乙草胺、甲胺磷及其复合对黑土真菌的生态效应

农药对土壤微生物区系结构和功能的影响以及潜在的生态风险成为人们关注的热点之一。本文以中科院海伦生态站农田黑土作为实验土壤，采用室内模拟的方法，利用传统的（CFU和ergosterol）及分子微生物生态学技术（DGGE，real-time PcR，clolle library）研究了乙草胺、甲胺磷及其复合对黑土真菌的生态效应，并得出以下结果：经8周处理，中、高浓度乙草胺（150和250mgkg-1）对土壤真菌数量、生物量和可培养真菌种群多样性具有长期抑制效应。乙草胺处理8周后可培养真菌和土壤固氮微生物n州基因的种群结构不能得到恢复，而总的真菌结构可基本恢复。甲胺磷对土壤可培养真菌数量和生物量具有促进作用，以高浓度（250mgkg~(-1)）尤为显著。高浓度甲胺磷（25omgkg~(-1)）对nifH基因多样性有长期抑制效应。甲胺磷处理8周后可培养真菌种群结构不可恢复，而总的真菌和n积基因种群结构可部分恢复。两者复合后对真菌数量，生物量，多样性及n担基因多样性的影响无论是促进还是抑制其作用强度都大于单因子。处理8周后可培养真菌、总的真菌和n州基因三者的种群结构均不可恢复。克隆测序分析发现乙草胺、甲胺磷及其复合可明显促进植物致病真菌（colletolrichum；truncatum，Rhizoctonia zeae，Fusarium oxysporum）的生长，同时使土壤中常见的青霉菌数量减少，使农药处理后具有潜在的植物病害爆发的风险。本试验结果表明，乙草胺、甲胺磷及其复合对土壤真菌数量、结构、多样性和功能基因nifH的多样性及其种群组成有不同程度的影响，甚至产生某些不可逆的长期生态效应。复合处理对土壤真菌的影响要大于两个单因子作用，表现了明显的复合生态效应。一般来说受到午扰的真菌种群结构不容易自然恢复，因此建议在施用这两种农药过程中要避免大量、频繁的单独或复合施用。

大气CO_2浓度升高对红松和长白赤松幼苗非根际土壤微生物的影响

以连续5 a不同CO2浓度处理的长白赤松和红松幼苗为对象,采用CFU(活细胞计数)菌落计数法研究了大气CO2浓度对幼苗非根际土壤微生物数量的影响。结果表明:高浓度CO2(700μmol.mol-1和500μmol.mol-1)处理对长白赤松和红松幼苗非根际土壤细菌数量具有显著的(p<0.01)抑制作用,对真菌数量亦有抑制作用。大气CO2浓度升高对红松幼苗非根际土壤放线菌数量具有抑制作用(p<0.05),而对长白赤松幼苗土壤放线菌数量没有明显的影响。

乙草胺和甲胺磷对农田黑土可培养真菌数量及种群结构的影响

应用传统及PCRDGGE方法(denaturinggradientgelelectrophoresis),分别对不同浓度乙草胺、甲胺磷胁迫下黑土中可培养真菌CFU(colonyformingunits)、种群丰富度(richness)及种群结构动态变化规律进行了研究.结果表明,在实验室微域条件下,乙草胺对黑土可培养真菌CFU的影响随处理浓度的增加而抑制作用增强,表现出由低浓度(50mg·kg-1)时的刺激生长到高浓度(250mg·kg-1)时的长期抑制效应;250mg·kg-1甲胺磷在8周处理过程中对土壤可培养真菌生长具有显著的刺激效应,使可培养真菌CFU比对照增加10倍,但50和150mg·kg-1甲胺磷处理对土壤可培养真菌CFU无显著影响.种群丰富度系数分析结果表明,高、中浓度乙草胺处理可使土壤可培养真菌种群丰富度不可逆地降低.土壤真菌rDNA特异PCRDGGE聚类分析结果表明,不同浓度乙草胺、甲胺磷处理均不同程度地对土壤可培养真菌的种群组成和结构造成影响,其中甲胺磷尤为显著.

Construction and characterization of a live, attenuated esrB mutant of Edwardsiella tarda and its potential as a vaccine against the haemorrhagic septicaemia in turbot, Scophthamus maximus (L.)

The esrB gene of Edwardsiella tarda, which encodes a regulator protein of the type III secretion system, was mutated by the unmarked deletion method and reintroduced by allelic exchange into the chromosome of E. tarda LSE40 by means of the suicide vector pRE 112. The LSE40 esrB mutant was highly attenuated when inoculated intraperitoneally into turbot Scophthamus maximus L., showing a 50% lethal dose of 10(8.1) cfu/fish. The esrB mutants were not recoverable from the internal organs at 14 days post-inoculation. Vaccination with a single dose of 10(5)-10(7) cfu/fish of the esrB mutant elicited significant protection against the wildtype strain of E. tarda LSE40 (relative percentage survival > 50%). The protection correlated well with the antibody titres in the serum of vaccinated fish. (c) 2006 Elsevier Ltd. All rights reserved.

Evidences of the intertidal red alga Grateloupia turuturu in turning Vibrio parahaemolyticus into non-culturable state in the presence of light

Grateloupia turuturu, previously known as Grateloupia doryphora, has been widely reported to be an invasive algal species. There are no studies to relate the impact of its existence on its surrounding environment. In this paper, we present our results to show that about 70% of individuals collected from the field could turn Vibrio parahaemolyticus into non-culturable state on both selective (TCBS) and non-selective (2216E) culture medium in 24 h in the presence of light in live algal culture. Total bacteria counts on TCBS and 2216E plates dropped from the initial 565 (174) and 1192 (60) cfu ml(-1) respectively to zero in 24 h. This effect disappeared when the alga was grown in darkness. The same effect was not found in two other intertidal macroalgae Laminaria japonica and Palmaria palmata. Further tests showed that the settlement ability of bacteria in seawater was impaired significantly in the presence of this alga in comparison with three other algal species. (c) 2006 Elsevier B.V. All rights reserved.

Relationship between differential retention of Escherichia coli and Enterococcus faecalis and variations in enzyme activity in the scallop Patinopecten yessoensis

Uptake of Escherichia coli and Enterococcus faecalis and variations of trypsin amylase activity acid phosphatase and superoxide dismutase in tissue of the scallop Patinopecten yessoensis were detected. The results showed that P. yessoensis accumulated E. faecalis in larger numbers and more rapidly than E. coli, both with the highest concentration in the digestive tract and lowest in hemolymph. Compared to E. coil, all scallops exposed to E. faecalis showed significantly higher trypsin and AMS activity. SOD activity in hemocytes and ACP activity in hemolymph was significantly higher in the treatments with 5 log(10)CFU/ml E. colt than with E. faecalis. But no significant differences in ACP activity of P. yessoensis exposed to a 3 log(10)CFU/ml inoculum of both bacteria were recorded. In conclusion, the mass retention of gut microflora in P. yessoensis is positively correlated with digestive enzymes activity and negatively correlated with ACP activity in the hemocyte. (C) 2010 Published by Elsevier Ltd.

大型藻类在工程治理海水富营养化和抑制病原微生物中的作用

沿海工农业生产的快速发展和人类活动对近海生态系统产生了很大影响，大量化肥的使用和工业污水、生活污水的排放导致近海环境污染，海水富营养化，赤潮频发。另外，由于近海养殖活动的迅猛发展以及养殖的不规范和不科学性导致近海生态系统结构和功能改变，一方面加重了海水富营养化，另一方面养殖动植物病害经常发生，严重影响了海产品的质量和效益。 大型海藻是海区重要的初级生产者，生命周期长、生长快，能通过光合作用吸收固定水体的C、N、P等营养物质来合成自身，同时增加水体溶解氧。因此，大型海藻被称为海洋环境中的生物过滤器。另外，由于大型藻类自身营养成分的复杂性和与藻共生的微生物多样性，大型海藻还可对生态系统中的浮游生物和微生物产生直接和间接影响。 在海洋环境，尤其是海水养殖水体环境存在着两个主要问题：海水富营养化和病源微生物控制，本文针对海洋环境中存在的这两个问题进行了探索研究。 以大型经济藻种长心卡帕藻（Kappaphycus alvarezzi）作为实验材料，分别在实验室内、室外藻类处理系统和海湾养殖现场三种条件下，进行藻类去除海水氮磷的一次性实验、半连续实验和连续实验，研究了其对海水中无机氮、无机磷的吸收速率和去除能力，初步评估了其生态价值。 构建了一种半封闭海域富营养化治理模式，以长心卡帕藻为实验材料，研究了其去除海水富营养化的能力，主要结果如下： （1）室内实验研究发现，长心卡帕藻对氮、磷的吸收速率随底物浓度升高而升高。在氮磷比为10:1，温度28℃条件下，氮浓度为50μmol • L-1时，藻对氮、磷的吸收速率达到最大，分别为0.93µmol • g-1（FW）• h-1和0.072µmol • g-1（FW）• h-1。 （2）人工修建的藻类养殖系统中进行的长心卡帕藻去除氮、磷的半连续实验，结果表明该藻具有连续去除海水DIN、DIP的能力。只要保持足够的底物浓度，长心卡帕藻对无机氮、无机磷的吸收速率达到最大，分别为0.3µmol • g-1（FW） • h-1和0.03µmol • g-1（FW）• h-1。但是对氮磷的吸收速率较室内实验有所降低。 （3）自然条件下，通过调查黎安海湾水质情况发现，长心卡帕藻具有较大的生态效益。在整个海湾大面积养殖卡帕藻，通过收获藻体，每年大约可以从海水中带走33吨氮素，7.5吨磷素。由于在海湾长心卡帕藻的作用，全年海湾水质保持在1-2级国家海水质量标准，产生了明显的生态效益。 另外，我们对大型藻类浒苔（Ulva clathrata）吸收氮磷和抑制鳗弧菌（Vibrio anguillarum）的效果进行了初步探索，结果表明：浒苔不仅对培养系统内无机氮和磷具有明显的去除作用，而且在异养细菌总量没有降低的情况下，对鳗弧菌有显著抑制作用，该抑制作用还受到水体中氮磷营养盐浓度的影响。在10g • L-1海藻的条件下，鳗弧菌以105－107 cfu • mL-1接入2天后，无论是否添加外源氮磷，鳗弧菌密度降到10 cfu • mL-1以下，鳗弧菌去除率几乎达到100%。实验数据还显示，添加氮磷营养盐可以增强浒苔对鳗弧菌的抑制作用，但没有降低其中的异养菌群数量，系统内异养细菌总量均维持在较高水平。进一步研究表明，培养浒苔24h后的海水，也对鳗弧菌65#产生抑制作用，这说明浒苔代谢释放到水体中某种化学成分或与藻共栖的微生物对鳗弧菌生长产生了抑制。

The characteristics of nutrient removal and inhibitory effect of Ulva clathrata on Vibrio anguillarum 65

To investigate the ecological effect of macroalgae on de-eutrophication and depuration of mariculture seawater, the variation of dissolved inorganic nitrogen (DIN) and phosphate (DIP), the amount of Vibrio anguillarum, and total heterotrophic bacteria in Ulva clathrata culture, as well as on the algal surface, were investigated by artificially adding nutrients and V. anguillarum strain 65 from February to April 2006. The results indicated that U. clathrata not only had strong DIN and DIP removal capacities, but also showed a significant inhibitory effect on V. anguillarum, although not reducing the total heterotrophic bacteria. Vibrio anguillarum 65 dropped from 5 similar to 8 x 10(7) cfu mL(-1) to 10 cfu mL(-1) (clone-forming units per mL) in 10 g L-1 of fresh U. clathrata culture within 2 days; i.e., almost all of the Vibrios were efficiently eradicated from the algal culture system. Our results also showed that the inhibitory effect of U. clathrata on V. anguillarum strain 65 was both DIN- and DIP-dependent. Addition of DIN and DIP could enhance the inhibitory effects of the algae on the Vibrio, but did not reduce the total heterotrophic bacteria. Further studies showed that the culture suspension in which U. clathrata was pre-cultured for 24 h also had an inhibitory effect on V. anguillarum strain 65. Some unknown chemical substances, either released from U. clathrata or produced by the alga associated microorganisms, inhibited the proliferation of V. anguillarum 65.

Monitoring microbial populations of sulfate-reducing bacteria using an impedimetric immunosensor based on agglutination assay

An impedimetric immunosensor was fabricated for rapid and non-labeled detection of sulfate-reducing bacteria, Desulforibrio caledoiensis (SRB) by immobilizing lectin-Concanavalin A using an agglutination assay. The immobilization of lectin was conducted using amine coupling on the surface of a gold (Au) electrode assembled with 11-Mercaptounclecanoic acid. Electrochemical impedance spectroscopy (EIS) was used to verify the stepwise assembly of the sensor system. The work conditions of the impedimetric immunosensor, such as pH of the buffer solutions and the incubation time of lectin, were optimized. Faradic impedance spectra for charge transfer for the redox probe Fe(CN)(6)(3-/4-) were measured to determine SRB concentrations. The diameter of the Nyquist diagram that is equal to the charge-transfer resistance (RI) increased with increasing SRB concentration. A linear relationship between R-ct and SRB concentration was obtained in SRB concentration range of 1.8 to 1.8 x 10(7) cfu/ml. The variation of the SRB population during the growth process was also monitored using the impedimetric immunosensor. This approach has great potential for simple, low-cost. and time-saving monitoring of microbial populations. (C) 2009 Elsevier B.V. All rights reserved.

Selective and specific detection of sulfate-reducing bacteria using potentiometric stripping analysis

A fast, sensitive and reliable potentiometric stripping analysis (PSA) is described for the selective detection of the marine pathogenic sulfate-reducing bacterium (SRB). Desulforibrio caledoiensis. The chemical and electrochemical parameters that exert influence on the deposition and stripping of lead ion, such as deposition potential, deposition time and pH value were carefully studied. The concentration of SRB was determined in acetate buffer solution (pH 5.2) under the optimized condition (deposition potential of -1.3 V. deposition time of 250 s, ionic strength of 0.2 mol L-1 and oxidant mercury (II) concentration of 40 mg L-1). A linear relationship between the stripping response and the logarithm of the bacterial concentration was observed in the range of 2.3 x 10 to 2.3 x 10(7) cfu mL(-1). In addition, the potentiometric stripping technique gave a distinct response to the SRB, but had no obvious response to Escherichia coli. The measurement system has a potential for further applications and provides a facile and sample method for detection of pathogenic bacteria. (C) 2010 Elsevier B.V. All rights reserved.

Evaluation of microbial adjuncts and their effect on the ripening of cheddar cheese

A bacteriocin-producing strain of Lactobacillus paracasei DPC 4715 was used as an adjunct culture in Cheddar cheese in order to control the growth of “wild” nonstarter lactic acid bacteria. No suppression of growth of the indicator strain was observed in the experimental cheese. The bacteriocin produced by Lactobacillus paracasei DPC 4715 was sensitive to chymosin and cathepsin D and it may have been cleaved by the rennet used for the cheese manufactured or by indigenous milk proteases. A series of studies were performed using various microbial adjuncts to influence cheese ripening. Microbacterium casei DPC 5281, Corynebacterium casei DPC 5293 and Corynebacterium variabile DPC 5305 were added to the cheesemilk at level of 109 cfu/ml resulting in a final concentration of 108 cfu/g in Cheddar cheese. The strains significantly increased the level of pH 4.6-soluble nitrogen, total free amino acids after 60 and 180 d of ripening and some individual free amino acids after 180 d. Yarrowia lipolytica DPC 6266, Yarrowia lipolytica DPC 6268 and Candida intermedia DPC 6271 were used to accelerate the ripening of Cheddar cheese. Strains were grown in YG broth to a final concentration of 107 cfu/ml, microfluidized, freeze-dried and added to the curd during salting at level of 2% w/w. The yeasts positively affected the primary, secondary proteolysis and lipolysis of cheeses and had aminopeptidase, dipeptidase, esterase and 5’ phosphodiestere activities that contributed to accelerate the ripening and improve the flavor of cheese. Hafia alvei was added to Cheddar cheesemilk at levels of 107 cfu/ml and 108 cfu/ml and its contribution during ripening was evaluated. The strain significantly increased the level of pH 4.6-soluble nitrogen, total free amino-acids, and some individual free amino-acids of Cheddar cheese, whereas no differences in the urea-polyacrylamide gel electrophoresis (urea-PAGE) electrophoretograms of the cheeses were detected. Hafia alvei also significantly increased the level of some biogenic amines. A low-fat Cheddar cheese was made with Bifidobacterium animalis subsp. lactis, strain BB-12® at level of 108 cfu/ml, as a probiotic adjunct culture and Hi-Maize® 260 (resistant high amylose maize starch) at level of 2% and 4% w/v, as a prebiotic fiber which also played the role of fat replacer. Bifidobacterium BB-12 decreased by 1 log cycle after 60 d of ripening and remained steady at level of ~107 cfu/g during ripening. The Young’s modulus also increased proportionally with increasing levels of Hi-maize. Hencky strain at fracture decreased over ripening and increased with increasing in fat replacer. A cheese based medium (CBM) was developed with the purpose of mimicking the cheese environment at an early ripening stage. The strains grown in CBM showed aminopeptidase activity against Gly-, Arg-, Pro- and Phe-p-nitroanalide, whereas, when grown in MRS they were active against all the substrates tested. Both Lb. danicus strains grown in MRS and in CBM had aminotransferase activity towards aromatic amino acids (Phe and Trp) and also branched-chain amino acids (Leu and Val). Esterase activity was expressed against p-nitrophenyl-acetate (C2), pnitrophenyl- butyrate (C4) and p-nitrophenyl-palmitate (C16) and was significantly higher in CBM than in MRS.

Use of oxygen sensors for the non destructive measurement of oxygen in packaged food and beverage products and its impact on product quality and shelf life

The principal objective of this thesis was to investigate the ability of reversible optical O2 sensors to be incorporated into food/beverage packaging systems to continuously monitor O2 levels in a non-destructive manner immediately postpackaging and over time. Residual levels of O2 present in packs can negatively affect product quality and subsequently, product shelf-life, especially for O2-sensitive foods/beverages. Therefore, the ability of O2 sensors to continuously monitor O2 levels present within food/beverage packages was considered commercially relevant in terms of identifying the consequences of residual O2 on product safety and quality over time. Research commenced with the development of a novel range of O2 sensors based on phosphorescent platinum and palladium octaethylporphyrin-ketones (OEPk) in nano-porous high density polyethylene (HDPE), polypropylene (PP) polytetrafluoroethylene (PTFE) polymer supports. Sensors were calibrated over a temperature range of -10°C to +40°C and deemed suitable for food and beverage packaging applications. This sensor technology was used and demonstrated itself effective in determining failures in packaging containment. This was clearly demonstrated in the packaging of cheese string products. The sensor technology was also assessed across a wide range of packaged products; beer, ready-to-eat salad products, bread and convenience-style, muscle-based processed food products. The O2 sensor technology performed extremely well within all packaging systems. The sensor technology adequately detected O2 levels in; beer bottles prior to and following pasteurisation, modified atmosphere (MA) packs of ready-to-eat salad packs as respiration progressed during product storage and MA packs of bread and convenience-style muscle-based products as mycological growth occurred in food packs over time in the presence and absence of ethanol emitters. The use of the technology, in conjunction with standard food quality assessment techniques, showed remarkable usefulness in determining the impact of actual levels of O2 on specific quality attributes. The O2 sensing probe was modified, miniaturised and automated to screen for the determination of total aerobic viable counts (TVC) in several fish species samples. The test showed good correlation with conventional TVC test (ISO:4833:2003), analytical performance and ruggedness with respect to variation of key assay parameters (probe concentration and pipetting volume). Overall, the respirometric fish TVC test was simple to use, possessed a dynamic microbial range (104-107 cfu/g sample), had an accuracy of +/- one log(cfu/g sample) and was rapid. Its ability to assess highly perishable products such as fish for total microbial growth in <12 hr demonstrates commercial potential.

Evaluation of rhizobacterial colonisation and the ability to induce Globodera pallida hatch

Three bacterial isolates, SB13 (Acinetobacter sp.), SB14 (Arthrobacter sp.) and SB15 (Bacillus sp.), were previously isolated from the rhizosphere of sugar beet (Beta vulgaris ssp. vulgaris) plants and shown to increase hatch of potato cyst nematodes in vitro. In this study, the three isolates were assayed for rhizosphere competence. Each isolate was applied to seeds at each of four concentrations (105-108 CFU ml−1) and the inoculated seeds were planted in plastic microcosms containing coarse sand. All three isolates were shown to colonise the rhizosphere, although to differing degrees, with the higher inoculation densities providing significantly better colonisation. The isolates increased sugar beet root and shoot dry weight. Isolates SB14 and SB15 were analysed for their ability to induce in vivo hatch of Globodera pallida in non-sterile soil planted with sugar beet. After 4 and 6 weeks, both isolates had induced significantly greater percentage hatch compared to controls.

Mycobacteriosis in Chesapeake Bay Striped Bass (Morone saxatilis): The Interaction of Nutrition and Disease

Field and laboratory studies were conducted from 1998 - 2005 to examine the relationship between nutritional status and mycobacteriosis in Chesapeake Bay striped bass (Morone saxatilis). A review of DNA from archived tissue blocks indicated that the disease has been present since at least 1984. Field surveys and feeding trials were conducted from 1998-1999 to determine the nutritional condition of striped bass and the association with disease state. Proximate composition revealed elevated moisture (~ 80%) and low storage lipids (< 0.5% ww), characteristic of a poorly nourished population. These findings were not consistent with data collected in 1990-1991, or with experimentally fed fish. Mycobacteriosis explained little of the variance in chemical composition (p > 0.2); however elevated moisture and low lipid concentration were associated with fish with ulcerative lesions (p < 0.05). This suggests that age 3 and 4 striped bass were in poor nutritional health in 1998-1999, which may be independent from the disease process. Challenge studies were performed to address the hypothesis that disease progression and severity may be altered by nutritional status of the host. Intraperitoneal inoculation of 104 CFU M. marinum resulted in high mortality, elevated bacterial density, and poor granuloma formation in low ration (0.15% bw/d) groups while adequately fed fish (1% bw/d) followed a normal course of granulomatous inflammation with low mortality to a steady, equilibrium state. Further, we demonstrated that an active inflammatory state could be reactivated in fish through reductions in total diet. The energetic demand of mycobacteriosis, was insignificant in comparison to sham inoculated controls in adequately fed fish (p > 0.05). Declines in total body energy were only apparent during active, inflammatory stages of disease. Overall, these findings suggest that: 1) mycobacteriosis is not a new disease of Chesapeake Bay striped bass, 2) the disease has little energetic demand in the normal, chronic progression, and 3) poor nutritional health can greatly enhance the progression and severity, and reactivation of disease. The implications of this research are that management strategies focused on enhancing the nutritional state of striped bass could potentially alter the disease dynamics in Chesapeake Bay.

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.