Senescence: the good the bad and the dysfunctional

Nearly 50 years have elapsed since Hayflick challenged the dogma that individual human cells were immortal by demonstrating that after a predictable number of cellular divisions, normal human fibroblasts eventually entered a state of permanent growth arrest [Hayflick L: The limited in vitro lifetime of human diploid cell strains. Exp Cell Res 1965, 37:614-636.; Hayflick L, Moorhead PS: The serial cultivation of human diploid cell strains. Exp Cell Res 1961, 25:585-621]. This growth arrest, referred to as senescence, was hypothesized to function as a tumor suppressive mechanism, capable of limiting the replicative capacity of an incipient tumor cell. While originally met with skepticism, the existence of senescence and its importance as a tumor suppressive mechanism is now accepted. Here, we highlight this work and introduce studies that indicate that while senescent cells themselves cannot produce a neoplasia, they possess the ability to promote the growth of nearby preneoplastic cells and in this way may contribute to age-related increases in tumor incidences. This added level of complexity suggests that senescence functions as a biological 'double edged sword.'     

Understanding the parts in terms of the whole

Metabolism is usually treated as a set of chemical reactions catalysed by separate enzymes. However, various complications, such as transport of molecules across membranes, physical association of different enzymes, giving the possibility of metabolite channelling, need to be taken into account. More generally, a proper understanding of the nature of life will require metabolism to be treated as a complete system, and not just as a collection of components. Certain properties of metabolic systems, such as feedback inhibition of the first committed step of a pathway, make sense only if one takes a broader view of a pathway than is usual in textbooks, so that one can appreciate ideas such as regulation of biosynthesis according to demand. More generally still, consideration of metabolism as a whole puts the emphasis on certain systemic aspects that are crucial but which can pass unnoticed if attention is always focussed on details. For example, a living organism, unlike any machine known or conceivable at present, makes and maintains itself and all of its components. Any serious investigation of how this can be possible implies an infinite regress in which each set of enzymes needed for the metabolic activity of the organism implies the existence of another set of enzymes to maintain them, which, in turn, implies another set, and so on indefinitely. Avoiding this implication of infinite regress represents a major challenge for future investigation.     

Theoretical study of the optimal shape of the front profile of the lens in the eye of the scallop,Pecten

The optimal shape of the front profile of the thick lens in the eye of the scallop,Pecten is theoretically, geometric optically investigated as a function of the refractive index of the lens and the retina, as well as of the geometrical parameters of the eye. The shape of the theoretical front surfaces is compared with that of the real, experimentally determined front face of the lens. The degree of correction of the lens for spherical aberration of the reflecting spherical mirror in thePecten eye is examined. The optimal shape of the front profile of the lens depends strongly on a set of parameters, such that a certain fine tuning is required among them to assure a full correction for spherical aberration. The extreme variability of the eye parameters and the shape of the front face of the lens in the scallop is inconsistent with this fine tuning requirement. The degree of correction of thePecten lens for spherical aberration might not be as good as it could be, a possible biooptical reason for which is discussed.     

Characterization of the channel constriction allowing the access of the substrate to the active site of yeast oxidosqualene cyclase

In oxidosqualene cyclases (OSCs), an enzyme which has been extensively studied as a target for hypocholesterolemic or antifungal drugs, a lipophilic channel connects the surface of the protein with the active site cavity. Active site and channel are separated by a narrow constriction operating as a mobile gate for the substrate passage. In Saccharomyces cerevisiae OSC, two aminoacidic residues of the channel/constriction apparatus, Ala525 and Glu526, were previously showed as critical for maintaining the enzyme functionality. In this work sixteen novel mutants, each bearing a substitution at or around the channel constrictions, were tested for their enzymatic activity. Modelling studies showed that the most functionality-lowering substitutions deeply alter the H-bond network involving the channel/constriction apparatus. A rotation of Tyr239 is proposed as part of the mechanism permitting the access of the substrate to the active site. The inhibition of OSC by squalene was used as a tool for understanding whether the residues under study are involved in a pre-catalytic selection and docking of the substrate oxidosqualene.     

Brazil at the third United Nations conference on the law of the sea

Abstract

As Brazil began to emerge as a major power in the years leading up to theThird United Nations Conference on the Law of the Sea (UNCLOS III), national ocean policy came to have a quite continuous, distinctive impact on global law of the sea negotiations. Brazil's participation at UNCLOS III offers a particularly good vantage point from which to analyze its more prominent international role as an emerging major power, its related growth as a maritime power, and its significant contribution to international organization.

UNCLOS III, in turn, affects Brazil. The broad implications of the emerging ocean order for both national and international jurisdiction issues, within which Brazilian ocean policy must operate, are analyzed. Brazil's distinctive position as an emerging power between the industrialized countries and the Third World has conditioned its involvement at UNCLOS III. As a developing state, Brazil has favored revision of the traditional order for the purpose of redressing the balance with the developed states. At the same time, as an emerging power, Brazil has an interest in supporting a stable, open international order. In spite of such policy dilemmas, Brazil stands out as one of the few big potential winners in the Third World from both the seabed and non‐seabed portions of the law of the sea negotiations.     

Non-universal usage of the leucine CUG codon and the molecular phylogeny of the genus Candida

CUG, a universal leucine codon, was reported to be read as serine in 10 species of the genus Candida. We used an in vitro cell-free translation system to identify the amino acid assignment of codon CUG in 78 species and 7 varieties of galactose-lacking Candida species equipped with Q9 as the major ubiquinone. Of these, only 11 species used codon CUG as a leucine codon. The remaining species decoded CUG as serine. Their small subunit ribosomal DNA sequences were also determined and analyzed using both Neighbor-Joining and Maximum Likelihood methods. The species decoding CUG as serine and leucine formed distinct clusters on both molecular phylogenetic trees. Our result suggests that non-universal decoding is not a rare event, and that it is widely distributed in the genus Candida.     

On the role of the pineal in thermoregulation in the pigeon

Diurnal rhythm in body temperature of pigeons subjected to different experimental conditions (pinealectomized, sham-operated, melatonin-implanted, cold-exposed) was studied under a 12 h light and 12 h dark regimen. The body temperature of pigeons during photophase was higher than that during scotophase in the normal as well as every treatment group studied. Pinealectomized pigeons showed higher body temperature in the photophase as well as scotophase, than that of the normal and sham-operated birds when examined 2 or 3 weeks following the post-surgical acclimatization to 25 or 3 degrees C. However, subcutaneous implantation of melatonin pellets into pinealectomized pigeons nullified or even reversed the hyperthermic effect of pinealectomy. Exposure of pigeons to--18 degrees C for 280 min during photophase as well as scotophase, produced a marked drop in body temperature in pinealectomized, sham-operated and normal pigeons. The pinealectomized pigeons exhibited a higher body temperature than that of the sham-operated and normal ones when exposed to--18 degrees C during the photophase, but not during the scotophase. It was concluded that while the pineal is not necessary for maintaining the daily thermal rhythm in the avian body, it has a thermoregulatory role, in that it prevents rise in body temperature in warm (25 degrees C) acclimatized and chronic cold (3 degrees C) exposed birds. In acute short-term cold (--18 degrees C) exposure however, the temperature regulatory role of the pineal was not effective during the scotophase.     

Editorial: Defining the membrane precursor supporting the nucleation of the phagophore

How does the phagophore form? Which membrane acts as a platform for its biogenesis? Over the years, extensive use of microscopy techniques have led to the controversial identification of multiple potential membranes as precursors for phagophore nucleation and/or for the supply of lipids to the expanding compartment. Nevertheless, none of these studies has established a direct functional link between membrane sources and autophagosome biogenesis. Addressing this point, in a recent study highlighted by a punctum in this issue, Ge and coworkers developed an in vitro approach to determine the identity of the membranes responsible for the lipidation of LC3, thus identifying the ER-Golgi intermediate compartment (ERGIC) as a potential key determinant of phagophore biogenesis.     

From the saltpan to the plate: An evaluation of the use of the edible halophyte Salicornia ramosissima in catering

The halophyte species Salicornia ramosissima has long been consumed as food and is currently regarded as a high-value gourmet item. However, given that these plants grow in estuarine areas, often impacted by pollution, and are prone to the accumulation of ions, the risks associated with food borne pathogens or toxic metals has to be carefully considered. The objective of this work was to gather evidence that S. ramossissima harvested locally in an estuarine system (Ria de Aveiro, Portugal) can be safely consumed as a healthy and catering-amenable food. Fresh shoots, taken as green vegetables, and dried powdered shoots (green salt) intended as seasoning, were analysed for total aerobic bacteria, total coliforms, Escherichia coli, Bacillus cereus and fungi (yeasts and moulds). The nutritional profile and the concentration of macro and micro elements, including potential toxic elements, was also established. Fresh shoots and green salt were incorporated in catering meals (soup and a meat dish) and subjected to sensory analyses. The microbiological quality of fresh shoots and green salt was compliant with the guidelines for salad greens and herbs and spices, respectively. The nutritional and elemental profile revealed that fresh shoots have a high content in fibre and NaCl. From the concentration of Na determined in green salt, a daily dose of 7 g was estimated as corresponding to the recommended daily dietary intake Na. None of the other elements was present in concentrations that could exceed the dietary intake limits. In the sensory tests, fresh shoots were well accepted as salad greens but green salt, used as seasoning, was considered as insufficient in terms of saltiness and does not completely substitute cooking salt. The results confirm the nutritional and sensory value of S. ramossisima and represent a promising prospect for the incorporation of locally harvested or crop cultivated plants in catering meals.     

MMP-1: the elder of the family

The matrix metalloproteinases (MMPs) are a family of zinc-containing endopeptidases that play a key role in both physiological and pathological tissue remodeling. Human fibroblast collagenase (MMP-1) was the first vertebrate collagenase purified as a protein and cloned as a cDNA, and is considered the prototype for all the interstitial collagenases. It is synthesized as a zymogen where N-terminal residues are removed by proteolysis and shares with other MMPs a catalytic domain and a carboxy terminal domain with sequence similarity to hemopexin. Importantly, MMP-1 should be considered a multifunctional molecule since it participates not only in the turnover of collagen fibrils in the extracellular space but also in the cleavage of a number of non-matrix substrates and cell surface molecules suggesting a role in the regulation of cellular behaviour. Furthermore, an extensive body of evidence indicates that MMP-1 plays an important role in diverse physiologic processes such as development, tissue morphogenesis, and wound repair. Likewise, it seems to be implicated in a variety of human diseases including cancer, rheumatoid arthritis, pulmonary emphysema and fibrotic disorders, suggesting that its inhibition or stimulation may open therapeutic avenues.     

On the kinematic modelling and the parameter estimation of the human shoulder.

This paper presents some results on the modelling and the corresponding parameter estimation of the human shoulder. This system consists of the clavicle, the scapula, the humerus and the various joints between these bodies and the trunk through the sternum; it will be represented as a succession of a rotational joint between the sternum and the clavicle and a constant distance joint, representing the scapula between, the clavicle and the humerus head. The parameters of this system are the components of the position vectors of the joint characteristic points (the corresponding centres of the rotations). Experimental results are presented as well as a validation of the proposed model.     

Youth and personality formation--the world belongs to the strength of the young and to the wisdom of the elderly (a point of view of the communicologist)

It is known from the pedagogic, didactic and experience coordinates that a man doesn't become better by using words but by his actions. They are matchless examples for the self-apprehension process and the perception of the action itself as well as the only worthy and accurate offer for the assessment of the range and the significance of the achieved result. From the earliest stage of their life, from the childhood and then later on in different stages of their development and growth, the human being as a social being has a double need: to feel himself in the range of his "I" and to feel himself as a member of a group, a family and of the society in general. Satisfying the sense and the level of those needs doubtlessly depends on the examples given by the life itself and the circumstances of the living within the family, the school and finally the society, that is, the surroundings where the individual is affirming himself by his individual creative capability and skills with which he realizes himself as a subject on its own as well as within the social group he lives and works in. The conditions of the life and work of the elderly are necessary for this important and precious task in the development of a young man so that the applications of their experiences could ensure reliable guidelines for the harmony and success of the life and work of the young. On this bridge of generations the experience of the old is affirmed along with the need for its aimed, creative and fruitful offer to the young in the dynamic process of their development to the maturity and creativity.     

When time and numerosity interfere: the longer the more, and the more the longer

There is strong evidence that magnitudes in different dimensions can interfere. A majority of previous studies on the interaction of temporal magnitudes on numerosity showed no interfering effect, while many studies have reported the interference of numerosity on judgement of temporal magnitudes. We speculated that this one-way interference is confounded by the magnitudes used in the studies. We used a methodology that allowed us to study this interaction reciprocally. Moreover, we selected magnitudes for two dimensions that enabled us to detect their interfering effects. Participants had to either judge which of two successive sets of items was more numerous (numerosity judgement task), or which set of items was presented longer (duration judgement task). We hypothesised that a longer presentation of a set will be judged as being more numerous, and vice versa, a more numerous set will be judged as being presented longer. Results confirmed our hypothesis. A positive correlation between duration of presentation and judged numerosity as well as a positive correlation between the number of items and judged duration of presentation was found. This observation supports the idea that duration and numerosity judgements are not completely independent and implies the existence of (partly) generalised and abstract components in the magnitude representations.     

On the Identity of the Amoeboflagllates Didascalus throntoni and Adelphamoeba galeacystis

ABSTRACT. Didascalus thorntoni , Singh 1952 has been classified alternately as a separate genus or as a species of Naegleria. In the 18th edition of the American Type Culture Collection catalogue it is classified as Naegleria thorntoni. To resolve the question of its identity we have used riboprinting and sequencing of the small subunit ribosomal DNA. The results indicate that D. thorntoni does not belong to the genus Naegleria. The sequence of the small subunit ribosomal DNA differs only in 20 nucleotides (1%) from that of the Paratetramitus jugosus. The difference is much smaller than between some species of Naegleria. Therefore, it is not clear whether D. thorntoni should be considered as a species of Paratetramitus or as a separate genus. The strain used in different laboratories as the type strain of Adelophamoeba gleacystis has been identified as a Naegleria strain. We believe that the type strain of A. galeacystis was mislabeled prior to submission to the American Type Culture Collection and to the Culture Collection of Algae and Protozoa. A recent isolate, which on the basis of morphology was identified as a strain of A. Galeacystis , has the identical small subunit ribosomal DNA sequence as D. throntoni. Our results prove Page was right when he stated that Adelphamoeba might be a synonym of Didascalus.     

Mining the pharmacogenomics literature--a survey of the state of the art

This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.     

Evaluation of the role of the adaptive result in the theory of the functional systems

The fundamental of the theory of the functional systems, i.e., the concept of the useful adaptive result as a universal system-forming factor is considered. It is suggested that the adaptive result is not system-forming in behaviors actualized exclusively due to activity of systems developed earlier. It is argued that positive mutations may serve as the system-forming factor for hereditary determined behavioral forms. In all other cases of goal-directed behavior (except conditioning) the aim of performance as a model of the future result plays the decisive role. Only in conditioning the classical concept of the system-forming role of the adaptive result seems to be undeniable. The refined ideas about the mechanisms of formation of the functional systems may be useful in analysis of a number of animal and human functions (learning, emotional stress, neuroses, etc.).     

Improving the Power of Structural Variation Detection by Augmenting the Reference

The uses of the Genome Reference Consortium’s human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.     

Doxorubicin inhibits the phosphate-transport protein reconstituted in liposomes. A study on the mechanism of the inhibition

Using Thr(P)-inhibitor-1 and Ser(P)-casein as substrates, studies on the activation of calcineurin purified from bovine brain have been carried out. The phosphatase requires the synergistic action of Ca2+, calmodulin and another divalent cation (Mg2+, Mn2+, Co2+ or Ni2+, but not Zn2+) for full expression of its activity. Ca2+ and Ca2+ X calmodulin act as allosteric activators to transform the phosphatase to a relaxed conformation, while Mg2+ acts solely as a cofactor for the catalytic action of the enzyme. In addition to their function as cofactors for catalysis, transition metal ions can also substitute for Ca2+ as allosteric activators. Ca2+ and calmodulin exert their activating effects mainly by increasing the Vm of the phosphatase reaction with little effect on the Km values for the substrates or on the KA values for the divalent cation cofactors. The predominant factor in dictating the catalytic properties of calcineurin is the divalent cation cofactor. For example, with Mg2+ as a cofactor, the phosphatase exhibits an optimum around pH 8.0-8.5; while with a transition metal ion as a cofactor, the optimum is around pH 7.0-7.5, regardless of whether Thr(P)-inhibitor-1 or Ser(P)-casein serves as a substrate, in the absence or the presence of Ca2+ X calmodulin.