Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications

One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information

Organizational Heterogeneity of Vertebrate Genomes

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as “texts” using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences

The evolution of transcription-associated biases of mutations across vertebrates

<p>Abstract</p> <p>Background</p> <p>The interplay between transcription and mutational processes can lead to particular mutation patterns in transcribed regions of the genome. Transcription introduces several biases in mutational patterns; in particular it invokes strand specific mutations. In order to understand the forces that have shaped transcripts during evolution, one has to study mutation patterns associated with transcription across animals.</p> <p>Results</p> <p>Using multiple alignments of related species we estimated the regional single-nucleotide substitution patterns along genes in four vertebrate taxa: primates, rodents, laurasiatheria and bony fishes. Our analysis is focused on intronic and intergenic regions and reveals differences in the patterns of substitution asymmetries between mammals and fishes. In mammals, the levels of asymmetries are stronger for genes starting within CpG islands than in genes lacking this property. In contrast to all other species analyzed, we found a mutational pressure in dog and stickleback, promoting an increase of GC-contents in the proximity to transcriptional start sites.</p> <p>Conclusions</p> <p>We propose that the asymmetric patterns in transcribed regions are results of transcription associated mutagenic processes and transcription coupled repair, which both seem to evolve in a taxon related manner. We also discuss alternative mechanisms that can generate strand biases and involves error prone DNA polymerases and reverse transcription. A localized increase of the GC content near the transcription start site is a signature of biased gene conversion (BGC) that occurs during recombination and heteroduplex formation. Since dog and stickleback are known to be subject to rapid adaptations due to population bottlenecks and breeding, we further hypothesize that an increase in recombination rates near gene starts has been part of an adaptive process.</p

Micro- y nanoestructuras de Zn2GeO4 : síntesis, caracterización y estudio de las propiedades ópticas

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias Físicas, leída el 05-11-2021In this PhD thesis work, the results obtained from the research on micro- and nanostructuresof zinc germanate (Zn2GeO4) are shown and discussed. This material is a wide bandgapsemiconductor, member of the transparent conducting oxide (TCO) family, which presentsseveral physical properties that make it a potential candidate for its integration in differentoptoelectronic or energy storage devices.The scope of applications of Zn2GeO4 can be extended or improved by controllingthe dimensions and morphology, as well as intrinsic defects and doping with impurities.Therefore, in this work, different synthesis or growth methods were employed in orderto achieve Zn2GeO4 structures with the desired dimensions, morphologies and physicalproperties. Thus, by means of the physical growth method of thermal evaporation, usingthe vapor-solid (VS) mechanism, both elongated Zn2GeO4 micro- and nanostructures wereobtained. This method was also used to dope the Zn2GeO4 structures by diffusion, includingthe dopant impurities during the growth stage. On the other hand, Zn2GeO4 nanocrystalswere synthesized via the chemical precipitation method...En el presente trabajo de tesis doctoral se muestran y discuten los resultados obtenidos durante la investigación realizada con micro- y nanoestructuras de germanato de zinc(Zn2GeO4). Este material es un semiconductor de gap ancho que forma parte de la familia de los óxidos conductores transparentes (TCO), y el cual presenta una serie de propiedades físicas que lo convierten en un potencial candidato para su incorporación en diversos dispositivos optoelectrónicos o de almacenamiento energético. El campo de aplicaciones del Zn2GeO4 se puede ampliar o mejorar mediante el control delas dimensiones y morfología, así como de los defectos intrínsecos y dopado con impurezas. Por ello, en este trabajo se emplearon diferentes métodos de síntesis o crecimiento, con el fin de lograr estructuras de Zn2GeO4 con las dimensiones, morfologías y propiedades físicas deseadas. Así, mediante el método de crecimiento físico de evaporación térmica, empleado el mecanismo vapor-sólido (VS), se obtuvieron tanto micro- y nanoestructuras alargadas de Zn2GeO4 como estructuras complejas. Este método fue también utilizado para doparlas estructuras de Zn2GeO4 mediante difusión, al incluir las impurezas dopantes durante la etapa de crecimiento. Por otro lado, se sintetizaron nanocristales de Zn2GeO4 a través del método de precipitación química...Fac. de Ciencias FísicasTRUEunpu

Study of Thin GaN/InGaN/GaN double graded structures for Future photovoltaic application

Indium gallium nitride (In_x Ga_(1-x) N) materials have displayed great potential for photovoltaic and optoelectronic devices due to their optical and electrical properties. Properties such as direct bandgap, strong bandgap absorption, thermal stability and high radiation resistance qualify them as great materials for photovoltaic devices. The tunable bandgap which absorbs the whole solar spectrum is the most significant feature which became attractive for scientists. The bandgap for these materials varies from 0.7 eV for InN to 3.4 eV for GaN covering from infrared to ultraviolet. In_x Ga_(1-x) N wurtzite crystal is grown on GaN buffer layer by Molecular Beam Epitaxy (MBE). Epitaxial growth of high quality In_x Ga_(1-x) N material, however, creates great challenges due to lattice mismatch between InN and GaN (up to 11%). This might be the actual reason of partially and fully strain at the interface relating to growth condition which affect optical properties of the materials. Therefore, studying solar cell parameters for different indium compositions (low to high) in the material is significant. In this work, graded composition In_x Ga_(1-x) N (44 nm ramping up followed by 44 nm ramping down) were grown on GaN/sapphire template. The growth was done at different indium compositions (low to high) in plasma-assisted MBE. Additionally, optical and structural characterizations of the materials were done. The results showed that by increasing indium composition, the composition was not linearly graded as expected and was accompanied by strain relaxation along the growth direction. In other words, for low indium composition, the results showed fully strained. However, for high indium composition partially strain relaxation was seen. The optical respond of three samples was studied with photoluminescence. For the first: to study the source of each peak in aspect of either exciton or different kinds of defect states. Second, peaks related to ground state transition. Furthermore, nextnano3 and nextnano+ software were used to simulate optical properties of 100 nm graded structures such as the band structure, ground state wave-function position as well as determine the optical transition probabilities among ground state hole and electrons as well as solar cell parameters for different structures under different strained conditions. Simulation continued for higher alloys (20% to 90%) under strain and (20%-100%) under relaxed condition. An equation like Vegard’s law was created to predict the energy bandgap under strain for different indium compositions. The simulation was performed for 100 nm -graded structure to find the optimum xmax for both conditions for maximum solar efficiency. In addition, the performance of graded structure in a Flat Base Graded (FBG) was studied to compare with Square well and Homojunction structure

Combinatorial Generalisation in Machine Vision

The human capacity for generalisation, i.e. the fact that we are able to successfully perform a familiar task in novel contexts, is one of the hallmarks of our intelligent behaviour. But what mechanisms enable this capacity that is at the same time so impressive but comes so naturally to us? This is a question that has driven copious amounts of research in both Cognitive Science and Artificial Intelligence for almost a century, with some advocating the need for symbolic systems and others the benefits of distributed representations. In this thesis we will explore which principles help AI systems to generalise to novel combinations of previously observed elements (such as color and shape) in the context of machine vision. We will show that while approaches such as disentangled representation learning showed initial promise, they are fundamentally unable to solve this generalisation problem. In doing so we will illustrate the need to perform severe tests of models in order to properly assess their limitations. We will also see how such failures are robust across different datasets, training modalities and in the internal representations of the models. We then show that a different type of system that attempts to learn object-centric representations is capable of solving the generalisation challenges that previous models could not. We conclude by discussing the implications of these results for long-standing questions regarding the kinds of cognitive systems that are required to solve generalisation problems

Materials sciences research

Research projects involving materials research conducted by various international test facilities are reported. Much of the materials research is classified in the following areas: (1) acousto-optic, acousto-electric, and ultrasonic research, (2) research for elucidating transport phenomena in well characterized oxides, (3) research in semiconductor materials and semiconductor devices, (4) the study of interfaces and interfacial phenomena, and (5) materials research relevant to natural resources. Descriptions of the individual research programs are listed alphabetically by the name of the author and show all personnel involved, resulting publications, and associated meeting speeches