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Identification And Cloning Of Putative Serine Protease Inhibitor (Serpin) Genes In Rice (Oryza Sativa) And A Preliminary Approach To Generate Rnai Using The Cloned Sequences, Santanu De Ph.D. 2019 Nova Southeastern University

Identification And Cloning Of Putative Serine Protease Inhibitor (Serpin) Genes In Rice (Oryza Sativa) And A Preliminary Approach To Generate Rnai Using The Cloned Sequences, Santanu De Ph.D.

Santanu De

Programmed Cell Death (PCD) is an important mechanism of plant immune response against diseases. Serine protease inhibitors (‘serpins’) are a conserved superfamily of proteins that inhibit serine protease targets and prevent programmed cell death (PCD) in plants, in absence of pathogen infection. In this project, putative serpin genes in rice (Oryza sativa) which are homologous to necrotic/‘Nec’ serpin genes in Drosophila are identified by bioinformatic analyses. This is followed by cloning of specific exon sequences of the rice serpin genes identified. Finally, one of the cloned sequences is utilized in a series of steps to produce interfering RNA (RNAi ...


Mechanisms Of Methane Transport Through Populus Trichocarpa, Ellynne Marie Kutschera, M. A. K. Khalil, Andrew Rice, Todd Rosenstiel 2019 Portland State University

Mechanisms Of Methane Transport Through Populus Trichocarpa, Ellynne Marie Kutschera, M. A. K. Khalil, Andrew Rice, Todd Rosenstiel

Todd N. Rosenstiel

Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global CH4 emission and the mechanisms of tree transport are relatively unknown. CH4 emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to CH4 enriched water and canopy emissions of CH4 were measured. The average flux for 34 trials (at temperatures ranging from 17 to 25 °C) was 2.8 ± 2 ...


Diversity And Abundance Of Soil Microbes Differ Along A Forest-Pasture Transect, Hannah Suli, Ashley Schumann, Cleo Bickley, Jasmine Rodriguez 2019 Humboldt State University

Diversity And Abundance Of Soil Microbes Differ Along A Forest-Pasture Transect, Hannah Suli, Ashley Schumann, Cleo Bickley, Jasmine Rodriguez

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Humboldt State University

No abstract provided.


Responses Of Bouteloua Eriopoda And Soil Stability To Precipitation Extremes In Chihuahuan Desert Grassland, Laura Kay Sadorf 2019 Humboldt State University

Responses Of Bouteloua Eriopoda And Soil Stability To Precipitation Extremes In Chihuahuan Desert Grassland, Laura Kay Sadorf

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Humboldt State University

No abstract provided.


Evaluating The Effect Of Time Of Day On Singing Behavior In Anna’S Hummingbirds, Adrian D. Macedo, Maxine R. Mota 2019 Humboldt State University

Evaluating The Effect Of Time Of Day On Singing Behavior In Anna’S Hummingbirds, Adrian D. Macedo, Maxine R. Mota

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Humboldt State University

No abstract provided.


Identification And Cloning Of Putative Serine Protease Inhibitor (Serpin) Genes In Rice (Oryza Sativa) And A Preliminary Approach To Generate Rnai Using The Cloned Sequences, Santanu De 2019 Nova Southeastern University

Identification And Cloning Of Putative Serine Protease Inhibitor (Serpin) Genes In Rice (Oryza Sativa) And A Preliminary Approach To Generate Rnai Using The Cloned Sequences, Santanu De

Biology Faculty Articles

Programmed Cell Death (PCD) is an important mechanism of plant immune response against diseases. Serine protease inhibitors (‘serpins’) are a conserved superfamily of proteins that inhibit serine protease targets and prevent programmed cell death (PCD) in plants, in absence of pathogen infection. In this project, putative serpin genes in rice (Oryza sativa) which are homologous to necrotic/‘Nec’ serpin genes in Drosophila are identified by bioinformatic analyses. This is followed by cloning of specific exon sequences of the rice serpin genes identified. Finally, one of the cloned sequences is utilized in a series of steps to produce interfering RNA (RNAi ...


Identification Of Bacterial Isolates Originating From The Human Hand, Leisa M. Rauch, Annette M. Golonka, Eran S. Kilpatrick 2019 University of South Carolina Columbia

Identification Of Bacterial Isolates Originating From The Human Hand, Leisa M. Rauch, Annette M. Golonka, Eran S. Kilpatrick

Journal of the South Carolina Academy of Science

The human body provides habitat for a diversity of bacterial species that are part of the normal human microbiota. Identification of various members of the normal microbiota to the species level requires a combination of biological staining procedures, biochemical tests, and molecular techniques. In this experiment, ten bacterial isolates originating from the hands of nine students and one faculty member at USC Salkehatchie were identified. Classification to a general taxonomic group was accomplished with standard staining and biochemical tests. Sequences for the 16S ribosomal RNA section of DNA for each isolate were analyzed with BLAST to generate a list of ...


A Comparison Of Lung Function Values Among A Scuba Diver Population And In Comparison To A Non-Diver Population, Gabriel C. Hutson, Jeremy D. Rentsch, Erin M. Eaton 2019 Francis Marion University

A Comparison Of Lung Function Values Among A Scuba Diver Population And In Comparison To A Non-Diver Population, Gabriel C. Hutson, Jeremy D. Rentsch, Erin M. Eaton

Journal of the South Carolina Academy of Science

The purpose of this study was to investigate possible correlations between lung function values (PEF, IRV, ERV, and FVC) among a diver population, as well as in comparison to a non-diver population. Independent variables for both populations were biological sex, age, and weekly physical activity. Independent variables for the diver population were dive tenure, number of logged dives, certification level, and gas mixture used. A spirometry test was conducted to collect lung function values of both populations. Data from this study suggest a statistically significant relationship between diver and non-diver sex and FVC, diver age and ERV, diver sex and ...


The Effect Of Combination Birth Control Pills On Heart Rate, Blood Pressure, Body Weight And Body Temperature, Scarlett E. Leigh, Marlee B. Marsh 2019 Columbia College - Columbia, South Carolina

The Effect Of Combination Birth Control Pills On Heart Rate, Blood Pressure, Body Weight And Body Temperature, Scarlett E. Leigh, Marlee B. Marsh

Journal of the South Carolina Academy of Science

Birth control pills are the most popular method of birth control for women. In the United States of America, roughly 10.2 million women use some type of birth control pills. The two main types of birth control pills available to women are combination pills, which contain both estrogen and progestin, and progestin-only birth control pills that do not contain any estrogen. Numerous biological research studies have been performed studying the effects of combination birth control pills on blood pressure and body weight. However, few studies have examined blood pressure combined with both heart rate, body temperature, and body weight ...


Table Of Contents, 2019 University of South Carolina

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.


5 Lipoxygenase's Role In Chondrogenesis Of The Atdc5 Cell Line, Tien My Tran 2019 Seton Hall University

5 Lipoxygenase's Role In Chondrogenesis Of The Atdc5 Cell Line, Tien My Tran

Seton Hall University Dissertations and Theses (ETDs)

5-Lipoxygenase metabolizes arachidonic acid (AA) to generate leukotrienes (LTs). Leukotrienes are very potent inflammatory mediators that can have negative effects on bone healing and cartilage tissue generation. Recent studies have shown that decreasing 5-lipoxygenase (5-LO) activity during fracture healing accelerates endochondral ossification and decreases healing time in animal fracture models, however, the roles of 5-LO in chondrogenesis is not fully investigated. In this study, we tested the hypothesis that 5-LO inhibition will increase the process of chondrogenesis. The ABT-761 is an N-hydroxyurea analog structurally similar to zileuton, which is a 5-LO enzyme inhibitor, The ATDC5 cell line which is derived ...


Implementing And Evaluating A Course-Based Undergraduate Research Experience (Cure) At A Hispanic-Serving Institution, Michele I. Shuster PhD, Jennifer Curtiss, Timothy F. Wright, Camilla Champion, Maryam Sharifi, Judith Bosland 2019 New Mexico State University

Implementing And Evaluating A Course-Based Undergraduate Research Experience (Cure) At A Hispanic-Serving Institution, Michele I. Shuster Phd, Jennifer Curtiss, Timothy F. Wright, Camilla Champion, Maryam Sharifi, Judith Bosland

Interdisciplinary Journal of Problem-Based Learning

We are examining the impact of a course-based undergraduate research experience (CURE) at a land-grant, Hispanic-serving institution in the southwestern United States. Students in our CURE completed one or two extended research projects over a single semester. Our CURE enrolled a high proportion of underrepresented minority students (70.3%), including 60.2% Hispanic students. One year after CURE completion, 31.5% of CURE students had graduated with a STEM degree, and 54.3% were enrolled in a STEM major. Pre- and postcourse surveys of indicators of persistence including scientific self-efficacy, scientific identity, valuing scientific community objectives, and intention to persist ...


The Efficacy Of Whole Human Genome Capture On Ancient Dental Calculus And Dentin, Kirsten A. Ziesemer, Jazmin Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-Garcia, Bruno Frohlich, George R. Miller, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis Jr., Corinne L. Hofman, Christina Warinner, Hannes Schroeder 2019 Leiden University,

The Efficacy Of Whole Human Genome Capture On Ancient Dental Calculus And Dentin, Kirsten A. Ziesemer, Jazmin Ramos-Madrigal, Allison E. Mann, Bernd W. Brandt, Krithivasan Sankaranarayanan, Andrew T. Ozga, Menno Hoogland, Courtney A. Hofman, Domingo C. Salazar-Garcia, Bruno Frohlich, George R. Miller, Anne C. Stone, Mark Aldenderfer, Cecil M. Lewis Jr., Corinne L. Hofman, Christina Warinner, Hannes Schroeder

Andrew Ozga

Objectives

Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.

Materials and methods

Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing.

Results

Total DNA from calculus exceeded that of dentin in ...


Successful Enrichment And Recovery Of Whole Mitochondrial Genomes From Ancient Human Dental Calculus, Andrew T. Ozga, Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, Christina Warinner 2019 University of Oklahoma

Successful Enrichment And Recovery Of Whole Mitochondrial Genomes From Ancient Human Dental Calculus, Andrew T. Ozga, Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, Christina Warinner

Andrew Ozga

Objectives

Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.

Materials ...


Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr. 2019 University of Oklahoma; Universidad Científica del Sur; City of Hope, NCI-designated Comprehensive Cancer Center

Subsistence Strategies In Traditional Societies Distinguish Gut Microbiomes, Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Zech Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, Paul Spicer, Paul Lawson, Luis Marin-Reyes, Omar Trujillo-Villarroel, Morris Foster, Emilio Guija-Poma, Luzmila Troncoso-Corzo, Christina Warinner, Andrew T. Ozga, Cecil M. Lewis Jr.

Andrew Ozga

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26 ...


Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. MacDonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner 2019 Leiden University

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Andrew Ozga

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon ...


Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raul Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra J. Obregon-Tito, Leslie Neal, Cecil M. Lewis Jr. 2019 University of Oklahoma

Origins Of An Unmarked Georgia Cemetery Using Ancient Dna Analysis, Andrew T. Ozga, Raul Y. Tito, Brian M. Kemp, Hugh Matternes, Alexandra J. Obregon-Tito, Leslie Neal, Cecil M. Lewis Jr.

Andrew Ozga

Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the ...


Comparison Of Two Ancient Dna Extraction Protocols For Skeletal Remains From Tropical Environments, Maria A. Nieves-Colon, Andrew T. Ozga, William J. Pestle, Andrea Cucina, Vera Tiesler, Travis W. Stanton, Anne C. Stone 2019 Arizona State University

Comparison Of Two Ancient Dna Extraction Protocols For Skeletal Remains From Tropical Environments, Maria A. Nieves-Colon, Andrew T. Ozga, William J. Pestle, Andrea Cucina, Vera Tiesler, Travis W. Stanton, Anne C. Stone

Andrew Ozga

Objectives

The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi‐tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12).

Materials and Methods

All samples were extracted twice, built into double‐stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed ...


Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner 2019 Max Planck Institute for the Science of Human History; University of Oklahoma

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Andrew Ozga

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is ...


Extracellular Vesicles At The Fetal-Maternal Interface In Cattle, Heloisa M. Rutigliano 2019 Utah State University

Extracellular Vesicles At The Fetal-Maternal Interface In Cattle, Heloisa M. Rutigliano

Funded Research Records

No abstract provided.


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