The Establishment and Regulation of Melanocyte Stem Cells in Zebrafish

Stem cells are the cells that regulate the growth and repair of tissues in adult organisms. In this thesis, I sought to develop methodologies to dissect the function and regulation of stem cells during zebrafish melanocyte regeneration. In the first part of this thesis, I develop a drug based method of ablating melanocytes in the adult zebrafish body. The drug is a copper chelator, neocuproine: NCP) that I show causes death specifically of melanocytes in adult, which allows for regeneration from melanocyte stem cells: MSCs). In the next part of the thesis, I employ clonal lineage statistical analyses to study the establishment, recruitment, and proliferation, differentiation, and survival of MSC daughter cells during larval melanocyte regeneration. These analyses suggest that MSCs are likely recruited at random for each regeneration event, and that approximately 84% of MSCs are recruited for any regeneration event. I demonstrate that kit signaling has a greater requirement during larval regeneration than during ontogeny and compare the regeneration of kit heterozygotes to wild type. The mutant heterozygotes have normal MSC recruitment and normal proliferation, differentiation, and survival of daughter cells. The mutant has defective MSC establishment, with this defect being quantitatively sufficient to explain the regeneration defect observed. I then used further clonal lineage analysis to suggest that reduction of kit signaling causes inappropriate differentiation of fated MSCs into ontogenetic melanocytes. These analyses are not unique for comparison of kit mutants to wild type, so can easily be applied to dissect any gene or drug which affects regeneration. In the final part of the thesis, I explore how many spermatagonia form the adult zebrafish male germline. An understanding of this number allows for efficient mutant screens, an essential part of the genetic dissection of any process. The zebrafish has approximately 485 spermatagonia, giving each male approximately 970 genomes which can be mutagenized. This number can be considered during mutant screen designs to eliminate redundant screening

A BDD-representation for the logic of equality and uninterpreted functions (a full version with proofs).

The logic of equality and uninterpreted functions (EUF) has been proposed for processor verification. This paper presents a new data structure called Binary Decision Diagrams for representing EUF formulas (EUF-BDDs). We define EUF-BDDs similar to BDDs, but we allow equalities between terms as labels instead of Boolean variables. We provide an approach to build a reduced ordered EUF-BDD (EUF-ROBDD) and prove that every path to a leaf is satisfiable by construction. Moreover, EUF-ROBDDs are logically equivalent representations of EUF-formulae, so they can also be used to represent state spaces in symbolic model checking with dat

Santa Teresa, mujer de letras y oración

Ningun

Synthesis and characterization of Nb2O5@C core-shell nanorods and Nb2O5nanorods by reacting Nb(OEt)5via RAPET (reaction under autogenic pressure at elevated temperatures) technique

The reaction of pentaethoxy niobate, Nb(OEt)5, at elevated temperature (800 °C) under autogenic pressure provides a chemical route to niobium oxide nanorods coated with amorphous carbon. This synthetic approach yielded nanocrystalline particles of Nb2O5@C. As prepared Nb2O5@C core-shell nanorods is annealed under air at 500 °C for 3 h (removing the carbon coating) results in neat Nb2O5nanorods. According to the TEM measurements, the Nb2O5crystals exhibit particle sizes between 25 nm and 100 nm, and the Nb2O5crystals display rod-like shapes without any indication of an amorphous character. The optical band gap of the Nb2O5nanorods was determined by diffuse reflectance spectroscopy (DRS) and was found to be 3.8 eV

Whole genome sequencing-based mapping and candidate identification of mutations from fixed zebrafish tissue

As forward genetic screens in zebrafish become more common, the number of mutants that cannot be identified by gross morphology or through transgenic approaches, such as many nervous system defects, has also increased. Screening for these difficult-to-visualize phenotypes demands techniques such as whole-mount in situ hybridization (WISH) or antibody staining, which require tissue fixation. To date, fixed tissue has not been amenable for generating libraries for whole genome sequencing (WGS). Here, we describe a method for using genomic DNA from fixed tissue and a bioinformatics suite for WGS-based mapping of zebrafish mutants. We tested our protocol using two known zebrafish mutant alleles, gpr126st49 and egr2bfh227, both of which cause myelin defects. As further proof of concept we mapped a novel mutation, stl64, identified in a zebrafish WISH screen for myelination defects. We linked stl64 to chromosome 1 and identified a candidate nonsense mutation in the F-box and WD repeat domain containing 7 (fbxw7) gene. Importantly, stl64 mutants phenocopy previously described fbxw7vu56 mutants, and knockdown of fbxw7 in wild-type animals produced similar defects, demonstrating that stl64 disrupts fbxw7. Together, these data show that our mapping protocol can map and identify causative lesions in mutant screens that require tissue fixation for phenotypic analysis

OpenFlow-based link dimensioning

In this demo we will demonstrate the possibility of using OpenFlow traffic measurements for link dimensioning purposes. Our solution runs on top of the Ryu OpenFlow controller and retrieves per-flow statistics metered at the OpenFlow switch. The statistics are obtained by using messages defined by the OpenFlow protocol. These statistics are then applied to a flow-based link dimensioning approach, originally proposed to operate with NetFlow input. By demonstrating our solution in a testbed, we are able to compare the OpenFlow-based approach with a NetFlow-based one and with the actual traffic demands calculated directly from the packet traces. With that, we show how quality of OpenFlow measurements affects the link dimensioning and how feasible their use in such applications is

Deep learning for inferring cause of data anomalies

Daily operation of a large-scale experiment is a resource consuming task, particularly from perspectives of routine data quality monitoring. Typically, data comes from different sub-detectors and the global quality of data depends on the combinatorial performance of each of them. In this paper, the problem of identifying channels in which anomalies occurred is considered. We introduce a generic deep learning model and prove that, under reasonable assumptions, the model learns to identify 'channels' which are affected by an anomaly. Such model could be used for data quality manager cross-check and assistance and identifying good channels in anomalous data samples. The main novelty of the method is that the model does not require ground truth labels for each channel, only global flag is used. This effectively distinguishes the model from classical classification methods. Being applied to CMS data collected in the year 2010, this approach proves its ability to decompose anomaly by separate channels.Comment: Presented at ACAT 2017 conference, Seattle, US

Production of new neutron-rich isotopes of heavy elements in fragmentation reactions of 238^{238}U projectiles at 1 A GeV

The production of heavy neutron-rich nuclei has been investigated using cold fragmentation reactions of $^{238}$U projectiles at relativistic energies. The experiment performed at the high-resolving-power magnetic spectrometer FRS at GSI allowed to identify 45 new heavy neutron-rich nuclei: $^{205}$Pt, $^{207-210}$Au, $^{211-216}$Hg, $^{213-217}$Tl, $^{215-220}$Pb, $^{219-224}$Bi, $^{221-227}$Po, $^{224-229}$At, $^{229-231}$Rn and $^{233}$Fr. The production cross sections of these nuclei were also determined and used to benchmark reaction codes that predict the production of nuclei far from stability.Comment: 5 pages, 2 figure