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PubMedDate not supplied

[Structure-function organization of neurokinin A and neurokinin B molecules. I. Theoretical conformational analysis of neurokinin A].

The spatial structure of the neurokinin A molecule was studied by the method of theoretical conformational analysis. On the basis of fragmental analysis, stable structures of the neurokinin A molecule under polar conditions were determined. The structures can be described by four families of low-energy conformations having a relatively labile tripeptide at the C-end and a conformationally rigid heptapeptide at the N-end. It was shown that two of these conformations are virtually isoenergetic structures. One of these is an alpha-helical structure and the other forms two beta-turns at the N-terminus, which change to the turn of the alpha-helix at the C-end.

Amino Acid Sequence↗

PubMed1991

[The effect of amino acid substitutions on the 3-dimensional structure of fragment 1--16 of the oncoprotein p21 ras].

Using the method of theoretical conformational analysis, spatial structure of fragment 1-16 of active [( Val12-Gly13], [Asp12-Gly13], [Gly12-Asp13]) and passive [( Gly12-Gly13] and [Pro12-Gly13]) modifications of oncoproteins family p21 ras have been investigated. The activation of these proteins has been shown to be accompanied by reorganization of three-dimensional structure of the polypeptide chain.

Amino Acids↗

PubMed1987

[Structural and functional research on polymyxins. 1H NMR analysis of the conformation of polymyxin M in water].

Spatial structure of polypeptide antibiotic polymyxin M in water was studied by one-and two-dimensional (COSY, COSY-45, RELAY) H NMR spectroscopy. Analysis of the signal spectral parameters revealed two intramolecular hydrogen bonds in the cyclic part of the molecule which was analogous to the structure of polymyxin B. However, configuration of both the beta-turns in the polymyxin M structure differed from that of the detected earlier beta-turns in the structure of polymyxin B.

Hydrogen↗

PubMed1993

Intracellular coordination by the ultradian clock.

Activity Cycles↗

PubMed1996

Structures of lantibiotics studied by NMR.

During the last decade, Nuclear Magnetic Resonance has played an important role in the unravelling of the primary and tertiary structures of lantibiotics. A short overview of these studies, together with typical spatial structures obtained, is presented.

Amino Acid Sequence↗

PubMed2004

Evolution of concentration field in a membrane system.

This paper deals with the evolution of concentration field at a single membrane system. Concentration field evolution is described by concentration effect of stable boundary layers, which originate in this system. The concentration effect of boundary layers (CBLE) is studied experimentally on the basis concentration profiles obtained from computer analysis of interferometric pictures of near-membrane regions. Besides experimental results, we also report theoretical investigations and numerical calculations of this effect for two models of membranes (an infinite thin wall and the wall of thickness l). Evolution of concentration field at different distances from membrane surface describes accurately the spatio-temporal structure of the concentration boundary layers (CBLs). Results have shown that their spatial structure is fully established and these layers develop diffusively.

Biological Transport↗

PubMed2001

First tryptophan-containing weak neurotoxin from cobra venom.

With the purpose of studying structure-function relationships among weak neurotoxins (called so because of their low toxicity), we have isolated a toxin (WTX) from the venom of cobra Naja kaouthia using a combination of gel-filtration and ion-exchange chromatography. The amino acid sequence of the isolated toxin was determined by means of Edman degradation and MALDI mass spectrometry, the primary structure obtained being confirmed by 1H-NMR in the course of spatial structure analysis. The WTX sequence differs slightly from that of the toxin CM-9a isolated earlier from the same venom (Joubert and Taljaard, Hoppe-Seyler's Z. Physiol. Chem., 361 (1980) 425). The differences include an extra residue (Trp36) between Ser35 and Arg37 as well as interchanging of two residues (Tyr52 and Lys50) in the C-terminal part of the toxin molecule. These changes improve the alignment that can be made with other weak neurotoxin sequences. An extended sequence comparison reveals that WTX is the first case of a tryptophan-containing weak neurotoxin isolated from cobra venom. WTX was found to compete with radioiodinated alpha-bungarotoxin for binding to the membrane-bound nicotinic acetylcholine receptor from Torpedo californica.

Amino Acid Sequence↗

PubMed1998

Circadian and ultradian clock-controlled rhythms in unicellular microorganisms.

The time structure of a biological system is at least as intricate as its spatial structure. Whereas we have detailed information about the latter, our understanding of the former is still rudimentary. As techniques for monitoring intracellular processes continuously in single cells become more refined, it becomes increasingly evident that periodic behaviour abounds in all time domains. Circadian timekeeping dominates in natural environments. Here the free-running period is about 24 h. Circadian rhythms in eukaryotes and prokaryotes allow predictive matching of intracellular states with environmental changes during the daily cycles. Unicellular organisms provide excellent systems for the study of these phenomena, which pervade all higher life forms. Intracellular timekeeping is essential. The presence of a temperature-compensated oscillator provides such a timer. The coupled outputs (epigenetic oscillations) of this ultradian clock constitute a special class of ultradian rhythm. These are undamped and endogenously driven by a device which shows biochemical properties characteristic of transcriptional and translational elements. Energy-yielding processes, protein turnover, motility and the timing of the cell-division cycle processes are all controlled by the ultradian clock. Different periods characterize different species, and this indicates a genetic determinant. Periods range from 30 min to 4 h. Mechanisms of clock control are being elucidated; it is becoming evident that many different control circuits can provide these functions.

Activity Cycles↗

PubMed2006

Spatial distribution pattern of oviposition in the mosquito Aedes aegypti in relation to urbanization in Buenos Aires: southern fringe bionomics of an introduced vector.

The distribution of Aedes aegypti (L) (Diptera: Culicidae) oviposition in Buenos Aires City is spatially heterogeneous. Oviposition activity was monitored for a year with a grid of 279 traps at 850-m intervals that were serviced weekly. Geostatistics were used for the spatial analysis and generalized linear regression to model oviposition as a function of demographic and environmental variables. The proportion of weeks infested and the total number of eggs showed spatial continuity and were higher in areas that had higher densities of houses and were closer to industrial sites; they were lower in areas with higher human populations or higher densities of flats. When all sites were considered, the spatial structure showed a strong trend, but after regression, the residuals presented lower spatial dependence. When only infested sites were considered, the oviposition variables were spatially autocorrelated and the regression residuals showed little or no spatial dependence. The spatial pattern of Ae. aegypti oviposition in a highly urbanized city such as Buenos Aires seems to be related to the urbanization gradient. These urban environments might present different resource availability or continuity between patches of resources.

Aedes↗

PubMed2004

Prefrontal cortical involvement in verbal encoding strategies.

The lateral prefrontal cortex is critical for the control and organization of information in working memory. In certain situations, effective reorganization can attenuate task difficulty, suggesting a dissociation between lateral prefrontal activity and basic memory demand. In a verbal working memory task, we investigated the enhancement of performance that occurs when incoming information can be reorganized into higher-level groups or chunks. In the fMRI scanner, volunteers heard and repeated a sequence of digits. Mathematically structured sequences, encouraging 'chunking', were compared with unstructured, random sequences. Though structured sequences were easier to remember, fMRI showed increased lateral prefrontal activation for these sequences. Specifically, both the dorsolateral and ventrolateral prefrontal cortices were activated preferentially for the structured sequences during encoding. When visual stimuli that can be chunked using spatial structure are used, similar results are observed. These results demonstrate that cognitively less demanding tasks may elicit greater lateral prefrontal recruitment. Thus, the lateral prefrontal cortex appears to play a general role in strategically recoding information from memory, in order to optimize performance.

Acoustic Stimulation↗

PubMed1996

Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified.

Base Sequence↗

PubMedDate not supplied

[The structure-function organization of neurokinin A and neurokinin B molecules. II. Theoretical conformational analysis of neurokinin B].

The spatial structure of a neurokinin B molecule was investigated by the method of theoretical conformational analysis. The conformational analysis of this molecule indicated that the possible structure of neurokinin B under polar conditions may be described by five families of low-energy conformations possessing a conformationally relatively rigid C-terminal heptapeptide and variable N-terminal fragments.

Animals↗

PubMed2001

Systems of spatial reference in human memory.

Seven experiments examined the spatial reference systems used in memory to represent the locations of objects in the environment. Participants learned the locations of common objects in a room and then made judgments of relative direction using their memories of the layout (e.g., "Imagine you are standing at the shoe, facing the lamp; point to the clock"). The experiments manipulated the number of views that observers were allowed to experience, the presence or absence of local and global reference systems (e.g., a rectangular mat on which objects were placed and the walls of the room, respectively), and the congruence of local and global reference systems. Judgments of relative direction were more accurate for imagined headings parallel to study views than for imagined headings parallel to novel views, even with up to three study views. However, study views misaligned with salient reference systems in the environment were not strongly represented if they were experienced in the context of aligned views. Novel views aligned with a local reference system were, under certain conditions, easier to imagine than were novel views misaligned with the local reference system. We propose that learning and remembering the spatial structure of the surrounding environment involves interpreting the layout in terms of a spatial reference system. This reference system is imposed on the environment but defined by egocentric experience.

Adult↗

PubMedDate not supplied

Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta3 integrin.

Computational tools can bridge the gap between sequence and protein 3D structure based on the notion that information is to be retrieved from the databases and that knowledge-based methods can help in approaching a solution of the protein-folding problem. To this aim our group has implemented neural network-based predictors capable of performing with some success in different tasks, including predictions of the secondary structure of globular and membrane proteins, the topology of membrane proteins and porins and stable alpha-helical segments suited for protein design. Moreover we have developed methods for predicting contact maps in proteins and the probability of finding a cysteine in a disulfide bridge, tools which can contribute to the goal of predicting the 3D structure starting from the sequence (the so called ab initio prediction). All our predictors take advantage of evolution information derived from the structural alignments of homologous (evolutionary related) proteins and taken from the sequence and structure databases. When it is necessary to build models for proteins of unknown spatial structure, which have very little homology with other proteins of known structure, non-standard techniques need to be developed and the tools for protein structure predictions may help in protein modeling. The results of a recent simulation performed in our lab highlights the role of high performing computing technology and of tools of computational biology in protein modeling and peptidomimetic design.

Databases, Factual↗

PubMed1987

Residual vision in patients with retrogeniculate lesions of the visual pathways.

Twenty-five subjects have been studied who, as a result of damage to the striate cortex, were 'blind' in extensive areas (scotomata) of the visual fields. Of these 25 subjects, 5 exhibited residual vision in response to transient lights presented within the scotoma, which enabled them to locate the stimuli by hand-reaching or by eye movements; the latter have been measured by electro-oculography. The residual vision underlying their responses was characterized by low flicker-fusion and by sensitivity in detection of movement which increased as target speed was raised. Discrimination for the direction of target movement was poor, but spatial resolution in the discrimination of target displacement was essentially normal. The subjects were unable to recognize or discriminate the spatial structure of targets located within the 'blind' field, and the observed dissociation between spatial discrimination of displacement and pattern is examined in relation to the 'two systems' hypothesis of visual function. There is no obvious correlation between the extent of neuronal damage as revealed by CT scans and the existence of residual vision.

Adult↗

PubMed2005

Practical lessons from protein structure prediction.

Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins. The development of high-quality prediction methods has been boosted in the last years by objective community-wide assessment experiments. This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed.

Algorithms↗

PubMed2004

Formation and structure of transport barriers during confinement transitions in toroidal plasma.

Density pedestal formation is studied experimentally during spontaneous low-to-high confinement transitions in the H-1 heliac. Poloidally extended potential structures, or zonal flows, seem to play the major role both in the spatial structure and in the temporal evolution of the pedestal formation. Zonal flows transiently generate radially localized maxima in the radial electric-field shear in L mode which coincides with the radial location of the pedestal in H mode.

Journal Article↗

PubMed2006

Spatial and temporal dynamics of overwintering Homalodisca coagulata (Hemiptera: Cicadellidae).

A 4-yr landscape-scale study was conducted to investigate spatial and temporal dynamics of overwintering Homalodisca coagulata (Say) (Hemiptera: Cicadellidae) in the lower San Joaquin Valley, California. Spatial structures of H. coagulata distributions were characterized with Moran's I index, and spatial associations between H. coagulata and the surrounding environment were investigated with a geographic information system. H. coagulata was caught consistently with sticky traps throughout the winter, and trap catches formed a distinctive peak in December or January, indicating active flight of H. coagulata during the winter. In 2000-2001, the mean +/-SE trap count was 4.8 +/- 1.21 per trap per wk, and H. coagulata trap catches were spatially autocorrelated within approximately 1.3 km. Approximately 49% of H. coagulata were caught in citrus, 23% in stone fruit, and 11% in grape. After a control program began in spring 2001, the mean trap count was considerably lower (0.041 +/- 0.0004 per trap per wk), and no spatial autocorrelations were detected in 2001-2004. H. coagulata trap catch-crop associations also changed after initiation of the control program. Between 25 and 38% of H. coagulata trap catches were from citrus, between 8 and 20% were from stone fruit, and between 11 and 25% were from grape. Potential for winter-season spread and management of Xylella fastidiosa Wells et al., a pathogen causing Pierce's disease, are discussed.

Animals↗