Thesis advisor: Welkin E. Johnson / Tetherin/BST2 is an interferon-inducible antiviral factor that restricts the egress of numerous enveloped viruses including HIV-1. Consequently, many viruses have evolved mechanisms to actively or passively evade restriction by tetherin. Most studies conducted to date focused on the tetherin-evasion mechanism of complex retroviruses like HIV and SIV, which encode accessory proteins like Vpu and Nef respectively to counteract tetherin-mediated restriction. However, there is a wide gap in knowledge in understanding how simple retroviruses (that includes alpharetroviruses, some betaretroviruses and gammaretroviruses) that lack obvious accessory proteins like HIV-1 Vpu and SIV-Nef, evade restriction by tetherin. In this dissertation, I have established that Simian retrovirus type-3, a prototypical type-D betaretrovirus, isolated from Asian macaques, is restricted by human tetherin but not by rhesus macaque tetherin. This differential sensitivity indicated that SRV-3 has a mechanism to evade tetherin-mediated restriction. I have identified the SRV-3 envelope (Env) glycoprotein as the viral determinant of tetherin antagonism, and have also found that SRV-3 envelope expression in-trans was sufficient to rescue a heterologous virus from tetherin. SRV-3 Env resulted in cell-surface down-modulation of rhesus tetherin, and this mechanism of tetherin-antagonism is independent of the SRV-3 Env trafficking pathway. The target specificity of SRV-3 Env overlapped a stretch of five residues (G14DIWK18) in the rhesus tetherin cytoplasmic tail that are absent from human tetherin. Additionally, I was able to show that SRV-3 Env physically interacts with rhesus tetherin by targeting the G14DIWK18 motif. SRV-3 belongs to a large supergroup of retroviruses, called the RDR Interference Supergroup. Due to this reason, I screened additional RDR envelope glycoproteins for their ability to antagonize a panel of tetherin homologs. All the RDR envelopes tested were sensitive to human tetherin but exhibited anti-tetherin activity when tested against a panel of tetherin homologs from squirrel monkey, baboon, dog and cat. I also found that several non-RDR gammaretroviral envelope glycoproteins also have anti-tetherin function. Thus, tetherin-antagonism is not just restricted to the envelope glycoproteins of retroviruses in the RDR interference supergroups but extends to other non-RDR gammaretroviruses as well. To my knowledge, this is the first characterization of gamma-type envelopes as tetherin antagonists. Thus, in the absence of a dedicated tetherin antagonist, many simple retroviruses in the beta- and gammaretrovirus genera may evade tetherin-mediated restriction through neo-functionalization of their envelope glycoproteins. We speculate that the evolutionary success of the gamma-type envelope may be due, at least in part, to this anti-tetherin function. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Thesis advisor: Welkin E. Johnson / Endogenous retroviruses (ERVs) make up a significant portion of vertebrate genomes, and serve as a fossil record of past retroviral infections. Although most ERV genes acquire inactivating mutations over time, some loci retain open reading frames (ORFs) across one or more of the viral genes. The ERV-Fc family, for example, endogenized in multiple mammalian hosts 10 to 30 million years ago, yet many copies maintain intact ORFs corresponding to the env gene, including loci in humans (HERV-Fc1-env) and baboons (babERV-Fc2-env). We previously identified intact ERV-Fc-related env sequences in eight additional mammalian species: chimpanzee, bonobo, aardvark, grey mouse lemur, squirrel monkey, marmoset, dog, and panda. Here we present the results of our assays of expression of these full-length Env proteins. We found that most of the precursors were not cleaved to form the functional surface (SU) and transmembrane (TM) subunits, even when a canonical furin cleavage site was still intact. An exception was babERV-Fc2, in which reconstruction of the cleavage site led to cleavage into SU and TM subunits. Furthermore, removal of 22 residues from the C-terminus of the cytoplasmic tail of babERV-Fc2 enhanced syncytia formation and the ability of babERV-Fc2 pseudotyped virions to infect 293T cells, suggesting the presence of an R-peptide cleavage mechanism. A survey of a small panel of cells revealed that only human cell lines were infectable by babERV-Fc2 pseudotyped murine leukemia virus (MLV) particles, whereas cells of old world monkey, canine, feline and chicken origin were not susceptible to infection. Ectopic expression of native Env codon optimized babERV-Fc2 Env can also inhibit infection by reconstructed babERV-Fc2 pseudotyped virus, raising the possibility that the endogenous glycoprotein encoded in the baboon genome may function as a viral entry inhibitor. Our results suggest that exaptation of ERV Env proteins as antiviral defense genes involves a combination of selective pressures: selection to preserve the receptor-binding and receptor interference functions of Env, but also selection to eliminate the membrane fusion related functions. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

The internal thermal climatic condition of a house is directly affected by how the building envelope (walls, windows and roof) is designed to suit the environment it is exposed to. The way in which the building envelope is constructed has a great affect on the energy required for heating and cooling to maintain human thermal comfort. Understanding how the internal climatic conditions react to the building envelope construction is therefore of great value. This study investigates how the thermal behaviour inside of a simple house reacts to changes made to the building envelope with the objective to predict how these changes will affect human thermal comfort when optimising the design of the house. A three-dimensional numerical model was created using computational fluid dynamic code (Ansys Fluent) to solve the governing equations that describe the thermal properties inside of a simple house. The geometries and thermophysical properties of the model were altered to simulate changes in the building envelope design to determine how these changes affect the internal thermal climate for both summer and winter environmental conditions. Changes that were made to the building envelope geometry and thermophysical properties include: thickness of the exterior walls, size of the window, and the walls and window glazing constant of emissivity. Results showed that there is a substantial difference in indoor temperatures, and heating and cooling patterns, between summer and winter environmental conditions. The thickness of the walls and size of the windows had a minimal effect on internal climate. It was found that the emissivity of the walls and window glazing had a significant effect on the internal climate conditions, where lowering the constant of emissivity allowed for more stable thermal conditions within the human comfort range.

The overall heat transfer coefficient of a building wall, the U value, is an interesting parameter to deduce the heat loss rate through the wall. The current method to determine this U value is well known, but is requires a lot of time to be performed. In this work a new idea of methodology is presented to get an accurate idea of the U value in a really smaller time, using an IR camera. IR thermography is a non destructive method that is mainly used today to carry out qualitative observations. In this work it is used as a quantitative tool to determine the conductivity of a wall knowing the external heat transfer coefficient. The error obtained on homogeneous and heterogeneous walls are smaller than 10 %, which is accurate enough for a fast measurement. The thermal mass of the wall can also be estimated with errors between 5 and 20 %, but only if the user has a good first guess of the real value. Finally some ideas are proposed when the heat transfer coefficient is not known, leading to less reliable results. More work is necessary to transform it as a usable method in everyday life. A part of the report concerns some attempts done with a simulation of the experiment, leading to no concrete results but it is still presented as it took some time to be studied.

This thesis seeks to tie into the underlying ideology of the middle landscape that has shaped housing development in the United States up to this point, and re-imagine its physical manifestation. An incremental approach is taken in imagining what housing might be in America, considering our myths surrounding the single family house, micro and macro community creation, density, sustainability (regarding the economics of the home and country, as well as our place in an ecosystem), emerging timber construction of tall buildings, and industrialized methods of building.  <br /><br />A mix of passive and active green building strategies are employed in making an expanded or "inhabited envelope", which surrounds a 22-story mass timber modular mid-rise residential tower in Red Hook Brooklyn. The base of the tower and development of the city block include a cooperative factory for wood based production, innovative bike storage, bike repair shop, shared use digital fabrication lab, shared use shops (wood, metal, and upholstery),  loading dock, laundry, gym, shared use office space, and café. / Master of Architecture

Le chloroplaste est un composant majeur de la cellule végétale. Cet organite est le fruit d’une endosymbiose, survenue entre une cellule eucaryote et une cyanobactérie. Ainsi, 95% des gènes codant pour les protéines plastidiales ont été transférés vers le génome nucléaire au cours de l’évolution. En conséquence, la plupart des protéines chloroplastiques sont aujourd’hui codées par le noyau, synthétisées dans le cytosol sous forme de précurseurs dotés d’une une extension N-terminale clivable (le "peptide de transit") et ensuite importées sans les chloroplastes via le système TOC/TIC (Translocons localisés au niveau des membranes externe et interne de l'enveloppe des chloroplastes). Jusqu'à récemment, toutes les protéines destinées aux compartiments chloroplastiques internes étaient censées posséder une séquence d’adressage N-terminale clivable et engager la machinerie d’import général TOC/TIC. Cependant, des études récentes reposant sur des approches protéomiques ont révélé l’existence de plusieurs protéines chloroplastiques dépourvues de la séquence additionnelle clivable. La première évidence de telles protéines dites non canoniques a été fournie par notre équipe, étudiant le protéome de l’enveloppe du chloroplaste d’Arabidopsis, qui a conduit à l’identification d’une protéine quinone oxidoréductase homologue nommée « ceQORH ». Bien que dépourvues de peptide de transit clivable, il s’est avéré que ces protéines sont capables de rejoindre les compartiments chloroplastiques internes. D’autre part, il a été également montré que l’import de ces protéines dans le chloroplaste n’est pas médiée par la machinerie de translocation générale TOC/TIC. De plus, il s’est avéré que ces protéines ont la particularité d’être multilocalisées dans les cellules de différents tissus de la feuille. Cependant, les mécanismes moléculaires qui contrôlent la localisation sub-cellulaire de telles protéines chloroplastiques non canoniques demeurent encore inconnus. Pour mieux caractériser fonctionnellement les composantes des systèmes d’import alternatifs de protéines chloroplastiques non canoniques, nous avons adopté une approche directe qui reposait sur des techniques biochimiques combinant le crosslink chimique, la purification par affinité et la spectrométrie de masse. Cette stratégie nous a permis d’identifier un partenaire, impliqué dans le contrôle de l’adressage de la protéine ceQORH dans le chloroplaste. Alternativement, nous avons réalisé une bio-analyse du protéome de l’enveloppe du chloroplaste et qui nous a permis de revisiter la composition du protéome de l’enveloppe du chloroplaste. Afin d’expliquer la localisation sub-cellulaire variable de la protéine ceQORH, les membres de l’équipe ont émis l’hypothèse d’une interaction probable de cette protéine avec un partenaire cytosolique. Dans la dernière partie de cette étude, nous avons validé l’interaction, in planta, entre ceQORH et son partenaire par une approche génétique qui portait sur l’analyse de l’impact de l’absence de ce dernier sur la régulation de la localisation sub-cellulaire de la protéine ceQORH. / Chloroplasts are a major component of plant cells. Their origin traces back to a cyanobacterial ancestor that was engulfed by an ancient eukaryotic cell and eventually integrated as an organelle during evolution. As a result, more than 95% of the ancestral cyanobacterial genes were transferred to the host cell nucleus. Proteins encoded by these relocated genes need to return to internal chloroplast compartments. This import is mainly achieved by the general TOC/TIC machinery located at the chloroplast surface. Until recently, all proteins destined to chloroplast were believed to possess an N-terminal and cleavable chloroplast targeting peptide, and to engage the TOC/TIC machinery. However, recent studies have revealed the existence of several non-canonical preproteins, lacking cleavable transit peptides. The first evidence for such ‘non-canonical’ chloroplast proteins was provided by our team studying the Arabidopsis chloroplast envelope proteome, leading to the identification of a quinone oxidoreductase homologue termed « ceQORH ». Furthermore, a few such proteins were demonstrated to use alternative targeting pathways, independent of the TOC/TIC machinery. To better characterize components of such alternative targeting machineries, a targeted study combining affinity purification and mass spectrometry aiming to identify alternative receptors at the chloroplast surface has been performed. This study allowed us to identify new “partner” involved in the control of chloroplast targeting of ceQORH protein. Alternatively, we also revisited the chloroplast envelope proteome composition and initiated a gene candidate approach. In addition, some non-canonical proteins are shared by plastids and other cell compartments. However, molecular mechanisms controlling subcellular localization of these non-canonical plastid proteins remain unknown. In order to explain the variable subcellular localization of ceQORH protein, our team hypothesized a probable interaction of ceQORH with a cytosolic partner. In the last part of this study, we validated the interaction between ceQORH and its partner in planta by a genetic approach analyzing the impact of the absence of the cytosolic partner on the regulation of the sub-cellular localization of ceQORH protein.

Fast neural oscillations known as beta (12-30Hz) and gamma (30-100Hz) rhythms are recorded across several brain areas of various species. They have been linked to diverse functions like perception, attention, cognition, or interareal brain communication. The majority of the tasks performed by the brain involves communication between brain areas. To efficiently perform communication, mathematical models of brain activity require representing neural oscillations as sustained and coherent rhythms. However, some recordings show that fast oscillations are not sustained or coherent. Rather they are noisy and appear as short and random epochs of sustained activity called bursts. Therefore, modeling such noisy oscillations and investigating their ability to show interareal coherence and phase synchronization are important questions that need to be addressed. In this thesis, we propose theoretical models of noisy oscillations in the gamma and beta bands with the same properties as those observed in in \textit{vivo}. Such models should exhibit dynamic and statistical features of the data and support dynamic phase synchronization. We consider networks composed of excitatory and inhibitory populations. Noise is the result of the finite size effect of the system or the synaptic inputs. The associated dynamics of the Local Field Potentials (LFPs) are modeled as linear equations, sustained by additive and/or multiplicative noises. Such oscillatory LFPs are also known as noise-induced or quasi-cycles oscillations. The LFPs are better described using the envelope-phase representation. In this framework, a burst is defined as an epoch during which the envelope magnitude exceeds a given threshold. Fortunately, to the lowest order, the envelope dynamics are uncoupled from the phase dynamics for both additive and multiplicative noises. For additive noise, we derive the mean burst duration via a mean first passage time approach and uncover an optimal range of parameters for healthy rhythms. Multiplicative noise is shown theoretically to further synchronize neural activities and better explain pathologies with an excess of neural synchronization. We used the stochastic averaging method (SAM) as a theoretical tool to derive the envelope-phase equations. The SAM is extended to extract the envelope-phase equations of two coupled brain areas. The goal is to tackle the question of phase synchronization of noise-induced oscillations with application to interareal brain communication. The results show that noise and propagation delay are essential ingredients for dynamic phase synchronization of quasi-cycles. This suggests that the noisy oscillations recorded in \textit{vivo} and modeled here as quasi-cycles are good candidates for such neural communication. We further extend the use of the SAM to describe several coupled networks subject to white and colored noises across the Hopf bifurcation ie in both quasi-cycle and limit cycle regimes. This allows the description of multiple brain areas in the envelope-phase framework. The SAM constitutes an appropriate and flexible theoretical tool to describe a large class of stochastic oscillatory phenomena through the envelope-phase framework.

Broiler birds have drastically increased in size over the past few decades through improvements in genetic selection. Physical measurements such as surface area, volume and physical dimensions are needed information in the construction of animal facilities and developing management guidelines. The objective of this study was to develop a three-dimensional scanning methodology to characterize surface area and envelope volume of poultry, livestock, and equine using a commercially available 3D digitizer system. The digitizing system used phase shift moiré to capture images of three test cylinders, four fiberglass animal models, and a live broiler bird. These images were spliced into physical models using image processing software. System accuracy (< 2%) was verified with cylinder models. Recommended camera orientations and placements were established with each species by the use of fiberglass models. The methods will have to be fine-tuned for live animals as observed in the live broiler test.

Broiler production requires significant expenditures for heating fuel year round. Poor thermal envelope performance leads to reduced live performance, increased energy use, and reduced profitability. Poultry house building component thermal resistance (R-value) is subject to change over time. To characterize the thermal envelope heat transmission and building component R-value of two broiler houses of different ages, conductive heat flux (W/m2) and temperature gradient (Delta T °C) were monitored with heat flux meter (HFM) arrays and temperature sensors over a 13-month period. Net heat loss and building component (walls and ceiling) thermal resistance were determined from the data. Results showed differences in net heat loss were observed for the ceiling zones where 84% more heat was lost through the ceiling of the older house than that of the newer house (P < 0.05). R-values determined from field measurements for both houses were below estimated theoretical composite R-values. Observed R-values were greater for ceiling envelope zones of the newer house when compared to the older house. Increased heat loss and reductions in ceiling envelope zone R-values for the older house were attributed to shifting and settling of the looseill cellulose attic insulation material, which was especially prevalent at the ceiling peak zone. To verify the feasibility of using sol-air temperature in lieu of outside air temperature to account for radiant load during warm conditions, field measurements of temperature (°C) (interior air, exterior air, and exterior surface) and solar radiation (W/m2) were recorded of a broiler house. Sol-air temperatures were calculated from these data. Observed maximum daily air temperatures were significantly different (P<0.0001) from maximum surface and sol-air temperatures. Maximum surface and sol-air temperatures were not significantly different (P=0.2144, P=0.1544). Simulations of conductive heat transfer by air and sol-air temperatures using climatic data showed heat gain as calculated by sol-air Delta T was considerably higher when compared to heat gain calculated by air Delta T. This study supports the rationale that the sol-air temperature concept results in improved estimates of conductive heat transfer during daytime conditions which can be used to optimize insulation and ventilation requirements for broiler houses during warm conditions.

No description available.