The evolution of phylogeographic data sets

Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next-generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic data sets over the past 20years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled and the total number of single nucleotide polymorphisms (SNPs) per data set has improved over time, with particularly dramatic increases within the past 5years. Interestingly, uniparentally inherited organellar markers (e.g. animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single-species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicates that the median number of SNPs per data set for studies published by the end of the year 2016 may approach similar to 20000. This survey provides baseline information for understanding the evolution of phylogeographic data sets and underscores the fact that development of analytical methods for handling very large genetic data sets will be critical for facilitating growth of the field.

Microsatellite in Aeschynomene falcata (Leguminosae): diversity, cross-amplification, and chromosome localization

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A relação teoria e prática em projetos de educação ambiental desenvolvidos em um bairro de Bauru, SP, Brasil

This study examines the relationship between theory and practice that emerges from two Environmental Projects that were carried out in a popular neighborhood of Bauru, SP, . In order to analyze the data, given the diversity of theoretical and practical approaches and concepts in environmental education, we chose as a theoretical foundation critical environmental education. Considering the techniques used in the methodological procedures of qualitative research in education, we elected, as a tool to collect information, content analysis. The results presented in this paper indicate the need to break the dichotomy between form (practice) and content (theory) in the environmental educational process, focusing on the systematized and historically constructed contents. Thus, we consider the environmental education process analyzed involve treating form and content as a dialectic unit.

State of the Arctic October 2006

This State of the Arctic Report presents a review of recent data by an international group of scientists who developed a consensus on the information content and reliability. The report highlights data primarily from 2000 to 2005 with a first look at winter 2006, providing an update to some of the records of physical processes discussed in the Arctic Climate Impact Assessment (ACIA, 2004, 2005). Of particular note: • Atmospheric climate patterns are shifting (Fig. 1). The late winter/spring pattern for 2000–2005 had new hot spots in northeast Canada and the East Siberian Sea relative to 1980–1999. Late winter 2006, however, shows a return to earlier climate patterns, with warm temperatures in the extended region near Svalbard. • Ocean salinity and temperature profiles at the North Pole and in the Beaufort Sea, which changed abruptly in the 1990s, show that conditions since 2000 have relaxed toward the pre-1990 climatology, although 2001–2004 has seen an increase in northward ocean heat transport through Bering Strait (Fig. 2), which is thought to impact sea ice loss. • Sea ice extent continues to decrease. The sea ice extent in September 2005 was the minimum observed in summer during the satellite era (beginning in 1979), marking an unprecedented series of extreme ice extent minima beginning in 2002 (Fig. 3). The sea ice extent in March 2006 was also the minimum observed in winter during the satellite era. • Tundra vegetation greenness increased, primarily due to an increase in the abundance of shrubs. Boreal forest vegetation greenness decreased, possibly due to drought conditions (Fig. 4). • There is increasing interest in the stability of the Greenland ice sheet. The velocity of outlet glaciers increased in 2005 relative to 2000 and 1995, but uncertainty remains with regard to the total mass balance. • Permafrost temperatures continue to increase. However, data on changes in the active layer thickness (the relatively thin layer of ground between the surface and permafrost that undergoes seasonal freezing and thawing) are less conclusive. While some of the sites show a barely noticeable increasing trend in the thickness of the active layer, most of them do not. • Globally, 2005 was the warmest year in the instrumental record (beginning in 1880), with the Arctic providing a large contribution toward this increase. Many of the trends documented in the ACIA are continuing, but some are not. Taken collectively, the observations presented in this report indicate that during 2000–2005 the Arctic system showed signs of continued warming. However, there are a few indications that certain elements may be recovering and returning to recent climatological norms (for example, the central Arctic Ocean and some wind patterns). These mixed tendencies further illustrate the sensitivity and complexity of the Arctic physical system. They underline the importance of maintaining and expanding efforts to observe and better understand this important component of the climate system to provide accurate predictions of its future state.

Isolation and characterisation of microsatellite loci in the wasp Mischocyttarus cassununga

Mischocyttarus cassununga, a primitively eusocial Brazilian wasp, commonly found in urban environments, is an interesting model for studies on the evolution of social behaviour in hymenopteran insects. In this study, we constructed a microsatellite-enriched genomic library and presented primers for 18 microsatellite loci. For the analysis, 20 unrelated females were screened and all loci obtained were polymorphic. PCR amplification revealed from 3 (Mcas5b) to 17 (Mcas53b) alleles per locus (). We detected the levels of observed (H (o)) and expected (H (e)) heterozygosities ranging from 0.150 to 0.950 and 0.261 to 0.920, respectively. The polymorphic information content ranged from 0.238 to 0.915, averaging 0.680. All loci were in Hardy-Weinberg equilibrium and linkage disequilibrium was not detected after sequential Bonferroni correction (P > 0.05). These molecular markers will allow further studies on sociogenetic structure, extensive population genetic analysis and diversity of M. cassununga and other Mischocyttarini species.

Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature

Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) and thereby potentially alter the information content and structure of cellular RNAs. Notably, although the overwhelming majority of such editing events occur in transcripts derived from Alu repeat elements, the biological function of non-coding RNA editing remains uncertain. Here, we show that mutations in ADAR1 (also known as ADAR) cause the autoimmune disorder Aicardi-Goutieres syndrome (AGS). As in Adar1-null mice, the human disease state is associated with upregulation of interferon-stimulated genes, indicating a possible role for ADAR1 as a suppressor of type I interferon signaling. Considering recent insights derived from the study of other AGS-related proteins, we speculate that ADAR1 may limit the cytoplasmic accumulation of the dsRNA generated from genomic repetitive elements.

DEVELOPMENT OF MICROSATELLITE MARKERS FOR QUALEA GRANDIFLORA (VOCHYSIACEAE), A TYPICAL SPECIES OF THE BRAZILIAN CERRADO

Premise of the study: Microsatellite primers were developed to investigate genetic diversity and population structure of Qualea grandiflora, a typical species of the Brazilian cerrado. Methods and Results: Eight microsatellite loci were isolated using an enrichment cloning protocol. These loci were tested on a population of 110 individuals of Q. grandiflora collected from a cerrado fragment in Sao Paulo State, Brazil. The loci polymorphism ranges from seven to 19 alleles and the average heterozygosity value is 0.568, while the average polymorphic information content is 0.799. Conclusions: The developed markers were found to be highly polymorphic, indicating their applicability to studies of population genetic diversity in Q. grandiflora

New microsatellite markers for garlic, Allium sativum (Alliaceae)

Premise of the study: A new set of microsatellite or simple sequence repeat (SSR) markers for garlic, an important medicinal spice, was developed to aid studies of genetic diversity and to define efficient strategies for germplasm conservation. Methods and Results: Using a (CT)(8)- and (GT)(8)-enriched library, a total of 16 SSR loci were developed and optimized in garlic. Ten loci were found to be polymorphic after screening 75 accessions. The parameters used to characterize the loci were observed and expected heterozygosity, number of alleles, Shannon Index, and polymorphism information content (PIC). A total of 44 alleles were identified, with an average of 4.4 alleles per loci. The vast majority of loci were moderate to highly informative according to PIC and the Shannon Index. Conclusion: The new SSR markers have the potential to be informative tools for genetic diversity, allele mining, mapping and associative studies, and in the management and conservation of garlic collections.

Functional markers for gene mapping and genetic diversity studies in sugarcane

Abstract Background The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database). Findings A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process. Conclusions These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.

Fourier-transform rheology on anionically synthesised polymer melts and solutions of various topology

Aim of this thesis was to further extend the applicability of the Fourier-transform (FT) rheology technique especially for non-linear mechanical characterisation of polymeric materials on the one hand and to investigated the influence of the degree of branching on the linear and non-linear relaxation behaviour of polymeric materials on the other hand. The latter was achieved by employing in particular FT-rheology and other rheological techniques to variously branched polymer melts and solutions. For these purposes, narrowly distributed linear and star-shaped polystyrene and polybutadiene homo-polymers with varying molecular weights were anionically synthesised using both high-vacuum and inert atmosphere techniques. Furthermore, differently entangled solutions of linear and star-shaped polystyrenes in di-sec-octyl phthalate (DOP) were prepared. The several linear polystyrene solutions were measured under large amplitude oscillatory shear (LAOS) conditions and the non-linear torque response was analysed in the Fourier space. Experimental results were compared with numerical predictions performed by Dr. B. Debbaut using a multi-mode differential viscoelastic fluid model obeying the Giesekus constitutive equation. Apart from the analysis of the relative intensities of the harmonics, a detailed examination of the phase information content was developed. Further on, FT-rheology allowed to distinguish polystyrene melts and solutions due to their different topologies where other rheological measurements failed. Significant differences occurred under LAOS conditions as particularly reflected in the phase difference of the third harmonic, Ħ3, which could be related to shear thinning and shear thickening behaviour.

Functional photoactive and electroactive nanodevices

Most of current ultra-miniaturized devices are obtained by the top-down approach, in which nanoscale components are fabricated by cutting down larger precursors. Since this physical-engineering method is reaching its limits, especially for components below 30 nm in size, alternative strategies are necessary. Of particular appeal to chemists is the supramolecular bottom-up approach to nanotechnology, a methodology that utilizes the principles of molecular recognition to build materials and devices from molecular components. The subject of this thesis is the photophysical and electrochemical investigation of nanodevices obtained harnessing the principles of supramolecular chemistry. These systems operate in solution-based environments and are investigated at the ensemble level. The majority of the chemical systems discussed here are based on pseudorotaxanes and catenanes. Such supramolecular systems represent prototypes of molecular machines since they are capable of performing simple controlled mechanical movements. Their properties and operation are strictly related to the supramolecular interactions between molecular components (generally photoactive or electroactive molecules) and to the possibility of modulating such interactions by means of external stimuli. The main issues addressed throughout the thesis are: (i) the analysis of the factors that can affect the architecture and perturb the stability of supramolecular systems; (ii) the possibility of controlling the direction of supramolecular motions exploiting the molecular information content; (iii) the development of switchable supramolecular polymers starting from simple host-guest complexes; (iv) the capability of some molecular machines to process information at molecular level, thus behaving as logic devices; (v) the behaviour of molecular machine components in a biological-type environment; (vi) the study of chemically functionalized metal nanoparticles by second harmonic generation spectroscopy.

Numeralklassifikatoren im Thai

Wie viele andere Sprachen Ost- und Südostasiens ist das Thai eine numerusneutrale Sprache, in der ein Nomen lediglich das Konzept benennt und keinen Hinweis auf die Anzahl der Objekte liefert. Um Nomina im Thai zählen zu können, ist der Klassifikator (Klf) nötig, der die Objekte anhand ihrer semantischen Schlüsseleigenschaft herausgreift und individualisiert. Neben der Klassifikation stellt die Individualisierung die Hauptfunktion des Klf dar. Weitere Kernfunktionen des Klf außerhalb des Zählkontextes sind die Markierung der Definitheit, des Numerus sowie des Kontrasts. Die wichtigsten neuen Ergebnisse dieser Arbeit, die sowohl die Ebenen der Grammatik und Semantik als auch die der Logik und Pragmatik integriert, sind folgende: Im Thai kann der Klf sowohl auf der Element- als auch auf der Mengenebene agieren. In der Verbindung mit einem Demonstrativ kann der Klf auch eine pluralische Interpretation hervorrufen, wenn er auf eine als pluralisch präsupponierte Gesamtmenge referiert oder die Gesamtmenge in einer Teil-Ganzes-Relation individualisiert. In einem Ausdruck, der bereits eine explizite Zahlangabe enthält, bewirkt die Klf-Demonstrativ-Konstruktion eine Kontrastierung von Mengen mit gleichen Eigenschaften. Wie auch der Individualbegriff besitzt der Klf Intension und Extension. Intension und Extension von Thai-Klf verhalten sich umgekehrt proportional, d.h. je spezifischer der Inhalt eines Klf ist, desto kleiner ist sein Umfang. Der Klf signalisiert das Schlüsselmerkmal, das mit der Intension des Nomens der Identifizierung des Objekts dient. Der Klf individualisiert das Nomen, indem er Teilmengen quantifiziert. Er kann sich auf ein Objekt, eine bestimmte Anzahl von Objekten oder auf alle Objekte beziehen. Formal logisch lassen sich diese Funktionen mithilfe des Existenz- und des Allquantors darstellen. Auch die Nullstelle (NST) läßt sich formal logisch darstellen. Auf ihren jeweiligen Informationsgehalt reduziert, ergeben sich für Klf und NST abhängig von ihrer Positionierung verschiedene Informationswerte: Die Opposition von Klf und NST bewirkt in den Fragebögen ausschließlich skalare Q-Implikaturen, die sich durch die Informationsformeln in Form einer Horn-Skala darstellen lassen. In einem sich aufbauenden Kontext transportieren sowohl Klf als auch NST in der Kontextmitte bekannte Informationen, wodurch Implikaturen des M- bzw. I-Prinzips ausgelöst werden. Durch die Verbindung der Informationswerte mit den Implikaturen des Q-, M- und I-Prinzips lässt sich anhand der Positionierung direkt erkennen, wann der Klf die Funktion der Numerus-, der Definitheits- oder der Kontrast-Markierung erfüllt.

Design And Implementation Of An End-To-End Simulator For The BepiColombo Rotation Experiment

Among the scientific objectives addressed by the Radio Science Experiment hosted on board the ESA mission BepiColombo is the retrieval of the rotational state of planet Mercury. In fact, the estimation of the obliquity and the librations amplitude were proven to be fundamental for constraining the interior composition of Mercury. This is accomplished by the Mercury Orbiter Radio science Experiment (MORE) via a strict interaction among different payloads thus making the experiment particularly challenging. The underlying idea consists in capturing images of the same landmark on the surface of the planet in different epochs in order to observe a displacement of the identified features with respect to a nominal rotation which allows to estimate the rotational parameters. Observations must be planned accurately in order to obtain image pairs carrying the highest information content for the following estimation process. This is not a trivial task especially in light of the several dynamical constraints involved. Another delicate issue is represented by the pattern matching process between image pairs for which the lowest correlation errors are desired. The research activity was conducted in the frame of the MORE rotation experiment and addressed the design and implementation of an end-to-end simulator of the experiment with the final objective of establishing an optimal science planning of the observations. In the thesis, the implementation of the singular modules forming the simulator is illustrated along with the simulations performed. The results obtained from the preliminary release of the optimization algorithm are finally presented although the software implemented is only at a preliminary release and will be improved and refined in the future also taking into account the developments of the mission.

Optical resonances of sphere-on-plane geometries

The optical resonances of metallic nanoparticles placed at nanometer distances from a metal plane were investigated. At certain wavelengths, these “sphere-on-plane” systems become resonant with the incident electromagnetic field and huge enhancements of the field are predicted localized in the small gaps created between the nanoparticle and the plane. An experimental architecture to fabricate sphere-on-plane systems was successfully achieved in which in addition to the commonly used alkanethiols, polyphenylene dendrimers were used as molecular spacers to separate the metallic nanoparticles from the metal planes. They allow for a defined nanoparticle-plane separation and some often are functionalized with a chromophore core which is therefore positioned exactly in the gap. The metal planes used in the system architecture consisted of evaporated thin films of gold or silver. Evaporated gold or silver films have a smooth interface with their substrate and a rougher top surface. To investigate the influence of surface roughness on the optical response of such a film, two gold films were prepared with a smooth and a rough side which were as similar as possible. Surface plasmons were excited in Kretschmann configuration both on the rough and on the smooth side. Their reflectivity could be well modeled by a single gold film for each individual measurement. The film has to be modeled as two layers with significantly different optical constants. The smooth side, although polycrystalline, had an optical response that was very similar to a monocrystalline surface while for the rough side the standard response of evaporated gold is retrieved. For investigations on thin non-absorbing dielectric films though, this heterogeneity introduces only a negligible error. To determine the resonant wavelength of the sphere-on-plane systems a strategy was developed which is based on multi-wavelength surface plasmon spectroscopy experiments in Kretschmann-configuration. The resonant behavior of the system lead to characteristic changes in the surface plasmon dispersion. A quantitative analysis was performed by calculating the polarisability per unit area /A treating the sphere-on-plane systems as an effective layer. This approach completely avoids the ambiguity in the determination of thickness and optical response of thin films in surface plasmon spectroscopy. Equal area densities of polarisable units yielded identical response irrespective of the thickness of the layer they are distributed in. The parameter range where the evaluation of surface plasmon data in terms of /A is applicable was determined for a typical experimental situation. It was shown that this analysis yields reasonable quantitative agreement with a simple theoretical model of the sphere-on-plane resonators and reproduces the results from standard extinction experiments having a higher information content and significantly increased signal-to-noise ratio. With the objective to acquire a better quantitative understanding of the dependence of the resonance wavelength on the geometry of the sphere-on-plane systems, different systems were fabricated in which the gold nanoparticle size, type of spacer and ambient medium were varied and the resonance wavelength of the system was determined. The gold nanoparticle radius was varied in the range from 10 nm to 80 nm. It could be shown that the polyphenylene dendrimers can be used as molecular spacers to fabricate systems which support gap resonances. The resonance wavelength of the systems could be tuned in the optical region between 550 nm and 800 nm. Based on a simple analytical model, a quantitative analysis was developed to relate the systems’ geometry with the resonant wavelength and surprisingly good agreement of this simple model with the experiment without any adjustable parameters was found. The key feature ascribed to sphere-on-plane systems is a very large electromagnetic field localized in volumes in the nanometer range. Experiments towards a quantitative understanding of the field enhancements taking place in the gap of the sphere-on-plane systems were done by monitoring the increase in fluorescence of a metal-supported monolayer of a dye-loaded dendrimer upon decoration of the surface with nanoparticles. The metal used (gold and silver), the colloid mean size and the surface roughness were varied. Large silver crystallites on evaporated silver surfaces lead to the most pronounced fluorescence enhancements in the order of 104. They constitute a very promising sample architecture for the study of field enhancements.

Matrix Designs and Methods for Secure and Efficient Compressed Sensing

The idea of balancing the resources spent in the acquisition and encoding of natural signals strictly to their intrinsic information content has interested nearly a decade of research under the name of compressed sensing. In this doctoral dissertation we develop some extensions and improvements upon this technique's foundations, by modifying the random sensing matrices on which the signals of interest are projected to achieve different objectives. Firstly, we propose two methods for the adaptation of sensing matrix ensembles to the second-order moments of natural signals. These techniques leverage the maximisation of different proxies for the quantity of information acquired by compressed sensing, and are efficiently applied in the encoding of electrocardiographic tracks with minimum-complexity digital hardware. Secondly, we focus on the possibility of using compressed sensing as a method to provide a partial, yet cryptanalysis-resistant form of encryption; in this context, we show how a random matrix generation strategy with a controlled amount of perturbations can be used to distinguish between multiple user classes with different quality of access to the encrypted information content. Finally, we explore the application of compressed sensing in the design of a multispectral imager, by implementing an optical scheme that entails a coded aperture array and Fabry-Pérot spectral filters. The signal recoveries obtained by processing real-world measurements show promising results, that leave room for an improvement of the sensing matrix calibration problem in the devised imager.