Molecular phylogenetics, evolution of sexual systems and historical biogeography of Darwin's favourite orchids (Catasetinae) and Swan orchids (Cycnoches Lindl.)

The Orchidaceae are one of the most species rich and widespread lineages among angiosperms. They have evolved numerous remarkable vegetative and reproductive traits that have allowed them to successfully adapt and diversify into a wide array of environments. More importantly, they have developed several intricate symbiotic relationships with different kinds of organisms (e.g. animals, fungi) that for centuries have attracted the attention of botanists, biologists, amateurs and naturalists. Nevertheless, despite the extensive research done so far on orchid biology and phylogenetics, very little is known about the biotic and environmental variables as well as the evolution of several key traits that seem to be linked with the successful diversification of this lineage. This dissertation is focused on three puzzling aspects of plant evolutionary biology, specifically the phylogenetic incongruence between nuclear and plastid genomes, the evolution of sexual systems, and lineage migration and isolation through time. To address these topics, I chose as a group of study the sub tribe Catasetinae, an orchid lineage including ca. 350 species restricted to the Neotropical region. They show a remarkable set of sexual systems, namely protandry and Environmental Sex Determination (ESD), that were never studied before in a phylogenetic context. My dissertation includes as well a minor part on taxonomic and floristic work devoted to other representative orchid lineages of the Neotropical flora (i.e. Epidendrum and Lepanthes). Based on vegetal material collected during field trips, my taxonomic research resulted in the description of several new species and new chorological reports contributing to the Colombian and Costa Rican Floras. Using a set of nuclear and chloroplast loci obtained from material cultivated at the Botanic Garden Munich and collected during field work in several Latin American countries, I produced a well-supported and insofar the most representatively sampled phylogeny of Catasetinae. While gathering vegetal material, I encountered several complications such as extreme scarcity of individuals and worrisome, extensive bureaucratic administrative processes to obtain collection and research permits that finally undermined my taxon sampling. By studying in detail the Catasetinae internal phylogenetic relationships independently derived from nuclear and plastid loci, I came across several well supported conflicting phylogenetic positions. Most of the traditional phylogenetic methods developed to address these conflicts aim at the inference of a species tree only. In chapter 5, I explored the utility of co-phylogenetic tools (i.e. PACo and ParaFit) to quantify the conflicts between nuclear and plastid genomes. These tools have been largely employed in host-parasite/endosymbiont studies, hence they have the power to assess the contribution of single Operational Terminal Units (OTUs) to the phylogenetic pattern observed. As a result, using the Catasetinae chloroplast and nuclear datasets and extensive simulation approaches, I demonstrate that PACo successfully detects conflicting OTUs and its performance is overall better than ParaFit. In addition, my research provided strong evidence towards the bias of input data type (i.e. phylograms and cladograms) on distance-based co-phylogenetic methods. A pipeline to execute PACo and ParaFit tools in the software R to detect conflicting sequences in either small or big datasets was designed After inferring a strongly supported phylogeny, and by carrying in-situ and ex-situ observations plus searches of specialized literature on reproductive biology, I investigated the evolution of sexual systems of Catasetinae. I relied on Ancestral State Reconstruction (ASR) approaches and Bayesian statistical frameworks (chapter 6). As a result, ASR revealed three independent gains of ESD, once in the Last Common Ancestor (LCA) of Catasetum, Cycnoches and part of Mormodes, respectively, always derived from a protandrous ancestors. In contrast, protandry appears to have evolved only once, at the LCA of Catasetum, Clowesia, Cycnoches, Dressleria and Mormodes. The last chapter of this dissertation deals with the impact of the Andean uplift, the most important orographic event in South America, on evolution of epiphytic lowland Neotropical lineages. I used as a group of study Cycnoches (a member of the Catasetinae), which includes ca. 34 species and is distributed in Neotropical lowland wet forests. To address this goal, I produced the most completely sampled phylogeny of Cycnoches, and relied on Bayesian dating and Ancestral Area Estimation (AAE) approaches. The LCA of Cycnoches lived ca. 6 million years ago (MYA) in the Amazonian region. From this area, it expanded towards Central America and Choco in multiple migrations well after main Andean mountain building episodes. In addition, stochastic character mapping showed that within-region speciation (i.e. speciation in sympatric lineages) was a key process linked to diversification and range distribution evolution in Cycnoches

Didactic Actions for a Learning of Contentses in University Students

Background The learning developer guarantees in the student the active appropriation and creator of the knowledge and prepares it to solve the problems that are presented in its professional practice Objective To design didactic actions guided to achieve a learning developer in university students Methods Was carried out a traverse descriptive study in the understood period of October 2017 to October 2018 it was applied a not structured interview and a questionnaire to students of Medicine and it was used mathematical methods for the absolute and relative values Results It was verified that in the process teaching learning from the first year in the career of Medicine features of the teaching memoristic are used Conclusions The students recognized not to know how to identify the essential of the content they have difficulties to still apply it before new situations with the books of text

Remote assessment of learning during the pandemic: junior high school teachers’ experiences

This paper explores the teachers’ experiences of remote assessment in the Junior High School of Rizal Technological University. The qualitative study was used to determine the assessment methods used during the remote learning in terms of written and performance task and identify the most effective among other difficulties faced by the teachers in comparison with face-to-face. Data of the paper were obtained by conducting interviews that use open-ended questions from 10 participants who teach in the School Year 2021-2022. The analysis of the study was done according to themes and categories and participants’ answers were quotes excerpted from the transcripts. The study’s conclusion emphasizes the significance of carefully planning exams to guarantee academic integrity. With emphasis on the need to focus on cognitive, emotional, and psychomotor abilities when designing learning exams, especially for online learning, as well as the use of technology tools to monitor results and prevent dishonest behavior during online assessments. Finally, a complementary technique for evaluating students while they are engaged in online learning through teaching resources or learning management systems must be available

Identificación y caracterización de una proteína de unión al gen icaA y evaluación de su potencial participación en la formación de biofilm en Staphylococcus aureus

Resumen: El biofilm es definido como una comunidad microbiana altamente estructurada, compleja, inmersas dentro de una matriz de biopolímeros y adheridas a un sustrato o interfase inerte o viviente. Las bacterias dentro del biofilm están protegidas del ataque del sistema inmune del hospedero, de los antibióticos y otros agentes antimicrobianos. Staphylococcus aureus es una bacteria Gram positiva considerada como un patógeno oportunista, ya que hace parte del microbioma humano pero tiene la capacidad de causar infecciones. Esta bacteria genera un gran impacto en la salud pública mundial, ya que es el cuarto microorganismo recuperado de infecciones de pacientes hospitalizados. Adicionalmente, S. aureus tiene la capacidad de formar biofilm sobre diferentes superficies, incluyendo implantes médicos. El biofilm en S. aureus es producido por el operón ica, el cual está conformado por los genes icaA, icaB, icaC e icaD, que codifican las enzimas relacionadas con la producción del polisacárido de adhesión intercelular (PIA), componente principal de la matriz extracelular del biofilm en este microorganismo. En trabajos realizados previamente en el Laboratorio de Genética Molecular Bacteriana (LGMB) de la Universidad el Bosque se determinó la existencia de una región dentro del gen icaA altamente conservada en varias especies de Staphylococcus spp y que además contiene una secuencia palindrómica. Además existen indicios de proteínas que se unen de manera específica a esta secuencia palindrómica. El objetivo de este estudio fue identificar y caracterizar una proteína de unión a esta secuencia palindrómica del gen icaA y determinar su posible participación en la formación del biofilm en S. aureus. A partir de ensayos de retardamiento en gel y un proceso de purificación basado en cromatografía de proteínas de alta resolución se logró establecer la existencia de dos proteínas que reconocen esta secuencia palindrómica, SarX y una proteína hipotética, previamente no descrita. Ya se ha determinado que SarX tiene la habilidad para unirse al gen icaA. Sin embargo, la proteína hipotética correspondió a un ortólogo de la proteína YheA de Bacillus subtilis y además contiene un dominio denominado com_ylbF, el cual también está presente en las proteínas YlbF y YmcA de esta misma bacteria. Adicionalmente, se realizó un análisis estructural “in silico” de la proteína YheA, y de las proteínas YlbF y YmcA de S. aureus y B. subtilis. Modelos tridimensionales (3D) de las tres proteínas fueron construidos usando los programas I-TASSER y Quark. A partir de este análisis dos nuevas características de YheA, YlbF y YmcA fueron encontradas: una estructura 3D altamente conservada, a pesar de sus bajos porcentajes de identidad 16% y la presencia de un motivo putativo específico de cada proteína localizado dentro del dominio com_ylbF. Esta proteína YheA tiene un alto contenido de glutamina (13,2%), a nivel general y en su motivo putativo (QQKQMQ), lo cual sugiere que este aminoácido podría estar participando en la función de la proteína. Basados en estos hallazgos, se sugiere renombrar YheA como proteína rica en glutamina o Qrp (por su nombre en inglés Glutamine-rich protein) en S. aureus. Usando ensayos de mutagénesis dirigida, la deleción del gen yheA/qrp, que codifica para la proteína Qrp/YheA, produce una disminución en la formación del biofilm y un aumento en la hemólisis de eritrocitos por S. aureus. Estos resultados señalan que S. aureus posee una nueva familia de proteínas que contienen el dominio com_ylbF, de las cuales una de ellas, Qrp/YheA, está participando en la formación de biofilm a través de una interacción, directa o indirecta, con una secuencia palindrómica presente dentro del gen icaA.Abstract: The biofilm is a complex and high structured microbial community, which is immersed within a matrix composed of biopolymers with ability to adhere to inert or living substrates. The bacteria within the biofilm are protected the host defenses, antibiotics and other antimicrobial compounds. Staphylococcus aureus is a Gram positive bacterium, an opportunistic pathogen that generates a high clinic impact in the public health due to that it is the fourth bacterium recovered from infections in hospitalized patients. In addition, S. aureus has the ability to form biofilm on different substrates, including medical implants. The biofilm in S. aureus is produced by ica operon, which is composed for the icaA, icaB, icaC and icaD genes, encoding the enzymes responsible for the Polysaccharide Intercellular Adhesin (PIA) synthesis, principal biopolymer of the biofilm. In previous studies performed in the Laboratorio de Genetica Molecular Bacteriana of the Universidad El Bosque, a high conserved region was identified within icaA gene of the several Staphylococcal species, and interestingly, this region contained a palindromic sequence. There are experimental evidences that suggest the existence of proteins that recognize specifically this palindromic sequence. For these reasons, the objective of this study was to identify and to characterize one protein that recognizes this palindromic sequence and to establish whether it participates in the biofilm formation in S. aureus. Using Electrophoretic Mobility Shift Assay (EMSA) and FPLC-based protein purification, we achieve to identify two proteins that recognize this palindromic sequence, SarX and a hypothetical protein, which has not been previously described. It is known that SarX protein has the ability for binding to icaA gene. However, the hypothetical protein was an ortholog of the YheA protein of Bacillus subtilis and it contains the com_ylbF domain, which has also been identified in the proteins YlbF and YmcA in this same bacterium. Then, we performed an “in silico” structural analysis of the YheA protein, as well as the YlbF and YmcA. Three-dimensional (3D) models of these three proteins, in both S. aureus and B. subtilis, were built using the I-TASSER and Quark programs. From these analysis two new and important characteristics for YheA, YlbF and YmcA were found: a highly conserved 3D structure (despite their low amino acid identity, 16%) and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. The YheA protein has a high content of glutamine (13.2%), even within its putative motif (QQKQMQ), which suggests that this amino acid could to be participating in the protein function. Based on these findings, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Interestingly, the yheA/qrp gene deletion in the S. aureus genome produces a decrease in the biofilm formation but an increase in the red blood cells hemolysis. Our results indicate that S. aureus possesses a new protein family that contain the com_ylbF domain, and that least one of these, Qrp/YheA, is participating in the biofilm formation through either direct or indirect interaction with a palindromic sequence located within the icaA gene.Doctorad

Photocatalytic Activity under Simulated Sunlight of Bi-Modified TiO2 Thin Films Obtained by Sol Gel

The synthesis of Bi-modified TiO2 thin films, with different Bi contents, is reported. The obtained materials were characterized by energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy (RS), X-ray diffraction (XRD), photoluminescence (PL), and diffuse reflectance spectroscopy (DRS), in order to obtain information on their chemical composition, vibrational features, and optical properties, respectively. Compositional characterization reveals that the bismuth content can be varied in an easy way from 0.5 to 25.4 at. %. Raman results show that the starting material corresponds to the anatase phase of crystalline TiO2, and Bi addition promotes the formation of bismuth titanates, Bi2Ti2O7 at Bi contents of 10.4 at. % and the Bi4Ti3O12 at Bi contents of 21.5 and 25.4 at. %. Optical measurements reveal that the band gap narrows from 3.3 eV to values as low as 2.7 eV. The photocatalytic activity was tested in the degradation reaction of the Malachite Green carbinol base dye (MG) as a model molecule under simulated sunlight, where the most relevant result is that photocatalytic formulations containing bismuth showed higher catalytic activity than pure TiO2. The higher photocatalytic activity of MG degradation of 67% reached by the photocatalytic formulation of 21.5 at. % of bismuth is attributed to the presence of the crystalline phase perovskite-type bismuth titanate, Bi4Ti3O12.SIEA UAEM 4488 CHT project, CONACyT CB-168827 and CB-24099