Local spin dynamics in magnetic molecular chains studied by NMR and μSR

We present NMR and μ⁺SR study of spin dynamics in one-dimensional and quasi-one-dimensional molecular magnets of recent synthesis. In particular, we focus on the so called Gd(hfac)₃NIT-R and CoPhOMe magnetic chains families. For Gd-R helimagnets we show some differences between “weakly frustrated systems” and “fully frustrated systems”. The different behaviour is due to the different radical inserted in the chains (R = Me, Ph for “weakly frustrated systems” and R = iPr, Et for “fully frustrated systems”). The existence of different phase transitions, particularly to 3D long-range magnetic order in Gd-Ph and to chiral order in Gd-iPr, is remarked together with a comparison between results obtained from macroscopic and microscopic investigating techniques. As regards CoPhOMe slowly relaxing chain, the ¹H NMR measurements confirm the freezing of the spins at low temperature, which prevents the 3D long-range order, and display the presence of two relaxation mechanisms related to distinct contributions to the local spin relaxation.     

Eradication-resolution dynamics with stochastic flare-ups

In infectious disease as well as in cancer, the ultimate outcome of the curative response, mediated by the body itself or through drug treatment, is either successful eradication or a resurgence of the disease (“flare-up” or “relapse”), depending on random fluctuations that dominate the dynamics of the system when the number of diseased cells has become very low. The presence of a low-numbers bottle-neck in the dynamics, which is unavoidable if eradication is to take place at all, renders at least one phase of the dynamics essentially stochastic. However, the eradicating agents (e.g. immune cells, drug molecules) generally remain at high numbers during the critical bottle-neck phase, sufficiently so to warrant a deterministic treatment. This leads us to consider a hybrid stochastic-deterministic approach where the infected cells are treated stochastically whereas the eradicating agents are treated deterministically. Exploiting the fact that the number of eradicating agents typically decreases monotonically during the resolution phase of the response, we derive a set of coupled first-order differential equations that describe the probability of ultimate eradication as a function of the system's state, and we consider a number of biomedical applications.     

The sense of water in the blowfly Protophormia terraenovae

The gustatory system of the blowfly, Protophormia terraenovae, is a relatively simple biological model for studies on chemosensory input and behavioral output. It appears to have renewed interest as a model for studies on the role of water channels, namely aquaporins or aquaglyceroporins, in water detection. To this end, we investigated the presence of water channels, their role in “water” and “salt” cell responsiveness and the transduction mechanism involved. For the first time our electrophysiological results point to the presence of an aquaglyceroporin in the chemoreceptor membrane of the “water” cell in the blowfly taste chemosensilla whose transduction mechanism ultimately involves an intracellular calcium increase and consequently cell depolarization. This hypothesis is also supported by calcium imaging data following proper stimulation. This mechanism is triggered by “water” cell stimulation with hypotonic solutions and/or solutes such as glycerol which crosses the membrane by way of aquaglyceroporins. Behavioral output indicates that the “sense” of water in blowflies is definitely not dependent on the “water” cell only, but also on the “salt” cell sensitivity. These findings also hypothesize a new role for aquaglyceroporin in spiking cell excitability.     

The kinetics of amylolysis : Part III. Effect of self-inhibition on the kinetic constants of beta-amylolysis

For beta-amylolysis, the number of bonds split per effective enzyme-substrate encounter has been determined with amyloses having various degrees of polymerization (d.p.), labelled with ¹⁴C. The degradation is shifted in the direction of the “single chain mechanism” with increasing d.p. By taking into account the “inactive, non-reacting” collisions leading to “self-inhibition”, the number of bonds split per “reactive” and “non-reactive” enzyme-substrate encounter was established. From these data, and from the inhibition constant of the inner D-glucose residues of the amylose chain, in conjunction with the Michaelis constant extrapolated to d.p.  4, the actual rate constants for the formation and dissociation of the “reactive” enzyme-substrate complexes and for the formation and dissociation of the “non-reactive” enzyme-substrate complexes were determined. It was found that the rate constants for the formation of the “reactive” complexes decrease slowly with the increase of “self-inhibition”, whereas those for the dissociation of these complexes decrease to a greater extent.     

Characterisation of physiological and immunological differences between Pacific oysters (Crassostrea gigas) genetically selected for high or low survival to summer mortalities and fed different rations under controlled conditions

Within the framework of a national scientific program named “MORtalités ESTivales de l'huître creuse Crassostrea gigas” (MOREST), a family-based experiment was developed to study the genetic basis of resistance to summer mortality in the Pacific oyster, Crassostrea gigas. As part of the MOREST project, the second generation of three resistant families and two susceptible families were chosen and pooled into two respective groups: “R” and “S”. These two groups of oysters were conditioned for 6 months on two food levels (4% and 12% of oyster soft-tissue dry weight in algal dry weight per day) with a temperature gradient that mimicked the Marennes-Oléron natural cycle during the oyster reproductive period. Oyster mortality remained low for the first two months, but then rapidly increased in July when seawater temperature reached 19 °C and above. Mortality was higher in “S” oysters than in “R” oysters, and also higher in oysters fed the 12% diet than those fed 4%, resulting in a decreasing, relative order in cumulative mortality as follows; 12% “S” > 12% “R” > 4% “S” > 4% “R”. Although the observed mortality rates were lower than those previously observed in the field, the mortality differential between “R” and “S” oysters was similar. Gonadal development, estimated by tissue lipid content, followed a relative order yielding a direct, positive relationship between reproductive effort and mortality as we reported precedently by quantitative histology. Regarding hemocyte parameters, one of the most striking observations was that reactive oxygen species (ROS) production was significantly higher in “S” oysters than in “R” oysters in May and June, regardless of food level. The absence of known environmental stress under these experimental conditions suggests that the ROS increase in “S” oyster could be related to their higher reproductive activity. Finally, a higher increase in hyalinocyte counts was observed for”S” oysters, compared to “R” oysters, in July, just before mortality. Taken together, our results suggest an association of genetically based resistance to summer mortality, reproductive strategy and hemocyte parameters.     

Configural processing of different topologically structured figures: an ERP Study

According to Chen’s theory, topological differences are perceived faster than feature differences in early visual perception. We hypothesized that topological perception is caused by the sensitivity in discriminating figures with and without “holes”. An ERP experiment was conducted utilizing a passive paradigm to investigate the differences in perceiving figures with “hole” and with “no-hole”. The results showed differences in N170 components between figures with “holes” and with “no-holes”. The inversion of the “hole” could influence the latency of N170, but the inversion of the “no-hole” could not, which indicated that global features are processed first in the “hole” perception whilst local features are given priority to the “no-hole” perception. This result was similar to studies concerning face and non-face objects, suggesting a configural processing of the “hole”.     

Comparing two methods of calculating the probability of absence: the Negative Predictive Value, and a Credible Interval

If sampling fails to reveal the presence of an invasive species with potential to actually be present, how may we calculate the probability that it is truly absent, e.g. didymo (Didymosphenia geminate) in New Zealand’s North Island. In statistical terms this is a Bayesian question, concerning the probability of a hypothesis (presence/absence), given the obtained data (all results negative). “Classical” theory doesn’t answer this question, because it inverts the required considerations by calculating the probability of all samples being absent if the invasive was actually present. Accordingly, the Bayesian view of “probability” must be adopted in order to answer the question. That definition differs from classical probability in that it always includes an element of subjective belief, particularly in the choice of an appropriate “prior probability” (this is our belief as to the presence of the invasive organism before collecting new data). Bayesian methods can therefore be somewhat controversial – but we seem forced to use them. One Bayesian approach is to use the “Negative Predictive Value”, in which a point estimate of the probability of presence (or absence) prior to sample collection (the “prior probability”) is updated using data once collected using Bayes’ rule. This is in common use in medical studies, where the prior probability is the background disease prevalence, which is generally well understood. It is sometimes used in environmental ‘hot-spot’ investigations. An alternative approach is to recognise the uncertainty in the prior belief by using a distribution of prior probability and updating that using data once collected to give a Credible Interval in which the probability of presence (or absence) should lie – if all our assumptions have been satisfied. We will compare the merits of these approaches considering didymo, southern salt marsh mosquito (Aedes camptorhychus) and the sea squirt Styela clava.     

干旱胁迫对鸭茅幼苗根系生长及光合特性的影响

以不同耐旱型鸭茅品种(系)“01998”(敏感型)和“宝兴”(耐旱型)为试材,采用盆栽控水试验方法,研究土壤干旱胁迫对鸭茅幼苗根系生长、生理特性及叶片光合作用的影响,探讨不同品种耐旱机制的差异.结果表明：干旱胁迫下,不同耐旱型鸭茅幼苗的根系活力和根系数量均呈先上升后下降的趋势,当土壤相对含水量降到30%时,根系活力和根数显著增加并达到最大值;干旱胁迫降低了两个品种鸭茅叶片的相对含水量、叶绿素含量、净光合速率、叶片蒸腾速率、气孔导度,提高了电导率和胞间CO₂浓度.干旱胁迫降低了两个品种鸭茅的单株叶面积,品种“01998”的地下及地上生物量下降,而“宝兴”无显著变化.     

How does the immune response get started?

An effective adaptive immune response requires the prior induction of the regulatory effector T-helper (eTh). There are two competing models of how this cell is induced to effectors. Under the Associative Recognition of Antigen (ARA) or “two signal” model, the T-helper requires eTh in order to be induced to eTh, an “autocatalytic” process. Under the “costimulation” model eTh are induced by an antigen-unspecific signal derived from an “activated” APC. Under the ARA model the problem of the origin of the primer eTh is posed. A nonself antigen-independent pathway to eTh is proposed as well as an experiment to reveal its existence. In the costimulation framework no primer eTh need be postulated but it lacks a mechanism that, in the absence of ARA, accounts for the self-nonself discrimination and the determination of effector class.     

Peach fruit ripening: A proteomic comparative analysis of the mesocarp of two cultivars with different flesh firmness at two ripening stages

A proteomic analysis was conducted on peach fruit mesocarp in order to better elucidate the biochemical and physiological events which characterize the transition of fruit from the “unripe” to the “ripe” phase.The first goal of the present work was to set-up a protocol suitable for improving protein extraction from peach mesocarp. The use of freeze-dried powdered tissue, together with the addition of phenol prior to the extraction with an aqueous buffer, significantly increased the protein yield and the quality of 2-DE gels. The proteomic profiles of the mesocarp from peach fruit of a non-melting flesh (NMF; ‘Oro A’) and a melting flesh (MF; ‘Bolero’) cultivar, at “unripe” and “ripe” stages as defined by some parameters typical of ripening, were then analyzed.The comparative analysis of the 2-DE gels showed that in NMF and MF peaches the relative volumes of 53 protein spots significantly changed in relation to both the ripening stage (“unripe” versus “ripe”) and/or the genetic background of the cultivar (‘Oro A’ versus ‘Bolero’).Thirty out of the 53 differently abundant spots were identified by LC-ESI-MS/MS. The analysis revealed enzymes involved in primary metabolism (e.g. C-compounds, carbohydrates, organic acids and amino acids) and in ethylene biosynthesis as well as proteins involved in secondary metabolism and responses to stress.Among these, 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) appeared to be one of the proteins with the largest change in relative abundance during the fruit transition from the pre-climacteric (“unripe”) to the climacteric (“ripe”) phase. Other proteins, such as S-adenosylmethionine synthetase and β-cyanoalanine synthase involved in ethylene metabolism, were also identified. Moreover, the changes in the relative abundances of a sucrose synthase and an α-amylase suggested differences between the two cultivars in the carbohydrate import activity of ripe fruit. The different accumulation of a few typical ROS-scavenger enzymes suggested that a higher oxidative stress occurred in MF with respect to NMF fruit. This result, together with data concerning the levels of total proteins and free amino acids and those regarding proteins involved in the maintenance of tissue integrity, was consistent with the hypothesis that the last phase of ripening in MF fruit is characterized by the appearance of a senescence status.The present study appears to define well some of the biochemical and physiological events that characterize the ripening of peach and, at the same time, provides interesting indications that could be employed in future marker assisted selection (MAS) programmes aimed to obtain MF fruits with higher ability to preserve tissue functionality maintaining for a longer time their organoleptic characteristics.     

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase

In many cytochrome c oxidases glutamic acid 242 is required for proton transfer to the binuclear heme a₃/Cu_B site, and for proton pumping. When present, the side chain of Glu-242 is orientated “down” towards the proton-transferring D-pathway in all available crystal structures. A nonpolar cavity “above” Glu-242 is empty in these structures. Yet, proton transfer from Glu-242 to the binuclear site, and for proton-pumping, is well established, and the cavity has been proposed to at least transiently contain water molecules that would mediate proton transfer. Such proton transfer has been proposed to require isomerisation of the Glu-242 side chain into an “up” position pointing towards the cavity. Here, we have explored the molecular dynamics of the protonated Glu-242 side chain. We find that the “up” position is preferred energetically when the cavity contains four water molecules, but the “down” position is favoured with less water. We conclude that the cavity might be deficient in water in the crystal structures, possibly reflecting the “resting” state of the enzyme, and that the “up/down” equilibrium of Glu-242 may be coupled to the presence of active-site water molecules produced by O₂ reduction.     

Merychippus (Mammalia, Perissodactyla, Equidae) from the Middle Miocene of state of Oaxaca, southeastern Mexico

Mexican material referable to Merychippus from two localities in eastern Oaxaca was described first nearly 50 years ago. Subsequent work there and in Central Oaxaca, spanning some 30 years, has allowed to establish the detail stratigraphy in both regions, and assembled a collection of merychippine material from the Matatlán (Central Oaxaca) and El Camarón (eastern Oaxaca) Formations, both K-Ar dated ~15 Ma (late early Barstovian). Detailed taxonomic analysis of this collection indicate the presence of two subhypsodont horse species referable to “Merychippus” cf. “M.” primus and “M.” cf. “M.” sejunctus in both regions. These records document the coexistence in tropical southern North America of basal and hipparionine affinity merychippine grade species, and provide a glimpse in to the diversity of subhypsodont equids in this region.     

A solid-state NMR study of changes in lipid phase induced by membrane-fusogenic LV-peptides

Membrane fusion requires restructuring of lipid bilayers mediated by fusogenic membrane proteins. Peptides that correspond to natural transmembrane sequences or that have been designed to mimic them, such as low-complexity “Leu-Val” (LV) peptide sequences, can drive membrane fusion, presumably by disturbing the lipid bilayer structure. Here, we assess how peptides of different fusogenicity affect membrane structure using solid state NMR techniques. We find that the more fusogenic variants induce an unaligned lipid phase component and a large degree of phase separation as observed in ³¹P 2D spectra. The data support the idea that fusogenic peptides accumulate PE in a non-bilayer phase which may be critical for the induction of fusion.     

Evolving an ecology of mathematical expressions with grammatical evolution

This paper describes the use of grammatical evolution to obtain an ecology of artificial beings associated with mathematical functions, whose fitness is also defined mathematically. The system allows “parasite” species and “parasites of parasites” to develop, and supports the simultaneous evolution of several ecological niches. The use of standard measurements makes it possible to explore the influence of the number of niches or the presence of parasites on “biological” diversity and similar functions. Our results suggest that some of the features of biological evolution depend more on the genetic substrate and natural selection than on the actual phenotypic expression of that substrate.     

Cerebral perfusion pressure in giraffe: modelling the effects of head-raising and -lowering

Loss of consciousness caused by positional changes of the head results from reduced cerebral blood flow (CBF). CBF is related to cerebral perfusion pressure (CPP). CPP is the difference between mean arterial pressure (MAP) at the head and intracranial pressure (ICP). The positional change of the giraffe head between ground level and standing upright is the largest of all animals yet loss of consciousness does not occur. We have investigated the possibility that an increase in CPP protects giraffe from fainting, using a mechanical model that functioned as an anatomical U-tube. It consisted of a rigid ascending “carotid” limb, a collapsible “brain” tube drained by a rigid, “vertebral venous plexus” (VVP) tube, and a collapsible “head” tube drained by a collapsible tube representing the “jugular vein”. The descending tubes could be rotated relative to the “carotid” tube to be horizontal, or at 30°, 45°, and 60° to the vertical to simulate changes in head position. Pressure at the top of the “carotid” tube was intracranial MAP, at the top of the “VVP” tube was ICP, and the difference CPP. In the simulated “head-up” position and a fluid flow rate of 4 L min⁻¹, CPP was ∼170 mmHg. With the VVP tube horizontal, CPP fell from ∼170 to 45 mmHg, but increased to ∼67 mmHg at 30° “down”, to ∼70 mmHg at 45° “down” and to ∼75 at 60° “down”. The fall in CPP in the head-down positions resulted from a decrease in viscous resistance in, and dissipation of pressure to, the “head” and “jugular” tubes. These data provide an estimate of cranial pressure changes in giraffe during positional changes of the head, and suggest that an increase in CPP plays a significant role in maintaining CBF during head-raising and that it may be an important mechanism for preventing fainting in giraffe.     

A new clustering of antibody CDR loop conformations

Previous analyses of the complementarity-determining regions (CDRs) of antibodies have focused on a small number of “canonical” conformations for each loop. This is primarily the result of the work of Chothia and coworkers, most recently in 1997. Because of the widespread utility of antibodies, we have revisited the clustering of conformations of the six CDR loops with the much larger amount of structural information currently available. In this work, we were careful to use a high-quality data set by eliminating low-resolution structures and CDRs with high B-factors or high conformational energies. We used a distance function based on directional statistics and an effective clustering algorithm with affinity propagation. With this data set of over 300 nonredundant antibody structures, we were able to cover 28 CDR-length combinations (e.g., L1 length 11, or “L1-11” in our CDR-length nomenclature) for L1, L2, L3, H1, and H2. The Chothia analysis covered only 20 CDR-lengths. Only four of these had more than one conformational cluster, of which two could easily be distinguished by gene source (mouse/human; κ/λ) and one could easily be distinguished purely by the presence and the positions of Pro residues (L3-9). Thus, using the Chothia analysis does not require the complicated set of “structure-determining residues” that is often assumed. Of our 28 CDR-lengths, 15 have multiple conformational clusters, including 10 for which the Chothia analysis had only one canonical class. We have a total of 72 clusters for non-H3 CDRs; approximately 85% of the non-H3 sequences can be assigned to a conformational cluster based on gene source and/or sequence. We found that earlier predictions of “bulged” versus “nonbulged” conformations based on the presence or the absence of anchor residues Arg/Lys94 and Asp101 of H3 have not held up, since all four combinations lead to a majority of conformations that are bulged. Thus, the earlier analyses have been significantly enhanced by the increased data. We believe that the new classification will lead to improved methods for antibody structure prediction and design.     

Effect of temperature, pH and buffer presence on ethanol production from synthesis gas by "Clostridium ragsdalei"

Fermentation pH, incubation temperature, and presence or absence of media buffer can alter the activity of microorganisms. For instance, carbon monoxide and hydrogen components of syngas show decreased solubility with increasing temperature, Clostridium species preferentially switch from acetogenesis to solventogenesis phase at pH below 5.0, and morpholinoethanesulfonic acid (MES) added as media buffer has been shown to increase lag time for ethanol production. The objective of the present study was to determine the effects of temperature, pH and MES buffer on ethanol production by “Clostridium ragsdalei”. This study showed syngas fermentation using “Clostridium ragsdalei” at 32 °C with media without buffer was associated with higher ethanol concentration and reduced lag time in switching to solventogenesis. Temperature above 40 °C and pH below 5.0 were outside the optimal range for growth and metabolism of the bacteria.     

The crystal structure analysis of group B Streptococcus sortase C1: a model for the "lid" movement upon substrate binding

A unique feature of the class-C-type sortases, enzymes essential for Gram-positive pilus biogenesis, is the presence of a flexible “lid” anchored in the active site. However, the mechanistic details of the “lid” displacement, suggested to be a critical prelude for enzyme catalysis, are not yet known. This is partly due to the absence of enzyme-substrate and enzyme-inhibitor complex crystal structures. We have recently described the crystal structures of the Streptococcus agalactiae SAG2603 V/R sortase SrtC1 in two space groups (type II and type III) and that of its “lid” mutant and proposed a role of the “lid” as a protector of the active-site hydrophobic environment. Here, we report the crystal structures of SAG2603 V/R sortase C1 in a different space group (type I) and that of its complex with a small-molecule cysteine protease inhibitor. We observe that the catalytic Cys residue is covalently linked to the small-molecule inhibitor without lid displacement. However, the type I structure provides a view of the sortase SrtC1 lid displacement while having structural elements similar to a substrate sorting motif suitably positioned in the active site. We propose that these major conformational changes seen in the presence of a substrate mimic in the active site may represent universal features of class C sortase substrate recognition and enzyme activation.     

Figurations de l’amas stellaire des Pléiades sur deux roches gravées de la région du Mont Bego Z IX. GII. R 4 et Z IX. GIII. R 6

Two engraved rocks are situated 140 m from each other at an altitude of about 2250 m. One of them is called “female dancer”, and the other, “the Pleiads”, and both show a group of seven small pitted areas, of which one is smaller than the others and ‘ identified as the “Pleiads stellar cluster”, often depicted or mentioned during Antiquity and also throughout various historical periods.On each of these rocks, a large halberd, whose handle is oriented east-west, was traced along a natural fissure in the rock and engraved in the center of the composition. The “Pleiads stellar cluster” is represented on each of the two rocks beside the halberd : although situated to the west above the halberd blade on the “female dancer” rock, it is placed to the south and to the left of the halberd handle on “the Pleiads” rock. This difference may mark two distinct calendar data.The position of the different figures in the compositions illustrated on these two rocks, in particular inversions in the representation of some of them may indicate two distinct periods of the agricultural yearly cycle: on the rock called “female dancer”, the “heliacal raise” at summer's end, marking the beginning of the harvest and, on the rock called “the Pleiads”, the “heliacal setting”, just before winter, after the end of the harvest, when the rains soaks the ground and it is time to plow.