How to analyze the anticoagulant and antithrombotic mechanisms of action in fucanome and galactanome?

Through the perspective of the current glycomics age, fucanomics and galactanomics denote the international projects concerned with the studies of the biomedically active marine sulfated fucose- or galactose-composed polysaccharides, named sulfated fucans (SFs), and sulfated galactans (SGs), respectively. SFs and SGs are isolated from algae or marine invertebrates. The range of therapeutic actions of SFs and SGs is impressively broad. When certain structural requirements are found, some SFs and SGs may exhibit beneficial properties in inflammation, nociception, hemostasis (coagulation and thrombosis), vascular biology (angiogenesis), oncology, oxidative-stress, and virus infections. Although many biomedical applications for SFs and SGs have been pointed out over the past two decades, only inflammation, hemostasis, cancer, and vascular biology have their mechanisms of action satisfactorily elucidated. In addition, advanced structure-function relationships have been achieved only for the anticoagulant and antithrombotic activities, in which glycans of well-defined structures have been assayed. Because of this, the activities of SFs and SGs in stopping the clot and thrombus formation represent the closest therapeutic areas of having these glycans truly explored for drug development. Here, through an analytical viewpoint, we present the common methods and protocols employed to achieve such advanced structure-function relationships of SFs and SGs in anticoagulation and antithrombosis.     

The action mode of the ribosome-inactivating protein α-sarcin

Based on the tertiary structure of the ribosome-inactivating protein alpha-sarcin, domains that are responsible for hydrolyzing ribosomes and naked RNA have been dissected. In this study, we found that the head-to-tail interaction between the first amino beta-strand and the last carboxyl beta-strand is not involved in catalyzing the hydrolysis of ribosomes or ribonucleic acids. Instead, a four-strand pleated beta-sheet is indispensable for catalyzing both substrates, suggesting that alpha-sarcin and ribonuclease T1 (RNase T1) share a similar catalytic center. The integrity of an amino beta-hairpin and that of the loop L3 in alpha-sarcin are crucial for recognizing and hydrolyzing ribosomes in vitro and in vivo. However, a mutant protein without the beta-hairpin structure, or with a disrupted loop L3, is still capable of digesting ribonucleic acids. The functional involvement of the beta-hairpin and the loop L3 in the sarcin stem/loop RNA of ribosomes is demonstrated by a docking model, suggesting that the two structures are in essence naturally designed to distinguish ribosome-inactivating proteins from RNase T1 to inactivate ribosomes.     

How random is the toss of a coin?

Background

The toss of a coin has been a method used to determine random outcomes for centuries. It is still used in some research studies as a method of randomization, although it has largely been discredited as a valid randomization method. We sought to provide evidence that the toss of a coin can be manipulated.

Methods

We performed a prospective experiment involving otolaryngology residents in Vancouver, Canada. The main outcome was the proportion of “heads” coin tosses achieved (out of 300 attempts) by each participant. Each of the participants attempted to flip the coin so as to achieve a heads result.

Results

All participants achieved more heads than tails results, with 7 of the 13 participants having significantly more heads results (p ≤ 0.05). The highest proportion of heads achieved was 0.68 (95% confidence interval 0.62–0.73, p < 0.001).

Interpretation

Certain people are able to successfully manipulate the toss of a coin. This throws into doubt the validity of using a coin toss to determine a chance result.The toss or flip of a coin to randomly assign a decision traditionally involves throwing a coin into the air and seeing which side lands facing up. This method may be used to resolve a dispute, see who goes first in a game or determine which type of treatment a patient receives in a clinical trial. There are only 2 possible outcomes, “heads” or “tails,” although, in theory, landing on an edge is possible. (Research suggests that when the coin is allowed to fall onto a hard surface, the chance of this happening is in the order of 1 in 6000 tosses.¹)When a coin is flipped into the air, it is supposedly made to rotate about an axis parallel to its flat surfaces. The coin is initially placed on a bent forefinger, and the thumb is released from under the coin surface, where it has been held under tension. The thumbnail strikes the part of the coin unsupported by the index finger, sending it rotating upward. All this is done with an upward movement of the hand and forearm. The coin may be allowed to fall to the floor or other surface or it may be caught by the “tosser” and sometimes turned onto the back of the opposite hand and then revealed. The catching method should not matter, provided it is consistent for each toss. The opponent often calls the toss when the coin is airborne, although in the case of randomization for clinical trials, this is unnecessary because one is simply looking for an outcome.Open in a separate windowThe appeal of the coin toss that it is a simple, seemingly unbiased, method of deciding between 2 options. Although the outcome of a coin toss should be at even odds, the outcome may well not be. Historically, the toss of a coin before a duel reputedly decided which person had his back to the sun — an obvious advantage when taking aim! In medical trials, a simple statistical manipulation can have a dramatic effect on the treatment a patient receives. Our hypothesis is that with minimal training, the outcome of the toss can be weighted heavily to the call of the tosser, thus abolishing the 50:50 chance result that is expected and allowing for manipulation of an apparently random event.     

How costly is the honest signaling of need?

ESS models of biological signaling have shown that costly signals can provide honest information. In the context of parent-offspring conflict over the allocation of resources by parents to their young, the theory explains costly offspring solicitation behavior as an accurate signal of offspring need to parents who cannot assess offspring condition directly. In this paper, we provide a simple but general characterization of the honest signaling of need in models of parent-offspring conflict: the offspring's signaling cost is proportional to the parent's fitness loss from satisfying the offspring's resource requirement. The factor of proportionality is given by a measure of the extent of parent-offspring conflict that depends only on coefficients of relatedness. These results hold for interbrood conflict with uniparental investment even if the relationship between offspring condition and resource requirement is not monotonic, and extend to cases of biparental care, uncertainty concerning the parent's condition, and intra-brood conflict. Copyright 1999 Academic Press.     

Just How Emergent is the Emergence of Semiosis?

Studying the origin of semiosis is a task obscured by terminological and metaphysical issues which create an ambiguous set of definitions for biosemiotics when referring to the concept of emergence. The question is, how emergent can semiosis be? And what are the conditions for semiosis to be an emergent of a certain type? This paper will attempt to briefly deal with the general terminology of emergence from a philosophical point of view and will discuss the characterization of semiosis as an emergent phenomenon based on the distinctions made by Bedau, Kim and Chalmers. Accordingly, we will consider the possibility of strong and weak emergence in an attempt to bring some clarity to what it means for something in biosemiotics to be an emergent and how the philosophical concepts play out when applied to biosemiotic research. In inquiring into the metaphysical status of semiosis, we change our semiotic theories to correspond to the assumptions contained in the elementary objects of our theories. This being the case, the way semiosis–the constitutive element that it is for semiotics–is taken to be with regards to its possible ontology, will conduct to different research objects for the long-term investigation of its origins and necessary conditions.     

How is the individuality of a face recognized?

A familiar face is instantly recognized in a crowd. This cannot be achieved through a feature by feature comparison of the observed face with either an average face (norm-based model of face recognition) or with a set of similarly constructed faces stored in memory (exemplar-based model of face recognition). A modified norm-based model is thus proposed. Instead of memorizing an average face, the normal variations for each facial feature are used to construct a multidimensional volume of face-space devoid of unusual features, here defined as features whose metrics lie below the 5th or above the 95th percentiles for that feature. A face consisting of 100 independently variable features will thus have, on average, 10 unusual features. Face identification then becomes exception-reporting. It requires only 10 such rare features to render a given face a one in 10¹³ faces (P=0.05¹⁰=9.8×10⁻¹⁴). In a world containing 6.7×10⁹ people, such a face would be unique. Faces remembered in this way can have their unusual features exaggerated or attenuated without loss of identity. This is the basis of caricatures and anti-caricatures. It also means that individuals belonging to a foreign race, possessing several features with modes beyond the “usual range” of the own-race population, will all look alike. Features that render a face unique in the own-race population are now shared by everyone in the foreign race.Average faces are more beautiful than the faces used in the averaging process. This makes evolutionary sense. Natural selection increases the frequency of fit features at the expense of maladaptive features. “Usual features” are therefore fitter than “unusual features”, and play an important role in mate selection. Such an existing fundamental sexual attribute could easily have been harnessed for the fast and efficient recognition of individuals in the community.     

How widespread is the phenomenon of dosage compensation?

The study of the phenomenon of dosage compensation by classical genetic and cytological means has led in the past to some fundamental observations on the nature and function of the genetic material. Modern molecular techniques applied to the study of the same phenomenon have helped to uncover elements of genetic regulation that have broad biological significance. Given that the vast majority of the work has been and is still performed in three model systems, the purpose of this paper is to evaluate the contribution of other organisms to our understanding of this phenomenon and to explore their potential use in future studies.     

Mast cell activation--a receptor-independent mode of substance P action?

Substance P is a representative of a group of amphiphilic neuropeptides which act as mast cell secretagogues. Our experiments with some new substance P derivatives suggest that these effects are dependent on two structural elements: (i) a hydrophobic chain which is not essentially a peptide, and (ii) a hydrophilic part with two positively charged amino acids. The mast cell triggering effect is unlikely to be mediated by a selective substance P receptor, but has strong similarities to the mode of action of polycations.     

How acidic is the lumen?

Proton motive force (pmf), established across the thylakoid membrane by photosynthetic electron transfer, functions both to drive the synthesis of ATP and initiate processes that down-regulate photosynthesis. At the same time, excessively low lumen pH can lead to the destruction of some lumenal components and sensitization of the photosynthetic apparatus to photoinhibition. Therefore, in order to understand the energy budget of photosynthesis, its regulation and responses to environmental stresses, it is essential to know the magnitude of pmf, its distribution between pH and the electric field () as well as the relationships between these parameters and G_ATP, and down-regulatory and inhibitory processes. We review past estimates of lumen pH and propose a model that can explain much of the divergent data in the literature. In this model, in intact plants under permissive conditions, photosynthesis is regulated so that lumen pH remains mod erate (between 5.8 and 6.5), where it modulates the activity of the violaxanthin deepoxidase, does not significantly restrict the turnover of the cytochrome b₆f complex, and does not destabilize the oxygen evolving complex. Only under stressed conditions, where light input exceeds the capacity of both photosynthesis and down-regulatory processes, does lumen pH decrease below 5, possibly contributing to photoinhibition. A value of n = 4 for the stoichiometry of protons pumped through the ATP synthase per ATP synthesized, and a minor contribution of to pmf, will allow moderate lumen pH to sustain the observed levels of G_ATP.     

The role and mode of action of apolipoproteins CIII and AV: synergistic actors in triglyceride metabolism?

PURPOSE OF REVIEW: Apolipoprotein (apo)CIII and apoAV play an important role in triglyceride metabolism as evidenced by the unambiguous and opposing phenotypes of transgenic and knockout mouse models. In this review we discuss studies on the genetics, protein structure, and regulation of apoCIII and apoAV and compare their potential molecular mechanisms of action in triglyceride metabolism. We examine the hypothesis that apoCIII and apoAV synergistically affect triglyceride metabolism. RECENT FINDINGS: It has now been firmly established that variation in plasma triglyceride levels in a wide range of human populations is strongly associated with genetic variation at the chromosomal locus encoding both the APOC3 and APOA5 genes, the APOA1/C3/A4/A5 gene cluster. The close physical linkage of these genes and the frequent concurrence of genetic variants, however, complicate the assignment of specific metabolic defects to specific polymorphisms. Recent insight into the regulation of APOC3 and APOA5 gene expression and structural modeling studies on the apoAV protein have provided novel clues for the potential molecular mechanisms responsible for the effects of apoCIII and apoAV on triglyceride metabolism. SUMMARY: Hypertriglyceridemia is a major independent risk factor in the development of cardiovascular disease. Moreover, triglyceride-derived fatty acids are thought to play a key role in the development and progression of the metabolic syndrome. As modulators of triglyceride metabolism, apoCIII and apoAV are key players and potential therapeutic targets. However, little is known of their molecular mechanism and potential cooperativity. Rational therapeutic application will require the filling of this hiatus in our knowledge.     

How useful is PCR in the diagnosis of malaria?

Polymerase chain reaction (PCR) assays are the most sensitive and specific method to detect malaria parasites, and have acknowledged value in research settings. However, the time lag between sample collection, transportation and processing, and dissemination of results back to the physician limits the usefulness of PCR in routine clinical practice. Furthermore, in most areas with malaria transmission, factors such as limited financial resources, persistent subclinical parasitaemia, inadequate laboratory infrastructures in the poorer, remote rural areas preclude PCR as a diagnostic method. Even in affluent, non-endemic countries, PCR is not a suitable method for routine use. Nonetheless, PCR could be clinically useful in selected situations.     

How strong is the mutagenicity of recombination in mammals?

It is commonly believed that a high recombination rate such as that in a pseudoautosomal region (PAR) greatly increases the mutation rate because a 170-fold increase was estimated for the mouse PAR region. However, sequencing PAR and non-PAR introns of the Fxy gene in four Mus taxa, we found an increase of only twofold to fivefold. Furthermore, analyses of sequence data from human and orangutan PAR and X-linked regions and from autosomal regions showed a weak effect of recombination on mutation rate (a slope of less than 0.2% per cM/Mb), although a much stronger effect on GC content (1% to 2% per cM/Mb). Because typical recombination rates in mammals are much lower than those in PARs, the mutagenicity of recombination is weak or, at best, moderate, although its effect on GC% is much stronger. In addition, contrary to a previous study, we found no Fxy duplicate in Mus spretus.     

How dim is dim? Precision of the celestial compass in moonlight and sunlight

Prominent in the sky, but not visible to humans, is a pattern of polarized skylight formed around both the Sun and the Moon. Dung beetles are, at present, the only animal group known to use the much dimmer polarization pattern formed around the Moon as a compass cue for maintaining travel direction. However, the Moon is not visible every night and the intensity of the celestial polarization pattern gradually declines as the Moon wanes. Therefore, for nocturnal orientation on all moonlit nights, the absolute sensitivity of the dung beetle's polarization detector may limit the precision of this behaviour. To test this, we studied the straight-line foraging behaviour of the nocturnal ball-rolling dung beetle Scarabaeus satyrus to establish when the Moon is too dim--and the polarization pattern too weak--to provide a reliable cue for orientation. Our results show that celestial orientation is as accurate during crescent Moon as it is during full Moon. Moreover, this orientation accuracy is equal to that measured for diurnal species that orient under the 100 million times brighter polarization pattern formed around the Sun. This indicates that, in nocturnal species, the sensitivity of the optical polarization compass can be greatly increased without any loss of precision.     

What is the role of putrescine accumulated under potassium deficiency?

Biomarker metabolites are of increasing interest in crops since they open avenues for precision agriculture, whereby nutritional needs and stresses can be monitored optimally. Putrescine has the potential to be a useful biomarker to reveal potassium (K⁺) deficiency. In fact, although this diamine has also been observed to increase during other stresses such as drought, cold or heavy metals, respective changes are comparably low. Due to its multifaceted biochemical properties, several roles for putrescine under K⁺ deficiency have been suggested, such as cation balance, antioxidant, reactive oxygen species mediated signalling, osmolyte or pH regulator. However, the specific association of putrescine build-up with low K⁺ availability in plants remains poorly understood, and possible regulatory roles must be consistent with putrescine concentration found in plant tissues. We hypothesize that the massive increase of putrescine upon K⁺ starvation plays an adaptive role. A distinction of putrescine function from that of other polyamines (spermine, spermidine) may be based either on its specificity or (which is probably more relevant under K⁺ deficiency) on a very high attainable concentration of putrescine, which far exceeds those for spermidine and spermine. putrescine and its catabolites appear to possess a strong potential in controlling cellular K⁺ and Ca²⁺, and mitochondria and chloroplasts bioenergetics under K⁺ stress.     

How thick is the layer of thermal volume surrounding the protein?

Investigation on the volume properties of protein hydration layers is reported. Presented results are based on combination of Monte Carlo modeling and available experimental data. Six globular proteins with known data are chosen for analysis. Analyzing the model and the experimental results we found that water molecules bound to proteins by hydrogen bond are preferentially located at the places with local depressions on the protein surface. Consequently, the hydration level is not strictly proportional to the area of charged and polar surfaces, but also depends on the shape of the molecular surface. The thickness of the thermal volume layer as calculated in the framework of the scaled particle theory is 0.6-0.65 A for chosen proteins. The obtained value is significantly lower than that presented for proteins in earlier papers (where proportionality between the hydration level and the area of charged and polar surfaces was assumed), but is close to the value published for small solute molecules. Discussion including the influence of protein size and the thermal motion of the surface is presented.