Heinz-Bernhard Kraatz and Sanela Martic
This books provides an introduction to current knowledge and practice of kinomics that covers a broad spectrum from human health to agriculture and drug discovery. This book is intended as a toolbox and reference for kinase researchers that provides information both to the novice and the established researchers.
NMR Spectroscopy: A Versatile Tool for Environmental Research
The challenges faced by environmental scientists today are vast, complex, and multi-faceted. For instance, predicting the fate of an environmental pollutant or understanding ecosystem responses to climate change, necessitate a firm understanding of molecular structure and dynamics of environmental media as well as the components that exist and interact within this media. Furthermore, linking information obtained at the molecular-scale to ecosystem-level processes is a major pursuit of modern environmental research. As such, NMR spectroscopy and its scalability from the molecular-scale to the macroscopic-scale, is facilitating rapid growth in environmental science. In addition, the versatility of NMR spectroscopy has resulted in the development and implementation of different types of NMR techniques to examine the structure of various types of environmental samples, living and non-living, as well as the study of critical environmental processes.
Date: July 2014
Nanobiosensors and Nanobioanalyses
Mun'delanji C. Vestergaard, Kagan Kerman, I-Ming Hsing, Eiichi Tamiya (Eds.)
Nanomaterials have become an essential part of biosensors and bioanalyses in the detection and monitoring of medical, pharmaceutical, and environmental conditions, from cancer to chemical warfare agents. This book, with its distinguished editors and international team of expert contributors, will be an essential guide for all those involved in the research, design, development, and application of nanomaterials in biosensors and bioanalyses.
Date: Jan 14th, 2015
Sean C. Thomas, Adam R. Martin and Erin E. Mycroft
- Tropical tree species adapted to high wind environments might be expected to differ systematically in terms of stem allometry and life-history patterns, as compared with species found in less windy forests. We quantified height-diameter (H-D) allometries and relative size at onset of maturity (RSOM) for rain forest tree and tree fern species native to Dominica, West Indies, an island that experiences some of the highest average wind speeds pantropically.
- H-D allometries for 17 Dominican angiosperm tree species were strongly concave on a log–log scale with asymptotic heights ranging from 9 to 32 m among species, averaging 25 m for canopy trees. H-D allometries for species-pooled data deviated strongly from recorded patterns for other tropical forest trees: asymptotic heights for trees in Dominica were 30–116% lower than those recorded for continental rain forest trees in Australia, South America, Africa and South-East Asia. In a subset of canopy trees sampled in steep, sheltered valleys, heights were 12–26% larger at a given diameter and approached those observed in other tropical regions, suggesting large phenotypic responses of H-D allometries to wind conditions.
- RSOM (quantified as the ratio of height at onset of reproduction to asymptotic maximum height) for Dominican angiosperm species was highly variable, ranging from 0.23 to 0.89 (mean 0.54), similar to patterns observed in Malaysia and Panama; very low RSOM values were estimated for two tree fern species. Pooling data from Dominica with published values from other tropical forests, we observed a significant negative correlation between RSOM and wood density.
- Synthesis. Our data suggest that wind regimes are a critical determinant of height-diameter (H-D) allometries of tropical trees at both the local and global scale. Although we found no evidence for a systematic differences in reproductive onset related to wind regime, RSOM was negatively correlated with species’ wood density, suggesting that more shade-tolerant tree species show a longer period of gradually increasing reproductive allocation through ontogeny.
Clickable 5′-γ-Ferrocenyl Adenosine Triphosphate Bioconjugates in Kinase-Catalyzed Phosphorylations
Dr. Nan Wang, Dr. Zhe She, Yen-Chun Lin, Prof. Sanela Martić, Dr. David J. Mann and Prof. Heinz-Bernhard Kraatz
A clickable site has been introduced into a tri-functional 5′-γ-ferrocenyl (Fc) adenosine triphosphate (Fc-ATP) derivative, which has been used as an effective co-substrate for kinase-catalyzed phosphorylation. The compound was also applied to the Fc-Ab1/Ab2 system, providing both electrochemical results and immunodetection. The clickable reaction site makes direct modification possible, which greatly expands its application.
LED-based interferometric reflectance imaging sensor for the detection of amyloid-β aggregation
Xin R. Cheng, George G. Daaboul, M. Selim Ünlü and Kagan Kerman
Self-aggregation of amyloid-β (Aβ) plays an important role in the pathogenesis of Alzheimer's disease (AD). Small molecule inhibitors of Aβ fibril formation reduce the Aβ-mediated neurotocixity. In this report, the interaction of amyloid-β (Aβ) with well-described modulators, (−)epigallocatechin-3-gallate (EGCG) and Zn(II), was detected using a LED-based interferometric reflectance imaging sensor (LED-IRIS) in a high-throughput and real-time format. Nucleation-based fibril growth strategy was employed, as the “seeds” of Aβ were prepared in the presence of EGCG and Zn(II). The seeds were then covalently immobilized on the chip surface. Using microfluidics, Aβ oligomers were exposed onto the seeds resulting in the elongation of fibrils, which was detected as the increase in the spot height. Monitoring the changes on the chip surface enabled to detect the efficacy of modulators to inhibit or facilitate the growth of Aβ fibrils. The proof-of-concept study reported here introduces a novel platform to facilitate the screening of small molecules towards the discovery of promising AD therapeutics.
Can We Model Snow Photochemistry? Problems with the Current Approaches
Florent Domine, Josué Bock, Didier Voisin, James Donaldson
Snow and the impurities contained therein form a complex multiphase photochemical reactor, releasing reactive molecules to the atmosphere and dramatically impacting the composition and reactivity of the lower polar troposphere. Challenges in our understanding and modeling abilities of this complex natural system are discussed.
Biological Activity of sym-Triazines with Acetylcholine-like Substitutions as Multitarget Modulators of Alzheimer's Disease
Veloso AJ, Chow AM, Dhar D, Tang DW, Ganesh HV, Mikhaylichenko S, Brown IR, Kerman K
Two novel sym-triazine derivatives were demonstrated as promising candidates against Alzheimer’s disease, supported by their capabilities in modulation of amyloid-β (Aβ1-42) fibril formation and inhibition of acetylcholinesterase activity. The cover figure shows that these sym-triazine derivatives were well tolerated and have potential beneficial effects on human neurons, promoting differentiation and extension of neurite processes, as highlighted with the cytoskeleton marker protein α-tubulin (green), and upregulating expression of the synaptic marker protein synaptophysin (red, indicated by white box). Art designers: Ari M. Chow and Anthony J. Veloso.
Versatile Strategy for Biochemical, Electrochemical and Immunoarray Detection of Protein Phosphorylations
S. Martic, M. Gabriel, J. P. Turowec, D. W. Litchfield, H. B. Kraatz
Protein kinases can use ferrocene-ATP conjugates to transfer the redox active ferrocene group to protein and peptide targets. Ferrocene transfer can be quantified electrochemically with the help of an antiferrocene antibody.
Introduction to the Focus Issue on Marine Boundary Layer: Ocean Atmosphere Interactions Processes
D. J. Donaldson and Christian George
The exchange of matter and energy between the sea surface and the atmosphere is a critical controller of the climate on Earth. This special issue on marine boundary layer processes contains several articles relating to the transport and reactions of chemical compounds at the air-sea boundary, and how such transformations influence the atmosphere in the overlying marine boundary layer.
Label-free methods for probing the interaction of clioquinol with amyloid-β
Xin Ran Cheng, Vinci Wing Sze Hung, Simona Scarano, Marco Mascini, Maria Minunni and Kagan Kerman
Kerman’s team and his Italian collaborators have developed label-free methods based on surface plasmon resonance (SPR) and thickness shear mode acoustic wave sensors (TSM-AWS) to detect the interaction between amyloid-β and clioquinol in real-time.
Glancing-angle Raman study of nitrate and nitric acid at the air–aqueous interface
Sumi N. Wren, D.J. Donaldson
Chemical Physics Letters 522 (2012) 1–10
Glancing-angle Raman spectra of aqueous KNO3 and HNO3 solutions were measured to determine the degree of nitric acid dissociation in the bulk and in the surface region. Acid dissociation in the surface region is similar to that in the bulk and depends strongly on water molecule availability to the dissociation process. The spectra were used to construct an adsorption isotherm for nitrate anion at the water surface; it exhibits an almost neutral surface affinity.
Mohtashim H. Shamsi and Heinz-Bernhard Kraatz
It describes the electrochemical identification of artificial oligonucleotides related to bovine species by scanning electrochemical microscopy and serves as an example for the identification of species based on mismatches in the mitochondrial cytochrome C1 oxidase gene.
Optical trapping for the characterization of amyloid-beta aggregation kinetics
Anthony J. Veloso, Hiroyuki Yoshikawa, Xin R. Cheng, Eiichi Tamiya and Kagan Kerman
Alzheimer’s disease (AD) is marked by the accumulation of neuronal plaques from insoluble amyloid- beta (Ab) peptides. Growing evidence for the role of Ab oligomers in neuronal cell cytotoxicity and pathogenesis has prompted the development of novel techniques to better understand the early stages of aggregation. K. Kerman and co-workers applied near infrared (NIR) optical trapping technique to characterize the early stages of Ab aggregation in the presence of a beta-sheet intercalating dye, Congo Red (CR), as the fluorescent marker. The integration of fluorescence analysis with NIR optical trapping has provided a new outlook into the first two hours of Ab aggregation.
Coriolis forces influence the secondary circulation of gravity currents flowing in large-scale sinuous submarine channel systems
Remo Cossu, Mathew G. Wells
A combination of centrifugal and Coriolis forces drive the secondary circulation of turbidity currents in sinuous channels, and hence determine where erosion and deposition of sediment occur. Using laboratory experiments we show that when centrifugal forces dominate, the density interface shows a superelevation at the outside of a channel bend. However when Coriolis forces dominate, the interface is always deflected to the right (in the Northern Hemisphere) for both left and right turning bends. The relative importance of either centrifugal or Coriolis forces can be described in terms of a Rossby number defined as Ro = U/fR, where U is the mean downstream velocity, f the Coriolis parameter and R the radius of curvature of the channel bend. Channels with larger bends at high latitudes have ∣Ro∣ < 1 and are dominated by Coriolis forces, whereas smaller, tighter bends at low latitudes have ∣Ro∣ ≫ 1 and are dominated by centrifugal forces.
Electrochemical probing of HIV enzymes using ferrocene-conjugated peptides on surfaces
One of the current pathways to develop inhibitors that target different steps in the life cycle of the human immunodeficiency virus (HIV) is blocking the function of the HIV-related proteins such as HIV-1 integrase (HIV-1 IN), HIV-1 reverse transcriptase (HIV-1 RT) and HIV-1 protease (HIV-1 PR), which are essential proteins that control the ability of HIV to infect cells, produce new copies of the virus, or cause disease. We have demonstrated for the first time the detection of these enzymes at nanomolar levels using ferrocene (Fc)-conjugated peptides on gold microelectrodes. The interaction between the Fc-conjugated peptides and the enzymes was studied by cyclic voltammetry. As the protein concentration increased, the electrochemical behaviour of the surface-bound Fc- bioconjugate changed, indicating that HIV protein was binding to the peptide film and encapsulating the Fc redox center on the surface. The electrochemical responses shifted to higher potentials and decreased in the current intensity, as the concentrations of the HIV-1 enzymes increased. The optimization studies were performed by changing the pH and NaCl concentration. Control experiments involved the exposure of the Fc-conjugated peptides with all the enzymes. This general procedure can be readily applied in the future to the multiplexed detection of several HIV-related proteins, as well as the high-throughput screening of candidate inhibitors for AIDS therapy.
Suppression of aqueous surface hydrolysis by monolayers of short chain organic amphiphiles
Daniel Clifford, Thorsten Bartels-Rausch and D.J. Donaldson Phys. Chem. Chem. Phys. , 2007 , 9 , 1362-1369
Aqueous aerosols and other water surfaces in the environment may be coated with organic films, which can give rise to significant effects on gas-solution transport and surface reactivity. We have used a surface active fluorescent pH probe to examine the hydrolysis of nitric acid and ammonia at both the uncoated and the organic-coated air-water interface. For uncoated samples, a transient change in pH is observed at the interface upon introduction of acid or base vapour, followed by a relaxation to a final pH which is different than the initial value, and equal to the final bulk pH. Solutions having monolayer and sub-monolayer films of 1-octanol do not display the transient, but do show the same long-time change in pH. The degree of suppression of the surface pH transient depends directly on the amount of octanol present at the surface, however when monolayers of butanol and of uncompressed stearic acid are present at the surface there is little difference seen from the clean interface. We propose that the surface component of the hydrolysis reaction depends directly on the concentration of available water at the interface.
In the upper half of the figure, the time dependence of surface pH is shown after gas phase nitric acid is introduced above a bare interface (in blue) and one having a monolayer of 1-octanol at the surface (red). Beside these traces are photos of the fluorescence observed with higher (top) and lower (bottom) values of the surface pH. The lower portion of the figure shows a cartoon depicting the inhibition of surface hydrolysis by an organic monolayer.