Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Oceans and human health: Sentinel habitats and sentinel species

The health of the oceans and people are inextricably linked. For many years we focused research and policy on anthropogenic impacts to oceans and coasts. Recently we have started to think about how the health of the oceans affects us. In response to the Oceans and Human Health Act of 2004, a NOAA initiative was created to explore the “One Health” of the oceans and coasts. The Center of Excellence in Oceans and Human Health at Hollings Marine Laboratory (HML) is one of three Centers dedicated to understanding the connections and forecasting changes in ocean and coastal health and human health. The Center at HML is developing new tools and approaches, including sentinel habitats and sentinel species, to evaluate linkages between ecological process and human health and wellbeing. The results provide environmental and public health managers, policy-makers and communities forecasts and assessments to improve ecosystem-based management that protects health and mitigates risks for the oceans, coasts and people.(PDF contains 4 pages)

Developing effective restoration plans to tackle the widespread impairment of coastal swimming and shellfishing waters

Congress established a legal imperative to restore the quality of our surface waters when it enacted the Clean Water Act in 1972. The act requires that existing uses of coastal waters such as swimming and shellfishing be protected and restored. Enforcement of this mandate is frequently measured in terms of the ability to swim and harvest shellfish in tidal creeks, rivers, sounds, bays, and ocean beaches. Public-health agencies carry out comprehensive water-quality sampling programs to check for bacteria contamination in coastal areas where swimming and shellfishing occur. Advisories that restrict swimming and shellfishing are issued when sampling indicates that bacteria concentrations exceed federal health standards. These actions place these coastal waters on the U.S. Environmental Protection Agencies’ (EPA) list of impaired waters, an action that triggers a federal mandate to prepare a Total Maximum Daily Load (TMDL) analysis that should result in management plans that will restore degraded waters to their designated uses. When coastal waters become polluted, most people think that improper sewage treatment is to blame. Water-quality studies conducted over the past several decades have shown that improper sewage treatment is a relatively minor source of this impairment. In states like North Carolina, it is estimated that about 80 percent of the pollution flowing into coastal waters is carried there by contaminated surface runoff. Studies show this runoff is the result of significant hydrologic modifications of the natural coastal landscape. There was virtually no surface runoff occurring when the coastal landscape was natural in places such as North Carolina. Most rainfall soaked into the ground, evaporated, or was used by vegetation. Surface runoff is largely an artificial condition that is created when land uses harden and drain the landscape surfaces. Roofs, parking lots, roads, fields, and even yards all result in dramatic changes in the natural hydrology of these coastal lands, and generate huge amounts of runoff that flow over the land’s surface into nearby waterways. (PDF contains 3 pages)

Design, operation and economics of a small-scale hatchery for the larval rearing of sugpo, Penaeus monodon Fab.

One of the major problems in the mass production of sugpo is how to obtain a constant supply of fry. Since ultimately it is the private sector which should produce the sugpo fry to fill the needs of the industry, the Barangay Hatchery Project under the Prawn Program of the Aquaculture Department of SEAFDEC has scaled down the hatchery technology from large tanks to a level which can be adopted by the private sector, especially in the villages, with a minimum of financial and technical inputs. This guide to small-scale hatchery operations is expected to generate more enthusiasm among fish farmers interested in venturing into sugpo culture.

Effects of extracts of dried seeds of Toloache, Datura innoxia as anaesthesia on the African catfish Clarias gariepinus fingerlings

The effects of crude extract, pure extract, aqueous, fraction of pure and lipid fraction of pure extract of dried seeds of toloache. Datura innoxia as anaesthesia on the African catfish. Clarias gariepinus fingerlings were studied. The fish were exposed to various doses of the extract in aquaria tanks and the time taken for each fish to reach anaesthesia was recorded. The fish were anaesthetized up to 3.00g/l fingerlings reached anaesthesia is significantly (P<0.05) shorter time (1.004 minutes at 0.05gl) in pure unseparated extract than in crude extract (58.50 minutes at 3.00g/l concentrated). The time to reach anaesthesia decreased with an increase in concentration of the seed extract. Out the two fractions the lipid fraction had significantly (P>0.05) better anaesthetic on the fish. The control produced no observable anaesthetic effect on the fish within three hours. This suggests that the anaesthetizing active ingredent resided in the lipid fraction. All fish recovered from anaesthesia, swam and fed actively and no mortality was observed throughout the exposure period and thereafter. It is therefore recommended for use on C. gariepinus fingerlings

Studying conscious and unconscious vision with functional Magnetic Resonance Imaging : the BOLD promise

Waking up from a dreamless sleep, I open my eyes, recognize my wife’s face and am filled with joy. In this thesis, I used functional Magnetic Resonance Imaging (fMRI) to gain insights into the mechanisms involved in this seemingly simple daily occurrence, which poses at least three great challenges to neuroscience: how does conscious experience arise from the activity of the brain? How does the brain process visual input to the point of recognizing individual faces? How does the brain store semantic knowledge about people that we know? To start tackling the first question, I studied the neural correlates of unconscious processing of invisible faces. I was unable to image significant activations related to the processing of completely invisible faces, despite existing reports in the literature. I thus moved on to the next question and studied how recognition of a familiar person was achieved in the brain; I focused on finding invariant representations of person identity – representations that would be activated any time we think of a familiar person, read their name, see their picture, hear them talk, etc. There again, I could not find significant evidence for such representations with fMRI, even in regions where they had previously been found with single unit recordings in human patients (the Jennifer Aniston neurons). Faced with these null outcomes, the scope of my investigations eventually turned back towards the technique that I had been using, fMRI, and the recently praised analytical tools that I had been trusting, Multivariate Pattern Analysis. After a mostly disappointing attempt at replicating a strong single unit finding of a categorical response to animals in the right human amygdala with fMRI, I put fMRI decoding to an ultimate test with a unique dataset acquired in the macaque monkey. There I showed a dissociation between the ability of fMRI to pick up face viewpoint information and its inability to pick up face identity information, which I mostly traced back to the poor clustering of identity selective units. Though fMRI decoding is a powerful new analytical tool, it does not rid fMRI of its inherent limitations as a hemodynamics-based measure.

Growth response and survival of F1 hybrid fry of Heterobranchus longifilis and Clarias gariepinus reared in glass aquaria and plastic basins

The growth response of F1 hybrid fry of female Heterobranchus longifilis and male Clarias gariepinus were investigated under laboratory conditions in glass aquaria glass tanks and plastic basins. The larvae were produced artificially after inducement with Ovarptim. The hatching percentage was very high. Weekly mean length and weight were monitored for 6 weeks. The average length increase was higher in aquaria glass tanks than in plastic basins. However, there were depressed and irregular weight increases in both types of rearing troughs while significant weight increase (P<0.05) was recorded at week 6 in the plastic basin. Generally, the growth rate and survival in both containers were not significantly different

Growth response of Heterobranchus longifilis fingerlings fed with varying levels of dietary freshwater mussel (Aspatharia sinuata)

A common bivalve: Freshwater mussel, Aspatharia sinuate was evaluated as a dietary protein supplement in the production diet for Heterobranchus longifilis fingerlings with mean body weight 8.34 plus or minus 10g reared in aquaria tanks. Four diets containing fishmeal protein at a rate of 25%, 50% and 75% along with the freshwater mussel flesh were formulated. The diet without the freshwater mussel served as the control. The fish fingerlings were fed at 5% body weight per day for 56 days. It was revealed at the end of the experiment that freshwater mussel was most suitable as a protein supplement when incorporated at 25% replacement. The body weight gain, specific growth rate and feed conversion ration values of 6.83g, 1.06% day and 0.62 respectively were highest in diet with 25% replacement closely followed by diet with 50% replacement. Beyond 75% inclusion level there was no significant growth (P>0.05). However, complete replacement of fishmeal by freshwater mussel decreases growth rates and should not be used in Heterobranchus longifilis diets

The survival and growth of hybrid Clarias gariepinus and Heterotis longifilis fed with live and frozen Dapthnids

Six glass tanks, each containing dechlorinated tap water and stocked with 3-day-old Heterobranchus, larvae hybrid between, Heterobranchus longifilis (male and Clarias gariepinus (female) were administered two types of feeding trials viz: live and frozen Dapthnids. Each treatment was replicated three times. The larvae were each fed approximately 50 Dapthnids per feeding time for fifteen days. Morphometric measurements of weigh and total length were taken before and after the experiment, and water quality parameters were monitored throughout the experimental period. At the end of the experiment, fish larvae fed frozen, Dapthnids, showed higher survival rate than Heterobranchus fed live Dapthnids. Even though the statistical analysis revealed that there was no significant difference (P>0.05) in survival. However, the Heteroclarias fed live dapthnids performed better in terms of growth rate than Heteroclarias fed frozen dapthnids. The statistical analysis did not show significant difference (P>0.05) between the final length and weight of two treatments. Heteroclarias fed live dapthnids had higher length and weight than Heteroclarias fed frozen dapthnids. It was therefore concluded that based on this experiment there is the likelihood that frozen zooplankton (Daphnids) do not encourage growth of Heteroclarias, but improves its survival. However, it's suggested that frozen zooplankton can be used to supplement live zooplankton in situation of sacrcity

Growth performance of Heteroclarias fed maggot meal at varying inclusion levels

70-day growth trial was conducted with Heteroclarias: Heterobranchus bidorsalis X Clarias gariepinus (mean weight 0.64~c0.006g) fed diets based on various inclusion levels of Maggot Meal. The fishmeal in the control diet was replaced with maggot meals at 25%, 50%, 75% and 100% levels to supply 40% crude protein in the final diets. The trails were conducted in glass tanks (60cmx30cmx30cm). Evaluation of growth parameters and nutrient utilization of the fish was based on weight gains, protein intake, protein efficiency ratio, net protein utilization, feed conversion efficiency and carcass analysis. Best growth and feed conversion efficiency were obtained with the 75% dietary inclusion of maggot meal. There was no significant differences (P>0.055) between the group of fish on 50% and 75% dietary inclusion maggot meal in growth performance and protein efficiency ratio but, there was a significant (P<0.05) difference in the NPU (Net Protein Utilization) and protein gain between the control diet and those fed on maggot meals. There was no marked variation in the survival rate of fish on all diets

Etorkinen seme-alaben jatorrizko hizkuntzen trataera eskolan

LABURPENA: EAEko hezkuntza sistemak gero eta ikasle etorkin kopuru handiagoa du. Horrek ikasgeletan hizkuntz aniztasuna sortzen du, ezinezkoa bihurtuz irakasleek ume guztien ama hizkuntza jakitea. Egoera berri horren aurrean, lan honen helburua da jatorri etorkina duten ikasleen ama hizkuntzei eskolan ematen zaien trataera ezagutzea. Asmo horrekin, adituek eskolako hizkuntzaren ikaskuntza prozesuan umeen ama hizkuntzek duten garrantziaz diotena aztertu dugu eta, ondoren, etorkin kopuru handia duen eskola publiko batean murgildu gara errealitate hori ikertzeko. Azterketa-lanean lorturiko emaitzak ikusita, ez du ematen ikastetxe horretan jarraitzen ari diren hezkuntza elebiduna modu egokiena denik egoera berriari erantzuteko eta badirudi interesgarria izan daitekeela antolakuntza, metodologia eta estrategia berritzaileetan pentsatzea.

Comunidade de mamíferos em uma paisagem fragmentada no município de Cachoeiras de Macacu, RJ

A Mata Atlântica sofre fortes pressões antrópicas desde o descobrimento do Brasil. Desse contexto surge a necessidades de estudos que busquem os efeitos dessa degradação sobre a biodiversidade desse bioma. Mamíferos são bons bioindicadores da qualidade ambiental dos ecossistemas a eles associados. Sendo assim, esse estudo objetivou a busca da relação entre a estrutura da comunidade de mamíferos e a estrutura da cobertura vegetal de uma paisagem do município de Cachoeiras de Macacu, RJ. Os resultados apontaram para uma relação entre a distância entre os fragmentos e sua composição, ou seja, quanto mais próximos os fragmentos estão entre si, mais semelhantes eles são em relação a composição da comunidade de mamíferos. Nessa perspectiva, refletimos sobre a importância da Teoria de Biogeografia de Ilhas e da Teoria de Metapopulações no pensar de estratégias conservacionistas e entendemos que elas podem ajudar na construção de modelos complexos sobre a composição das espécies de mamíferos.

Carga de trabalho de enfermeiros: uma análise do Nursing Activities Score (NAS)

Este estudo tem como objeto a carga de trabalho de enfermeiros que trabalham em unidades de cuidados semi-intensivos. Seu objetivo geral foi identificar e analisar a percepção dos enfermeiros de uma unidade semi-intensiva acerca do instrumento Nursing Activities Score - NAS, tendo como foco o conceito de carga de trabalho. Os objetivos específicos foram: identificar domínios do NAS considerados pelos enfermeiros como capazes de avaliar a carga de trabalho; identificar os itens que os enfermeiros consideram relevantes e manteriam no instrumento, os itens que excluiriam e os que acrescentariam; identificar itens que os enfermeiros consideram subdimensionados, para os quais aumentariam a pontuação, os superdimensionados, para os quais diminuiriam a pontuação; e, ao final, discutir implicações dessa avaliação para a organização do trabalho e seus impactos na saúde do trabalhador de enfermagem. Estudo de abordagem quantitativa do tipo descritivo exploratória, com breve aporte qualitativo, utilizando a triangulação metodológica. O local de estudo foi uma unidade de média complexidade com 35 leitos em um hospital privado do Rio de Janeiro. Participaram do estudo 28 enfermeiros e os dados foram coletados por meio de um questionário com perguntas fechadas e abertas no período de abril a maio de 2008. O tratamento dos dados foi realizado com apoio do software Excel, utilizando estatística descritiva. O material qualitativo foi organizado em categorias, usando elementos da Análise de Conteúdo Temática. Entre os domínios, verificou-se que os enfermeiros consideram o que mais avalia a carga real de trabalho o Suporte Ventilatório, com 89%, e o domínio que não avalia a carga de trabalho foi o Suporte Neurológico, com 25%. Os três domínios mais citados para serem acrescidos de atividades foram o Suporte Renal, com 25%, seguido Intervenção Especificas, com 21%, e Suporte Metabólico, respectivamente. Quanto à exclusão de atividades, só dois domínios foram mencionados: Suporte Ventilatório, com 25%, e Atividade Básica, com 21%. Os enfermeiros acham que 69% da pontuação era adequada aos itens e 31% acreditam não estar adequada. No grupo, 27% aumentariam a pontuação em alguns itens e 4% diminuiriam a pontuação. Sobre a mensuração da carga de trabalho, acreditam que essa colabora no processo de trabalho, 79%, e 57% acham que mensurar a carga de trabalho através do NAS pode auxiliar na preservação de sua saúde. Concluímos que esse instrumento mensura a carga de trabalho na opinião dos enfermeiros, mas precisa ser adaptado à realidade da unidade onde está sendo aplicada. Além disso, os enfermeiros alteraram mais os itens relacionados à carga física sem identificar a carga psíquica de trabalho como relevante, evidenciando que o trabalho de enfermagem precisa ser mais bem conhecido pelos enfermeiros no que se refere às dimensões de impacto na sua saúde.

Determination of optimum stocking density of Macrobrachium rosenbergii larvae using multiple feed in a commercial hatchery at Cox’s Bazar, Bangladesh

Experimental stocking density of Macrobrachium rosenbergii in larval rearing was conducted in A.G. Aqua Hatchery, Chakaria, Bangladesh to study the effect of different stocking densities on growth, survival rate and diseases stress under hatchery condition. The research work was conducted using six cemented rectangular tanks having 3m3 capacity (1.5mX2mX1m) each. Stocking density were maintained in three experimental setup as 200, 150 and 100ind/L of the T1, T2 and T3 respectively with one replicate each. The larvae were fed with Artemia nauplii, Custard, Maxima and brine shrimp flakes. Water quality was maintained by exchanging 20-30% (12ppt saline water) daily. During the study period, temperature, pH, DO, salinity, nitrite-nitrogen, ammonia and alkalinity were maintained from 28.5-31.5ºC, 7.5-7.8, 5.8-5.9mg/L, 12-13ppt, 0.14-0.2 mg/L, 0.22-0.3mg/L, and 140-160mg/L respectively. The growth rates of larvae at 11th stage were recorded in terms of body length 0.115, 0.136, and 0.169 mm/day whereas body weight were observed 0.000115, 0.000180, and 0.000240g/day. The survival rate of larvae were found 21.8%, 30.4% and 51.3% in treatments T1, T2 and T3 respectively. PL was obtained as 43, 45, and 51PL/L and days required of 41, 38 and 34 days in stocking density of 200, 150, and 100ind/L respectively. It was found that the minimum of 34 days was required to attain the PL (12th stage) using the stocking density of 100 individuals/L. Cannibalism, Zoothamnium, Exuvia Entrapment Disease (EED), and Bacterial Necrosis (BN) were found to be the threat to the commercial hatchery operation that might responsible for potential larval damages which can be reduced by lowering the stocking densities in larval rearing tank that also increased the survival and growth rate.

Gestão em saúde, uma perspectiva ergológica: com quantos gestos se faz uma gestão

Baseado na convicção de que trabalhar é gerir fruto das pesquisas com a perspectiva da Ergologia , procura-se nesta tese pensar gestão como um conceito ampliado, algo que todos os humanos operam ao trabalhar, e não somente como uma função exclusiva de administradores, no sentido restrito do termo (referido apenas aos chefes, diretores, etc.). Tendo como campo empírico o Sistema Único de Saúde (SUS) e investigando-se as proposições de alguns dos principais autores sobre o tema da Gestão e Planejamento em Saúde, verificou-se que uma exaustiva busca vem sendo empreendida por diversos agentes do campo da Saúde e por pesquisadores para aproximarem-se, compreenderem e desenvolverem melhor as habilidades, os conhecimentos, as competências e os dispositivos que permitiriam uma gestão mais eficiente do SUS e, mais especificamente, no âmbito de uma Unidade de Saúde Pública no Brasil. Estiveram em análise as práticas de gestão desenvolvidas em um Centro Municipal de Saúde do estado do Rio de Janeiro (Brasil), no qual o autor da tese, além das atividades de pesquisa, exercia a função de diretor geral. A tese teve como objetivo principal analisar, do ponto de vista da atividade, a dimensão gestionária do trabalho na Unidade de Saúde citada, a fim de discutir a viabilidade naquele local e, possivelmente em outras Unidades de Saúde do exercício de uma ergogestão, isto é, uma gestão com base nos princípios propostos pela Ergologia quando o ponto de vista da atividade tem cidadania no meio de trabalho. O referencial teórico constituiu-se de algumas abordagens clínicas do trabalho (Ergonomia da Atividade, Psicopatologia do Trabalho, Psicodinâmica do Trabalho e Clínica da Atividade, esta última em menor proporção) com elementos das contribuições do educador brasileiro Paulo Freire, do psicanalista inglês Donald Winnicott e do biólogo chileno Humberto Maturana, todas colocadas em sinergia dialética sob a orientação da perspectiva ergológica. No curso da investigação foram utilizados métodos e técnicas pertinentes a este quadro e que objetivaram possibilitar a aproximação e o diálogo com os protagonistas da atividade na Unidade de Saúde em análise. Destacam-se as influências da pesquisa-intervenção e da pesquisa etnográfica, sendo o principal dispositivo técnico utilizado aquele denominado Encontros sobre o Trabalho. A pesquisa empreendida, conjuntamente com a experiência concreta de gerenciamento (como diretor geral), permitiu concluir que o esforço de implantação da modalidade que se denomina ergogestão, privilegiando o ponto de vista da atividade, pôde colaborar para promover transformações positivas no cotidiano da Unidade posta em análise. Contudo, sua aceitação por um maior número de atores e seu desenvolvimento dependem do atendimento de algumas necessidades, apontadas pelo coletivo de trabalho como entraves a superar. Os achados aqui presentes podem contribuir para a construção de um patrimônio de informações acerca da Unidade. A partir desse patrimônio outras experiências de gerenciamento podem vir a se desenvolver, obtendo-se assim, cada vez maior êxito na gestão do processo de trabalho e na melhoria das condições do atendimento oferecido aos usuários.