734 research outputs found
A conserved supergene locus controls colour pattern diversity in Heliconius butterflies
No full textWe studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a “supergene”, determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic “supergene” polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection
No full textWith the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)-RNA molecules that are not translated to protein products-has become more evident. A subclass of ncRNA transcripts are encoded by highly regulated, multi-exon, transcriptional units, are processed like typical protein-coding mRNAs and are increasingly implicated in regulation of many cellular functions in eukaryotes. This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences, by using a systematic computational filtering approach. We initially searched for previously reported ncRNAs and found nine murine ncRNAs and homologs of several previously described nonmouse ncRNAs. Through our computational approach to filter artifact-free clones that lack protein coding potential, we extracted 4280 transcripts as the largest-candidate set. Many clones in the set had EST hits, potential CpG islands surrounding the transcription start sites, and homologies with the human genome. This implies that many candidates are indeed transcribed in a regulated manner. Our results demonstrate that ncRNAs are a major functional subclass of processed transcripts in mammals
Kinematic differences in left-right side in blocking among college women's volleyball players in Japan
No full textLink to publisher's homepage at http://www.mohejournal.com/index.php/moheIn recent years, the attacking tactics of top-level teams have been dominated by a combination of four attackers. The basic approach to defending against this move is to block in the direction of the toss (Read Block System). This study compares and examines the difference between the left and right sides of the crossover step of women's volleyball players using the read block system. Fifteen Japanese college women's volleyball players (age: 20.1±1.1 years, height: 169.3±5.5 cm) were eligible for the study. A time-synchronized 16 camera Mac3D optical motion capture systems (Motion Analysis Co.) and 10 force plates (Tec Gihan Co.) were used to determine three dimensional (3-D) coordinates of 38 retroreflective markers. The players were told that the toss from the setter would go up randomly in one of the left or right direction, and they were asked to block in response to the toss from the centre of the net. The results showed that the performance of the jump height (p = 0.04, d =0.50), maximum block reach (p = 0.01, d =0.51), and motion time (p =0.02, d =0.75) was better than the left, and the effect size was large. Since most of the subjects in this study were right-handed (two of the Opposites were left-handed), it is assumed that they tended to perform better on the left side, which is a block stepping similar to spike stepping. However, some players may not use the spiking hand, so individualized instruction is required
Statistische Mechanik unter Anwendung der Werkzeuge der Informationstheorie
No full text0 Cover and acknowledgements i-xiv 1 Introduction 1 1.1 Biological
thermodynamics 1 1.2 An intuitive notion of energy and entropy 2 1.3 From
steam engines to actin filaments: the laws of thermodynamics 5 1.4 Free energy
in processes involving proteins 6 1.4.1 Predicting ligand binding and protein-
protein interactions 7 1.4.2 Conformational entropy 8 1.5 The statistical in
mechanics 9 1.5.1 Information over matter and energy 10 1.6 Entropy is a
logarithmic counting of microstates 11 1.6.1 Stabilization by conformational
entropy 13 1.6.2 Acceptable errors in theoretical estimations of protein
thermodynamics 15 1.7 The entropy of polymers 16 1.7.1 Connection of
thermodynamics to information theory 17 1.8 Medical applications of protein
and drug thermodynamics 17 1.9 Aim of this work 19 1.10 References for Chapter
1 20 2 Balanced and bias-free computation of conformational entropy
differences for molecular trajectories 27 2.1 Introduction 27 2.1.1
Experimental measurements of conformational entropy 28 2.1.2 Theoretical
estimation of conformational entropy 29 2.2 Analytical derivation:
Configurational entropy of a macromolecule 30 2.2.1 Absolute and relative
configurational entropies 30 2.2.2 Sackur-Tetrode equation as a limiting case
for ideal gas 33 2.2.3 Entropy using local spherical polar (BAT) coordinates
34 2.2.3.1 Relative conformational entropy in terms of BAT coordinates 37 2.3
Numerical method to estimate conformational entropy differences 38 2.3.1
Automated selection of BAT coordinates 39 2.3.1.1 Continuity maximization for
torsions 39 2.3.1.2 Phase angles 40 2.3.2 Mutual Information expansion in low
dimensional subspaces 40 2.3.3 Discretization 42 2.3.4 Bias-Removal 44 2.3.5
Balancing 44 2.3.6 Generating molecular conformations in a canonical ensemble
46 2.3.7 Benchmark Entropy 46 2.4 Model system 1: Monte Carlo simulation of a
three-atom molecule in a cage 48 2.4.1 Simulation procedure 48 2.4.1.1 Monte
Carlo algorithm 49 2.4.2 Clustering of conformations 49 2.4.3 Entropy
estimation 50 2.5 Model system 2: Molecular Dynamics simulation of trialanine
52 2.5.1 Simulation procedure 52 2.5.2 Clustering of conformations 53 2.5.3
Entropy estimation 54 2.5.4 Convergence of benchmark entropy, energy and free
energy 54 2.5.5 Detailed results for entropy estimates using the MI expansion
(MIE) 57 2.5.5.1 MIE1 using all BAT coordinates 57 2.5.5.2 MIE2 using all BAT
coordinates 58 2.5.5.3 MIE3 using all BAT coordinates 59 2.5.5.4 MIE Using
only soft degrees of freedom 60 2.5.6 Convergence of the entropy estimates 63
2.5.6.1 Importance of choosing frames at random in the balancing method 64
2.5.7 Summary of results for model system 2 64 2.6 Discussion 69 2.6.1.1 BAT
coordinates represent phase space compactly 69 2.6.1.2 Approximate
cancellation of the Jacobian term of the entropy 70 2.6.1.3 Entropy estimation
in signal processing versus molecular simulations 70 2.7 Conclusion 71 2.8
References for Chapter 2 74 3 Influence of Spacer-Receptor Interactions on the
Stability of Bivalent Ligand-Receptor Complexes 81 3.1 Introduction 81 3.1.1
Biological and pharmaceutical relevance of multivalency 81 3.1.2 Polymer
spacer-receptor interactions 82 3.1.3 Comparison of our model to experiment 82
3.2 Conclusions 83 3.2.1 Receptor topography: concave, planar or convex 83
3.2.2 Interaction thermodynamics: repulsive or attractive 83 3.3 References
for Chapter 3 84 4 Summary 87 4.1 Abstract in English 87 4.1.1 Balanced and
bias-free computation of conformational entropy differences for molecular
trajectories 87 4.1.2 Influence of spacer-receptor interactions on the
stability of bivalent ligand-receptor complexes 88 4.2 Zusammenfassung in
deutscher Sprache 90 4.2.1 Ausbalancierte und von systematischen Fehlern
bereinigte Berechnung konformationeller Entropiedifferenzen für molekulare
Trajektorien 90 4.2.2 Einfluss von Spacer-Rezeptor-Wechselwirkungen auf die
Stabilität von bivalenten Ligand-Rezeptor-Komplexen 91 Submitted manuscript
Influence of Spacer-Receptor Interactions on the Stability of Bivalent Ligand-
Receptor Complexes (print version only) 94 Supporting information for
manuscript (print version only) 119Although thermodynamics was born from the desire to optimize industrial
processes, its wide applicability has recently afforded it a place in biology.
Accurate estimation of thermodynamic variables for processes involving
biological macromolecules is an important goal in theoretical chemistry. For
macromolecules and soft matter in general, understanding of the driving forces
that comprise a given free energy or binding constant requires consideration
of flexibility for all molecular degrees of freedom. The entropic contribution
to free energy is thus an essential ingredient, whether explicitly quantified
or included in a model in the form of a correct enumeration of the
multiplicity of conformations. This doctoral thesis offers two contributions
to the problem of computing entropy: (a) A numerical method for estimating
conformational entropy differences for macromolecules was developed. It uses
techniques borrowed from information theory and applies them to statistical
mechanics. The method is applicable to conformational transitions and protein-
ligand binding. (b) A model to describe the enhancement of the binding
affinity for a bivalent ligand tethered with a polymer spacer was expounded.
The novelty of the model consists in the inclusion of spacer-receptor
interactions. (a) Balanced and bias-free computation of conformational entropy
differences for molecular trajectories The mutual information expansion (MIE)
is applied to estimate conformational entropy differences of macromolecules
applicable to molecular dynamics or Monte Carlo simulation data on
oligopeptides, polymers, proteins and ligands. The MIE serves to reduce the
high dimensionality of the probability density of the conformational space of
a macromolecule. The individual terms of the MIE are evaluated with a
histogram method. Internal bond-angle-torsion (BAT) coordinates are used to
avoid spurious correlations present when using Cartesian coordinates, which
would demand using higher order terms in the MIE. Practically all entropy
estimation methods from finite samples suffer from an inherent systematic
error or bias. Two approaches are applied that compensate for systematic
errors that occur with a histogram method: (1) Simulation data are balanced by
using the same number of coordinate sets (frames) for both conformer domains.
Balancing puts fluctuations of the histogram bin contents on the same level
for both conformers, allowing for efficient error cancellation. (2) Bias-
removal corrects for systematic deviations due to finite number of frames per
bin. Applying both corrections improves the precision of entropy differences
enormously. Estimates of entropy differences are compared to thermodynamic
benchmarks of polymer and peptide models, where excellent agreement is found.
For trialanine as model system, the average error for the estimated
conformational entropy difference is only 0.3 J/(mol K), which is 100 times
smaller than without applying the two corrections. Guidelines are provided for
efficiently estimating conformational entropies. The complete method,
including 1st to 3rd order MI expansion, balancing and bias-removal can be
performed with the program ENTROPICAL. It can be obtained from the author and
used with CHARMM and NAMD topologies and trajectories. (b) Influence of
spacer-receptor interactions on the stability of bivalent ligand-receptor
complexes Experiments show that a ligand-receptor complex formed by binding a
bivalent ligand (D) in which the two ligating units are joined covalently by a
flexible polymeric spacer (S) can be orders of magnitude more stable than the
corresponding complex formed with monomeric ligands. Up until now, the
molecular models that have been proposed to rationalize this "enhancement
effect" neglect spacer-receptor (S-R) interactions. These interactions can
nevertheless substantially influence the relative stability of complexes.
Here, the results of a computational study designed to assess the impact of
S-R interactions in the prototypic bivalent complex are presented and compared
with results of experiments. The S-R interactions mimicking general features
of biological systems are modeled by contoured R surfaces with hills (or
depressions) at the binding sites. In the fictitious limit of vanishing S-R
interactions, the enhancement is pronounced. This enhancement is in line with
the experimental observations, although the S-R interactions, which surely
occur in reality, were neglected. For strictly repulsive S-R interactions
(hard R surface) the enhancement vanishes, or even reverses. This is
particularly the case if the R surface is convex (i.e. rising between the
binding sites), while the enhancement is only moderately reduced if the R
surface is concave. Alternatively, a weak S-R attraction close to the R
surface can increase the enhancement. It is concluded that large enhancement
should be observed only if both features are present: a concave R surface plus
a weak S-R attraction. The latter occurs for spacer material such as
polyethylene glycol (PEG), which is weakly hydrophobic and thus attracted by
protein surfaces. It is shown that the enhancement of bivalent binding can be
characterized by a single key parameter, which may also provide guidelines for
the design of multivalent complexes with large enhancement effect.Obwohl die Thermodynamik ursprünglich zur Optimierung industrieller Prozesse
entwickelt wurde, hat sie sich durch ihre breiten Anwendungsmöglichkeiten in
letzter Zeit auch einen Platz in der Biologie gesichert. Ein wichtiges Ziel in
der theoretischen Chemie stellt die genaue Abschätzung thermodynamischer
Variablen für Prozesse dar, an denen biologische Makromoleküle beteiligt sind.
Das Verständnis der Triebkräfte, die eine gewisse freie Energie bei
Makromolekülen und allgemein weicher Materie ausmachen, bedarf der
Miteinbeziehung der Flexibilität aller molekularen Freiheitsgrade. Der
entropische Beitrag zur freien Energie ist also ein unentbehrlicher
Bestandteil, unabhängig davon, ob er explizit quantifiziert wird oder bei
einem Modell in Form einer richtigen Aufzählung der Vielfachheit der
Konformationen mit einbezogen wird. Die vorliegende Dissertation liefert zu
dem Problem der Entropieberechnung zwei Beiträge: (1) Eine numerische Methode
zur Berechnung von Entropiedifferenzen bei Makromolekülen wurde entwickelt.
Sie entlehnt Techniken aus der Informationstheorie und wendet sie in der
statistischen Mechanik an. Die Methode ist bei Konformationsänderungen und
Protein-Ligandbindung verwendbar. (2) Zur Beschreibung der Verstärkung der
Bindungsaffinität bei bivalenten Liganden, die mit einem Polymer-Spacer
verknüpft sind, wurde ein geeignetes Modell entwickelt. Neu bei diesem Modell
ist die Einbeziehung von Spacer-Rezeptor-Wechselwirkungen. (a) Ausbalancierte
und von systematischen Fehlern bereinigte Berechnung konformationeller
Entropiedifferenzen für molekulare Trajektorien Die Reihenentwicklung der
wechselseitigen Information (mutual information expansion, MIE) wird benutzt,
um Differenzen in konformationeller Entropie bei Makromolekülen zu berechnen.
Die Methode ist auf Moleküldynamik- oder Monte-Carlo-Simulationsdaten von
Polymeren, Proteinen und Liganden anwendbar. Die MIE dient der
Dimensionsreduktion der Wahrscheinlichkeitsdichte des konformationellen Raums
eines Makromoleküls. Die einzelnen Entwickungsterme der MIE werden mit Hilfe
einer Histogrammmethode ausgewertet. Ein internes Koordinatensystem
(Bindungslänge, Bindungswinkel und Torsionswinkel, das sogenannte BAT-System)
wird benutzt, um die, bei kartesischen Koordinaten anwesenden, störenden
Korrelationen zu vermeiden, die Entwickungsterme höherer Ordnung in der MIE
benötigen würden. Praktisch alle Entropieschätzungsmethoden, die über eine
endliche Menge von Daten verfügen, leiden an systematischen Fehlern (Bias).
Zwei Korrekturmethoden werden eingesetzt, um diese systematischen Fehler von
Histogrammmethoden auszugleichen: (1) Die Simulationsdaten werden
ausbalanciert, indem die gleiche Anzahl von Koordinatensätzen (Einzelbildern)
für beide Konformerdomänen benutzt wird. Durch dieses Ausbalancieren werden
die Schwankungen der Belegungen einzelner Histogrammsäulen für beide
Konformere im Mittel gleich groß. Dies führt zu einem effizienten
Fehlerausgleich. (2) Die Bereinigung der systematischen Fehler (Bias)
kompensiert Abweichungen, die auf Grund der endlichen Menge von Daten pro
Histogrammsäule entstanden sind. Die gleichzeitige Verwendung beider
Korrekturen verbessert die Genauigkeit der Abschätzung von Entropiedifferenzen
erheblich. Die geschätzten Entropiedifferenzen werden mit thermodynamischen
Bezugswerten für Polymer- und Peptidmodelle verglichen und stimmen mit diesen
ausgezeichnet überein. Für das Modellsystem Trialanin betrug der
durchschnittliche Fehler für die geschätzte konformationelle Entropiedifferenz
nur 0.3 J (mol K), welcher 100-mal kleiner ist als bei Weglassen beider
Korrekturmethoden. Leitlinien zur effizienten Berechnung konformationeller
Entropie werden angegeben. Die komplette Methode, einschließlich MIE 1. bis 3.
Grad, Ausbalancieren und Bereinigung von systematischen Fehlern, kann mit
Hilfe des Programms ENTROPICAL ausgeführt werden. Das Programm arbeitet auf
CHARMM- und NAMD-Topologien und -Trajektorien und wird vom Autor auf Anfrage
zur Verfügung gestellt. (b) Einfluss von Spacer-Rezeptor-Wechselwirkungen auf
die Stabilität von bivalenten Ligand-Rezeptor-Komplexen Experimente zeigen,
dass ein durch einen bivalenten Liganden (D) gebildeter Ligand-Rezeptor-
Komplex, in dem beide bindenden Einheiten mit Hilfe eines flexiblen Polymer-
Spacers kovalent verknüpft werden, um Größenordnungen stabiler sein kann als
der entsprechende, durch monomere Liganden gebildete Komplex. Bislang haben
molekulare Modelle der bivalenten Bindung den Verstärkungseffekt erklärt, ohne
die Wechselwirkungen zwischen Spacer und Rezeptor (S-R) zu berücksichtigen.
Letztere können aber die relative Stabilität der Komplexe entscheidend
beeinflussen. Wir haben Computersimulationen an geeigneten, prototypischen
Modellsystemen für den bivalenten Komplexe durchgeführt, um die Auswirkungen
der S-R-Wechselwirkungen auf die Bindungseffizienz zu untersuchen und mit
experimentellen Ergebnissen verglichen. Die modellierten S-R-Wechselwirkungen
bilden die allgemeinen Merkmale biologischer Systeme nach und werden als
R-Oberfläche mit Bergen (bzw. Tälern) an den Bindungsstellen modelliert. Im
fiktiven Grenzfall verschwindender S-R-Wechselwirkungen ist die Verstärkung
der Bindungseffizienz groß. Dies deckt sich mit experimentellen Beobachtungen,
obwohl die in der Realität sicher auftretenden S-R-Wechselwirkungen
vernachlässigt wurden. Bei rein abstoßenden S-R-Wechselwirkungen (harter
R-Oberfläche) verschwindet die Verstärkung oder kehrt sich gar um. Das ist
insbesondere bei konvexer (also zwischen den Bindungsstellen gewölbter)
R-Oberfläche der Fall, wobei die Verstärkung bei einer konkaven Oberfläche nur
unwesentlich verringert ist. Alternativ kann eine schwache S-R-Anziehung nahe
der R-Oberfläche die Verstärkung erhöhen. Es wird geschlussfolgert, dass nur
in dem Fall, dass beide Merkmale anwesend sind, eine hohe Verstärkung zu
erwarten ist: d. h. bei einer konkaven R-Oberfläche und einer schwachen
S-R-Anziehung. Letzteres tritt bei Spacermaterialien wie Polyethylenglycol
(PEG) auf, welches geringfügig hydrophob ist und aus diesem Grund von
Proteinoberflächen angezogen wird. Es wird gezeigt, dass die Verstärkung
bivalenter Bindung mit einem einzelnen Parameter gekennzeichnet werden kann,
woraus sich Leitlinien für den Entwurf multivalenter Komplexe mit hoher
Verstärkung gewinnen lassen
Contrast-enchanced Ultrasound of Pancreatic Lesions: PAMUS (Pancreatic Multicenter Ultrasound Study) Results
No full textScientific Papers SSM!=-0
Matsumuramata Xing & Chen, 2014, nom. nov.
No full textGenus Matsumuramata nom. nov. Numata Matsumura, 1935: 139 (Hemiptera: Fulgoromorpha: Delphacidae). Preoccupied by Numata Busck, 1906: 724 (Lepidoptera: Gelechioidea: Gelechiidae). Type species: Stenocranus sacchari Matsumura, 1910 Etymology. The generic name is dedicated to Prof. Shōnen Matsumura who is the author of the preexisting generic name Numata. Gender: feminine.Published as part of Xing, Ji-Chun & Chen, Xiang-Sheng, 2014, Nomenclatural changes for the genus Discophorellus Tsaur & Hsu, 1991 and new replacement name for Numata Matsumura, 1935 (Hemiptera: Fulgoromorpha), pp. 149-150 in Zootaxa 3856 (1) on page 150, DOI: 10.11646/zootaxa.3856.1.8, http://zenodo.org/record/492985
Fundamental Study of the Fill-in Minimization Problem
No full textIn this paper the fill-in minimization problem which arises
at the application of the sparse matrix method for a large sparse set of linear equations is discussed from the graph-theoretic viewpoint and also through the numerical experiments. Therefore, this investigation consists of two parts, and in the former part the author shows, at first, that the elimination process of a sparse matrix is equivalently replaced to the vertex eliminations for a graph obtained from the matrix, and by use of some concepts
in the theory of graph he proves that the vertex elimination process for the minimum fill-in is equivalent to the vertex eliminations for vertices in each subgraph which is obtained by the appropriate dissection of whole graph, and that there are only two types of vertex eliminations through the process. This results in the proposal of a new model of the vertex elimination process. The latter part of this investigation is used for the verification of the results from the theoretic investigation. Through the numerical experiments he concludes that the new model of the vertex elimination process is valid, at least, for a graph like a regular finite element mesh. Furthermore, he shows that this model coincides with Nested Dissection Method which can give the minimum value of fill-in, at present
Pancreatic multicenter ultrasound study (PAMUS)
No full textAIM: To describe the typical CEUS pattern of pancreatic lesions and to evaluate the diagnostic accuracy of Contrast-enhanced ultrasound (CEUS) in their characterization.MATERIALS AND METHODS: All US and CEUS examinations of focal pancreatic masses performed in six centers during a period of five years were reviewed. Inclusion criteria were: focal pancreatic mass pathologically proved, visible at ultrasound (US) and studied with CEUS. All lesions were then evaluated for size, aspect and enhancement pattern. Sensitivity, specificity, positive and negative predictive values with 95% CIs were calculated to define diagnostic accuracy of CEUS in respect to pathology. Diagnostic confidence of US and CEUS, discerning between benign and malignant lesions, were represented by using ROC (receiver operating characteristics) curves. Agreement was evaluated by means of k statistics.RESULTS: 1439 pancreatic lesions were included. At CEUS the lesions were divided into solid (89%) and cystic (12%) masses and classified into six and eight categories, respectively. Among the solid lesions, adenocarcinomas were characterized with an accuracy of 87.8%. Among the cystic lesions, cystic tumors were diagnosed with an accuracy of 97.1%. ROC curve area increased from 0.637 for US to 0.877 for CEUS (p<0.0001). Inter-observer agreement was slightly higher for solid (k=0.78) than cystic (k=0.62) lesions. In none of the centers side effects were reported.CONCLUSION: CEUS is accurate in the characterization of pancreatic lesions. CEUS should be considered as a complementary imaging method for pancreatic lesions characterization
Hydration-Induced Local Molecular Structures in Nano-Layered Clay Particles
No full textPositronium (Ps) annihilation spectroscopy and thermogravimetry and differential thermal analysis (TG-DTA) were conducted for synthetic smectite clay minerals to investigate local molecular structures induced by water adsorption and desorption. The TG curves indicate the weight loss of ~ 3.5 wt %, ~ 2.5 wt %, and ~ 2.0 wt % for saponite, hectorite, and stevensite due to dehydration, in accordance with DTA endothermic peaks around 332 K, 350 K, and 345 K. It is found based on the results of Ps lifetime spectroscopy that the presence of angstrom-scale open space is sensitively dependent on water adsorption and desorption in smectite clay minerals
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