The Escherichia coli cell cycle

This review summarizes present knowledge of the bacterial cell cycle with particular emphasis on Escherichia coli. We discuss data coming from three different types of approaches to the study of cell extension and division: The search for discrete events occurring once per division cycle. It is generally agreed that the initiation and termination of DNA replication and cell septation are discrete events; there is less agreement on the sudden doubling in rate of cell surface extension, murein biosynthesis and the synthesis of membrane proteins and phospholipids. We discuss what is known about the temporal relationship amongst the various cyclic events studied. The search for discrete growth zones in the cell envelope layers. We discuss conflicting reports on the existence of murein growth zones and protein insertion sites in the inner and outer membranes. Elucidation of the mechanism regulating the initiation of DNA replication. The concept of "critical initiation mass" is examined. We review data suggesting that the DNA is attached to the envelope and discuss the role of the latter in the initiation of DNA replication.     

Psychiatric Aspects of Artificial Insemination (Donor)

Artificial insemination (donor) [A.I.D.] in humans is a medical procedure that has been carried out for roughly 50 years. Its legal status has not yet been established; its moral implications are still hotly contested, and its psychological and psychiatric implications are only now coming under scientific scrutiny.The use of this procedure in couples who are psychologically unsuited for it can have unfortunate consequences. The obstetrician should seek the assistance of a dynamically oriented psychiatrist in screening couples who ask for artificial insemination (donor).Parenthood, in line with psychoanalytic ego psychology, is seen as a phase of ego development. The potential for mothering and fathering children is a later stage in growth than the capacity to conceive and sire them. It is the psychiatrist''s role to assess the couple''s motivation for A.I.D. in the light of the extent to which they have achieved this degree of ego development.     

Brain physiology and origin of the human subjective experience

The modern approaches to the problem of the brain basis of subjective experience are reviewed in the paper. The main hypothesis proposes that the events of subjective experience emerge as a result of information comparison and synthesis in crucial for this mental function cortical areas. This synthesis is provided by the special organization of brain processes which includes circulation of nerve impulses in the brain structures. Memory traces are retrieved during this process, and then the appropriate centers of motivations and emotions are activated. Afterwards, the excitation returns to the sites of initial projections, where the synthesis of new information and that retrieved from memory is performed. The hypothesis has been proposed by the author more than twenty years ago and is based on the experimental study of the brain mechanisms of sensation and thinking. It is also shown that the frontal cortex and, particularly, the verbal centers are involved in recognition and decision making. The last part of the paper deals with the problem of the functional significance of subjective events. The possible double bottom-up and top-down determination of brain and mental events is considered and the importance of the search for experimental approaches to these problems is argued.     

Human brain reflexes: from stimulus to recognition and from decision to action

The paper presents a survey of the data, obtained in laboratories, directed by the author, on the problem of the brain bases of psychics. Phenomena of perception, thinking and taking decision about behavioural response correspond to the afferent, central and efferent parts of the reflex arch. Psychic function arises on the basis of complex organization and integration of the processes in the brain. It is shown that sensation is based on the synthesis in the cortical projection area of the information on physical and signal properties of the stimulus. By means of the method developed in the laboratory, of mapping of intracortical interaction the participation is studied of different cortical zones in the process of mental creation of visual image. The process of taking decision is studied by a new method: "reaction choice potential" recorded in the case of decision, about the character of reaction to signal controlled by consciousness.     

« Sens et essence du monde et du moi onirique » dans <Emphasis Type="Italic">Rêve et Existence</Emphasis> de Ludwig Binswanger

This paper reflects on one of Ludwig Binswanger’s best-known essays, in an effort to clarify the mode of existence of the person within the oneiric world and, therefore, the manifestation mode of that world itself. The author argues that what matters most in the expression of that world is not that it consists of images, but that it is devoid of syntax. This makes it both global and perfective and explains why nothing in it is actually determined by the ego of the dreamer. Its space has no horizon, no perspective and no vantage point, and its temporality is in gestation (chronogenetics), with no concept of the separation of present, past and future. It is characterised by process and lacking in structure. In addition, it is strangely familiar, because it echoes the past in a way that indicates inevitable fate. While the dreaming ego is well folded into that world, its mode of existence remains impersonal; it doesn’t decide for itself, and it doesn’t confront what is coming. The strangeness encountered is not that of the Other, but that of the stranger the ego perceives within itself. Dreaming, therefore, offers the opportunity for human beings to experience existence when it is still undecided — Freud called it the id and Schelling Gemüt — in a place where the ego has not yet become a person. It is only in the waking world that people can integrate their still inchoative egos and give them a destination.     

Specific features of lateralization of a stationary auditory image by a human under condition of stimulation without interaural differences: a neurophysiological analysis

Analysis of the lateralization phenomena of a fused auditory image (FAI) was performed on the basis of the previously developed model of the binaural directional hearing. It was found earlier that, under conditions of auditory stimulation without interaural differences, the FAI was localized at the head midline only in about a quarter of subjects. In a greater part of the listeners, the FAI was lateralized within the range of -4.6 ... +11.2 degrees from the midline. It was shown that FAI localization with reference to the head midline may be determined by the extent of asymmetry and spatial contrast between the "active" neural zones in the left and right halves of the subjective auditory space. In turn, the asymmetry (or its absence) of these "active" zones fully depends on a distribution of neurons by characteristic time delays in the left and right halves of the subjective auditory field. The model also explains the fact of a decrease in localization precision with the FAI position just at the midline.     

The LSD Syndrome—A Review

lsd (lysergic acid diethylamide) is a powerful bio-active substance related to serotonin in structure. Its actions generally affect autonomic, sensory and psychological functions. Autonomic stimulation is varied. Sensory responses are usually visual, involving heightened and distorted color perception and fusion of sensory impressions. Psychological responses include a feeling that a unique experience is occurring; feelings of depersonalization; pronounced fluctuation of mood; time and space distortions; autistic phenomena; fluctuation of aggressive drives (usually reduction); and spontaneous reoccurrence of the lsd experience.The subjective responses can be related to three basic phenomena: (1) expectation; (2) loss of characteristic modes of perceptual and cognitive patterning; and (3) hypersuggestibility.The major adverse reactions are: (1) chronic drug dependence including subsequent personality changes and depressive reactions; and (2) acute ego dissolution. These reactions usually occur in already emotionally ill people. Most of these users fall into two groups, those with unresolved identity problems and those with severe ego abnormality. The majority of adverse reactions are of the chronic drug dependence type and are usually seen in adolescents and young adults who have not negotiated the age-appropriate tasks of forming and integrating the various identities that are the composite of their life experiences.lsd helps alleviate these stresses via some of its psychological properties as discussed. It also provides a nidus for the formation of a subculture where goals for social, sexual and vocational achievement are lower and idiosyncratic modes of adaptation are better tolerated. A smaller group of users who have serious reactions such as psychosis, rage reactions, homicidal and suicidal ideation are usually found to have preexisting ego abnormality such as ambulatory schizophrenia, chronic impulse disorders and borderline states. Although adverse reactions most often appear to be related to pre-morbid psychopathology, this is not invariably so. Further, there is as yet no reliable method to determine who will have an adverse reaction and what the nature of that reaction will be.     

The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast

The refinement and high-throughput of protein interaction detection methods offer us a protein–protein interaction network in yeast. The challenge coming along with the network is to find better ways to make it accessible for biological investigation. Visualization would be helpful for extraction of meaningful biological information from the network. However, traditional ways of visualizing the network are unsuitable because of the large number of proteins. Here, we provide a simple but information-rich approach for visualization which integrates topological and biological information. In our method, the topological information such as quasi-cliques or spoke-like modules of the network is extracted into a clustering tree, where biological information spanning from protein functional annotation to expression profile correlations can be annotated onto the representation of it. We have developed a software named PINC based on our approach. Compared with previous clustering methods, our clustering method ADJW performs well both in retaining a meaningful image of the protein interaction network as well as in enriching the image with biological information, therefore is more suitable in visualization of the network.     

THEA: ontology-driven analysis of microarray data

MOTIVATION: Microarray technology makes it possible to measure thousands of variables and to compare their values under hundreds of conditions. Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information available. Currently, data interpretation clearly constitutes the bottleneck of such analyses and there is an obvious need for tools able to fill the gap between data processed with mathematical methods and existing biological knowledge. RESULTS: THEA (Tools for High-throughput Experiments Analysis) is an integrated information processing system allowing convenient handling of data. It allows to automatically annotate data issued from classification systems with selected biological information coming from a knowledge base and to either manually search and browse through these annotations or automatically generate meaningful generalizations according to statistical criteria (data mining). AVAILABILITY: The software is available on the website http://thea.unice.fr/     

DO SUTURE ZONES EXIST?

Remington (1968) argued that 13 suture zones exist in North America. Remington defined a suture zone as, "a band of geographic overlap between major biotic assemblages, including some pairs of species or semispecies which hybridize in the zone" (p. 322). Although initially controversial, the idea that suture zones exist has picked up momentum over the past decade, due largely to the phylogeographic work of Hewitt, Avise, and their colleagues. Nevertheless, the reality of suture zones has not yet been subjected to rigorous analysis using statistical and geographic information system (GIS) approaches. To test for the existence of Remington's suture zones, we first identified 117 terrestrial hybrid zones in Canada and the United States through a literature search for the key words "cline," "contact zone," "hybrid zone," and "hybridization" in articles published between 1970 and 2002. The 117 hybrid zones were mapped using a GIS approach and compared with a digitized version of Remington's original suture zone map. Overall, there does appear to be an association between hybrid zones and suture zones, but this association is largely attributable to clustering of hybrid zones in only two of the 13 suture zones recognized by Remington. The results suggest that evolutionary biologists should retain some skepticism toward Remington's suture zones.     

Neurons that express the AMPA receptor GluR2/3 subunits in suprachiasmatic nuclei of Syrian hamsters colocalize either vasoactive intestinal peptide, peptide histidine isoleucine or gastrin-releasing peptide

In mammals, many circadian rhythms are driven by a clock located inside the suprachiasmatic nucleus of the hypothalamus. They are synchronized to environmental light-dark cycles by information coming directly from the retina via glutamatergic afferents. In rodents, retinal fibres make direct synaptic contacts with neurons synthesizing vasoactive intestinal peptide and gastrin-releasing peptide. These two neuropeptides, administered alone or combined with the peptide histidine isoleucine, phase-shift the clock in the same way that light does. Using ICC and light and electron microscopy, our study demonstrates that subunits 2 and 3 of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid-type glutamatergic receptors are colocalized in neurons expressing one or other of these three neuropeptides. Double-labelled neurons were located in the ventral and lateral ventral parts and near the symmetrical plane of the intermediate and caudal thirds of the nucleus. In light microscopy, brown and granular blue stainings of chromogens revealing both antigens were easily identifiable and spatially separated in perikarya. In electron microscopy, almost all the cells observed in these zones expressed the receptor subunits. A few labelled dendritic profiles, some of them post-synaptic, were observed; axon terminals were always unlabelled. Colocalization with vasoactive intestinal peptide and gastrin-releasing peptide was confirmed by the immunogold technique in perikarya and some dendrites. The present study suggests that peptidergic neurons expressing the AMPA receptors are involved in photic entrainment of the clock by the retina without excluding some glutamatergic information coming from other hypothalamic nuclei.     

The polymorphism of the genes/enzymes involved in the last two reductive steps of monolignol synthesis: what is the functional significance?

The polymorphism of genes and enzymes involved in the last two steps of monolignol synthesis is examined in the light of recent data coming from genomic studies and mutant/transformant analyses. The two catalytic activities considered--cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD)--are encoded by small multigene families. While some degree of diversification can be noted at the sequence level, it is often difficult to use this information to assign substrate specificities to each member of a gene family. Expression profiles, however, suggest for both CAD and CCR the existence of two sub-families: one devoted to developmental lignification, and the other involved in the synthesis of defence-related compounds.     

Estimation of metabolite networks with regard to a specific covariable: applications to plant and human data

Introduction

In systems biology, where a main goal is acquiring knowledge of biological systems, one of the challenges is inferring biochemical interactions from different molecular entities such as metabolites. In this area, the metabolome possesses a unique place for reflecting “true exposure” by being sensitive to variation coming from genetics, time, and environmental stimuli. While influenced by many different reactions, often the research interest needs to be focused on variation coming from a certain source, i.e. a certain covariable \(\mathbf {X}_m\).

Objective

Here, we use network analysis methods to recover a set of metabolite relationships, by finding metabolites sharing a similar relation to \(\mathbf {X}_m\). Metabolite values are based on information coming from individuals’ \(\mathbf {X}_m\) status which might interact with other covariables.

Methods

Alternative to using the original metabolite values, the total information is decomposed by utilizing a linear regression model and the part relevant to \(\mathbf {X}_m\) is further used. For two datasets, two different network estimation methods are considered. The first is weighted gene co-expression network analysis based on correlation coefficients. The second method is graphical LASSO based on partial correlations.

Results

We observed that when using the parts related to the specific covariable of interest, resulting estimated networks display higher interconnectedness. Additionally, several groups of biologically associated metabolites (very large density lipoproteins, lipoproteins, etc.) were identified in the human data example.

Conclusions

This work demonstrates how information on the study design can be incorporated to estimate metabolite networks. As a result, sets of interconnected metabolites can be clustered together with respect to their relation to a covariable of interest.

     

East-West cranial differentiation in pre-Columbian human populations of South America.

South Amerindians are frequently thought of as a rather biologically homogeneous megapopulation. However, when native South Americans are assessed by information coming from DNA variability analysis, they resolve into two, major distinct entities of Eastern and Western zones. The purpose of this study is to investigate if the same dual pattern emerges from craniometric data. We approached this question by means of functional craniometric variables. We found strong evidence that Westerners and Easterners constitute two distinct and independent microevolutionary universes when cranial morphology is assessed. The existence of a third universe, Northwest, cannot be completely ruled out, but needs further investigation. We also discovered that Westerners and Easterners present similar degrees of internal variation, contrary to the findings of geneticists and molecular biologists. Palaeoamericans seem to be more similar to Easterners than to Westerners and North-Westerners. Our results suggest that this East-West cranial differentiation is more probably the result of differential rates of genetic drift and gene flow acting on each side of the Cordillera. However, different intensities of gene flow between Palaeoamericans and Amerindians in the highlands and in the lowlands cannot be completely dismissed as a possible explanation for the differentiation found.     

A model study of the role of proteins CLV1, CLV2, CLV3, and WUS in regulation of the structure of the shoot apical meristem

In order to elucidate the role of proteins CLV1, CLV2, CLV3, and WUS in the mechanism underlying the maintenance of compartmental structure (spatial arrangement of the zones of biosynthesis of marker proteins) of the shoot apical meristem, a model of such mechanism was developed. Computational experiments led to biologically plausible solutions only when synthesis of substance W in a space between the organizing center and meristem apex was limited by the mechanism based on interaction of CLV3 with membrane receptor CLV1/CKV2 and lower boundary of the zone of W synthesis was determined by isoline of the corresponding threshold level of substance Y concentration. The model of the "reaction-diffusion" type formalizing the role proteins CLV1, CLV2, CLV3, and WUS can describe the basis of the mechanism underlying regulation of the compartmental structure of the shoot apical meristem and positioning of the organizing center in a certain site of the cell ensemble of such meristem.     

Negative BOLD differentiates visual imagery and perception

Recent studies emphasize the overlap between the neural substrates of visual perception and visual imagery. However, the subjective experiences of imagining and seeing are clearly different. Here we demonstrate that deactivation of auditory cortex (and to some extent of somatosensory and subcortical visual structures) as measured by BOLD functional magnetic resonance imaging unequivocally differentiates visual imagery from visual perception. During visual imagery, auditory cortex deactivation negatively correlates with activation in visual cortex and with the score in the subjective vividness of visual imagery questionnaire (VVIQ). Perception of the world requires the merging of multisensory information so that, during seeing, information from other sensory systems modifies visual cortical activity and shapes experience. We suggest that pure visual imagery corresponds to the isolated activation of visual cortical areas with concurrent deactivation of "irrelevant" sensory processing that could disrupt the image created by our "mind's eye."     

Structural NMR of protein oligomers using hybrid methods

Solving structures of native oligomeric protein complexes using traditional high-resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice.     

From biological fundamentals to practice, and back

It has become evident that advances in farm animal reproduction have become increasingly dependent on fundamental scientific research in addition to an understanding of the physiological processes involved in reproduction. As a consequence, most innovations are now coming from a long linear process starting with fundamental scientific research to their application on the farm and lastly, consumer acceptance. The emerging perception of life's complexity is also indicating that technical advances must be better understood before they are implemented by the producer and accepted by the public. To the biological complexity, one must now add the complexity of human interaction on a global level through regulation, international trade and public information. In this context, more than ever, advancements in animal reproduction must be developed in parallel with the scientific understanding of the cause and consequences of human intervention.