Methods for analyzing the influence of molecular dynamics on neuronal activity

Magdeburg, Univ., Fak. für Informatik, Diss., 2015

The aggregation of Chauliognathus species (Coleoptera, Cantharidae) and its possible role for coexistence and mimicry

The relative population sizes of a species complex of Chauliognathus are reported, as well as their spatial distribution associated with different patches of food plants. Field work was done at Fazenda Santa Isabel, municipality of Guaíba, State of Rio Grande do Sul, Brazil. The results suggest that two mechanisms account for the reduction in food competition among the species involved: one is asynchrony in the appearance of the species in the area, and the other is aggregation in different patches of food plants. Since the species here reported show a similar colour pattern (yellow-black) the possibility of the occurrence of serial mimicry in this complex of species is dicussed.

Molecular systematics of the frog genus Leptodactylus (Amphibia: Leptodactylidae) / Linda R. Maxson, W. Ronald Heyer.

n.s. no.41(1988)

Molecular phylogenies, chromosomes and dispersion in Brazilian akodontines (Rodentia, Sigmodontinae)

A new molecular phylogeny for akodontine rodents from Brazil was proposed. The phylogenetic tree was enriched with the area of occurrence and with information on the karyotype of the samples. Based on this enriched tree, and with a described methodology, hypotheses were proposed on the karyotype and area of occurrence of the ancestors of each Clade. Thus it was possible to discuss hypotheses on chromosome evolution of the group, and on dispersion events from the "area of original differentiation" of akodontines in the Andes. Chromosome evolution started with high diploid numbers (2n=52) and showed a tendency to reduction (until 2n=14 in more recent clades). Independent side-branches of the tree showed 2n reduction and in one case the 2n increased. At least four dispersion events from the Andes down to South-eastern Brazil were proposed. The results should suggest the direction of new studies on comparative karyology.

A molecular contribution to the controversial taxonomical status of some freshwater snails (Caenogastropoda: Rissooidea, Cochliopidae) from the Central Andes desert to Patagonia

For over 40 years malacologists have been discussing the taxonomical status of Heleobia species, an enigmatic genus from Cochliopidae family (Caenogastropoda: Rissooidea). As with other rissooidean families, the considerable character convergence and the paucity of anatomical synapomorphies has proved to be a problem in resolving cochliopid phylogenetic relations and establishing the validity of several nominal cochliopid species. Here we present a molecular contribution to solve the taxonomical status of one of the most abundant Southern South America cochliopid genera which has many endemic species. We report molecular evidence that supports three of the four Heleobia groups described for this region, the "australis", "parchappii" and "piscium" groups. The fourth, the "hatcheri" group, belongs not to Heleobia but to a different genus which itself should not be considered as part of the family Cochliopidae but closely related to genus Potamolithus Pilsbry & Rush, 1896.

Firm Size and Geographical Aggregation: An Empirical Appraisal in Industrial Location

This paper assesses empirically the importance of size discrimination and disaggregate data for deciding where to locate a start-up concern. We compare three econometric specifications using Catalan data: a multinomial logit with 4 and 41 alternatives (provinces and comarques, respectively) in which firm size is the main covariate; a conditional logit with 4 and 41 alternatives including attributes of the sites as well as size-site interactions; and a Poisson model on the comarques and the full spatial choice set (942 municipalities) with site-specific variables. Our results suggest that if these two issues are ignored, conclusions may be misleading. We provide evidence that large and small firms behave differently and conclude that Catalan firms tend to choose between comarques rather than between municipalities. Moreover, labour-intensive firms seem more likely to be located in the city of Barcelona. Keywords: Catalonia, industrial location, multinomial response model. JEL: C250, E30, R00, R12

Infinite time aggregation for the critical Patlak-Keller-Segel model in R2

We analyze the two-dimensional parabolic-elliptic Patlak-Keller-Segel model in the whole Euclidean space R2. Under the hypotheses of integrable initial data with finite second moment and entropy, we first show local in time existence for any mass of "free-energy solutions", namely weak solutions with some free energy estimates. We also prove that the solution exists as long as the entropy is controlled from above. The main result of the paper is to show the global existence of free-energy solutions with initial data as before for the critical mass 8 Π/Χ. Actually, we prove that solutions blow-up as a delta dirac at the center of mass when t→∞ keeping constant their second moment at any time. Furthermore, all moments larger than 2 blow-up as t→∞ if initially bounded.

Caracterización agronómica, fenológica, cualitativa y molecular de la colección nuclear de cebadas españolas

El presente proyecto planteaba el paso siguiente a la construcción, por nosotros mismos, de la Colección Nuclear de Cebadas Españolas, que es una representación esquemática de la variabilidad genética de las cebadas ancestralmente cultivadas en nuestro país. Para la explotación completa de estos materiales autóctonos en el Programa Nacional de Mejora de Cebadas, que estamos llevando a cabo los grupos integrantes de este proyecto, se realizó el mismo, que ha comprendido los objetivos siguientes: - Caracterización agronómica, mediante ensayos de campo en ambientes contrastantes y representativos, incluyendo la evaluación de respuestas a factores productores de estreses bióticos y abióticos. - Caracterización fenológica, mediante ensayos en invernadero con protocolos desarrollados por nosotros, para identificar la respuesta de estos genotipos a la vernalización y el fotoperiodo. - Caracterización maltero-cervecera/pienso, mediante análisis de cebada y malta. - Caracterización molecular, mediante el uso de marcadores SSRs y STS.

Estudis funcionals i de plegament dels dominis d'activació de les procarboxipeptidases

Els dominis d’activació (ADs) de les procarboxipeptidases de la subfamília A/B sempre han sorprès ja que representen una quarta part del proenzim. S’han realitzat alguns estudis per intentar descobrir-ne alguna possible funció alternativa, però no han estat fructífers. El descobriment de l’elevada velocitat de plegament del domini d’activació de la procarboxipeptidasa A2 humana, (ADA2h), emperò, va portar a proposar la possibilitat de que realitzessin una funció d’assistència al plegament del domini enzimàtic. Posteriorment, l’anàlisi del plegament d’ADA2h a pH baix va revelar la capacitat d’aquest domini per formar fibres amiloides, a més de demostrar que un increment de l’estabilitat proteica podia prevenir la formació d’aquests agregats. La profunda caracterització del plegament d’ADA2h va fer que aquesta proteïna fos un bon model amiloidogènic, de manera que es van proposar un seguit d’experiments que s’han desenvolupat en el present treball per tal de conèixer millor aquest procés. S’han dut a terme estudis cinètics d’agregació per tal de valorar la contribució dels diferents aminoàcids de la seqüència polipeptídica, utilitzant 29 variants puntuals d’ADA2h. Es va eliminar la contribució de l’estabilitat mitjançant la utilització d’urea, i per dicroïsme circular conjuntament amb un aparell de flux detingut, es van obtenir dues velocitats diferents, v1 i v2, que corresponen a la formació d’un intermediari i a la seva reorganització, respectivament. Experiments complementaris utilitzant espectroscòpia d’infraroig (IR) revelaren la reorganització de l’estat natiu (en aquest cas) per a donar la forma agregada. Les cinètiques d’IR van mostrar que ADA2h forma l’estructura _ típica de les fibres amiloides, previ desplegament les seves hèlixs-_. Finalment, s’han realitzat estudis de biocomputació per tal d’esbrinar possibles funcions alternatives dels ADs. Les superposicions estructurals semblen mostrar similaritat dels ADs amb dominis de reconeixement d’RNA (RRM). Aquesta hipòtesi s’ha comprovat experimentalment amb ADA4h, mostrant una dèbil, però existent, unió a RNA.

PET Molecular Imaging of Hypoxia in Ischemic Stroke: An Update.

Hypoxia, a condition of insufficient oxygen availability to support metabolism, occurs when the vascular supply is interrupted, as in stroke. The identification of the hypoxic and viable tissue in stroke as compared with irreversible lesions (necrosis) has relevant implications for the treatment of ischemic stroke. Traditionally, imaging by positron emission tomography (PET), using 15O-based radiotracers, allowed the measurement of perfusion and oxygen extraction in stroke, providing important insights in its pathophysiology. However, these multitracer evaluations are of limited applicability in clinical settings. More recently, specific tracers have been developed, which accumulate with an inverse relationship to oxygen concentration and thus allow visualizing the hypoxic tissue non invasively. These belong to two main groups: nitroimidazoles, and among these the 18F-Fluoroimidazole (18F-FMISO) is the most widely used, and the copper-based tracers, represented mainly by Cu-ATSM. While these tracers have been at first developed and tested in order to image hypoxia in tumors, they have also shown promising results in stroke models and preliminary clinical studies in patients with cardiovascular disorders, allowing the detection of hypoxic tissue and the prediction of the extent of subsequent ischemia and clinical outcome. These tracers have therefore the potential to select an appropriate subgroup of patients who could benefit from a hypoxia-directed treatment and provide prognosis relevant imaging. The molecular imaging of hypoxia made important progress over the last decade and has a potential for integration into the diagnostic and therapeutic workup of patients with ischemic stroke.

Ab initio modeling and molecular dynamics simulation of the alpha 1b-adrenergic receptor activation.

This work describes the ab initio procedure employed to build an activation model for the alpha 1b-adrenergic receptor (alpha 1b-AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and experimental mutagenesis approach was used to determine the structural and dynamic features characterizing the inactive and active states of alpha 1b-AR. The latest version of the model has been successfully challenged with respect to its ability to interpret and predict the functional properties of a large number of mutants. The iterative approach employed to describe alpha 1b-AR activation in terms of molecular structure and dynamics allows further complications of the model to allow prediction and interpretation of an ever-increasing number of experimental data.

Peroxisome proliferator-activated receptor structures: ligand specificity, molecular switch and interactions with regulators.

Peroxisome proliferator-activated receptors (PPARs) compose a family of nuclear receptors that mediate the effects of lipidic ligands at the transcriptional level. In this review, we highlight advances in the understanding of the PPAR ligand binding domain (LBD) structure at the atomic level. The overall structure of PPARs LBD is described, and important protein ligand interactions are presented. Structure-activity relationships between isotypes structures and ligand specificity are addressed. It is shown that the numerous experimental three-dimensional structures available, together with in silico simulations, help understanding the role played by the activating function-2 (AF-2) in PPARs activation and its underlying molecular mechanism. The relation between the PPARs constitutive activity and the intrinsic stability of the active conformation is discussed. Finally, the interactions of PPARs LBD with co-activators or co-repressors, as well as with the retinoid X receptor (RXR) are described and considered in relation to PPARs activation.