Forest Sciences Commons^™

Long Oligodeoxynucleotides: Chemical Synthesis, Isolation Via Catching-By-Polymerization, Verification Via Sequencing, And Gene Expression Demonstration, Yipeng Yin, Reed Arneson, Alexander Apostle, Adikari M.D.N. Eriyagama, Komal Chillar, Emily Burke, Martina Jahfetson, Yinan Yuan, Shiyue Fang

Michigan Tech Publications, Part 2

Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex …

Regulation Of Regeneration In Arabidopsis Thaliana, Md Khairul Islam, Sai Teja Mummadi, Sanzhen Liu, Hairong Wei

Michigan Tech Publications, Part 2

We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. …

Reconstructing 42 Years (1979–2020) Of Great Lakes Surface Temperature Through A Deep Learning Approach, Miraj Kayastha, Tao Liu, Daniel Titze, Timothy C. Havens, Chenfu Huang, Pengfei Xue

Michigan Tech Publications, Part 2

Accurate estimates for the lake surface temperature (LST) of the Great Lakes are critical to understanding the regional climate. Dedicated lake models of various complexity have been used to simulate LST but they suffer from noticeable biases and can be computationally expensive. Additionally, the available historical LST datasets are limited by either short temporal coverage (<30 >years) or lower spatial resolution (0.25° × 0.25°). Therefore, in this study, we employed a deep learning model based on Long Short-Term Memory (LSTM) neural networks to produce a daily LST dataset for the Great Lakes that spans an unparalleled 42 years (1979–2020) at …

Invasive Buckthorn Mapping: A Uav-Based Approach Utilizing Machine Learning, Gis, And Remote Sensing Techniques In The Upper Peninsula Of Michigan, Vikranth Madeppa

Dissertations, Master's Theses and Master's Reports

An Invasive species is a species that is alien or non-native to the ecosystem which causes harm to economic, environmental, or human health (E.O. 13112 of Feb 3, 1999). Invasive species have posed a serious threat to ecosystems across the globe. These invasive species have impacts on the biodiversity and productivity of invaded forests. Remotely sensed data is a valuable resource for understanding and addressing issues related to invasive species. This study presents a novel approach for mapping the distribution of two invasive plant species, Common and Glossy Buckthorn, using unmanned aerial vehicles (UAVs), machine learning algorithms, geographic information systems …

Integrating Deep Learning And Hydrodynamic Modeling To Improve The Great Lakes Forecast, Pengfei Xue, Aditya Wagh, Gangfeng Ma, Yilin Wang, Yongchao Yang, Tao Liu, Chenfu Huang

Michigan Tech Publications

The Laurentian Great Lakes, one of the world’s largest surface freshwater systems, pose a modeling challenge in seasonal forecast and climate projection. While physics-based hydrodynamic modeling is a fundamental approach, improving the forecast accuracy remains critical. In recent years, machine learning (ML) has quickly emerged in geoscience applications, but its application to the Great Lakes hydrodynamic prediction is still in its early stages. This work is the first one to explore a deep learning approach to predicting spatiotemporal distributions of the lake surface temperature (LST) in the Great Lakes. Our study shows that the Long Short-Term Memory (LSTM) neural network, …

Emissions, Shawn Urbanski, Susan O'Neill, Amara L. Holder, Sarah Green, Rick L. Graw

Michigan Tech Publications

This chapter assesses the current state of the science regarding the composition, intensity, and drivers of wildland fire emissions in the USA and Canada. Globally and in the USA wildland fires are a major source of gases and aerosols which have significant air quality impacts and climate interactions. Wildland fire smoke can trigger severe pollution episodes with substantial effects on public health. Fire emissions can degrade air quality at considerable distances downwind, hampering efforts by air regulators to meet air standards. Fires are a major global source of aerosols which affect the climate system by absorbing and scattering radiation and …

Fine Scale Mapping Of Laurentian Mixed Forest Natural Habitat Communities Using Multispectral Naip And Uav Datasets Combined With Machine Learning Methods, Parth P. Bhatt

Dissertations, Master's Theses and Master's Reports

Natural habitat communities are an important element of any forest ecosystem. Mapping and monitoring Laurentian Mixed Forest natural communities using high spatial resolution imagery is vital for management and conservation purposes. This study developed integrated spatial, spectral and Machine Learning (ML) approaches for mapping complex vegetation communities. The study utilized ultra-high and high spatial resolution National Agriculture Imagery Program (NAIP) and Unmanned Aerial Vehicle (UAV) datasets, and Digital Elevation Model (DEM). Complex natural vegetation community habitats in the Laurentian Mixed Forest of the Upper Midwest. A detailed workflow is presented to effectively process UAV imageries in a dense forest environment …

Hb-Pls: A Statistical Method For Identifying Biological Process Or Pathway Regulators By Integrating Huber Loss And Berhu Penalty With Partial Least Squares Regression, Wenping Deng, Kui Zhang, Cheng He, Sanzhen Liu, Hairong Wei

Michigan Tech Publications

Gene expression data features high dimensionality, multicollinearity, and non-Gaussian distribution noise, posing hurdles for identification of true regulatory genes controlling a biological process or pathway. In this study, we integrated the Huber loss function and the Berhu penalty (HB) into partial least squares (PLS) framework to deal with the high dimension and multicollinearity property of gene expression data, and developed a new method called HB-PLS regression to model the relationships between regulatory genes and pathway genes. To solve the Huber-Berhu optimization problem, an accelerated proximal gradient descent algorithm with at least 10 times faster than the general convex optimization solver …

Regional Impacts Of Invasive Species And Climate Change On Black Ash Wetlands, Joseph Shannon

Dissertations, Master's Theses and Master's Reports

For more than a decade intensive research on the ecohydrology of black ash wetland ecosystems has been performed to understand these systems before they are drastically altered by the invasive species, emerald ash borer (EAB). In that time there has been little research aimed at the scale and persistence of the alterations. Three distinct but related research articles will be presented to demonstrate a method for moderate resolution mapping of black ash across its entire range, understand the relative impacts of EAB and climate change on probable future wetland conditions, and develop an experimental and modeling approach to quantify and …

Insights On Dissolved Organic Matter Production Revealed By Removal Of Charge-Transfer Interactions In Senescent Leaf Leachates, Karl M. Meingast, Brice K. Grunert, Sarah A. Green, Evan S. Kane, Nastaran Khademimoshgenani

Michigan Tech Publications

Dissolved organic matter (DOM) is a critical part of the global carbon cycle. Currently, it is understood that at least a portion of the chromophoric DOM (CDOM) character can be described through an electronic interaction of charge transfer (CT) complexes. While much work has been done to understand the influence of CT on soil and aquatic reference standard DOM, little is known about the influence of CT in fresh terrestrially derived DOM. In this study, leaf litter leachates from three tree species were treated (reduced) with sodium borohydride to determine the contribution of CT on a source of fresh terrestrial …

Mid-Atlantic Forest Ecosystem Vulnerability Assessment And Synthesis: A Report From The Mid-Atlantic Climate Change Response Framework Project, Patricia Leopold, Louis Iverson, Frank R. Thompson Iii, Leslie A. Brandt, Stephen D. Handler, Danielle Shannon, Matt Kelly, Et. Al.

College of Forest Resources and Environmental Science Publications

Forest ecosystems will be affected directly and indirectly by a changing climate over the 21st century. This assessment evaluates the vulnerability of 11 forest ecosystems in the Mid-Atlantic region (Pennsylvania, New Jersey, Delaware, eastern Maryland, and southern New York) under a range of future climates. We synthesized and summarized information on the contemporary landscape, provided information on past climate trends, and described a range of projected future climates. This information was used to parameterize and run multiple forest impact models, which provided a range of potential tree responses to climate. Finally, we brought these results before two multidisciplinary panels of …

Tgmi: An Efficient Algorithm For Identifying Pathway Regulators Through Evaluation Of Triple-Gene Mutual Interaction, Chathura J. Gunasekara, Kui Zhang, Wenping Deng, Laura E. Brown, Hairong Wei

Michigan Tech Publications

Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene mutual interaction (TGMI) for identifying these regulators using high-throughput gene expression data. It first calculated the regulatory interactions among triple gene blocks (two pathway genes and one transcription factor (TF)), using conditional mutual information, and then identifies significantly interacted triple genes using a newly identified novel mutual interaction measure (MIM), which was substantiated to reflect strengths of regulatory interactions within each triple gene …

Growth Performance, Organ-Level Ionic Relations And Organic Osmoregulation Of Elaeagnus Angustifolia In Response To Salt Stress, Zhengxiang Liu, Jiangfeng Zhu, Xiuyan Yang, Haiwen Wu, Qi Wei, Hairong Wei, Huaxin Zhang

Michigan Tech Publications

Elaeagnus angustifolia is one of the most extensively afforested tree species in environment-harsh regions of northern China. Despite its exceptional tolerance to saline soil, the intrinsic adaptive physiology has not been revealed. In this study, we investigated the growth, organ-level ionic relations and organic osmoregulation of the seedlings hydroponically treated with 0, 100 and 200 mM NaCl for 30 days. We found that the growth characteristics and the whole-plant dry weight were not obviously stunted, but instead, were even slightly stimulated by the treatment of 100 mM NaCl. In contrast, these traits were significantly inhibited by 200 mM NaCl treatment. …

The Effect Of Poplar Psngs1.2 Overexpression On Growth, Secondary Cell Wall, And Fiber Characteristics In Tobacco, Tingting Lu, Lulu Liu, Minjing Wei, Yingying Liu, Zianshang Qu, Chuanping Yang, Hairong Wei, Zhigang Wei

Michigan Tech Publications

The glutamine synthetase (GS1) is a key enzyme that catalyzes the reaction of glutamate and ammonia to produce glutamine in the nitrogen (N) metabolism. Previous studies on GS1s in several plant species suggest that overexpression of GS1s can enhance N utilization, accelerate plant vegetative growth, and change wood formation. In this study, we isolated a GS1 gene, termed PsnGS1.2, from Populus simonii × Populus nigra. This gene was expressed at a higher level in roots, and relatively lower but detectable levels in xylem, leaves and phloem of P. simonii × P. nigra. The protein encoded by PsnGS1.2 is …

Dynamics Of Wild Red Raspberry (Rubus Idaeus L.) And The Influence On Tree Regeneration Within Silvicultural Openings In A Northern Hardwood Stand, Matthew J. Widen

Dissertations, Master's Theses and Master's Reports

Previous studies have investigated how the abundance of raspberries (Rubus idaeus L.) impacts tree regeneration, but few have linked these impacts to location within canopy openings with a legacy tree. To fill this knowledge gap, we investigated the presence, abundance, and location of raspberries within openings containing legacy trees and the resulting impacts on tree regeneration. During the winter of 2003, 49 openings were created of three sizes: small, medium, large and 20 reference single-tree selection sites in a northern hardwood stand in Ford Forest near Alberta, Michigan. Tree regeneration and vegetative species cover were recorded in 2005 and …

The Effects Of Early Pruning On The Near-Ground Branch Density Of Four Live Fencing Species, Aric Devens

Dissertations, Master's Theses and Master's Reports

Crop losses in home gardens greatly impact the wellbeing of rural West African families. Herbivory by migratory or local livestock represents a significant source of crop loss. Live-fencing gardens with thorny hedges is a low-cost and sustainable strategy for reducing losses due to herbivory. However, guidance on the establishment of thorny hedges is inconsistent, poorly publicized, and often anecdotal. Therefore, this study evaluated the effects of three early pruning treatments on near-ground branch density of four thorny species: Vachellia nilotica, Senegalia laeta, Senegalia mellifera, and Prosopis juliflora. Physical measurements and photographic data indicated that after one growing season, V. …

Failure To Communicate: Inefficiencies In Voluntary Incentive Programs For Private Forest Owners In Michigan, Mark. D. Rouleau, Jennifer F. Lind-Riehl, Miranda N. Smith, Audrey L. Mayer

College of Forest Resources and Environmental Science Publications

Coordinating forest management across thousands of nonindustrial private forest (NIPF) owners is a difficult yet necessary task for state land management agencies. Voluntary Incentive Programs (VIPs) can coordinate the decentralized activities of these owners in return for services or financial incentives. However, many VIPs typically have low enrollment. Our study investigates the implementation of VIPs to increase forest management coordination among NIPFs in Michigan. We present findings from 20 semi-structured interviews with leaders of state and local land management organizations, and government officials at state natural resource agencies, and contrast their answers with those recorded from 37 interviews of NIPF …

Bottom-Up Ggm Algorithm For Constructing Multilayered Hierarchical Gene Regulatory Networks That Govern Biological Pathways Or Processes, Sapna Kupari, Wenping Deng, Chathura J. Gunasekara, Vincent Chiang, Huann-Sheng Chen, Hairong Wei, Et. Al.

Michigan Tech Publications

Background: Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways.

Results: A bottom-up graphic Gaussian model (GGM) algorithm was developed for constructing ML-hGRN operating above a biological pathway using small- to medium-sized microarray or RNA-seq data sets. The algorithm first placed genes of a pathway at the bottom layer and began to construct an ML-hGRN by evaluating all combined triple genes: two pathway genes and one regulatory gene. The algorithm retained all triple genes where a regulatory …

Effects Of Wildfire And Post-Fire Salvage Logging On Rill Networks And Sediment Delivery In California Forests, Will Olsen

Dissertations, Master's Theses and Master's Reports

Wildfires can increase soil erosion by orders of magnitude over rates in unburned forests and negatively impact aquatic resources. Rill erosion is a dominant erosion and sediment transport mechanism in burned forests, and hydrologically connected rills can form networks on burned hillslopes. At the swale scale (< 10,000 m²), little is known about how rill networks develop under different burn severities over time, their relationship with sediment yields, and the effect of post-fire salvage logging on rill networks and sediment yields.

The first study assessed rill networks and sediment yields in three burn severities in the inland Coast Range of …

Using An Obcd Approach And Landsat Tm Data To Detect Harvesting On Nonindustrial Private Property In Upper Michigan, Riccardo Tortini, Audrey L. Mayer, Pieralberto Maianti

College of Forest Resources and Environmental Science Publications

Forest dynamics influence climate, biodiversity, and livelihoods at multiple scales, yet current resource policy addressing these dynamics is ineffective without reliable land use land cover change data. The collective impact of harvest decisions by many small forest owners can be substantial at the landscape scale, yet monitoring harvests and regrowth in these forests is challenging. Remote sensing is an obvious route to detect and monitor small-scale land use dynamics over large areas. Using an annual series of Landsat-5 Thematic Mapper (TM) images and a GIS shapefile of property boundaries, we identified units where harvests occurred from 2005 to 2011 using …

Rapid Response Tools And Datasets For Post-Fire Modeling: Linking Earth Observations And Process-Based Hydrological Models To Support Post-Fire Remediation, Mary Ellen Miller, Michael Billmire, William J. Elliot, K. A. Endsley, P. R. Robichaud

Michigan Tech Research Institute Publications

Preparation is key to utilizing Earth Observations and process-based models to support post-wildfire mitigation. Post-fire flooding and erosion can pose a serious threat to life, property and municipal water supplies. Increased runoff and sediment delivery due to the loss of surface cover and fire-induced changes in soil properties are of great concern. Remediation plans and treatments must be developed and implemented before the first major storms in order to be effective. One of the primary sources of information for making remediation decisions is a soil burn severity map derived from Earth Observation data (typically Landsat) that reflects fire induced changes …

Using The Landsat Data Archive To Assess Long-Term Regional Forest Dynamics Assessment In Eastern Europe, 1985-2012, S. Turubanova, P. Potapov, A. Krylov, A. Tyukavina, Jessica L. Mccarty, V. C. Radeloff, M. C. Hansen

Michigan Tech Research Institute Publications

Abstract. Dramatic political and economic changes in Eastern European countries following the dissolution of the “Eastern Bloc” and the collapse of the Soviet Union greatly affected land-cover and land-use trends. In particular, changes in forest cover dynamics may be attributed to the collapse of the planned economy, agricultural land abandonment, economy liberalization, and market conditions. However, changes in forest cover are hard to quantify given inconsistent forest statistics collected by different countries over the last 30 years. The objective of our research was to consistently quantify forest cover change across Eastern Europe from 1985 until 2012 using the complete Landsat …

Understanding Farmers’ Perceptions And The Effects Of Shea Tree Vitellaria Paradoxa Distribution In Agroforestry Parklands Of The Upper West Region, Ghana, Fahimeh Baziari

Dissertations, Master's Theses and Master's Reports - Open

Agroforestry parklands represent a vast majority of the agricultural landscape under subsistent-oriented farming in semi-arid West Africa. Parklands are characterized by the growth of well- maintained trees (e.g., shea) on cultivated fields as a result of both environmental and human influences. Shea (Vitellaria paradoxa) provides a cultural and economic benefit to the local people of Ghana, especially women. Periods between traditional fallow rotation systems have reduced recently due to agricultural development and a demand for higher production. As a result, shea trees, which regenerate during fallow periods, has decreased over the landscape. The aim of this study was …

Restoration Of Headwater And Coastal Fens In The Lake Superior Basin Of Upper Michigan, James A. Bess

Dissertations, Master's Theses and Master's Reports - Open

In 2009, research projects were initiated at Michigan Technological University to develop restoration techniques for headwater fens and coastal wetlands in the southern Lake Superior Basin in Michigan’s Upper Peninsula. The primary focus of these was to quantify the efficacy of using locally collected seeds as a technique for wetland restoration. Two primary sites were selected, the Sleeper Lake Fen complex in Luce County and the Portage Waterway-Keweenaw Bay region of Lake Superior in Baraga and Houghton Counties. At the Sleeper Lake site, a combination of heavy machinery, seeding and mulch application was used to restore a 1.6 km ditch …

Biomass Burning Fuel Consumption Rates: A Field Measurement Database, T. T. Van Leeuwen, G. R. Van Der Werf, A. A. Hoffmann, R. G. Detmers, G. Rücker, Nancy H. F. French, S. Archibald, J. A. Carvalho Jr, G. D. Cook, William J. De Groot, C. Hély, Eric S. Kasischke, S. Kloster, Jessica Mccarty, M. L. Pettinari, P. Savadogo, E. C. Alvarado, L. Boschetti, S. Manuri, C. P. Meyer, F. Siegert, L. A. Trollope, W. S. W. Trollope

Michigan Tech Research Institute Publications

Landscape fires show large variability in the amount of biomass or fuel consumed per unit area burned. Fuel consumption (FC) depends on the biomass available to burn and the fraction of the biomass that is actually combusted, and can be combined with estimates of area burned to assess emissions. While burned area can be detected from space and estimates are becoming more reliable due to improved algorithms and sensors, FC is usually modeled or taken selectively from the literature. We compiled the peer-reviewed literature on FC for various biomes and fuel categories to understand FC and its variability better, and …

Remote Sensing Estimates Of Stand-Replacement Fires In Russia, 2002–2011, Alexander Krylov, Jessica L. Mccarty, Peter Potapov, Tatiana Loboda, Alexandra Tyukavina, Svetlana Turubanova, Matthew Hansen

Michigan Tech Research Institute Publications

The presented study quantifies the proportion of stand-replacement fires in Russian forests through the integrated analysis of Landsat and Moderate Resolution Imaging Spectroradiometer (MODIS) data products. We employed 30 m Landsat Enhanced Thematic Mapper Plus derived tree canopy cover and decadal (2001–2012) forest cover loss (Hansen et al 2013 High-resolution global maps of 21st-century forest cover change Science 342 850–53) to identify forest extent and disturbance. These data were overlaid with 1 km MODIS active fire (earthdata.nasa.gov/data/near-real-time-data/firms) and 500 m regional burned area data (Loboda et al 2007 Regionally adaptable dNBR-based algorithm for burned area mapping from …

Information And Entropy Theory For The Sustainability Of Coupled Human And Natural Systems, Audrey L. Mayer, Richard P. Donovan, Christopher W. Pawlowski

College of Forest Resources and Environmental Science Publications

For coupled human and natural systems (CHANS), sustainability can be defined operationally as a feasible, desirable set of flows (material, currency, information, energy, individuals, etc.) that can be maintained despite internal changes and changes in the environment. Sustainable development can be defined as the process by which CHANS can be moved toward sustainability. Specific indicators that give insight into the structure and behavior of feedbacks in CHANS are of particular interest because they would aid in the sustainable management of these systems through an understanding of the structures that govern system behavior. However, the use of specific feedbacks as monitoring …

Modeling Regional-Scale Wildland Fire Emissions With The Wildland Fire Emissions Information System, Nancy H. F. French, Donald Mckenzie, Tyler Erickson, Benjamin Koziol, Michael Billmire, K. A. Endsley, Naomi K. Yager Scheinerman, Liza K. Jenkins, Mary Ellen Miller, Roger Ottmar, Susan Prichard

Michigan Tech Research Institute Publications

As carbon modeling tools become more comprehensive, spatial data are needed to improve quantitative maps of carbon emissions from fire. The Wildland Fire Emissions Information System (WFEIS) provides mapped estimates of carbon emissions from historical forest fires in the United States through a web browser. WFEIS improves access to data and provides a consistent approach to estimating emissions at landscape, regional, and continental scales. The system taps into data and tools developed by the U.S. Forest Service to describe fuels, fuel loadings, and fuel consumption and merges information from the U.S. Geological Survey (USGS) and National Aeronautics and Space Administration …

Volume Yields Of Smallholder Eucalyptus Grandis W. Hill Ex Maiden Stands In Eastern Paraguay, Brook F. Alloway

Dissertations, Master's Theses and Master's Reports - Open

Smallholders in eastern Paraguay plant small stands of Eucalyptus grandis W. Hill ex Maiden intended for sale on the local market. Smallholders have been encouraged to plant E. grandis by local forestry extension agents who offer both forestry education and incentive programs. Smallholders who practice recommended forestry techniques geared towards growing large diameter trees of good form are financially rewarded by the local markets which desire saw log quality trees. The question was posed, are smallholders engaging in recommended silvicultural practices and producing reasonable volume yields? It was hypothesized that smallholders, having received forestry education and having financial incentives from …

Application Of An Imputation Method For Geospatial Inventory Of Forest Structural Attributes Across Multiple Spatial Scales In The Lake States, U.S.A., Ram K. Deo

Dissertations, Master's Theses and Master's Reports - Open

Credible spatial information characterizing the structure and site quality of forests is critical to sustainable forest management and planning, especially given the increasing demands and threats to forest products and services. Forest managers and planners are required to evaluate forest conditions over a broad range of scales, contingent on operational or reporting requirements. Traditionally, forest inventory estimates are generated via a design-based approach that involves generalizing sample plot measurements to characterize an unknown population across a larger area of interest. However, field plot measurements are costly and as a consequence spatial coverage is limited. Remote sensing technologies have shown remarkable …