Selectivity control in Pt-catalyzed cinnamaldehyde hydrogenation

Chemoselectivity is a cornerstone of catalysis, permitting the targeted modification of specific functional groups within complex starting materials. Here we elucidate key structural and electronic factors controlling the liquid phase hydrogenation of cinnamaldehyde and related benzylic aldehydes over Pt nanoparticles. Mechanistic insight from kinetic mapping reveals cinnamaldehyde hydrogenation is structure-insensitive over metallic platinum, proceeding with a common Turnover Frequency independent of precursor, particle size or support architecture. In contrast, selectivity to the desired cinnamyl alcohol product is highly structure sensitive, with large nanoparticles and high hydrogen pressures favoring C=O over C=C hydrogenation, attributed to molecular surface crowding and suppression of sterically-demanding adsorption modes. In situ vibrational spectroscopies highlight the role of support polarity in enhancing C=O hydrogenation (through cinnamaldehyde reorientation), a general phenomenon extending to alkyl-substituted benzaldehydes. Tuning nanoparticle size and support polarity affords a flexible means to control the chemoselective hydrogenation of aromatic aldehydes.

Specific binding of the mammalian high mobility group protein AT-hook 2 to the minor groove of AT -rich DNAs: Thermodynamic and specificity studies

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a small transcriptional factor involved in cell development and oncogenesis. It contains three "AT-hook" DNA binding domains, which specifically recognize the minor groove of AT-rich DNA sequences. It also has an acidic C-terminal motif. Previous studies showed that HMGA2 mediates all its biological effects through interactions with AT-rich DNA sequences in the promoter regions. In this dissertation, I used a variety of biochemical and biophysical methods to examine the physical properties of HMGA2 and to further investigate HMGA2's interactions with AT-rich DNA sequences. The following are three avenues perused in this study: (1) due to the asymmetrical charge distribution of HMGA2, I have developed a rapid procedure to purify HMGA2 in the milligram range. Preparation of large amounts of HMGA2 makes biophysical studies possible; (2) Since HMGA2 binds to different AT-rich sequences in the promoter regions, I used a combination of isothermal titration calorimetry (ITC) and DNA UV melting experiment to characterize interactions of HMGA2 with poly(dA-dT) 2 and poly(dA)poly(dT). My results demonstrated that (i) each HMGA2 molecule binds to 15 AT bp; (ii) HMGA2 binds to both AT DNAs with very high affinity. However, the binding reaction of HMGA2 to poly(dA-dT) 2 is enthalpy-driven and the binding reaction of HMGA2 with poly(dA)poly(dT) is entropy-driven; (iii) the binding reactions are strongly depended on salt concentrations; (3) Previous studies showed that HMGA2 may have sequence specificity. In this study, I used a PCR-based SELEX procedure to examine the DNA binding specificity of HMGA2. Two consensus sequences for HMGA2 have been identified: 5'-ATATTCGCGAWWATT-3' and 5'-ATATTGCGCAWWATT-3', where W represents A or T. These consensus sequences have a unique feature: the first five base pairs are AT-rich, the middle four to five base pairs are GC-rich, and the last five to six base pairs are AT-rich. All three segments are critical for high affinity binding. Replacing either one of the AT-rich sequences to a non-AT-rich sequence causes at least 100-fold decrease in the binding affinity. Intriguingly, if the GC-segment is substituted by an AT-rich segment, the binding affinity of HMGA2 is reduced approximately 5-fold. Identification of the consensus sequences for HMGA2 represents an important step towards finding its binding sites within the genome.

Tailoring heme -thiolate proteins into efficient biocatalysts with high specificity and selectivity

Cytochrome P450 monooxygenases, one of the most important classes of heme-thiolate proteins, have attracted considerable interest in the biochemical community because of its catalytic versatility, substrate diversity and great number in the superfamily. Although P450s are capable of catalyzing numerous difficult oxidation reactions, the relatively low stability, low turnover rates and the need of electron-donating cofactors have limited their practical biotechnological and pharmaceutical applications as isolated enzymes. The goal of this study is to tailor such heme-thiolate proteins into efficient biocatalysts with high specificity and selectivity by protein engineering and to better understand the structure-function relationship in cytochromes P450. In the effort to engineer P450cam, the prototype member of the P450 superfamily, into an efficient peroxygenase that utilizes hydrogen peroxide via the “peroxide-shunt” pathway, site-directed mutagenesis has been used to elucidate the critical roles of hydrophobic residues in the active site. Various biophysical, biochemical and spectroscopic techniques have been utilized to investigate the wild-type and mutant proteins. Three important P450cam variants were obtained showing distinct structural and functional features. In P450camV247H mutant, which exhibited almost identical spectral properties with the wild-type, it is demonstrated that a single amino acid switch turned the monooxygenase into an efficient preoxidase by increasing the peroxidase activity nearly one thousand folds. In order to tune the distal pocket of P450cam with polar residues, Leu 246 was replaced with a basic residue, lysine, resulting in a mutant with spectral features identical to P420, the inactive species of P450. But this inactive-species-like mutant showed catalytic activities without the facilitation of any cofactors. By substituting Gly 248 with a histidine, a novel Cys-Fe-His ligation set was obtained in P450cam which represented the very rare case of His ligation in heme-thiolate proteins. In addition to serving as a convenient model for hemoprotein structural studies, the G248H mutant also provided evidence about the nature of the axial ligand in cytochrome P420 and other engineered hemoproteins with thiolate ligations. Furthermore, attempts have been made to replace the proximal ligand in sperm whale myoglobin to construct a heme-thiolate protein model by mimicking the protein environment of cytochrome P450cam and chloroperoxidase.

Tailoring Heme-Thiolate Proteins into Efficient Biocatalysts with High Specificity and Selectivity

Cytochrome P450 monooxygenases, one of the most important classes of heme-thiolate proteins, have attracted considerable interest in the biochemical community because of its catalytic versatility, substrate diversity and great number in the superfamily. Although P450s are capable of catalyzing numerous difficult oxidation reactions, the relatively low stability, low turnover rates and the need of electron-donating cofactors have limited their practical biotechnological and pharmaceutical applications as isolated enzymes. The goal of this study is to tailor such heme-thiolate proteins into efficient biocatalysts with high specificity and selectivity by protein engineering and to better understand the structure-function relationship in cytochromes P450. In the effort to engineer P450cam, the prototype member of the P450 superfamily, into an efficient peroxygenase that utilizes hydrogen peroxide via the “peroxide-shunt” pathway, site-directed mutagenesis has been used to elucidate the critical roles of hydrophobic residues in the active site. Various biophysical, biochemical and spectroscopic techniques have been utilized to investigate the wild-type and mutant proteins. Three important P450cam variants were obtained showing distinct structural and functional features. In P450camV247H mutant, which exhibited almost identical spectral properties with the wild-type, it is demonstrated that a single amino acid switch turned the monooxygenase into an efficient preoxidase by increasing the peroxidase activity nearly one thousand folds. In order to tune the distal pocket of P450cam with polar residues, Leu 246 was replaced with a basic residue, lysine, resulting in a mutant with spectral features identical to P420, the inactive species of P450. But this inactive-species-like mutant showed catalytic activities without the facilitation of any cofactors. By substituting Gly 248 with a histidine, a novel Cys-Fe-His ligation set was obtained in P450cam which represented the very rare case of His ligation in heme-thiolate proteins. In addition to serving as a convenient model for hemoprotein structural studies, the G248H mutant also provided evidence about the nature of the axial ligand in cytochrome P420 and other engineered hemoproteins with thiolate ligations. Furthermore, attempts have been made to replace the proximal ligand in sperm whale myoglobin to construct a heme-thiolate protein model by mimicking the protein environment of cytochrome P450cam and chloroperoxidase.

Hook removal from a juvenile bull shark in Tarpon Bay

http://digitalcommons.fiu.edu/fce_lter_photos/1261/thumbnail.jpg

Food selectivity and processing by the cold-water coral Lophelia pertusa

Cold-water corals form prominent reef ecosystems along ocean margins that depend on suspended resources produced in surface waters. In this study, we investigated food processing of 13C and 15N labelled bacteria and algae by the cold-water coral Lophelia pertusa. Coral respiration, tissue incorporation of C and N and metabolic-derived C incorporation into the skeleton were traced following the additions of different food concentrations (100, 300, 1300 µg C/l) and two ratios of suspended bacterial and algal biomass (1:1, 3:1). Respiration and tissue incorporation by L. pertusa increased markedly following exposure to higher food concentrations. The net growth efficiency of L. pertusa was low (0.08±0.03), which is consistent with their slow growth rates. The contribution of algae and bacteria to total coral assimilation was proportional to the food mixture in the two lowest food concentrations, but algae were preferred over bacteria as food source at the highest food concentration. Similarly, the stoichiometric uptake of C and N was coupled in the low and medium food treatment, but was uncoupled in the high food treatment and indicated a comparatively higher uptake or retention of bacterial carbon as compared to algal nitrogen. We argue that behavioural responses for these small-sized food particles, such as tentacle behaviour, mucus trapping and physiological processing, are more likely to explain the observed food selectivity as compared to physical-mechanical considerations. A comparison of the experimental food conditions to natural organic carbon concentrations above CWC reefs suggests that L. pertusa is well adapted to exploit temporal pulses of high organic matter concentrations in the bottom water caused by internal waves and down-welling events.

Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity

Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.

Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity

Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.

A Machine Learning Analysis of Twitter Sentiment to the Sandy Hook Shootings

Gun related violence is a complex issue and accounts for a large proportion of violent incidents. In the research reported in this paper, we set out to investigate the pro-gun and anti-gun sentiments expressed on a social media platform, namely Twitter, in response to the 2012 Sandy Hook Elementary School shooting in Connecticut, USA. Machine learning techniques are applied to classify a data corpus of over 700,000 tweets. The sentiments are captured using a public sentiment score that considers the volume of tweets as well as population. A web-based interactive tool is developed to visualise the sentiments and is available at this http://www.gunsontwitter.com. The key findings from this research are: (i) There are elevated rates of both pro-gun and anti-gun sentiments on the day of the shooting. Surprisingly, the pro-gun sentiment remains high for a number of days following the event but the anti-gun sentiment quickly falls to pre-event levels. (ii) There is a different public response from each state, with the highest pro-gun sentiment not coming from those with highest gun ownership levels but rather from California, Texas and New York.

Analyse von Schüler-Versuchsprotokollen beim eigenständigen Experimentieren am Beispiel des Hook'schen Gesetzes

Mit der Einführung der Bildungsstandards für den mittleren Schulabschluss im Fach Physik ist vor allem der Prozess der Erkenntnisgewinnung stärker in den Mittelpunkt didaktischer und unterrichtlicher Arbeit gerückt. Damit erhält insbesondere das Experiment eine noch größere Rolle für den naturwissenschaftlichen Unterricht als ihm bereits vor der Einführung zukam. Im erkenntnistheoretischen Sinn gilt es neben der Entwicklung von Fragestellungen als eine der zentralen naturwissenschaftlichen Arbeitsweisen in der Physik. Ein besonderes Potential für den Physikunterricht bietet in diesem Zusammenhang das Schülerexperiment, dem trotz umstrittener Wirksamkeit zahlreiche Vorzüge zugeschrieben werden können. Neben der Förderung von praktischen experimentellen Fähigkeiten zählen dazu vor allem die Einführung in naturwissenschaftliche Denk- und Arbeitsprozesse und die Steigerung der Motivation bei den Lernenden. Um als Lehrperson konkret mit den auftretenden Problemen im Unterricht umgehen zu können und die Schülerinnen und Schüler angesichts wachsender Heterogenität individuell fördern zu können, ist es jedoch unerlässlich, über die Bandbreite der Schwierigkeiten Bescheid zu wissen und diese wiederum bei der Unterrichtsplanung zu berücksichtigen. Daher sollen im Rahmen dieser Arbeit Schüler-Versuchsprotokolle im Hinblick auf mögliche Schwierigkeiten der Lernenden analysiert werden. Die auszuwertenden Protokolle sind bereits im Rahmen des DiSiE-Projektes der Universität Kassel, das sich mit der Diagnose von Schülerschwierigkeiten beim eigenständigen Experimentieren beschäftigt, entstanden und wurden von Schülerinnen und Schüler während der Bearbeitung einer Experimentieraufgabe zum Hook’schen Gesetz angefertigt.

Fishing gear selectivity for Lates niloticus L., Oreochromis niloticus L. and Rastrineobola argentea P. in Lakes Victoria, Kyoga and Nabugabo

Catch effort data on which fisheries management regulations are sometimes based are not available for most lakes in Uganda. However, failure to regulate fishing gears and methods has been a major cause of collapse of fisheries in the country. Fisheries have been damaged by destructive and non-selective fishing gears and methods such as trawling and beach seining, by use of gill nets of mesh size which crop immature fish and by introduction of mechanised fishing. Selectivity of gears used to crop Lates niloticus L.(Nile perch), Oreochromis niloticus L. (Nile tilapia) and Rastrineobola argentea Pellegrin (Mukene) which are currently the most important commercial species in Uganda were examined in order to recommend the most suitable types, sizes and methods that should be used in exploiting these fisheries. Gill nets of less than 127 mm mainly cropped immature Nile tilapia and Nile perch. To protect these fisheries, the minimum mesh size of gill nets should be set at 127 mm. Seine nets of 5 mm caught high proportions in immature Mukene while those of 10 mm caught mainly mature Mukene. When operated inshore, both sizes caught immature Nile perch and Nile tilapia as by-catch. To protect the Mukene fishery and avoid catching immature bye-catch, a minimum mesh size of the Mukene net should be 10 mm operated as Lampara type net offshore, but since most fishermen have been using 5 mm seine nets for over five years the minimum size should not be allowed to drop below 5 mm pending further thorough investigations. Beach seining and trawling are destructive to fisheries and should be prohibited until data that may justify their use is available.

The effect of hook size on the catch rate and size of the Nile perch Lates niloticus (Linne) fishery in the Napoleon Gulf, Lake Victoria, Uganda

This study was undertaken in Napoleon gulf, Lake Victoria Uganda from July – December 2009. It was conducted in four landing sites; Bukaya (0.41103N, 33.19133E), Bugungu (0.40216N, 33.2028E), Busana (0.39062N, 33.25228E) and Kikondo (0.3995N, 33.21848E) all from Buikwe district (Formerly part of Mukono district). The main aim was to determine the effect of both hook size and bait type on the catch rate (mean weight) and size composition of Nile perch (Lates niloticus) (LINNE) fishery in the Napoleon Gulf, Lake Victoria. The main hook sizes investigated during the experiment were 7, 8, 9, 10, 11 and 12 that were dominantly used in harvesting Nile perch in Napoleon Gulf, Lake Victoria. In this study length, weight and bait type data were collected on site from each boat at that particular fishing spot; since most fishermen in the Napoleon Gulf could sell their fish immediately the catch is caught there and then. The results indicated a total of 873 Nile perch fish samples collected during the study. Statistical tests, descriptive statistics, regression and correlation were all carried out using the Statistical Package for the Social Sciences (SPSS) in addition to Microsoft excel. The bait types in the Gulf ranged from 5-10 cm Total length (TL) haplochromine, 24.5-27 cm TL Mormyrus kannume and 9-24 cm TL Clarias species. The bait types had a significant effect on the catch rate and also on the size composition the fish harvested measured as Total length (ANCOVA F=8.231; P<0.05) despite the fact that bait type had no influence on mean weight of fish captured (ANCOVA F=2.898; P>0.05). Hook sizes used by the fishers had a significant effect on the both the size (TL) composition (ANCOVA F=3.847; P<0.05) and the mean weight (ANCOVA F=4.599; P<0.005) of the Nile perch captured. Investigations indicated hook sizes seven (7) and eight (8) were the ones that harvested the Nile perch above the slot size of 50 cm total length. In general hook sizes indicated to be the main drive in the harvesting of the Nile perch though bait type also contributed toward that. Generally there is need for management to put a law in place on the minimum hook size to be used on the harvesting of the Nile perch and also monitored by the Fisheries Management as a regulatory measure. In addition to that aquaculture should be encouraged to farm the fish for bait at a higher scale in the region in order to avoid depleting the wild stocks already in danger of extinction. Through this kind of venture, both biodiversity conservation and environmental sustainability will be observed in the Lake Victoria basin.

Map of the bays, harbors, and rivers around New York : showing the channels, soundings, lighthouses, buoys &c., and the complete topography of the surrounding country : including Hempstead, Sandy-Hook, South-Amboy, Newark, Yonkers, N. Rochelle & Glen Cove /

Relief shown by hachures. Depths shown by contours and soundings.

Assessment of grazing selectivity in relation to land cover: a comparison between sheep and goats

Portugal’s Northeast production of sheep and goats are based on the exploitation of landscape by-products such as spontaneous native vegetation and agriculture leftovers. Shepherds tend the flocks throughout grazing itineraries every day, crossing a mosaic of patches of varied land uses. During the journey, the shepherd acts together with the sheep and goats to select each patch in creating an ordered sequence of land uses. The focus of the research is on the land-use composition of the grazing itineraries; determinate how they depend on the patterns of the landscape mosaic. It is utilized a data set of 26 monthly herd’s itineraries, 13 of sheep and 13 of goats, to investigate the relationship of the land uses crossed by the flocks and the land uses of the landscape, evaluating the land-use preferences and selectivity of the sheep and goats. It is utilized the divergences in the time spent and distance travelled by the herds and the area of the land uses in the landscape, the chi-square test to relate the preferred land used and the season, and the discriminate analysis to distinguish the preferences and the selectivity of the herd of sheep and the herd of goats. The herds of the sheep and the goats presented different land-use preferences over the seasons and the discriminant analysis shows that they have different landscape preferences. The herd of sheep has the highest selectivity indexes for the annual irrigated crops, the agricultural complex systems and the agroforestry land uses. The highest selectivity indexes for the herd of goats were found for the deciduous forest, the agriculture with natural and semi-natural spaces and the shrublands land uses. It was concluded that the landscape management for sheep and goats herding has to be different: the agricultural land uses are essential to the flocks of sheep and the forest land uses are decisive to the flocks of goats.

Dual layer solid phase extraction based on molecular imprinting technology: Seeking a route to enhance selectivity for trace analysis of pesticide residues in olive oil.

Aiming to introduce a multiresidue analysis for the trace detection of pesticide residues belonging to organophosphorus and triazine classes from olive oil samples, a new sample preparation methodology comprising the use of a dual layer of “tailor-made” molecularly imprinted polymers (MIPs) SPE for the simultaneous extraction of both pesticides in a single procedure has been attempted. This work has focused on the implementation of a dual MIP-layer SPE procedure (DL-MISPE) encompassing the use of two MIP layers as specific sorbents. In order to achieve higher recovery rates, the amount of MIP layers has been optimized as well as the influence of MIP packaging order. The optimized DL-MISPE approach has been used in the preconcentration of spiked organic olive oil samples with concentrations of dimethoate and terbuthylazine similar to the maximum residue limits and further quantification by HPLC. High recovery rates for dimethoate (95%) and terbuthylazine (94%) have been achieved with good accuracy and precision. Overall, this work constitutes the first attempt on the development of a dual pesticide residue methodology for the trace analysis of pesticide residues based on molecular imprinting technology. Thus, DL-MISPE constitutes a reliable, robust, and sensitive sample preparation methodology that enables preconcentration of the target pesticides in complex olive oil samples, even at levels similar to the maximum residue limits enforced by the legislation.