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1
Shanmugam, Sivamoorthy. "Automatic Sub-assembly detection, disassembly sequencing and disassembly direction prediction for an assembly model." Cincinnati, Ohio : University of Cincinnati, 2005. http://www.ohiolink.edu/etd/view.cgi?acc%5Fnum=ucin1109252927.
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2
SHANMUGAM, SIVAMOORTHY. "AUTOMATIC SUB-ASSEMBLY DETECTION, DISASSEMBLY SEQUENCING AND DISASSEMBLY DIRECTION PREDICTOR FOR AN ASSEMBLY MODEL." University of Cincinnati / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1109252927.
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3
Baker, Michael. "The assembly and disassembly of clathrin cages." Thesis, University of Warwick, 2016. http://wrap.warwick.ac.uk/89475/.
Full textAbstract:
Clathrin mediated endocytosis (CME) is an integral process in eukaryotic cells and governs a wide range of processes in higher organisms including neurotransmitter release and cell signalling, to development and cell polarity. Due to its wide ranging roles this mechanism has been implicated in various disease states such as Huntington’s disease and various cancers as well as being a method of entry into cells for many viruses and bacteria. The process of CME involves the formation of a clathrin coat, primarily consisting of the protein clathrin, that drives uptake of cargo at the plasma membrane. These interactions are facilitated through a large family of proteins known as adaptor proteins, which drive the process of CME through specific interactions with clathrin, cargo, the plasma membrane and the cytoskeleton. Once the cargo has been endocytosed the process must be reversed through the actions of the disassembly proteins auxilin/GAK and Hsc70. A number of questions remain as to how adaptors promote assembly and how auxilin and Hsc70 drive disassembly through interaction with clathrin and potentially through interactions with the adaptor proteins. By purifying adaptor proteins and clathrin I have used various biochemical and biophysical techniques to investigate these interactions in vitro. Using a novel assembly assay based on dynamic light scattering I have shown that it is possible to measure the effect of adaptors on clathrin cage size distribution during assembly. In disassembly I have shown how mutations in the disassembly protein auxilin affect its ability to catalyse the disassembly of clathrin cages and how the presence of various adaptor proteins alters the ability of auxilin and Hsc70 to disassemble these structures. Finally, I demonstrate an inhibitory effect on disassembly by the adaptor protein epsin and propose a mechanism of interaction with clathrin that can be disrupted through mutations to epsin clathrin-binding motifs and discuss the implications of this effect for the role of adaptors in vivo.
4
Schoen, Timothy Ryan. "Constraint-aware distributed robotic assembly and disassembly." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/77078.
Full textAbstract:
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 83-85).
In this work, we present a distributed robotic system capable of the efficient assembly and disassembly of complex three-dimensional structures. We introduce algorithms for equitable partitioning of work across robots and for the efficient ordering of assembly or disassembly tasks while taking physical constraints into consideration. We then extend these algorithms to a variety of real-world situations, including when component parts are unavailable or when the time requirements of assembly tasks are non-uniform. We demonstrate the correctness and efficiency of these algorithms through a multitude of simulations. Finally, we introduce a mobile robotic platform and implement these algorithms on them. We present experimental data from this platform on the effectiveness and applicability of our algorithms.
by Timothy Ryan Schoen.
M.Eng.
5
Sung, Raymond Chun Wai. "Automatic assembly feature recognition and disassembly sequence generation." Thesis, Heriot-Watt University, 2001. http://hdl.handle.net/10399/478.
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6
Mohd, Rashid Aiman. "Disassembly and assembly in the Malay building culture." Thesis, University of Sheffield, 2018. http://etheses.whiterose.ac.uk/22827/.
Full textAbstract:
Asian vernacular architecture is generally dynamic, progressing and constantly transforming. The significance of Asian vernacular values lies in the culture, identity and memory of the people rather than the fabric or preserved artefacts. Likewise, the vernacular traditional Malay houses are a manifestation of the craft process and meanings embodied in the people, their building practice and artefacts. However, the Malay building culture is diminishing while the numbers of tukang or master craftsmen is declining, which adds to the loss of traditional knowledge and skills in Malay house building culture. The study investigates the traditional craft of Malay house-building within the present in order to identify the legacy of Malay craftsmanship concerning knowledge and skills of tukang and their apprentices. Furthermore, the study explores contemporary Malay building practice and inquiring how traditions were and continued to be conveyed towards building participants. The unstructured interviews with tukang, experts and non-experts, while observing building activities were used to provide insights of the Malay house building culture within contemporary. The methodology adopted is relevant as much of the craft knowledge and skills are embodied and performed, rather than articulated in oral or literature. The study concluded that Malay architecture is rooted not in the tangible built fabric but in the knowledge and dexterity of tukang and the craft process relating to materials, tools, measurement and bodily movement. Similarly, the meaning of Malay craftsmanship is defined by tukang and embodied in their practice. However, tukang is more than simply a builder but has a spiritual role that connects the Malay cultural beliefs to the Malay house and the building process. Hence, the study implies that the Malay house building is a form of a spiritual practice emphasising the value of culture, memory and religious identity rather than purely narrating the structures. Furthermore, the findings of the study suggest that essential qualities of craftsmanship, knowledge and skills in Malay house-building are exemplified subliminally within the actions of buka-pasang or disassembly and assembly. The study demonstrates that the practice of disassembling and assembling existing Malay structures, was and still remain as a socially communicative act in transmitting building traditions. The study characterised the disassembly and assembly as a building process involving dyadic knowledge of technical (strategy) and spiritual (cultural) that manifest the poetics, procedural, ritual and somatic means of Malay house-building culture. Therefore the study asserted that performing disassembly and assembly afford to a sense of retracing footsteps of past mastery as an embodied heritage experience - hence comparable to the apprenticeship-style of learning that demonstrates the process of mimetic, causal learning and reflective cognitive process. Eventually, the study expresses that the values of Malay cultural heritage are not in the static heritage artefact, but the physical and spiritual interaction between artefacts and the people in the present. The answer to the loss of heritage and the decline of traditional building practice and knowledge it offers is through disassembly and assembly, where the study views this process as a catalyst in overcoming these shortcomings.
7
Duggan, James. "Soluble factors affecting the assembly and disassembly of membrane rafts." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.495061.
Full textAbstract:
The presence of membrane microdomains or rafts within cell membranes is an area of intensive research and debate, with the notion of intracellular membrane rafts proving particularly contentious. The full extent of their biological importance is unknown but, they do appear to have vital roles in key processes such as membrane transport and cell signalling. They have been shown to have significant involvement in the formation of the immunological synapse and subsequent immune cell activation. Their cellular functions are also hijacked by various pathogens such as the human immunodeficiency virus and prion diseases, establishing them as important pharmaceutical targets.
8
Lane, Laura Alexandra. "Assembly and disassembly of protein complexes : insights from mass spectrometry." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.608969.
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9
Chromy, Laura R. "The role of HSP70 chaperones in papovavirus disassembly and assembly /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2007.
Find full textAbstract:
Thesis (Ph.D. in Molecular Biology) -- University of Colorado Denver, 2007.Typescript. Includes bibliographical references (leaves 142-165). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;
10
Chang, Piyen. "Selection and evaluation of joint types and joining processes for concurrent assembly/disassembly-based design." Thesis, This resource online, 1996. http://scholar.lib.vt.edu/theses/available/etd-09182008-063034/.
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11
Lurgi, Rivera Miguel. "The assembly and disassembly of ecological networks in a changing world." Doctoral thesis, Universitat Autònoma de Barcelona, 2014. http://hdl.handle.net/10803/133289.
Full textAbstract:
El
ensamblaje,
estructuración
y
funcionamiento
de
las
comunidades
naturales,
compuestas
de
muchas
especies
que
forman
redes
complejas
de
interacciones
ecológicas,
ha
desconcertado
a
los
ecólogos
durante
muchas
generaciones.
Investigación
ecológica
pionera
determinó
que
el
tamaño
de
la
comunidad
y
su
complejidad
(medida
como
la
conectividad
en
la
red
de
interacciones
ecológicas)
limita
la
estabilidad
de
la
comunidad,
y
por
lo
tanto
impiden
que
las
comunidades
sean
indefinidamente
complejas
o
ricas
en
especies.
Investigación
sobre
el
ensamblaje
y
la
estabilidad
en
comunidades
naturales
ha
descubierto
que
la
arquitectura
de
la
red
trófica
es
la
clave
para
la
estabilidad
de
la
comunidad
y
su
persistencia.
Así,
los
científicos
comenzaron
a
centrarse
en
la
comprensión
de
las
complejas
redes
de
interacciones
entre
especies,
y
pronto
se
dieron
cuenta
de
que
la
dinámica
de
las
poblaciones
de
las
comunidades
naturales
se
rigen
por
la
estructura
de
estas
redes.
Por
otra
parte,
ciertas
características
observadas
en
la
estructura
de
las
redes
ecológicas
son
responsables
del
mantenimiento
de
la
estabilidad
en
diferentes
tipos
de
comunidades
ecológicas.
El
siguiente
paso
en
la
investigación
de
las
redes
ecológicas
es
incorporar
varios
tipos
de
interacción
en
un
escenario
ecológico
más
amplio.
Esto
incrementará
el
conocimiento
de
la
estructura
y
la
estabilidad
de
la
comunidad.
El
cambio
global
está
afectando
los
ecosistemas
de
todo
el
mundo,
con
profundos
impactos
sobre
el
delicado
equilibrio
de
la
naturaleza.
Ya
ha
causado
un
número
sin
precedentes
de
extinciones,
y
el
consiguiente
daño
en
la
estructura
y
funcionamiento
del
ecosistema
ha
llevado
a
muchos
a
sugerir
que
en
estos
momentos
estamos
presenciando
la
sexta
extinción
masiva
en
la
historia
de
la
Tierra.
El
principal
desafío
para
la
investigación
ecológica
que
tenemos
por
delante
es
entender
y
predecir
cómo
el
cambio
global
está
afectando,
y
es
probable
que
afecte
en
el
futuro,
los
ecosistemas
complejos.
En
esta
tesis
enfrento
este
desafío
utilizando
una
aproximación
empírico-‐teórica
integradora
para
explorar
los
efectos
del
cambio
global
-‐cambio
climático,
pérdida
de
biodiversidad
e
invasión
de
especies-‐
en
comunidades
compuestas
por
múltiples
especies.
Adicionalmente,
investigo
qué
hace
que
las
comunidades
ecológicas
sean
estables
durante
su
ensamblaje,
y
cómo
esta
estabilidad
puede
verse
afectada
por
el
cambio
global.
En
concreto,
he
empleado
una
combinación
de
revisión
de
resultados
y
análisis
de
datos
empíricos,
un
novedoso
marco
conceptual
para
el
análisis
de
las
relaciones
entre
diferentes
dimensiones
de
la
estabilidad
ecológica,
modelos
teóricos
fundamentados
en
redes
tróficas
con
estructuras
realista
y
ecuaciones
diferenciales
ordinarias
para
simular
la
dinámica
de
las
poblaciones,
y
modelos
espacialmente
explícitos
basados
en
el
individuo
con
una
mezcla
de
tipos
de
interacciones
ecológicas;
con
el
fin
de
obtener
una
visión
predictiva
de
los
efectos
de
los
diferentes
componentes
del
cambio
global
sobre
las
comunidades
naturales
y
sobre
los
factores
que
explican
la
estabilidad
de
estos
conjuntos
de
especies.
Algunos
de
mis
principales
hallazgos
son:
(1)
cambios
de
distribuciones
de
especies
provocados
por
el
cambio
climático
están
generando
comunidades
nuevas
.
Estas
últimas
se
caracterizan
por
nuevos
patrones
en
que
las
distribuciones
de
tamaño
corporal
dentro
de
las
redes
tróficas
se
están
desplazando
hacia
tamaños
más
pequeños,
las
interacciones
especialistas
se
están
perdiendo,
y
las
fuerzas
de
interacción
son
cada
vez
más
fuertes
en
general,
con
consecuencias
importantes
para
la
dinámica
de
la
comunidad.
(2)
Las
diferentes
dimensiones
de
la
estabilidad
ecológica
se
correlacionan
de
manera
no
trivial.
La
pérdida
de
biodiversidad
lleva
a
un
desacoplamiento
de
estas
correlaciones.
Esto
conduce
a
dinámicas
altamente
impredecibles
en
comunidades
ecológicas
sujetas
a
perturbaciones.
(3)
Enfocándonos
en
las
invasiones
biológicas
vemos
que
la
estructura
de
la
red
trófica
es
un
factor
determinante
para
éxito
de
la
invasión.
Comunidades
menos
conectadas,
más
modulares,
y
más
heterogéneas
en
términos
de
amplitud
de
la
dieta
de
las
especies
que
las
componen
son
más
robustas
a
las
invasiones
biológicas.
Las
invasiones
hacen
a
las
comunidades
más
conectadas
y
menos
modulares
en
general,
lo
que
las
hace
aún
más
frágiles
a
las
invasiones.
Algunos
rasgos
de
las
especies
invasoras,
como
su
tamaño
corporal
y
su
capacidad
de
capturar
la
presa,
también
son
fuertes
determinantes
del
éxito
de
la
invasión.
(4)
Por
último,
las
interacciones
mutualistas
incrementan
tanto
la
estabilidad
temporal
como
la
estabilidad
espacial,
mediante
el
mantenimiento
de
una
agregación
espacial
más
constante.
Las
distribuciones
de
las
fuerzas
de
interacción
en
la
red
se
desplazan
hacia
valores
más
bajos
a
medida
que
la
fracción
de
mutualismos
en
la
comunidad
aumenta.The assembly, structuring and functioning of natural communities, composed of many species forming complex networks of ecological interactions, has puzzled ecologists for many generations. Early ecological research determined that community size and complexity (measured as connectivity in the network of ecological interactions) limit community stability, and hence impose constraints to communities to become indefinitely complex or speciose. Community assembly and stability research uncovered the fact that food web architecture is the key to community stability and persistence. Scientists thus started to focus on the understanding of complex networks of interactions between species, and it was soon realised that species population dynamics are influenced by biotic interactions within the overall network. Moreover, certain features observed in the structure of ecological networks are responsible for the maintenance of stability and species persistence in different kinds of ecological communities. The next step in ecological networks research is to incorporate several interaction types into a broader ecological scenario. This will further our knowledge in community structure and stability. Global change is affecting all ecosystems across the globe, having profound impacts over the delicate balance of nature. It has already caused an unprecedented number of extinctions, and the consequent damage to ecosystem structure and functioning has prompted many to suggest that we are currently witnessing the sixth mass extinction in the history of the Earth. The main big challenge for ecological research that lies ahead is to understand and predict how different components of global change are affecting and will likely affect complex ecosystems. In this thesis I tackle this challenge following an integrative empirical-‐theoretical approximation exploring the effects of global change –climatic warming, biodiversity loss and species invasion-‐ on multispecies communities. In addition, I investigate what makes ecological communities stable through their assembly, and how this stability may be affected by global change. Specifically, I employed a combination of empirical results review and data analysis, a novel conceptual framework for the analysis of relationships between different dimensions of stability, theoretical models grounded on realistic food web structure and ordinary differential equations to simulate populations dynamics, and individual-‐based spatially explicit models with a mixture of ecological interaction types in order to gain predictive insights on the effects of different components of global change on natural communities and several factors behind the stability of these assemblages of species. Some of my key findings are: (1) Species range shifts triggered by climate change are generating novel communities. These are characterized by consistent novel patterns where body size distributions within the food webs are getting shifted towards smaller sizes, specialised interactions are getting lost, and interaction strengths are getting stronger in general, with further consequences for community dynamics. (2) Different dimensions of ecological stability are correlated in non-‐trivial ways. Biodiversity loss leads to a decoupling of the correlations previously observed between stability measures. This leads to highly unpredictable dynamics of ecological communities after major disturbances. (3) When focusing on biological invasions I find that food web structure is a strong determinant of invasion success. Less connected, more modular, and more heterogeneous communities in terms of diet breadth are more robust to biological invasions. Invasions make communities more connected and less modular in general, rendering them even more fragile to invasions. Species traits of the invasive species, such as body size and the ability to capture prey, are also strong determinants of invasion success. (4) Finally, mutualistic interactions increase both temporal stability and spatial stability, by keeping spatial aggregation more constant. Distributions of interaction strengths across the entire food web are shifted towards lower values as mutualism increases.
12
Vaillant, Dominique. "Evaluation of mammalian cell-free systems of nuclear assembly and disassembly." Thesis, University of Ottawa (Canada), 2005. http://hdl.handle.net/10393/27066.
Full textAbstract:
Mammalian cell-free systems are very useful for the biochemical and structural study of nuclear disassembly and assembly. Through manipulation, the role of specific proteins in these processes can be investigated. I first intended to examine the involvement of integral and peripheral inner nuclear membrane proteins in nuclear disassembly and assembly. However, I was unable to achieve disassembly when isolated interphase HeLa nuclei were exposed to mitotic soluble extracts containing cyclin B1. Homogenates of synchronized mitotic HeLa cells left to reassemble nuclei resulted in incomplete nuclear envelope assembly on chromatin masses. Digitonin permeabilized mitotic cells also assembled incomplete nuclei, generating a lot of cytoplasmic inclusions of inner nuclear membrane proteins as an intermediate. These results were therefore used as a basis for the experimental evaluation of mammalian cell-free systems. Synchronization itself induced incomplete nuclear assembly. This may be caused by the prior aberrant nuclear disassembly, or by the abnormal number of mitotic spindles.
13
Sept, David S. "Models of assembly and disassembly of individual microtubules and their ensembles." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/nq23068.pdf.
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14
DESAI, ANOOP. "AN INTEGRATED METHODOLOGY FOR ASSEMBLY, DISASSEMBLY AND MAINTENANCE FOR CONSUMER PRODUCTS." University of Cincinnati / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1154100938.
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15
Tison, Christopher Kirby. "Programmable, isothermal disassembly of DNA-linked colloidal particles." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28189.
Full textAbstract:
Thesis (M. S.)--Materials Science and Engineering, Georgia Institute of Technology, 2009.Committee Chair: Milam, Valeria; Committee Member: Boyan, Barbara; Committee Member: Li, Mo; Committee Member: McDevitt, Todd; Committee Member: Sandhage, Ken.
16
Eze, Ngozi A. "Implementing locked nucleic acids as a bioinspired colloidal assembly and disassembly tool." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/51789.
Full textAbstract:
Oligonucleotides are popular recognition-based biomaterials assembly and disassembly tools due to their specificity and ease of control. Their susceptibility to degradation by nucleases and false positive signals under certain conditions, however, has led to great interest in chemically modified oligonucleotides such as locked nucleic acids (LNA) that enhance both nuclease resistance and target specificity. This dissertation extends prior work with DNA sequences to investigate incorporating locked nucleic acid (LNA), a synthetic oligonucleotide, in isothermal colloidal assembly and disassembly schemes as well as on hybridization kinetics between single-stranded and double-stranded probes immobilized on microspheres. Incorporation of LNA nucleotides into DNA sequences is of particular interest as a means of enhancing the performance of DNA in a biomaterials context due to the increased resistance of LNA to nuclease degradation, its greater intrinsic affinity for oligonucleotide targets, and low cytotoxicity effects. The effects of LNA modification, target sequence length, sequence fidelity, and salt concentration are key variables explored. After providing an overview of DNA and its properties, synthetic oligonucleotides, colloidal particles, and previous applications of DNA and LNA in colloidal assembly schemes, this work then discusses the selection and characteristics of appropriate pairs of hybridization partners for reversible colloidal assembly scenarios. A comparative investigation of the in situ primary hybridization kinetics between select LNA or DNA targets and single-stranded probes immobilized on colloidal surfaces is performed. To support the disassembly studies, the in situ competitive displacement kinetics of hybridized LNA primary targets by either LNA or DNA secondary targets is discussed. For these in situ studies, flow cytometry was used to quantify the hybridization reactions as they occur on microsphere surfaces. While comparable rate constants were typically observed between target and single-stranded probes, LNA typically exhibited more extensive primary and secondary hybridization activity. Optimizing hybridization parameters, such as duplex concentration, sequence fidelity, and LNA content in the probe and target strands, allows for the extent of colloidal disassembly to be tuned, an important step in developing a multifunctional colloid-based biomaterial system.
17
Geerts, Sjirk. "Assembly and disassembly of bird pollination communities at the Cape of Africa." Thesis, Stellenbosch : Stellenbosch University, 2011. http://hdl.handle.net/10019.1/6904.
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Thesis (PhD (Botany and Zoology))--Stellenbosch University, 2011.ENGLISH ABSTRACT: With the current global decline in pollinators, and the concurrent decline in plant species, pollination research is becoming increasingly important. However, studies outside Europe and North-America and on groups other than insects are needed to make generalisations possible. In this thesis I study how pollination structures plant and bird communities in a biodiversity hotspot, the Cape Floristic Region of South Africa. I show that bird-plant pollination mutualisms are an important ecological factor structuring ornithophilous Proteaceae and nectar-feeding bird communities. This close association between plant and bird communities suggests an important role for community wide pollination mutualisms. How these mutualisms disassemble in reaction to a range of anthropogenic impacts is determined. Firstly, I use experimental manipulation of honeybee density to test whether honeybee farming affects nectar-feeding birds. Hive addition increased honeybee abundance far above natural levels but nectar-feeding bird pollinators were not consistently affected. Secondly, I document the impact of a two lane tar road on the bird pollination community. The two-fold decline found in pollination along roadsides, should have important implications for the way we view and manage road verges for ecological processes. Thirdly, I investigated how fragmentation affects bird-pollination communities by assessing an endangered, bird-pollinated plant, Brunsvigia litoralis. The only flower visitor at the urban sites, the shorter billed Greater Double-collared Sunbird is unable to access the nectar due to a long perianth tube. The longer billed Malachite Sunbird was the sole pollinator of B. litoralis at the rural site, significantly increased seed set. The lack of ecological analogs in these urban fragments might place pollinator specialist plants, such as B. litoralis, at risk. Fourthly, fire is a frequent disturbance in communities of bird-pollinated plants. In a before/after fire observation study and a burnt/unburnt transplant study, birds visited flowers in the “before fire” and “unburnt” areas only. The results are surprising given the large number of bird-pollinated plants flowering in the early post-fire vegetation. Lastly, I find that alien invasive plant species are incorporated into the native pollination community in a spectacular way; sunbirds adapt to a hummingbird-like, hovering lifestyle to obtain nectar. Alien invasive plants greatly increase nectar-feeding bird abundance; in turn, birds enhance seed set in these alien plants. I conclude by asking whether the disassembling of bird pollination communities really matters. To answer this question I report on a decade of demographic data on the geophytic bird-pollinated Brunsvigia orientalis. In the demographic analysis, the elasticity component for reproduction was more important than expected for a long lived plant. Reduced population growth in the shade and a large investment in a winged inflorescence, suggest B. orientalis is a light demanding, well dispersed, gap colonising species. The link between pollination and seed has been made before, but I take this one step further and show that pollination intensity predicts population growth rate. By linking plant demography and pollination, I was able to predict the future of plant populations under variable pollination conditions. The disassembly of bird pollination communities only becomes important for population persistence once the mutualism has almost entirely broken down.
AFRIKAANSE OPSOMMING: Met die huidige globale afname in bestuiwers en die gelyktydige afname in plant spesies, word bestuiwing navorsing toenemend belangrik. Studies buite Europa en Noord-Amerika en op groepe anders dan insekte is nodig on veralgemenings moontlik te maak. In hierdie tesis bestudeer ek hoe bestuiwing struktuur gee and plant en voël gemeenskappe in 'n biodiversiteit hotspot, die Kaapse Floristiese Ryk van Suid-Afrika. Ek wys dat voël-plant bestuiwings mutualismes 'n belangrike ekologiese faktor is in die strukturering van voël bestuifde Proteaceae gemeenskappe en nektar-etende voël gemeenskappe. Hierdie noue assosiasie tussen plant en voël gemeenskappe impliseer 'n belangrike rol vir gemeenskapwye bestuiwings meganismes. Ek bepaal hoe hierdie mutualismes aftakel in reaksie op 'n verskeidenheid van antropogeniese impakte. Eerstens gebruik ek 'n eksperimentele manipulasie van heuningby getalle om te toets of bye boerdery nektar-etende voëls affekteer. Byekorf toevoeging het heuningby getalle laat toeneem tot ver bo natuurlike vlakke maar nektar-etende voël bestuiwers is nie konsekwent beïnvloed nie. Tweedens dokumenteer ek die impakte van 'n twee baan teerpad op die voël bestuiwings gemeenskap. Die twee-malige afname in bestuiwing langs paaie sal belangrike implikasies hê vir die manier hoe ons pad reserwes sien en bestuur met betrekking tot ekologiese prosesse. Derdens bestudeer ek hoe fragmentasie die voël-plant gemeenskappe affekteer deur die bedreigde voël-bestuifde Brunsvigia litoralis te assesseer. Die enigste besoeker in die meer stedelike area, die Groot-rooibandsuikerbekkie, wat 'n korter snawel het, is nie in staat om die nektar te bereik nie, weens 'n te lang blombuis. Die Jangroentjie suikerbekkie met sy langer snawel is die enigste bestuiwer van B. litoralis in die meer landelike area, met 'n betekenisvolle vermeerdering in saad vorming. Die gebrek aan ekologies analogiese spesies in die stedelike fragmente kan 'n risiko inhou vir bestuiwer gespesialiseerde plante soos B. litoralis. Vierdens, vuur is 'n gereelde versteuring van voël-plant gemeenskappe. In 'n voor/na vuur observasie studie en 'n brand/nie-brand verplasing studie, het voëls blomme net in die “voor brand” en “nie-brand” areas besoek. Hierdie resultate is verrassend siende die groot hoeveelheid voël-bestuifde plante wat blom direk na brande. Laastens het ek gevind dat uitheemse indringer plante geïnkorporeer word in die inheemse bestuiwers gemeenskappe op 'n skouspelagtige manier; suikerbekkies pas aan tot 'n kolibri-tipe, fladderende lewenswyse om nektar te bekom. Uitheemse indringer plante het nektar-etende voël hoeveelhede laat toeneem; in reaksie het voëls saad opbrengs vermeerder. In konklusie vra ek of hierdie aftakeling van die voël bestuiwers gemeenskap belangrik is. Om hierdie vraag te antwoord assesseer ek 'n dekade van demografiese data van die geofietiese, voël-bestuifde plant, Brunsvigia orientalis. In die demografiese analises was die elastisiteit komponent van reproduksie belangriker as verwag vir 'n langlewende plant. Verminderde populasie groei in die skaduwee en 'n hoë investering in 'n gevlerkte bloeiwyse suggereer dat B. orientalis 'n lig afhanklike, goed verspreide, gaping koloniserende spesie is. Die skakel tussen bestuiwing en saadvorming is voorheen gemaak, maar ek neem dit een stap verder en wys dat bestuiwings intensiteit populasie groeikoers voorspel. Deur plant demografie en bestuiwing te koppel was ek in staat om die toekoms van populasies onder variërende bestuiwings kondisies te voorspel. Die aftakeling van voël bestuiwings gemeenskappe word slegs belangrik vir populasies se voortbestaan wanneer die mutualisme amper heeltemal verdwyn het.
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June, Stephen Matthew. "Step-Growth Polymerization Towards the Design of Polymers: Assembly and Disassembly of Macromolecules." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/37619.
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Step-growth polymerization provided an effective method for the preparation of several high performance polymers. Step-growth polymerization was used for syntheses of poly(siloxane imides), polyesters, poly(triazole esters), poly(triazole ether esters), and epoxy networks. Each of these polymeric systems exhibited novel structures, and either photoreactive capabilities, or high performance properties.
There is an increasing trend towards the development of photoactive adhesives. In particular these polymers are often used in flip bonding, lithography, stimuli responsive polymers, drug delivery, and reversible adhesives. The ability to tailor polymer properties carefully with exposure to light allows for very unique stimuli responsive properties for many applications. This dissertation primarily investigates photoreactive polymers for reversible adhesion for use in the fabrication of microelectronic devices. In particular cyclobutane diimide functionality within polyimides and poly(siloxane imides) and o-nitro benzyl ester functionality within polyesters acted effectively as chromophores to this end.
Thermal solution imidization allowed for the effective synthesis of polyimides and poly(siloxane imides). 1,2,3,4-Cyclobutane tetracarboxylic dianhydride acted as the chromophore within the polymer backbone. The polyimides obtained exhibited dispersibility only in dipolar, aprotic, high boiling solvents such as DMAc or NMP. The obtained poly(siloxane imides) demonstrated enhanced dispersibility in lower boiling organic solvents such as THF and CHCl3. Dynamic mechanical analysis and tensile testing effectively measure the mechanical properties of the photoactive poly(siloxane imides) and confirmed elastomeric properties. Atomic force microscopy confirmed microphase separation of the photoactive poly(siloxane imides). 1H NMR spectroscopy confirmed formation of maleimide peaks upon exposure to narrow band UV light with a wavelength of 254 nm. This suggested photo-cleavage of the cyclobutane diimide units within the polymer backbone.
Melt transesterification offered a facile method for the synthesis of o-nitro benzyl ester-containing polyesters. 1H NMR spectroscopy confirmed the structures of the photoactive polyesters and size exclusion chromatography confirmed reasonable molecular weights and polydispersities of the obtained samples. 1H NMR spectroscopy also demonstrated a decrease in the integration of the resonance corresponding to the o-nitro benzyl ester functionality relative to the photo-stable m-nitro benzyl ester functionality upon exposure to high-intensity UV light, suggesting photo-degradation of the adhesive. ASTM wedge testing verified a decrease in fracture energy of the adhesive upon UV exposure, comparable to the decrease in fracture energy of a commercial hot-melt adhesive upon an increase in temperature.
Click chemistry was used to synthesize polyesters and segmented block copolyesters. Triazole-containing homopolyesters exhibited a marked increase (~40 °C) in Tg, relative to structurally analogous classical polyesters synthesized in the melt. However, the triazole-containing homopolyesters exhibited insignificant dispersibility in many organic solvents and melt-pressed films exhibited poor flexibility. Incorporation of azide-functionalized poly(propylene glycol) difunctional oligomers in the synthesis of triazole-containing polyesters resulted in segmented block copolyesters which exhibited enhanced dispersibility and film robustness relative to the triazole-containing homopolyesters. The segmented triazole-containing polyesters all demonstrated a soft segment Tg near -62 °C, indicating microphase separation. Dynamic mechanical analysis confirmed the presence of a rubbery plateau, with increasing plateau moduli as a function of hard segment content, as well as increasing flow temperatures as a function of hard segment content. Tensile testing revealed increasing tensile strength as a function of hard segment, approaching 10 MPa for the 50 wt % HS sample. Atomic force microscopy confirmed the presence of microphase separated domains, as well as semicrystalline domains. These results indicated the effectiveness of click chemistry towards the synthesis of polyesters and segmented block copolyesters.
Click chemistry was also used for the synthesis of photoactive polyesters and segmented block polyesters. The preparation of 2-nitro-p-xylylene glycol bispropiolate allowed for the synthesis of triazole-containing polyesters, which exhibited poor dispersibility and flexibility of melt-pressed films. The synthesis of segmented photoactive polyesters afforded photoactive polyesters with improved dispersibility and film robustness. 1H NMR spectroscopy confirmed the photodegradation of the o-nitro benzyl functional groups within the triazole-containing polyesters, which indicated the potential utility of these polyesters for reversible adhesion.
Synthesis of the glycidyl ether of 2,2,4,4-tetramethyl-1,3-cyclobutane diol (CBDOGE) allowed for the subsequent preparation of epoxy networks which did not contain bisphenol-A or bisphenol-A derivatives. Preparation of analogous epoxy networks from the glycidyl ether of bisphenol-A (BPA-GE) provided a method for control experiments. Tensile testing demonstrated that, dependent on network Tg, the epoxy networks prepared from CBDOGE exhibited similar Youngâ s moduli and tensile strain at break as epoxy networks prepared from BPAGE. Dynamic mechanical analysis demonstrated similar glassy moduli for the epoxy networks, regardless of the glycidyl ether utilized. Tg and rubbery plateau moduli varied as a function of diamine molecular weight. Melt rheology demonstrated a gel time of 150 minutes for the preparation of epoxy networks from CBDO-GE and 78 minutes for the preparation of epoxy networks from BPA-GE, with the difference attributed to increased sterics surrounding CBDO-GE. These results indicated the suitability of CBDO-GE as a replacement for BPA-GE in many applications.Ph. D.
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Coutee, Adam S. "Virtual Assembly and Disassembly Analysis: An Exploration into Virtual Object Interactions and Haptic Feedback." Diss., Available online, Georgia Institute of Technology, 2004:, 2004. http://etd.gatech.edu/theses/available/etd-05272004-174324/unrestricted/coutee%5adam%5s%5200407%5phd.pdf.
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Thesis (Ph. D.)--School of Mechanical Engineering, Georgia Institute of Technology, 2005. Directed by Bert Bras.Bras, Bert, Committee Chair ; Baker, Nelson, Committee Member ; Griffin, Paul, Committee Member ; Paredis, Chris, Committee Member ; Rosen, David, Committee Member. Vita. Includes bibliographical references.
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Cheng, Xi. "Dynamic assembly, disassembly and bundling of the bacterial cell division protein FtsZ and YgfE (ZapA)." Thesis, University of Warwick, 2011. http://wrap.warwick.ac.uk/49617/.
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The protein FtsZ is a tubulin-like GTPase, which plays an essential role in prokaryotic cell division. In vivo it assembles into a dynamic ring (the Z-ring) at the future site of cell division on the inner surface of the cytoplasmatic membrane. The Z-ring then serves as a scaffold which recruits all other division proteins to form the cytokinetic machinery. The constriction of the ring facilitates the separation of two daughter cells. In vitro, FtsZ polymerizes in the presence of GTP to form single-stranded protofilaments. It is assumed that FtsZ association and assembly reactions studied in vitro will play an important role in understanding the mechanism of Z-ring assembly and disassembly in vivo. In this work, we therefore have studied the dynamics of FtsZ polymerization in vitro, especially the bundling induced with YgfE. YgfE, the putative Escherichia coli ZapA orthologue, is one of these division proteins recruited by FtsZ. It acts to enhance lateral associations between FtsZ fibres to form larger bundles. In this study, we have demonstrated that YgfE exists as a tetramer in solution at the concentrations reported in this study, and the bundling activity is exerted more efficiently on preformed FtsZ protofilaments. We also investigate the importance of the tetramerisation of YgfE on function. A number of mutant forms of ZapA were generated with the aim of disrupting the dimer:dimer interface. Using those mutants we show that tetramerisation is a requirement for both FtsZ bundling, and GTPase modulation activities. In addition, a novel technique, continuous channel flow linear dichroism (LD) spectroscopy, has been first developed in this work. LD is a simple spectroscopy technique for structural characterization of long biomacromolecules in solutions. Continuous channel flow Flow LD has overcome the limitation of Couette flow LD due to the time required to assemble and fill the cell.
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Ford, Robert John. "The roles of RNA in the assembly and disassembly of single-stranded RNA icosahedral viruses." Thesis, University of Leeds, 2012. http://etheses.whiterose.ac.uk/4135/.
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Single-stranded, positive-sense icosahedral viruses are major pathogens in every kingdom of life. Despite this, their capsid assembly and uncoating mechanisms remain poorly understood. This work describes these processes in two model systems; satellite tobacco necrosis virus and turnip crinkle virus. For satellite tobacco necrosis virus, several aptamers were previously raised against the coat protein, where each aptamer folded into stem-loops displaying the motif AXXA. Aptamer B3 contained the strongest sequence similarity to the cognate genome, including a 10/10 contiguous stretch. Capsid assembly using the purified coat protein shows that RNA is critical for capsid assembly, and that stem-loops displaying the motif AXXA can efficiently trigger this process. There is a clear preference for this loop motif, which is unaffected by the sequence of the base paired stem. The structure of the B3-encapsidated virus-like particle has been solved by X-ray crystallography to 2.3 Å, together with a lower resolution map encompassing the RNA. The presence of B3 results in an extension of the N-terminal helices by roughly one and a half turns, such that residues 8-11 that are disordered in all previous X-ray structures are now visualised, including R8 and K9. The binding of B3 facilitates charge neutralisation and trimer formation in the coat protein, resulting in the assembly of a T=1 capsid. This assembly mechanism is consistent with additional assembly studies using longer RNAs, in which the first step in assembly is genomic compaction. This compaction event is driven by multiple binding events of coat proteins with packaging signals in the form of stem-loops displaying the preferred loop sequence. In turnip crinkle virus, a putative disassembly mechanism has been suggested. Expansion and proteolysis mediates extrusion of the viral genome, such that the formation of “striposomes”, which are thought to be polysomal arrays of ribosomes on extruding RNA, can be visualised by TEM. Purification of proteolysed capsids revealed that the cleaved coat proteins become dissociated and the remaining protein shells lose their icosahedral symmetry, often appearing to begin release of RNA from unique sites in the absence of ribosomes. These results explain why coat proteins are essential for wild-type infections because they facilitate a ribosome-mediated uncoating mechanism avoiding host RNA silencing. The results in this thesis suggest new paradigms for capsid assembly and uncoating, which may be exploited by other members of the same family of viruses, especially those having similar coat protein folds.
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Campos, González Roberto. "Calmodulin and the assembly and disassembly of microtubules during the mitogenic stimulation of mouse T lymphocytes." Thesis, University of Ottawa (Canada), 1987. http://hdl.handle.net/10393/5323.
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English, Christine Marie. "Insights into chromatin assembly through the characterization of the histone chaperone ASF1 bound to histones H3-H4 /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.
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Thesis (Ph.D. in Biochemistry & Molecular Genetics) -- University of Colorado at Denver and Health Sciences Center, 2006.Typescript. Includes bibliographical references (leaves 169-185). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;
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Keenen, Bridget A. "The role of SWI/SNF chromatin remodeling enzymes in melanoma." Toledo, Ohio : University of Toledo, 2010. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=mco1271819328.
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Dissertation (Ph.D.)--University of Toledo, 2010."Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Doctor of Philosophy Degree in Biomedical Sciences." Title from title page of PDF document. "A Dissertation entitled"--at head of title. Bibliography: p. 63-71, 126-140.
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Swygert, Sarah G. "The Shape of Silence: The Solution-State Conformation of Sir Heterochromatin: A Dissertation." eScholarship@UMMS, 2015. http://escholarship.umassmed.edu/gsbs_diss/790.
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Heterochromatin is a silenced chromatin region essential for maintaining genomic stability in eukaryotes and for driving developmental processes in higher organisms. A hallmark of heterochromatin is the presence of specialized architectural proteins that alter chromatin structure to inhibit transcription and recombination. Although it is generally assumed that heterochromatin is highly condensed, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, heterochromatin assembly at telomeres and the HM silent mating type loci requires the Sir proteins: Sir3, believed to be the major structural component of SIR heterochromatin, and the Sir2/4 complex, responsible for SIR recruitment to silencing regions and deacetylation of lysine 16 of the histone H4 tail, a mark associated with active chromatin. A combination of sedimentation velocity, atomic force microscopy, and nucleosomal array capture was used to characterize the stoichiometry and conformation of SIR nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome, and that Sir2/4 may additionally bind at a ratio of one per nucleosome. Despite Sir3’s ability to repress transcription in vivo and homologous recombination in vitro in the absence of Sir2/4, Sir3 fibers were found to be significantly less compact than canonical magnesium-induced 30 nanometer fibers. However, heterochromatin fibers composed of all three Sir proteins did adopt a more condensed, globular structure. These results suggest that heterochromatic silencing is mediated both by the creation of more stable nucleosomes and by the steric exclusion of external factors.
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Letienne, Justine [Verfasser], and Christine [Akademischer Betreuer] Blattner. "Impact of Mdm2-p53 on the proteasome assembly and disassembly Role of the ubiquitination of some 19S subunits / Justine Letienne. Betreuer: Christine Blattner." Karlsruhe : KIT-Bibliothek, 2011. http://d-nb.info/101691959X/34.
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Alam, Syed Benazir. "Study of the role of viral coat protein and host factor HSP70 homologs in the assembly and disassembly of Cucumber necrosis virus particles." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/61781.
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Virion assembly and disassembly are crucial aspects of the virus multiplication cycle, however, relatively little is known about these processes in plant viruses. While the former helps to produce multiple copies of stable infectious progeny virions, the latter is required for release of the encapsidated viral genome into a host cell for initiating new rounds of virus multiplication. In this thesis, I aimed to study Cucumber necrosis virus (CNV) particle assembly and disassembly and the role of CNV coat protein (CP) and host HSP70 homologs in these processes. It was found that CNV infection of Nicotiana benthamiana causes a significant upregulation of HSP70 homologs, and that, in turn, HSP70 is co-opted by the virus at several stages of the multiplication cycle to promote various aspects of the infection cycle including viral RNA, CP and particle accumulation. HSP70 homologs were also found to assist CNV CP in chloroplast targeting possibly to attenuate chloroplast-mediated plant defence and thereby allow further spread of the virus. It was also determined that the HSP70 homologue, Hsc70-2 is bound to CNV virions and that this association appears to facilitate the uncoating efficiency of CNV particles likely via triggering a conformational change in particles. This is the first report that a plant virus utilizes HSP70 homologs for disassembly.
A highly basic “KGRKPR” sequence in the ε-region of the CNV CP arm was also examined for its role in virion assembly and encapsidation of viral RNA. Through mutational analysis, it was found that the basic residues promote T=3 versus T=1 virion formation and encapsidation of full-length viral RNA in vivo. Moreover, mutants lacking 2-4 of the basic residues encapsidated proportionately greater amounts of host RNA suggesting the role of these basic residues in selection of viral RNA during assembly.
It was also shown that heat shock enhances transcription of heat-inducible ONSEN-like retrotransposons known to be induced during CNV infection. Since retrotransposons are known to play an important role in genome variation, the described studies may be helpful in understanding the importance of plant viruses in inducing genome variation and perhaps adaptation of plants to changes in the environment.Land and Food Systems, Faculty of
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Manning, Benjamin J. "ATP-Dependent Heterochromatin Remodeling: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/795.
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Eukaryotic DNA is incorporated into the nucleoprotein structure of chromatin. This structure is essential for the proper storage, maintenance, regulation, and function of the genomes’ constituent genes and genomic sequences. Importantly, cells generate discrete types of chromatin that impart distinct properties on genomic loci; euchromatin is an open and active compartment of the genome, and heterochromatin is a restricted and inactive compartment. Heterochromatin serves many purposes in vivo, from heritably silencing key gene loci during embryonic development, to preventing aberrant DNA repeat recombination. Despite this generally repressive role, the DNA contained within heterochromatin must still be repaired and replicated, creating a need for regulated dynamic access into silent heterochromatin. In this work, we discover and characterize activities that the ATP-dependent chromatin remodeling enzyme SWI/SNF uses to disrupt repressive heterochromatin structure.
First, we find two specific physical interactions between the SWI/SNF core subunit Swi2p and the heterochromatin structural protein Sir3p. We find that disrupting these physical interactions results in a SWI/SNF complex that can hydrolyze ATP and slide nucleosomes like normal, but is defective in its ability to evict Sir3p off of heterochromatin. In vivo, we find that this Sir3p eviction activity is required for proper DNA replication, and for establishment of silent chromatin, but not for SWI/SNF’s traditional roles in transcription. These data establish new roles for ATP-dependent chromatin remodeling in regulating heterochromatin.
Second, we discover that SWI/SNF can disrupt heterochromatin structures that contain all three Sir proteins: Sir2p, Sir3p and Sir4p. This new disruption activity requires nucleosomal contacts that are essential for silent chromatin formation in vivo. We find that SWI/SNF evicts all three heterochromatin proteins off of chromatin. Surprisingly, we also find that the presence of Sir2p and Sir4p on chromatin stimulates SWI/SNF to evict histone proteins H2A and H2B from nucleosomes. Apart from discovering a new potential mechanism of heterochromatin dynamics, these data also establish a new paradigm of chromatin remodeling enzyme regulation by nonhistone proteins present on the substrate.
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Manning, Benjamin J. "ATP-Dependent Heterochromatin Remodeling: A Dissertation." eScholarship@UMMS, 2009. http://escholarship.umassmed.edu/gsbs_diss/795.
Full textAbstract:
Eukaryotic DNA is incorporated into the nucleoprotein structure of chromatin. This structure is essential for the proper storage, maintenance, regulation, and function of the genomes’ constituent genes and genomic sequences. Importantly, cells generate discrete types of chromatin that impart distinct properties on genomic loci; euchromatin is an open and active compartment of the genome, and heterochromatin is a restricted and inactive compartment. Heterochromatin serves many purposes in vivo, from heritably silencing key gene loci during embryonic development, to preventing aberrant DNA repeat recombination. Despite this generally repressive role, the DNA contained within heterochromatin must still be repaired and replicated, creating a need for regulated dynamic access into silent heterochromatin. In this work, we discover and characterize activities that the ATP-dependent chromatin remodeling enzyme SWI/SNF uses to disrupt repressive heterochromatin structure.
First, we find two specific physical interactions between the SWI/SNF core subunit Swi2p and the heterochromatin structural protein Sir3p. We find that disrupting these physical interactions results in a SWI/SNF complex that can hydrolyze ATP and slide nucleosomes like normal, but is defective in its ability to evict Sir3p off of heterochromatin. In vivo, we find that this Sir3p eviction activity is required for proper DNA replication, and for establishment of silent chromatin, but not for SWI/SNF’s traditional roles in transcription. These data establish new roles for ATP-dependent chromatin remodeling in regulating heterochromatin.
Second, we discover that SWI/SNF can disrupt heterochromatin structures that contain all three Sir proteins: Sir2p, Sir3p and Sir4p. This new disruption activity requires nucleosomal contacts that are essential for silent chromatin formation in vivo. We find that SWI/SNF evicts all three heterochromatin proteins off of chromatin. Surprisingly, we also find that the presence of Sir2p and Sir4p on chromatin stimulates SWI/SNF to evict histone proteins H2A and H2B from nucleosomes. Apart from discovering a new potential mechanism of heterochromatin dynamics, these data also establish a new paradigm of chromatin remodeling enzyme regulation by nonhistone proteins present on the substrate.
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Silveira, Alexandra C. "Characterization of SUDS3 as a BRMS1 family member in breast cancer." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2008p/silveira.pdf.
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Hughes, Amanda L. "Dissecting cis and trans Determinants of Nucleosome Positioning: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/743.
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Eukaryotic DNA is packaged in chromatin, whose repeating subunit, the nucleosome, consists of an octamer of histone proteins wrapped by about 147bp of DNA. This packaging affects the accessibility of DNA and hence any process that occurs on DNA, such as replication, repair, and transcription. An early observation from genome-wide nucleosome mapping in yeast was that genes had a surprisingly characteristic structure, which has motivated studies to understand what determines this architecture. Both sequence and trans acting factors are known to influence chromatin packaging, but the relative contributions of cis and trans determinants of nucleosome positioning is debated. Here we present data using genetic approaches to examine the contributions of cis and trans acting factors on nucleosome positioning in budding yeast.
We developed the use of yeast artificial chromosomes to exploit quantitative differences in the chromatin structures of different yeast species. This allows us to place approximately 150kb of sequence from any species into the S.cerevisiae cellular environment and compare the nucleosome positions on this same sequence in different environments to discover what features are variant and hence regulated by trans acting factors. This method allowed us to conclusively show that the great preponderance of nucleosomes are positioned by trans acting factors. We observe the maintenance of nucleosome depletion over some promoter sequences, but partial fill-in of NDRs in some of the YAC v promoters indicates that even this feature is regulated to varying extents by trans acting factors.
We are able to extend our use of evolutionary divergence in order to search for specific trans regulators whose effects vary between the species. We find that a subset of transcription factors can compete with histones to help generate some NDRs, with clear effects documented in a cbf1 deletion mutant. In addition, we find that Chd1p acts as a potential “molecular ruler” involved in defining the nucleosome repeat length differences between S.cerevisiae and K.lactis. The mechanism of this measurement is unclear as the alteration in activity is partially attributable to the N-terminal portion of the protein, for which there is no structural data. Our observations of a specialized chromatin structure at de novo transcriptional units along with results from nucleosome mapping in the absence of active transcription indicate that transcription plays a role in engineering genic nucleosome architecture. This work strongly supports the role of trans acting factors in setting up a dynamic, regulated chromatin structure that allows for robustness and fine-tuning of gene expression.
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Hughes, Amanda L. "Dissecting cis and trans Determinants of Nucleosome Positioning: A Dissertation." eScholarship@UMMS, 2011. http://escholarship.umassmed.edu/gsbs_diss/743.
Full textAbstract:
Eukaryotic DNA is packaged in chromatin, whose repeating subunit, the nucleosome, consists of an octamer of histone proteins wrapped by about 147bp of DNA. This packaging affects the accessibility of DNA and hence any process that occurs on DNA, such as replication, repair, and transcription. An early observation from genome-wide nucleosome mapping in yeast was that genes had a surprisingly characteristic structure, which has motivated studies to understand what determines this architecture. Both sequence and trans acting factors are known to influence chromatin packaging, but the relative contributions of cis and trans determinants of nucleosome positioning is debated. Here we present data using genetic approaches to examine the contributions of cis and trans acting factors on nucleosome positioning in budding yeast.
We developed the use of yeast artificial chromosomes to exploit quantitative differences in the chromatin structures of different yeast species. This allows us to place approximately 150kb of sequence from any species into the S.cerevisiae cellular environment and compare the nucleosome positions on this same sequence in different environments to discover what features are variant and hence regulated by trans acting factors. This method allowed us to conclusively show that the great preponderance of nucleosomes are positioned by trans acting factors. We observe the maintenance of nucleosome depletion over some promoter sequences, but partial fill-in of NDRs in some of the YAC v promoters indicates that even this feature is regulated to varying extents by trans acting factors.
We are able to extend our use of evolutionary divergence in order to search for specific trans regulators whose effects vary between the species. We find that a subset of transcription factors can compete with histones to help generate some NDRs, with clear effects documented in a cbf1 deletion mutant. In addition, we find that Chd1p acts as a potential “molecular ruler” involved in defining the nucleosome repeat length differences between S.cerevisiae and K.lactis. The mechanism of this measurement is unclear as the alteration in activity is partially attributable to the N-terminal portion of the protein, for which there is no structural data. Our observations of a specialized chromatin structure at de novo transcriptional units along with results from nucleosome mapping in the absence of active transcription indicate that transcription plays a role in engineering genic nucleosome architecture. This work strongly supports the role of trans acting factors in setting up a dynamic, regulated chromatin structure that allows for robustness and fine-tuning of gene expression.
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Walfridsson, Julian. "The CHD chromatin remodeling factors in schizosaccharomyces pombe /." Stockholm, 2007. http://diss.kib.ki.se/2007/978-91-7357-106-7/.
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Junius, Meike Pauline Wilhelmine [Verfasser], Ulf [Akademischer Betreuer] [Gutachter] Diederichsen, and Reinhard [Gutachter] Jahn. "Synthesis and Analysis of Modified SNARE Proteins with Respect to Assembly and Disassembly of the SNARE Complex / Meike Pauline Wilhelmine Junius ; Gutachter: Ulf Diederichsen, Reinhard Jahn ; Betreuer: Ulf Diederichsen." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2017. http://d-nb.info/1123283036/34.
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Linger, Jeffrey G. "The role of histone chaperones in double-strand DNA repair and replication-independent histone exchange /." Connect to full text via ProQuest. IP filtered, 2006.
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Thesis (Ph.D. in Biochemistry) -- University of Colorado, 2006.Typescript. Includes bibliographical references (leaves 153-171). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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Yang, Xiaofang. "Functional and Structural Dissection of the SWI/SNF Chromatin Remodeling Complex: A Dissertation." eScholarship@UMMS, 2007. https://escholarship.umassmed.edu/gsbs_diss/330.
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The yeast SWI/SNF complex is the prototype of a subfamily of ATP-dependent chromatin remodeling complexes. It consists of eleven stoichiometric subunits including Swi2p/Snf2p, Swi1p, Snf5p, Swi3p, Swp82p, Swp73p, Arp7p, Arp9p, Snf6p, Snf11p, and Swp29p, with a molecular weight of 1.14 mega Daltons. Swi2p/Snf2p, the catalytic subunit of SWI/SNF, is evolutionally conserved from yeast to human cells. Genetic evidence suggests that SWI/SNF is required for the transcriptional regulation of a subset of genes, especially inducible genes. SWI/SNF can be recruited to target promotors by gene specific activators, and in some cases, SWI/SNF facilitates activator binding. Biochemical studies have demonstrated that purified SWI/SNF complex can hydrolyze ATP, and it can use the energy from ATP hydrolysis to generate superhelical torsion, mobilize mononucleosomes, enhance the accessibility of endonucleases to nucleosomal DNA, displace H2A/H2B dimers, induce dinucleosome and altosome formation, or evict nucleosomes. A human homolog of Swi2p/Snf2p, BRG1, is the catalytic subunit of the human SWI/SNF complex. Interestingly, isolated BRG1 alone is able to remodel a mononucleosome substrate. Importantly, mutations in mammalian SWI/SNF core subunits are implicated in tumorigenesis. Therefore, it remains interesting to characterize the role(s) of each subunit for SWI/SNF function. In this thesis project, I dissected SWI/SNF chromatin remodeling function by investigating the role of the SANT domain of the Swi3p subunit. Swi3p is one of the core components of SWI/SNF complex, and it contains an uncharacterized SANT domain that has been found in many chromatin regulatory proteins. Earlier studies suggested that the SANT domain of Ada2p may serve as the histone tail recognition module. For Swi3p, a small deletion of eleven amino acids from the SANT domain caused a growth phenotype similar to that of other swi/snf mutants.
In chapter I, I have reviewed recent findings in the function of chromatin remodeling complexes and discuss the molecular mechanism of their action.
In chapter II, I characterized the role of the SANT domain of Swi3p. I found that deletion of the SANT domain caused a defect in a genome-wide transcriptional profile, SWI/SNF recruitment, and more interestingly impairment of the SANT domain caused the dissociation of SWI/SNF into several subcomplexes: 1) Swi2p/Arp7p/Arp9p, 2) Swi3p/Swp73p/Snf6p, 3) Snf5p, and 4) Swi1p. Artificial tethering of SWI/SNF onto a LacZ reporter promoter failed to activate the reporter gene in the absence of the SANT domain, although Swi2p can be recruited to the LacZ promoter. We thus demonstrated that the Swi3p SANT domain is critical for Swi3p function and serves as a protein scaffold to integrate these subcomplexes into an intact SWI/SNF complex.
In Chapter III, I first characterized the enzymatic activity of the subcomplexes, especially the minimal complex of Swi2p/Arp7p/Arp9p. We found that this minimal subcomplex is fully functional for chromatin remodeling in assays including cruciform formation, restriction enzyme accessibility in mononucleosomal and nucleosomal array substrates, and mononucleosome mobility shift. However, it is defective in ATP-dependent removal of H2A/H2B dimers. Moreover, we found that Swi3p and the N-terminal acidic domain of Swi3p strongly interact with GST-H2A and H2B but not GST-H3 or H4 tails. We purified a SWI/SNF mutant (SWI/SNF-Δ2N) that lacks 200 amino acids within the N-terminal acidic domain of Swi3p. Intriguingly, SWI/SNF-Δ2N failed to catalyze ATP-dependent dimer loss, although this mutant SWI/SNF contains all the subunits and has intact ATP-dependent activity in enhancing restriction enzyme accessibility. These data help to further understand the molecular mechanism of SWI/SNF, and show that H2A/H2B dimer loss is not an obligatory consequence of ATP-dependent DNA translocation, but requires the histone chaperone function of the Swi3p subunit. Based on these findings, we proposed a new model of the structural and functional organization of the SWI/SNF chromatin remodeling machinery: SWI/SNF contains at least four distinct modules that function at distinct stages of the chromatin remodeling process. 1) Swi1p and Snf5p modules directly interact with gene specific activators and function as the recruiter; 2) Swi2p/Arp7p/Arp9p generates energy from ATP hydrolysis and disrupts histone/DNA interactions; and 3) Swi3p/Swp73p/Snf6p may play dual roles by integrating each module into a large remodeling complex, as well as functioning as a histone H2A/H2B chaperone to remove dimers from remodeled nucleosomes.
Chapter IV is a perspective from current work in this project. I first discuss the interest in further characterizing the essential role of Snf6p, based on its activation of LacZ reporter on its own. Using in vitro translated protein and co-IP studies, I tried to pinpoint the requirement of the SANT domain for SWI/SNF assembly. I found that Swi3p directly interacts with Swp73p, but not with other subunits. When Swi3p is first incubated with Swp73p, Swi3p also interacts with Snf6p, indicating that Swi3p indirectly interacts with Snf6p, therefore forming a subcomplex of Swi3p/Swp73p/Snf6p. This subcomplex can also be reconstituted using in vitro co-translation. Consistent with the TAP preparation of this subcomplex, partial deletion of the SANT domain of Swi3p does not affect the assembly of Swi3p/Swp73p/Snf6p in vitro. However, the assembly of SWI/SNF complex was not detected in the presence of eight essential in vitro translated subunits or from co-translation of all the subunits. I have discussed the interest in further characterizing the histone chaperone role of the Swi3p N-terminal acidic domain and the role of other core subunits of SWI/SNF such as Snf6p for transcriptional regulation.
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Marfella, Concetta G. A. "The Role of CHD2 in Mammalian Development and Disease: a Dissertation." eScholarship@UMMS, 2007. http://escholarship.umassmed.edu/gsbs_diss/334.
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Chromatin structure is intricately involved in the mechanisms of eukaryotic gene regulation. In general, the compact nature of chromatin blocks DNA accessibility such that components of the transcriptional machinery are unable to access regulatory sequences and gene activation is repressed. These repressive effects can be overcome or augmented by the actions of chromatin remodeling enzymes. Numerous studies highlight two classes of these enzymes: those that covalently modify nucleosomal histones and those that utilize energy derived from ATP hydrolysis to destabilize the histone-DNA contacts within the nucleosome (13, 14, 92). Members of each of these groups of chromatin remodeling enzymes play pivotal roles in modulating chromatin structure and in facilitating or blocking the binding of transcription factors. Mutations in genes encoding these enzymes can result in transcriptional deregulation and improper protein expression. Therefore, the regulation of chromatin structure is critical for precise regulation of almost all aspects of gene expression. Consequently, enzymes regulating chromatin structure are important modulators of cellular processes such as cell viability, growth, and differentiation. There remain many uncharacterized members of the ATP-dependent class of remodeling enzymes; characterization of these proteins will further elucidate the cellular functions these enzymes control.
Here, we focus primarily on the ATP-dependent remodeling complexes, specifically the chromodomain helicase DNA-binding (CHD) family. The CHD proteins are distinguished from other ATP-dependent complexes by the presence of two N-terminal chromodomains that function as interaction surfaces for a variety of chromatin components. These proteins also contain a SNF2-like ATPase motif and are further classified based on the presence or absence of additional domains. Genetic, biochemical, and structural studies demonstrate that CHD proteins are important regulators of transcription and play critical roles during developmental processes. Numerous CHD proteins have also been implicated in human disease.
The first CHD family member, mChd1, was identified in 1993 in a search for DNA-binding proteins with an affinity for immunoglobin promoters. Since then, additional CHD genes have been identified based on sequence and structural homology to mChd1. Despite an increase in the number of studies relating to CHD proteins, the function of most remains unknown or poorly characterized. Using embryonic stem (ES) cells containing an insertional mutation in the murine Chd2 locus, we generated a Chd2-mutant mouse model to address the biological effects of Chd2 in development and disease. The targeted Chd2 allele resulted in a stable Chd2-βgeo fusion protein that contained the tandem chromodomains, the SNF2-like ATPase motif, but lacked the C-terminal portion of the DNA-binding domain.
We demonstrated that the mutation in Chd2 resulted in a general growth delay in homozygous mutants late in embryogenesis as well as perinatal lethality. Similarly, heterozygous mice showed a decreased neonatal viability. Moreover, the surviving heterozygous mice showed a general growth delay during the neonatal period and increased susceptibility to non-neoplastic lesions affecting multiple organs, most notably the kidneys.
We further examined the connection between Chd2 and kidney disease in this murine model. Our findings revealed that the kidney phenotype observed in Chd2 mutant mice led to the development of membranous glomerulopathy, proteinuria, and ultimately to impaired kidney function. Additionally, serum analysis revealed decreased hematocrit levels in the Chd2-mutant mice, suggesting that the membranous glomerulopathy observed in these mice is associated with anemia.
Lastly, we investigated whether the type of anemia observed in the Chd2-mutant mice. Red blood cell (RBC) indices and morphological examination of the RBCs indicated that the anemia seen in the Chd2-mutant mice can be classified as normocytic and normochromic. Further analyses have been initiated to determine if the anemia is due to an intrinsic effect in erythropoiesis or a secondary consequence of the glomerular disease.
In summary, our findings have contributed to our understanding of the putative chromatin remodeling enzyme Chd2. Although much remains to be studied, these findings demonstrate a role for Chd2 in mammalian development and have revealed a link between Chd2 and disease.
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Kolpa, Heather J. "XIST and CoT-1 Repeat RNAs are Integral Components of a Complex Nuclear Scaffold Required to Maintain SAF-A and Modify Chromosome Architecture: A Dissertation." eScholarship@UMMS, 2016. https://escholarship.umassmed.edu/gsbs_diss/825.
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XIST RNA established the precedent for a noncoding RNA that stably associates with and regulates chromatin, however it remains poorly understood how such RNAs structurally associate with the interphase chromosome territory. I demonstrate that transgenic XIST RNA localizes in cis to an autosome as it does to the inactive X chromosome, hence the RNA recognizes a structure common to all chromosomes. I reassess the prevalent thinking in the field that a single protein, Scaffold Attachment Factor-A (SAF-A/hnRNP U), provides a single molecule bridge required to directly tether the RNA to DNA. In an extensive series of experiments in multiple cell types, I examine the effects of SAF-A depletion or different SAF-A mutations on XIST RNA localization, and I force XIST RNA retention at mitosis to examine the effect on SAF-A. I find that SAF-A is not required to localize XIST RNA but is one of multiple proteins involved, some of which frequently become lost or compromised in cancer. I additionally examine SAF-A’s potential role localizing repeat-rich CoT-1 RNA, a class of abundant RNAs that we show tightly and stably localize to euchromatic interphase chromosome territories, but release upon disruption of the nuclear scaffold. Overall, findings suggest that instead of “tethering” chromosomal RNAs to the scaffold, SAF-A is one component of a multi-component matrix/scaffold supporting interphase nuclear architecture. Results indicate that Cot-1 and XIST RNAs form integral components of this scaffold and are required to maintain the chromosomal association of SAF-A, substantially advancing understanding of how chromatin-associated RNAs contribute to nuclear structure.
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Kolpa, Heather J. "XIST and CoT-1 Repeat RNAs are Integral Components of a Complex Nuclear Scaffold Required to Maintain SAF-A and Modify Chromosome Architecture: A Dissertation." eScholarship@UMMS, 2004. http://escholarship.umassmed.edu/gsbs_diss/825.
Full textAbstract:
XIST RNA established the precedent for a noncoding RNA that stably associates with and regulates chromatin, however it remains poorly understood how such RNAs structurally associate with the interphase chromosome territory. I demonstrate that transgenic XIST RNA localizes in cis to an autosome as it does to the inactive X chromosome, hence the RNA recognizes a structure common to all chromosomes. I reassess the prevalent thinking in the field that a single protein, Scaffold Attachment Factor-A (SAF-A/hnRNP U), provides a single molecule bridge required to directly tether the RNA to DNA. In an extensive series of experiments in multiple cell types, I examine the effects of SAF-A depletion or different SAF-A mutations on XIST RNA localization, and I force XIST RNA retention at mitosis to examine the effect on SAF-A. I find that SAF-A is not required to localize XIST RNA but is one of multiple proteins involved, some of which frequently become lost or compromised in cancer. I additionally examine SAF-A’s potential role localizing repeat-rich CoT-1 RNA, a class of abundant RNAs that we show tightly and stably localize to euchromatic interphase chromosome territories, but release upon disruption of the nuclear scaffold. Overall, findings suggest that instead of “tethering” chromosomal RNAs to the scaffold, SAF-A is one component of a multi-component matrix/scaffold supporting interphase nuclear architecture. Results indicate that Cot-1 and XIST RNAs form integral components of this scaffold and are required to maintain the chromosomal association of SAF-A, substantially advancing understanding of how chromatin-associated RNAs contribute to nuclear structure.
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Burns, Loree Griffin. "In Vivo Functional Analysis of the Saccharomyces Cerevisiae SWI/SNF Complex: A Dissertation." eScholarship@UMMS, 1997. https://escholarship.umassmed.edu/gsbs_diss/202.
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Chromatin remodeling is crucial to transcriptional regulation in vivo and a number of protein complexes capable of altering genomic architecture in the budding yeast Saccaromyces cerevisiaehave been identified. Among these, the SWI/SNF complex, a 2 MDa, eleven subunit protein assembly, has been the most extensively characterized. The SWI/SNF complex is required for the proper expression of a number of genes in yeast, although it is completely dispensable for the expression of others. Likewise, some, but not all, transcriptional activator proteins require SWI/SNF activity in order to function in vivo. The goal of this thesis work was to identify those components of the transcription process which dictate this dependence on SWI/SNF activity.
Using the well characterized UASGALsystem, we have determined that one of these components is the nucleosome state of activator binding sites within a promoter. We find that while SWI/SNF activity is not required for the GAL4 activator to bind to and activate transcription from nucleosome-free binding sites, the complex is required for GAL4 to bind and function at low affinity, nucleosomal binding sites in vivo. The SWI/SNF -dependence of these nucleosomal binding sites can be overcome by 1) replacing the low affinity sites with higher affinity, consensus GAL4 binding sequences, or 2) placing the low affinity sites into a nucleosme-free region. These results provide the first in vivo evidence that the SWI/SNF complex can regulate gene expression by modulating the DNA binding of a transcriptional activator protein.
To determine whether specific components of the GAL4 protein are necessary in order for the SWI/SNF complex to modulate binding to nucleosomal sites in our model system, we tested the SWI/SNF-dependent DNA binding of various derivative GAL4 proteins. We find that a functional activation domain is not required for SWI/SNF to modulate GAL4 binding in vivo. Interestingly, like the full length protein, GAL4 derivatives in which the activation domain has been mutated are able to partially occupy nucleosomal sites in the absence of SWI/SNF (binding in the absence of SWI/SNF is at least forty percent lower than in the presence of SWI/SNF), indicating the activation domain is also not required for SWI/SNF-independent DNA binding.
These results support a model in which the SWI/SNF-dependence of a gene reflects the nucleosomal context of its important regulatory sequences, e.g. binding sites for transcriptional regulatory proteins. Although nucleosomal promoter regions have been correlated with SWI/SNF-dependence in the past, there has of yet been no gene at which nucleosome location has correlated with a specific genetic function. In the final part of this thesis work, we initiated a search for an endogenous SWI/SNF-dependent gene for which the nucleosome state of activator binding sites could be determined.
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Bennett, Gwendolyn M. "Chromatin Regulators and DNA Repair: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/742.
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DNA double-strand break (DSB) repair is essential for maintenance of genome stability. However, the compaction of the eukaryotic genome into chromatin creates an inherent barrier to any DNA-mediated event, such as during DNA repair. This demands that there be mechanisms to modify the chromatin structure and thus access DNA. Recent work has implicated a host of chromatin regulators in the DNA damage response and several functional roles have been defined. Yet the mechanisms that control their recruitment to DNA lesions, and their relationship with concurrent histone modifications, remain unclear. We find that efficient DSB recruitment of many yeast chromatin regulators is cell-cycle dependent. Furthering this, we find recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather that their recruitment coincides with reduced levels of γH2AX. We go on to determine the chromatin remodeling enzyme Fun30 functions in histone dynamics surround a DSB, but does not significantly affect γH2AX dynamics. Additionally, we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X. Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.
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Bennett, Gwendolyn M. "Chromatin Regulators and DNA Repair: A Dissertation." eScholarship@UMMS, 2012. http://escholarship.umassmed.edu/gsbs_diss/742.
Full textAbstract:
DNA double-strand break (DSB) repair is essential for maintenance of genome stability. However, the compaction of the eukaryotic genome into chromatin creates an inherent barrier to any DNA-mediated event, such as during DNA repair. This demands that there be mechanisms to modify the chromatin structure and thus access DNA. Recent work has implicated a host of chromatin regulators in the DNA damage response and several functional roles have been defined. Yet the mechanisms that control their recruitment to DNA lesions, and their relationship with concurrent histone modifications, remain unclear. We find that efficient DSB recruitment of many yeast chromatin regulators is cell-cycle dependent. Furthering this, we find recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather that their recruitment coincides with reduced levels of γH2AX. We go on to determine the chromatin remodeling enzyme Fun30 functions in histone dynamics surround a DSB, but does not significantly affect γH2AX dynamics. Additionally, we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X. Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.
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Chevreuil, Maelenn. "Phénomènes dynamiques d’auto-assemblage et de désassemblage dans des virus icosaédriques." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS043.
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L’auto-assemblage et le désassemblage de la capside des virus, étapes critiques du cycle viral, est un sujet qui suscite beaucoup d’intérêt. Cependant, les mécanismes sous-jacents et, en particulier, les chemins dynamique d’assemblage et de désassemblage des capsides, vides ou pleines, des virus ne sont pas entièrement résolues. La diffusion des rayons X aux petits angles résolue en temps, combinée à la décomposition en valeur singulière, est une technique qui permet d’étudier des processus impliquant des espèces de taille nanométrique avec une résolution temporelle de l’ordre de la milliseconde. La technique de criblage de thermo-stabilité des protéines par fluorescence, couplée à un modèle théorique de champ moyen, permet d’estimer expérimentalement les énergies d’interactions entre les protéines et la charge effective de celles-ci. Dans le cas du virus de la marbrure chlorotique de la cornille, ces techniques nous ont permis d’étudier la dynamique d’autoassemblage des protéines des capsides autour de leur formation de complexes amorphes via un chemin cinétique appelé en masse tandis que leur relaxation en virions s’effectue via un chemin cinétique dit synchrone. Les énergies de liaison des protéines avec le génome se sont révélées modérées tandis qu’une barrière d’énergie élevée sépare les complexes des virions. Des expériences complémentaires ont également montré que cette barrière pouvait être abaissée, de sorte que des capsides pleines se forment directement. Dans le cas du virus de l’hépatite B, nous avons étudié les dynamiques d’assemblage et de désassemblage des capsides vides. Nous avons pu identifier un chemin cinétique probable de désassemblage avec la présence d’une espèce intermédiaire assimilable à une structure fractale-branchée. Les expériences d’assemblage ont révélé un chemin cinétique en trois phases, i.e. agglomération, croissance et relaxation, dirigé par l’attraction hydrophobe et modulé par la répulsion électrostatique. De plus, certaines expériences ont également montré que la dernière phase pouvait être facilement inhibéeThe self-assembly and disassembly of virus capsids, critical stages of the viral cycle, is a subject that arouses a lot of interest. However, the underlying mechanisms and, in particular, the kinetic pathways of assembly and disassembly, whether the capsid is empty or full, are not entirely solved. Time-resolved small-angle X-ray scattering is a technique for tracking processes involving nano-sized species with a time resolution of the millisecond order. Combined with the singular value decomposition, a modelindependent method of analysis, the technique allows the investigation of the kinetics of capsid selfassembly and disassembly. In addition, the fluorescence thermal shift assays, coupled with a theoretical mean-field model, makes it possible to experimentally estimate the interaction energies between the proteins as well as their effective charge. Thus, in the case of the cowpea chlorotic mottle virus (CCMV), we have studied the self-assembly dynamics of capsid proteins with their genetic material. The experiments revealed the formation of amorphous complexes via a kinetic pathway called en masse whereas their relaxation into virions occurs via a socalled synchronous kinetic path. The binding energies of proteins with the genome showed to be moderate, while the energetic barrier separating the complexes of virions is high. The experiments performed with a synthetic polyelectrolyte showed that this barrier could be lowered, so that full capsids form under conditions where virions cannot. In the case of the hepatitis B virus (HBV), we studied the self-assembly and disassembly dynamics of empty capsids. First, we were able to identify a probable disassembly kinetic path with the presence of an intermediate species organised like a fractal-branched structure. Finally, the assembly experiments revealed a kinetic pathway in three phases, i.e. agglomeration, growth and relaxation, directed by hydrophobic attraction and modulated by electrostatic repulsion. Due to the low effective charge of the protein, the last phase could be inhibited by raising the salinity, thus trapping the capsids in a conformation containing defects
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Guiras, Zouhour. "Contribution à l'optimisation des politiques de maintenance et l'analyse de risque dans la planification des opérations d’assemblage - désassemblage à deux niveaux." Thesis, Université de Lorraine, 2019. http://www.theses.fr/2019LORR0016/document.
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La réalité des marchés économiques impose des contraintes aux entreprises manufacturières qui sont de plus en plus difficiles à réaliser, comme la diversification des produits, l'amélioration de leur qualité, la réduction des coûts et la diminution des retards. Ces contraintes sont satisfaites par une meilleure organisation des systèmes de fabrication en utilisant les ressources techniques existantes. Notre présente thèse met l’accent sur deux contributions majeures, la première consiste à modéliser différents cas du système industriel (Système de production simple, système d’assemblage, système de désassemblage) en intégrant des politiques de maintenance adéquates. La deuxième contribution repose sur l’évaluation des risques de pertes de profit d’une décision prise suite à l’optimisation des différents systèmes industriels étudiés. Trois différents problèmes industriels sont étudiés, le premier concerne le développement des méthodes d’évaluation de risque de perte de profit résultant du choix d'un algorithme d’optimisation pour résoudre un problème de planification conjointe de production et de maintenance. Pour atteindre nos objectifs, nous commençons par calculer les plans de production et de maintenance en utilisant différents algorithmes d’optimisation. En outre, nous proposons des modèles analytiques pour quantifier le risque de perte de profit résultant des retours de produits et de la prise en compte des durées de réparation de pannes non nulles. Cette étude fournit des informations sur les algorithmes d’optimisations les plus efficaces pour les problématiques rencontrés pour aider et orienter les décideurs dans l'analyse et l'évaluation de leurs décisions. La deuxième problématique concerne l'optimisation de la planification du système d'assemblage à deux niveaux. Un modèle mathématique est développé pour incorporer une planification de l'approvisionnement pour les systèmes d'assemblage à deux niveaux dont les délais d’approvisionnement et les pannes du système sont stochastiques. La planification de maintenance optimale obtenue est utilisée dans l'évaluation des risques afin de trouver la période seuil de réparation qui réduit les pertes de profit. La troisième problématique étudiée concerne l’optimisation de la planification dans le cadre d’assemblage à base de désassemblage des produits usagés en tenant compte de la dégradation du système de production. Un modèle analytique est développé pour envisager le désassemblage, la remise à neuf des produits usagés qui contribuent à l’assemblage des produits finis. En effet, ces derniers peuvent être constitués de composants neufs ou remis à neuf. Une politique de maintenance est séquentiellement intégrée pour réduire l'indisponibilité du système. Le but de cette étude est d'aider les décideurs, dans certaines conditions, à choisir le processus le plus rentable pour satisfaire le client et qui peut également s'adapter aux risques potentiels qui peuvent perturber le système de désassemblage-assemblage. Le risque lié aux périodes de réparation du système est discuté, ce qui a un impact sur la prise de décision managérialeThe reality of the economic markets places constraints on manufacturing companies that are increasingly difficult to achieve, such as product diversification, quality improvement, cost reduction and fewer delays. These constraints are satisfied by a better organization of manufacturing systems using existing technical resources. Our thesis focuses on two major contributions, the first is to model different industrial systems (simple production system, assembly system, disassembly system) by integrating maintenance policies. The second contribution is based on risk assessment of profit loss following a decision taken after an optimization of an industrial system. Three different industrial problems are studied; the first concerns the development of risk assessment methods of profit loss resulting from the choice of an optimization algorithm to solve a problem of joint production and maintenance planning. To achieve our goals, we start by calculating production and maintenance plans using different optimization algorithms. In addition, we propose analytical models to quantify the risk of profit loss resulting from product returns and of repair times. This study provides information on the most effective optimization algorithms for the problems encountered to help and guide decision-makers in the analysis and evaluation of their decisions. The second problem concerns the optimization of two-level assembly system planning. A mathematical model is developed to incorporate supply planning for two-level assembly system with stochastic lead times and failures. The optimal maintenance planning obtained is used in the risk assessment to find the threshold repair period that reduces the profit loss. The third problem studied concerns the optimization of disassembly system of returned products (used or end of life products), remanufacturing and assembly of finished products taking into account the degradation of the production system. An analytical model is developed to consider disassembly, remanufacturing of returned products that contribute to the assembly of finished products. Indeed, the latter may consist of new or remanufactured components. A maintenance policy is sequentially integrated to reduce the unavailability of the system. The goal of this study is to help decision makers, under certain conditions, choose the most cost-effective process to satisfy the customer and who can also adapt to the potential risks that can disrupt the disassembly-remanufacturing-assembly system. The risk associated with system repair periods is discussed, which has an impact on managerial decision-making
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Salma, Nunciada. "Transcriptional Regulation During Adipocyte Differentiation: A Role for SWI/SNF Chromatin Remodeling Enzymes: A Dissertation." eScholarship@UMMS, 2006. https://escholarship.umassmed.edu/gsbs_diss/50.
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Chromatin has a compact organization in which most DNA sequences are structurally inaccessible and functionally inactive. Reconfiguration of thechromatir required to activate transcription. This reconfiguration is achieved by the action of enzymes that covalently modify nucleosomal core histones, and by enzymes that disrupt histone-DNA interactions via ATP hydrolysis.
TheSWI/SNF family of ATP-dependent chromatin remodeling enzymes has been implicated not only in gene activation but also in numerous cellular processes including differentiation, gene repression, cell cycle control, recombination and DNA repair. PPARγ, C/EBPα and C/EBPβ are transcription factors with well established roles in adipogenesis. Ectopical expression of each of these factors in non-adipogenic cells is sufficient to convert them to adipocyte-like cells.
To determine the requirements of SWI/SNF enzymes in adipocyte differentiation, we introduced PPARγ, C/EBPα or C/EBPβ into fibroblasts that inducibly express dominant-negative versions of the Brahma-Related Gene 1 (BRG1) or human Brahma (BRM), which are the ATPase subunits of the SWI/SNF enzymes. We found that adipogenesis and expression of adipocyte genes were inhibited in the presence of mutant SWI/SNF enzymes. Additionally, in cells expressing C/EBPα or C/EBPβ, PPARγ expression was SWI/SNF dependent. These data indicate the importance of these remodeling enzymes in both early and late gene activation events.
Subsequently, we examined by chromatin immunoprecipitation (ChIP) assay the functional role of SWI/SNF enzymes in the activation of PPARγ2, the master regulator of adipogenesis. Temporal analysis of factors binding to the PPARγ2 promoter showed that SWI/SNF enzymes are required to promote preinitiation complex assembly and function.
Additionally, our studies concentrated on the role of C/EBP family members in the activation of early and late genes during adipocyte differentiation. During adipogenesis, C/EBPβ and δ are rapidly and transiently expressed and are involved in the expression of PPARγ and C/EBPα, which together activate the majority of the adipocyte genes. Our studies determined the temporal recruitment of the C/EBP family at the promoters of early and late genes by ChIP assay during adipocyte differentiation. We found that all of the C/EBP members evaluated are present at the promoters of early and late genes, and the binding correlated with the kinetics of the C/EBPs expression. Binding of C/EBPβ and δ is transient, subsequently being replaced by C/EBPα. These studies demonstrated that C/EBPβ and δ are not only involved in the regulation of PPARγ and C/EBPα, but also in the activation of late expressed adipocyte genes.
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Sinha, Manisha. "Recombinational Repair of a Chromosomal DNA Double Strand Break: A Dissertation." eScholarship@UMMS, 2009. https://escholarship.umassmed.edu/gsbs_diss/412.
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Repairing a chromosomal DNA double strand break is essential for survival and maintenance of genomic integrity of a eukaryotic organism. The eukaryotic cell has therefore evolved intricate mechanisms to counteract all sorts of genomic insults in the context of chromatin structure. Modulating chromatin structure has been crucial and integral in regulating a number of conserved repair processes along with other fundamental genomic processes like replication and transcription.
The work in this dissertation has focused on understanding the role of chromatin remodeling enzymes in the repair of a chromosomal DNA double strand break by homologous recombination. This has been approached by recapitulating the biochemical formation of recombination intermediates on chromatin in vitro. In this study, we have demonstrated that the mere packaging of DNA into nucleosomal structure does not present a barrier for successful capture of homologous DNA sequences, a central step of the biochemical pathway of recombinational repair. It is only the assembly of heterochromatin-like more complex nucleo-protein structure that presents additional constraints to this key step. And, this additional constraint can be overcome by the activities of ATP-dependent chromatin remodeling enzymes. These findings have great implications for our perception of the mechanism of the recombinational repair process of a chromosomal DNA double strand break within the eukaryotic genome.
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Iacob, Robert-Eugen. "Modélisation cinématique des mobilités de composants pour des opérations d’assemblage et de désassemblage." Grenoble INPG, 2010. http://www.theses.fr/2010INPG0139.
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La conception assistée par ordinateur (CAO) a été l'un des domaines de recherche fondamental dans la conception automatisée pendant de nombreuses années. Les centres d'intérêt principaux sont les processus exigés pour concevoir différentes pièces, pour simuler leur comportement et pour les inspecter. Le module d’ensemble, qui adresse actuellement le produit entier, par comparaison ; est beaucoup moins étudié et un des processus peu compris dans la conception, sachant que presque tous les logiciels de CAO sont orientés vers les pièces seules. Afin d'offrir un outil pour l'analyse du modèle de produit cette recherche se concentre sur la simulation des opérations d'assemblage et de désassemblage (A/D), une plateforme de simulation étant proposée. Des simulations d'A/D peuvent être effectuées de manière automatisées ou interactives utilisant le matériel informatique standard ou par des simulations immersives en temps réel. Par conséquent, la plateforme proposée est basée sur un nouveau type de processus de simulation adressant jusqu'à deux types de représentations de forme (B-Rep NURBS et polydrique). Cet environnement peut aider les concepteurs pour réaliser une analyse satisfaisante d'ensembles rapidement et peut réduire le temps du développement de produits. Un autre bénéfice de ce travail est la capacité de produire des modèles et des traitements qui améliorent l'intégration des modèles d'assemblages dans des environnements immersifs avec les modèles haptiques et visuels requis. En plus, un opérateur spécifique qui produit des contraintes cinématiques dans le voisinage des configurations de contact est proposé pour déterminer à tout moment les mouvements valides entre les composants. Ainsi, la complexité des algorithmes de détection de collision dans les environnements de simulation en temps réel est réduite. Cette opération est basée sur le modèle mathématique et sur une représentation qui offre la possibilité de décrire toutes les combinaisons valides des phases de montage et de démontage d'un produitAssembly/Disassembly (A/D) simulations are important to improve design and efficiency of product development processes. In order to get efficient simulation processes it is important to simulate all the possible relative movements between the components in a mechanical assembly. This is important both in the context of interactive simulation and in the context of immersive/real time simulations. If some categories of movements are missing, simulations can loose key configurations, hence they may be no longer meaningful. The scope in research, whiting this thesis deals, in the first time, with a theoretical approach for developing of a kinematical model able to represent all the valid relative movements of a reference component with respect to its surrounding ones, which form a family of trajectories. It is based on the analysis of the three basic movements: translation, rotation and helical ones. In order to determine the compatibility between different families of trajectories, a bi-quaternion is associated to each contact area between the different components. All possible trajectories for each component are analyzed, for the three basic type of movements, in order to find the compatible ones, which leads to the specification of an operator. Thus, the results of all the possible associations are determined and a general combination operator is proposed. The properties of this later are demonstrated as well. The operator can form, in a real time simulation environment, the basis for determining at each moment, the valid movements between components, thus reducing the complexity of collision detection algorithms. The A/D simulations can be performed either from an automated or interactive point of view using standard computer equipment or through immersive and real-time simulation schemes. In order to address this diversity of configurations, a simulation framework was developed. It is based on a new simulation preparation process which allows a simulation process to address up to two types of shape representations, i. E. B-Rep NURBS and polyhedral ones, at the same time, thus handling efficiently the configurations where 3D shape representations of assemblies play a key role. In order to illustrate the simulation process the automatic identification of contacts in a 3D product model and their corresponding list is described. After the identification stage, an interpretation of the results is needed in order to have the complete list with the mechanical contacts for a product. The preparation process is performed within three major stages : model tessellation, surface merging and contacts identification. The framework is based on STEP exchange format. This software environment can assist designers to achieve a satisfactory assembly analysis rapidly and can reduce the lead-time of product development. Further consequences of the present work is its ability to produce models and treatments that improve integration of assembly models in immersive environments taking into account of the haptic and visual models needed. Assembly/Disassembly simulations using haptic devices are facing difficulties while simulating insertion/extraction operations such as removing cylinders from holes for example. In order to address this configuration as well as others, an approach based on the kinematic model and on the simulation framework is proposed
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Young, Daniel W. "Regulation of Cell Growth and Differentiation within the Context of Nuclear Architecture by the Runx2 Transcription Factor: a Dissertation." eScholarship@UMMS, 2005. https://escholarship.umassmed.edu/gsbs_diss/19.
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The Runx family of transcription factors performs an essential role in animal development by controlling gene expression programs that mediate cell proliferation, growth and differentiation. The work described in this thesis is concerned with understanding mechanisms by which Runx proteins support this program of gene expression within the architectural context of the mammalian cell nucleus. Multiple aspects of nuclear architecture are influenced by Runx2 proteins including sequence-specific DNA binding at gene regulatory regions, organization of promoter chromatin structure, and higher-order compartmentalization of proteins in nuclear foci. This work provides evidence for several functional activities of Runx2 in relation to architectural parameters of gene. expression for the control of cell growth and differentiation. First, the coordination of SWI/SNF mediated chromatin alterations by Runx2 proteins is found to be a critical component of osteoblast differentiation for skeletal development. Several chromatin modifying enzymes and signaling factors interact with the developmentally essential Runx2 C-terminus. A patent-pending microscopic image analysis strategy invented as part of this thesis work - called intranuclear informatics - has contributed to defining the C-terminal portion of Runx2 as a molecular determinant for the nuclear organization of Runx2 foci and directly links Runx2 function with its organization in the nucleus. Intranuclear informatics also led to the discovery that nuclear organization of Runx2 foci is equivalently restored in progeny cells following mitotic division - a natural perturbation in nuclear structure and function. Additional microscopic studies revealed the sequential and selective reorganization of transcriptional regulators and RNA processing factors during progression of cell division to render progeny cells equivalently competent to support Runx2 mediated gene expression. Molecular studies provide evidence that the Runx proteins have an active role in retaining phenotype by interacting with target gene promoters through sequence-specific DNA binding during cell division to support lineage-specific control of transcriptional programs in progeny cells. Immunolocalization of Runx2 foci on mitotic chromosome spreads revealed several large foci with pairwise symmetry on sister chromatids; these foci co-localize with the RNA polymerase I transcription factor, Upstream Binding Factor (UBFl) at nucleolar organizing regions. A series of experiments were carried out to reveal that Runx2 interacts directly with ribosomal DNA loci in a cell cycle dependent manner; that Runx2 is localized to UBF foci within nucleoli during interphase; that Runx2 attenuates rRNA synthesis; and that this repression of ribosomal gene expression by Runx2 is associated with cell growth inhibition and induction of osteoblast-specific gene expression. This thesis has identified multiple novel mechanisms by which Runx2 proteins function within the hierarchy of nuclear architecture to control cell proliferation, growth and differentiation.
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Pennini, Meghan E. "Toll-like Receptor 2-dependent Inhibition of Interferon gamma Signaling by Mycobacterium tuberculosis." Connect to text online, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=case1152115234.
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Martins, Mateus Jose. "Projeto de um microcomputador de 8 bits para aplicações em pesquisa e ensino." Universidade de São Paulo, 1990. http://www.teses.usp.br/teses/disponiveis/54/54132/tde-11092007-110931/.
Full textAbstract:
O presente trabalho descreve o desenvolvimento de um microcomputador de 8 bits. O projeto inclui além dos circuitos básicos, lógica adicional para extender a memória contornando o limite normal de endereçamento. Um disco virtual uma interface em RAM e uma interface para \"Winchester\" foram desenvolvidas para extender a capacidade de armazenamento secundário e a velocidade de execução. Suporte para o coprocessador AM9511 é fornecido para freqüentes cálculos em ponto flutuante. Rotinas para operações básicas de E/,. manipulação da memória e \"Caching\" de disco, foram desenvolvidas para suportar o sistema operacional CP/M. Um monitor residente com montador, desmontador e funções de E/S de alto nível, foi construído para ajudar no desenvolvimento de aplicações dedicadas.The present works describes the development of an 8 bits microcomputer system. The project includes, besides the basic circuity, additional logic for memory extension behind the regular address limit. A virtual RAM disk and a Winchester interface were developed to extend secondary storage and execution speed. For floating point intensive calculations support for an AM9511 coprocessor is given. Routines for basic I/O operations, memory management and disk \"Caching\" were developed to support the CP/M operating system. A resident monitor with assembly, disassembly and high level I/O functions was constructed to aid the development of dedicated application.