Thesis advisor: Welkin Johnson / Endogenous Retroviruses (ERVs) are “fossilized” retroviruses of a once exogenous retrovirus located in the genome of extant vertebrates. Retroviral infection results in a provirus integration into the host genome. An infection of a germline cell could lead to the provirus potentially being inherited by the offspring of the infected individual. Once in the genome, the provirus becomes subject to evolutionary processes and can become either lost or fixed in a population, remaining as “fossils” long after the exogenous retrovirus has gone extinct23. Notably, 8% of the human genome consists of ERVs30. Human Endogenous Retrovirus Type K (HERV-K)(HML-2) family is of particular interest. HERV-K integrations are as old as 30-35 million years, endogenizing before the separation of humans and Old World Monkeys. However, there are human specific insertions, some as young as 150,000 – 250,000 years, making them the youngest insertion in the human genome. There are over 90 insertions in the human genome; the bulk is shared by all humans44,47. Transcripts of HERV-K genes are upregulated in multiple cancer and tumor cell lines 14,39,46, as well as in HIV-1 infected patients 7,11,29. Just as there are human specific insertions of ERV-K, there are also Old World Monkey specific insertions44. I have identified an intact endogenous retroviral envelope open reading frame on chromosome 12 of the rhesus macaque genome. This viral envelope-encoding sequence, which I refer to as rhERV-K env, retains all the canonical features of a retroviral Env protein. An alignment between rhERV-K env and a consensus sequence of HERV-K, HERV-Kcon env, shows a 70% amino acid sequence identity. For experimental purposes, reconstructed HERV-K envelopes have been incorporated into virions of Human Immunodeficiency virus (HIV-1)19,26,49, Murine Leukemia Virus (MLV)12, and Vesicular stomatitis Virus (VSV)26,41,49. While these approaches have illuminated some aspects of HERV-K Env-mediated entry, to date a cell-surface receptor has not been identified for any ERV-K Env. This could be due to its low infectivity levels12,26,49, its seemingly broad cell tropism limiting identification of null cell lines26,49, or possibly the HERV-K consensus reconstructions are not an accurate representation of the progenitor HERV-K virus. I am interested in understanding how the ERV-K retrovirus accessed the human germline (some 150,000 – 250,000 years ago). To do this, I focused specifically on the envelope proteins of HERV-K and rhERV-K, with the goal of analyzing the ERV-K entry process. The identification and inclusion of rhERV-K Env in this study is meant to circumvent the possibility that the previously described consensus reconstructions of human HERV-K Env are not representative, and may also provide a means to compare the endogenization process in the human/ape and old-world monkey lineages. I focused on developing two systems for single-cycle infection, one based on Mason-Pfizer Monkey Virus (MPMV) (which has not been done before), and a second based on MLV, which has previously been reported on. MPMV, like HERV-K, is a betaretrovirus, and I reasoned that possibly using a betaretrovirus would overcome some of the low-infectivity issues associated with prior attempts using HIV and MLV. To develop a system for examining function of the ERV-K Env proteins, I addressed 3 issues: 1. Are the HERV-K Env and rhERV-K Env proteins expressed and properly processed? 2. Can they be incorporated into virions of a heterologous virus? 3. Are ERV-K pseudotyped virions infectious? I have answered these questions in the following thesis. / Thesis (MS) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

<p>The demand for more accurate measurements is increasing in today’s industry. One reason for this is to optimize production and thus maximize profits. Another reason is that in some cases government regulations dictate that supervision of certain parameters must be followed. At Preemraff Lysekil there are basically four reasons for measuring skin temperatures inside fired process heaters, namely; because of government regulations, in order to estimate the load of the fired process heater, to estimate the lifetime of the tubes inside the fired process heater and finally, to determine the need of decoking. However, only the first three of these reasons are applied to H2301/2/3. The current skin thermocouple design has been in use for many years and now the question of how well it measures surface temperature has risen. Furthermore a new weld-free design is under consideration to replace the old skin thermocouple design. Another question is therefore how well the new design can measure the surface temperature under the same operating conditions as the old one. In order to evaluate this, three–dimensional computer simulations were made of the different designs. As this thesis will show, the differences in calculated skin thermocouple temperature and calculated surface temperature is about the same for the two designs. However, the current design will show a lower temperature than the surface temperature, while the new design will show a higher temperature. Regarding the core of the skin thermocouple designs, namely the thermocouple, no hard conclusions can be drawn, although the industry appears to favor type ’N’ over type ’K’.</p>

The demand for more accurate measurements is increasing in today’s industry. One reason for this is to optimize production and thus maximize profits. Another reason is that in some cases government regulations dictate that supervision of certain parameters must be followed. At Preemraff Lysekil there are basically four reasons for measuring skin temperatures inside fired process heaters, namely; because of government regulations, in order to estimate the load of the fired process heater, to estimate the lifetime of the tubes inside the fired process heater and finally, to determine the need of decoking. However, only the first three of these reasons are applied to H2301/2/3. The current skin thermocouple design has been in use for many years and now the question of how well it measures surface temperature has risen. Furthermore a new weld-free design is under consideration to replace the old skin thermocouple design. Another question is therefore how well the new design can measure the surface temperature under the same operating conditions as the old one. In order to evaluate this, three–dimensional computer simulations were made of the different designs. As this thesis will show, the differences in calculated skin thermocouple temperature and calculated surface temperature is about the same for the two designs. However, the current design will show a lower temperature than the surface temperature, while the new design will show a higher temperature. Regarding the core of the skin thermocouple designs, namely the thermocouple, no hard conclusions can be drawn, although the industry appears to favor type ’N’ over type ’K’.

[pt] A presente Dissertação de Mestrado, intitulada Avaliação metrológica da estabilidade termoelétrica do termopar tipo K, refere-se à verificação de desvios de estabilidade da força eletromotriz induzidos pelo uso de termopares tipo k com isolação mineral de 3mm de diâmetro. Foram analisadas oito amostras de quatro fabricantes nacionais de termopares, após sua exposição a um campo de temperatura de 995 diferente de 0,5 graus Celsius, portanto próximo ao seu limite de aplicabilidade (1070 graus Celsius), simulando uma condição de uso em regime contínuo. As amostras foram recozidas a uma temperatura de 1000 graus Celsius para regularizar o estado de tensão antes dos ensaios realizados e suas condições físico-químicas avaliadas antes dos experimentos, com base em analises química e metalográficas. As variações da força eletromotriz, induzidas pelo uso, foram avaliadas com base em calibrações que antecederam e sucederam a exposição das amostras ao campo de temperatura previamente determinado, realizadas contra temperaturas de referência obtidas pelo uso de seis células de pontos fixos (Ag, Al, Zn, Sn, In e Ga). Como contextualização, a dissertação também apresenta um breve histórico relacionado à medição da temperatura e ao uso de termopares tipo K, além de fundamentar a teoria que sustenta o desenvolvimento da pesquisa, suas conclusões, estabelecendo, assim, as bases para recomendações de novos trabalhos neste campo. Como resultado central da investigação conduzida, comprovou- se que, para as condições de trabalhos impostas (calibração em células de ponto fixo e exposição à temperatura de 995 graus Celsius em regime contínuo), todas as amostras apresentaram desvios nas suas curvas de calibração que variam na faixa de 0,2 a 4,0 graus Celsius, explicitando intervalos superiores às expectativas dos usuários. O período de vida dos experimentos completou-se com um intervalo de tempo de 134 h de submissão ao campo de temperatura. A pesquisa é de relevância no contexto industrial e científico pelo fato de o termopar tipo K representar cerca de 70 por cento do mercado brasileiro de termopares, e ser uma expectativa e recomendação do Instituto Nacional de Metrologia do Brasil, o Instituto Nacional de Metrologia, Normalização e Qualidade Industrial (INMETRO). / [en] The present masters dissertation entitled Metrological Assessment of Thermoelectric Stability of Type K Thermocouple, refers to the verification of stability deviations in the electromotive force induced by the use of type K thermocouple with 3mm diameter mineral insulation. Eight samples from four national thermocouples manufacturers were analyzed, after their exposure to a 995 different to 0,5 temperature field, thus very close to its applicability threshold (1070 Celsius degree), simulating a continuous regime condition of use. The samples were annealed at 1000 Celsius degree to regulate the strain state before the tests; their physical-chemical conditions were assessed before the essays based on chemical and metallographic analyses. The variations in electromotive forces induced by use were assessed based on calibrations made before and after the exposure of the samples to the temperature field previously determined,performed against reference temperatures obtained with the use of six fixed- point cells (Ag, Al, Zn, Sn, In and Ga). The dissertation also presents a brief history on temperature gauging and the use of type K thermocouples, in addition to showing the basis of the theory that supports research development, its conclusions, thus establishing the basis for recommendations of new research in this field. The main result of the research carried out enabled us to prove that, for the imposed working conditions (calibration on fixed-point cells and exposure to temperatures of 995 Celsius degree under a continuous regime), all the samples presented deviations in their calibration curves which varied from 0.2 to 4.0 Celsius degree, which made explicit higher intervals than those expected by the users. The test s lifetime was completed with a 134 hour time interval submission to the temperature field. The research is relevant in the industrial and scientific context because type K thermocouples represent approximately 70percent of the Brazilian thermocouple market, and because it is an expectation and a recommendation of the National Metrology Institute of Brazil - the Instituto Nacional de Metrologia,Normalização e Qualidade Industrial (INMETRO).