De novo evolution of genetic function from random sequences

The study of de novo gene birth has opened the doors for evolutionary biologists to approach old questions about the origin of innovation from new perspectives. There are still many questions about what makes a functional gene, how likely it is for a non-coding sequence to become one, how common is this phenomenon in nature, and how do novel genes become essential for an organism. In this thesis, I present three projects that aim to explore some of these questions. In chapter 1, I revisit a study published in 2017 that used a library of random sequences in E. coli, in order to quantify the likelihood that a random sequence expressed in a cell provides a fitness advantage. I successfully replicated these results, and I improved the analysis pipeline to examine sequences in greater depth. I confirmed that expression of random DNA sequences is well tolerated by E. coli, and found that sequence length is a determinant factor of its effect on fitness. In chapter 2, I transferred the random sequence experiment to a eukaryotic model to determine what proportion of random sequences are well tolerated by eukaryotic cells despite the different complexity. The results indicate that eukaryotic cells are at least as tolerant to the expression of random sequences as bacteria. However, no specific feature of the sequences correlated with their tolerability. Finally, in chapter 3, I expressed three putative de novo genes identified in mouse in a human cell line. The selected genes are taxonomically restricted to species of mice, with transcription and proteomic evidence. Interestingly, expression of the novel genes had little effect on the transcriptome of the cells. The results presented in this thesis add to the mounting evidence that cells are much more tolerant to the expression of new sequences than previously thought. This insight generates new questions about the birth of genes that should be explored in the future

Senior Voice Recital

This is a copy of the program and notes for Evelyn Fajardo\u27s Senior Voice Recital given on April 2nd, 2016 from 8pm-9pm. This document provides background about each composer and piece included in the program

Lateral vibration effects in atomic-scale friction

The influence of lateral vibrations on the stick-slip motion of a nanotip elastically pulled on a flat crystal surface is studied by atomic force microscopy (AFM) measurements on a NaCl(001) surface in ultra-high vacuum. The slippage of the nanotip across the crystal lattice is anticipated at increasing driving amplitude, similarly to what is observed in presence of normal vibrations. This lowers the average friction force, as explained by the Prandtl-Tomlinson model with lateral vibrations superimposed at finite temperature. Nevertheless, the peak values of the lateral force, and the total energy losses, are expected to increase with the excitation amplitude, which may limit the practical relevance of this effect.Comment: To appear in Applied Physics Letter

The Ecclesiology and the Theology of Ministerial Priesthood in Fulton J. Sheen

This is a theological analysis directed towards elucidating the notion of the Church and ministerial priesthood in Sheen’s writings. His view of the Church’s nature as the prism of the diffusion of Divine Life serves as the theological basis for understanding his notion of the evangelizing mission of the Church. In line with Sheen’s ecclesiology, his theology of ministerial priesthood is elaborated within the theological framework of the so-called Divine Equation. In the analysis of Sheen’s theological ideas in reference to Vatican Council II, certain similarities and differences come to light, between his notion of the Church and priesthood, and some key conciliar teachings.Este es un análisis teológico dirigido a dilucidar la noción de la Iglesia y el sacerdocio ministerial en el pensamiento de Sheen. Su visión de la Iglesia como prisma de la difusión de la Vida Divina es el fundamento clave para comprender su noción de la misión evangelizadora de la Iglesia. De acuerdo con su eclesiología, se elabora su teología del sacerdocio ministerial en el marco teológico de la llamada Ecuación Divina. En el análisis de su noción de la Iglesia y del sacerdocio en referencia al Concilio Vaticano II, sus ideas teológicas muestran ciertas similitudes y diferencias en comparación con algunas de las enseñanzas conciliares

A totally laparoscopic associating liver partition and portal vein ligation for staged hepatectomy assisted with radiofrequency (radiofrequency assisted liver partition with portal vein ligation) for staged liver resection

In order to induce liver hypertrophy to enable liver resection in patients with a small future liver remnant, various methods have been proposed in addition to portal vein embolisation. Most recently, the ALPPS technique has gained significant international interest. This technique is limited by the high morbidity associated with an in-situ liver splitting and the patient undergoing two open operations. We present the case of a variant ALPPS technique performed entirely laparoscopically with no major morbidity or mortality. An increased liver volume of 57.9% was seen after 14 days. This technique is feasible to perform and compares favourably to other ALPPS methods whilst gaining the advantages of laparoscopic surgery

Towards the Refinement of DHTs

The implications of cooperative configurations have been far-reaching and pervasive. After years of private research into the memory bus, we prove the investigation of evolutionary programming, demonstrates the important importance of artificial intelligence. We motivate a “fuzzy” tool for simulating context-free grammar, which we call Cacochymy