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Genomic Reconstruction Of The Tree Of Life, Sambriddhi Mainali

Electronic Theses and Dissertations Archive

A new methodology is presented for molecular phylogenetic analysis addressing a fundamental problem in biology, name the reconstruction of the Tree of Life (TOL). Here, phylogenies are based on patterns of hybridization similarity in their DNA. Furthermore, phylogenies are based on a set of universal biomarkers (so-called nxh chips) chosen a priori, independently of the target group of organisms. Therefore, this methodology enables analyses of groups with biologically distant organisms, hence could be scaled to obtain a universal tree of life. Unlike conventional molecular methods, it produces a hypothesis in a single run, without optimizing across numerous hypotheses for consensus. …

Fiberblender: A Realistic Computer Model Of Nerve Bundles For Simulating And Validating The Acquisition Of Diffusion Tensor Imaging, Teddy Salan

Electronic Theses and Dissertations Archive

Diffusion Tensor Imaging (DTI) is a powerful medical imaging technique that provides a unique method to investigate the structure and connectivity of neural pathways. DTI is a special magnetic resonance imaging (MRI) modality that combines the principles of magnetic resonance with molecular diffusion to trace the motion of water molecules. In the central nervous system, where nerve fibers are packed in highly-directional bundles, these molecules diffuse along the orientation of the fibers. Hence, characterizing the motion of water with DTI delivers a non-invasive in vivo technique to capture the connectivity of nerves themselves. Despite its promises and successful clinical applications …

Reducing Biomass Recalcitrance By Heterologous Expression Of A Bacterial Peroxidase In Tobacco (Nicotiana Benthamiana), Ayalew Ligaba-Osena, Bertrand Hankoua, Kay Dimarco, Robert Pace, Mark Crocker, Jesse Mcatee, Nivedita Nagachar, Ming Tien, Tom L. Richard

Center for Applied Energy Research Faculty and Staff Publications

Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and …

Development And Testing Of An Agricultural Nozzle Clog Detection Device Prototype, Chin Nee Vong

Student Theses and Dissertations

Nozzle clogging during spray application results in poor weed management and increased cost in re-spraying. A device that can detect nozzle clogging during the spraying operation is necessary. A novel method and device for detecting clogged nozzles that is externally attachable to each nozzle on the sprayer’s boom has been developed in the Precision Application Technology Lab at Arkansas State University. The study’s objectives include developing prototypes of this device and comparing the spray droplet size and spray pattern in controlled condition and spray coverage in field condition with and without using the device. The research demonstrated that this new …

Strategic Leadership Newsletter: Volume 3, Number 4, Larry M. Starr Phd

Leadership Doctorates Newsletter (Formerly Strategic Leadership Newsletter)

Jefferson Strategic Leadership Newsletter reports information relevant to the Jefferson (Philadelphia University + Thomas Jefferson University) Doctor of Management Program in Strategic Leadership (DSL) and its community including personal and professional events and accomplishments, new practices, research, opportunities, and suggestions. You are encouraged to forward the Newsletter to friends and colleagues to expand awareness and to brand yourself as a community member. You are also invited to recommend people or organizations to be added to the mailing list. Contact Jefferson Strategic Leadership Newsletter by emailing [email protected].

General Engineers: The Medical Field Is An Option, Karoline Kouk

University of Mississippi News

Problem-solving skills learned in engineering are valuable in medicine

Comparative Analysis Of Double-Stranded Rna Degradation And Processing In Insects, Indrakant K. Singh, Satnam Singh, Kanakachari Mogilicherla, Jayendra Nath Shukla, Subba R. Palli

Entomology Faculty Publications

RNA interference (RNAi) based methods are being developed for pest management. A few products for control of coleopteran pests are expected to be commercialized soon. However, variability in RNAi efficiency among insects is preventing the widespread use of this technology. In this study, we conducted research to identify reasons for variability in RNAi efficiency among thirty-seven (37) insects belonging to five orders. Studies on double-stranded RNA (dsRNA) degradation by dsRNases and processing of labeled dsRNA to siRNA showed that both dsRNA degradation and processing are variable among insects belonging to different orders as well as among different insect species within …

Investigation Of The Effectiveness Of N, N-Dimethylformamide As A Solvent For Cdte Electrodeposition, Joshua Aaron Vangilder

Student Theses and Dissertations

The goal of this dissertation project was to investigate the viability of N, N-dimethylformamide (DMF) as a solvent for CdTe electrodeposition. The Taguchi Method was used to design a minimal set of experiments to determine this. The factors chosen were deposition voltage, solution composition, stir rate, and temperature. There were a total of nine experiments and 18 samples produced (2 per experiment). Optical absorbance data was collected for each film to approximate the bandgap of the material. This data was used to determine the optimal set of conditions and the relative significance of each factor to one another. It was …

Methylglyoxal Requires Ac1 And Trpa1 To Produce Pain And Spinal Neuron Activation, Ryan B. Griggs, Don E. Laird, Renee R. Donahue, Weisi Fu, Bradley K. Taylor

Physiology Faculty Publications

Methylglyoxal (MG) is a metabolite of glucose that may contribute to peripheral neuropathy and pain in diabetic patients. MG increases intracellular calcium in sensory neurons and produces behavioral nociception via the cation channel transient receptor potential ankyrin 1 (TRPA1). However, rigorous characterization of an animal model of methylglyoxal-evoked pain is needed, including testing whether methylglyoxal promotes negative pain affect. Furthermore, it remains unknown whether methylglyoxal is sufficient to activate neurons in the spinal cord dorsal horn, whether this requires TRPA1, and if the calcium-sensitive adenylyl cyclase 1 isoform (AC1) contributes to MG-evoked pain. We administered intraplantar methylglyoxal and then evaluated …

Modeling And Implementation Of Hfo2-Based Ferroelectric Tunnel Junctions, Spencer Allen Pringle

Theses

HfO2-based ferroelectric tunnel junctions (FTJs) represent a unique opportunity as both a next-generation digital non-volatile memory and as synapse devices in braininspired logic systems, owing to their higher reliability compared to filamentary resistive random-access memory (ReRAM) and higher speed and lower power consumption compared to competing devices, including phase-change memory (PCM) and state-of-the-art FTJ. Ferroelectrics are often easier to deposit and have simpler material structure than films for magnetic tunnel junctions (MTJs). Ferroelectric HfO2 also enables complementary metal-oxide-semiconductor (CMOS) compatibility, since lead zirconate titanate (PZT) and BaTiO3-based FTJs often are not.

No other groups have yet demonstrated a HfO2-based FTJ …

The Anchor, Volume 131.12: December 6, 2017, Hope College

The Anchor: 2017

The Anchor began in 1887 and was first issued weekly in 1914. Covering national and campus news alike, Hope College’s student-run newspaper has grown over the years to encompass over two-dozen editors, reporters, and staff. For much of The Anchor's history, the latest issue was distributed across campus each Wednesday throughout the academic school year (with few exceptions). In recent years The Anchor moved to monthly print issues and a more frequently updated website. The Anchor is now published in print twice per academic semester. Occasionally, the volume and/or issue numbering is irregular.

Peran Konservasi Tanah Terhadap Cadangan Karbon Tanah, Bahan Organik, Dan Pertumbuhan Kelapa Sawit (Elaeis Guineensis Jacq.), Yenni Asbur, Mira Ariyanti

Jurnal Kultivasi

Penerapan konservasi tanah di perkebunan kelapa sawit dapat dilakukan secara vegetatif dan mekanik. Secara vegetatif dengan memanfaatkan tanaman yang banyak tumbuh di bawah tegakan kelapa sawit seperti Asystasia gangetica dan Nephrolepis biserrata sebagai tanaman penutup tanah, sedangkan secara mekanik dengan memotong panjang lereng melalui pembuatan teras gulud. Penelitian ini bertujuan mengetahui peran konservasi tanah terhadap cadangan karbon tanah, bahan organik, dan pertumbuhan kelapa sawit. Penelitian dilaksanakan dari Agustus 2014-April 2015 di perkebunan kelapa sawit (tahun tanam 2005) PTPN VII, Lampung Selatan. Penelitian menggunakan rancangan tersarang faktorial dengan enam ulangan tersarang di dalam perlakuan. Perlakuan terdiri dari teras gulud (tanpa teras …

A Teachable Unit On Soft Corals With Instructional Method Variances, Emily Breech

Honors Projects

The soft coral Sinularia flexibilis contains an aqueous alcohol extract that has shown antineoplastic activity against lymphocytic leukemia (Weinheimer and Matson, 1977). It also has other biological properties that work as antimicrobials, anti-inflammatory agents, and cytotoxicity activities (Kamel and Slattery, 2005). There is much research on the effects of flow rate on growth and morphology (Khalesi, Beeftink, & Wijffels, 2007) and the effects of light-dependency on growth rate (Khalesi, Beeftink, & Wijffels, 2009). The purpose of this student project was to further research on S. flexibilis, as well as incorporate that research into evaluating the effects of lecture-based teaching …

A Novel Mutation In St14 At A Functionally Significant Amino Acid Residue Expands The Spectrum Of Ichthyosis-Hypotrichosis Syndrome., Leila Youssefian, Andrew Touati, Amir Hossein Saeidian, Omid Zargari, Sirous Zeinali, Hassan Vahidnezhad, Jouni Uitto

Department of Dermatology and Cutaneous Biology Faculty Papers

BACKGROUND: Mutations in the ST14 gene, encoding the serine protease matriptase, have been associated with ichthyosis-hypotrichosis syndrome (IHS), a Mendelian disorder with skin and hair manifestations which include, in addition to ichthyosis and hypotrichosis, hypohidrosis and follicular atrophoderma. However, the understanding of the specific consequences of mutations in ST14 on the development of this syndrome is incomplete.

RESULTS: Using a targeted next-generation sequencing array of 38 ichthyosis-associated genes on a large cohort of 180 ichthyosis patients from a primarily consanguineous background, a previously unreported homozygous p.Asp482Asn mutation in ST14 was identified in a patient with IHS. This mutation affects an …

The Pul37 Tegument Protein Guides Alphaherpesvirus Retrograde Axonal Transport To Promote Neuroinvasion, Alexsia L. Richards, Patricia J. Sollars, Jared D. Pitts, Austin M. Stults, Ekaterina E. Heldwein, Gary E. Pickard, Gregory A. Smith

School of Veterinary and Biomedical Sciences: Faculty Publications

A hallmark property of the neurotropic alpha-herpesvirinae is the dissemination of infection to sensory and autonomic ganglia of the peripheral nervous system following an initial exposure at mucosal surfaces. The peripheral ganglia serve as the latent virus reservoir and the source of recurrent infections such as cold sores (herpes simplex virus type I) and shingles (varicella zoster virus). However, the means by which these viruses routinely invade the nervous system is not fully understood. We report that an internal virion component, the pUL37 tegument protein, has a surface region that is an essential neuroinvasion effector. Mutation of this region rendered …

Using Milk Urea Nitrogen To Calculate Urine And Urinary Nitrogen Output, Peter S. Erickson

Faculty Publications

No abstract provided.

Validation Of Minimally-Invasive Sample Collection Methods For Measurement Of Telomere Length, Stephanie A. Stout, Jue Lin, Natalie Hernandez, Elysia Poggi Davis, Elizabeth Blackburn, Judith E. Carroll, Laura M. Glynn

Psychology: Faculty Scholarship

Objective: The discovery of telomere length (TL) as a biomarker of cellular aging and correlate of age-related disease has generated a new field of research in the biology of healthy aging. Although the most common method of sample collection for TL is venous blood draw, less-invasive DNA collection methods are becoming more widely used. However, how TL relates across tissues derived from these sample collection methods is poorly understood. The current study is the first to characterize the associations in TL across three sample collection methods: venous whole blood, finger prick dried blood spot and saliva.

Methods: TL …

Validation Of Minimally-Invasive Sample Collection Methods For Measurement Of Telomere Length, Stephanie A. Stout, Jue Lin, Natalie Hernandez, Elyssia Poggi Davis, Judith E. Carroll, Laura M. Glynn

Psychology Faculty Articles and Research

Objective: The discovery of telomere length (TL) as a biomarker of cellular aging and correlate of age-related disease has generated a new field of research in the biology of healthy aging. Although the most common method of sample collection for TL is venous blood draw, less-invasive DNA collection methods are becoming more widely used. However, how TL relates across tissues derived from these sample collection methods is poorly understood. The current study is the first to characterize the associations in TL across three sample collection methods: venous whole blood, finger prick dried blood spot and saliva.

Methods: TL …

In Silico Study Of Newly Synthesized Opioid Analgesics Bound To Three Opioid Receptors, Abdullah Allaoa, Mai Zahran

Publications and Research

Opioids are the most widely used drugs for the treatment of moderate to severe, chronic pain. They achieve antinociception by activation of mu (MOR-1), kappa (KOR-1), and delta (DOR-1) opioid receptors. Natural products found in kratom plant, Mitragyna speciosa, represent diverse chemical groups with opioid activity, providing opportunities to better understand opioid pharmacology. Pharmacology studies show that Mitragynine pseudoindoxyl is a mu agonist/delta antagonist opioid with a signaling bias for G-protein-mediated signaling pathways in vitro and which produced potent antinociception in vivo. Respiratory depression assays along with other behavioral testing also showed that some of the major problems …

Developmental Nonlinearity Drives Phenotypic Robustness, Rebecca M. Green, Jennifer L. Fish, Nathan M. Young, Francis J. Smith, Benjamin Roberts, Katie Dolan, Irene Choi, Courtney L. Leach, Paul Gordon, James M. Cheverud, Charles C. Roseman, Trevor J. Williams, Ralph S. Marcucio, Benedikt Hallgrímsson

Biology: Faculty Publications and Other Works

Robustness to perturbation is a fundamental feature of complex organisms. Mutations are the raw material for evolution, yet robustness to their effects is required for species survival. The mechanisms that produce robustness are poorly understood. Nonlinearities are a ubiquitous feature of development that may link variation in development to phenotypic robustness. Here, we manipulate the gene dosage of a signaling molecule, Fgf8, a critical regulator of vertebrate development. We demonstrate that variation in Fgf8 expression has a nonlinear relationship to phenotypic variation, predicting levels of robustness among genotypes. Differences in robustness are not due to gene expression variance or …

A Redescription Of The Ichnospecies Koreanaornis Anhuiensis (Aves) From The Lower Cretaceous Qiuzhuang Formation At Mingguang City, Anhui Province, China, Li-Da Xing, Yuan-Chao Hu, Jian-Dong Huang, Qing He, Martin G. Lockley, Michael E. Burns, Jun Fang

Research, Publications & Creative Work

The Cretaceous bird trackway originally labeled Aquatilavipes anhuiensis, in 1994, had previously been examined, photographed and replicated, but never described or illustrated in detail. However, it has been part of a widening discussion about the distribution of Aquatilavipes and Koreanaornis in China (and Korea). Here we illustrate and formally describe the holotype in detail and assign it to Koreanaornis (Koreanaornis anhuiensis) as informally proposed by previous authors. We also demonstrate that most authenticated reports of Koreanaornis, including the Anhui occurrence, are from the Lower Cretaceous, not from the Upper Cretaceous as previously reported.

The Effect Of Drought On Phytochemical Active Compounds Content In Chamomile And Yarrow, H Rihan, B Mahmood, M Foulkes, S Burchett

School of Biological and Marine Sciences

The effect of drought stress conditions on the phytochemical compounds content of German chamomile (Matricaia chamomilla L.), common yarrow and summer berries yarrow (Achillea millefolium L.) was investigated. Treatments contained drought stress 70% field capacity (FC) pots and control (well-watered 100% FC) pots under controlled glasshouse conditions. Freeze dried and ground leaves were extracted at room temperature using Shaking extraction with methanol (99.9%) as an efficient solvent in order to determine the phytochemical compositions of phenols and flavonoids from dried chamomile and yarrow leaves. Samples were then analysed using High performance liquid chromatography with ultra-violet detection (HPLC-UV). Five times sample …

Failing Food Supply: Permaculture's Potential, John Faltin

Department of Environmental Studies: Undergraduate Student Theses

Conventional agriculture is the currently leading production method to grow crops in the western hemisphere. Long-term sustainability of the system and all the components is secondary to producing high yields each growing season, which leads to issues such as erosion and reduced soil quality. Other agricultural production methods such as permaculture aim to build soil and improve quality every growing season. This experiment intends to look at the potential of permaculture to improve soil quality on small-scales at the end of each growing season. The parameters to gauge success are a larger concentration of macronutrients at the end of the …

Prep-Hplc Method Development To Isolate Potentially-Carcinogenic, Arginine-Based Heterocyclic Amines, Victoria S. Kim

Honors Theses

Heterocyclic amines (HCAs) are carcinogenic molecules generated from the reaction of creatin(in)e and amino acids at high cooking temperatures in meat. Previous research has shown that replacing creatine with arginine leads to new, uncharacterized HCA molecules. This research entails implementing and optimizing the preparative HPLC analysis of extracts from multiple burnings of arginine with phenylalanine. Isolated fractions from the prep-HPLC analysis were further analyzed using the Ames test to identify mutagenic compounds. Prep-HPLC provides quality control to the burning process along with isolation of larger quantities of materials for further characterization and molecular structure identification.

Helping Children Understand: Using Picture Books To Age – Appropriately Explain Dance-Movement Therapy And Childhood Cancer, Megan Schaefer

Honors Theses

Cancer is the leading cause of childhood death by disease, and there are many different therapies available to patients. One of the most promising forms of therapy is Dance/Movement Therapy (DMT). DMT is an engaging and creative form of rehabilitation, and focuses on the interaction between the body and mind. With this exercise, patients are able to express their emotional processes through physical movement, allowing for an alternate form of communication.

The way that children engage in DMT is highly influenced by their age and developmental stage. When children are presented with a new task, it may be necessary for …

Pembentukan Ubi Mikro Kentang (Solanum Tuberosum L.) Pada Berbagai Komposisi Media In Vitro, Inneke Amalia, Anne Nuraini, Sumadi, Syariful Mubarok, Erni Suminar

Jurnal Kultivasi

Permasalahan umum terkait pada produksi kentang adalah penggunaan benih sumber yang kurang bermutu dan mengalami kemunduran benih. Penelitian bertujuan untuk menentukan zat penghambat tumbuh coumarin, jasmonic acid dan paklobutrazol yang tepat untuk pertumbuhan stek dan pembentukan ubi mikro kentang secara in vitrosehingga dapat digunakan untuk penyediaan bibit berkualitas. Percobaan dilaksanakan di Laboratorium Kultur Jaringan Teknologi Benih Fakultas Pertanian Universitas Padjadjaran Jatinangor, Sumedang, pada bulan Oktober 2015 sampai Mei 2016. Metode percobaan yang digunakan adalah Rancangan Acak Lengkap (RAL) yang merupakan kombinasi dari media, retardan coumarin (105 mg L-1 dan 120 mg L-1), paklobutrazol (0.4 mg L-1 dan 1 mg L-1) …

Pertumbuhan Dan Produksi Pucuk Kolesom Pada Intensitas Cahaya Rendah, Rina Ekawati

Jurnal Kultivasi

Intensitas cahaya rendah merupakan salah satu faktor eksternal lingkungan yang dapat mempengaruhi pertumbuhan suatu tanaman. Intensitas cahaya yang optimal dapat meningkatkan pertumbuhan tanaman. Kolesom merupakan salah satu jenis sayuran fungsional yang dapat digunakan sebagai tanaman obat. Penelitian ini bertujuan untuk mempelajari pengaruh intensitas cahaya rendah terhadap pertumbuhan dan hasil pucuk kolesom. Percobaan ini dilakukan di Politeknik Lembaga Pendidikan Perkebunan (LPP) Yogyakarta, dari bulan Maret hingga September 2016. Penelitian ini menggunakan rancangan acak kelompok faktor tunggal dengan 2 taraf perlakuan, yaitu tanpa naungan (N0) dan naungan (N1). Setiap perlakuan diulang tiga kali sehingga terdapat 6 satuan percobaan. Hasil percobaan menunjuk-kan bahwa …

Respon Pertumbuhan Bibit Nilam Aceh (Pogostemon Cablin Benth.) Klon Sidikalang Pada Media Tanam Subsoil Dengan Pemberian Pati Beras Dan Pupuk Hayati, Mira Ariyanti, Cucu Suherman, Intan Ratna Dewi Anjarsari, Dewi Santika

Jurnal Kultivasi

Media tanam berupa topsoil masih menjadi andalan untuk mendukung pertumbuhan tanaman nilam karena kandungan mineral dan bahan organiknya yang tinggi. Seiring dengan pemanfaatannya, ketersediaan topsoil semakin berkurang dan dirasa perlu untuk mencari alternatif lain yaitu dengan memanfaatkan subsoil. Peningkatan unsur hara dalam subsoil dilakukan dengan cara pemberian pupuk organik berupa pati beras dan pupuk hayati. Percobaan dilakukan di Kebun Percobaan Fakultas Pertanian Universitas Padjadjaran Jatinangor pada Juni 2011- September 2011. Penelitian menggunakan rancangan acak kelompok terdiri dari 11 kombinasi perlakuan diulang tiga kali. Perlakuan percobaan meliputi top soil, sub soil + pupuk anorganik N 1.75 g, sub soil + 25 …

The Antelope, University Of Nebraska At Kearney

The Antelope

No abstract provided.

Seafarer Citizen Scientist Ocean Transparency Data As A Resource For Phytoplankton And Climate Research, Sd Seafarers, S Lavender, G Beaugrand, N Outram, Et Al

School of Engineering, Computing and Mathematics

The oceans' phytoplankton that underpin the marine food chain appear to be changing in abundance due to global climate change. Here, we compare the first four years of data from a citizen science ocean transparency study, conducted by seafarers using home-made Secchi Disks and a free Smartphone application called Secchi, with contemporaneous satellite ocean colour measurements. Our results show seafarers collect useful Secchi Disk measurements of ocean transparency that could help future assessments of climate-induced changes in the phytoplankton when used to extend historical Secchi Disk data.