular carcinoma and papillary carcinoma. In follicular tumours, we found marked reduction of the tumour suppressor and therapeutic target extracellular protein decorin. We made the novel observation that TGFβ-induced protein ig-h3 (TGFBI) was found frequently overexpressed in follicular carcinoma compared with follicular adenoma. Proteomic pathway analysis showed changes in papillary carcinoma were associated with disruption of cell contacts (loss of E-cadherin), actin cytoskeleton dynamics and loss of differentiation markers, all hallmarks of an invasive phenotype. PMID:27025787

  11. Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures

    PubMed Central

    Rosas-Trigueros, Jorge Luis; Correa-Basurto, José; Guadalupe Benítez-Cardoza, Claudia; Zamorano-Carrillo, Absalom

    2011-01-01

    Bax is a member of the Bcl-2 protein family that participates in mitochondrion-mediated apoptosis. In the early stages of the apoptotic pathway, this protein migrates from the cytosol to the outer mitochondrial membrane, where it is inserted and usually oligomerizes, making cytochrome c-compatible pores. Although several cellular and structural studies have been reported, a description of the stability of Bax at the molecular level remains elusive. This article reports molecular dynamics simulations of monomeric Bax at 300, 400, and 500 K, focusing on the most relevant structural changes and relating them to biological experimental results. Bax gradually loses its α-helices when it is submitted to high temperatures, yet it maintains its globular conformation. The resistance of Bax to adopt an extended conformation could be due to several interactions that were found to be responsible for maintaining the structural stability of this protein. Among these interactions, we found salt bridges, hydrophobic interactions, and hydrogen bonds. Remarkably, salt bridges were the most relevant to prevent the elongation of the structure. In addition, the analysis of our results suggests which conformational movements are implicated in the activation/oligomerization of Bax. This atomistic description might have important implications for understanding the functionality and stability of Bax in vitro as well as within the cellular environment. PMID:21936009

  12. The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes.

    PubMed

    Slapeta, Jan; Moreira, David; López-García, Purificación

    2005-10-01

    Classical studies on protist diversity of freshwater environments worldwide have led to the idea that most species of microbial eukaryotes are known. One exemplary case would be constituted by the ciliates, which have been claimed to encompass a few thousands of ubiquitous species, most of them already described. Recently, molecular methods have revealed an unsuspected protist diversity, especially in oceanic as well as some extreme environments, suggesting the occurrence of a hidden diversity of eukaryotic lineages. In order to test if this holds also for freshwater environments, we have carried out a molecular survey of small subunit ribosomal RNA genes in water and sediment samples of two ponds, one oxic and another suboxic, from the same geographic area. Our results show that protist diversity is very high. The majority of phylotypes affiliated within a few well established eukaryotic kingdoms or phyla, including alveolates, cryptophytes, heterokonts, Cercozoa, Centroheliozoa and haptophytes, although a few sequences did not display a clear taxonomic affiliation. The diversity of sequences within groups was very large, particularly that of ciliates, and a number of them were very divergent from known species, which could define new intra-phylum groups. This suggests that, contrary to current ideas, the diversity of freshwater protists is far from being completely described. PMID:16191619

  13. A Critical Review of the Concept of Transgenic Plants: Insights into Pharmaceutical Biotechnology and Molecular Farming.

    PubMed

    Abiri, Rambod; Valdiani, Alireza; Maziah, Mahmood; Shaharuddin, Noor Azmi; Sahebi, Mahbod; Yusof, Zett yNorhana Balia; Atabaki, Narges; Talei, Daryush

    2016-01-01

    Using transgenic plants for the production of high-value recombinant proteins for industrial and clinical applications has become a promising alternative to using conventional bioproduction systems, such as bacteria, yeast, and cultured insect and animal cells. This novel system offers several advantages over conventional systems in terms of safety, scale, cost-effectiveness, and the ease of distribution and storage. Currently, plant systems are being utilised as recombinant bio-factories for the expression of various proteins, including potential vaccines and pharmaceuticals, through employing several adaptations of recombinant processes and utilizing the most suitable tools and strategies. The level of protein expression is a critical factor in plant molecular farming, and this level fluctuates according to the plant species and the organs involved. The production of recombinant native and engineered proteins is a complicated procedure that requires an inter- and multi-disciplinary effort involving a wide variety of scientific and technological disciplines, ranging from basic biotechnology, biochemistry, and cell biology to advanced production systems. This review considers important plant resources, affecting factors, and the recombinant-protein expression techniques relevant to the plant molecular farming process. PMID:25944541

  14. Molecular underpinnings of prefrontal cortex development in rodents provide insights into the etiology of neurodevelopmental disorders

    PubMed Central

    Schubert, D; Martens, G J M; Kolk, S M

    2015-01-01

    The prefrontal cortex (PFC), seat of the highest-order cognitive functions, constitutes a conglomerate of highly specialized brain areas and has been implicated to have a role in the onset and installation of various neurodevelopmental disorders. The development of a properly functioning PFC is directed by transcription factors, guidance cues and other regulatory molecules and requires the intricate and temporal orchestration of a number of developmental processes. Disturbance or failure of any of these processes causing neurodevelopmental abnormalities within the PFC may contribute to several of the cognitive deficits seen in patients with neurodevelopmental disorders. In this review, we elaborate on the specific processes underlying prefrontal development, such as induction and patterning of the prefrontal area, proliferation, migration and axonal guidance of medial prefrontal progenitors, and their eventual efferent and afferent connections. We furthermore integrate for the first time the available knowledge from genome-wide studies that have revealed genes linked to neurodevelopmental disorders with experimental molecular evidence in rodents. The integrated data suggest that the pathogenic variants in the neurodevelopmental disorder-associated genes induce prefrontal cytoarchitectonical impairments. This enhances our understanding of the molecular mechanisms of prefrontal (mis)development underlying the four major neurodevelopmental disorders in humans, that is, intellectual disability, autism spectrum disorders, attention deficit hyperactivity disorder and schizophrenia, and may thus provide clues for the development of novel therapies. PMID:25450230

  15. Molecular characterization of human skin response to diphencyprone at peak and resolution phases: therapeutic insights.

    PubMed

    Gulati, Nicholas; Suárez-Fariñas, Mayte; Fuentes-Duculan, Judilyn; Gilleaudeau, Patricia; Sullivan-Whalen, Mary; Correa da Rosa, Joel; Cueto, Inna; Mitsui, Hiroshi; Krueger, James G

    2014-10-01

    Diphencyprone (DPCP) is a hapten that induces delayed-type hypersensitivity (DTH) reactions. It is used as an immune-modulating therapeutic, but its molecular effects in human skin are largely unknown. We studied cellular and molecular characteristics of a recall response to 0.04% DPCP at 3-day (peak) and 14-day (resolution) time points using immune markers, reverse-transcriptase-PCR (RT-PCR), and gene array approaches. A peak response showed modulation of ∼7,500 mRNA transcripts, with high expression of cytokines that define all major effector T-cell subsets. Concomitant increases in T-cell and CD11c+ dendritic cell (DC) infiltrates were measured. The resolution reaction was characterized by unexpectedly high levels of T cells and mature (DC-lysosome-associated membrane glycoprotein positive (DC-LAMP+)) DCs, but with marked decreases in expression of IL-2, IFNγ, and other T cell-derived cytokines. However, negative immune regulators such as IDO1 that were high in peak reactions, continued to have high expression in resolution reactions. In the resolution reaction, ∼1,500 mRNA transcripts were significantly different from placebo-treated skin. These data suggest that the response to DPCP evolves from an inflammatory/effector peak at day 3 to a more regulated immune response after 14 days. This model system could be useful for further dissection of mechanisms of immune activation or negative immune regulation in human skin. PMID:24751728

  16. Molecular characterization of human skin response to diphencyprone at peak and resolution phases: therapeutic insights

    PubMed Central

    Gulati, Nicholas; Suárez-Fariñas, Mayte; Fuentes-Duculan, Judilyn; Gilleaudeau, Patricia; Sullivan-Whalen, Mary; da Rosa, Joel Correa; Cueto, Inna; Mitsui, Hiroshi; Krueger, James G.

    2014-01-01

    Diphencyprone (DPCP) is a hapten that induces delayed-type hypersensitivity (DTH) reactions. It is used as an immune modulating therapeutic, but its molecular effects in human skin are largely unknown. We studied cellular and molecular characteristics of a recall response to 0.04% DPCP at 3 day (peak) and 14 day (resolution) timepoints using immune markers, RT-PCR and gene array approaches. A peak response showed modulation of ~7,500 mRNA transcripts, with high expression of cytokines that define all major effector T-cell subsets. Concomitant increases in T-cell and CD11c+ dendritic cell (DC) infiltrates were measured. The resolution reaction was characterized by unexpectedly high levels of T-cells and mature (DC-LAMP+) DCs, but with marked decreases in expression of IL-2, IFNγ, and other T-cell derived cytokines. However, negative immune regulators such as IDO1 that were high in peak reactions, continued to have high expression in resolution reactions. In the resolution reaction, ~1,500 mRNA transcripts were significantly different from placebo-treated skin. These data suggest the response to DPCP evolves from an inflammatory/effector peak at day 3 to a more regulated immune response after 14 days. This model system could be useful for further dissection of mechanisms of immune activation or negative immune regulation in human skin. PMID:24751728

  17. Molecular insights into the boundary conditions in the Stokes-Einstein relation

    NASA Astrophysics Data System (ADS)

    Ishii, Yoshiki; Ohtori, Norikazu

    2016-05-01

    In order to mimic the Brownian particle in liquid, molecular dynamics calculations of dilute solutions of spherical fullerene molecules with various sizes in liquid Ar were performed. To establish the scaling equation for self-diffusion coefficient, D , of the fullerenes, the dependence of D was examined on the mass ratio of solute to solvent and on the energy-parameter ratio used in the Lennard-Jones potentials. The dependence on the energy-parameter ratio remains up to C540, whereas D rapidly becomes independent of the mass ratio with increasing mass of the solute. The product of the scaling equations obtained for the D of the solute and for shear viscosity, ηsv, for the solvent gives a relation which replaces the Stokes-Einstein relation based on the hydrodynamics. The present expression does not need both the boundary conditions and the hydrodynamic particle size, but instead the energy-parameter ratio, packing fraction of solvent, and bare size of solute. From the viewpoint of the tackiness at the boundary, the cage correlation function around the diffusing particle was examined; it was found that the decay time of the function depends mainly on the the energy-parameter ratio. Therefore, the energy-parameter ratio accounts for the main part of both the boundary conditions and the hydrodynamic particle size in the Stokes equation, which have so far been ill-defined in any molecular theories.

  18. Molecular insights into the boundary conditions in the Stokes-Einstein relation.

    PubMed

    Ishii, Yoshiki; Ohtori, Norikazu

    2016-05-01

    In order to mimic the Brownian particle in liquid, molecular dynamics calculations of dilute solutions of spherical fullerene molecules with various sizes in liquid Ar were performed. To establish the scaling equation for self-diffusion coefficient, D, of the fullerenes, the dependence of D was examined on the mass ratio of solute to solvent and on the energy-parameter ratio used in the Lennard-Jones potentials. The dependence on the energy-parameter ratio remains up to C_{540}, whereas D rapidly becomes independent of the mass ratio with increasing mass of the solute. The product of the scaling equations obtained for the D of the solute and for shear viscosity, η_{sv}, for the solvent gives a relation which replaces the Stokes-Einstein relation based on the hydrodynamics. The present expression does not need both the boundary conditions and the hydrodynamic particle size, but instead the energy-parameter ratio, packing fraction of solvent, and bare size of solute. From the viewpoint of the tackiness at the boundary, the cage correlation function around the diffusing particle was examined; it was found that the decay time of the function depends mainly on the the energy-parameter ratio. Therefore, the energy-parameter ratio accounts for the main part of both the boundary conditions and the hydrodynamic particle size in the Stokes equation, which have so far been ill-defined in any molecular theories. PMID:27300813

  19. Insights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies.

    PubMed

    Karthikeyan, Subramani; Bharanidharan, Ganesan; Kesherwani, Manish; Mani, Karthik Ananth; Srinivasan, Narasimhan; Velmurugan, Devadasan; Aruna, Prakasarao; Ganesan, Singaravelu

    2016-06-01

    4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl acetate [Ace semi],4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl propanoate [Pro semi] from the family of thiosemicarbazones derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and it is also less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiosemicarbazone derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance (r) between donor (HSA) and acceptor (thiosemicarbazone derivative) was estimated according to Forster's theory of non-radiative energy transfer using fluorescence spectroscopy. The binding dynamics has been elaborated using synchronous fluorescence spectroscopy, and the feature of thiosemicarbazone derivative induced structural changes of HSA has been studied by circular dichorism, Fourier transform infrared spectroscopy. Molecular modelling simulations explore the hydrophobic interaction and hydrogen bonding which stabilizes the interaction. PMID:26368536

  20. Atomistic Insights into Regulatory Mechanisms of the HER2 Tyrosine Kinase Domain: A Molecular Dynamics Study

    PubMed Central

    Telesco, Shannon E.; Radhakrishnan, Ravi

    2009-01-01

    HER2 (ErbB2/Neu) is a receptor tyrosine kinase belonging to the epidermal growth factor receptor (EGFR)/ErbB family and is overexpressed in 20–30% of human breast cancers. Although several crystal structures of ErbB kinases have been solved, the precise mechanism of HER2 activation remains unknown, and it has been suggested that HER2 is unique in its requirement for phosphorylation of Y877, a key tyrosine residue located in the activation loop. To elucidate mechanistic details of kinase domain regulation, we performed molecular dynamics simulations of a homology-modeled HER2 kinase structure in active and inactive conformations. Principal component analysis of the atomistic fluctuations reveals a tight coupling between the activation loop and catalytic loop that may contribute to alignment of residues required for catalysis in the active kinase. The free energy perturbation method is also employed to predict a role for phosphorylated Y877 in stabilizing the kinase conformations. Finally, simulation results are presented for a HER2/EGFR heterodimer and reveal that the dimeric interface induces a rearrangement of the αC helix toward the active conformation. Elucidation of the molecular regulatory mechanisms in HER2 will help establish structure-function relationships in the wild-type kinase, as well as predict mutations with a propensity for constitutive activation in HER2-mediated cancers. PMID:19289058

  1. Age-associated Cognitive Decline: Insights into Molecular Switches and Recovery Avenues

    PubMed Central

    Konar, Arpita; Singh, Padmanabh; Thakur, Mahendra K.

    2016-01-01

    Age-associated cognitive decline is an inevitable phenomenon that predisposes individuals for neurological and psychiatric disorders eventually affecting the quality of life. Scientists have endeavored to identify the key molecular switches that drive cognitive decline with advancing age. These newly identified molecules are then targeted as recovery of cognitive aging and related disorders. Cognitive decline during aging is multi-factorial and amongst several factors influencing this trajectory, gene expression changes are pivotal. Identifying these genes would elucidate the neurobiological underpinnings as well as offer clues that make certain individuals resilient to withstand the inevitable age-related deteriorations. Our laboratory has focused on this aspect and investigated a wide spectrum of genes involved in crucial brain functions that attribute to senescence induced cognitive deficits. We have recently identified master switches in the epigenome regulating gene expression alteration during brain aging. Interestingly, these factors when manipulated by chemical or genetic strategies successfully reverse the age-related cognitive impairments. In the present article, we review findings from our laboratory and others combined with supporting literary evidences on molecular switches of brain aging and their potential as recovery targets. PMID:27114845

  2. Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

    PubMed

    Ramya, L; Ramakrishnan, Vigneshwar

    2016-07-01

    Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. PMID:27492241

  3. Electronic structure of carbon dioxide under pressure and insights into the molecular-to-nonmolecular transition.

    PubMed

    Shieh, Sean R; Jarrige, Ignace; Wu, Min; Hiraoka, Nozomu; Tse, John S; Mi, Zhongying; Kaci, Linada; Jiang, Jian-Zhong; Cai, Yong Q

    2013-11-12

    Knowledge of the high-pressure behavior of carbon dioxide (CO2), an important planetary material found in Venus, Earth, and Mars, is vital to the study of the evolution and dynamics of the planetary interiors as well as to the fundamental understanding of the C-O bonding and interaction between the molecules. Recent studies have revealed a number of crystalline polymorphs (CO2-I to -VII) and an amorphous phase under high pressure-temperature conditions. Nevertheless, the reported phase stability field and transition pressures at room temperature are poorly defined, especially for the amorphous phase. Here we shed light on the successive pressure-induced local structural changes and the molecular-to-nonmolecular transition of CO2 at room temperature by performing an in situ study of the local electronic structure using X-ray Raman scattering, aided by first-principle exciton calculations. We show that the transition from CO2-I to CO2-III was initiated at around 7.4 GPa, and completed at about 17 GPa. The present study also shows that at ~37 GPa, molecular CO2 starts to polymerize to an extended structure with fourfold coordinated carbon and minor CO3 and CO-like species. The observed pressure is more than 10 GPa below previously reported. The disappearance of the minority species at 63(± 3) GPa suggests that a previously unknown phase transition within the nonmolecular phase of CO2 has occurred. PMID:24167283

  4. The peptide-receptive transition state of MHC-1 molecules: Insight from structure and molecular dynamics

    SciTech Connect

    Robinson H.; Mage, M.; Dolan, M.; Wang, R.; Boyd, L.; Revilleza, M.; Natarajan, K.; Myers, N.; Hansen, T.; Margulies, D.

    2012-05-01

    MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed 'open' position in the PR transition state to a 'closed' position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.

  5. Aqueous electrolyte surfaces in strong electric fields: molecular insight into nanoscale jets and bridges

    NASA Astrophysics Data System (ADS)

    Jirsák, Jan; Moučka, Filip; Škvor, Jiří; Nezbeda, Ivo

    2015-04-01

    Exposing aqueous surfaces to a strong electric field gives rise to interesting phenomena, such as formation of a floating water bridge or an eruption of a jet in electrospinning. In an effort to account for the phenomena at the molecular level, we performed molecular dynamics simulations using several protocols on both pure water and aqueous solutions of sodium chloride subjected to an electrostatic field. All simulations consistently point to the same mechanisms which govern the rearrangement of the originally planar surface. The results show that the phenomena are primarily governed by an orientational reordering of the water molecules driven by the applied field. It is demonstrated that, for pure water, a sufficiently strong field yields a columnar structure parallel to the field with an anisotropic arrangement of the water molecules with their dipole moments aligned along the applied field not only in the surface layer but over the entire cross section of the column. Nonetheless, the number of hydrogen bonds per molecule does not seem to be affected by the field regardless of its strength and molecule's orientation. In the electrolyte solutions, the ionic charge is able to overcome the effect of the external field tending to arrange the water molecules radially in the first coordination shell of an ion. The ion-water interaction interferes thus with the water-electric field interaction, and the competition between these two forces (i.e., strength of the field versus concentration) provides the key mechanism determining the stability of the observed structures.

  6. Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy.

    PubMed

    Martínez-Aguilar, Juan; Clifton-Bligh, Roderick; Molloy, Mark P

    2016-01-01

    Around 5% of the general population have palpable thyroid nodules. Although most thyroid tumours are benign, thyroid cancer represents the most common malignancy of the endocrine system, comprising mainly follicular and papillary thyroid carcinomas. Previous studies have shed some light on the molecular pathogenesis of thyroid cancer but there have not been any comprehensive mass spectrometry-based proteomic studies of large scale to reveal protein expression differences between thyroid tumours and the molecular alterations associated with tumour malignancy. We applied data-independent acquisition mass spectrometry which enabled quantitative expression analysis of over 1,600 proteins from 32 specimens to compare normal thyroid tissue with the three most common tumours of the thyroid gland: follicular adenoma, follicular carcinoma and papillary carcinoma. In follicular tumours, we found marked reduction of the tumour suppressor and therapeutic target extracellular protein decorin. We made the novel observation that TGFβ-induced protein ig-h3 (TGFBI) was found frequently overexpressed in follicular carcinoma compared with follicular adenoma. Proteomic pathway analysis showed changes in papillary carcinoma were associated with disruption of cell contacts (loss of E-cadherin), actin cytoskeleton dynamics and loss of differentiation markers, all hallmarks of an invasive phenotype. PMID:27025787

  7. Molecular signature of pancreatic adenocarcinoma: an insight from genotype to phenotype and challenges for targeted therapy

    PubMed Central

    Sahin, Ibrahim H; Iacobuzio-Donahue, Christine A; O’Reilly, Eileen M

    2016-01-01

    Introduction Pancreatic adenocarcinoma remains one of the most clinically challenging cancers despite an in-depth characterization of the molecular underpinnings and biology of this disease. Recent whole-genome-wide studies have elucidated the diverse and complex genetic alterations which generate a unique oncogenic signature for an individual pancreatic cancer patient and which may explain diverse disease behavior in a clinical setting. Areas covered In this review article, we discuss the key oncogenic pathways of pancreatic cancer including RAS-MAPK, PI3KCA and TGF-β signaling, as well as the impact of these pathways on the disease behavior and their potential targetability. The role of tumor suppressors particularly BRCA1 and BRCA2 genes and their role in pancreatic cancer treatment are elaborated upon. We further review recent genomic studies and their impact on future pancreatic cancer treatment. Expert opinion Targeted therapies inhibiting pro-survival pathways have limited impact on pancreatic cancer outcomes. Activation of pro-apoptotic pathways along with suppression of cancer-stem-related pathways may reverse treatment resistance in pancreatic cancer. While targeted therapy or a ‘precision medicine’ approach in pancreatic adenocarcinoma remains an elusive challenge for the majority of patients, there is a real sense of optimism that the strides made in understanding the molecular underpinnings of this disease will translate into improved outcomes. PMID:26439702

  8. Structural insights into the molecular mechanism of the m(6)A writer complex.

    PubMed

    Śledź, Paweł; Jinek, Martin

    2016-01-01

    Methylation of adenosines at the N(6) position (m(6)A) is a dynamic and abundant epitranscriptomic mark that regulates critical aspects of eukaryotic RNA metabolism in numerous biological processes. The RNA methyltransferases METTL3 and METTL14 are components of a multisubunit m(6)A writer complex whose enzymatic activity is substantially higher than the activities of METTL3 or METTL14 alone. The molecular mechanism underpinning this synergistic effect is poorly understood. Here we report the crystal structure of the catalytic core of the human m(6)A writer complex comprising METTL3 and METTL14. The structure reveals the heterodimeric architecture of the complex and donor substrate binding by METTL3. Structure-guided mutagenesis indicates that METTL3 is the catalytic subunit of the complex, whereas METTL14 has a degenerate active site and plays non-catalytic roles in maintaining complex integrity and substrate RNA binding. These studies illuminate the molecular mechanism and evolutionary history of eukaryotic m(6)A modification in post-transcriptional genome regulation. PMID:27627798

  9. Enhanced heme accessibility in horse heart mini-myoglobin: Insights from molecular modelling and reactivity studies.

    PubMed

    Polticelli, Fabio; Zobnina, Veranika; Ciaccio, Chiara; de Sanctis, Giampiero; Ascenzi, Paolo; Coletta, Massimo

    2015-11-01

    Mini-myoglobin (mini-HHMb) is a fragment of horse-heart myoglobin (HHMb) considered to be the prototype of the product encoded by the central exon of the HHMb gene. For this reason, mini-HHMb has been studied extensively showing that carbonylation and oxygenation properties of the ferrous form are similar to those of the full-length protein, while kinetics and thermodynamics of azide binding to the ferric form are significantly different from those of HHMb. To analyze the structure-function relationships in mini-HHMb and the role of conformational fluctuations in ligand accessibility, the molecular model of mini-HHMb has been built and refined by molecular dynamics simulations, and analyzed in parallel with that of full length HHMb. Moreover, imidazole binding parameters of ferric mini-HHMb and HHMb have been determined. Furthermore, structural data of ferric mini-HHMb and HHMb have been correlated with the imidazole and previously determined azide binding properties. Present results indicate that, despite the extensive trimming, the heme-α-helices E-F substructure is essentially unaltered in mini-HHMb with respect to HHMb. However, the heme-Fe atom displays an enhanced accessibility in mini-HHMb, which may affect both ligand association and dissociation kinetics. PMID:26363214

  10. Molecular underpinnings of prefrontal cortex development in rodents provide insights into the etiology of neurodevelopmental disorders.

    PubMed

    Schubert, D; Martens, G J M; Kolk, S M

    2015-07-01

    The prefrontal cortex (PFC), seat of the highest-order cognitive functions, constitutes a conglomerate of highly specialized brain areas and has been implicated to have a role in the onset and installation of various neurodevelopmental disorders. The development of a properly functioning PFC is directed by transcription factors, guidance cues and other regulatory molecules and requires the intricate and temporal orchestration of a number of developmental processes. Disturbance or failure of any of these processes causing neurodevelopmental abnormalities within the PFC may contribute to several of the cognitive deficits seen in patients with neurodevelopmental disorders. In this review, we elaborate on the specific processes underlying prefrontal development, such as induction and patterning of the prefrontal area, proliferation, migration and axonal guidance of medial prefrontal progenitors, and their eventual efferent and afferent connections. We furthermore integrate for the first time the available knowledge from genome-wide studies that have revealed genes linked to neurodevelopmental disorders with experimental molecular evidence in rodents. The integrated data suggest that the pathogenic variants in the neurodevelopmental disorder-associated genes induce prefrontal cytoarchitectonical impairments. This enhances our understanding of the molecular mechanisms of prefrontal (mis)development underlying the four major neurodevelopmental disorders in humans, that is, intellectual disability, autism spectrum disorders, attention deficit hyperactivity disorder and schizophrenia, and may thus provide clues for the development of novel therapies. PMID:25450230

  11. Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor.

    PubMed

    Holmes, Tracy C; May, Aaron E; Zaleta-Rivera, Kathia; Ruby, J Graham; Skewes-Cox, Peter; Fischbach, Michael A; DeRisi, Joseph L; Iwatsuki, Masato; Ōmura, Satoshi; Khosla, Chaitan

    2012-10-24

    Guadinomines are a recently discovered family of anti-infective compounds produced by Streptomyces sp. K01-0509 with a novel mode of action. With an IC(50) of 14 nM, guadinomine B is the most potent known inhibitor of the type III secretion system (TTSS) of Gram-negative bacteria. TTSS activity is required for the virulence of many pathogenic Gram-negative bacteria including Escherichia coli , Salmonella spp., Yersinia spp., Chlamydia spp., Vibrio spp., and Pseudomonas spp. The guadinomine (gdn) biosynthetic gene cluster has been cloned and sequenced and includes 26 open reading frames spanning 51.2 kb. It encodes a chimeric multimodular polyketide synthase, a nonribosomal peptide synthetase, along with enzymes responsible for the biosynthesis of the unusual aminomalonyl-acyl carrier protein extender unit and the signature carbamoylated cyclic guanidine. Its identity was established by targeted disruption of the gene cluster as well as by heterologous expression and analysis of key enzymes in the biosynthetic pathway. Identifying the guadinomine gene cluster provides critical insight into the biosynthesis of these scarce but potentially important natural products. PMID:23030602

  12. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding

    PubMed Central

    Du, Qi-Shi; Chen, Dong; Xie, Neng-Zhong; Huang, Ri-Bo; Chou, Kuo-Chen

    2015-01-01

    Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen–π interaction (Hp–π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp–π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the ‘point-to-plane’ one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop’s unique stability and flexibility feature, as well as the driving force of the protein global folding. PMID:25375237

  13. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.

    PubMed

    Du, Qi-Shi; Chen, Dong; Xie, Neng-Zhong; Huang, Ri-Bo; Chou, Kuo-Chen

    2015-09-01

    Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding. PMID:25375237

  14. Molecular insights into Rab7-mediated endosomal recruitment of core retromer: deciphering the role of Vps26 and Vps35.

    PubMed

    Priya, Amulya; Kalaidzidis, Inna V; Kalaidzidis, Yannis; Lambright, David; Datta, Sunando

    2015-01-01

    Retromer, a peripheral membrane protein complex, plays an instrumental role in host of cellular processes by its ability to recycle receptors from endosomes to the trans-Golgi network. It consists of two distinct sub-complexes, a membrane recognizing, sorting nexins (SNX) complex and a cargo recognition, vacuolar protein sorting (Vps) complex. Small GTPase, Rab7 is known to recruit retromer on endosomal membrane via interactions with the Vps sub-complex. The molecular mechanism underlying the recruitment process including the role of individual Vps proteins is yet to be deciphered. In this study, we developed a FRET-based assay in HeLa cells that demonstrated the interaction of Rab7 with Vps35 and Vps26 in vivo. Furthermore, we showed that Rab7 recruits retromer to late endosomes via direct interactions with N-terminal conserved regions in Vps35. However, the single point mutation, which disrupts the interaction between Vps35 and Vps26, perturbed the Rab7-mediated recruitment of retromer in HeLa cells. Using biophysical measurements, we demonstrate that the association of Vps26 with Vps35 resulted in high affinity binding between the Vps sub-complex and the activated Rab7 suggesting for a possible allosteric role of Vps26. Thus, this study provides molecular insights into the essential role of Vps26 and Vps35 in Rab7-mediated recruitment of the core retromer complex. PMID:25367362

  15. 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 Central

    Afonso, Philippe V.; Gessain, Antoine

    2013-01-01

    Background 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. Findings 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). Conclusions 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. PMID:24086779

  16. Insights into Himalayan biogeography from geckos: a molecular phylogeny of Cyrtodactylus (Squamata: Gekkonidae).

    PubMed

    Agarwal, Ishan; Bauer, Aaron M; Jackman, Todd R; Karanth, K Praveen

    2014-11-01

    The India-Asia collision profoundly influenced the climate, topography and biodiversity of Asia, causing the formation of the biodiverse Himalayas. The species-rich gekkonid genus Cyrtodactylus is an ideal clade for exploring the biological impacts of the India-Asia collision, as previous phylogenetic hypotheses suggest basal divergences occurred within the Himalayas and Indo-Burma during the Eocene. To this end, we sampled for Cyrtodactylus across Indian areas of the Himalayas and Indo-Burma Hotspots and used three genes to reconstruct relationships and estimate divergence times. Basal divergences in Cyrtodactylus, Hemidactylus and the Palaearctic naked-toed geckos were simultaneous with or just preceded the start of the India-Asia collision. Diversification within Cyrtodactylus tracks the India-Asia collision and subsequent geological events. A number of geographically concordant clades are resolved within Indo-Burmese Cyrtodactylus. Our study reveals 17 divergent lineages that may represent undescribed species, underscoring the previously undocumented diversity of the region. The importance of rocky habitats for Cyrtodactylus indicates the Indo-Gangetic flood plains and the Garo-Rajmahal Gap are likely to have been important historical barriers for this group. PMID:25108260

  17. Insights into the molecular phylogeny and historical biogeography of the white-clawed crayfish (Decapoda, Astacidae).

    PubMed

    Jelić, Mišel; Klobučar, Göran I V; Grandjean, Frédéric; Puillandre, Nicolas; Franjević, Damjan; Futo, Momir; Amouret, Julien; Maguire, Ivana

    2016-10-01

    In this study, the evolutionary history of the white-clawed crayfish (WCC) was evaluated using large-scale datasets comprising >1350 specimens from the entire distribution range. Using species delimitation methods on mitochondrial DNA (mtDNA) sequences, we propose four primary species hypotheses for WCC. Sequences for several nuclear regions were screened but none showed significant variation within WCC. This result favours a single secondary species hypothesis and indicates the existence of a mito-nuclear discordance in WCC. Therefore, mtDNA groups were considered only as genetic units that carry information about ancient divergences within WCC and not as taxonomic units. The reconstruction of ancestral ranges and divergence time estimates were used to link the current genetic structure with paleogeographic processes. These results showed that the emergence of mtDNA groups in WCC could be related to the Messinian Salinity Crisis, the climate cooling during the Pliocene and Pleistocene, and (paleo)shifting of the Adriatic Sea coastline in the Padanovenezian Plain. The most recent common ancestor of the mtDNA groups most likely originated from Dalmatia (eastern Adriatic coast) as indicated by the reconstruction of ancestral ranges. This ecoregion, along with the Gulf of Venice Drainages, harbours a high genetic diversity and should be emphasised as an area of the highest conservation priority. PMID:27404041

  18. Aggregation in concentrated protein solutions: Insights from rheology, neutron scattering and molecular simulations

    NASA Astrophysics Data System (ADS)

    Castellanos, Maria Monica

    Aggregation of therapeutic proteins is currently one of the major challenges in the bio-pharmaceutical industry, because aggregates could induce immunogenic responses and compromise the quality of the product. Current scientific efforts, both in industry and academia, are focused on developing rational approaches to screen different drug candidates and predict their stability under different conditions. Moreover, aggregation is promoted in highly concentrated protein solutions, which are typically required for subcutaneous injection. In order to gain further understanding about the mechanisms that lead to aggregation, an approach that combined rheology, neutron scattering, and molecular simulations was undertaken. Two model systems were studied in this work: Bovine Serum Albumin in surfactant-free Phosphate Buffered Saline at pH = 7.4 at concentrations from 11 mg/mL up to ˜519 mg/mL, and a monoclonal antibody in 20 mM Histidine/Histidine Hydrochloride at pH = 6.0 with 60 mg/mL trehalose and 0.2 mg/mL polysorbate-80 at concentrations from 53 mg/mL up to ˜220 mg/mL. The antibody used here has three mutations in the CH2 domain, which result in lower stability upon incubation at 40 °C with respect to the wild-type protein, based on size-exclusion chromatography assays. This temperature is below 49 °C, where unfolding of the least stable, CH2 domain occurs, according to differential scanning calorimetry. This dissertation focuses on identifying the role of aggregation on the viscosity of protein solutions. The protein solutions of this work show an increase in the low shear viscosity in the absence of surfactants, because proteins adsorb at the air/water interface forming a viscoelastic film that affects the measured rheology. Stable surfactant-laden protein solutions behave as simple Newtonian fluids. However, the surfactant-laden antibody solution also shows an increase in the low shear viscosity from bulk aggregation, after prolonged incubation at 40 °C. Small

  19. Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa.

    PubMed

    Bron, Peter A; van Baarlen, Peter; Kleerebezem, Michiel

    2012-01-01

    Probiotic bacteria can modulate immune responses in the host gastrointestinal tract to promote health. The genomics era has provided novel opportunities for the discovery and characterization of bacterial probiotic effector molecules that elicit specific responses in the intestinal system. Furthermore, nutrigenomic analyses of the response to probiotics have unravelled the signalling and immune response pathways which are modulated by probiotic bacteria. Together, these genomic approaches and nutrigenomic analyses have identified several bacterial factors that are involved in modulation of the immune system and the mucosal barrier, and have revealed that a molecular 'bandwidth of human health' could represent a key determinant in an individual's physiological responsiveness to probiotics. These approaches may lead to improved stratification of consumers and to subpopulation-level probiotic supplementation to maintain or improve health, or to reduce the risk of disease. PMID:22101918

  20. Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs.

    PubMed

    Tatsumi, Norifumi; Kobayashi, Ritsuko; Yano, Tohru; Noda, Masatsugu; Fujimura, Koji; Okada, Norihiro; Okabe, Masataka

    2016-01-01

    The lung is an important organ for air breathing in tetrapods and originated well before the terrestrialization of vertebrates. Therefore, to better understand lung evolution, we investigated lung development in the extant basal actinopterygian fish Senegal bichir (Polypterus senegalus). First, we histologically confirmed that lung development in this species is very similar to that of tetrapods. We also found that the mesenchymal expression patterns of three genes that are known to play important roles in early lung development in tetrapods (Fgf10, Tbx4, and Tbx5) were quite similar to those of tetrapods. Moreover, we found a Tbx4 core lung mesenchyme-specific enhancer (C-LME) in the genomes of bichir and coelacanth (Latimeria chalumnae) and experimentally confirmed that these were functional in tetrapods. These findings provide the first molecular evidence that the developmental program for lung was already established in the common ancestor of actinopterygians and sarcopterygians. PMID:27466206

  1. Primary and Secondary Lymphatic Valve Development: Molecular, Functional and Mechanical Insights

    PubMed Central

    Bazigou, Eleni; Wilson, John T.; Moore, James E.

    2015-01-01

    Fluid homeostasis in vertebrates critically relies on the lymphatic system forming a hierarchical network of lymphatic capillaries and collecting lymphatics, for the efficient drainage and transport of extravasated fluid back to the cardiovascular system. Blind–ended lymphatic capillaries employ specialized junctions and anchoring filaments to encourage a unidirectional flow of the interstitial fluid into the initial lymphatic vessels, whereas collecting lymphatics are responsible for the active propulsion of the lymph to the venous circulation via the combined action of lymphatic muscle cells and intraluminal valves. Here we describe recent findings on molecular and physical factors regulating the development and maturation of these two types of valves and examine their role in tissue-fluid homeostasis. PMID:25086182

  2. Insight into lattice thermal impedance via equilibrium molecular dynamics: case study on Al

    NASA Astrophysics Data System (ADS)

    Evteev, Alexander V.; Levchenko, Elena V.; Momenzadeh, Leila; Belova, Irina V.; Murch, Graeme E.

    2016-02-01

    Using results of equilibrium molecular dynamics simulation in conjunction with the Green-Kubo formalism, we present a general treatment of thermal impedance of a crystal lattice with a monatomic unit cell. The treatment is based on an analytical expression for the heat current autocorrelation function which reveals, in a monatomic lattice, an energy gap between the origin of the phonon states and the beginning of the energy spectrum of the so-called acoustic short-range phonon modes. Although, we consider here the f.c.c. Al model as a case example, the analytical expression is shown to be consistent for different models of elemental f.c.c. crystals over a wide temperature range. Furthermore, we predict a frequency 'window' where the thermal waves can be generated in a monatomic lattice by an external periodic temperature perturbation.

  3. New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics.

    PubMed

    Furmanchuk, Al'ona; Shishkin, Oleg V; Isayev, Olexandr; Gorb, Leonid; Leszczynski, Jerzy

    2010-09-01

    The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface. PMID:20532343

  4. Molecular Insights into Carbon Nanotube Supercapacitors: Capacitance Independent of Voltage and Temperature

    SciTech Connect

    Feng, Guang; Li, Song; Atchison, Jennifer S.; Presser, Volker; Cummings, Peter T.

    2013-04-12

    Molecular dynamics (MD) simulations of supercapacitors with single-walled carbon nanotube (SWCNT) electrodes in room-temperature ionic liquids were performed to investigate the influences of the applied electrical potential, the radius/curvature of SWCNTs, and temperature on their capacitive behavior. It is found that (1) SWCNTs-based supercapacitors exhibit a near-flat capacitance–potential curve, (2) the capacitance increases as the tube radius decreases, and (3) the capacitance depends little on the temperature. We report the first MD study showing the influence of the electrode curvature on the capacitance–potential curve and negligible dependence of temperature on capacitance of tubular electrode. The latter is in good agreement with recent experimental findings and is attributed to the similarity of the electrical double layer (EDL) microstructure with temperature varying from 260 to 400 K. The electrode curvature effect is explained by the dominance of charge overscreening and increased ion density per unit area of electrode surface.

  5. Puffs and gene regulation--molecular insights into the Drosophila ecdysone regulatory hierarchy.

    PubMed

    Thummel, C S

    1990-12-01

    Sixteen years ago, Michael Ashburner and his colleagues proposed a hierarchical model for the genetic control of polytene chromosome puffing by the steroid hormone ecdysone. The recent molecular isolation and characterization of three early ecdysone-inducible genes has confirmed many aspects of this model--these genes are directly induced by ecdysone, repressed by ecdysone-induced proteins, and appear to encode DNA binding regulatory proteins. The three early genes are also remarkably similar in structure. They are all unusually long and complex, with multiple transcripts that direct the synthesis of several related proteins from each locus. Proteins encoded by two of the early genes bind to both early and late ecdysone-induced puffs, implying that they are key regulators in the hierarchy. PMID:2127884

  6. Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs

    PubMed Central

    Tatsumi, Norifumi; Kobayashi, Ritsuko; Yano, Tohru; Noda, Masatsugu; Fujimura, Koji; Okada, Norihiro; Okabe, Masataka

    2016-01-01

    The lung is an important organ for air breathing in tetrapods and originated well before the terrestrialization of vertebrates. Therefore, to better understand lung evolution, we investigated lung development in the extant basal actinopterygian fish Senegal bichir (Polypterus senegalus). First, we histologically confirmed that lung development in this species is very similar to that of tetrapods. We also found that the mesenchymal expression patterns of three genes that are known to play important roles in early lung development in tetrapods (Fgf10, Tbx4, and Tbx5) were quite similar to those of tetrapods. Moreover, we found a Tbx4 core lung mesenchyme-specific enhancer (C-LME) in the genomes of bichir and coelacanth (Latimeria chalumnae) and experimentally confirmed that these were functional in tetrapods. These findings provide the first molecular evidence that the developmental program for lung was already established in the common ancestor of actinopterygians and sarcopterygians. PMID:27466206

  7. Clear cell carcinoma of the ovary: molecular insights and future therapeutic perspectives

    PubMed Central

    2016-01-01

    Clear cell carcinoma (CCC) of the ovary is known to show poorer sensitivity to chemotherapeutic agents and to be associated with a worse prognosis than the more common serous adenocarcinoma or endometrioid adenocarcinoma. To improve the survival of patients with ovarian CCC, the deeper understanding of the mechanism of CCC carcinogenesis as well as the efforts to develop novel treatment strategies in the setting of both front-line treatment and salvage treatment for recurrent disease are needed. In this presentation, we first summarize the mechanism responsible for carcinogenesis. Then, we highlight the promising therapeutic targets in ovarian CCC and provide information on the novel agents which inhibit these molecular targets. Moreover, we discuss on the cytotoxic anti-cancer agents that can be best combined with targeted agents in the treatment of ovarian CCC. PMID:27029752

  8. Revisiting glucose uptake and metabolism in schistosomes: new molecular insights for improved schistosomiasis therapies

    PubMed Central

    You, Hong; Stephenson, Rachel J.; Gobert, Geoffrey N.; McManus, Donald P.

    2014-01-01

    A better understanding of the molecular mechanisms required for schistosomes to take up glucose, the major nutritional source exploited by these blood flukes from their mammalian hosts and the subsequent metabolism required to fuel growth and fecundity, can provide new avenues for developing novel interventions for the control of schistosomiasis. This aspect of parasitism is particularly important to paired adult schistosomes, due to their considerable requirements for the energy needed to produce the extensive numbers of eggs laid daily by the female worm. This review describes recent advances in characterizing glucose metabolism in adult schistosomes. Potential intervention targets are discussed within the insulin signaling and glycolysis pathways, both of which play critical roles in the carbohydrate and energy requirements of schistosomes. PMID:24966871

  9. Structural, vibrational, and thermal properties of densified silicates: Insights from molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bauchy, M.

    2012-07-01

    Structural, vibrational, and thermal properties of densified sodium silicate (close to NS2) are investigated with classical molecular dynamics simulations of the glass and the liquid state. A systematic investigation of the glass structure with respect to density was performed. We observe a repolymerization of the network manifested by a transition from a tetrahedral to an octahedral silicon environment, the decrease of the amount of non-bridging oxygen atoms and the appearance of threefold coordinated oxygen atoms (triclusters). Anomalous changes in the medium range order are observed, the first sharp diffraction peak showing a minimum of its full-width at half maximum according to density. Generic vibrational trends are observed, such as the shift of the Boson peak intensity to higher frequencies and the decrease of its intensity. Finally, we show that the thermal behavior of the liquid can be reproduced by the Birch-Murnaghan equation of states, thus allowing us to compute the isothermal compressibility.

  10. Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies.

    PubMed

    Chen, Huilun; Rao, Honghao; Yang, Jian; Qiao, Yongxiang; Wang, Fei; Yao, Jun

    2016-01-01

    This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 10(4) L mol(-1) at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II). PMID:26671830

  11. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    PubMed

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation. PMID:27121070

  12. Novel therapeutics in metastatic colorectal cancer: molecular insights and pharmacogenomic implications.

    PubMed

    Hanna, Diana L; Lenz, Heinz-Josef

    2016-08-01

    Although the survival of metastatic colorectal cancer (mCRC) patients has improved five-fold over the last century, CRC remains a significant global health burden. Impressive strides have been made in identifying new regimens, employing maintenance strategies to limit treatment toxicities, and combining multidisciplinary approaches to achieve cure in oligometastatic disease. Attempts at personalized integration of targeted agents have been limited by the ability to identify molecularly enriched patient populations most likely to benefit. In this review, we discuss novel therapeutics and regimens recently approved and in development for mCRC. In addition, we discuss using older agents in novel combination and maintenance strategies, and highlight evidence for implementing pharmacogenomic data and non-invasive monitoring into the personalized management of mCRC patients. PMID:27031164

  13. Biological and molecular profile of fracture non-union tissue: current insights

    PubMed Central

    Panteli, Michalis; Pountos, Ippokratis; Jones, Elena; Giannoudis, Peter V

    2015-01-01

    Delayed bone healing and non-union occur in approximately 10% of long bone fractures. Despite intense investigations and progress in understanding the processes governing bone healing, the specific pathophysiological characteristics of the local microenvironment leading to non-union remain obscure. The clinical findings and radiographic features remain the two important landmarks of diagnosing non-unions and even when the diagnosis is established there is debate on the ideal timing and mode of intervention. In an attempt to understand better the pathophysiological processes involved in the development of fracture non-union, a number of studies have endeavoured to investigate the biological profile of tissue obtained from the non-union site and analyse any differences or similarities of tissue obtained from different types of non-unions. In the herein study, we present the existing evidence of the biological and molecular profile of fracture non-union tissue. PMID:25726940

  14. Primary and secondary lymphatic valve development: molecular, functional and mechanical insights.

    PubMed

    Bazigou, Eleni; Wilson, John T; Moore, James E

    2014-11-01

    Fluid homeostasis in vertebrates critically relies on the lymphatic system forming a hierarchical network of lymphatic capillaries and collecting lymphatics, for the efficient drainage and transport of extravasated fluid back to the cardiovascular system. Blind-ended lymphatic capillaries employ specialized junctions and anchoring filaments to encourage a unidirectional flow of the interstitial fluid into the initial lymphatic vessels, whereas collecting lymphatics are responsible for the active propulsion of the lymph to the venous circulation via the combined action of lymphatic muscle cells and intraluminal valves. Here we describe recent findings on molecular and physical factors regulating the development and maturation of these two types of valves and examine their role in tissue-fluid homeostasis. PMID:25086182

  15. Water adsorption and proton conduction in metal-organic frameworks: Insights from molecular simulations

    NASA Astrophysics Data System (ADS)

    Paesani, Francesco

    2014-03-01

    Metal-organic frameworks (MOFs) are a relatively new class of porous materials that hold great potential for a wide range of applications in chemistry, materials science, and nanoengineering. Compared to other porous materials such as zeolites, MOF properties are highly tunable. In particular, it has been shown that both size and shape of the MOF pores can be rationally designed for specific applications. For example, the ability to modify the framework properties with respect to hydrophilicity/hydrophobicity and acidity/basicity can enable the direct control of proton conduction through carrier molecules adsorbed inside the pores. Here, I report on our current efforts aimed at providing a molecular-level characterization of water-mediated proton conduction through the MOF pores. Particular emphasis will be put on correlation between proton conduction and both structural and chemical properties of the frameworks as well as on the dynamical behavior of water confined in the MOF pores. NSF award number: DMR-130510

  16. Molecular Insights on Post-chemotherapy Retinoblastoma by Microarray Gene Expression Analysis

    PubMed Central

    Nalini, Venkatesan; Segu, Ramya; Deepa, Perinkulam Ravi; Khetan, Vikas; Vasudevan, Madavan; Krishnakumar, Subramanian

    2013-01-01

    Purpose Management of Retinoblastoma (RB), a pediatric ocular cancer is limited by drug-resistance and drug-dosage related side effects during chemotherapy. Molecular de-regulation in post-chemotherapy RB tumors was investigated. Materials and Methods cDNA microarray analysis of two post-chemotherapy and one pre-chemotherapy RB tumor tissues was performed, followed by Principle Component Analysis, Gene ontology, Pathway Enrichment analysis and Biological Analysis Network (BAN) modeling. The drug modulation role of two significantly up-regulated genes (p≤0.05) − Ect2 (Epithelial-cell-transforming-sequence-2), and PRAME (preferentially-expressed-Antigen-in-Melanoma) was assessed by qRT-PCR, immunohistochemistry and cell viability assays. Results Differential up-regulation of 1672 genes and down-regulation of 2538 genes was observed in RB tissues (relative to normal adult retina), while 1419 genes were commonly de-regulated between pre-chemotherapy and post- chemotherapy RB. Twenty one key gene ontology categories, pathways, biomarkers and phenotype groups harboring 250 differentially expressed genes were dys-regulated (EZH2, NCoR1, MYBL2, RB1, STAMN1, SYK, JAK1/2, STAT1/2, PLK2/4, BIRC5, LAMN1, Ect2, PRAME and ABCC4). Differential molecular expressions of PRAME and Ect2 in RB tumors with and without chemotherapy were analyzed. There was neither up- regulation of MRP1, nor any significant shift in chemotherapeutic IC50, in PRAME over-expressed versus non-transfected RB cells. Conclusion Cell cycle regulatory genes were dys-regulated post-chemotherapy. Ect2 gene was expressed in response to chemotherapy-induced stress. PRAME does not contribute to drug resistance in RB, yet its nuclear localization and BAN information, points to its possible regulatory role in RB. PMID:24092970

  17. Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.

    PubMed

    Malan-Müller, Stefanie; Fairbairn, Lorren; Daniels, Willie M U; Dashti, Mahjoubeh Jalali Sefid; Oakeley, Edward J; Altorfer, Marc; Kidd, Martin; Seedat, Soraya; Gamieldien, Junaid; Hemmings, Sîan Megan Joanna

    2016-02-01

    D-cycloserine (DCS) has been shown to be effective in facilitating fear extinction in animal and human studies, however the precise mechanisms whereby the co-administration of DCS and behavioural fear extinction reduce fear are still unclear. This study investigated the molecular mechanisms of intrahippocampally administered D-cycloserine in facilitating fear extinction in a contextual fear conditioning animal model. Male Sprague Dawley rats (n = 120) were grouped into four experimental groups (n = 30) based on fear conditioning and intrahippocampal administration of either DCS or saline. The light/dark avoidance test was used to differentiate maladapted (MA) (anxious) from well-adapted (WA) (not anxious) subgroups. RNA extracted from the left dorsal hippocampus was used for RNA sequencing and gene expression data was compared between six fear-conditioned + saline MA (FEAR + SALINE MA) and six fear-conditioned + DCS WA (FEAR + DCS WA) animals. Of the 424 significantly downregulated and 25 significantly upregulated genes identified in the FEAR + DCS WA group compared to the FEAR + SALINE MA group, 121 downregulated and nine upregulated genes were predicted to be relevant to fear conditioning and anxiety and stress-related disorders. The majority of downregulated genes transcribed immune, proinflammatory and oxidative stress systems molecules. These molecules mediate neuroinflammation and cause neuronal damage. DCS also regulated genes involved in learning and memory processes, and genes associated with anxiety, stress-related disorders and co-occurring diseases (e.g., cardiovascular diseases, digestive system diseases and nervous system diseases). Identifying the molecular underpinnings of DCS-mediated fear extinction brings us closer to understanding the process of fear extinction. PMID:26400817

  18. Lessons from mammalian hibernators: molecular insights into striated muscle plasticity and remodeling.

    PubMed

    Tessier, Shannon N; Storey, Kenneth B

    2016-05-01

    Striated muscle shows an amazing ability to adapt its structural apparatus based on contractile activity, loading conditions, fuel supply, or environmental factors. Studies with mammalian hibernators have identified a variety of molecular pathways which are strategically regulated and allow animals to endure multiple stresses associated with the hibernating season. Of particular interest is the observation that hibernators show little skeletal muscle atrophy despite the profound metabolic rate depression and mechanical unloading that they experience during long weeks of torpor. Additionally, the cardiac muscle of hibernators must adjust to low temperature and reduced perfusion, while the strength of contraction increases in order to pump cold, viscous blood. Consequently, hibernators hold a wealth of knowledge as it pertains to understanding the natural capacity of myocytes to alter structural, contractile and metabolic properties in response to environmental stimuli. The present review outlines the molecular and biochemical mechanisms which play a role in muscular atrophy, hypertrophy, and remodeling. In this capacity, four main networks are highlighted: (1) antioxidant defenses, (2) the regulation of structural, contractile and metabolic proteins, (3) ubiquitin proteosomal machinery, and (4) macroautophagy pathways. Subsequently, we discuss the role of transcription factors nuclear factor (erythroid-derived 2)-like 2 (Nrf2), Myocyte enhancer factor 2 (MEF2), and Forkhead box (FOXO) and their associated posttranslational modifications as it pertains to regulating each of these networks. Finally, we propose that comparing and contrasting these concepts to data collected from model organisms able to withstand dramatic changes in muscular function without injury will allow researchers to delineate physiological versus pathological responses. PMID:26982616

  19. Sodium ion interactions with aqueous glucose: insights from quantum mechanics, molecular dynamics, and experiment.

    PubMed

    Mayes, Heather B; Tian, Jianhui; Nolte, Michael W; Shanks, Brent H; Beckham, Gregg T; Gnanakaran, S; Broadbelt, Linda J

    2014-02-27

    In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on β-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na(+) suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na(+) interacts similarly with α- and β-glucose. PMID:24308866

  20. Molecular insight into arsenic toxicity via the genome-wide deletion mutant screening of Saccharomyces cerevisiae.

    PubMed

    Johnson, Adam J; Veljanoski, Filip; O'Doherty, Patrick J; Zaman, Mohammad S; Petersingham, Gayani; Bailey, Trevor D; Münch, Gerald; Kersaitis, Cindy; Wu, Ming J

    2016-02-01

    Arsenic is omnipresent in soil, air, food and water. Chronic exposure to arsenic is a serious problem to human health. In-depth understanding of this metalloid's toxicity is a fundamental step towards development of arsenic-free foods and measures for bioremediation. By screening the complete set of gene deletion mutants (4873) of Saccharomyces cerevisiae, this study uncovered 75 sensitive and 39 resistant mutants against arsenite [As(III)]. Functional analysis of the corresponding genes revealed the molecular details for its uptake, toxicity and detoxification. On the basis of the hypersensitivity of yap3Δ, the transcription factor, Yap3p, is for the first time linked to the cell's detoxification against As(III). Apart from confirming the previously described role of the mitogen-activated protein kinase (MAPK) Hog1 pathway in combating arsenic toxicity, the results show that the regulatory subunits (Ckb1p and Ckb2p) of protein kinase CK2 are also involved in the process, suggesting possible crosstalk between the two key protein kinases. The sensitivity to As(III) conferred by deletion of the genes involved in protein degradation and chromatin remodelling demonstrates protein damage is the key mode of toxicity for the metalloid. Furthermore, the resistant phenotype of fps1Δ, snf3Δ and pho81Δ against As(III) links arsenic uptake with the corresponding plasma membrane-bound transporters-aquaglyceroporin (Fps1p), hexose (Snf3p) and phosphate transporters. The molecular details obtained in this screen for As(III) uptake, detoxification and toxicity provide the basis for future investigations into arsenic-related problems in the environment, agriculture and human health. PMID:26688044

  1. A new gating site in human aquaporin-4: Insights from molecular dynamics simulations.

    PubMed

    Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Nicchia, Grazia Paola; Frigeri, Antonio; Pisani, Francesco; Benfenati, Valentina; Mangiatordi, Giuseppe Felice

    2014-12-01

    Aquaporin-4 (AQP4) is the predominant water channel in different organs and tissues. An alteration of its physiological functioning is responsible for several disorders of water regulation and, thus, is considered an attractive target with a promising therapeutic and diagnostic potential. Molecular dynamics (MD) simulations performed on the AQP4 tetramer embedded in a bilayer of lipid molecules allowed us to analyze the role of spontaneous fluctuations occurring inside the pore. Following the approach by Hashido et al. [Hashido M, Kidera A, Ikeguchi M (2007) Biophys J 93: 373-385], our analysis on 200ns trajectory discloses three domains inside the pore as key elements for water permeation. Herein, we describe the gating mechanism associated with the well-known selectivity filter on the extracellular side of the pore and the crucial regulation ensured by the NPA motifs (asparagine, proline, alanine). Notably, on the cytoplasmic side, we find a putative gate formed by two residues, namely, a cysteine belonging to the loop D (C178) and a histidine from loop B (H95). We observed that the spontaneous reorientation of the imidazole ring of H95 acts as a molecular switch enabling H-bond interaction with C178. The occurrence of such local interaction seems to be responsible for the narrowing of the pore and thus of a remarkable decrease in water flux rate. Our results are in agreement with recent experimental observations and may represent a promising starting point to pave the way for the discovery of chemical modulators of AQP4 water permeability. PMID:25150048

  2. Insights using a molecular approach into the life cycle of a tapeworm infecting great white sharks.

    PubMed

    Randhawa, Haseeb S

    2011-04-01

    The great white shark Carcharodon carcharias Linnaeus, 1758 is a versatile and fierce predator (and responsible for many shark attacks on humans). This apex predator feeds on a wide range of organisms including teleosts, other elasmobranchs, cephalopods, pinnipeds, and cetaceans. Although much is known about its diet, no trophic links have been empirically identified as being involved in the transmission of its tapeworm parasites. Recently, the use of molecular tools combined with phylogenetics has proven useful to identify larval and immature stages of marine tapeworms; utilization of the technique has been increasing rapidly. However, the usefulness of this approach remains limited by the availability of molecular data. Here, I employed gene sequence data from the D2 region of the large subunit of ribosomal DNA to link adults of the tapeworm Clistobothrium carcharodoni Dailey and Vogelbein, 1990 (Cestoda: Tetraphyllidea) to larvae for which sequence data for this gene are available. The sequences from the adult tapeworms were genetically identical (0% sequence divergence) to those available on GenBank for "SP" 'small' Scolex pleuronectis recovered from the striped dolphin (Stenella coeruleoalba) and Risso's dolphin (Grampus griseus). This study is the first to provide empirical evidence linking the trophic interaction between great white sharks and cetaceans as a definitive route for the successful transmission of a tetraphyllidean tapeworm. Using the intensity of infection data from this shark and from cetaceans as proxies for the extent of predation, I estimate that this individual shark would have consumed between 9 to 83 G. griseus , fresh, dead, or both, in its lifetime. PMID:21506792

  3. Molecular Phylogeny of the Neotropical Genus Christensonella (Orchidaceae, Maxillariinae): Species Delimitation and Insights into Chromosome Evolution

    PubMed Central

    Koehler, Samantha; Cabral, Juliano S.; Whitten, W. Mark; Williams, Norris H.; Singer, Rodrigo B.; Neubig, Kurt M.; Guerra, Marcelo; Souza, Anete P.; Amaral, Maria do Carmo E.

    2008-01-01

    Background and Aims Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification. Methods Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes. Key Results Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands. Conclusions The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent

  4. A Molecular Analysis Provides Novel Insights into Androgen Receptor Signalling in Breast Cancer

    PubMed Central

    Mehta, Jatin; Asthana, Shailendra; Mandal, Chandi Charan; Saxena, Sunita

    2015-01-01

    Background Androgen Receptor (AR) is an essential transcription factor for the development of secondary sex characteristics, spermatogenesis and carcinogenesis. Recently AR has been implicated in the development and progression of breast and prostate cancers. Although some of the functions of the AR are known but the mechanistic details of these divergent processes are still not clear. Therefore understanding the regulatory mechanisms of the functioning of the AR in ER-/AR+ breast cancer will provide many novel targets for the purpose of therapeutic intervention. Methods/Results Using bioinformatics tools, we have identified 75 AR targets having prominent roles in cell cycle, apoptosis and metabolism. Herein, we validated 10 genes as AR targets by studying the regulation of these genes in MDA-MB-453 cell line on stimulation by androgens like 5α-dihydrotestosterone (DHT), using RT-qPCR and ChIP assay. It was observed that all the identified genes involved in cell cycle except MAD1L1 were found to be up regulated whereas expression of apoptosis related genes was decreased in response to DHT treatment. We performed an exhaustive, rigid-body docking between individual ARE and DNA binding domain (DBD) of the AR protein and it was found that novel residues K567, K588, K591 and R592 are involved in the process of DNA binding. To verify these specific DNA-protein interactions electrostatic energy term calculations for each residue was determined using the linearized Poisson–Boltzmann equation. Our experimental data showed that treatment of breast cancer cells with DHT promotes cell proliferation and decreases apoptosis. It was observed that bicalutamide treatment was able to reverse the effect of DHT. Conclusion Taken together, our results provide new insights into the mechanism by which AR promotes breast cancer progression. Moreover our work proposes to use bicalutamide along with taxanes as novel therapy for the treatment of TNBCs, which are positive for downstream

  5. Comparative molecular epidemiology provides new insights into Zucchini yellow mosaic virus occurrence in France.

    PubMed

    Lecoq, H; Wipf-Scheibel, C; Nozeran, K; Millot, P; Desbiez, C

    2014-06-24

    Zucchini yellow mosaic virus (ZYMV, genus Potyvirus) causes important crop losses in cucurbits worldwide. In France, ZYMV epidemics are sporadic but occasionally very severe. This contrasts with Watermelon mosaic virus (WMV, genus Potyvirus) which causes regular and early epidemics. Factors influencing ZYMV epidemiology are still poorly understood. In order to gain new insights on the ecology and epidemiology of this virus, a 5-year multilocation trial was conducted in which ZYMV spread and populations were studied in each of the 20 plot/year combinations and compared with WMV. Search for ZYMV alternative hosts was conducted by testing weeds growing naturally around one plot and also by checking ZYMV natural infections in selected ornamental species. Although similar ZYMV populations were observed occasionally in the same plot in two successive years suggesting the occurrence of overwintering hosts nearby, only two Lamium amplexicaule plants were found to be infected by ZYMV of 3459 weed samples that were tested. The scarcity of ZYMV reservoirs contrasts with the frequent detection of WMV in the same samples. Since ZYMV and WMV have many aphid vectors in common and are transmitted with similar efficiencies, the differences observed in ZYMV and WMV reservoir abundances could be a major explanatory factor for the differences observed in the typology of ZYMV and WMV epidemics in France. Other potential ZYMV alternative hosts have been identified in ornamental species including begonia. Although possible in a few cases, exchanges of populations between different plots located from 500 m to 4 km apart seem uncommon. Therefore, the potential dissemination range of ZYMV by its aphid vectors seems to be rather limited in a fragmented landscape. PMID:24486486

  6. Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects.

    PubMed

    Kandiah, D A; Sali, A; Sheng, Y; Victoria, E J; Marquis, D M; Coutts, S M; Krilis, S A

    1998-01-01

    Advances in defining the target antigen(s) for the autoantibodies in the APS highlight the inadequacies of the current classification of these autoantibodies into anticardiolipin and LA antibodies. The discovery that beta 2GPI is the target antigen for the autoantibodies detected in solid-phase immunoassays has opened a number of areas of research linking these autoantibodies to atherogenesis and thrombus formation. Although the role of beta 2GPI in the regulation of blood coagulation in unclear, current evidence suggests that anti-beta 2GPI antibodies interfere with its "normal" role and appear to promote a procoagulant tendency. The expansion of research in this area and the diversity of the clinical manifestations of patients with APS have resulted in the inclusion of molecular biologists and pharmaceutical companies joining immunologists, hematologists, rheumatologists, obstetricians, neurologists, vascular surgeons, and protein and lipid biochemists in attempting to understand the pathophysiology of this condition. Although the published literature may result in conflicting results and introduce new controversies, developing standardized laboratory methods and extrapolation of in vitro experimental results to the vivo situation will advance our understanding of the regulation of the immune system and its interaction with normal hemostatic mechanisms. Since the authors' last review in 1991, the study and understanding of the pathophysiology of APS have evolved from lipid biochemistry to molecular techniques that may eventually provide specific therapies for the clinical manifestations of this condition. Although current treatment has improved the morbidity associated with this condition, especially in improving pregnancy outcomes, future therapies, as outlined in this review, may specifically address the biological abnormalities and have fewer side effects. Better diagnostic tools, such as magnetic resonance imaging with perfusion studies, will allow the study

  7. Phenotypic and molecular insights into spinal muscular atrophy due to mutations in BICD2.

    PubMed

    Rossor, Alexander M; Oates, Emily C; Salter, Hannah K; Liu, Yang; Murphy, Sinead M; Schule, Rebecca; Gonzalez, Michael A; Scoto, Mariacristina; Phadke, Rahul; Sewry, Caroline A; Houlden, Henry; Jordanova, Albena; Tournev, Iyailo; Chamova, Teodora; Litvinenko, Ivan; Zuchner, Stephan; Herrmann, David N; Blake, Julian; Sowden, Janet E; Acsadi, Gyuda; Rodriguez, Michael L; Menezes, Manoj P; Clarke, Nigel F; Auer Grumbach, Michaela; Bullock, Simon L; Muntoni, Francesco; Reilly, Mary M; North, Kathryn N

    2015-02-01

    Spinal muscular atrophy is a disorder of lower motor neurons, most commonly caused by recessive mutations in SMN1 on chromosome 5q. Cases without SMN1 mutations are subclassified according to phenotype. Spinal muscular atrophy, lower extremity-predominant, is characterized by lower limb muscle weakness and wasting, associated with reduced numbers of lumbar motor neurons and is caused by mutations in DYNC1H1, which encodes a microtubule motor protein in the dynein-dynactin complex and one of its cargo adaptors, BICD2. We have now identified 32 patients with BICD2 mutations from nine different families, providing detailed insights into the clinical phenotype and natural history of BICD2 disease. BICD2 spinal muscular atrophy, lower extremity predominant most commonly presents with delayed motor milestones and ankle contractures. Additional features at presentation include arthrogryposis and congenital dislocation of the hips. In all affected individuals, weakness and wasting is lower-limb predominant, and typically involves both proximal and distal muscle groups. There is no evidence of sensory nerve involvement. Upper motor neuron signs are a prominent feature in a subset of individuals, including one family with exclusively adult-onset upper motor neuron features, consistent with a diagnosis of hereditary spastic paraplegia. In all cohort members, lower motor neuron features were static or only slowly progressive, and the majority remained ambulant throughout life. Muscle MRI in six individuals showed a common pattern of muscle involvement with fat deposition in most thigh muscles, but sparing of the adductors and semitendinosus. Muscle pathology findings were highly variable and included pseudomyopathic features, neuropathic features, and minimal change. The six causative mutations, including one not previously reported, result in amino acid changes within all three coiled-coil domains of the BICD2 protein, and include a possible 'hot spot' mutation, p.Ser107Leu

  8. Phenotypic and molecular insights into spinal muscular atrophy due to mutations in BICD2

    PubMed Central

    Rossor, Alexander M.; Oates, Emily C.; Salter, Hannah K.; Liu, Yang; Murphy, Sinead M.; Schule, Rebecca; Gonzalez, Michael A.; Scoto, Mariacristina; Phadke, Rahul; Sewry, Caroline A.; Houlden, Henry; Jordanova, Albena; Tournev, Iyailo; Chamova, Teodora; Litvinenko, Ivan; Zuchner, Stephan; Herrmann, David N.; Blake, Julian; Sowden, Janet E.; Acsadi, Gyuda; Rodriguez, Michael L.; Menezes, Manoj P.; Clarke, Nigel F.; Auer Grumbach, Michaela; Bullock, Simon L.; Muntoni, Francesco; North, Kathryn N.

    2015-01-01

    Spinal muscular atrophy is a disorder of lower motor neurons, most commonly caused by recessive mutations in SMN1 on chromosome 5q. Cases without SMN1 mutations are subclassified according to phenotype. Spinal muscular atrophy, lower extremity-predominant, is characterized by lower limb muscle weakness and wasting, associated with reduced numbers of lumbar motor neurons and is caused by mutations in DYNC1H1, which encodes a microtubule motor protein in the dynein-dynactin complex and one of its cargo adaptors, BICD2. We have now identified 32 patients with BICD2 mutations from nine different families, providing detailed insights into the clinical phenotype and natural history of BICD2 disease. BICD2 spinal muscular atrophy, lower extremity predominant most commonly presents with delayed motor milestones and ankle contractures. Additional features at presentation include arthrogryposis and congenital dislocation of the hips. In all affected individuals, weakness and wasting is lower-limb predominant, and typically involves both proximal and distal muscle groups. There is no evidence of sensory nerve involvement. Upper motor neuron signs are a prominent feature in a subset of individuals, including one family with exclusively adult-onset upper motor neuron features, consistent with a diagnosis of hereditary spastic paraplegia. In all cohort members, lower motor neuron features were static or only slowly progressive, and the majority remained ambulant throughout life. Muscle MRI in six individuals showed a common pattern of muscle involvement with fat deposition in most thigh muscles, but sparing of the adductors and semitendinosus. Muscle pathology findings were highly variable and included pseudomyopathic features, neuropathic features, and minimal change. The six causative mutations, including one not previously reported, result in amino acid changes within all three coiled-coil domains of the BICD2 protein, and include a possible ‘hot spot’ mutation, p.Ser107

  9. Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System*

    PubMed Central

    Koh, Serry; Hwang, Jungwon; Guchhait, Koushik; Lee, Eun-Gyeong; Kim, Sang-Yoon; Kim, Sujin; Lee, Sangmin; Chung, Jeong Min; Jung, Hyun Suk; Lee, Sang Jun; Ryu, Choong-Min; Lee, Seung-Goo; Oh, Tae-Kwang; Kwon, Ohsuk; Kim, Myung Hee

    2016-01-01

    TodS is a sensor kinase that responds to various monoaromatic compounds, which either cause an agonistic or antagonistic effect on phosphorylation of its cognate response regulator TodT, and controls tod operon expression in Pseudomonas putida strains. We describe a molecular sensing mechanism of TodS that is activated in response to toluene. The crystal structures of the TodS Per-Arnt-Sim (PAS) 1 sensor domain (residues 43–164) and its complex with toluene (agonist) or 1,2,4-trimethylbenzene (antagonist) show a typical β2α3β3 PAS fold structure (residues 45–149), forming a hydrophobic ligand-binding site. A signal transfer region (residues 150–163) located immediately after the canonical PAS fold may be intrinsically flexible and disordered in both apo-PAS1 and antagonist-bound forms and dramatically adapt an α-helix upon toluene binding. This structural change in the signal transfer region is proposed to result in signal transmission to activate the TodS/TodT two-component signal transduction system. Site-directed mutagenesis and β-galactosidase assays using a P. putida reporter strain system verified the essential residues involved in ligand sensing and signal transfer and suggest that the Phe46 residue acts as a ligand-specific switch. PMID:26903514

  10. Molecular insight into the viral biology and clinical features of trichodysplasia spinulosa.

    PubMed

    Wu, J H; Nguyen, H P; Rady, P L; Tyring, S K

    2016-03-01

    Trichodysplasia spinulosa (TS) is a disfiguring skin disease that occurs most frequently in patients receiving immunosuppressive therapies, and is thus frequently associated with organ transplantation. TS is characterized clinically by folliculocentric papular eruption, keratin spine formation and development of leonine face; and histologically by expansion of the inner root sheath epithelium and high expression of the proliferative marker Ki-67. Recent discovery of the TS-associated polyomavirus (TSPyV) and emerging studies demonstrating the role of TSPyV tumour antigens in cell proliferation pathways have opened a new corridor for research on TS. In this brief review, we summarize the clinical and histological features of TS and evaluate the current options for therapy. Furthermore, we address the viral aetiology of the disease and explore the mechanisms by which TSPyV may influence TS development and progression. As reports of TS continue to rise, clinician recognition of TS, as well as accompanying research on its underlying pathogenesis and therapeutic options, is becoming increasingly important. It is our hope that heightened clinical suspicion for TS will increase rates of diagnosis and will galvanize both molecular and clinical interest in this disease. PMID:26479880

  11. Endemic nephropathy and upper urothelial carcinoma--new insights in molecular biology.

    PubMed

    Jankovic Velickovic, Ljubinka; Dolicanin, Zana; Stefanovic, Vladisav

    2014-01-01

    Upper Tract Urothelial Carcinoma (UTUC) is an uncommon disease which occurs more frequently in some regions of Balkan countries than in other areas in the world. Investigation of UTUC in the South Morava River basin and its tributaries where BEN is endemic revealed increased frequency not only of tumour of the renal pelvis and ureter but also of urinary bladder tumours. A comparative morphological and immunohistochemical study of UTUC in the BEN region and control rural and city populations free of BEN, identify growth pattern as the best morphological characteristic which differentiated BEN and control tumours, i.e. solid growth for BEN tumours and papillary for control tumours. Overexpression of tumour suppressor p53 as well as decreased expression of E-CD was detected in BEN tumours. Other cells cycle related molecular markers--Cyclin D1, p16, and HER-2 showed no difference in expression between groups, as well as the proliferative marker Ki-67. Investigation of apoptosis-related markers identifies Bax as a specific marker of BEN-associated UTUC. Decrease of the pro-apoptotic protein Bax together with alteration of Survivin may be indicative of specific disturbances of an intrinsic apoptotic pathway in UTUC arising in endemic areas. PMID:24802310

  12. Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species.

    PubMed

    Denver, D R; Clark, K A; Raboin, M J

    2011-11-01

    The Phylum Nematoda has long been known to contain a great diversity of species that vary in reproductive mode, though our understanding of the evolutionary origins, causes and consequences of nematode reproductive mode change have only recently started to mature. Here we bring together and analyze recent progress on reproductive mode evolution throughout the phylum, resulting from the application of molecular phylogenetic approaches and newly discovered nematode species. Reproductive mode variation is reviewed in multiple free-living, animal-parasitic and plant-parasitic nematode groups. Discussion ranges from the model nematode Caenorhabditis elegans and its close relatives, to the plant-parasitic nematodes of the Meloidogyne genus where there is extreme variation in reproductive mode between and even within species, to the vertebrate-parasitic genus Strongyloides and related genera where reproductive mode varies across generations (heterogony). Multiple evolutionary transitions from dioecous (obligately outcrossing) to hermaphroditism and parthenogenesis in the phylum are discussed, along with one case of an evolutionary transition from hermaphroditism to doioecy in the Oscheius genus. We consider the roles of underlying genetic mechanisms in promoting reproductive plasticity in this phylum, as well as the potential evolutionary forces promoting transitions in reproductive mode. PMID:21787872

  13. Molecular Background of miRNA Role in Asthma and COPD: An Updated Insight

    PubMed Central

    Szymczak, Izabela; Wieczfinska, Joanna; Pawliczak, Rafal

    2016-01-01

    Inflammatory airway diseases are a significant health problems requiring new approaches to the existing therapies and addressing fundamental issues. Difficulties in developing effective therapeutic strategies might be caused by lack of understanding of their exact molecular mechanism. MicroRNAs (miRNAs) are a class of regulators that already revolutionized the view of gene expression regulation. A cumulating number of investigations show a pivotal role of miRNAs in the pathogenesis of asthma, chronic obstructive pulmonary disease (COPD), or airway remodeling through the regulation of many pathways involved in their pathogenesis. Expression changes of several miRNAs have also been found to play a role in the development and/or improvement in asthma or COPD. Still, relatively little is known about the role of miRNAs in inflammatory disorders. The microRNA profiles may differ depending on the cell type or antigen-presenting cell. Based on the newest literature, this review discusses the current knowledge concerning miRNA contribution and influence on lung inflammation and chosen inflammatory airway diseases: asthma and COPD. PMID:27376086

  14. Molecular insights into chronotype and time-of-day effects on decision-making.

    PubMed

    Ingram, Krista K; Ay, Ahmet; Kwon, Soo Bin; Woods, Kerri; Escobar, Sue; Gordon, Molly; Smith, Isaac H; Bearden, Neil; Filipowicz, Allan; Jain, Kriti

    2016-01-01

    Recent reports highlight that human decision-making is influenced by the time of day and whether one is a morning or evening person (i.e., chronotype). Here, we test whether these behavioral effects are associated with endogenous biological rhythms. We asked participants to complete two well-established decision-making tasks in the morning or evening: the matrix task (an ethical decision task) and the balloon analog risk task (BART; a risk-taking task), and we measured their chronotype in two ways. First, participants completed a self-report measure, the Horne-Östberg Morningness-Eveningness Questionnaire (MEQ). Second, we measured the expression of two circadian clock-regulated genes-Per3 and Nr1d2-from peripheral clock cells in participants' hair follicle samples. Using a cosinor model, we estimated the phase of the peripheral clock and assigned RNA chronotypes to participants with advanced (larks) or delayed (owls) phases. The behavioral data were analyzed independently for self-reported (MEQ) and RNA-based chronotypes. We find that significant chronotype and/or time-of-day effects between larks and owls in decision-making tasks occur only in RNA-based chronotypes. Our results provide evidence that time-of-day effects on decision-making can be explained by phase differences in oscillating clock genes and suggest that variation in the molecular clockwork may influence inter-individual differences in decision-making behavior. PMID:27388366

  15. Molecular insight into activated sludge producing polyhydroxyalkanoates under aerobic-anaerobic conditions.

    PubMed

    Ciesielski, Slawomir; Pokoj, Tomasz; Klimiuk, Ewa

    2008-08-01

    One of the options enabling more economic production of polyhydroxyalkanoates compared to pure cultures is the application of mixed cultures. The use of a microbial community in a sequencing batch reactor has a few advantages: a simple process control, no necessity for sterile processing, and possibilities of using cheap substrates as a source of carbon. Nevertheless, while cultivation methods to achieve high PHAs biomass concentration and high productivity in wild and recombinant strains are defined, knowledge about the cultivation strategy for PHAs production by mixed culture and species composition of bacterial communities is still very limited. The main object of this study was to characterize on the molecular level the composition and activity of PHAs producing microorganism in activated sludge cultivated under oxygen limitation conditions. PHAs producers were detected using a PCR technique and the created PHA synthase gene library was analyzed by DNA sequencing. The obtained results indicate that PHAs-producers belonged to Pseudomonas sp., and possessed genes coding for mcl-PHA synthase. The kinetics of mcl-PHA synthase expression was relatively estimated using real-time PCR technology at several timepoints. Performed quantitative and qualitative analysis of total bacterial activity showed that there were differences in total activity during the process but differential expression of various groups of microorganisms examined by using DGGE was not observed. PMID:18418634

  16. Paratransgenesis: an approach to improve colony health and molecular insight in honey bees (Apis mellifera)?

    PubMed

    Rangberg, Anbjørg; Diep, Dzung B; Rudi, Knut; Amdam, Gro V

    2012-07-01

    The honey bee (Apis mellifera) is highly valued as a commercial crop pollinator and a model animal in research. Over the past several years, governments, beekeepers, and the general public in the United States and Europe have become concerned by increased losses of honey bee colonies, calling for more research on how to keep colonies healthy while still employing them extensively in agriculture. The honey bee, like virtually all multicellular organisms, has a mutually beneficial relationship with specific microbes. The microbiota of the gut can contribute essential nutrients and vitamins and prevent colonization by non-indigenous and potentially harmful species. The gut microbiota is also of interest as a resource for paratransgenesis; a Trojan horse strategy based on genetically modified symbiotic microbes that express effector molecules antagonizing development or transmission of pathogens. Paratransgenesis was originally engineered to combat human diseases and agricultural pests that are vectored by insects. We suggest an alternative use, as a method to promote health of honey bees and to expand the molecular toolbox for research on this beneficial social insect. The honey bees' gut microbiota contains lactic acid bacteria including the genus Lactobacillus that has paratransgenic potential. We present a strategy for transforming one Lactobacillus species, L. kunkeei, for use as a vector to promote health of honey bees and functional genetic research. PMID:22659204

  17. Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization.

    PubMed

    Jeon, Joohyun; Mills, Carolyn E; Shell, M Scott

    2013-04-18

    Self-assembling peptides represent a growing class of inexpensive, environmentally benign, nanostructured materials. In particular, diphenylalanine (FF) self-assembles into nanotubes with remarkable strength and thermal stability that have found use in a wide variety of applications, including as sacrificial templates and scaffolds for structuring inorganic materials and as interfacial "nanoforests" for superhydrophobic surfaces and high-performance supercapacitors and biosensors. However, little is known about the assembly mechanisms of FF nanotubes or the forces underlying their stability. Here, we perform a variety of molecular dynamics simulations on both zwitterionic and capped (uncharged) versions of the FF peptide to understand the early stages of self-assembly. We compare these results to simulations of the proposed nanotube X-ray crystal structure. When comparing the zwitterionic and uncharged FF peptides, we find that, while electrostatic interactions steer the former into more ordered dimers and trimers, the hydrophobic side chain interactions play a strong role in determining the structures of larger oligomers. Simulations of the crystal structure fragment also suggest that the strongest interactions occur between side chains, not between the charged termini that form salt bridges. We conclude that the amphiphilic nature of FF is key to understanding its self-assembly, and that the early precursors to nanotube structures are likely to involve substantial hydrophobic clustering, rather than hexamer ring motifs as has been previously suggested. PMID:23521630

  18. ART and health: clinical outcomes and insights on molecular mechanisms from rodent studies

    PubMed Central

    Feuer, S.K.; Camarano, L.; Rinaudo, P.F.

    2013-01-01

    Since the birth of the first IVF-conceived child in 1978, the use of assisted reproductive technologies (ART) has grown dramatically, contributing to the successful birth of 5 million individuals worldwide. However, there are several reported associations of ART with pregnancy complications, such as low birthweight (LBW), preterm birth, birth defects, epigenetic disorders, cancer and poor metabolic health. Whether this is attributed to ART procedures or to the subset of the population seeking ART remains a controversy, but the most relevant question today concerns the potential long-term implications of assisted conception. Recent evidence has emerged suggesting that ART-conceived children have distinct metabolic profiles that may predispose to cardiovascular pathologies in adulthood. Because the eldest IVF individuals are still too young to exhibit components of chronic middle-aged syndromes, the use of animal models has become particularly useful in describing the effects of unusual or stressful preimplantation experiences on adult fitness. Elucidating the molecular mechanisms by which embryos integrate environmental signals into development and metabolic gene expression programs will be essential for optimizing ART procedures such as in vitro culture conditions, embryo selection and transfer. In the future, additional animal studies to identify mechanisms underlying unfavorable ART outcomes, as well as more epidemiological reviews to monitor the long-term health of ART children are required, given that ART procedures have become routine medical practice. PMID:23264495

  19. Insight into the mechanism of polyphenols on the activity of HMGR by molecular docking.

    PubMed

    Islam, Barira; Sharma, Charu; Adem, Abdu; Aburawi, Elhadi; Ojha, Shreesh

    2015-01-01

    Statins are hypolipidemic drugs that are effective in the treatment of hypercholesterolemia by attenuating cholesterol synthesis in the liver via competitive inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase. Recently, dietary changes associated with drug therapy have garnered attention as novel drugs to mitigate or ameliorate hypercholesterolemia. The present study was undertaken to observe different dietary polyphenols that can bind to the active site of HMGR and inhibit it. Results from the 12 dietary polyphenols tested reveal that polyphenols can bind to HMGR and block the binding of nicotinamide adenine dinucleotide phosphate (NADP(+)). We observed that the rigidity of phenolic rings prevents the polyphenols from docking to the enzyme activity site. The presence of an ester linkage between the phenolic rings in (-)-epigallocatechin-3-gallate (EGCG) and the alkyl chain in curcumin allows them to orient in the active site of the HMGR and bind to the catalytic residues. EGCG and curcumin showed binding to the active site residues with a low GRID score, which may be a potential inhibitor of HMGR. Kaempferol showed binding to HMG-CoA, but with low binding affinity. These observations provide a rationale for the consistent hypolipidemic effect of EGCG and curcumin, which has been previously reported in several epidemiological and animal studies. Therefore, this study substantiates the mechanism of polyphenols on the activity of HMGR by molecular docking and provides the impetus for drug design involving further structure-function relationship studies. PMID:26357462

  20. Neurodevelopmental sequelae of postnatal maternal care in rodents: clinical and research implications of molecular insights.

    PubMed

    Kaffman, Arie; Meaney, Michael J

    2007-01-01

    Parental care plays an important role in the emotional and cognitive development of the offspring. Children who have been exposed to abuse or neglect are more likely to develop numerous psychopathologies, while good parent-infant bonding is associated with improved resiliency to stress. Similar observations have also been reported in non-human primates and rodents, suggesting that at least some neurodevelopmental aspects of parent-offspring interactions are conserved among mammals and could therefore be studied in animals. We present data to suggest that frequency of licking and grooming provided by the dam during a critical period in development plays an important role in modifying neurodevelopment. These findings are examined in the broader context in which exposure to other sensory modalities such as vision or hearing during a specific period in development shapes brain development with functional consequences that persist into adulthood. We also discuss recent rodent work showing that increased frequency of licking and grooming provided by the dam during the first week of life is associated with changes in DNA methylation of promoter elements that control expression of these genes and behavior. The stability of DNA methylation in postmitotic cells provides a possible molecular scaffold by which changes in gene expression and behavioral traits induced by postnatal maternal care are maintained throughout life. Finally, the relevance of findings reported in rodents to those noted in non-human primates and humans are assessed and the research and clinical implications of these observations for future work are explored. PMID:17355397

  1. Nephrogenic Diabetes Insipidus: Essential Insights into the Molecular Background and Potential Therapies for Treatment

    PubMed Central

    Rittig, Søren

    2013-01-01

    The water channel aquaporin-2 (AQP2), expressed in the kidney collecting ducts, plays a pivotal role in maintaining body water balance. The channel is regulated by the peptide hormone arginine vasopressin (AVP), which exerts its effects through the type 2 vasopressin receptor (AVPR2). Disrupted function or regulation of AQP2 or the AVPR2 results in nephrogenic diabetes insipidus (NDI), a common clinical condition of renal origin characterized by polydipsia and polyuria. Over several years, major research efforts have advanced our understanding of NDI at the genetic, cellular, molecular, and biological levels. NDI is commonly characterized as hereditary (congenital) NDI, arising from genetic mutations in the AVPR2 or AQP2; or acquired NDI, due to for exmple medical treatment or electrolyte disturbances. In this article, we provide a comprehensive overview of the genetic, cell biological, and pathophysiological causes of NDI, with emphasis on the congenital forms and the acquired forms arising from lithium and other drug therapies, acute and chronic renal failure, and disturbed levels of calcium and potassium. Additionally, we provide an overview of the exciting new treatment strategies that have been recently proposed for alleviating the symptoms of some forms of the disease and for bypassing G protein-coupled receptor signaling. PMID:23360744

  2. Insights into molecular and metabolic events associated with fruit response to post-harvest fungal pathogens.

    PubMed

    Alkan, Noam; Fortes, Ana M

    2015-01-01

    Due to post-harvest losses more than 30% of harvested fruits will not reach the consumers' plate. Fungal pathogens play a key role in those losses, as they cause most of the fruit rots and the customer complaints. Many of the fungal pathogens are already present in the unripe fruit but remain quiescent during fruit growth until a particular phase of fruit ripening and senescence. The pathogens sense the developmental change and switch into the devastating necrotrophic life style that causes fruit rotting. Colonization of unripe fruit by the fungus initiates defensive responses that limit fungal growth and development. However, during fruit ripening several physiological processes occur that correlate with increased fruit susceptibility. In contrast to plant defenses in unripe fruit, the defense posture of ripe fruit entails a different subset of defense responses that will end with fruit rotting and losses. This review will focus on several aspects of molecular and metabolic events associated with fleshy fruit responses induced by post-harvest fungal pathogens during fruit ripening. PMID:26539204

  3. Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight

    NASA Astrophysics Data System (ADS)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary

    The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.

  4. Insight into the mechanism of polyphenols on the activity of HMGR by molecular docking

    PubMed Central

    Islam, Barira; Sharma, Charu; Adem, Abdu; Aburawi, Elhadi; Ojha, Shreesh

    2015-01-01

    Statins are hypolipidemic drugs that are effective in the treatment of hypercholesterolemia by attenuating cholesterol synthesis in the liver via competitive inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase. Recently, dietary changes associated with drug therapy have garnered attention as novel drugs to mitigate or ameliorate hypercholesterolemia. The present study was undertaken to observe different dietary polyphenols that can bind to the active site of HMGR and inhibit it. Results from the 12 dietary polyphenols tested reveal that polyphenols can bind to HMGR and block the binding of nicotinamide adenine dinucleotide phosphate (NADP+). We observed that the rigidity of phenolic rings prevents the polyphenols from docking to the enzyme activity site. The presence of an ester linkage between the phenolic rings in (–)-epigallocatechin-3-gallate (EGCG) and the alkyl chain in curcumin allows them to orient in the active site of the HMGR and bind to the catalytic residues. EGCG and curcumin showed binding to the active site residues with a low GRID score, which may be a potential inhibitor of HMGR. Kaempferol showed binding to HMG-CoA, but with low binding affinity. These observations provide a rationale for the consistent hypolipidemic effect of EGCG and curcumin, which has been previously reported in several epidemiological and animal studies. Therefore, this study substantiates the mechanism of polyphenols on the activity of HMGR by molecular docking and provides the impetus for drug design involving further structure–function relationship studies. PMID:26357462

  5. Molecular insights into the origin of the Hox-TALE patterning system

    PubMed Central

    Hudry, Bruno; Thomas-Chollier, Morgane; Volovik, Yael; Duffraisse, Marilyne; Dard, Amélie; Frank, Dale; Technau, Ulrich; Merabet, Samir

    2014-01-01

    Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI: http://dx.doi.org/10.7554/eLife.01939.001 PMID:24642410

  6. Effect of Zn(2+) ions on the assembly of amylin oligomers: insight into the molecular mechanisms.

    PubMed

    Wineman-Fisher, Vered; Miller, Yifat

    2016-08-01

    Amylin is an endocrine hormone and is a member of the family of amyloid peptides and proteins that emerge as potential scaffolds by self-assembly processes. Zn(2+) ions can bind to amylin peptides to form self-assembled Zn(2+)-amylin oligomers. In the current work the binding sites of Zn(2+) ions in the self-assembled amylin oligomers at various concentrations of zinc have been investigated. Our results yield two conclusions. First, in the absence of Zn(2+) ions polymorphic states (i.e. various classes of amylin oligomers) are obtained, but when Zn(2+) ions bind to amylin peptides to form Zn(2+)-amylin oligomers, the polymorphism is decreased, i.e. Zn(2+) ions bind only to specific classes of amylin. At low concentrations of Zn(2+) ions the polymorphism is smaller than at high concentrations. Second, the structural features of the self-assembled amylin oligomers are not affected by the presence of Zn(2+) ions. This study proposes new molecular mechanisms of the self-assembly of Zn(2+)-amylin oligomers. PMID:27425207

  7. Merkel Cell Polyomavirus: Molecular Insights into the Most Recently Discovered Human Tumour Virus

    PubMed Central

    Stakaitytė, Gabrielė; Wood, Jennifer J.; Knight, Laura M.; Abdul-Sada, Hussein; Adzahar, Noor Suhana; Nwogu, Nnenna; Macdonald, Andrew; Whitehouse, Adrian

    2014-01-01

    A fifth of worldwide cancer cases have an infectious origin, with viral infection being the foremost. One such cancer is Merkel cell carcinoma (MCC), a rare but aggressive skin malignancy. In 2008, Merkel cell polyomavirus (MCPyV) was discovered as the causative agent of MCC. It is found clonally integrated into the majority of MCC tumours, which require MCPyV oncoproteins to survive. Since its discovery, research has begun to reveal the molecular virology of MCPyV, as well as how it induces tumourigenesis. It is thought to be a common skin commensal, found at low levels in healthy individuals. Upon loss of immunosurveillance, MCPyV reactivates, and a heavy viral load is associated with MCC pathogenesis. Although MCPyV is in many ways similar to classical oncogenic polyomaviruses, such as SV40, subtle differences are beginning to emerge. These unique features highlight the singular position MCPyV has as the only human oncogenic polyomavirus, and open up new avenues for therapies against MCC. PMID:24978434

  8. Molecular Dynamics Simulations of the Cx26 Hemichannel: Insights into Voltage-Dependent Loop-Gating

    PubMed Central

    Kwon, Taekyung; Roux, Benoît; Jo, Sunhwan; Klauda, Jeffery B.; Harris, Andrew L.; Bargiello, Thaddeus A.

    2012-01-01

    Loop-gating is one of two voltage-dependent mechanisms that regulate the open probability of connexin channels. The loop-gate permeability barrier is formed by a segment of the first extracellular loop (E1) (the parahelix) and appears to be accompanied by straightening of the bend angle between E1 and the first transmembrane domain (TM1). Here, all-atom molecular dynamics simulations are used to identify and characterize interacting van der Waals and electrostatic networks that stabilize the parahelices and TM1/E1 bend angles of the open Cx26 hemichannel. Dynamic fluctuations in an electrostatic network in each subunit are directly linked to the stability of parahelix structure and TM1/E1 bend angle in adjacent subunits. The electrostatic network includes charged residues that are pore-lining and thus positioned to be voltage sensors. We propose that the transition to the closed state is initiated by voltage-driven disruption of the networks that stabilize the open-state parahelix configuration, allowing the parahelix to protrude into the channel pore to form the loop-gate barrier. Straightening of the TM1/E1 bend appears to be a consequence of the reorganization of the interacting networks that accompany the conformational change of the parahelix. The electrostatic network extends across subunit boundaries, suggesting a concerted gating mechanism. PMID:22455917

  9. Cholesterol behavior in asymmetric lipid bilayers: insights from molecular dynamics simulations.

    PubMed

    Yesylevskyy, Semen O; Demchenko, Alexander P

    2015-01-01

    Asymmetric lipid composition of the cell membranes plays an important role in the multitude of important biological functions. Much less is known, however, about the distribution and dynamics of cholesterol in asymmetric biological membranes. In this work we show how this issue could be addressed computationally by molecular dynamics simulations. The influence of the lipid head group charge, acyl chain saturation, spontaneous membrane curvature and the surface tension of the membrane on cholesterol distribution in asymmetric lipid bilayers is investigated. Four asymmetric bilayers containing DOPC, DOPS, DSPC, or DSPS lipids, were simulated on the time scale extended to tens of microseconds. We show that cholesterol strongly prefers anionic lipids to neutral and saturated lipid tails to unsaturated with distribution ratio ~0.4-0.6. Multiple flip-flop transitions of cholesterol were observed directly and their mean times range from 350 to 2,000 ns. It was shown that the distribution of cholesterol in the asymmetric bilayer depends not only on the type of lipids but also on the local membrane curvature and the surface tension. The geometric shape of spontaneously curved asymmetric bilayer changes dramatically in the presence of cholesterol. The membrane curvature becomes less homogeneous with large patches of flattened regions interleaved by rather sharp bends. PMID:25331142

  10. Insights into the uranium(VI) speciation with Pseudomonas fluorescens on a molecular level.

    PubMed

    Lütke, Laura; Moll, Henry; Bernhard, Gert

    2012-11-21

    Microorganisms have great potential to bind and thus transport actinides in the environment. Thus microbes indigenous to designated nuclear waste disposal sites have to be investigated regarding their interaction mechanisms with soluble actinyl ions when assessing the safety of a planned repository. This paper presents results on the pH-dependent sorption of U(VI) onto Pseudomonas fluorescens isolated from the granitic rock aquifers at Äspö Hard Rock Laboratory, Sweden. To characterize the U(VI) interaction on a molecular level, potentiometric titration in combination with time-resolved laser-induced fluorescence spectroscopy (TRLFS) were applied. This paper as a result is one of the very few sources which provide stability constants of U(VI) complexed by cell surface functional groups. In addition the bacteria-mediated liberation of inorganic phosphate in dependence on [U(VI)] at different pHs was studied to judge the influence of phosphate release on U(VI) mobilization. The results demonstrate that in the acidic pH range U(VI) is bound by the cells mainly via protonated phosphoryl and carboxylic sites. The complexation by carboxylic groups can be observed over a wide pH range up to around pH 7. At neutral pH fully deprotonated phosphoryl groups are mainly responsible for U(VI) binding. U(VI) can be bound by P. fluorescens with relatively high thermodynamic stability. PMID:23007661

  11. ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations

    PubMed Central

    Pérez-Villa, Andrea; Darvas, Maria; Bussi, Giovanni

    2015-01-01

    Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures. We also construct and simulate putative intermediates for the translocation process, and we perform non-equilibrium targeted simulations to estimate their relative stability. For each of the simulated structures we carefully characterize the available conformational space, the ligand binding pocket, and the RNA binding cleft. The analysis of the hydrogen bond network and of the non-equilibrium trajectories indicates an ATP-dependent stabilization of one of the protein conformers. Additionally, enthalpy calculations suggest that entropic effects might be crucial for the stabilization of the experimentally observed structures. PMID:26358809

  12. Signaling mechanisms of LOV domains: New insights from molecular dynamics studies

    PubMed Central

    Freddolino, Peter L.; Gardner, Kevin H.; Schulten, Klaus

    2013-01-01

    Phototropins are one of several classes of photoreceptors used by plants and algae to respond to light. These proteins contain flavin-binding LOV (Light-Oxygen-Voltage) domains that form covalent cysteine-flavin adducts upon exposure to blue light, leading to the enhancement of phototropin kinase activity. Several lines of evidence suggest that adduct formation in the phototropin LOV2 domains leads to the dissociation of an alpha helix (Jα) from these domains as part of the light-induced activation process. However, crystal structures of LOV domains both in the presence and absence of the Jα helix show very few differences between dark and illuminated states, and thus the precise mechanism through which adduct formation triggers helical dissociation remains poorly understood. Using Avena sativa phototropin 1 LOV2 as a model system, we have studied the interactions of the LOV domain core with the Jα helix through a series of equilibrium molecular dynamics simulations. Here we show that conformational transitions of a conserved glutamine residue in the flavin binding pocket are coupled to altered dynamics of the Jα helix both through a shift in dynamics of the main β-sheet of the LOV domain core and through a secondary pathway involving the N-terminal A′α helix. PMID:23407663

  13. Aqua Ions-Graphene Interfacial and Confinement Behavior: Insights from isobaric-isothermal molecular dynamics

    SciTech Connect

    Chialvo, Ariel A; Cummings, Peter T

    2011-01-01

    We carry out a systematic micro-structural characterization of the solidfluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a free standing plate or with two such plates separated by an inter-plate distance 0 ! h( ) ! 30 at ambient conditions via isothermalisobaric molecular dynamics. With this characterization we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the external and internal (confined) SFI s, the effect of the differential hydration behavior among species and its link to species expulsion from confinement. For water at ambient conditions we found that the structure of the external SFI s is independent of the interplate distance h in the range 0 ! h( ) ! 30 , i.e., the absence of wallmediated correlation effects between external and internal SFI s, and that for h < 9 the slit-pores de-wet. Moreover, we observed a selective expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters including tetrahedral configuration, hydrogen bonding, and species coordination numbers.

  14. Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System.

    PubMed

    Koh, Serry; Hwang, Jungwon; Guchhait, Koushik; Lee, Eun-Gyeong; Kim, Sang-Yoon; Kim, Sujin; Lee, Sangmin; Chung, Jeong Min; Jung, Hyun Suk; Lee, Sang Jun; Ryu, Choong-Min; Lee, Seung-Goo; Oh, Tae-Kwang; Kwon, Ohsuk; Kim, Myung Hee

    2016-04-15

    TodS is a sensor kinase that responds to various monoaromatic compounds, which either cause an agonistic or antagonistic effect on phosphorylation of its cognate response regulator TodT, and controls tod operon expression in Pseudomonas putida strains. We describe a molecular sensing mechanism of TodS that is activated in response to toluene. The crystal structures of the TodS Per-Arnt-Sim (PAS) 1 sensor domain (residues 43-164) and its complex with toluene (agonist) or 1,2,4-trimethylbenzene (antagonist) show a typical β2α3β3 PAS fold structure (residues 45-149), forming a hydrophobic ligand-binding site. A signal transfer region (residues 150-163) located immediately after the canonical PAS fold may be intrinsically flexible and disordered in both apo-PAS1 and antagonist-bound forms and dramatically adapt an α-helix upon toluene binding. This structural change in the signal transfer region is proposed to result in signal transmission to activate the TodS/TodT two-component signal transduction system. Site-directed mutagenesis and β-galactosidase assays using a P. putida reporter strain system verified the essential residues involved in ligand sensing and signal transfer and suggest that the Phe(46) residue acts as a ligand-specific switch. PMID:26903514

  15. Postcollision multifragmentation in fullerene-surface impact: Microscopic insights via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Bernstein, Victor; Kolodney, Eli

    2016-07-01

    Postcollision multifragmentation which we have recently observed experimentally in C60 - -surface impact is the phenomenon of a delayed multiparticle breakup of a highly collisionally vibrationally excited large molecule/cluster (the precursor species) into several polyatomic fragments, after leaving the surface. In this paper, we show that the molecular dynamics simulations of near-grazing C60 collisions with a gold surface at 300 eV impact energy (very similar to the experimental conditions) successfully reproduce the experimentally observed characteristics of the postcollision multifragmentation process. The calculated mass resolved kinetic energy distributions and the time dependent yield curves of the Cn fragments revealed a precursor mediated, velocity correlated, delayed fragmentation event along the outgoing trajectory, far away from the surface. Most of the large fragments (n ≥ 5) are formed within a time window of 2-20 ps after leaving the surface, corresponding to the vertical distances of 3-30 nm from the surface. Analysis of delay times and actual time duration for multifragmentation reveal that a large part can be described as simultaneous postcollision (delayed) multifragmentation events. The delayed nature of the event seems to be due to an early sequence of structural transformations of the precursor.

  16. Postcollision multifragmentation in fullerene-surface impact: Microscopic insights via molecular dynamics simulations.

    PubMed

    Bernstein, Victor; Kolodney, Eli

    2016-07-28

    Postcollision multifragmentation which we have recently observed experimentally in C60 (-)-surface impact is the phenomenon of a delayed multiparticle breakup of a highly collisionally vibrationally excited large molecule/cluster (the precursor species) into several polyatomic fragments, after leaving the surface. In this paper, we show that the molecular dynamics simulations of near-grazing C60 collisions with a gold surface at 300 eV impact energy (very similar to the experimental conditions) successfully reproduce the experimentally observed characteristics of the postcollision multifragmentation process. The calculated mass resolved kinetic energy distributions and the time dependent yield curves of the Cn fragments revealed a precursor mediated, velocity correlated, delayed fragmentation event along the outgoing trajectory, far away from the surface. Most of the large fragments (n ≥ 5) are formed within a time window of 2-20 ps after leaving the surface, corresponding to the vertical distances of 3-30 nm from the surface. Analysis of delay times and actual time duration for multifragmentation reveal that a large part can be described as simultaneous postcollision (delayed) multifragmentation events. The delayed nature of the event seems to be due to an early sequence of structural transformations of the precursor. PMID:27475357

  17. Merkel cell polyomavirus: molecular insights into the most recently discovered human tumour virus.

    PubMed

    Stakaitytė, Gabrielė; Wood, Jennifer J; Knight, Laura M; Abdul-Sada, Hussein; Adzahar, Noor Suhana; Nwogu, Nnenna; Macdonald, Andrew; Whitehouse, Adrian

    2014-01-01

    A fifth of worldwide cancer cases have an infectious origin, with viral infection being the foremost. One such cancer is Merkel cell carcinoma (MCC), a rare but aggressive skin malignancy. In 2008, Merkel cell polyomavirus (MCPyV) was discovered as the causative agent of MCC. It is found clonally integrated into the majority of MCC tumours, which require MCPyV oncoproteins to survive. Since its discovery, research has begun to reveal the molecular virology of MCPyV, as well as how it induces tumourigenesis. It is thought to be a common skin commensal, found at low levels in healthy individuals. Upon loss of immunosurveillance, MCPyV reactivates, and a heavy viral load is associated with MCC pathogenesis. Although MCPyV is in many ways similar to classical oncogenic polyomaviruses, such as SV40, subtle differences are beginning to emerge. These unique features highlight the singular position MCPyV has as the only human oncogenic polyomavirus, and open up new avenues for therapies against MCC. PMID:24978434

  18. Insights into the Interactions between Maleimide Derivates and GSK3β Combining Molecular Docking and QSAR

    PubMed Central

    Quesada-Romero, Luisa; Mena-Ulecia, Karel; Tiznado, William; Caballero, Julio

    2014-01-01

    Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3β) using docking experiments. We found that the orientations that these compounds adopt inside GSK3β binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure–activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. We found a model to explain the structure–activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q2 value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors. PMID:25010341

  19. Insights into the interactions between maleimide derivates and GSK3β combining molecular docking and QSAR.

    PubMed

    Quesada-Romero, Luisa; Mena-Ulecia, Karel; Tiznado, William; Caballero, Julio

    2014-01-01

    Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3β) using docking experiments. We found that the orientations that these compounds adopt inside GSK3β binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure-activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. We found a model to explain the structure-activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q(2) value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors. PMID:25010341

  20. Towards New Insights in the Sterol/Amphotericin Nanochannels Formation: A Molecular Dynamic Simulation Study.

    PubMed

    Boukari, Khaoula; Balme, Sébastien; Janot, Jean-Marc; Picaud, Fabien

    2016-06-01

    Amphotericin B (AmB) is a well-known polyene which self-organizes into membrane cell in order to cause the cell death. Its specific action towards fungal cell is not fully understood but was proved to become from sterol composition. The mechanism was shown experimentally to require the formation of stable sterol/polyene couples which could then organize in a nanochannel. This would allow the leakage of ions responsible for the death of fungal cells, only. In this present study, we investigate the arrangement of AmB/sterols in biological membrane using molecular dynamic simulations in order to understand the role of the sterol structure on the antifungal action of the polyene. We show in particular that the nanochannels tend to close up when cell was composed with cholesterol (animal cell) due to strong interaction between amphotericin and sterol. On the other side, with ergosterol (fungal cell) the largest interactions between amphotericin and lipid membrane lead to the appearance of large hole that could favor the important leakage of ions and thus, the fungal cell death. This work appears as a good complement in the extensive studies linked to the understanding of the antifungal molecules in membrane cells. PMID:26700625

  1. Molecular insights into chronotype and time-of-day effects on decision-making

    PubMed Central

    Ingram, Krista K; Ay, Ahmet; Kwon, Soo Bin; Woods, Kerri; Escobar, Sue; Gordon, Molly; Smith, Isaac H.; Bearden, Neil; Filipowicz, Allan; Jain, Kriti

    2016-01-01

    Recent reports highlight that human decision-making is influenced by the time of day and whether one is a morning or evening person (i.e., chronotype). Here, we test whether these behavioral effects are associated with endogenous biological rhythms. We asked participants to complete two well-established decision-making tasks in the morning or evening: the matrix task (an ethical decision task) and the balloon analog risk task (BART; a risk-taking task), and we measured their chronotype in two ways. First, participants completed a self-report measure, the Horne-Östberg Morningness-Eveningness Questionnaire (MEQ). Second, we measured the expression of two circadian clock-regulated genes—Per3 and Nr1d2—from peripheral clock cells in participants’ hair follicle samples. Using a cosinor model, we estimated the phase of the peripheral clock and assigned RNA chronotypes to participants with advanced (larks) or delayed (owls) phases. The behavioral data were analyzed independently for self-reported (MEQ) and RNA-based chronotypes. We find that significant chronotype and/or time-of-day effects between larks and owls in decision-making tasks occur only in RNA-based chronotypes. Our results provide evidence that time-of-day effects on decision-making can be explained by phase differences in oscillating clock genes and suggest that variation in the molecular clockwork may influence inter-individual differences in decision-making behavior. PMID:27388366

  2. Insights into photodissociation dynamics of acetaldehyde from ab initio calculations and molecular dynamics simulations

    SciTech Connect

    Chen Shilu; Fang Weihai

    2009-08-07

    In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH{sub 3}CHO). Stationary structures for H{sub 2} and CO eliminations in the ground state (S{sub 0}) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH{sub 3}CHO (265 nm<{lambda}<318 nm), the T{sub 1} C-C bond fission following intersystem crossing from the S{sub 1} state is the predominant channel and the minor channel, the ground-state elimination to CH{sub 4}+CO after internal conversion (IC) from S{sub 1} to S{sub 0}, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S{sub 1}/S{sub 0} intersection point resulting from the S{sub 1} C-C bond fission, becomes accessible and increases the yield of CH{sub 4}+CO.

  3. Thermophysical properties of energetic ionic liquids/nitric acid mixtures: Insights from molecular dynamics simulationsa)

    NASA Astrophysics Data System (ADS)

    Hooper, Justin B.; Smith, Grant D.; Bedrov, Dmitry

    2013-09-01

    Molecular dynamics (MD) simulations of mixtures of the room temperature ionic liquids (ILs) 1-butyl-4-methyl imidazolium [BMIM]/dicyanoamide [DCA] and [BMIM][NO3-] with HNO3 have been performed utilizing the polarizable, quantum chemistry based APPLE&P® potential. Experimentally it has been observed that [BMIM][DCA] exhibits hypergolic behavior when mixed with HNO3 while [BMIM][NO3-] does not. The structural, thermodynamic, and transport properties of the IL/HNO3 mixtures have been determined from equilibrium MD simulations over the entire composition range (pure IL to pure HNO3) based on bulk simulations. Additional (non-equilibrium) simulations of the composition profile for IL/HNO3 interfaces as a function of time have been utilized to estimate the composition dependent mutual diffusion coefficients for the mixtures. The latter have been employed in continuum-level simulations in order to examine the nature (composition and width) of the IL/HNO3 interfaces on the millisecond time scale.

  4. Forced Desorption of Bovine Serum Albumin and Lysozyme from Graphite: Insights from Molecular Dynamics Simulation.

    PubMed

    Mücksch, Christian; Urbassek, Herbert M

    2016-08-18

    We use molecular dynamics (MD) simulation to study the adsorption and desorption of two widely different proteins, bovine serum albumin (BSA) and lysozyme, on a graphite surface. The adsorption is modeled using accelerated MD to allow the proteins to find optimum conformations on the surface. Our results demonstrate that the "hard protein" lysozyme retains much of its secondary structure during adsorption, whereas BSA loses it almost completely. BSA has a considerably larger adsorption energy compared to that of lysozyme, which does not scale with chain length. Desorption simulations are carried out using classical steered MD. The BSA molecule becomes fully unzipped during pull-off, whereas several helices survive this process in lysozyme. The unzipping process shows up in the force-distance curve of BSA as a series of peaks, whereas only a single or few, depending on protein orientation, force peaks occur for lysozyme. The maximum desorption force is larger for BSA than for lysozyme, but only by a factor of about 2.3. PMID:27421144

  5. Molecular basis of floral petaloidy: insights from androecia of Canna indica

    PubMed Central

    Fu, Qian; Liu, Huanfang; Almeida, Ana M. R.; Kuang, Yanfeng; Zou, Pu; Liao, Jingping

    2014-01-01

    Floral organs that take on the characteristics of petals can occur in all whorls of the monocot order Zingiberales. In Canna indica, the most ornamental or ‘petaloid’ parts of the flowers are of androecial origin and are considered staminodes. However, the precise nature of these petaloid organs is yet to be determined. In order to gain a better understanding of the genetic basis of androecial identity, a molecular investigation of B- and C-class genes was carried out. Two MADS-box genes GLOBOSA (GLO) and AGAMOUS (AG) were isolated from young inflorescences of C. indica by 3′ rapid amplification of cDNA ends polymerase chain reaction (3′-RACE PCR). Sequence characterization and phylogenetic analyses show that CiGLO and CiAG belong to the B- and C-class MADS-box gene family, respectively. CiAG is expressed in petaloid staminodes, the labellum, the fertile stamen and carpels. CiGLO is expressed in petals, petaloid staminodes, the labellum, the fertile stamen and carpels. Expression patterns in mature tissues of CiGLO and CiAG suggest that petaloid staminodes and the labellum are of androecial identity, in agreement with their position within the flower and with described Arabidopsis thaliana expression patterns. Although B- and C-class genes are important components of androecial determination, their expression patterns are not sufficient to explain the distinct morphology observed in staminodes and the fertile stamen in C. indica. PMID:24876297

  6. Domestication of Plants in the Americas: Insights from Mendelian and Molecular Genetics

    PubMed Central

    Pickersgill, Barbara

    2007-01-01

    Background Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. Genetic and Molecular Analyses of Domestication Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. Conclusions Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas. PMID:17766847

  7. Insights into molecular and metabolic events associated with fruit response to post-harvest fungal pathogens

    PubMed Central

    Alkan, Noam; Fortes, Ana M.

    2015-01-01

    Due to post-harvest losses more than 30% of harvested fruits will not reach the consumers’ plate. Fungal pathogens play a key role in those losses, as they cause most of the fruit rots and the customer complaints. Many of the fungal pathogens are already present in the unripe fruit but remain quiescent during fruit growth until a particular phase of fruit ripening and senescence. The pathogens sense the developmental change and switch into the devastating necrotrophic life style that causes fruit rotting. Colonization of unripe fruit by the fungus initiates defensive responses that limit fungal growth and development. However, during fruit ripening several physiological processes occur that correlate with increased fruit susceptibility. In contrast to plant defenses in unripe fruit, the defense posture of ripe fruit entails a different subset of defense responses that will end with fruit rotting and losses. This review will focus on several aspects of molecular and metabolic events associated with fleshy fruit responses induced by post-harvest fungal pathogens during fruit ripening. PMID:26539204

  8. Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding.

    PubMed

    Park, Jiho; Czapla, Luke; Amaro, Rommie E

    2013-08-26

    CYP19A1, also known as aromatase or estrogen synthetase, is the rate-limiting enzyme in the biosynthesis of estrogens from their corresponding androgens. Several clinically used breast cancer therapies target aromatase. In this work, explicitly solvated all-atom molecular dynamics simulations of aromatase with a model of the lipid bilayer and the transmembrane helix are performed. The dynamics of aromatase and the role of titration of an important amino acid residue involved in aromatization of androgens are investigated via two 250-ns long simulations. One simulation treats the protonated form of the catalytic aspartate 309, which appears more consistent with crystallographic data for the active site, while the simulation of the deprotonated form shows some notable conformational shifts. Ensemble-based computational solvent mapping experiments indicate possible novel druggable binding sites that could be utilized by next-generation inhibitors. In addition, the effects of protonation on the ligand positioning and channel dynamics are investigated using geometrical models that estimate the opening width of critical channels. Significant differences in channel dynamics between the protonated and deprotonated trajectories are exhibited, suggesting that the mechanism for substrate and product entry and the aromatization process may be coupled to a "locking" mechanism and channel opening. Our results may be particularly relevant in the design of novel drugs, which may be useful therapeutic treatments of cancers such as those of the breast and prostate. PMID:23927370

  9. Minireview: Insights Into the Structural and Molecular Consequences of the TSH-β Mutation C105Vfs114X.

    PubMed

    Kleinau, Gunnar; Kalveram, Laura; Köhrle, Josef; Szkudlinski, Mariusz; Schomburg, Lutz; Biebermann, Heike; Grüters-Kieslich, Annette

    2016-09-01

    Naturally occurring thyrotropin (TSH) mutations are rare, which is also the case for the homologous heterodimeric glycoprotein hormones (GPHs) follitropin (FSH), lutropin (LH), and choriogonadotropin (CG). Patients with TSH-inactivating mutations present with central congenital hypothyroidism. Here, we summarize insights into the most frequent loss-of-function β-subunit of TSH mutation C105Vfs114X, which is associated with isolated TSH deficiency. This review will address the following question. What is currently known on the molecular background of this TSH variant on a protein level? It has not yet been clarified how C105Vfs114X causes early symptoms in affected patients, which are comparably severe to those observed in newborns lacking any functional thyroid tissue (athyreosis). To better understand the mechanisms of this mutant, we have summarized published reports and complemented this information with a structural perspective on GPHs. By including the ancestral TSH receptor agonist thyrostimulin and pathogenic mutations reported for FSH, LH, and choriogonadotropin in the analysis, insightful structure function and evolutionary restrictions become apparent. However, comparisons of immunogenicity and bioactivity of different GPH variants is hindered by a lack of consensus for functional analysis and the diversity of used GPH assays. Accordingly, relevant gaps of knowledge concerning details of GPH mutation-related effects are identified and highlighted in this review. These issues are of general importance as several previous and recent studies point towards the high impact of GPH variants in differential signaling regulation at GPH receptors (GPHRs), both endogenously and under diseased conditions. Further improvement in this area is of decisive importance for the development of novel targeted therapies. PMID:27387040

  10. Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study.

    PubMed

    Xue, Weiwei; Wang, Panpan; Li, Bo; Li, Yinghong; Xu, Xiaofei; Yang, Fengyuan; Yao, Xiaojun; Chen, Yu Zong; Xu, Feng; Zhu, Feng

    2016-01-28

    Antidepressants selectively inhibiting serotonin reuptake (SSRIs) represent a highly effective drug class, and novel therapeutic strategies were proposed to improve SSRIs' drug efficacy. The knowledge of the inhibitory mechanism of FDA approved SSRIs could provide great insights and act as important starting points to discover privileged drug scaffolds with improved efficacy. However, the structure of human serotonin transporter (hSERT) is yet to be determined and the inhibitory mechanism underlying SSRIs still needs to be further explored. In this study, the inhibitory mechanism of 4 approved SSRIs treating major depression (fluoxetine, sertraline, paroxetine and escitalopram) was identified by integrating multiple computational methods. Firstly, a recently published template with high sequence identity was adopted for the first time to generate hSERT's homology model. Then, docking poses of 4 SSRIs were used as the initial conformation for molecular dynamics (MD) simulation followed by MM/GBSA binding free energy calculation and per-residue free energy decomposition. Finally, the binding mode shared by the 4 studied SSRIs was identified by hierarchically clustering per-residue free energies. The identified binding mode was composed of collective interactions between 3 chemical groups in SSRIs and 11 hot spot residues in hSERT. 6 out of these 11 were validated by previous mutagenesis studies or pharmacophore models, and the remaining 5 (Ala169, Ala173, Thr439, Gly442 and Leu443) found in this work were not yet been identified as common determinants of all the 4 studied SSRIs in binding hSERT. Moreover, changes in SSRIs' binding induced by mutation on hot spot residues were further explored, and 3 mechanisms underlining their drug sensitivity were summarized. In summary, the identified binding mode provided important insights into the inhibitory mechanism of approved SSRIs treating major depression, which could be further utilized as a framework for assessing and

  11. Phylogeny, evolutionary trends and classification of the Spathelia–Ptaeroxylon clade: morphological and molecular insights

    PubMed Central

    Appelhans, M. S.; Smets, E.; Razafimandimbison, S. G.; Haevermans, T.; van Marle, E. J.; Couloux, A.; Rabarison, H.; Randrianarivelojosia, M.; Keßler, P. J. A.

    2011-01-01

    Background and Aims The Spathelia–Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia–Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. Methods A species-level phylogenetic analysis of the Spathelia–Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL–trnF, rps16 and psbA–trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. Key Results With the exception of Spathelia, all genera of the Spathelila–Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. Conclusions The Spathelia–Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities

  12. Molecular Analysis of a Leprosy Immunotherapeutic Bacillus Provides Insights into Mycobacterium Evolution

    PubMed Central

    Raghuvanshi, Saurabh; Khurana, Jitendra P.; Tyagi, Akhilesh K.; Tyagi, Anil K.; Hasnain, Seyed E.

    2007-01-01

    Background Evolutionary dynamics plays a central role in facilitating the mechanisms of species divergence among pathogenic and saprophytic mycobacteria. The ability of mycobacteria to colonize hosts, to proliferate and to cause diseases has evolved due to its predisposition to various evolutionary forces acting over a period of time. Mycobacterium indicus pranii (MIP), a taxonomically unknown ‘generalist’ mycobacterium, acts as an immunotherapeutic against leprosy and is approved for use as a vaccine against it. The large-scale field trials of this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and adjuvant property has led to human clinical evaluations of MIP in interventions against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as ‘Immuvac’, is currently the focus of advanced phase III clinical trials for its antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-à-vis evolutionary path, underpinning its immanent immunomodulating properties is of the highest desiderata. Principal Findings Genome wide comparisons together with molecular phylogenetic analyses by fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) based genotyping and candidate orthologues sequencing revealed that MIP has been the predecessor of highly pathogenic Mycobacterium avium intracellulare complex (MAIC) that did not resort to parasitic adaptation by reductional gene evolution and therefore, preferred a free living life-style. Further analysis suggested a shared aquatic phase of MAIC bacilli with the early pathogenic forms of Mycobacterium, well before the latter diverged as ‘specialists’. Conclusions/Significance This evolutionary paradigm possibly affirms to marshal our understanding about the acquisition and optimization of virulence in mycobacteria and determinants of boundaries therein. PMID:17912347

  13. Way back for fructose and liver metabolism: Bench side to molecular insights

    PubMed Central

    Rebollo, Alba; Roglans, Núria; Alegret, Marta; Laguna, Juan C

    2012-01-01

    The World Health Organization recommends that the daily intake of added sugars should make up no more than 10% of total energy. The consumption of sugar-sweetened beverages is the main source of added sugars. Fructose, together with glucose, as a component of high fructose corn syrups or as a component of the sucrose molecule, is one of the main sweeteners present in this kind of beverages. Data from prospective and intervention studies clearly point to high fructose consumption, mainly in the form of sweetened beverages, as a risk factor for several metabolic diseases in humans. The incidence of hypertension, nonalcoholic fatty liver disease (NAFLD), dyslipidemia (mainly hypertriglyceridemia), insulin resistance, type 2 diabetes mellitus, obesity, and the cluster of many of these pathologies in the form of metabolic syndrome is higher in human population segments that show high intake of fructose. Adolescent and young adults from low-income families are especially at risk. We recently reviewed evidence from experimental animals and human data that confirms the deleterious effect of fructose on lipid and glucose metabolism. In this present review we update the information generated in the past 2 years about high consumption of fructose-enriched beverages and the occurrence of metabolic disturbances, especially NAFLD, type 2 diabetes mellitus, and metabolic syndrome. We have explored recent data from observational and experimental human studies, as well as experimental data from animal and cell models. Finally, using information generated in our laboratory and others, we provide a view of the molecular mechanisms that may be specifically involved in the development of liver lipid and glucose metabolic alterations after fructose consumption in liquid form. PMID:23236229

  14. Calcium Induced Regulation of Skeletal Troponin — Computational Insights from Molecular Dynamics Simulations

    PubMed Central

    Genchev, Georgi Z.; Kobayashi, Tomoyoshi; Lu, Hui

    2013-01-01

    The interaction between calcium and the regulatory site(s) of striated muscle regulatory protein troponin switches on and off muscle contraction. In skeletal troponin binding of calcium to sites I and II of the TnC subunit results in a set of structural changes in the troponin complex, displaces tropomyosin along the actin filament and allows myosin-actin interaction to produce mechanical force. In this study, we used molecular dynamics simulations to characterize the calcium dependent dynamics of the fast skeletal troponin molecule and its TnC subunit in the calcium saturated and depleted states. We focused on the N-lobe and on describing the atomic level events that take place subsequent to removal of the calcium ion from the regulatory sites I and II. A main structural event - a closure of the A/B helix hydrophobic pocket results from the integrated effect of the following conformational changes: the breakage of H-bond interactions between the backbone nitrogen atoms of the residues at positions 2, 9 and sidechain oxygen atoms of the residue at position 12 (N2-OE12/N9-OE12) in sites I and II; expansion of sites I and II and increased site II N-terminal end-segment flexibility; strengthening of the β-sheet scaffold; and the subsequent re-packing of the N-lobe hydrophobic residues. Additionally, the calcium release allows the N-lobe to rotate relative to the rest of the Tn molecule. Based on the findings presented herein we propose a novel model of skeletal thin filament regulation. PMID:23554884

  15. CAM and cell fate targeting: molecular and energetic insights into cell growth and differentiation.

    PubMed

    Ventura, Carlo

    2005-09-01

    Evidence-based medicine is switching from the analysis of single diseases at a time toward an integrated assessment of a diseased person. Complementary and alternative medicine (CAM) offers multiple holistic approaches, including osteopathy, homeopathy, chiropractic, acupuncture, herbal and energy medicine and meditation, all potentially impacting on major human diseases. It is now becoming evident that acupuncture can modify the expression of different endorphin genes and the expression of genes encoding for crucial transcription factors in cellular homeostasis. Extremely low frequency magnetic fields have been found to prime the commitment to a myocardial lineage in mouse embryonic stem cells, suggesting that magnetic energy may direct stem cell differentiation into specific cellular phenotypes without the aid of gene transfer technologies. This finding may pave the way to novel approaches in tissue engineering and regeneration. Different ginseng extracts have been shown to modulate growth and differentiation in pluripotent cells and to exert wound-healing and antitumor effects through opposing activities on the vascular system, prompting the hypothesis that ancient compounds may be the target for new logics in cell therapy. These observations and the subtle entanglement among different CAM systems suggest that CAM modalities may deeply affect both the signaling and transcriptional level of cellular homeostasis. Such a perception holds promises for a new era in CAM, prompting reproducible documentation of biological responses to CAM-related strategies and compounds. To this end, functional genomics and proteomics and the comprehension of the cell signaling networks may substantially contribute to the development of a molecular evidence-based CAM. PMID:16136206

  16. Molecular analysis of the anaerobic rumen fungus Orpinomyces - insights into an AT-rich genome.

    PubMed

    Nicholson, Matthew J; Theodorou, Michael K; Brookman, Jayne L

    2005-01-01

    The anaerobic gut fungi occupy a unique niche in the intestinal tract of large herbivorous animals and are thought to act as primary colonizers of plant material during digestion. They are the only known obligately anaerobic fungi but molecular analysis of this group has been hampered by difficulties in their culture and manipulation, and by their extremely high A+T nucleotide content. This study begins to answer some of the fundamental questions about the structure and organization of the anaerobic gut fungal genome. Directed plasmid libraries using genomic DNA digested with highly or moderately rich AT-specific restriction enzymes (VspI and EcoRI) were prepared from a polycentric Orpinomyces isolate. Clones were sequenced from these libraries and the breadth of genomic inserts, both genic and intergenic, was characterized. Genes encoding numerous functions not previously characterized for these fungi were identified, including cytoskeletal, secretory pathway and transporter genes. A peptidase gene with no introns and having sequence similarity to a gene encoding a bacterial peptidase was also identified, extending the range of metabolic enzymes resulting from apparent trans-kingdom transfer from bacteria to fungi, as previously characterized largely for genes encoding plant-degrading enzymes. This paper presents the first thorough analysis of the genic, intergenic and rDNA regions of a variety of genomic segments from an anaerobic gut fungus and provides observations on rules governing intron boundaries, the codon biases observed with different types of genes, and the sequence of only the second anaerobic gut fungal promoter reported. Large numbers of retrotransposon sequences of different types were found and the authors speculate on the possible consequences of any such transposon activity in the genome. The coding sequences identified included several orphan gene sequences, including one with regions strongly suggestive of structural proteins such as collagens

  17. Molecular and pathologic insights from latent HIV-1 infection in the human brain

    PubMed Central

    Desplats, Paula; Dumaop, Wilmar; Smith, David; Adame, Anthony; Everall, Ian; Letendre, Scott; Ellis, Ronald; Cherner, Mariana; Grant, Igor

    2013-01-01

    Objective: We aimed to investigate whether HIV latency in the CNS might have adverse molecular, pathologic, and clinical consequences. Methods: This was a case-control comparison of HIV-1 seropositive (HIV+) patients with clinical and neuropathologic examination. Based on the levels of HIV-1 DNA, RNA, and p24 in the brain, cases were classified as controls, latent HIV CNS infection, and HIV encephalitis (HIVE). Analysis of epigenetic markers including BCL11B, neurodegeneration, and neuroinflammation was performed utilizing immunoblot, confocal microscopy, immunochemistry/image analysis, and qPCR. Detailed antemortem neurocognitive data were available for 23 out of the 32 cases. Results: HIV+ controls (n = 12) had no detectable HIV-1 DNA, RNA, or p24 in the CNS; latent HIV+ cases (n = 10) showed high levels of HIV-1 DNA but no HIV RNA or p24; and HIVE cases (n = 10) had high levels of HIV-1 DNA, RNA, and p24. Compared to HIV+ controls, the HIV+ latent cases displayed moderate cognitive impairment with neurodegenerative and neuroinflammatory alterations, although to a lesser extent than HIVE cases. Remarkably, HIV+ latent cases showed higher levels of BCL11B and other chromatin modifiers involved in silencing. Increased BCL11B was associated with deregulation of proinflammatory genes like interleukin-6, tumor necrosis factor–α, and CD74. Conclusion: Persistence of latent HIV-1 infection in the CNS was associated with increased levels of chromatin modifiers, including BCL11B. Alteration of these epigenetic factors might result in abnormal transcriptomes, leading to inflammation, neurodegeneration, and neurocognitive impairment. BCL11B and other epigenetic factors involved in silencing might represent potential targets for HIV-1 involvement of the CNS. PMID:23486877

  18. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies.

    PubMed

    Gogoi, Prerana; Chandravanshi, Monika; Mandal, Suraj Kumar; Srivastava, Ambuj; Kanaujia, Shankar Prasad

    2016-07-01

    About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature. PMID:26248730

  19. A promiscuous recognition mechanism between GPR17 and SDF-1: Molecular insights.

    PubMed

    Parravicini, Chiara; Daniele, Simona; Palazzolo, Luca; Trincavelli, Maria Letizia; Martini, Claudia; Zaratin, Paola; Primi, Roberto; Coppolino, Giusy; Gianazza, Elisabetta; Abbracchio, Maria P; Eberini, Ivano

    2016-06-01

    Recent data and publications suggest a promiscuous behaviour for GPR17, a class-A GPCR operated by different classes of ligands, such as uracil nucleotides, cysteinyl-leukotrienes and oxysterols. This observation, together with the ability of several class-A GPCRs to form homo- and hetero-dimers, is likely to unveil new pathophysiological roles and novel emerging pharmacological properties for some of these GPCRs, including GPR17. This receptor shares structural, phylogenetic and functional properties with some chemokine receptors, CXCRs. Both GPR17 and CXCR2 are operated by oxysterols, and both GPR17 and CXCR ligands have been demonstrated to have a role in orchestrating inflammatory responses and oligodendrocyte precursor cell differentiation to myelinating cells in acute and chronic diseases of the central nervous system. Here, by combining in silico modelling data with in vitro validation in (i) a classical reference pharmacological assay for GPCR activity and (ii) a model of maturation of primary oligodendrocyte precursor cells, we demonstrate that GPR17 can be activated by SDF-1, a ligand of chemokine receptors CXCR4 and CXCR7, and investigate the underlying molecular recognition mechanism. We also demonstrate that cangrelor, a GPR17 orthosteric antagonist, can block the SDF-1-mediated activation of GPR17 in a concentration-dependent manner. The ability of GPR17 to respond to different classes of GPCR ligands suggests that this receptor modifies its function depending on the extracellular mileu changes occurring under specific pathophysiological conditions and advocates it as a strategic target for neurodegenerative diseases with an inflammatory/immune component. PMID:26971834

  20. Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A.

    PubMed

    Oanca, Gabriel; Purg, Miha; Mavri, Janez; Shih, Jean C; Stare, Jernej

    2016-05-21

    The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier. PMID:27121693

  1. New insights into the enigma of boron carbide inverse molecular behavior

    SciTech Connect

    Dera, Przemyslaw; Manghnani, Murli H.; Hushur, Anwar; Hu, Yi; Tkachev, Sergey

    2014-07-01

    Equation of state and compression mechanism of nearly stoichiometric boron carbide B{sub 4}C were investigated using diamond anvil cell single crystal synchrotron X-ray diffraction technique up to a maximum quasi-hydrostatic pressure of 74.0(1) GPa in neon pressure transmitting medium at ambient temperature. No signatures of structural phase transitions were observed on compression. Crystal structure refinements indicate that the icosahedral units are less compressible (13% volume reduction at 60 GPa) than the unit cell volume (18% volume reduction at 60 GPa), contrary to expectations based on the inverse molecular behavior hypothesis, but consistent with spectroscopic evidence and first principles calculations. The high-pressure crystallographic refinements reveal that the nature of the chemical bonds (two, versus three centered character) has marginal effect on the bond compressibility and the compression of the crystal is mainly governed by the force transfer between the rigid icosahedral structural units. - Graphical abstract: Single crystal measurements of equation of state and compression mechanism of B{sub 4}C show that the icosahedral units are less compressibe than the unit cell volume, despite the threei-ceneterd nature of some icosahedral bonds. - Highlights: • Equation of state and compression mechanism of B{sub 4}C were measured to 75 GPa. • No signatures of structural phase transitions were observed on compression. • Icosahedral units are less compressibe than the unit cell volume. • The nature of the chemical bonds has mariginal effect on the bond compressibility. • The compression is governed by force transfer between the rigid icosahedra.

  2. Molecular insights into connective tissue growth factor action in rat pancreatic stellate cells.

    PubMed

    Karger, Anna; Fitzner, Brit; Brock, Peter; Sparmann, Gisela; Emmrich, Jörg; Liebe, Stefan; Jaster, Robert

    2008-10-01

    Pancreatic fibrosis, a key feature of chronic pancreatitis and pancreatic cancer, is mediated by activated pancreatic stellate cells (PSC). Connective tissue growth factor (CTGF) has been suggested to play a major role in fibrogenesis by enhancing PSC activation after binding to alpha5beta1 integrin. Here, we have focussed on molecular determinants of CTGF action. Inhibition of CTGF expression in PSC by siRNA was associated with decreased proliferation, while application of exogenous CTGF stimulated both cell growth and collagen synthesis. Real-time PCR studies revealed that CTGF target genes in PSC not only include mediators of matrix remodelling but also the proinflammatory cytokines interleukin (IL)-1beta and IL-6. CTGF stimulated binding of NF-kappaB to the IL-6 promoter, and siRNA targeting the NF-kappaB subunit RelA interfered with CTGF-induced IL-6 expression, implicating the NF-kappaB pathway in the mediation of the CTGF effect. In further studies, we have analyzed regulation of CTGF expression in PSC. Transforming growth factor-beta1, activin A and tumor necrosis factor-alpha enhanced expression of the CTGF gene, while interferon-gamma displayed the opposite effect. The region from -74 to -125 of the CTGF promoter was revealed to be critical for its activity in PSC as well as for the inhibitory effect of interferon-gamma. Taken together, our results indicate a tight control of CTGF expression in PSC at the transcriptional level. CTGF promotes fibrogenesis both directly by enhancing PSC proliferation and matrix protein synthesis, and indirectly through the release of proinflammatory cytokines that may accelerate the process of chronic inflammation. PMID:18639630

  3. TRANSMISSION OF LEPROSY IN QIUBEI COUNTY, YUNNAN, CHINA: INSIGHTS FROM AN EIGHT YEAR MOLECULAR EPIDEMIOLOGY INVESTIGATION

    PubMed Central

    WENG, XIAOMAN; VANDER HEIDEN, JASON; XING, YAN; LIU, JIAN; VISSA, VARALAKSHMI

    2010-01-01

    Leprosy continues to be endemic in parts of China. To track the occurrence of leprosy and determine at risk communities, molecular strain typing based on variable number of tandem repeats (VNTRs) was applied in Qiubei County, Wenshan Prefecture, Yunnan Province of the People’s Republic of China, a multiethnic region that is home to four predominant ethnic minorities. A previous study, conducted between 2002 and 2005, provided the first descriptions of Mycobacterium leprae strains in the region. M. leprae strains in Qiubei are highly conserved, so only sufficiently polymorphic loci can distinguish strains. A balance between mutation rate and loci stability is needed, so that secondary transmissions can be identified as genotypic matches. The long incubation period of leprosy necessitated an extension of the study to assess the validity of VNTR typing and observe allelic shifts in the same multiethnic population. From 2006 to early 2010 the extension was performed to yield a cumulative total of 164 enrolled patients and 130 skin samples suitable for VNTR typing. Patient demographic information revealed that the case detection rate among certain minority populations in the county is considerably higher than the national rate. Cluster analysis of allele frequencies showed similar strain types within family groups and neighboring townships. Allele frequencies were not found to significantly differ between genders or clinical presentations. The percentage of cases showing near-matching genotypes varied with geography; showing a considerably higher rate in the northern townships. The northern townships continue to show strain types falling into the groups previously defined. Southern genotypes were distinct from those in the north, but clonal genetic relationships were indiscernible in the south. Social interactions and the physical, residential and occupational environments may be more conducive to transmission of community strains in the north. PMID:21129505

  4. Way back for fructose and liver metabolism: bench side to molecular insights.

    PubMed

    Rebollo, Alba; Roglans, Núria; Alegret, Marta; Laguna, Juan C

    2012-12-01

    The World Health Organization recommends that the daily intake of added sugars should make up no more than 10% of total energy. The consumption of sugar-sweetened beverages is the main source of added sugars. Fructose, together with glucose, as a component of high fructose corn syrups or as a component of the sucrose molecule, is one of the main sweeteners present in this kind of beverages. Data from prospective and intervention studies clearly point to high fructose consumption, mainly in the form of sweetened beverages, as a risk factor for several metabolic diseases in humans. The incidence of hypertension, nonalcoholic fatty liver disease (NAFLD), dyslipidemia (mainly hypertriglyceridemia), insulin resistance, type 2 diabetes mellitus, obesity, and the cluster of many of these pathologies in the form of metabolic syndrome is higher in human population segments that show high intake of fructose. Adolescent and young adults from low-income families are especially at risk. We recently reviewed evidence from experimental animals and human data that confirms the deleterious effect of fructose on lipid and glucose metabolism. In this present review we update the information generated in the past 2 years about high consumption of fructose-enriched beverages and the occurrence of metabolic disturbances, especially NAFLD, type 2 diabetes mellitus, and metabolic syndrome. We have explored recent data from observational and experimental human studies, as well as experimental data from animal and cell models. Finally, using information generated in our laboratory and others, we provide a view of the molecular mechanisms that may be specifically involved in the development of liver lipid and glucose metabolic alterations after fructose consumption in liquid form. PMID:23236229

  5. Filler reinforcement in cross-linked elastomer nanocomposites: insights from fully atomistic molecular dynamics simulation.

    PubMed

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

    Using a fully atomistic model, we perform large-scale molecular dynamics simulations of sulfur-cured polybutadiene (PB) and nanosilica-filled PB composites. A well-integrated network without sol fraction is built dynamically by cross-linking the coarse-grained precursor chains in the presence of embedded silica nanoparticles. Initial configurations for subsequent atomistic simulations are obtained by reverse mapping of the well-equilibrated coarse-grained systems. Based on the concept of "maximally inflated knot" introduced by Grosberg et al., we show that the networks simulated in this study behave as mechanically isotropic systems. Analysis of the network topology in terms of graph theory reveals that mechanically inactive tree-like structures are the dominant structural components of the weakly cross-linked elastomer, while cycles are mainly responsible for the transmission of mechanical forces through the network. We demonstrate that quantities such as the system density, thermal expansion coefficient, glass transition temperature and initial Young's modulus can be predicted in qualitative and sometimes even in quantitative agreement with experiments. The nano-filled system demonstrates a notable increase in the glass transition temperature and an approximately two-fold increase in the nearly equilibrium value of elastic modulus relative to the unfilled elastomer even at relatively small amounts of filler particles. We also examine the structural rearrangement of the nanocomposite subjected to tensile deformation. Under high strain-rate loading, the formation of structural defects (microcavities) within the polymer bulk is observed. The nucleation and growth of cavities in the post-yielding strain hardening regime mainly take place at the elastomer/nanoparticle interfaces. As a result, the cavities are concentrated just near the embedded nanoparticles. Therefore, while the silica nanofiller increases the elastic modulus of the elastomer, it also creates a more

  6. Mechanism of Titin Unfolding by Force: Insight from Quasi-Equilibrium Molecular Dynamics Calculations

    PubMed Central

    Pabón, Germán; Amzel, L. Mario

    2006-01-01

    We have studied the unfolding by force of one of the immunoglobulin domains of the muscle protein titin using molecular dynamics simulations at 300 K. Previous studies, done at constant pulling rates, showed that under the effect of the force two strands connected to each other by six backbone H-bonds are pulled apart. No details about the mechanism of H-bond breaking were provided. Our simulation protocol “pull and wait” was designed to correspond to very slow pulling, more similar to the rates used in experiments than are the protocols used in previous computational studies. Under these conditions interstrand backbone H-bonds are not “ripped apart” by the application of the force. Instead, small elongations produced by the force weaken specific backbone H-bonds with respect to water-backbone H-bonds. These weakened bonds allow a single water molecule to make H-bonds to the CO and the NH of the same backbone H-bond while they are still bound to each other. The backbone H-bond then breaks (distance >3.6 Å), but its donor and acceptor atoms remain bound to the same water molecule. Further separation of the chains takes place when a second water molecule makes an H-bond with either the protein backbone donor or acceptor atom. Thus, the force does not directly break the main chain H-bonds: it destabilizes them in such a way that they are replaced by H-bonds to water. With this mechanism, the force necessary to break all the H-bonds required to separate the two strands will be strongly dependent on the pulling speed. Further simulations carried out at low forces but long waiting times (≥ 500 ps, ≤ 10 ns) show that, given enough time, even a very small pulling force (<400 pN) is sufficient to destabilize the interstrand H-bonds and allow them to be replaced by H-bonds to two water molecules. As expected, increasing the temperature to 350 K allows the interstrand H-bonds to break at lower forces than those required at 300 K. PMID:16632514

  7. New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis

    PubMed Central

    Tingaud-Sequeira, Angèle; Chauvigné, François; Lozano, Juanjo; Agulleiro, María J; Asensio, Esther; Cerdà, Joan

    2009-01-01

    Background The Senegalese sole (Solea senegalensis) is a marine flatfish of increasing commercial interest. However, the reproduction of this species in captivity is not yet controlled mainly because of the poor knowledge on its reproductive physiology, as it occurs for other non-salmonid marine teleosts that exhibit group-synchronous ovarian follicle development. In order to investigate intra-ovarian molecular mechanisms in Senegalese sole, the aim of the present study was to identify differentially expressed genes in the ovary during oocyte growth (vitellogenesis), maturation and ovarian follicle atresia using a recently developed oligonucleotide microarray. Results Microarray analysis led to the identification of 118 differentially expressed transcripts, of which 20 and 8 were monitored by real-time PCR and in situ hybridization, respectively. During vitellogenesis, many up-regulated ovarian transcripts had putative mitochondrial function/location suggesting high energy production (NADH dehydrogenase subunits, cytochromes) and increased antioxidant protection (selenoprotein W2a), whereas other regulated transcripts were related to cytoskeleton and zona radiata organization (zona glycoprotein 3, alpha and beta actin, keratin 8), intracellular signalling pathways (heat shock protein 90, Ras homolog member G), cell-to-cell and cell-to-matrix interactions (beta 1 integrin, thrombospondin 4b), and the maternal RNA pool (transducer of ERBB2 1a, neurexin 1a). Transcripts up-regulated in the ovary during oocyte maturation included ion transporters (Na+-K+-ATPase subunits), probably required for oocyte hydration, as well as a proteinase inhibitor (alpha-2-macroglobulin) and a vesicle calcium sensor protein (extended synaptotagmin-2-A). During follicular atresia, few transcripts were found to be up-regulated, but remarkably most of them were localized in follicular cells of atretic follicles, and they had inferred roles in lipid transport (apolipoprotein C-I), chemotaxis

  8. Molecular and pathological insights into Chlamydia pecorum-associated sporadic bovine encephalomyelitis (SBE) in Western Australia

    PubMed Central

    2014-01-01

    Background Despite its global recognition as a ruminant pathogen, cases of Chlamydia pecorum infection in Australian livestock are poorly documented. In this report, a C. pecorum specific Multi Locus Sequence Analysis scheme was used to characterise the C. pecorum strains implicated in two cases of sporadic bovine encephalomyelitis confirmed by necropsy, histopathology and immunohistochemistry. This report provides the first molecular evidence for the presence of mixed infections of C. pecorum strains in Australian cattle. Case presentation Affected animals were two markedly depressed, dehydrated and blind calves, 12 and 16 weeks old. The calves were euthanized and necropsied. In one calf, a severe fibrinous polyserositis was noted with excess joint fluid in all joints whereas in the other, no significant lesions were seen. No gross abnormalities were noted in the brain of either calf. Histopathological lesions seen in both calves included: multifocal, severe, subacute meningoencephalitis with vasculitis, fibrinocellular thrombosis and malacia; diffuse, mild, acute interstitial pneumonia; and diffuse, subacute epicarditis, severe in the calf with gross serositis. Immunohistochemical labelling of chlamydial antigen in brain, spleen and lung from the two affected calves and brain from two archived cases, localised the antigen to the cytoplasm of endothelium, mesothelium and macrophages. C. pecorum specific qPCR, showed dissemination of the pathogen to multiple organs. Phylogenetic comparisons with other C. pecorum bovine strains from Australia, Europe and the USA revealed the presence of two genetically distinct sequence types (ST). The predominant ST detected in the brain, heart, lung and liver of both calves was identical to the C. pecorum ST previously described in cases of SBE. A second ST detected in an ileal tissue sample from one of the calves, clustered with previously typed faecal bovine isolates. Conclusion This report provides the first data to suggest

  9. Transport processes at alpha-quartz-water interfaces: insights from first-principles molecular dynamics simulations.

    PubMed

    Adeagbo, Waheed A; Doltsinis, Nikos L; Klevakina, Ksenia; Renner, Jörg

    2008-05-16

    Car-Parrinello molecular dynamics (CP-MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the alpha-quartz-water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H(2)O molecules into H(+) and OH(-) is observed at the Si-terminated surface. The OH(-) fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO(2) present as Si(OH)(4) in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)(4) molecule as would have been indicated by a substantial lowering of the Si(OH)(4) diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP-MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si--O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si--O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si--O bond. The final solute species is Si(OH)(4). PMID:18404743

  10. Impact of Mutation on Proton Transfer Reactions in Ketosteroid Isomerase: Insights from Molecular Dynamics Simulations

    PubMed Central

    Chakravorty, Dhruva K.; Hammes-Schiffer, Sharon

    2010-01-01

    The two proton transfer reactions catalyzed by ketosteroid isomerase (KSI) involve a dienolate intermediate stabilized by hydrogen bonds with Tyr14 and Asp99. Molecular dynamics simulations based on an empirical valence bond model are used to examine the impact of mutating these residues on the hydrogen-bonding patterns, conformational changes, and van der Waals and electrostatic interactions during the proton transfer reactions. While the rate constants for the two proton transfer steps are similar for wild-type (WT) KSI, the simulations suggest that the rate constant for the first proton transfer step is smaller in the mutants due to the significantly higher free energy of the dienolate intermediate relative to the reactant. The calculated rate constants for the mutants D99L, Y14F, and Y14F/D99L relative to WT KSI are qualitatively consistent with the kinetic experiments indicating a significant reduction in the catalytic rates along the series of mutants. In the simulations, WT KSI retained two hydrogen-bonding interactions between the substrate and the active site, while the mutants typically retained only one hydrogen-bonding interaction. A new hydrogen-bonding interaction between the substrate and Tyr55 was observed in the double mutant, leading to the prediction that mutation of Tyr55 will have a greater impact on the proton transfer rates for the double mutant than for WT KSI. The electrostatic stabilization of the dienolate intermediate relative to the reactant was greater for WT KSI than for the mutants, providing a qualitative explanation for the significantly reduced rates of the mutants. The active site exhibited highly restricted motion during the proton transfer reactions, but small conformational changes occurred to facilitate the proton transfer reactions by strengthening the hydrogen-bonding interactions and by bringing the proton donor and acceptor closer to each other with the proper orientation for proton transfer. Thus, these calculations

  11. An unusual H2 sorption mechanism in PCN-14: insights from molecular simulation.

    PubMed

    Pham, Tony; Forrest, Katherine A; Space, Brian

    2016-08-01

    Simulations of H2 sorption were performed in PCN-14, a metal-organic framework (MOF) that consists of Cu(2+) ions coordinated to 5,5'-(9,10-anthracenediyl)diisophthalate (adip) linkers. This MOF displays an excess H2 uptake of 2.70 wt% at 77 K and 1.0 atm and an initial H2Qst value of 8.6 kJ mol(-1) according to previous experimental measurements. The experimental H2 sorption isotherms and Qst values in PCN-14 were reproduced in simulations using well-known H2 potentials that have been widely used for MOF-H2 theoretical studies. H2 sorption in PCN-14 was dominated by repulsion/dispersion energetics; this allowed the experimental observables to be reproduced by a model that includes only Lennard-Jones parameters. The most energetically favorable H2 sorption site in PCN-14 corresponds to sorption within a small cage that is enclosed by three [Cu2(O2CR)4] units and three adip linkers. The anthracenyl rings of the adip linkers represent the secondary sorption sites within the MOF. In contrast to expectations, sorption of H2 onto the Cu(2+) ions of the copper paddlewheels was not observed within the simulations at low loading. The simulations revealed that the open-metal sites in PCN-14 were occupied at high loading. Control simulations of H2 sorption in PCN-14 for different cases in which the partial positive charge of one of the paddlewheel Cu(2+) ions was increased relative to the other revealed that sorption onto the open-metal sites can be captured if there is a very high positive charge on the metal. Otherwise, the calculated partial charge for the Cu(2+) ions in PCN-14 in this work was not high enough in magnitude to facilitate strong H2-metal interactions in simulation. This study shows the power of using molecular simulations to elucidate an unusual H2 sorption behavior in a MOF. PMID:27426916

  12. Insights into molecular assembly of ACCase heteromeric complex in Chlorella variabilis--a homology modelling, docking and molecular dynamic simulation study.

    PubMed

    Misra, Namrata; Panda, Prasanna Kumar; Patra, Mahesh Chandra; Pradhan, Sukanta Kumar; Mishra, Barada Kanta

    2013-07-01

    Acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that catalyses the first committed step of fatty acid biosynthesis, is considered as a potential target for improving lipid accumulation in oleaginous feedstocks, including microalgae. ACCase is composed of three distinct conserved domains, and understanding the structural details of each catalytic domain assumes great significance to gain insights into the molecular basis of the complex formation and mechanism of biotin transport. In the absence of a crystal structure for any single heteromeric ACCase till date, here we report the first heteromeric association model of ACCase from an oleaginous green microalga, Chlorella variabilis, using a combination of homology modelling, docking and molecular dynamic simulations. The binding site of the docked biotin carboxylase (BC) and carboxyltransferase (CT) were predicted to be contiguous but distinct in biotin carboxyl carrier protein (BCCP) molecule. Simulation studies revealed considerable flexibility for the BC and CT domains in the BCCP-bound forms, thus indicating the adaptive behaviour of BCCP. Further, principal component analysis revealed that in the presence of BCCP, the BC and CT domains exhibited an open-state conformation via the outward clockwise rotation of the binding helices. These conformational changes might be responsible for binding of BCCP domain and its translocation to the respective active sites. Various rearrangements of inter-domain hydrogen bonds (H-bonds) contributed to conformational changes in the structures. H-bond interactions between the interacting residue pairs involving Glu201BCCP/Arg255BC and Asp224BCCP/Gln228CT were found to be essential for the intermolecular assembly. The present findings are consistent with previous biochemical studies. PMID:23677812

  13. Structure based investigation on the binding interaction of transport proteins in leishmaniasis: insights from molecular simulation.

    PubMed

    Singh, Shailza; Mandlik, Vineetha

    2015-05-01

    Leishmania major is the causative agent of cutaneous leishmaniasis which affects over 1 million people in 88 different countries. The incidence of this disease is on the rise due to the current problems associated with the present chemotherapeutics. In addition, Leishmania confronts resistance to the traditional drugs like sodium stibogluconate and newer repurposed drugs like miltefosine. ABC transporters are involved in the development of drug resistance. Miltefosine, the drug used for the treatment of leishmaniasis, is effluxed by P4 ATPase and ABC transporter, which is the prime focus of our study in this paper. P4 ATPase (MDR1) along with an unnamed protein (cdc50) translocates miltefosine from the outer to the inner leaflet by the process of flipping which is ATP driven. In contrast, miltefosine also escapes from the cells by an energy dependent mechanism that involves the ABC transporter protein (ABC). It is known that certain genes in the parasite amplify the portions of a gene which encodes ABC transporter and P4 ATPase involved in translocating phospholipids and hence resistance to miltefosine. We observed the ABC and P4 ATPase genes, 39 T-box elements were observed in the ABC transporter protein and three elements were observed in the P4 ATPase gene suggesting its role in transcription regulation. To the best of our knowledge, there are no structural and regulatory reports on these two proteins in L. major. Computational structural biology tools may aid in understanding the interaction of miltefosine with the P4-ATPase-cdc50 complex and the ABC transporter. This can be achieved by modeling the target protein structures, studying the dynamics associated with the different domains of the protein and later using activators and inhibitors to alter the functioning of the protein. Molecular dynamics simulation with a lipid bilayer is performed to investigate the conformational changes and structure-activity relationship. As transporters are difficult to model

  14. Reactivity of aldehydes at the air-water interface. Insights from molecular dynamics simulations and ab initio calculations.

    PubMed

    Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F

    2015-02-14

    Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments. PMID:25451554

  15. Conduction and Reactivity in Heterogeneous-Molecular Catalysis: New Insights in Water Oxidation Catalysis by Phosphate Cobalt Oxide Films.

    PubMed

    Costentin, Cyrille; Porter, Thomas R; Savéant, Jean-Michel

    2016-05-01

    Cyclic voltammetry of phosphate cobalt oxide (CoPi) films catalyzing O2-evolution from water oxidation as a function of scan rate, phosphate concentration and film thickness allowed for new insights into the coupling between charge transport and catalysis. At pH = 7 and low buffer concentrations, the film is insulating below 0.8 (V vs SHE) but becomes conductive above 0.9 (V vs SHE). Between 1.0 to 1.3 (V vs SHE), the mesoporous structure of the film gives rise to a large thickness-dependent capacitance. At higher buffer concentrations, two reversible proton-coupled redox couples appear over the capacitive response with 0.94 and 1.19 (V vs SHE) pH = 7 standard potentials. The latter is, at most, very weakly catalytic and not responsible for the large catalytic current observed at higher potentials. CV-response analysis showed that the amount of redox-active cobalt-species in the film is small, less than 10% of total. The catalytic process involves a further proton-coupled-electron-transfer and is so fast that it is controlled by diffusion of phosphate, the catalyst cofactor. CV-analysis with newly derived relationships led to a combination of the catalyst standard potential with the catalytic rate constant and a lower-limit estimation of these parameters. The large currents resulting from the fast catalytic reaction result in significant potential losses related to charge transport through the film. CoPi films appear to combine molecular catalysis with semiconductor-type charge transport. This mode of heterogeneous molecular catalysis is likely to occur in many other catalytic films. PMID:26981886

  16. 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

    2016-04-01

    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. PMID:26273990

  17. Integrated Molecular and Microscopic Scale Insight into Morphology and Ion Dynamics in Ca2+-Mediated Natural Organic Matter Floccs

    SciTech Connect

    Bowers, Geoffrey M.; Argersinger, Haley E.; Reddy, Venkataswara; Johnson, Timothy A.; Arey, Bruce W.; Bowden, Mark E.; Kirkpatrick, Robert J.

    2015-08-06

    Combined X-ray diffraction (XRD), helium ion microscopy (HeIM), and Ca-43 nuclear magnetic resonance (NMR) results provide novel insight into the nano- and microstructure of flocculated NOM; the molecular-scale interaction among natural organic matter (NOM), dissolved Ca2+ ions, and water in NOM floccs; and the effects of pH and ionic strength on these characteristics. Suwannee River humic acid (HA), fulvic acid (FA), and NOM flocculated from Ca2+ bearing solutions share similar morphological characteristics on the 100 nm to micron scales, including micron-sized equant fragments and rounded, rough areas with features on the 100 nm scale. HeIM suggests that the NOM floccs are built from a fundamental spheroidal structure that is similar to 10 nm in diameter, in agreement with published AFM and small-angle X-ray scattering results. Calcium is incorporated into these floccs at 100% relative humidity in a wide range of disordered structural environments, with basic pH leading to shorter mean Ca-O distances and lower mean coordination numbers with respect to floccs formed under acidic conditions. The NMR results show that dynamical processes involving water and Ca2+ occurring at frequencies >10(4) Hz are important for hydrated OM floccs, in agreement with published molecular dynamics simulations of OM in solution. From the NMR results, we find evidence for two Ca2+ dynamic averaging mechanisms: one related to rapid exchange (>100 kHz) between surface proximity-restricted (those within 5 angstrom of a surface) and bulk solution environments when excess Ca2+ is present in the pore solution when pore water is unfrozen and a second consisting of intermediate scale (tens of kHz) site exchange among strongly sorbed inner-sphere sites when excess Ca2+ is absent and the carboxylic and phenolic functional groups of the NOM are deprotonated.

  18. Insight into the formation of molecular species in laser-induced plasma of isotopically labeled organic samples.

    PubMed

    Glaus, Reto; Riedel, Jens; Gornushkin, Igor

    2015-10-01

    Recently, the detection of molecular species in laser-induced breakdown spectroscopy (LIBS) has gained increasing interest, particularly for isotopic analysis. In LIBS of organic materials, it is predominantly CN and C2 species that are formed, and multiple mechanisms may contribute to their formation. To gain deeper insight into the formation of these species, laser-induced plasma of (13)C and (15)N labeled organic materials was investigated in a temporally and spatially resolved manner. LIBS on fumaric acid with a (13)C labeled double bond allowed the formation mechanism of C2 to be investigated by analyzing relative signal intensities of (12)C2, (12)C(13)C, and (13)C2 molecules. In the early plasma (<5 μs), the majority of C2 originates from association of completely atomized target molecules, whereas in the late plasma, the increased concentration of (13)C2 is due to incomplete dissociation of the carbon double bond. The degree of this fragmentation was found to be up to 80% and to depend on the type of the atmospheric gas. Spatial distributions of C2 revealed distinct differences for plasma generated in nitrogen and argon. A study of the interaction of ablated organics with ambient nitrogen showed that the ambient nitrogen contributed mainly to CN formation. The pronounced anisotropy of the C(15)N to C(14)N ratio across the diameter of the plasma was observed in the early plasma, indicating poor initial mixing of the plasma with the ambient gas. Overall, for accurate isotope analysis of organics, LIBS in argon with relatively short integration times (<10 μs) provides the most robust results. On the other hand, if information about the original molecular structure is of interest, then experiments in nitrogen (or air) with long integration times appear to be the most promising. PMID:26402464

  19. Insights into the Formation and Structures of Molecular Gels by Diimidazolium Salt Gelators in Ionic Liquids or "Normal" Solvents.

    PubMed

    Rizzo, Carla; D'Anna, Francesca; Noto, Renato; Zhang, Mohan; Weiss, Richard G

    2016-08-01

    Insights are provided into the properties of molecular gels formed by diimidazolium salts both in "normal" solvents and ionic liquids. These materials can be interesting for applications in green and sustainable chemistry in which ionic liquids play a significant role, like catalysis and energy. In particular, two positional isomers of a diimidazolium cation have been examined with a wide range of anions for their ability to form gel phases. In particular, di-, tri-, and tetravalent anions bearing aliphatic or aromatic spacers were paired with the divalent cations. The properties of the organo- and ionogels formed have been analyzed by means of several different techniques, including calorimetry, rheology, resonance light scattering, UV/Vis absorption, polarizing optical microscopy, and powder X-ray diffraction measurements. The investigations performed enabled us to obtain a wide range of conductive materials characterized by a high thermal stability and a low corrosiveness of the gelator (organogels) or of both gelator and solvent (ionogels). The information gained should be useful in the broader quest to identify and promote their applications. PMID:27359108

  20. Insights into the potential aggregation liabilities of the b12 Fab fragment via elevated temperature molecular dynamics.

    PubMed

    Buck, Patrick M; Kumar, Sandeep; Singh, Satish K

    2013-03-01

    Aggregation is a common hurdle faced during the development of antibody therapeutics. In this study, we explore the potential aggregation liabilities of the Fab (fragment antigen-binding) from a human IgG1κ antibody via multiple elevated temperature molecular dynamic simulations, analogous to accelerated stability studies performed during formulation development. Deformation and solvent exposure changes in response to thermal stress were monitored for individual structural domains (V(H), V(L), C(H)1 and C(L)), their interfaces (V(H):V(L) and C(H)1:C(L)), edge beta-strands and sequence-predicted aggregation-prone regions (APRs). During simulations, domain interfaces deformed prior to the unfolding of individual domains. However, interfacial beta-strands retained their secondary structure and remained solvent protected longer than all other strands or loops. Thus, APRs located in interfacial beta-strands are effectively blocked from self-association. Structural deformations were also observed in complementarity-determining regions, edge beta-strands and adjoining framework beta-strands, which increased their solvent-accessible surface area and exposed APRs in these regions. From the analysis of these structural changes, two potential aggregation liabilities were identified in the V(H) domain of this Fab. Insights gained from this investigation should be useful in devising a rational structure-based strategy for the design and selection of antibody candidates with high potency and improved developability. PMID:23188804

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

    PubMed

    Kilymis, D A; Delaye, J-M; Ispas, S

    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 important 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. PMID:27475379

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

    NASA Astrophysics Data System (ADS)

    Kilymis, D. A.; Delaye, J.-M.; Ispas, S.

    2016-07-01

    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 important 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.

  3. Comparative Genomic and Sequence Analysis Provides Insight into the Molecular Functionality of NOD1 and NOD2

    PubMed Central

    Boyle, Joseph P.; Mayle, Sophie; Parkhouse, Rhiannon; Monie, Tom P.

    2013-01-01

    Amino acids with functional or key structural roles display higher degrees of conservation through evolution. The comparative analysis of protein sequences from multiple species and/or between homologous proteins can be highly informative in the identification of key structural and functional residues. Residues which in turn provide insight into the molecular mechanisms of protein function. We have explored the genomic and amino acid conservation of the prototypic innate immune genes NOD1 and NOD2. NOD1 orthologs were found in all vertebrate species analyzed, whilst NOD2 was absent from the genomes of avian, reptilian and amphibian species. Evolutionary trace analysis was used to identify highly conserved regions of NOD1 and NOD2 across multiple species. Consistent with the known functions of NOD1 and NOD2 highly conserved patches were identified that matched the Walker A and B motifs and provided interaction surfaces for the adaptor protein RIP2. Other patches of high conservation reflect key structural functions as predicted by homology models. In addition, the pattern of residue conservation within the leucine-rich repeat (LRR) region of NOD1 and NOD2 is indicative of a conserved mechanism of ligand recognition involving the concave surface of the LRRs. PMID:24109482

  4. New insights in the capability of climate models to simulate the impact of LUC based on temperature decomposition of paired site observations

    NASA Astrophysics Data System (ADS)

    Vanden Broucke, Sam; Luyssaert, Sebastiaan; Davin, Edouard L.; Janssens, Ivan; Lipzig, Nicole

    2015-06-01

    In this study, we present a new methodology for evaluating the biogeophysical impact of land use change (LUC) in regional climate models. For this, we use observational data from paired eddy covariance flux towers in Europe, representing a LUC from forest to open land (deforestation). Two model simulations with the regional climate model COSMO-CLM2 (The Consortium for Small-Scale Modelling model in climate mode COSMO-CLM coupled to the Community Land Model CLM) are performed which differ only in prescribed land use for site pair locations. The model is evaluated by comparing the observed and simulated difference in surface temperature (Ts) between open land and forests. Next, we identify the biogeophysical mechanisms responsible for Ts differences by applying a decomposition method to both observations and model simulations. This allows us to determine which LUC-related mechanisms were well represented in COSMO-CLM2, and which were not. Results from observations show that deforestation leads to a significant cooling at night, which is severely underestimated by COSMO-CLM2. It appears that the model is missing one crucial impact of deforestation on the nighttime surface energy budget: a reduction in downwelling longwave radiation. Results are better for daytime, as the model is able to simulate the increase in albedo and associated surface cooling following deforestation reasonably well. Also well simulated, albeit underestimated slightly, is the decrease in sensible heat flux caused by reduced surface roughness. Overall, these results stress the importance of differentiating between daytime and nighttime climate when discussing the effect of LUC on climate. Finally, we believe that they provide new insights supporting a wider application of the methodology (to other regional climate models).

  5. 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

  6. Environmental and Climatic Determinants of Molecular Diversity and Genetic Population Structure in a Coenagrionid Damselfly

    PubMed Central

    Wellenreuther, Maren; Sánchez-Guillén, Rosa A.; Cordero-Rivera, Adolfo; Svensson, Erik I.; Hansson, Bengt

    2011-01-01

    Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the target of many ecological and evolutionary studies. We addressed the following questions: (i) Is the population structure affected by longitudinal or latitudinal gradients?; (ii) Do geographic boundaries limit gene flow?; (iii) Does geographic distance affect connectivity and is there a signature of past bottlenecks?; (iv) Is there evidence of a recent range expansion and (vi) what is the effect of geography and climatic factors on population structure? We found low to moderate genetic sub-structuring between populations (mean FST = 0.06, Dest = 0.12), and an effect of longitude, but not latitude, on genetic diversity. No significant effects of geographic boundaries (e.g. water bodies) were found. FST-and Dest-values increased with geographic distance; however, there was no evidence for recent bottlenecks. Finally, we did not detect any molecular signatures of range expansions or an effect of geographic suitability, although local precipitation had a strong effect on genetic differentiation. The population structure of this small insect has probably been shaped by ecological factors that are correlated with longitudinal gradients, geographic distances, and local precipitation. The relatively weak global population structure and high degree of genetic variation within populations suggest that I. elegans has high dispersal ability, which is consistent with this species being an effective and early coloniser of new habitats. PMID:21655216

  7. Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity

    PubMed Central

    Solomon, Scott E.; Bacci, Mauricio; Martins, Joaquim; Vinha, Giovanna Gonçalves; Mueller, Ulrich G.

    2008-01-01

    The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene—or both—have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area. PMID:18648512

  8. Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights.

    PubMed

    Trontin, Jean-François; Klimaszewska, Krystyna; Morel, Alexandre; Hargreaves, Catherine; Lelu-Walter, Marie-Anne

    2016-01-01

    Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics. PMID:26619863

  9. Impacts of climate and humans on the vegetation in northwestern Turkey: palynological insights from Lake Iznik since the Last Glacial

    NASA Astrophysics Data System (ADS)

    Miebach, Andrea; Niestrath, Phoebe; Roeser, Patricia; Litt, Thomas

    2016-03-01

    The Marmara region in northwestern Turkey provides a unique opportunity for studying the vegetation history in response to climate changes and anthropogenic impacts because of its location between different climate and vegetation zones and its long settlement history. Geochemical and mineralogical investigations of the largest lake in the region, Lake Iznik, already registered climate-related changes of the lake level and the lake mixing. However, a palynological investigation encompassing the Late Pleistocene to Middle Holocene was still missing. Here, we present the first pollen record of the last ca. 31 ka cal BP (calibrated kilo years before 1950) inferred from Lake Iznik sediments as an independent proxy for paleoecological reconstructions. Our study reveals that the vegetation in the Iznik area changed generally between (a) steppe during glacials and stadials indicating dry and cold climatic conditions, (b) forest-steppe during interstadials indicating milder and moister climatic conditions, and (c) oak-dominated mesic forest during interglacials indicating warm and moist climatic conditions. Moreover, a pronounced succession of pioneer trees, cold temperate, warm temperate, and Mediterranean trees appeared since the Lateglacial. Rapid climate changes, which are reflected by vegetation changes, can be correlated with Dansgaard-Oeschger (DO) events such as DO-4, DO-3, and DO-1, the Younger Dryas, and probably also the 8.2 event. Since the mid-Holocene, the vegetation was influenced by anthropogenic activities. During early settlement phases, the distinction between climate-induced and human-induced changes of the vegetation is challenging. Still, evidence for human activities consolidates since the Early Bronze Age (ca. 4.8 ka cal BP): cultivated trees, crops, and secondary human indicator taxa appeared, and forests were cleared. Subsequent fluctuations between extensive agricultural uses and regenerations of the natural vegetation become apparent.

  10. Sensitivity of Groundwater Recharge Estimations to Climate Change and Frequency Distribution of Precipitation Events: Insights from a Lysimeter Modelling Study

    NASA Astrophysics Data System (ADS)

    von Freyberg, J.; Moeck, C.; Schirmer, M.

    2014-12-01

    An adequate quantification of groundwater recharge is required for sustainable water resource management and robust hydrological model predictions. However, estimation of the future temporal evolution of groundwater recharge rates at annual, seasonal or daily time scales remains a challenging task due to the strong linkage of infiltration processes with predicted changes of the frequency distribution of precipitation. While many studies have addressed recharge processes under climate change scenarios, only limited work has been carried out systematically focusing on the impact of precipitation variability. Thus, we simulated groundwater recharge in the Swiss pre-Alpine Rietholzbach research catchment based on a water balance model, that was calibrated to daily direct recharge measured at a weighting lysimeter. Three approaches, employing different degrees of complexity, were utilized to obtain future climatic forcing functions. First, a relatively simple delta change factors approach for three stationary time periods was applied. For this scenario 10 different climate model chains were used to determine the predictive uncertainty accompanied with the different GCM (Global Circulation Model) x RCM (Regional Climate Model) combinations. Second, these delta change values were combined with a stochastic weather generator, which allows for a more realistic simulation of climatic variability compared to the simple delta change downscaling approach. Further, additional uncertainty, linked to natural climate variability in the climatic forcing functions, can be determined more efficiently. Finally, the frequency distribution of precipitation events was artificially adjusted to account for a larger amount of extreme events, thus simulating what is expected for the future. The first simulations indicate that annual recharge is less affected by changes of the frequency distribution of precipitation, however there was a marked impact on the seasonal signal. All approaches

  11. 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

  12. Insights into the molecular mechanism of inhibition and drug resistance for HIV-1 RT with carbovir triphosphate.

    PubMed

    Ray, Adrian S; Yang, Zhenjun; Shi, Junxing; Hobbs, Ann; Schinazi, Raymond F; Chu, Chung K; Anderson, Karen S

    2002-04-23

    Abacavir (1592U89, or Ziagen) is a powerful and selective inhibitor of HIV-1 viral replication that has been approved by the FDA for treatment of acquired immunodeficiency syndrome. Abacavir is metabolized to the active compound carbovir triphosphate (CBVTP). This compound is a guanosine analogue containing a 2',3'-unsaturation in its planar carbocyclic deoxyribose ring that acts on HIV-1 reverse transcriptase (RT(WT)) as a molecular target, resulting in chain termination of DNA synthesis. A single amino acid change from methionine 184 to valine in HIV-1 RT (RT(M184V)) has been observed clinically in response to abacavir treatment. The ability of the natural substrate, dGTP, or CBVTP to be utilized during DNA- and RNA-directed polymerization by RT(WT) and RT(M184V) was defined by pre-steady-state kinetic parameters. In the case of RT(WT), CBVTP was found to be a surprisingly poor substrate relative to dGTP. In both DNA- and RNA-directed polymerization, a decrease in the efficiency of CBVTP utilization with respect to dGTP was found with RT(M184V), suggesting that this mutation confers resistance at the level of CBVMP incorporation. The relatively low incorporation efficiency for RT(WT) was unanticipated considering earlier studies showing that the triphosphate form of a thymidine nucleoside analogue containing a planar 2',3'-unsaturated ribose ring, D4TTP, was incorporated with high efficiency relative to the natural substrate, dTTP. The difference may be related to the isosteric replacement of oxygen in the deoxyribose ring with carbon. This hypothesis was tested by synthesizing and evaluating D4GTP (the planar 2',3'-unsaturated deoxyribose guanosine analogue that is complementary to D4TTP). In contrast to CBVTP, D4GTP was found to be an excellent substrate for RT(WT) and no resistance was conferred by the M184V mutation, thus providing novel insight into structure-activity relationships for nucleoside-based inhibitors. In this work, we illustrate how an

  13. Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

    PubMed Central

    2013-01-01

    Background Penstemon’s unique phenotypic diversity, hardiness, and drought-tolerance give it great potential for the xeric landscaping industry. Molecular markers will accelerate the breeding and domestication of drought tolerant Penstemon cultivars by, creating genetic maps, and clarifying of phylogenetic relationships. Our objectives were to identify and validate interspecific molecular markers from four diverse Penstemon species in order to gain specific insights into the Penstemon genome. Results We used a 454 pyrosequencing and GR-RSC (genome reduction using restriction site conservation) to identify homologous loci across four Penstemon species (P. cyananthus, P. davidsonii, P. dissectus, and P. fruticosus) representing three diverse subgenera with considerable genome size variation. From these genomic data, we identified 133 unique interspecific markers containing SSRs and INDELs of which 51 produced viable PCR-based markers. These markers produced simple banding patterns in 90% of the species × marker interactions (~84% were polymorphic). Twelve of the markers were tested across 93, mostly xeric, Penstemon taxa (72 species), of which ~98% produced reproducible marker data. Additionally, we identified an average of one SNP per 2,890 bp per species and one per 97 bp between any two apparent homologous sequences from the four source species. We selected 192 homologous sequences, meeting stringent parameters, to create SNP markers. Of these, 75 demonstrated repeatable polymorphic marker functionality across the four sequence source species. Finally, sequence analysis indicated that repetitive elements were approximately 70% more prevalent in the P. cyananthus genome, the largest genome in the study, than in the smallest genome surveyed (P. dissectus). Conclusions We demonstrated the utility of GR-RSC to identify homologous loci across related Penstemon taxa. Though PCR primer regions were conserved across a broadly sampled survey of Penstemon species

  14. Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction*

    PubMed Central

    Sharadamma, Narayanaswamy; Harshavardhana, Yadumurthy; Ravishankar, Apoorva; Anand, Praveen; Chandra, Nagasuma; Muniyappa, K.

    2014-01-01

    The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins. PMID:25324543

  15. Molecular Level Insights on Collagen-Polyphenols Interaction Using Spin-Relaxation and Saturation Transfer Difference NMR.

    PubMed

    Reddy, R Ravikanth; Phani Kumar, Bandaru V N; Shanmugam, Ganesh; Madhan, Balaraman; Mandal, Asit B

    2015-11-01

    Interaction of small molecules with collagen has far reaching consequences in biological and industrial processes. The interaction between collagen and selected polyphenols, viz., gallic acid (GA), pyrogallol (PG), catechin (CA), and epigallocatechin gallate (EGCG), has been investigated by various solution NMR measurements, viz., (1)H and (13)C chemical shifts (δH and δC), (1)H nonselective spin-lattice relaxation times (T1NS) and selective spin-lattice relaxation times (T1SEL), as well as spin-spin relaxation times (T2). Furthermore, we have employed saturation transfer difference (STD) NMR method to monitor the site of GA, CA, PG, and EGCG which are in close proximity to collagen. It is found that -COOH group of GA provides an important contribution for the interaction of GA with collagen, as evidenced from (13)C analysis, while PG, which is devoid of -COOH group in comparison to GA, does not show any significant interaction with collagen. STD NMR data indicates that the resonances of A-ring (H2', H5' and H6') and C-ring (H6 and H8) protons of CA, and A-ring (H2' and H6'), C-ring (H6 and H8), and D-ring (H2″and H6″) protons of EGCG persist in the spectra, demonstrating that these protons are in spatial proximity to collagen, which is further validated by independent proton spin-relaxation measurement and analysis. The selective (1)H T1 measurements of polyphenols in the presence of protein at various concentrations have enabled us to determine their binding affinities with collagen. EGCG exhibits high binding affinity with collagen followed by CA, GA, and PG. Further, NMR results propose that presence of gallic acid moiety in a small molecule increases its affinity with collagen. Our experimental findings provide molecular insights on the binding of collagen and plant polyphenols. PMID:26447653

  16. Release of Native-like Gaseous Proteins from Electrospray Droplets via the Charged Residue Mechanism: Insights from Molecular Dynamics Simulations.

    PubMed

    McAllister, Robert G; Metwally, Haidy; Sun, Yu; Konermann, Lars

    2015-10-01

    The mechanism whereby gaseous protein ions are released from charged solvent droplets during electrospray ionization (ESI) remains a matter of debate. Also, it is unclear to what extent electrosprayed proteins retain their solution structure. Molecular dynamics (MD) simulations offer insights into the temporal evolution of protein systems. Surprisingly, there have been no all-atom simulations of the protein ESI process to date. The current work closes this gap by investigating the behavior of protein-containing aqueous nanodroplets that carry excess positive charge. We focus on "native ESI", where proteins initially adopt their biologically active solution structures. ESI proceeds while the protein remains entrapped within the droplet. Protein release into the gas phase occurs upon solvent evaporation to dryness. Droplet shrinkage is accompanied by ejection of charge carriers (Na(+) for the conditions chosen here), keeping the droplet at ∼85% of the Rayleigh limit throughout its life cycle. Any remaining charge carriers bind to the protein as the final solvent molecules evaporate. The outcome of these events is largely independent of the initial protein charge and the mode of charge carrier binding. ESI charge states and collision cross sections of the MD structures agree with experimental data. Our results confirm the Rayleigh/charged residue model (CRM). Field emission of excess Na(+) plays an ancillary role by governing the net charge of the shrinking droplet. Models that envision protein ejection from the droplet are not supported. Most nascent CRM ions retain native-like conformations. For unfolded proteins ESI likely proceeds along routes that are different from the native state mechanism explored here. PMID:26325619

  17. 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. PMID:26979697

  18. 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.

  19. 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

  20. Influence of Climate Warming on Arctic Mammals? New Insights from Ancient DNA Studies of the collared lemming Dicrostonyx torquatus.

    NASA Astrophysics Data System (ADS)

    Prost, Stefan; Smirnov, Nickolay; Fedorov, Vadim B.; Sommer, Robert S.; Stiller, Mathias; Nagel, Doris; Knapp, Michael; Hofreiter, Michael

    2010-05-01

    Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographic distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum (LGM) had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with cold and dry climate. Using three dimensional network reconstruction and model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference we show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Blling/Allerd) warming phase at 14.5 kyrs BP. Our results show that previous climate warming events had a strong influence on collard lemming populations. A similar population reduction due to predicted future climate change would have severe effects on the arctic ecosystem, as collared lemmings are a key species in the trophic interactions and ecosystem processes in the Arctic.

  1. Simple Indices Provide Insight to Climate Attributes Delineating the Geographic Range of Aedes albopictus (Diptera: Culicidae) Prior to Worldwide Invasion.

    PubMed

    Mogi, Motoyoshi; Armbruster, Peter; Tuno, Nobuko; Campos, Raúl; Eritja, Roger

    2015-07-01

    Aedes albopictus (Skuse) has expanded its distribution worldwide during the past decades. Despite attempts to explain and predict its geographic occurrence, analyses of the distribution of Ae. albopictus in the context of broad climatic regions (biomes) has not been performed. We analyzed climate conditions at its distribution sites in the range before the worldwide invasions (from the easternmost Hawaii through westernmost Madagascar) by using thermal and aridity-humidity indices descriptive of major biomes. A significant advantage of this approach is that it uses simple indices clearly related to the population dynamics of Ae. albopictus. Although Ae. albopictus has been regarded as a forest species preferring humid climate, in areas with significant human habitation, the distribution sites extended from the perhumid, rain forest zone to the semiarid, steppe zone. This pattern was common from the tropics through the temperate zone. Across the distribution range, there was no seasonal discordance between temperature and precipitation; at sites where winter prevents Ae. albopictus reproduction (monthly means<10°C), precipitation was concentrated in warm months (>10°C) under the Asian summer monsoon. Absence of the species in northern and eastern coastal Australia and eastern coastal Africa was not attributable solely to climate conditions. However, Asia west of the summer monsoon range was climatically unsuitable because of low precipitation throughout the year or in warm months favorable to reproduction (concentration of precipitation in winter). We hypothesized that Ae. albopictus originated in continental Asia under the monsoon climate with distinct dry seasons and hot, wet summer, enabling rapid population growth. PMID:26335471

  2. Climate, people, fire and vegetation: new insights into vegetation dynamics in the Eastern Mediterranean since the 1st century AD

    NASA Astrophysics Data System (ADS)

    Bakker, J.; Paulissen, E.; Kaniewski, D.; Poblome, J.; De Laet, V.; Verstraeten, G.; Waelkens, M.

    2012-08-01

    Anatolia forms a bridge between Europe, Africa and Asia and is influenced by all three continents in terms of climate, vegetation and human civilisation. Unfortunately, well dated palynological records focussing on the period from the end of the classical Roman period until subrecent times are rare for Anatolia and completely absent for southwest Turkey, resulting in a lacuna in knowledge concerning the interactions of climatic change, human impact, and environmental change in this important region. Two well dated palaeoecological records from the Western Taurus Mountains, Turkey, provide a first relatively detailed record of vegetation dynamics from late Roman times until the present in SW Turkey. Combining pollen, non-pollen palynomorphs, charcoal, sedimentological, archaeological data, and newly developed multivariate numerical analyses, allows for the disentangling of climatic and anthropogenic influences on vegetation change. Results show both the regional pollen signal as well as local soil sediment characteristics respond accurately to shifts in regional climatic conditions. Both climatic as well as anthropogenic change had a strong influence on vegetation dynamics and land use. A moist environmental trend during the late 3rd century caused an increase in marshes and wetlands in the moister valley floors, limiting possibilities for intensive crop cultivation at such locations. A mid 7th century shift to pastoralism coincided with a climatic deterioration as well as the start of Arab incursions into the region, the former driving the way in which the vegetation developed afterwards. Resurgence in agriculture was observed in the study during the mid 10th century AD, coinciding with the Medieval Climate Anomaly. An abrupt mid 12th century decrease in agriculture is linked to socio-political change, rather than the onset of the Little Ice Age. Similarly, gradual deforestation occurring from the 16th century onwards has been linked to changes in lands use during

  3. Functional adjustments of xylem anatomy to climatic variability: insights from long-term Ilex aquifolium tree-ring series.

    PubMed

    Rita, Angelo; Cherubini, Paolo; Leonardi, Stefano; Todaro, Luigi; Borghetti, Marco

    2015-08-01

    The present study assessed the effects of climatic conditions on radial growth and functional anatomical traits, including ring width, vessel size, vessel frequency and derived variables, i.e., potential hydraulic conductivity and xylem vulnerability to cavitation in Ilex aquifolium L. trees using long-term tree-ring time series obtained at two climatically contrasting sites, one mesic site in Switzerland (CH) and one drought-prone site in Italy (ITA). Relationships were explored by examining different xylem traits, and point pattern analysis was applied to investigate vessel clustering. We also used generalized additive models and bootstrap correlation functions to describe temperature and precipitation effects. Results indicated modified radial growth and xylem anatomy in trees over the last century; in particular, vessel frequency increased markedly at both sites in recent years, and all xylem traits examined, with the exception of xylem cavitation vulnerability, were higher at the CH mesic compared with the ITA drought site. A significant vessel clustering was observed at the ITA site, which could contribute to an enhanced tolerance to drought-induced embolism. Flat and negative relationships between vessel size and ring width were observed, suggesting carbon was not allocated to radial growth under conditions which favored stem water conduction. Finally, in most cases results indicated that climatic conditions influenced functional anatomical traits more substantially than tree radial growth, suggesting a crucial role of functional xylem anatomy in plant acclimation to future climatic conditions. PMID:26142450

  4. Denudational slope processes and slope response to global climate changes and other disturbances: insights from the Nepal Himalayas.

    NASA Astrophysics Data System (ADS)

    Fort, Monique

    2016-04-01

    Hillslope geomorphology results from a large range of denudational processes mainly controlled by relief, structure, lithology, climate, land-cover and land use. In most areas of the world, the "critical zone" concept is a good integrator of denudation that operates on a long-term scale. However, in large and high mountain areas, short-time scale factors often play a significant role in the denudational pattern, accelerating and/or delaying the transfer of denudation products and fluxes, and creating specific, spatially limited disturbances. We focus on the Nepal Himalayas, where the wide altitudinal range of bio-climatic zones and the intense geodynamic activity create a complex mosaic of landforms, as expressed by the present geomorphology of mountain slopes. On the basis of examples selected in the different Himalayan mountain belts (Siwaliks hills, middle mountains, High Himalaya), we illustrate different types of slopes and disturbances induced by active tectonics, climate extremes, and climate warming trends. Special attention is paid to recent events, such as landslide damming, triggered by either intense rainfalls (Kali Gandaki and Sun Kosi valleys) or the last April-May 2015 Gorkha seismic sequence (southern Khumbu). Lastly, references to older, larger events show that despite the highly dynamic environment, landforms caused by large magnitude disturbances may persist in the landscape in the long term.

  5. Southern African continental climate since the late Pleistocene: Insights from biomarker analyses of Kalahari salt pan sediments

    NASA Astrophysics Data System (ADS)

    Belz, Lukas; Schüller, Irka; Wehrmann, Achim; Wilkes, Heinz

    2016-04-01

    The climate system of sub-tropical southern Africa is mainly controlled by large scale atmospheric and marine circulation processes and, therefore, very sensitive to global climate change. This underlines the importance of paleoenvironmental reconstructions in order to estimate regional implications of current global changes. However, the majority of studies on southern African paleoclimate are based on the investigation of marine sedimentary archives and past climate development especially in continental areas is still poorly understood. This emphasizes the necessity of continental proxy-data from this area. Proxy datasets from local geoarchives especially of the southwestern Kalahari region are still scarce. A main problem is the absence of conventional continental climatic archives, due to the lack of lacustrine systems. In this study we are exploring the utility of sediments from western Kalahari salt pans, i.e. local depressions which are flooded temporarily during rainfall events. An age model based on 14C dating of total organic carbon (TOC) shows evidence that sedimentation predominates over erosional processes with respect to pan formation. Besides the analyses of basic geochemical bulk parameters including TOC, δ13CTOC, total inorganic carbon, δ13CTIC, δ18OTIC, total nitrogen and δ15N, our paleo-climatic approach focuses on reconstruction of local vegetation assemblages to identify changes in the ecosystem. This is pursued using plant biomarkers, particularly leaf wax n-alkanes and n-alcohols and their stable carbon and hydrogen isotopic signatures. Results show prominent shifts in n-alkane and n-alkanol distributions and compound specific carbon isotope values, pointing to changes to a more grass dominated environment during Heinrich Stadial 1 (18.5-14.6 ka BP), while hydrogen isotope values suggest wetter phases during Holocene and LGM. This high variability indicates the local vulnerability to global change.

  6. Impacts of climate and humans on the vegetation in NW Turkey: palynological insights from Lake Iznik since the Last Glacial

    NASA Astrophysics Data System (ADS)

    Miebach, A.; Niestrath, P.; Roeser, P.; Litt, T.

    2015-11-01

    The Marmara region in northwestern Turkey provides a unique opportunity for studying the vegetation history in response to climate changes and anthropogenic impacts because of its location between different climate and vegetation zones and its long settlement history. Geochemical and mineralogical investigations of the largest lake in the region, Lake Iznik, already registered climate related changes of the lake level and the lake mixing. However, a palynological investigation encompassing the Late Pleistocene to Middle Holocene was still missing. Here, we present the first pollen record of the last ca. 31 ka cal BP (calibrated kilo years before 1950) inferred from Lake Iznik sediments as an independent proxy for paleoecological reconstructions. Our study reveals that the vegetation in the Iznik area changed generally between steppe during glacial/stadial conditions, forest-steppe during interstadial conditions, and oak dominated mesic forest during interglacial conditions. Moreover, a pronounced succession of pioneer trees, cold temperate, warm temperate, and Mediterranean trees appeared since the Lateglacial. Rapid climate changes, which are reflected by vegetation changes, can be correlated with Dansgaard-Oeschger (DO) events such as DO-4, DO-3, and DO-1, the Younger Dryas, and probably also the 8.2 event. Since the mid-Holocene, the vegetation was influenced by anthropogenic activities. During early settlement phases, the distinction between climate-induced and human-induced changes of the vegetation is challenging. Still, evidence for human activities consolidates since the Early Bronze Age (ca. 4.8 ka cal BP): cultivated trees, crops, and secondary human indicator taxa appeared, and forests got cleared. Subsequent fluctuations between extensive agricultural use and regeneration of the natural vegetation become apparent.

  7. Climate suitability estimates offer insight into fundamental revegetation challenges among post-mining rehabilitated landscapes in eastern Australia

    NASA Astrophysics Data System (ADS)

    Audet, P.; Arnold, S.; Lechner, A. M.; Mulligan, D. R.; Baumgartl, T.

    2012-12-01

    Rehabilitation of post-mining sites in semi-arid/subtropical environments of eastern Australia have a general objective to establish specific types of native vegetation communities as defined in mine closure plans and in relation to the specific biotic and abiotic requirements of such communities. Critical for the success of rehabilitation is the availability of water and hence the climatic characteristic of this geographical region which is defined by a number of weather-bound factors (e.g. potentially erratic rainfall and periods of drought and flooding). However, specific estimates of climate suitability are seldom incorporated into current mined land rehabilitation design. To address this, our analysis combined various broad-scale climatic parameters (i.e. primarily relating to rainfall) to assess bioregional suitability-susceptibility within the context of plant early-establishment in the objective of informing rehabilitation schemes as to the inherent environmental challenges influencing both short- and long-term ecological development. Following our survey of available climate data, we derived site suitability-susceptibility indexes (that are otherwise currently not available within rehabilitation schemes) and compared the performance of 9 mine site locations in which our Centre has been engaged in environmental monitoring (Weipa, Mt. Isa, Ernest Henry, Eromanga, Kidston, Curragh, Tarong, North Stradbroke Island, and Newnes Plateau). More specifically, the sites were ranked from most-to-least suitable and compared with natural vegetation patterns (as estimated by the mean NDVI). Overall, it was determined that regular rainfall and relatively short periods of water-deficit are key characteristics of climate suitability (as found among the relatively more temperate coastal-hinterland sites), whereas high rainfall variability and (or) prolonged seasonal drought are primary characteristics of unsuitability (as found among the arid central-inland sites

  8. Neotectonic deformation versus climate control in the Central Andes of Argentina, insights from 10Be Surface Exposure Dating

    NASA Astrophysics Data System (ADS)

    Terrizzano, Carla; Zech, Roland; Garcia Morabito, Ezequiel; Yamin, Marcela; Haghipour, Negar; Wüthrich, Lorenz; Christl, Marcus

    2015-04-01

    Mountainous regions and their forelands commonly supports a suite of landforms sensitive to climate change and tectonics, providing -if addressed with appropriate geomorphological and geochronological approaches- record for landscape, climate, and tectonic evolution. In particular, alluvial fans are valuable archives of Quaternary climate and tectonics. The southern Central Andes and their forelands provide a perfect setting to study such forcings, since first, the extreme aridity favors the geomorphological preservation of the fan surfaces, so that 10Be surface exposure dating can be applied to establish robust and precise chronologies. And second, the neotectonic activity in this region results in widespread deformation of Quaternary deposits and recent devastating earthquakes. However, rates of uplift and shortening on the reverse faults remain largely unknown and very little is known yet about the Pleistocene climate history in the southern Central Andes, which limits a robust evaluation of the role of climate for the alluvial fan formation and landscape evolution. We combined structural and geomorphic investigations with 10Be surface exposure dating in the western Precordillera of the Southern Central Andes of Argentina (31°30'-31°53' SL/69°20' WL) in order to establish a numeric chronology for four deformed alluvial fan surfaces, to estimate uplift rates and to evaluate the potential climate role in controlling the fan construction and evolution. Surface exposure ages were determined for a few large boulders, amalgamated pebbles, and via depth profiles on sand samples. Boulder ages range from 145 to 212 ka for the oldest well-preserved fan remnants (Q1a, n=3), from 63 to 108 ka (Q2, n=3) and 21-28 ka (Q3, n=2), amalgamated pebbles yield ages range from 106 to 127 ka for the oldest fan surface (Q1b, n=79), all calculations assuming no erosion and using the scaling scheme for spallation based on Lal 1991, Stone 2000. Boulders from current channels have 10Be

  9. Influence of Climate Warming on Arctic Mammals? New Insights from Ancient DNA Studies of the Collared Lemming Dicrostonyx torquatus

    PubMed Central

    Prost, Stefan; Smirnov, Nickolay; Fedorov, Vadim B.; Sommer, Robert S.; Stiller, Mathias; Nagel, Doris; Knapp, Michael; Hofreiter, Michael

    2010-01-01

    Background Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. Results Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød) warming phase at 14.5 kyrs BP. Conclusion Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population extinctions of collared

  10. Climate and human impacts on the vegetation in NW Turkey: palynological insights from Lake Iznik since the Last Glacial

    NASA Astrophysics Data System (ADS)

    Miebach, Andrea; Niestrath, Phoebe; Roeser, Patricia A.; Litt, Thomas

    2015-04-01

    The reconstruction of the climate and vegetation history of the Marmara region in northwestern Turkey is of particular interest because of its long occupation history and its location between different climate and vegetation zones. Geochemical and mineralogical investigations of the largest lake in the region, Lake Iznik, already registered climate related changes of the lake level and the lake mixing during the last 31 ka cal BP (Roeser 2014). However, a palynological investigation, encompassing the Late Pleistocene to Middle Holocene, was still missing. Here, we present the first pollen record of the last 31 ka cal BP from Lake Iznik sediments as an independent proxy for paleoecological reconstructions. Lake Iznik is situated east of the Marmara Sea. Its catchment area is located in a climatic transition zone between the Mediterranean and Pontic climate zones. Today, the region is highly influenced by (sub-) Euxinian temperate deciduous and mixed forests dominated by deciduous oak and beech. Coastal areas of the southeastern Marmara Sea and the Aegean Sea are dominated by (sub-) Mediterranean woods and shrubs with sclerophyllous and evergreen elements (Zohary 1973). The pollen record of Lake Iznik reflects typical Eastern Mediterranean vegetation pattern and northern hemispheric climate changes. In contrast to the recent vegetation, a steppe vegetation dominated during the Late Pleistocene. In response to Dansgaard-Oeschger events, the vegetation changed rapidly into a steppe-forest. A remarkable expansion of deciduous oak forest, indicating warmer temperatures, is registered since the Bölling-Alleröd. A short period of dryer and/or cooler climate, corresponding to the Younger Dryas, is marked by an increase of steppe components and by a decrease of several trees. Deciduous oaks predominated the vegetation since the Early Holocene. They were successively accompanied by cold temperate, warm temperate, and Mediterranean trees. In addition to the climate impact

  11. Climate, people, fire and vegetation: new insights into vegetation dynamics in the Eastern Mediterranean since the 1st century AD

    NASA Astrophysics Data System (ADS)

    Bakker, J.; Paulissen, E.; Kaniewski, D.; Poblome, J.; De Laet, V.; Verstraeten, G.; Waelkens, M.

    2013-01-01

    Anatolia forms a bridge between Europe, Africa and Asia and is influenced by all three continents in terms of climate, vegetation and human civilisation. Unfortunately, well-dated palynological records focussing on the period from the end of the classical Roman period until subrecent times are rare for Anatolia and completely absent for southwest Turkey, resulting in a lacuna in knowledge concerning the interactions of climatic change, human impact, and environmental change in this important region. Two well-dated palaeoecological records from the Western Taurus Mountains, Turkey, provide a first relatively detailed record of vegetation dynamics from late Roman times until the present in SW Turkey. Combining pollen, non-pollen palynomorphs, charcoal, sedimentological, archaeological data, and newly developed multivariate numerical analyses allows for the disentangling of climatic and anthropogenic influences on vegetation change. Results show changes in both the regional pollen signal as well as local soil sediment characteristics match shifts in regional climatic conditions. Both climatic as well as anthropogenic change had a strong influence on vegetation dynamics and land use. A moist environmental trend during the late-3rd century caused an increase in marshes and wetlands in the moister valley floors, limiting possibilities for intensive crop cultivation at such locations. A mid-7th century shift to pastoralism coincided with a climatic deterioration as well as the start of Arab incursions into the region, the former driving the way in which the vegetation developed afterwards. Resurgence in agriculture was observed in the study during the mid-10th century AD, coinciding with the Medieval Climate Anomaly. An abrupt mid-12th century decrease in agriculture is linked to socio-political change, rather than the onset of the Little Ice Age. Similarly, gradual deforestation occurring from the 16th century onwards has been linked to changes in land use during Ottoman

  12. Decadal-to-centennial-scale climate variability: Insights into the rise and fall of the Great Salt Lake

    NASA Technical Reports Server (NTRS)

    Mann, Michael E.; Lall, Upmanu; Saltzman, Barry

    1995-01-01

    We demonstrate connections between decadal and secular global climatic variations, and historical variations in the volume of the Great Salt Lake. The decadal variations correspond to a low-frequency shifting of storm tracks which influence winter precipitation and explain nearly 18% of the interannual and longer-term variance in the record of monthly volume change. The secular trend accounts for a more modest approximately 1.5% of the variance.

  13. Insights into soil carbon dynamics across climatic and geologic gradients from time-series and fraction-specific radiocarbon analysis

    NASA Astrophysics Data System (ADS)

    van der Voort, Tessa Sophia; Hagedorn, Frank; Zell, Claudia; McIntyre, Cameron; Eglinton, Tim

    2016-04-01

    Understanding the interaction between soil organic matter (SOM) and climatic, geologic and ecological factors is essential for the understanding of potential susceptibility and vulnerability to climate and land use change. Radiocarbon constitutes a powerful tool for unraveling SOM dynamics and is increasingly used in studies of carbon turnover. The complex and inherently heterogeneous nature of SOM renders it challenging to assess the processes that govern SOM stability by solely looking at the bulk signature on a plot-scale level. This project combines bulk radiocarbon measurements on a regional-scale spanning wide climatic and geologic gradients with a more in-depth approach for a subset of locations. For this subset, time-series and carbon pool-specific radiocarbon data has been acquired for both topsoil and deeper soils. These well-studied sites are part of the Long-Term Forest Ecosystem Research (LWF) program of the Swiss Federal Institute for Forest, Snow and Landscape research (WSL). Statistical analysis was performed to examine relationships of radiocarbon signatures with variables such as temperature, precipitation and elevation. Bomb-curve modeling was applied determine carbon turnover using time-series data. Results indicate that (1) there is no significant correlation between Δ14C signature and environmental conditions except a weak positive correlation with mean annual temperature, (2) vertical gradients in Δ14C signatures in surface and deeper soils are highly similar despite covering disparate soil-types and climatic systems, and (3) radiocarbon signatures vary significantly between time-series samples and carbon pools. Overall, this study provides a uniquely comprehensive dataset that allows for a better understanding of links between carbon dynamics and environmental settings, as well as for pool-specific and long-term trends in carbon (de)stabilization.

  14. Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale

    PubMed Central

    Sahoo, Bikash Ranjan; Fujiwara, Toshimichi

    2016-01-01

    The cathelicidin derived bovine antimicrobial peptide BMAP27 exhibits an effective microbicidal activity and moderate cytotoxicity towards erythrocytes. Irrespective of its therapeutic and multidimensional potentiality, the structural studies are still elusive. Moreover, the mechanism of BMAP27 mediated pore formation in heterogeneous lipid membrane systems is poorly explored. Here, we studied the effect of BMAP27 in model cell-membrane systems such as zwitterionic, anionic, thymocytes-like (TLM) and leukemia-like membranes (LLM) by performing molecular dynamics (MD) simulation longer than 100 μs. All-atom MD studies revealed a stable helical conformation in the presence of anionic lipids, however, significant loss of helicity was identified in TLM and zwitterionic systems. A peptide tilt (~45˚) and central kink (at residue F10) was found in anionic and LLM models, respectively, with an average membrane penetration of < 0.5 nm. Coarse-grained (CG) MD analysis on a multi-μs scale shed light on the membrane-dependent peptide and lipid organization. Stable micelle and end-to-end like oligomers were formed in zwitterionic and TLM models, respectively. In contrast, unstable oligomer formation and monomeric BMAP27 penetration were observed in anionic and LLM systems with selective anionic lipid aggregation (in LLM). Peptide penetration up to ~1.5 nm was observed in CG-MD systems with the BMAP27 C-terminal oriented towards the bilayer core. Structural inspection suggested membrane penetration by micelle/end-to-end like peptide oligomers (carpet-model like) in the zwitterionic/TLM systems, and transmembrane-mode (toroidal-pore like) in the anionic/LLM systems, respectively. Structural insights and energetic interpretation in BMAP27 mutant highlighted the role of F10 and hydrophobic residues in mediating a membrane-specific peptide interaction. Free energy profiling showed a favorable (-4.58 kcal mol-1 for LLM) and unfavorable (+0.17 kcal mol-1 for TLM) peptide insertion

  15. The Climate Potentials and Side-Effects of Large-Scale terrestrial CO2 Removal - Insights from Quantitative Model Assessments

    NASA Astrophysics Data System (ADS)

    Boysen, L.; Heck, V.; Lucht, W.; Gerten, D.

    2015-12-01

    Terrestrial carbon dioxide removal (tCDR) through dedicated biomass plantations is considered as one climate engineering (CE) option if implemented at large-scale. While the risks and costs are supposed to be small, the effectiveness depends strongly on spatial and temporal scales of implementation. Based on simulations with a dynamic global vegetation model (LPJmL) we comprehensively assess the effectiveness, biogeochemical side-effects and tradeoffs from an earth system-analytic perspective. We analyzed systematic land-use scenarios in which all, 25%, or 10% of natural and/or agricultural areas are converted to tCDR plantations including the assumption that biomass plantations are established once the 2°C target is crossed in a business-as-usual climate change trajectory. The resulting tCDR potentials in year 2100 include the net accumulated annual biomass harvests and changes in all land carbon pools. We find that only the most spatially excessive, and thus undesirable, scenario would be capable to restore the 2° target by 2100 under continuing high emissions (with a cooling of 3.02°C). Large-scale biomass plantations covering areas between 1.1 - 4.2 Gha would produce a climate reduction potential of 0.8 - 1.4°C. tCDR plantations at smaller scales do not build up enough biomass over this considered period and the potentials to achieve global warming reductions are substantially lowered to no more than 0.5-0.6°C. Finally, we demonstrate that the (non-economic) costs for the Earth system include negative impacts on the water cycle and on ecosystems, which are already under pressure due to both land use change and climate change. Overall, tCDR may lead to a further transgression of land- and water-related planetary boundaries while not being able to set back the crossing of the planetary boundary for climate change. tCDR could still be considered in the near-future mitigation portfolio if implemented on small scales on wisely chosen areas.

  16. Molecular records of climate variability and vegetation response since the Late Pleistocene in the Lake Victoria basin, East Africa

    NASA Astrophysics Data System (ADS)

    Berke, Melissa A.; Johnson, Thomas C.; Werne, Josef P.; Grice, Kliti; Schouten, Stefan; Sinninghe Damsté, Jaap S.

    2012-11-01

    New molecular proxies of temperature and hydrology are helping to constrain tropical climate change and elucidate possible forcing mechanisms during the Holocene. Here, we examine a ˜14,000 year record of climate variability from Lake Victoria, East Africa, the world's second largest freshwater lake by surface area. We determined variations in local hydroclimate using compound specific δD of terrestrial leaf waxes, and compared these results to a new record of temperature utilizing the TEX86 paleotemperature proxy, based on aquatic Thaumarchaeotal membrane lipids. In order to assess the impact of changing climate on the terrestrial environment, we generated a record of compound specific δ13C from terrestrial leaf waxes, a proxy for ecosystem-level C3/C4 plant abundances, and compared the results to previously published pollen-inferred regional vegetation shifts. We observe a general coherence between temperature and rainfall, with a warm, wet interval peaking ˜10-9 ka and subsequent gradual cooling and drying over the remainder of the Holocene. These results, particularly those of rainfall, are in general agreement with other tropical African climate records, indicating a somewhat consistent view of climate over a wide region of tropical East Africa. The δ13C record from Lake Victoria leaf waxes does not appear to reflect changes in regional climate or vegetation. However, palynological analyses document an abrupt shift from a Poaceae (grasses)-dominated ecosystem during the cooler, arid late Pleistocene to a Moraceae-dominated (trees/shrubs) landscape during the warm, wet early Holocene. We theorize that these proxies are reflecting vegetation in different locations around Lake Victoria. Our results suggest a predominantly insolation-forced climate, with warm, wet conditions peaking at the maximum interhemispheric seasonal insolation contrast, likely intensifying monsoonal precipitation, while maximum aridity coincides with the rainy season insolation and the

  17. A molecular perspective on Late Quaternary climate and vegetation change in the Lake Tanganyika basin, East Africa

    NASA Astrophysics Data System (ADS)

    Tierney, Jessica E.; Russell, James M.; Huang, Yongsong

    2010-03-01

    Characterizing the nature of past hydrological change and its interactions with vegetation is fundamental to acquiring a better understanding of continental tropical climate dynamics. Here, we outline major shifts in the climate and ecosystem of tropical East Africa for the past 60,000 years (60 ka) by examining molecular records of hydrology, vegetation, and temperature from a sediment sequence from Lake Tanganyika. We demonstrate, via comparison with pollen spectra, that stable carbon isotopes measured on higher plant leaf waxes ( δ13C wax) are a reliable proxy for vegetation change. In addition we argue that the D/H ratio of higher plant leaf waxes ( δD wax) is a robust and independent indicator of past changes in aridity, and is not affected by regional vegetation change directly. Our paired, compound-specific isotope data show that shifts in vegetation lead major changes in hydrology in the Tanganyika basin at several major climate transitions during the past 60,000 years, suggesting that vegetation in the Tanganyika basin is not as sensitive to aridity as previous studies have suggested and that variations in carbon dioxide, temperature, and internal ecosystem dynamics are equally, if not more, important. We hypothesize that regional vegetation change may exert a positive feedback on regional hydrology, thus partially accounting for the abrupt threshold behavior evident in our paleohydrological data. Furthermore, we find that past changes in Tanganyika basin climate and ecology are closely linked to concentrations of atmospheric trace gases, highlighting the paramount influence of global climatic shifts upon regional tropical climate over glacial/interglacial timescales.

  18. Insights into the molecular level composition, sources, and formation mechanisms of dissolved organic matter in aerosols and precipitation

    NASA Astrophysics Data System (ADS)

    Altieri, Katye Elisabeth

    Atmospheric aerosols scatter and absorb light influencing the global radiation budget and climate, and are associated with adverse effects on human health. Precipitation is an important removal mechanism for atmospheric dissolved organic matter (DOM), and a potentially important input for receiving ecosystems. However, the sources, formation, and composition of atmospheric DOM in aerosols and precipitation are not well understood. This dissertation investigates the composition and formation mechanisms of secondary organic aerosol (SOA) formed through cloud processing reactions, elucidates the composition and sources of DOM in rainwater, and provides links connecting the two. Photochemical batch aqueous-phase reactions of organics with both biogenic and anthropogenic sources (i.e., methylglyoxal, pyruvic acid) and OH radical were performed to simulate cloud processing. The composition of products formed through cloud processing experiments and rainwater collected in New Jersey, USA was investigated using a combination of electrospray ionization mass spectrometry techniques, including ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry. This dissertation has resulted in the first evidence that oligomers form through cloud processing reactions, the first detailed chemical mechanism of aqueous phase oligomerization, the first identification of oligomers, organosulfates, and nitrooxy organosulfates in precipitation, and the first molecular level chemical characterization of organic nitrogen in precipitation. The formation of oligomers in SOA helps to explain the presence of large multifunctional compounds and humic like substances (HULIS) that dominate particulate organic mass. Oligomers have low vapor pressures and remain in the particle phase after cloud evaporation, enhancing SOA. The chemical properties of the oligomers suggest that they are less hygroscopic than the monomeric reaction products (i.e., organic acids). Their elemental

  19. A tale of two spartinas: Climatic, photobiological and isotopic insights on the fitness of non-indigenous versus native species

    NASA Astrophysics Data System (ADS)

    Duarte, B.; Baeta, A.; Rousseau-Gueutin, M.; Ainouche, M.; Marques, J. C.; Caçador, I.

    2015-12-01

    Salt marshes are facing a new threat: the invasion by non-indigenous species (NIS), Although its introduction time is not established yet, in 1999 Spartina versicolor was already identified as a NIS in the Mediterranean marshes, significantly spreading its area of colonization. Using the Mediterranean native Spartina maritima as a reference, the present research studied the ecophysiological fitness of this NIS in its new environment, as a tool to understand its potential invasiveness. It was found that Spartina versicolor had a stable photobiological pattern, with only minor fluctuations during an annual cycle, and lower efficiencies comparated to S. maritima. The NIS seems to be rather insensitive to the observed abiotic factors fluctuations (salinity and pH of the sediment), and thus contrasts with the native S. maritima, known to be salinity dependent with higher productivity values in higher salinity environments. Most of the differences observed between the photobiology of these species could be explained by their nitrogen nutrition (here evaluated by the δ15N stable isotope) and directly related with the Mediterranean climate. Enhanced by a higher N availability during winter, the primary production of S. maritima which lead to dilution of the foliar δ15N concentration in the newly formed biomass, similarly to what is observed along a rainfall gradient. On the other hand, S. versicolor showed an increased δ15N in its tissues along the annual rainfall gradient, probably due to a δ15N concentration effect during low biomass production periods (winter and autumn). Together with the photobiological traits, these isotopic data point out to a climatic misfit of S. versicolor to the Mediterranean climate compared to the native S. maritima. This appears to be the major constrain shaping the ecophysiological fitness of this NIS, its primary production and consequently, its spreading rate along the Mediterranean marshes.

  20. Holocene climate variability in the NE Pacific: Insight from connections between the Gulf of Alaska and the California Current System

    NASA Astrophysics Data System (ADS)

    Finney, B. P.; Addison, J. A.

    2009-12-01

    Historically, decadal-scale climatic change in the North Pacific region appears to be characterized by circulation modes with coherent and recognizable spatial patterns (i.e., PDO). Examination of trends in paleo-records from widespread regions, allow recognition of how these modes have varied over time. Changes in patterns of correlations of proxies between regions suggest several periods of reorganization of ocean-atmospheric circulation during the Holocene. Major shifts appear to have occurred during climatic transitions into the Neoglacial period (ca 4000 BP), and into and out of the Little Ice Age (LIA; ca. AD 1200 and 1850). Recent paleoclimatic studies from Mt, Logan ice cores and elsewhere suggest these transitions reflect shifts between atmospheric circulation modes of more zonal vs. more meridional flow. These shifts in climate can be tracked into variability in primary productivity and higher trophic levels, such as pelagic fish, in the North Pacific marine ecosystem. Within the Gulf of Alaska, new high-resolution reconstructions of ocean paleoproductivity based on multiproxy analysis of sediment cores suggest persistent variability over multidecadal scales, punctuated by abrupt state changes in overall productivity level. Such “mega-regime shifts” are of a different nature and larger amplitude than historical regime-shifts. Records of Alaskan salmon are generally positively correlated with Gulf of Alaska productivity. Interestingly, records of California Current sardine and anchovy abundance reveal different relationships to Alaska salmon abundance during the LIA relative to historical observations. It is likely that a different pattern of ocean-atmospheric circulation during the LIA, resulted in different relationships between these regional ecosystems.

  1. New insights into the Weichselian environment and climate of the East Siberian Arctic, derived from fossil insects, plants, and mammals

    NASA Astrophysics Data System (ADS)

    Sher, A. V.; Kuzmina, S. A.; Kuznetsova, T. V.; Sulerzhitsky, L. D.

    2005-03-01

    Multidisciplinary study of a key section on the Laptev Sea Coast (Bykovsky Peninsula, east Lena Delta) in 1998-2001 provides the most complete record of Middle and Late Weichselian environments in the East Siberian Arctic. The 40-m high Mamontovy Khayata cliff is a typical Ice Complex section built of icy silts with a network of large syngenetic polygonal ice wedges, and is richly fossiliferous. In combination with pollen, plant macrofossil and mammal fossils, a sequence of ca 70 insect samples provides a new interpretation of the environment and climate of the area between ca 50 and 12 ka. The large number of radiocarbon dates from the section, together with an extensive 14C database on mammal bones, allows chronological correlation of the various proxies. The Bykovsky record shows how climate change, and the Last Glacial Maximum in particular, affected terrestrial organisms such as insects and large grazing mammals. Both during the presumed "Karginsky Interstadial" (MIS 3) and the Sartanian Glacial (MIS 2), the vegetation remained a mosaic arctic grassland with relatively high diversity of grasses and herbs and dominance of xeric habitats: the tundra-steppe type. This biome was supported by a constantly very continental climate, caused by low sea level and enormous extension of shelf land. Variations within the broad pattern were caused mainly by fluctuations in summer temperature, related to global trends but overprinted by the effect of continentality. No major changes in humidity were observed nor were advances of modern-type forest or forest-tundra recorded, suggesting a major revision of the "Karginsky Interstadial" paradigm. The changing subtypes of the tundra-steppe environment were persistently favourable for mammalian grazers, which inhabited the shelf lowlands throughout the studied period. Mammal population numbers were lowered during the LGM, especially toward its end, and then flourished in a short, but impressive peak in the latest Weichselian, just

  2. Assessing tectonic and climatic causal mechanisms in foreland-basin stratal architecture: insights from the Alborz Mountains, northern Iran

    NASA Astrophysics Data System (ADS)

    Ballato, Paolo; Strecker, Manfred

    2015-04-01

    The southern foreland basin of the Alborz Mountains of northern Iran is characterized by an approximately 7.3-km-thick sequence of Miocene sedimentary rocks, constituting three basin-wide coarsening-upward units spanning a period of 106 years. We assess available magnetostratigraphy, paleoclimatic reconstructions, stratal architecture, records of depositional environments, and sediment-provenance data to characterize the relationships between tectonically-generated accommodation space (A) and sediment supply (S). Our analysis allows an inversion of the stratigraphy for particular forcing mechanisms, documenting causal relationships, and providing a basis to decipher the relative contributions of tectonics and climate (inferred changes in precipitation) in controlling sediment supply to the foreland basin. Specifically, A/S > 1, typical of each basal unit (17.5-16.0, 13.8-13.1 and 10.3-9.6 Ma), is associated with sharp facies retrogradation and reflects substantial tectonic subsidence. Within these time intervals, arid climatic conditions, changes in sediment provenance, and accelerated exhumation in the orogen suggest that sediment supply was most likely driven by high uplift rates. Conversely, A/S < 1 (13.8 and 13.8-11 Ma, units 1, and 2) reflects facies progradation during a sharp decline in tectonic subsidence caused by localized intra-basinal uplift. During these time intervals, climate continued to be arid and exhumation active, suggesting that sediment supply was again controlled by tectonics. A/S < 1, at 11-10.3 Ma and 9-6-7.6 Ma (and possibly 6.2; top of units 2 and 3), is also associated with two episodes of extensive progradation, but during wetter phases. The first episode appears to have been linked to a pulse in sediment supply driven by an increase in precipitation. The second episode reflects a balance between a climatically-induced increase in sediment supply and a reduction of subsidence through the incorporation of the proximal foreland into the

  3. Climate Warming and Soil Carbon in Tropical Forests: Insights from an Elevation Gradient in the Peruvian Andes

    PubMed Central

    Nottingham, Andrew T.; Whitaker, Jeanette; Turner, Benjamin L.; Salinas, Norma; Zimmermann, Michael; Malhi, Yadvinder; Meir, Patrick

    2015-01-01

    The temperature sensitivity of soil organic matter (SOM) decomposition in tropical forests will influence future climate. Studies of a 3.5-kilometer elevation gradient in the Peruvian Andes, including short-term translocation experiments and the examination of the long-term adaptation of biota to local thermal and edaphic conditions, have revealed several factors that may regulate this sensitivity. Collectively this work suggests that, in the absence of a moisture constraint, the temperature sensitivity of decomposition is regulated by the chemical composition of plant debris (litter) and both the physical and chemical composition of preexisting SOM: higher temperature sensitivities are found in litter or SOM that is more chemically complex and in SOM that is less occluded within aggregates. In addition, the temperature sensitivity of SOM in tropical montane forests may be larger than previously recognized because of the presence of “cold-adapted” and nitrogen-limited microbial decomposers and the possible future alterations in plant and microbial communities associated with warming. Studies along elevation transects, such as those reviewed here, can reveal factors that will regulate the temperature sensitivity of SOM. They can also complement and guide in situ soil-warming experiments, which will be needed to understand how this vulnerability to temperature may be mediated by altered plant productivity under future climatic change. PMID:26955086

  4. How will coral reef fish communities respond to climate-driven disturbances? Insight from landscape-scale perturbations.

    PubMed

    Adam, Thomas C; Brooks, Andrew J; Holbrook, Sally J; Schmitt, Russell J; Washburn, Libe; Bernardi, Giacomo

    2014-09-01

    Global climate change is rapidly altering disturbance regimes in many ecosystems including coral reefs, yet the long-term impacts of these changes on ecosystem structure and function are difficult to predict. A major ecosystem service provided by coral reefs is the provisioning of physical habitat for other organisms, and consequently, many of the effects of climate change on coral reefs will be mediated by their impacts on habitat structure. Therefore, there is an urgent need to understand the independent and combined effects of coral mortality and loss of physical habitat on reef-associated biota. Here, we use a unique series of events affecting the coral reefs around the Pacific island of Moorea, French Polynesia to differentiate between the impacts of coral mortality and the degradation of physical habitat on the structure of reef fish communities. We found that, by removing large amounts of physical habitat, a tropical cyclone had larger impacts on reef fish communities than an outbreak of coral-eating sea stars that caused widespread coral mortality but left the physical structure intact. In addition, the impacts of declining structural complexity on reef fish assemblages accelerated as structure became increasingly rare. Structure provided by dead coral colonies can take up to decades to erode following coral mortality, and, consequently, our results suggest that predictions based on short-term studies are likely to grossly underestimate the long-term impacts of coral decline on reef fish communities. PMID:25070649

  5. Cool episode and platform demise in the Early Aptian: New insights on the links between climate and carbonate production

    NASA Astrophysics Data System (ADS)

    Bonin, Aurélie; Pucéat, Emmanuelle; Vennin, Emmanuelle; Mattioli, Emanuela; Aurell, Marcos; Joachimski, Michael; Barbarin, Nicolas; Laffont, Rémi

    2016-01-01

    The Early Aptian encountered several crises in neritic and pelagic carbonate production, major perturbations in the carbon cycle, and an oceanic anoxic event (OAE1a). Yet the causal links between these perturbations and climate changes remain poorly understood, partly because temperature records spanning the Early Aptian interval are still scant. We present new δ18O data from well-preserved bivalves from a carbonate platform of the Galve subbasin (Spain) that document a major cooling event postdating most of OAE1a. Our data show that cooling postdates the global platform demise and cannot have triggered this event that occurred during the warmest interval. The warmest temperatures coincide with the time equivalent of OAE1a and with platform biotic assemblages dominated by microbialites at Aliaga as well as on other Tethyan platforms. Coral-dominated assemblages then replace microbialites during the subsequent cooling. Nannoconids are absent during most of the time equivalent of the OAE1a, probably related to the well-known crisis affecting this group. Yet they present a transient recovery in the upper part of this interval with an increase in both size and abundance during the cool interval portion that postdates OAE1a. An evolution toward cooler and drier climatic conditions may have induced the regional change from microbial to coral assemblages as well as nannoconids size and abundance increase by limiting continent-derived input of nutrients.

  6. Response of lightning NOx emissions and ozone production to climate change: Insights from the Atmospheric Chemistry and Climate Model Intercomparison Project

    NASA Astrophysics Data System (ADS)

    Finney, D. L.; Doherty, R. M.; Wild, O.; Young, P. J.; Butler, A.

    2016-05-01

    Results from an ensemble of models are used to investigate the response of lightning nitrogen oxide emissions to climate change and the consequent impacts on ozone production. Most models generate lightning using a parameterization based on cloud top height. With this approach and a present-day global emission of 5 TgN, we estimate a linear response with respect to changes in global surface temperature of +0.44 ± 0.05 TgN K-1. However, two models using alternative approaches give +0.14 and -0.55 TgN K-1 suggesting that the simulated response is highly dependent on lightning parameterization. Lightning NOx is found to have an ozone production efficiency of 6.5 ± 4.7 times that of surface NOx sources. This wide range of efficiencies across models is partly due to the assumed vertical distribution of the lightning source and partly to the treatment of nonmethane volatile organic compound (NMVOC) chemistry. Careful consideration of the vertical distribution of emissions is needed, given its large influence on ozone production.

  7. Acid treatment biasing to C/N, δ13C and δ15N of organic matter: A Molecular insight

    NASA Astrophysics Data System (ADS)

    Brodie, C.; Casford, J.; Leng, M. J.; Zong, Y.

    2011-12-01

    It is known that acid treatment methods employed to remove inorganic carbon (IC) from sample material prior to analysis for C/N, δ13C and δ15N cause non-linear, unpredictable biasing to the organic matter (OM) fraction [1, 2, 3]. Consequently, measured C/N, δ13C and δ15N have an uncertainty much greater than instrument precision with biases for C/N reported in the range of 1 - 100, for δ13C in the range of 0.2 - 6.8 % and for δ15N in the range of 0.2 - 1.5 % [1, 2, 3], in both modern and palaeo environmental materials. Brodie et al [3] extended this investigation to a down-core lake sedimentary archive (Lake Tianyang, South China) and noted the potential for this biasing to preclude "common" interpretations of the data (e.g., C/N values as an OM provenance tool; δ13C as a proxy for changes in C3 and C4 vegetation). It is evident that the size of biasing between sample horizons varies considerably implying a differential relative reaction to acid treatment down-core (i.e., as the type, relative amount and physical state of organic components changes. We now investigate this biasing at the molecular level by employing 13C-NMR and GC-IRMS techniques on a suite of modern and palaeo environmental materials and on a lake sedimentary archive. This will provide an important insight into the effect of acid treatment on organic compounds (i.e. removal from the sample, breakdown of compounds and partial removal) and associated isotopic fractionation. From an improved understanding of the type of compounds most susceptible to alteration/removal during the acid treatment processes it will be possible to consider refinements to the acid pre-treatment process and provide information on the relative down-core changes in those compounds susceptible to change (which we may be able to glean environmental information from). [1] Brodie, C.R., Leng, M.J., Casford, J.S.L., Kendrick, C.K., Lloyd, J.M., Zong, Y.Q., and Bird, M.I. (2011) Evidence for bias in C and N concentrations

  8. The relationships between temperature changes and reproductive investment in a Mediterranean goby: Insights for the assessment of climate change effects

    NASA Astrophysics Data System (ADS)

    Zucchetta, M.; Cipolato, G.; Pranovi, F.; Antonetti, P.; Torricelli, P.; Franzoi, P.; Malavasi, S.

    2012-04-01

    The relationships between changes in water temperature and the timing and level of reproductive investment were investigated in an estuarine fish, inhabiting the Venice lagoon: the grass goby Zosterisessor ophiocephalus. A time series of the mean monthly values of gonado-somatic index was coupled with thermal profiles of lagoon water temperatures over 14 years, from 1997 to 2010. Results showed that the reproductive investment was positively affected by water temperature changes, both in terms of monthly thermal anomalies and cumulative degree days. A predictive model was also developed to assess the temporal shift of reproductive peaks as a response to inter-annual thermal fluctuations. This model allowed the detection of deviations from the median level, indicating that during warmer years, the reproductive peak tended to occur earlier than during colder years. The model is therefore proposed as a tool to predict anticipated consequences of climate change on fish phenology in transitional waters, regarding recurrent biological phenomena, such as reproduction and recruitment.

  9. Centennial-scale vegetation and climate changes in the Middle Atlas, Morocco: new insights from multi-proxy investigations at Lake Sidi Ali

    NASA Astrophysics Data System (ADS)

    Fletcher, William; Campbell, Jennifer; Joannin, Sebastien; Mischke, Steffen; Zielhofer, Christoph; de Batist, Marc; Mikdad, Abdes

    2016-04-01

    The karstic lakes of the Middle Atlas, Morocco, represent a valuable archive of environmental and climatic change for Northwest Africa. Here we present the results of centennial-scale palynological and charcoal analyses as part of a multiproxy palaeolimnological study of sediment cores from Lake Sidi Ali in the Middle Atlas, Morocco (33° 03 N, 05° 00 W; 2,080 m a.s.l.). Supported by absolute dating including 23 more than twenty AMS 14C dates on pollen concentrates, the record covers the entire Holocene and offers insights into vegetation and climate change at a regionally unprecedented centennial-scale. Pollen assemblages are dominated by steppic herbs, evergreen oaks (Quercus), junipers (Cupressaceae) and Atlantic cedar (Cedrus atlantica). A long-term evolution of the montane vegetation is recorded, reflecting progressive changes in the dominant arboreal taxa and leading to the full establishment of the emblematic cedar forests of the area during the mid-Holocene by 6000 cal BP. Orbital-scale changes in seasonality and growing season moisture availability linked to declining summer insolation are implicated, with a transition from (a) warm, dry summers associated with summer drought tolerant taxa especially evergreen Quercus, high algal productivity in the lake, and high background levels of microcharcoal reflecting distant fire activity during the early Holocene, to (b) cool, relatively humid summers with dominance of montane conifers, declining algal productivity in the lake, and episodic local fire activity during the mid- to late Holocene. Superimposed on the long-term environmental changes are recurrent centennial-scale fluctuations in vegetation composition, reflecting competitive dynamics between the major taxa, initially between steppic and arboreal elements, and later between the major tree taxa. Parallels with hydrological proxies including stable O and C isotopes suggest common responses to climatic drivers (fluctuations in moisture sources and

  10. Aeolian beach ridges and their significance for climate and sea level: Concept and insight from the Levant coast (East Mediterranean)

    NASA Astrophysics Data System (ADS)

    Mauz, B.; Hijma, M. P.; Amorosi, A.; Porat, N.; Galili, E.; Bloemendal, J.

    2013-06-01

    Relict beach ridges of aeolian origin and associated soils are often used for inferring relative sea level and climate with contrasting results. Most studies link the aeolian coastal deposits to regressive phases, some to high sea-level stands, and a few to intermediate relative sea-level positions. We interpret the apparent contradictions as indicating the lack of an over-arching concept and the inconsistent usage of sea level-related terms. In this paper we present an integrated morpho-sedimentological concept for a microtidal, mid-latitudinal coast and review existing data from the Levant (East Mediterranean) coast to evaluate the concept and to eliminate nomenclatural confusion. A coastal depositional environment in a semi-arid environment consists of shallow-marine, aeolian and alluvial facies which together form an aeolian beach-ridge complex as a package of strata which respond simultaneously to sea-level change. A transgressive complex forms through reworking or overstepping of the coastal foredune and a regressive complex forms by downstepping. Under transgression the aeolian beach ridge represents the highstand deposit and its adjacent shallow marine sediment is the transgressive deposit. Under regression the complex represents the falling stage and the associated downdip surface marks the lowstand. On the Levant coast we find chronologically well-constrained, offlapping aeolian beach ridges as parts of six downstepping beach ridge complexes formed between ~ 200 ka and 10 ka. The complexes represent the falling stage systems tract (FSST) of a short-lived (5th-order) depositional sequence when the shoreline shifted from a position close to the modern coastline to the shelf or below the shelf edge. Three of these FSSTs and their up dip and down dip super bounding surface together form the 4th order (~ 100 ka) sequence of the last interglacial/glacial cycle. The absence of transgressive, highstand and lowstand systems tract is explained by the poor

  11. Sedimentary provenance insights to East Antarctic ice sheet oscillations and growth during the mid-Miocene Climate Transition

    NASA Astrophysics Data System (ADS)

    Pierce, E. L.; van de Flierdt, T.; Williams, T.; Hemming, S. R.; Cook, C.; Passchier, S.

    2012-12-01

    A major step in the evolution of the East Antarctic ice sheet (EAIS) occurred ~ 14 Ma during the Mid-Miocene Climate Transition (MMCT), a period with a global climatic shift that had a profound effect on many components of the Earth system, including terrestrial biota, ocean circulation, both ocean and terrestrial temperatures, sea-level, and ice volume. Of particular interest during this transition is the variability in the extent of the EAIS at its marine-grounded margins. Despite inferences on the total amount of ice growth on Antarctica as a whole, little is known of the temporal and spatial evolution of the East Antarctic ice expansion at this time. Here we apply isotopic provenance studies in order to determine the source of glacially derived sediments deposited ca. 14.7 to 12.6 Ma off the coast of East Antarctica at IODP Site U1356. A total of 672 hornblendes grains from 40 samples were analyzed for their 40Ar/39Ar ages, showing a dominant and unvarying age population of 1400 -1550 Ma for all of the samples. Neodymium (Nd) isotope measurements on the terrigenous <63 μm sediment fraction in contrast show a large range of 8 epsilon units (-8.4 to -16.4). We interpret our results to indicate a greatly retreated EAIS in the Wilkes subglacial basin prior to and during the MMCT. Observed Ar ages are best explained by an ice sheet that sat along the extension of the Mertz Shear Zone, at the western edge of the Wilkes Basin. Three distinct excursions to more radiogenic Nd isotope values require significant input from a more radiogenic source, such as the Ferrar Group, which consists of the Ferrar Doloerite, Kirkpatrick Basalt and Dufek Gabbro, and has epsilon Nd values of approximately -5. The Ferrar Group outcrops extensively along the spine of the Transantarctic Mountains, and geophysical surveys (Ferraccioli et al., 2009, Tectonophysics) indicate that Ferrar dolerite intrudes Beacon Sandstone in areas within the Wilkes subglacial basin. Given the decoupling in

  12. Insights into Ocean Acidification During the Middle Eocene Climatic Optimum from Boron Isotopes at Southern Ocean Site 738

    NASA Astrophysics Data System (ADS)

    Moebius, I.; Hoenisch, B.; Friedrich, O.

    2015-12-01

    The Middle Eocene Climatic Optimum (MECO) is a ~650-kyr interval of global warming, with a brief ~50 ky long peak warming interval, and an abrupt termination. Deep sea and surface ocean temperature evolution across this interval are fairly well constrained, but thus far we have little understanding of the mechanisms responsible for the gradual warming and rapid recovery. Carbonate mass accumulation rates suggest a shoaling of the carbonate compensation depth, and studies on alkenones indicate increasing atmospheric CO2 levels during the MECO. This suggests an increase in surface ocean CO2, and consequently ocean acidification. However, the severity and timing of the proposed ocean acidification with respect to the onset, peak warming and the termination are currently not well resolved. The boron isotopic composition (δ11B) recorded in planktic foraminifer shells offers an opportunity to infer oceanic pH across this interval. We are working on a boron isotope reconstruction from Southern Ocean IODP site 738 and South Atlantic IODP site 1263, covering 42.0 to 38.5 Ma. These sites are characterized by good carbonate preservation and well-defined age models have been established. Additionally, ecology, nutrient content and bottom-water oxygenation have been shown to change significantly across the event towards a more eutrophic, periodically oxygen-depleted environment supporting different biological communities. We selected the planktic foraminifera species Acarinina spinuloinflata for this study because it is symbiont-bearing, suggesting a near-surface habitat and little vertical migration in the water column, and because of its abundance in the samples. δ11B data will be translated to surface ocean pH and atmospheric pCO2 will be approximated to refine knowledge about the carbon cycle during this time. Parallel analysis of two core sites will help to evaluate the tenacity of the data.

  13. Storm surges and climate change implications for tidal marshes: Insight from the San Francisco Bay Estuary, California, USA

    USGS Publications Warehouse

    Thorne, Karen M.; Buffington, Kevin J.; Swanson, Kathleen; Takekawa, John Y.

    2013-01-01

    Tidal marshes are dynamic ecosystems that are influenced by oceanic and freshwater processes and daily changes in sea level. Projected sea-level rise and changes in storm frequency and intensity will affect tidal marshes by altering suspended sediment supply, plant and wildlife communities, and the inundation duration and depth of the marsh platform. The objective of this research was to evaluate how regional weather conditions resulting in low-pressure storms changed tidal conditions locally within three tidal marshes. We hypothesized that regional storms will increase sea level heights locally, resulting in increased inundation of the tidal marsh platform and plant communities. Using site-level measurements of elevation, plant communities, and water levels, we present results from two storm events in 2010 and 2011 from the San Francisco Bay Estuary (SFBE), California, USA. The January 2010 storm had the lowest recorded sea level pressure in the last 30 years for this region. During the storm episodes, the duration of tidal marsh inundation was 1.8 and 3.1 times greater than average for that time of year in 2010 and 2011, respectively. At peak storm surges, over 65% in 2010 and 93% in 2011 of the plant community was under water. We also discuss the implications of these types of storms and projected sea-level rise on the structure and function of tidal marshes and how that may affect the hydrogeomorphic processes and marsh biotic communities. This type of information is useful to managers for incorporating local climate change into developing their monitoring, management, and adaptation strategies.

  14. How fast is Arctic climate really changing? An insight from recent past, present day and near future coupled model simulations

    NASA Astrophysics Data System (ADS)

    Koenigk, Torben; Brodeau, Laurent

    2016-04-01

    Three quasi-equilibrium simulations using constant greenhouse gas forcing corresponding to years 2000, 2015 and 2030 have been performed with the global coupled model EC-Earth in order to analyze recent past and possible near future changes in the Arctic climate. The model simulations indicate an accelerated warming and ice extent reduction in the Arctic in near future conditions compared to the recent past. Both Arctic warming and sea ice reduction are closely linked to the increase of ocean heat transport into the Arctic, particularly through the Barents Sea Opening. Decadal variations of Arctic sea ice extent and ice volume are of the same order of magnitude as the observed ice extent reductions in the last 30 years and are dominated by the variability of the ocean heat transports through the Barents Sea Opening and the Bering Strait. Despite a general warming of mid and high northern latitudes, a substantial cooling is found in the subpolar gyre of the North Atlantic in the near future simulation. This cooling is related to a strong reduction in the AMOC, which is mainly caused by reduced deep water formation in the Labrador Sea. The observed trend towards a more negative phase of the North Atlantic Oscillation (NAO) and the observed linkage between autumn Arctic ice variations and NAO are reproduced in our model simulations for selected 30-year periods but are not robust over longer time periods. This indicates that the observed linkages between ice and NAO might not be robust in reality either, and that the observational time period is still too short to reliably separate the trend from the natural variability.

  15. Insights into mechanism of pyrido[2,3-d]pyrimidines as DYRK1A inhibitors based on molecular dynamic simulations.

    PubMed

    Li, Jiao Jiao; Tian, Yue Li; Zhai, Hong Lin; Lv, Min; Zhang, Xiao Yun

    2016-08-01

    DYRK1A is characterized by the early development and regulation of neuronal proliferation, and its over expression gives rise to neurological abnormalities. As the promising DYRK1A inhibitors, the binding mechanism between DYRK1A and pyrido[2,3-d]pyrimidines derivatives at molecular level are still veiled. In this article, it was achieved to get the structural insights into pyrido[2,3-d]pyrimidines derivatives as DYRK1A inhibitors by means of comprehensive computational approaches involving molecular docking, molecular dynamics simulation, free energy calculation, and energy decomposition analysis. The calculated energy values were highly consistent with the experimental activities. Based on the individual energy terms analysis, the van der Waals interaction was the major leading force in the DYRK1A-ligand interaction. Lys188 was the important residue that formed the hydrogen bond, which improved the inhibitory activity. Furthermore, four novel inhibitors with higher predicted activity were designed based on the obtained findings and confirmed by molecular simulations. Our study is expected to provide significant drug design strategy for the development of more promising DYRK1A inhibitors. Proteins 2016; 84:1108-1123. © 2016 Wiley Periodicals, Inc. PMID:27119584

  16. 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. PMID:25077523

  17. VIP and PACAP. Recent insights into their functions/roles in physiology and disease from molecular and genetic studies

    PubMed Central

    Moody, Terry W.; Ito, Tetsuhide; Osefo, Nuramy; Jensen, Robert T.

    2010-01-01

    Purpose of review VIP and PACAP as well as the three classes of G-protein-coupled receptors mediating their effects, are widely distributed in the CNS and peripheral tissues. These peptides are reported to have many effects in different tissues, which are physiological or pharmacological, and which receptor mediates which effect, has been difficult to determine, primarily due to lack of potent, stable, selective agonists/antagonists. Recently the use of animals with targeted knockout (KO) of the peptide or a specific receptor has provided important insights into the role of their role in normal physiology and disease states. Recent findings During the review period, considerable progress and insights has occurred in the understanding of the role of VIP/PACAP as well as their receptors in a number of different disorders/areas. Particularly, insights into their roles in energy metabolism, glucose regulation, various gastrointestinal processes including GI inflammatory conditions and motility and their role in the CNS as well as CNS diseases has greatly expanded. Summary PACAP/VIP as well as there three classes of receptors are important in many physiological/pathophysiological processes, some of which are identified in these studies using knockout animals. These studies may lead to new novel treatment approaches. Particularly important are their roles in glucose metabolism and on islets leading to possible novel approaches in diabetes; their novel anti-inflammatory, cytoprotective effects, their CNS neuroprotective effects, and their possible roles in diseases such as schizophrenia and chronic depression. PMID:21157320

  18. 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 Central

    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

  19. Symbiosis between hydra and chlorella: molecular phylogenetic analysis and experimental study provide insight into its origin and evolution.

    PubMed

    Kawaida, Hitomi; Ohba, Kohki; Koutake, Yuhki; Shimizu, Hiroshi; Tachida, Hidenori; Kobayakawa, Yoshitaka

    2013-03-01

    Although many physiological studies have been reported on the symbiosis between hydra and green algae, very little information from a molecular phylogenetic aspect of symbiosis is available. In order to understand the origin and evolution of symbiosis between the two organisms, we compared the phylogenetic relationships among symbiotic green algae with the phylogenetic relationships among host hydra strains. To do so, we reconstructed molecular phylogenetic trees of several strains of symbiotic chlorella harbored in the endodermal epithelial cells of viridissima group hydra strains and investigated their congruence with the molecular phylogenetic trees of the host hydra strains. To examine the species specificity between the host and the symbiont with respect to the genetic distance, we also tried to introduce chlorella strains into two aposymbiotic strains of viridissima group hydra in which symbiotic chlorella had been eliminated in advance. We discussed the origin and history of symbiosis between hydra and green algae based on the analysis. PMID:23219706

  20. TRPV1 function is modulated by Cdk5-mediated phosphorylation: insights into the molecular mechanism of nociception

    PubMed Central

    Jendryke, Thomas; Prochazkova, Michaela; Hall, Bradford E.; Nordmann, Grégory C.; Schladt, Moritz; Milenkovic, Vladimir M.; Kulkarni, Ashok B.; Wetzel, Christian H.

    2016-01-01

    TRPV1 is a polymodally activated cation channel acting as key receptor in nociceptive neurons. Its function is strongly affected by kinase-mediated phosphorylation leading to hyperalgesia and allodynia. We present behavioral and molecular data indicating that TRPV1 is strongly modulated by Cdk5-mediated phosphorylation at position threonine-407(mouse)/T406(rat). Increasing or decreasing Cdk5 activity in genetically engineered mice has severe consequences on TRPV1-mediated pain perception leading to altered capsaicin consumption and sensitivity to heat. To understand the molecular and structural/functional consequences of TRPV1 phosphorylation, we generated various rTRPV1T406 receptor variants to mimic phosphorylated or dephosphorylated receptor protein. We performed detailed functional characterization by means of electrophysiological whole-cell and single-channel recordings as well as Ca2+-imaging and challenged recombinant rTRPV1 receptors with capsaicin, low pH, or heat. We found that position T406 is critical for the function of TRPV1 by modulating ligand-sensitivity, activation, and desensitization kinetics as well as voltage-dependence. Based on high resolution structures of TRPV1, we discuss T406 being involved in the molecular transition pathway, its phosphorylation leading to a conformational change and influencing the gating of the receptor. Cdk5-mediated phosphorylation of T406 can be regarded as an important molecular switch modulating TRPV1-related behavior and pain sensitivity. PMID:26902776

  1. TRPV1 function is modulated by Cdk5-mediated phosphorylation: insights into the molecular mechanism of nociception.

    PubMed

    Jendryke, Thomas; Prochazkova, Michaela; Hall, Bradford E; Nordmann, Grégory C; Schladt, Moritz; Milenkovic, Vladimir M; Kulkarni, Ashok B; Wetzel, Christian H

    2016-01-01

    TRPV1 is a polymodally activated cation channel acting as key receptor in nociceptive neurons. Its function is strongly affected by kinase-mediated phosphorylation leading to hyperalgesia and allodynia. We present behavioral and molecular data indicating that TRPV1 is strongly modulated by Cdk5-mediated phosphorylation at position threonine-407(mouse)/T406(rat). Increasing or decreasing Cdk5 activity in genetically engineered mice has severe consequences on TRPV1-mediated pain perception leading to altered capsaicin consumption and sensitivity to heat. To understand the molecular and structural/functional consequences of TRPV1 phosphorylation, we generated various rTRPV1T406 receptor variants to mimic phosphorylated or dephosphorylated receptor protein. We performed detailed functional characterization by means of electrophysiological whole-cell and single-channel recordings as well as Ca(2+)-imaging and challenged recombinant rTRPV1 receptors with capsaicin, low pH, or heat. We found that position T406 is critical for the function of TRPV1 by modulating ligand-sensitivity, activation, and desensitization kinetics as well as voltage-dependence. Based on high resolution structures of TRPV1, we discuss T406 being involved in the molecular transition pathway, its phosphorylation leading to a conformational change and influencing the gating of the receptor. Cdk5-mediated phosphorylation of T406 can be regarded as an important molecular switch modulating TRPV1-related behavior and pain sensitivity. PMID:26902776

  2. AC electrical characterisation and insight to charge transfer mechanisms in DNA molecular wires through temperature and UV effects.

    PubMed

    Kassegne, Sam; Wibowo, Denni; Chi, James; Ramesh, Varsha; Narenji, Alaleh; Khosla, Ajit; Mokili, John

    2015-06-01

    In this study, AC characterisation of DNA molecular wires, effects of frequency, temperature and UV irradiation on their conductivity is presented. λ-DNA molecular wires suspended between high aspect-ratio electrodes exhibit highly frequency-dependent conductivity that approaches metal-like behaviour at high frequencies (∼MHz). Detailed temperature dependence experiments were performed that traced the impedance response of λ-DNA until its denaturation. UV irradiation experiments where conductivity was lost at higher and longer UV exposures helped to establish that it is indeed λ-DNA molecular wires that generate conductivity. The subsequent renaturation of λ-DNA resulted in the recovery of current conduction, providing yet another proof of the conducting DNA molecular wire bridge. The temperature results also revealed hysteretic and bi-modal impedance responses that could make DNA a candidate for nanoelectronics components like thermal transistors and switches. Further, these experiments shed light on the charge transfer mechanism in DNA. At higher temperatures, the expected increase in thermal-induced charge hopping may account for the decrease in impedance supporting the 'charge hopping mechanism' theory. UV light, on the other hand, causes damage to GC base-pairs and phosphate groups reducing the path available both for hopping and short-range tunneling mechanisms, and hence increasing impedance--this again supporting both the 'charge hopping' and 'tunneling' mechanism theories. PMID:26023159

  3. Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein

    PubMed Central

    Schumacher, Maria A.; Lee, Jeehyun; Zeng, Wenjie

    2016-01-01

    During Bacillus subtilis sporulation, segregating sister chromosomes are anchored to cell poles and the chromosome is remodeled into an elongated structure called the axial filament. Data indicate that a developmentally regulated protein called RacA is involved in these functions. To gain insight into how RacA performs these diverse processes we performed a battery of structural and biochemical analyses. These studies show that RacA contains an N-terminal winged-helix-turn-helix module connected by a disordered region to a predicted coiled-coil domain. Structures capture RacA binding the DNA using distinct protein–protein interfaces and employing adjustable DNA docking modes. This unique DNA binding mechanism indicates how RacA can both specifically recognize its GC-rich centromere and also non-specifically bind the DNA. Adjacent RacA molecules within the protein–DNA structure interact leading to DNA compaction, suggesting a mechanism for axial filament formation. We also show that the RacA C-domain coiled coil directly contacts the coiled coil region of the polar protein DivIVA, which anchors RacA and hence the chromosome to the pole. Thus, our combined data reveal unique DNA binding properties by RacA and provide insight into the DNA remodeling and polar anchorage functions of the protein. PMID:27085804

  4. Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein.

    PubMed

    Schumacher, Maria A; Lee, Jeehyun; Zeng, Wenjie

    2016-06-20

    During Bacillus subtilis sporulation, segregating sister chromosomes are anchored to cell poles and the chromosome is remodeled into an elongated structure called the axial filament. Data indicate that a developmentally regulated protein called RacA is involved in these functions. To gain insight into how RacA performs these diverse processes we performed a battery of structural and biochemical analyses. These studies show that RacA contains an N-terminal winged-helix-turn-helix module connected by a disordered region to a predicted coiled-coil domain. Structures capture RacA binding the DNA using distinct protein-protein interfaces and employing adjustable DNA docking modes. This unique DNA binding mechanism indicates how RacA can both specifically recognize its GC-rich centromere and also non-specifically bind the DNA. Adjacent RacA molecules within the protein-DNA structure interact leading to DNA compaction, suggesting a mechanism for axial filament formation. We also show that the RacA C-domain coiled coil directly contacts the coiled coil region of the polar protein DivIVA, which anchors RacA and hence the chromosome to the pole. Thus, our combined data reveal unique DNA binding properties by RacA and provide insight into the DNA remodeling and polar anchorage functions of the protein. PMID:27085804

  5. From climate change to molecular response: redox proteomics of ozone-induced responses in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ozone (O3) causes significant agricultural losses with soybean being highly sensitive to this oxidant. Here we assess the effect of elevated seasonal O3 exposure on the total and redox proteomes of soybean. To understand the molecular responses to O3 exposure, soybean grown at the Soybean Free Air C...

  6. High molecular weight SOA formation during limonene ozonolysis: insights from ultrahigh-resolution FT-ICR mass spectrometry characterization

    NASA Astrophysics Data System (ADS)

    Kundu, S.; Fisseha, R.; Putman, A. L.; Rahn, T. A.; Mazzoleni, L. R.

    2012-06-01

    The detailed molecular composition of laboratory generated limonene ozonolysis secondary organic aerosol (SOA) was studied using ultrahigh-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Approximately 1200 molecular formulas were identified in the SOA over the mass range of 140 to 850 Da. Four characteristic groups of high relative abundance species were observed; they indicate an array of accretion products that retain a large fraction of the limonene skeleton. The identified molecular formulas of each of the groups are related to one another by CH2, O and CH2O homologous series. The CH2 and O homologous series of the low molecular weight (MW) SOA (m/z < 300) are explained with a combination of functionalization and fragmentation of radical intermediates and reactive uptake of gas-phase carbonyls. They include isomerization and elimination reactions of Criegee radicals, reactions between alkyl peroxy radicals, and scission of alkoxy radicals resulting from the Criegee radicals. The presence of compounds with 10-15 carbon atoms in the first group (e.g. C11H18O6) provides evidence for SOA formation by the reactive uptake of gas-phase carbonyls during limonene ozonolysis. The high MW compounds (m/z > 300) were found to constitute a significant number fraction of the identified SOA components. The formation of high MW compounds was evaluated by molecular formula trends, fragmentation analysis of select high MW compounds and a comprehensive reaction matrix including the identified low MW SOA, hydroperoxides and Criegee radicals as building blocks. Although the formation of high MW SOA may occur via a variety of radical and non-radical reaction channels, the combined approach indicates a greater importance of the non-condensation reactions over aldol and ester condensation reaction channels. Among these hemi-acetal reactions appear to be most dominant followed by hydroperoxide and Criegee reaction channels.

  7. 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.

    2016-01-01

    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.

  8. Coexistence of spinodal instability and thermal nucleation in thin-film rupture:Insights from molecular levels

    SciTech Connect

    Nguyen, Trung D; Fuentes-Cabrera, Miguel A; Fowlkes, Jason Davidson; Rack, Philip D

    2014-01-01

    Despite extensive investigation using hydrodynamic models and experiments over the past decades, there remain open questions regarding the origin of the initial rupture of thin liquid films. One of the reasons that makes it difficult to identify the rupture origin is the coexistence of two dewettingmechanisms, namely, thermal nucleation and spinodal instability, as observed in many experimental studies. Using a coarse-grained model and large-scale molecular dynamics simulations, we are able to characterize the very early stage of dewetting in nanometer-thick liquid-metal films wetting a solid substrate. We observe the features characteristic of both spinodal instability and thermal nucleation in the spontaneously dewetting films and show that these two macroscopic mechanisms share a common origin at molecular levels.

  9. In Silico Identification of Novel APRIL Peptide Antagonists and Binding Insights by Molecular Modeling and Immunosorbent Assays.

    PubMed

    Silva, Joao H M da; Calmon-Hamaty, Flavia; Savino, Wilson; Hahne, Michael; Caffarena, Ernesto R

    2015-01-01

    The "A proliferation inducing ligand" protein (APRIL) is a cytokine over-expressed in many transformed and tumoral cells acting onto two distinct receptors of the Tumoral Necrosis Factor B cell maturation antigen (BCMA) and the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). We herein describe, through a detailed computational approach, the molecular interactions between TACI and its ligands APRIL and another structurally similar protein called B-cell activating factor (BAFF) by means of molecular dynamics. Dynamical analysis suggests R84 and D85 residues from TACI as possible mutation candidates, yielding increased affinity between TACI and APRIL. The association of computational simulations, site directed mutagenesis and peptide design could be a powerful tool, driving to better in vitro experiments. Our results contribute to the elucidation of APRIL signaling and help clarify the effects of blocking interaction between APRIL and its receptors through the use of particular peptides. PMID:25731591

  10. Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints

    PubMed Central

    Hornak, Viktor; Ahuja, Shivani; Eilers, Markus; Goncalves, Joseph A.; Sheves, Mordechai; Reeves, Philip J.; Smith, Steven O.

    2009-01-01

    Structural restraints provided by solid-state NMR measurements of the metarhodopsin II intermediate are combined with molecular dynamics simulations to help visualize the structural changes in the light activation of rhodopsin. Since the time scale for the formation of the metarhodopsin II intermediate (> 1 ms) is beyond that readily accessible by molecular dynamics, we use NMR distance restraints derived from 13C dipolar recoupling measurements to guide the simulations. The simulations yield a working model for how photoisomerization of the 11-cis retinylidene chromophore bound within the interior of rhodopsin is coupled to transmembrane helix motion and receptor activation. The mechanism of activation that emerges is that multiple switches on the extracellular (or intradiscal) side of rhodopsin trigger structural changes that converge to disrupt the ionic lock between helices H3 and H6 on the intracellular side of the receptor. PMID:20004206

  11. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships.

    PubMed

    Gupta, Radhey S; Bhandari, Vaibhav; Naushad, Hafiz Sohail

    2012-01-01

    The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, along with the Lentisphaerae, Poribacteria, and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, six conserved signature indels (CSIs) in the proteins Cyt c oxidase, UvrD helicase, urease, and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase, and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia, and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae, and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms. PMID:23060863

  12. Ion Pairing and Counterion Condensation in Aqueous Electrolyte and Poly-electrolyte Solutions: Insights from Molecular Simulation

    SciTech Connect

    Chialvo, Ariel A; Simonson, J Michael {Mike}

    2007-01-01

    We discuss the molecular-based study of ion-pair formation in LiCl aqueous solutions and its implications on the interpretation of the raw data from neutron diffraction with isotopic substitution experiments, the counterion condensation in aqueous polyelectrolyte solutions comprising short-chain lithium poly-styrene sulfonate (Li{sup +}-PSS{sup -}), as well as their interplay leading to the occurrence of 'like-charge' attractive interactions in the presence of salts of polyvalent counterions.

  13. Molecular modeling, mutational analysis and conformational switching in IL27: An in silico structural insight towards AIDS research.

    PubMed

    Banerjee, Arundhati; Ray, Sujay

    2016-01-15

    The advancement in proteomics and bioinformatics provokes to discern the molecular-level probe for HIV inhibitor; human interleukin-27 (IL27). Documentation documents that tyrosine residues in IL27 play a pivotal role for interacting with HIV, causing apoptosis of the HIV+ cells. Primarily, 3D structure of human wild-type (WT) IL27 was built through manifold molecular modeling techniques after the satisfaction of stereo-chemical properties. Its essential tyrosine residues were identified. Two mutant models for IL27 were prepared following the similar protocol by first substituting the tyrosine residues with glycine (MT_G) and then with alanine (MT_A) in the WT protein. Molecular dynamics (MD) simulation was performed to obtain a stable conformation. Conformational alterations in WT, MT_G and MT_A (before and after MD simulation) disclosed that MT_A was the steadiest one with the best secondary structure conformation supported by statistical significances. Though huge RMSD variations were observed on superimposing the MT structures on WT individually, the MTs were examined to share similar SCOP/CATH fold with TM-score=0.8, indicating that they retained their functionality even after mutation. Electrostatic surface potential again unveiled MT_A to be the most stable one. MT_A was thereby revealed to be the potent peptide inhibitor for HIV. This probe presents a pathway to investigate and compare the bio-molecular interaction of WT IL27 and MT_A IL27 (strongest model) with HIV in the future. This is the first report regarding the structural biology of IL27 accompanied by alteration at its genetic level and delving into the unknown residue-level and functional biochemistry for bringing about an annihilation towards AIDS. PMID:26432006

  14. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships

    PubMed Central

    Gupta, Radhey S.; Bhandari, Vaibhav; Naushad, Hafiz Sohail

    2012-01-01

    The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, along with the Lentisphaerae, Poribacteria, and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, six conserved signature indels (CSIs) in the proteins Cyt c oxidase, UvrD helicase, urease, and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase, and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia, and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae, and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms. PMID:23060863

  15. Neuroendocrine Tumors of the Prostate: Emerging Insights from Molecular Data and Updates to the 2016 World Health Organization Classification.