Life Sciences Commons^™

An Intelligent System For Automated Dna Base Calling, Mohamad T. Musavi

University of Maine Office of Research Administration: Grant Reports

An investigation into improving the performance of DNA base calling algorithms was conducted. The results have shown that the preprocessing steps performed by ABI sequencer on raw data adversely affects the accuracy of DNA sequencing. This adverse effect has been responsible for relatively high error rates, between 3.5% to 6%, in both ABI and Phred sequencing software. Please note that Phred also uses the processed data generated by ABI sequencer; only their base-calling algorithm is different. To remedy this effect, we have developed and implemented a new filtering technique that preserves the initial information contained in the raw data. This …

Distribution And Impact Of The Oyster Parasite Bonamia Ostreae In Maine, And Its Detection Using Dna Probes, Ryan Carnegie

Electronic Theses and Dissertations

Health management efforts in Maine related to the flat oyster (Ostrea edulis) parasite Bonamia ostreae are limited by a lack of knowledge of the parasite’s distribution and impact in both wild and cultured populations. This information would be more readily obtainable with improved diagnostic tools. The objectives of this dissertation were to design sensitive and specific DNA probes for detection of B. ostreae; to assess the prevalence and intensity of parasite infections in wild oyster populations in Maine; and to evaluate growth and mortality of cultured oysters in the Damariscotta River, where B. ostreae is enzootic. A polymerase …

Leaf Area, Stemwood Volume Growth, And Stand Structure In A Mixed-Species, Multi-Aged Northern Conifer Forest, Laura Kenefic

Electronic Theses and Dissertations

Tree- and stand-level leaf area (LA) - stemwood volume growth relationships were explored in mixed-species, multi-aged northern conifer stands dominated by Tsuga canadensis (L.) Carr. (eastern hemlock), Abies balsameu (L.) Mill. (balsam fir), and Piceu rubens Sarg. (red spruce). A T. cunudensis LA model was developed to supplement published equations for A. bulsumeu and P. rubens. Sapwood area was an effective T. cunudensis LA surrogate, though nonsapwood-based models using stem cross-sectional area and modified live crown ratio produced results comparable to sapwood-based models. Equations for predicting tree-level stemwood volume increment (AVINC) were derived, and implied growth efficiencies (GE) were …

Creating Virtual Wood Particulate Composites, Huaijun Wang

Electronic Theses and Dissertations

Wood particulate composites are inhomogeneous, short fiber materials. The behavior of such materials depends on the properties of the constituent elements (wood particles, fibers, and adhesives) and the manner in which they are organized (the microstructure). Research on the microstructure of these composites has been carried out for several decades. However, due to the complexity of the engineered structures, most existing works are either over-simplified or lacking in general representations. While experimental approaches to improve material performance are necessary, this thesis presents another approach for better depictions of such complex systems. In this research project, digital surrogates of the composite …

Factors Influencing Net Primary Production In Red Spruce, Michael Day

Electronic Theses and Dissertations

Management of forest resources, even when practiced at the scale of ecosystems, is implicitly based on managing photosynthetic acquisition of carbon by trees. This thesis examines several aspects of carbon balance at the scale of individual trees, using red spruce (Picea rubens Sarg.) as a model species. Age-related declines in net primary productivity have been described for many species, including red spruce. A potential explanation is that ontogenetic changes in meristems lead to lower photosynthetic rates, which was confirmed here for red spruce. A grafting study used scions from juvenile, 6Oy, and 120~ trees to demonstrate that age-related morphological …

The Position Of Acoelomorph Turbellarians Among Lower Worms, Seth Tyler

University of Maine Office of Research Administration: Grant Reports

The Acoelomorpha is a group of worms of comparatively simple structure, and, accordingly, some biologists consider them to represent the most basic form of all multicellular animals. Acoelomorphs digest their food with a multinucleate mass of tissue instead of in the lumen or cavity of a gut, and their nervous system is only loosely organized into concentrations that could be compared to the brain and nerve cords of other animals. Taxonomists divide the group into 17 families, largely on the basis of the structure of the reproductive organs, but have fallen short of explaining how these families relate to each …

170 Years Of Caring: The Animal Welfare Movement In Bangor, Maine, John D. Blaisdell

Maine History

The history of the animal welfare movement in Bangor, Maine dates to the first decades of the nineteenth century: Over the course of its long history, the movement's emphasis shifted from a focus on livestock and urban workhorses in the nineteenth century to children and animals at the turn of the century and finally to companion animals, primarily cats and dogs. These shifts, the author argues, reflect economic and technological changes as well as a transformation in society's perception of animals. A Maine native, John Blaisdell, is currently working on a book exploring the history of Maine's animal welfare movement. …

Additional Evidence That Juvenile Oyster Disease Is Caused By A Member Of The Roseobacter Group And Colonization Of Nonaffected Animals By Stappia Stellulata-Like Strains, K. J. Boettcher, B. J. Barber, J. T. Singer

Biology and Ecology Faculty Scholarship

Juvenile oyster disease (JOD) causes significant annual mortalities of hatchery-produced Eastern oysters, Crassostrea virginica, cultured in the Northeast. We have reported that a novel species of the α-proteobacteria Roseobacter group (designated CVSP) was numerically dominant in JOD-affected animals sampled during the 1997 epizootic on the Damariscotta River, Maine. In this study we report the isolation of CVSP bacteria from JOD-affected oysters during three separate epizootics in 1998. These bacteria were not detected in nonaffected oysters at the enzootic site, nor in animals raised at a JOD-free site. Animals raised at the JOD enzootic site that were unaffected by JOD were …

Tb177: Evaluation Of An Experimental Filter Medium For Water Re-Use Systems, John Riley, David Cole, Robert Bayer

Technical Bulletins

This report describes the development and testing of a new material for use as a filter medium in recirculating aquaculture systems and other water quality control situations. The material consists of a combination of activated carbon and a hydrophilic urethane foam in a homogeneous matrix. Its physical properties relevant to filtration were determined. It was then tested for its ability to remove various dissolved organic compounds and inorganic nitrogenous compounds in the form of a synthetic waste-water containing ammonia and nitrite. Finally it was subjected to long-term use in the biofilter of a fish culture system. It proved to be …

Does Elevated Nitrogen And Sulfur Deposition Lead To Net Base Cation Losses In Northern New England Forest Soils?, Ivan J. Fernandez, Stephen A. Norton, Jeffrey Kahl, Lindsey E. Rustad

University of Maine Office of Research Administration: Grant Reports

The aims of this research are to continue treatment and monitoring of a paired watershed experiment at Bear Brook in northern Maine, with an emphasis on changes in soil base cations, particularly calcium. Base cation depletion is well-recognised as a potential problem in soils that have been subjected to acidic N deposition but few data exist from well-controlled, long-term experiments. The Bear Brook watershed has been periodically treated with ammonium sulfate since the fall of 1989 and is believed to be approaching N saturation. Since 1993 the relationship between base cations and strong acid anions has changed, such that labile …

Tb172: Evaluation Of Entomopathogens For Biological Control Of Insect Pests Of Lowbush (Wild) Blueberry, Francis A. Drummond, Eleanor Groden

Technical Bulletins

To maintain the economic viability of Maine’s blueberry farms, to offer alternative pest control strategies in light of the implementation of the Food Quality Protection Act of 1996, and to reduce the human health and environmental risks associated with pest management, these researchers have been researching biological control tactics. This technical bulletin outlines protocols and experimental design necessary for evaluation of entomopathogens targeted against the significant direct and indirect pests associated with lowbush blueberry.

Mp742: 4th Annual Munsungan Conference Proceedings: Forest Health, William D. Ostrofsky, T. J. Dragon

Miscellaneous Publications

These conference proceedings provide viewpoints on a variety of important and defining aspects of forest health. Forest managers, landowners, and scientists have long appreciated the direct effects that insects, diseases and damaging weather can have on forests. Over the past fifty years the Maine landscape has been affected by numerous outbreaks of defoliators such as the gypsy moth and the spruce budworm, by white pine blister rust and beech bark disease, and most recently by severe ice storm damage, along with countless other pests and catastrophic storms. During the past several years, the public also has become increasingly aware of …

Mr415: Why Not Tame The Wild Blueberry, Walter Litten, John M. Smagula

Miscellaneous Reports

A discussion of two studies of different methods of propagating lowbush blueberry plants. These methods could be used for introducing blueberry plants into existing fields to improve field cover, or to start a blueberry field from scratch.

Mr416: An Evaluation Of Turfgrass Species And Varieties: Perennial Ryegrass, Alan R. Langille, Annamarie Pennucci

Miscellaneous Reports

The ryegrasses include those popular and extensively used turfgrasses noted for their rapid germination and subsequent swift development into a suitable turf. These grasses are broadly adapted to cool temperate climates and find use in a wide array of habitats: from the seashore to mountain slopes, and in nearly all soil conditions. This report presents the results of a trial of 97 perennial ryegrass varieties at the University of Maine.

An Investigation Of The Evolution Of Autotrophic Endosymbioses In Bivalves By Comparative Molecular Phylogenetic Analysis Of Host And Symbiont Rrna Sequences, Daniel L. Distel

University of Maine Office of Research Administration: Grant Reports

Symbiotic associations between animals and bacteria are extremely diverse and commonplace in nature. In fact, it is difficult to find examples of animal species whose existence is not profoundly influenced by symbiotic associations with bacteria. For example, mitochondria (the structures within human cells that generate the energy for metabolic processes) are thought to have arisen from ancient bacteria that long ago formed a symbiotic association with the ancestor of all living animals. The support provided for this project will allow investigation of a type of symbiosis commonly found in clams and worms from deep-sea hydrothermal vents (marine hot springs) that …

1999-2000 Piscataquis County Cooperative Extension Annual Report, Donna Coffin

Maine County Extension Associations

1999-2000 annual report of activities for the Piscataquis County Cooperative Extension Office.

Wild Blueberries 1999 Csrees Progress Reports, Alfred A. Bushway, Bodhan Slabyj, Russell Hazen, Darrell W. Donahue, Frank A. Drummond, Judith A. Collins, Rodney J. Bushway, Brian Perkins, Seanna L. Annis, Connie S. Stubbs, John M. Smagula, Walter Litten, Richard Dyer, Karen Loennecker, David E. Yarborough, Timothy M. Hess, David Lambert, John Jemison

Wild Blueberry Research Reports

The 1999 edition of the Wild Blueberries CSREES Progress Reports was prepared for the Maine Blueberry Commission and the University of Maine Blueberry Advisory Committee by researchers at the University of Maine, Orono. Projects in this report include:

1. Effects of QF Processing on Microbiological Quality of Maine Wild Blueberries

2. Separation of Maggot-Infested Blueberries in the IQF Processing Line

3. Determination of Pesticide Residue Levels in Fresh and Processed Wild Blueberries

4. Control Tactics for Blueberry Pest Insects

5. IPM Strategies

6. Biology and Ecology of Blueberry Pest Insects

7. Survey of Stem Blight and Leaf Spot Diseases in …

Evaluating The Durability Of Wood/Frp Bonds Through Chemical Kinetics Using A Range Of Mechanical Test Methods, Jonathan Philip Alexander

Electronic Theses and Dissertations

Hybrid composites of wood and fiber reinforced polymers (FRP) exhibit a flexibility of design properties through choices in fiber type, amount, orientation and resin type. With this flexibility comes the need to measure the durability of the composite material system, especially the bond between these two materials due to their markedly different responses to moisture. This study is two-fold; the first section examines methods for the mechanical testing and durability of wood/FRP laminations. Six mechanical tests were evaluated and a modified block shear method was identified as the most suitable due to its ability to provide representative results independent of …

Maine Forests: A Century Of Change, 1900-2000…And Elements Of Policy Change For A New Century, Lloyd Irland

Maine Policy Review

At the close of the 19th century, the state’s forest area was at an all time low; land ownership was changing rapidly with the emergence of new paper companies; a growing number of wildlife species were threatened; and widespread unease over the future of Maine’s forests was evident. Today a similar unease is evident. Many believe the state’s spruce-fir forest is being overcut; land ownership is changing rapidly; fear exists that the sustainability of Maine’s forests; and wildlife populations have been severely compromised. Given the similarity in circumstance, one might ask whether there has been any change over the past …

Fish Or Foul? Will Aquaculture Carve Out A Niche In The Gulf Of Maine?, Philip W. Conkling

Maine Policy Review

Despite early promise and an optimal environment, aquaculture has grown more slowly in Maine than it has in other parts of the United States and the world. As Philip Conkling explains, this is due to market forces, scientific and technical issues, cultural opposition, and, more recently, the threat of an endangered species listing for Atlantic salmon. While near-term prospects for significant expansion of the industry appear bleak, Conkling suggests that a fresh generation of pioneers may be able to carve out a new niche, but only by conducting “old fashioned” research and development—on the job, on the water, and in …

Evolution Of The Maine Lobster Co-Management Law, James Acheson, Terry Stockwell, James A. Wilson

Maine Policy Review

In fisheries management circles, there is growing realization that traditional ways of managing marine resources are not working and that new approaches to management need to be tried. One of the most promising of these new approaches is co-management, where authority for managing fish stocks is shared between the industry and government agencies. This paper discusses the implementation of the new co-management system, which was initiated in the Maine lobster industry in 1995. The law has clearly been successful; it has been framed in a way to allow lobster fishermen to be able to generate rules to constrain their own …

Developing A Cooperative Research Agenda For Maine’S Commercial Fisheries, Robin Alden, Linda Mercer

Maine Policy Review

This past year the Maine Department of Marine Resources sponsored a unique series of meetings involving fishermen, academic and government scientists, and fishery managers. The goal was to define a shared research agenda for Maine’s marine fisheries. Robin Alden and Linda Mercer summarize the results of these meetings. In doing so they address the question: “What do we need to know to properly manage Maine's major marine resources?” Alden and Mercer also conclude that the collaborative process these meetings helped to establish is one of the keys to the successful management of Maine’s marine resources.

Best Practices In Endangered Species Recovery Planning: Lessons For The Conservation Of Maine’S Atlantic Salmon, Raymond J. O’Connor, Ray B. Owen, Judith Rhymer

Maine Policy Review

The call for federal listing of Atlantic salmon as endangered implies that such action will result in a recovery plan for the species that is superior to Maine ’s Atlantic Salmon Conservation Plan. In this article the authors compare the Maine plan against the findings of a recent review of Endangered Species Act recovery plans. The review, conducted by the Society for Conservation Biology in collaboration with the U.S. Fish and Wildlife Service, assessed the quality of a national sample of Endangered Species Act recovery plans with the intention of identifying “best practice.” By comparing the Maine plan to the …

Weed Population Dynamics In Potato Cropping Systems As Affected By Rotation Crop, Cultivation, And Primary Tillage, Silke Ullrich

Electronic Theses and Dissertations

Reduction of dependence on herbicides in potato production is important to limit environmental contamination and reduce production costs. An experiment was conducted from 1992 to 1997 in northern Maine to examine the effects of two rotation crops (a green-manure mixture of oat, pea and hairy vetch vs. barley) and two tillage practices (chisel vs. moldboard) on weed population dynamics in two-year potato rotations without the use of herbicides. Chenopodium album, Gnaphalium uliainosum, and a complex of cruciferous weeds (Brassica rapa, Brassica kaber, and Raphanus raphanistrum) were dominant. Oat-pea-vetch was more weed-suppressive than barley, however, crucifer density increased in both rotations. …