Enzymatic Polymerization of High Molecular Weight DNA

The use of DNA as a polymeric building material transcends its function in biology and is exciting in bionanotechnology for applications ranging from biosensing, to diagnostics, and to targeted drug delivery. These applications are enabled by DNA’s unique structural and chemical properties, embodied as a directional polyanion that exhibits molecular recognition capabilities. Hence, the efficient and precise synthesis of high molecular weight DNA materials has become key to advance DNA bionanotechnology. Current synthesis methods largely rely on either solid phase chemical synthesis or template-dependent polymerase amplification. The inherent step-by-step fashion of solid phase synthesis limits the length of the resulting DNA to typically less than 150 nucleotides. In contrast, polymerase based enzymatic synthesis methods (e.g., polymerase chain reaction) are not limited by product length, but require a DNA template to guide the synthesis. Furthermore, advanced DNA bionanotechnology requires tailorable structural and self-assembly properties. Current synthesis methods, however, often involve multiple conjugating reactions and extensive purification steps.

The research described in this dissertation aims to develop a facile method to synthesize high molecular weight, single stranded DNA (or polynucleotide) with versatile functionalities. We exploit the ability of a template-independent DNA polymerase−terminal deoxynucleotidyl transferase (TdT) to catalyze the polymerization of 2’-deoxyribonucleoside 5’-triphosphates (dNTP, monomer) from the 3’-hydroxyl group of an oligodeoxyribonucleotide (initiator). We termed this enzymatic synthesis method: TdT catalyzed enzymatic polymerization, or TcEP.

Specifically, this dissertation is structured to address three specific research aims. With the objective to generate high molecular weight polynucleotides, Specific Aim 1 studies the reaction kinetics of TcEP by investigating the polymerization of 2’-deoxythymidine 5’-triphosphates (monomer) from the 3’-hydroxyl group of oligodeoxyribothymidine (initiator) using in situ 1H NMR and fluorescent gel electrophoresis. We found that TcEP kinetics follows the “living” chain-growth polycondensation mechanism, and like in “living” polymerizations, the molecular weight of the final product is determined by the starting molar ratio of monomer to initiator. The distribution of the molecular weight is crucially influenced by the molar ratio of initiator to TdT. We developed a reaction kinetics model that allows us to quantitatively describe the reaction and predict the molecular weight of the reaction products.

Specific Aim 2 further explores TcEP’s ability to transcend homo-polynucleotide synthesis by varying the choices of initiators and monomers. We investigated the effects of initiator length and sequence on TcEP, and found that the minimum length of an effective initiator should be 10 nucleotides and that the formation of secondary structures close to the 3’-hydroxyl group can impede the polymerization reaction. We also demonstrated TcEP’s capacity to incorporate a wide range of unnatural dNTPs into the growing chain, such as, hydrophobic fluorescent dNTP and fluoro modified dNTP. By harnessing the encoded nucleotide sequence of an initiator and the chemical diversity of monomers, TcEP enables us to introduce molecular recognition capabilities and chemical functionalities on the 5’-terminus and 3’-terminus, respectively.

Building on TcEP’s synthesis capacities, in Specific Aim 3 we invented a two-step strategy to synthesize diblock amphiphilic polynucleotides, in which the first, hydrophilic block serves as a macro-initiator for the growth of the second block, comprised of natural and/or unnatural nucleotides. By tuning the hydrophilic length, we synthesized the amphiphilic diblock polynucleotides that can self-assemble into micellar structures ranging from star-like to crew-cut morphologies. The observed self-assembly behaviors agree with predictions from dissipative particle dynamics simulations as well as scaling law for polyelectrolyte block copolymers.

In summary, we developed an enzymatic synthesis method (i.e., TcEP) that enables the facile synthesis of high molecular weight polynucleotides with low polydispersity. Although we can control the nucleotide sequence only to a limited extent, TcEP offers a method to integrate an oligodeoxyribonucleotide with specific sequence at the 5’-terminus and to incorporate functional groups along the growing chains simultaneously. Additionally, we used TcEP to synthesize amphiphilic polynucleotides that display self-assemble ability. We anticipate that our facile synthesis method will not only advance molecular biology, but also invigorate materials science and bionanotechnology.

Utilizing ICT to prevent loneliness and social isolation of the elderly. A literature review

Ageing of the population is a worldwide phenomenon. Numerous ICT-based solutions have been developed for elderly care but mainly connected to the physiological and nursing aspects in services for the elderly. Social work is a profession that should pay attention to the comprehensive wellbeing and social needs of the elderly. Many people experience loneliness and depression in their old age, either as a result of living alone or due to a lack of close family ties and reduced connections with their culture of origin, which results in an inability to participate actively in community activities (Singh & Misra, 2009). Participation in society would enhance the quality of life. With the development of information technology, the use of technology in social work practice has risen dramatically. The aim of this literature review is to map out the state of the art of knowledge about the usage of ICT in elderly care and to figure out research-based knowledge about the usability of ICT for the prevention of loneliness and social isolation of elderly people. The data for the current research comes from the core collection of the Web of Science and the data searching was performed using Boolean? The searching resulted in 216 published English articles. After going through the topics and abstracts, 34 articles were selected for the data analysis that is based on a multi approach framework. The analysis of the research approach is categorized according to some aspects of using ICT by older adults from the adoption of ICT to the impact of usage, and the social services for them. This literature review focused on the function of communication by excluding the applications that mainly relate to physical nursing. The results show that the so-called ‘digital divide’ still exists, but the older adults have the willingness to learn and utilise ICT in daily life, especially for communication. The data shows that the usage of ICT can prevent the loneliness and social isolation of older adults, and they are eager for technical support in using ICT. The results of data analysis on theoretical frames and concepts show that this research field applies different theoretical frames from various scientific fields, while a social work approach is lacking. However, a synergic frame of applied theories will be suggested from the perspective of social work.

Falls and the Social Isolation of Older Adults in the National Health and Aging Trends Study

Thesis (Ph.D.)--University of Washington, 2016-08

Ground Plane Slot Structures for Isolation of Cosited Microstrip Antennas

Ground plane slot structures have been shown to reduce coupling between cosited antennas. Although some such structures have already been reported, no analytical model exists to describe their behavior and there are no design guidelines. In this work, the behavior of reported ground plane structures is used as a clue to obtain generalizable information about such structures' behavior. The structures' scalability and excitation behavior is investigated. Next a circuit model is derived that describes the interaction of microstrip patch antennas with a ground plane slot structure based on mutual admittances between the ground plane slots and the effective slots at the antennas' radiating edges. The circuit model leads to design guidelines for the ground plane slot structure and an approximate relationship between mutual admittances which must be satisfied in order to isolate the antennas. Finally, we present a novel ground plane slot structure that mitigates some of the disadvantages of earlier designs.

Enzymatic upgrading of eucalypt paper-grade kraft pulp within dissolving pulp production

Dissolving-grade pulps are commonly used for the production of cellulose derivatives and regenerated cellulose. High cellulose content, low content of non-cellulosic material, high brightness, a uniform molecular weight distribution and high cellulose reactivity are the key features that determine the quality of a dissolving pulp. The first part of this work was an optimization study regarding the application of selected enzymes in different stages of a new purification process recently developed in Novozymes for purifying an eucalypt Kraft pulp into dissolving pulp, as an alternative to the pre-hydrolysis kraft (PHK) process. In addition, a viscosity reduction was achieved by cellulase (endoglucanase) treatment in the beginning of the sequence, while the GH11 and GH10 xylanases contributed to boost the brightness of the final pulp. The second part of the work aimed at exploring different auxiliary enzyme activities together with a key xylanase towards further removal of recalcitrant hemicelluloses from a partially bleached Eucalypt Kraft pulp. The resistant fraction (ca. 6% xylan in pulp) was not hydrolysable by the different combinations of enzymes tested. Production of a dissolving pulp was successful when using a cold caustic extraction (CCE) stage in the end of the sequence O-X-DHCE-X-HCE-D-CCE. The application of enzymes improved process efficiency. The main requirements for the production of a dissolving pulp (suitable for viscose making) were fulfilled: 2,7% residual xylan, 92,4% of brightness, a viscosity within the values of a commercial dissolving pulp and increased reactivity.

Extraction, identification, fractionation and isolation of phenolic compounds in plants with hepatoprotective effects

The liver is one of the most important organs of human body, being involved in several vital functions and regulation of physiological processes. Given its pivotal role in the excretion of waste metabolites and drugs detoxification, the liver is often subjected to oxidative stress that leads to lipid peroxidation and severe cellular damage. The conventional treatments of liver diseases such as cirrhosis, fatty liver and chronic hepatitis are frequently inadequate due to side effects caused by hepatotoxic chemical drugs. To overcome this problematic paradox, medicinal plants, owing to their natural richness in phenolic compounds, have been intensively exploited concerning their extracts and fraction composition in order to find bioactive compounds that could be isolated and applied in the treatment of liver ailments. The present review aimed to collect the main results of recent studies carried out in this field and systematize the information for a better understanding of the hepatoprotective capacity of medicinal plants in in vitro and in vivo systems. Generally, the assessed plant extracts revealed good hepatoprotective properties, justifying the fractionation and further isolation of phenolic compounds from different parts of the plant. Twenty-five phenolic compounds, including flavonoids, lignan compounds, phenolic acids and other phenolic compounds, have been isolated and identified, and proved to be effective in the prevention and/or treatment of chemically induced liver damage. In this perspective, the use of medicinal plant extracts, fractions and phenolic compounds seems to be a promising strategy to avoid side effects caused by hepatotoxic chemicals.

Effects of Low Molecular Weight Sulfated Galactan Fragments From Botryocladia Occidentalis on the Pharmacological and Enzymatic Activity of Spla2 From Crotalus Durissus Cascavella

Low molecular weight fragments of sulfated galactans (Boc-5 and Boc-10) from the red algae Botryocladia occidentalis significantly inhibited Crotalus durissus cascavella sPLA2 enzymatic activity. Equimolar ratios of sPLA2 to Boc-5 or Boc-10 resulted in allosteric inhibition of sPLA2. Under the conditions tested, we observed that both Boc-5 and Boc-10 strongly decreased edema, myonecrosis, and neurotoxicity induced by native sPLA2.

Isolation of micropropagated strawberry endophytic bacteria and assessment of their potential for plant growth promotion.

Twenty endophytic bacteria were isolated from the meristematic tissues of three varieties of strawberry cultivated in vitro, and further identified, by FAME profile, into the genera Bacillus and Sphingopyxis. The strains were also characterized according to indole acetic acid production, phosphate solubilization and potential for plant growth promotion. Results showed that 15 strains produced high levels of IAA and all 20 showed potential for solubilizing inorganic phosphate. Plant growth promotion evaluated under greenhouse conditions revealed the ability of the strains to enhance the root number, length and dry weight and also the leaf number, petiole length and dry weight of the aerial portion. Seven Bacillus spp. strains promoted root development and one strain of Sphingopyxis sp. promoted the development of plant shoots. The plant growth promotion showed to be correlated to IAA production and phosphate solubilization. The data also suggested that bacterial effects could potentially be harnessed to promote plant growth during seedling acclimatization in strawberry

Isolation of a potential anticancer agent with protein phosphatase inhibitory activity from soil-derived Penicillium sp strain H9318

Purpose: To determine the effect of the secondary metabolites from Penicillium sp. H9318 on cytotoxicity and cell cycle progression. Methods: A yeast PP1 inhibitory screening system was carried out to confirm the presence of anti- PP1c activity in crude acetone extracts of strain H9318. The extracts were fractionated and identified as Fraction S1 and Citrinin 9318 (CTN9318). Various cancer cell lines were used to test for the toxicity of the crude acetone extracts, Fraction S1 and Citrinin 9318, using MTT viability assay. Results: It was found that a colorectal cancer cell line, HT-29, was susceptible to Fraction S1 and Citrinin 9318. A propidium iodide (PI)-incorporated DNA assay was used to show that there was G2/M arrest in HT-29 by Citrinin 9318. Conclusion: Citrinin 9318 inhibits the viability of HT-29 via mitotic block. The results suggest that Citrinin 9318 is capable of exerting cytotoxicity and mitotic arrest in a colon cancer cell line, HT29

水稻胚囊发育畸变的细胞学和遗传学研究

1．水稻多卵卵器的起源：被子植物的卵器中通常只有一个卵细胞。我们在水稻多胚品系胚囊中观察到二卵卵器和三卵卵器，本研究对其大孢子发生和胚囊发育进行了细胞胚胎学观察，揭示了水稻多卵卵器的起源．观察结果表明，该品系能进行正常的大孢子发生。大孢子母细胞进行正常的减数分裂形成四个大孢子靠近合点端的大孢子发育，其它三个退化。功能大孢子第一次有丝分裂后两个子核被一中央大液泡分隔在胚囊珠孔端和合点端，与此同时胚囊出现不均衡生长，珠孔端迅速膨大，合点端几乎不增大，致使二核末期的胚囊呈倒梨形．紧接着发生第二次有丝分裂，合点端核分裂时纺锤丝与胚囊纵轴平行，而珠孔端核分裂时纺锤丝与胚囊纵轴成4 5度夹角．由此产生的四核胚囊中，合点端一核向胚囊中部或中上部（胚囊珠孔端）迁移，四核胚囊再经一次有丝分裂形成两种类型的核分布偏离蓼型的八核胚囊。一种类型是珠孔端四个核，中部与合点各二个核，在胚囊细胞化过程中，珠孔端四核 分化成四细胞卵器，其中卵细胞和助细胞各二个，中部的二核分化成二极核中央细胞，合点 端的二核形成反足细胞。另一种类型是珠孔端六个核，合点端二个核，在胚囊细胞化过程中， 两端各一核向中部迁移分化成二极核中央细胞，珠孔端剩余的五核分化成五细胞卵器，其 中卵细胞三个，助细胞二个，合点端的一核迅速分裂形成反足细胞． 2．水稻同源三倍体TAR的生殖特性：TAR的单穗结实率平均可达10%，核型分析表明此三倍体产生的后代个体仍为具有36条染色体的三倍体．细胞胚胎学初步观察显示TAR为一具兼性无融合生殖特性的水稻新种质，其胚珠几乎都能进行胚囊的分化，但其中仅有33%的胚囊有较正常的结构，9%的胚囊在散粉前进行胚胎发生，58%的胚囊发育显著异常，表现为极性紊乱、多极核或缺失雌性生殖单位等。 3．水稻亚种间杂种败育的细胞学基础：对普通栽培稻不同品种类型间杂种颖花败育的细胞学基础及雌性败育的过程进行的细胞学研究表明：1）引起杂种颖花败育的原因有胚囊败育，花粉败育、开花时花药不开裂和雌雄异熟．其中胚囊败育而丧失受精能力是引起低结实率的最重要的因素，开花时花药不开裂和雌雄异熟在一定程度上形成了雌雄性细胞时间和空间的隔离屏障。2）杂种植株的所有大孢子母细胞都能进行正常的减数分裂形成四个大孢子，败育主要发生在靠近合点端的功能大孢子分化形成胚囊的早期，有的胚囊母细胞在进行第一次有丝分裂前便萎缩解体，多数能完成一次或二次有丝分裂形成二核或四核败育胚囊．败育的共同特征是无液泡的分化，细胞质少或退化，在败育胚囊残迹部位，解体的珠心细胞和萎缩的胚囊残溃混杂垛叠．已受精的杂种子房没有观察到胚及胚乳发育的异常．籼粳杂种胚囊败育频率较高． 4．籼粳杂种生殖障碍的基因定位：应用具有1 37个标记位点的籼粳杂交窄叶青8号/京系17)F1花药培养获得的127个双单倍体OH）群体构建的R FLP图谱，对控制籼粳杂种颖花败育的基因座位进行了定位研究。结果在第1、3、4、5、6、7、8、1 2染色体上检测到1 0个基因座位，其中第3、12染色体上的2个不育基因位点str3和str12与同一杂交组合F2分离群体中发现的异常分离热点处于相同的染色体区段．stj-6的基因加性效应为负值，有增加籼粳亲和性的作用;其余的不育基因座位皆有增加籼梗杂种不育性的作用． 5．籼粳杂种胚囊败育的遗传分析和基因定位：利用DH系构建的分子图谱及DH系衍生的2个回交群体定位了引起籼梗杂种胚囊败育的2个互补的主效基因esa-l（E1或e1位点）和esa-2（E2或e2位点），它们分别位于第6和第1 2染色体．在不育基因位点，籼稻基因型为EIEle2e2，粳稻基因型为elelE 2E 2，杂交后代中基因型为EIE2，Ele2、elE 2的雌配子体正常发育，携带ele2基因型的雌配子体表现败育．胚囊育性受配子体基因型控制，孢予体遗传背景影响胚囊败育基因的表达.

Ontogenia do óvulo e da Antera de Cybistax antisyphilitica (Mart.) Mart. (Bignoniaceae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Effect of preantral follicle isolation technique on in-vitro follicular growth, oocyte maturation and embryo development in mice

Background: The use of mechanical and enzymatic techniques to isolate preantral follicles before in-vitro culture has been previously described. The aim of this study was to assess the effect of the isolation procedure of mouse preantral follicles on their subsequent development in vitro. Methods: Follicles were isolated either mechanically or enzymatically and cultured using an individual non-spherical culture system. Follicular development and steroidogenesis, oocyte in-vitro maturation and embryo development were assessed for both groups. Results: After 12 days of culture, follicles isolated mechanically had a higher survival rate but a lower antral-like cavity formation rate than follicles isolated enzymatically. Enzymatic follicle isolation was associated with a higher production of testosterone and estradiol compared with mechanical isolation. A stronger phosphatase alkaline reaction was observed after enzymatic isolation, suggesting that follicles isolated enzymatically had more theca cells than those isolated mechanically. However, both isolation techniques resulted in similar oocyte maturation and embryo development rates. Conclusions: Enzymatic follicular isolation did not affect theca cell development. Follicular steroidogenesis was enhanced after enzymatic isolation but the developmental capacity of oocytes was comparable to that obtained after mechanical isolation.

The isolation, partial purification and preliminary characterization of a growth factor from chick embryo brains

Chicl( brain growth factor (CBGF) is a mitogen isolated from embryonic chick brains thought to have a potential role as a trophic factor involved in nerve dependent amphibian limb regeneration. In addition, CBGF stimulates 3H-thymidine incorporation in chick embryo brain astrocytes in vitro. In this study, cultured chick embryo brain non-neuronal cells were employed in a bioassay to monitor CBGF activity throughout various stages of its pllrification. Cell culture and assay conditions were optimized. Nonneuronal cells grew best on collagen-coated culture dishes in complete medium, were most responsive to a growth stimulus [10% fetal bovine serum (FBS)] at the second and third subcultures, and were healthiest when rendered "quiescent" in medium supplemented with 1% FBS. The most effective bioassay conditions consisted of a minimum 14.5 hour "quiescence" time (24 hours was used), a 6 hour "prestimulation" time, and a 24 hour 3H-thymidine labeling time. Four-day subconfluent primary non-neuronal cells consisted of 6.63% GFAP positive cells; as a result cultures were thought to be mainly composed of astroblasts. CBGF was purified from 18-day chick embryo brains by ultrafiltration through Amicon PM-30 and YM-2 membranes, size exclusion chromatography through a Biogel P6 column, and analytical reverse-phase high-performance liquid chromatography (rp-HPLC). The greatest activity resided in rp-HPLC fraction #7 (10 ng/ml) which was as effective as 10% FBS at stimulating 3H-thymidine incorporation in chick embryo brain nonneuronal cells. Although other researchers report the isolation of a mitogenic fraction consisting of 5'-GMP from the embryonic chick brain, UV absorbance spectra, rp-HPLC elution profiles, and fast atom bombardment (FAB) mass spectra indicated that CBGF is neither 5'-GMP nor 51-AMP. 2 Moreover, commercially available 5t-GMP was inhibitory to 3H-thymidine incorporation in the chick non-neuronal cells, while Sf-AMP had no effect. Upon treatment with pronase, the biological activity of fraction P6-3 increased; this increase was nearly 30% greater than what would be expected from a simple additive effect of any mitogenic activity of pronase alone together with P6-3 alone. This may suggest the presence of an inhibitor protein. The bioactive component may be a protein protected by a nucleoside/nucleotide or simply a nucleoside/nucleotide acting alone. While the FAB mass spectrum of rp-HPLC fraction #7 did not reveal molecular weight or sequence information, the ion of highest molecular weight was observed at m/z 1610; this is consistent with previous estimations of CBGF's size. 3