On the composition of oceanic and littoral manganese nodules (published online 2015)

The following analyses were made some years ago, principally with the object of ascertaining the state of oxidation of the manganese in the nodules. The nodules examined came from three different localities, two of them oceanic and the third littoral. Samples marked I., II., and III. are from nodules brought up in the trawl on board the "Challenger," on 13th March 1874, in lat. 42° 42' S., long. 134° 10' E. The depth of the water was 2600 fathoms, and the temperature of the bottom water 0·2° C. The density of the bottom water was 1·02570 at 15·56° C. Being from a high southern latitude, and therefore near the source of surface aeration, the water is highly charged with atmospheric gases, especially oxygen. It contained, per litre, 18·4 c.c. of mixed nitrogen and oxygen, of which 31·81 per cent, was oxygen, and 27·33 c.c, or 53·7 milligrammes, loosely-bound carbonic acid. The position of the station is about 400 miles south-west of the nearest part of the Australian coast, and about 500 miles west of Tasmania. It was the deepest water observed in the Antarctic voyage between the Cape of Good Hope and Melbourne. The haul was a very abundant one, and a few notes which I made at the time may be interesting: -"The water was found unexpectedly deep, the bottom being red clay, with some Foraminifera.

A host–guest system to study structure–function relationships of membrane fusion peptides

We designed a host–guest fusion peptide system, which is completely soluble in water and has a high affinity for biological and lipid model membranes. The guest sequences are those of the fusion peptides of influenza hemagglutinin, which are solubilized by a highly charged unstructured C-terminal host sequence. These peptides partition to the surface of negatively charged liposomes or erythrocytes and elicit membrane fusion or hemolysis. They undergo a conformational change from random coil to an obliquely inserted (≈33° from the surface) α-helix on binding to model membranes. Partition coefficients for membrane insertion were measured for influenza fusion peptides of increasing lengths (n = 8, 13, 16, and 20). The hydrophobic contribution to the free energy of binding of the 20-residue fusion peptide at pH 5.0 is −7.6 kcal/mol (1 cal = 4.18 J). This energy is sufficient to stabilize a “stalk” intermediate if a typical number of fusion peptides assemble at the site of membrane fusion. The fusion activity of the fusion peptides increases with each increment in length, and this increase strictly correlates with the hydrophobic binding energy and the angle of insertion.

Molecular cloning of violaxanthin de-epoxidase from romaine lettuce and expression in Escherichia coli.

Plants need to avoid or dissipate excess light energy to protect photosystem II (PSII) from photoinhibitory damage. Higher plants have a conserved system that dissipates excess energy as heat in the light-harvesting complexes of PSII that depends on the transthylakoid delta pH and violaxanthin de-epoxidase (VDE) activity. To our knowledge, we report the first cloning of a cDNA encoding VDE and expression of functional enzyme in Escherichia coli. VDE is nuclear encoded and has a transit peptide with characteristic features of other lumen-localized proteins. The cDNA encodes a putative polypeptide of 473 aa with a calculated molecular mass of 54,447 Da. Cleavage of the transit peptide results in a mature putative polypeptide of 348 aa with a calculated molecular mass of 39,929 Da, close to the apparent mass of the purified enzyme (43 kDa). The protein has three interesting domains including (i) a cysteine-rich region, (ii) a lipocalin signature, and (iii) a highly charged region. The E. coli expressed enzyme de-epoxidizes violaxanthin sequentially to antheraxanthin and zeaxanthin, and is inhibited by dithiothreitol, similar to VDE purified from chloroplasts. This confirms that the cDNA encodes an authentic VDE of a higher plant and is unequivocal evidence that the same enzyme catalyzes the two-step mono de-epoxidation reaction. The cloning of VDE opens new opportunities for examining the function and evolution of the xanthophyll cycle, and possibly enhancing light-stress tolerance of plants.

Sequence verification of human creatine kinase (43 kDa) isozymes by high-resolution tandem mass spectrometry.

Amino acid sequencing by recombinant DNA technology, although dramatically useful, is subject to base reading errors, is indirect, and is insensitive to posttranslational processing. Mass spectrometry techniques can provide molecular weight data from even relatively large proteins for such cDNA sequences and can serve as a check of an enzyme's purity and sequence integrity. Multiply-charged ions from electrospray ionization can be dissociated to yield structural information by tandem mass spectrometry, providing a second method for gaining additional confidence in primary sequence confirmation. Here, accurate (+/- 1 Da) molecular weight and molecular ion dissociation information for human muscle and brain creatine kinases has been obtained by electrospray ionization coupled with Fourier-transform mass spectrometry to help distinguish which of several published amino acid sequences for both enzymes are correct. The results herein are consistent with one published sequence for each isozyme, and the heterogeneity indicated by isoelectric focusing due to 1-Da deamidation changes. This approach appears generally useful for detailed sequence verification of recombinant proteins.

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae.

Mutations in the Saccharomyces cerevisiae SSU71 gene were isolated as suppressors of a transcription factor TFIIB defect that confers both a cold-sensitive growth defect and a downstream shift in transcription start-site selection at the cyc1 locus. The ssu71-1 suppressor not only suppresses the conditional phenotype but also restores the normal pattern of transcription initiation at cyc1. In addition, the ssu71-1 suppressor confers a heat-sensitive phenotype that is dependent upon the presence of the defective form of TFIIB. Molecular and genetic analysis of the cloned SSU71 gene demonstrated that SSU71 is a single-copy essential gene encoding a highly charged protein with a molecular mass of 82,194 daltons. Comparison of the deduced Ssu71 amino acid sequence with the protein data banks revealed significant similarity to RAP74, the larger subunit of the human general transcription factor TFIIF. Moreover, Ssu71 is identical to p105, a component of yeast TFIIF. Taken together, these data demonstrate a functional interaction between TFIIB and the large subunit of TFIIF and that this interaction can affect start-site selection in vivo.

Turkey’s new election: War or peace? EPC Commentary, 30 October 2015

Turkey is headed to its second parliamentary election in five months with snap polls slated for November 1. The election will take place in a highly charged atmosphere with escalating violence and financial volatility. The renewed conflict between Turkey and the terrorist Kurdistan Workers' Party (PKK) is spreading throughout the country with the rise of ethnic tensions posing a big threat to internal harmony. Even a peace rally in the capital Ankara was hit by suicide bombers marking the deadliest terror attack in Turkey's history. Turkey, which has always been the most stable country in a turbulent region, risks its security being seriously jeopardised unless the violence is urgently stopped and the political ambiguity is ended through a stable government.

The AKP rebooted – What next for Turkey? EPC Commentary, 30 October 2015

Turkey is headed to its second parliamentary election in five months with snap polls slated for November 1. The election will take place in a highly charged atmosphere with escalating violence and financial volatility. The renewed conflict between Turkey and the terrorist Kurdistan Workers' Party (PKK) is spreading throughout the country with the rise of ethnic tensions posing a big threat to internal harmony. Even a peace rally in the capital Ankara was hit by suicide bombers marking the deadliest terror attack in Turkey's history. Turkey, which has always been the most stable country in a turbulent region, risks its security being seriously jeopardised unless the violence is urgently stopped and the political ambiguity is ended through a stable government.

Learning Environments in Design Studio Culture

The paper reports on a study of design studio culture from a student perspective. Learning in design studio culture has been theorised variously as a signature pedagogy emulating professional practice models, as a community of practice and as a form of problem-based learning, all largely based on the study of teaching events in studio. The focus of this research has extended beyond formally recognized activities to encompass the student’s experience of their social and community networks, working places and study set-ups, to examine how these have contributed to studio culture and how there have been supported by studio teaching. Semi-structured interviews with final year undergraduate students of architecture formed the basis of the study using an interpretivist approach informed by Actor-network theory, with studio culture featured as the focal actor, enrolling students and engaging with other actors, together constituting an actor-network of studio culture. The other actors included social community patterns and activities; the numerous working spaces (including but not limited to the studio space itself); the equipment, tools of trade and material pre-requisites for working; the portfolio enrolling the other actors to produce work for it; and the various formal and informal events associated with the course itself. Studio culture is a highly charged social arena: The question is how, and in particular, which aspects of it support learning? Theoretical models of situated learning and communities of practice models have informed the analysis, with Bourdieu’s theory of practice, and his interrelated concepts of habitus, field and capital providing a means of relating individually acquired habits and modes of working to social contexts. Bourdieu’s model of habitus involves the externalisation through the social realm of habits and knowledge previously internalised. It is therefore a useful model for considering whole individual learning activities; shared repertoires and practices located in the social realm. The social milieu of the studio provides a scene for the exercise and display of ‘practicing’ and the accumulation of a form of ‘practicing-capital’. This capital is a property of the social milieu rather than the space, so working or practicing in the company of others (in space and through social media) becomes a more valued aspect of studio than space or facilities alone. This practicing-capital involves the acquisition of a habitus of studio culture, with the transformation of physical practices or habits into social dispositions, acquiring social capital (driving the social milieu) and cultural capital (practicing-knowledge) in the process. The research drew on students’ experiences, and their practicing ‘getting a feel for the game’ by exploring the limits or boundaries of the field of studio culture. The research demonstrated that a notional studio community was in effect a social context for supporting learning; a range of settings to explore and test out newly internalised knowledge, demonstrate or display ideas, modes of thinking and practicing. The study presents a nuanced interpretation of how students relate to a studio culture that involves a notional community, and a developing habitus within a field of practicing that extends beyond teaching scenarios.

Benchmarking a modified version of the civ3 nonrelativistic atomic-structure code within Na-like-tungsten R -matrix calculations

In this work we explore the validity of employing a modified version of the nonrelativistic structure code civ3 for heavy, highly charged systems, using Na-like tungsten as a simple benchmark. Consequently, we present radiative and subsequent collisional atomic data compared with corresponding results from a fully relativistic structure and collisional model. Our motivation for this line of study is to benchmark civ3 against the relativistic grasp0 structure code. This is an important study as civ3 wave functions in nonrelativistic R-matrix calculations are computationally less expensive than their Dirac counterparts. There are very few existing data for the W LXIV ion in the literature with which we can compare except for an incomplete set of energy levels available from the NIST database. The overall accuracy of the present results is thus determined by the comparison between the civ3 and grasp0 structure codes alongside collisional atomic data computed by the R-matrix Breit-Pauli and Dirac codes. It is found that the electron-impact collision strengths and effective collision strengths computed by these differing methods are in good general agreement for the majority of the transitions considered, across a broad range of electron temperatures.

Avaliação do potencial anti-inflamatório, anticoagulante e hemorrágico de heparinóides presentes em "Artemia franciscana"

Heparan sulfate (HS) and Heparin (Hep) glycosaminoglycans (GAGs) are heterogeneous and highly charged polysaccharides. HS is structurally related to Hep but is much less substituted with sulfo groups than heparin and has a more varied structure (or sequence). Because of structural similiarities between these two polymers, they have been described together as heparinoids . Both chains bind a variety of proteins and mediate various physiologically important processes including, blood coagulation, cell adhesion and growth factor regulation. Heparinoids with structural characteristics similar to these described from HS and/or Hep from mammalian tissues have been isolated from different species of invertebrates, although only a few heparinoids from unusual sources have been characterized. The present study describes the presence of unusual heparinoids population from Artemia franciscana, isolated after proteolysis and fractionation by ion exchange resin and named, F-3.0M. The study model in vivo were hemostasis (rat tail scarification) and inflamatoty activity. The tests in vitro were used for coagulations assays (PT and APTT). The analyse of the heparinoids eluted with 3,0M NaCl showed electrophoretic migration in different buffer systems a single band with a behaviour intermediate between those of mammalian HEP and HS. The main products obtained from Artemia heparinoids after enzymatic degradation with heparitinases I and II from F. heparinum were N-sulphated disaccharides (∆U-GlcNS,6S/ ∆U,2S-GlcNS and ∆U-GlcNS) and N-acetylated disaccharides (∆U, GlcNAc). This heparinoid had a lower hemorrhagic effect (400μg/ml) when compared to unfractiionated heparins(25μg/ml).The results also suggest a negligible APTT activity of this heparinoid (62.2s). No action was observed on PT indicating that F-3.0M haven t action on the extrinsic pathway. The results showed that the fraction F- 3.0M have inhibitory effect on migration of leukocytes, 64.5% in the concentration of 10 μg/ml (P<0.001). The search for new heparin and/or heparan sulphates analogs devoid of anticoagulant activity is an atractive alternative and may open up a wide variety of new therapeutic applications

Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.

Ronald Reagan Rain

RONALD REAGAN RAIN is a collection of poems that explore the wildness and terror lurking beneath the surface of contemporary suburban landscapes in a largely imagined America. Images of menacing policemen, bears, fast food restaurants, and dead film stars appear as substantive figures that embody loss and a preoccupation with aging, money woes, and a failed national confidence. Influenced by Russel Edson and Georg Trakl, poets whose work is characterized by Hermeticism and Expressionism, the poems in RONALD REAGAN RAIN suggest a similar dual need for autonomy and compromise in both highly charged poetic fragments and longer prose passages that examine issues of civil and personal estrangement as the outside world calls for constant introspection and reassessments of identity.

Ion-acoustic waves in a complex plasma with negative ions

Negative ions and negatively charged micro- to nano-meter sized dust grains are ubiquitous in astrophysical as well as industrial processing plasmas. The negative ions can appear in electro-negative plasmas as a result of elementary processes such as dissociative or non-dissociative electron attachment to neutrals. They are usually rather small in number, and in general do not affect the overall plasma behavior. On the other hand, since the dust grains are almost always highly negative, even in small numbers they can take up a considerable proportion of the total negative charge in the system. The presence of dusts can affect the characteristics of most collective processes of the plasma since the charge balance in both the steady and dynamic states can be significantly altered. Another situation that often occurs is that the electron number density becomes small because of their absorption by the dust grains or the discharge walls. In this case the negative ions in the plasma can play a very important role. Here, a self-consistent theory of linear waves in complex laboratory plasmas containing dust grains and negative ions is presented. A comprehensive model for such plasmas including source and sink effects associated with the presence of dust grains and negative ions is introduced. The stationary state of the plasma as well as the dispersion and damping characteristics of the waves are investigated. All relevant processes, such as ionization, diffusion, electron attachment, negative-positive ion recombination, dust charge relaxation, and dissipation due to electron and ion elastic collisions with neutrals and dust particles, as well as charging collisions with the dusts, are taken into consideration.

Charged particles and cluster ions produced during cooking activities

Previous studies showed that a significant number of the particles present in indoor air are generated by cooking activities, and measured particle concentrations and exposures have been used to estimate the related human dose. The dose evaluation can be affected by the particle charge level which is usually not considered in particle deposition models. To this purpose, in this paper we show, for the very first time, the electric charge of particles generated during cooking activities and thus extending the interest on particle charging characterization to indoor micro-environments, so far essentially focused on outdoors. Particle number, together with positive and negative cluster ion concentrations, was monitored using a condensation particle counter and two air ion counters, respectively, during different cooking events. Positively-charged particle distribution fractions during gas combustion, bacon grilling, and eggplant grilling events were measured by two Scanning Mobility Particle Sizer spectrometers, used with and without a neutralizer. Finally, a Tandem Differential Mobility Analyzer was used to measure the charge specific particle distributions of bacon and eggplant grilling experiments, selecting particles of 30, 50, 80 and 100 nm in mobility diameter. The total fraction of positively-charged particles was 4.0%, 7.9%, and 5.6% for gas combustion, bacon grilling, and eggplant grilling events, respectively, then lower than other typical outdoor combustion-generated particles.