Matching Items (13)

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Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Description

Background
Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse

Background
Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.
Results
Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.
Conclusions
Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.

Contributors

Created

Date Created
  • 2017-03-27

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Xerostomia and the Microbiome of the Mouth

Description

Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that

Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore, the relationship between the microbiome and its host is mutually beneficial because the host is providing microbes with an environment in which they can flourish and, in turn, keep their host healthy. Reviewing examples of larger scale environmental shifts could provide a window by which scientists can make hypotheses. Certain medications and healthcare treatments have been proven to cause xerostomia. This disorder is characterized by a dry mouth, and known to be associated with a change in the composition, and reduction, of saliva. Two case studies performed by Bardow et al, and Leal et al, tested and studied the relationships of certain medications and confirmed their side effects on the salivary glands [2,3]. Their results confirmed a relationship between specific medicines, and the correlating complaints of xerostomia. In addition, Vissink et al conducted case studies that helped to further identify how radiotherapy causes hyposalivation of the salivary glands [4]. Specifically patients that have been diagnosed with oral cancer, and are treated by radiotherapy, have been diagnosed with xerostomia. As stated prior, studies have shown that patients having an ecologically balanced and diverse microbiome tend to have healthier mouths. The oral cavity is like any biome, consisting of commensalism within itself and mutualism with its host. Due to the decreased salivary output, caused by xerostomia, increased parasitic bacteria build up within the oral cavity thus causing dental disease. Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The Human Oral Microbiomics Database (HOMD) is a set of reference 16S rRNA gene sequences. These are then used to define individual human oral taxa. By conducting metagenomic experiments at the molecular and cellular level, scientists can identify and label micro species that inhabit the mouth during parasitic outbreaks or a shifting of the microbiome. Because the HOMD is incomplete, so is our ability to cure, or prevent, oral disease. The purpose of the thesis is to research what is known about xerostomia and its effects on the complex microbiome of the oral cavity. It is important that researchers determine whether this particular perspective is worth considering. In addition, the goal is to create novel experiments for treatment and prevention of dental diseases.

Contributors

Agent

Created

Date Created
  • 2015-05

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Investigating the Skin Immune Proteome of the White-Nose Syndrome Resistant Gray Bat, Myotis grisescens

Description

White-nose syndrome (WNS) is a cutaneous fungal infection caused by Pseudogymnoascus destructans (Pd) which was first observed in the United States in 2006. Pd infects bats during hibernation and leads

White-nose syndrome (WNS) is a cutaneous fungal infection caused by Pseudogymnoascus destructans (Pd) which was first observed in the United States in 2006. Pd infects bats during hibernation and leads to the development of cutaneous lesions and behavioral changes that can result in the animal's death. This study generated the first complete bat skin proteome for the WNS resistant gray bat (Myotis grisescens) to optimize sample preparation methods and identify immune proteins that may signal resistance. Wing tissue was collected from a female gray bat and processed in a Barocycler using 4M or 8M urea followed by an in-gel trypsin digestion of pooled samples and processing of separate samples without digestion specifically to capture and identify small antimicrobial peptides. Both undigested and digested samples were analyzed using a Thermo Fisher LTQ Orbitrap Velos mass spectrometer and interpreted using PEAKS software. A total of 29 immune proteins were identified including the antimicrobial peptide dermcidin. This method will be applied to a larger range of samples from five species variably impacted by WNS to compare skin proteomes with the aim of identifying immune proteins that are responsible for resistance at the barrier where Pd invades.

Contributors

Agent

Created

Date Created
  • 2017-05

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Genetics of Athletic Performance

Description

Abstract
Purpose—Use a framework of genetic knowledge to investigate the association between the genotypes of various genes with phenotypes, specifically the traits of elite athletes, in order to establish a

Abstract
Purpose—Use a framework of genetic knowledge to investigate the association between the genotypes of various genes with phenotypes, specifically the traits of elite athletes, in order to establish a personal opinion on their relevance to athletic performance.
Methods—Assemble and analyze selected published scientific studies on genotype and athletic performance and lastly to formulate a personal opinion on the value of genetic testing of athletes. ACTN3, ACE, MSTN, and apoE were the genes selected for analyses.
Results—Two genes, ACTN3 and ACE, showed a significant relationship of genotype to phenotypic traits related to athletic performance. ApoE did not demonstrate a phenotypic association with athletic performance, however it showed a correlation with injury susceptibility leading to traumatic brain injury (TBI). MSTN did not show a phenotypic association with athletic performance.
Conclusion—When considering the multifactorial nature of athletics, each sport must be investigated individually due to the different individual requirements. ACTN3 and ACE are the most widely studied genes, therefore, considerable data on their relevance to athletic performance was easily obtained and supported a relationship between genotype and athletic performance.

Contributors

Agent

Created

Date Created
  • 2017-05

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Understanding Differences Between Susceptibility and Resistance to White-Nose Syndrome in Bats: Methodological Optimization

Description

White-nose syndrome (WNS) is a fungal disease that infects hibernating bats of multiple species across large portions of eastern North America. To date, WNS has been responsible for the deaths

White-nose syndrome (WNS) is a fungal disease that infects hibernating bats of multiple species across large portions of eastern North America. To date, WNS has been responsible for the deaths of over seven million bats. It is not yet known why certain species are able to resist infection. Since the fungus invades the skin and some resistant species show no signs of the characteristic cutaneous lesions, it seems likely that resistant species contain specific defense mechanisms within their skin, such as antimicrobial peptides (AMPs) and other immunologically relevant proteins expressed by specific cell types or as secreted soluble components. Proteomics could be a useful tool for understanding differences in susceptibility, and could help identify AMPs that could be synthesized and used as control agents against the spread of the causative fungus. This study is the first to optimize proteomics methods for bat wing tissues in order to compare the skin proteomes of species variably impacted by WNS, including those of two endangered species. Further tests are planned to investigate methods of increasing protein yield without altering the size of the tissue sample collected, as well as the analysis of mass spectrometry data from processed skin tissues of five bat species differentially affected by WNS.

Contributors

Agent

Created

Date Created
  • 2018-05

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Canine Obesity Awareness and Owner Responsiveness

Description

Pet obesity is higher than ever in the United States. According to the Association for Pet Obesity Prevention, 52.5% of dogs and 58.3% of cats were either overweight or obese

Pet obesity is higher than ever in the United States. According to the Association for Pet Obesity Prevention, 52.5% of dogs and 58.3% of cats were either overweight or obese in 20121. Obesity has been linked to health issues such as cardiovascular disease, diabetes, muscular disorders and some cancers to name a few.2 A pet at the recommended healthy weight is important to avoid these diseases. It is important that owners realize this and if their pet is at an unhealthy weight, work with their veterinarian to help the pet lose weight. This study looks at how committed dog owners are to help their pet lose weight and the problems they face while doing so.

Contributors

Agent

Created

Date Created
  • 2014-05

Species delimitation of flowering plant genus Medicago section Buceras (Fabaceae)

Description

There is a relative lack of basic information about early diverging species of the genus Medicago that, for the most part, were formerly considered to be in the genus Trigonella.

There is a relative lack of basic information about early diverging species of the genus Medicago that, for the most part, were formerly considered to be in the genus Trigonella. Species boundaries are not always clear, for example, the most recent treatment of the genus Medicago submerged four previously recognized species into Medicago monantha, a widely distributed species in the Middle East. These species are recognized on the basis of morphological characters such as fruit number, shape, length and areole shape and size, but species identification is still challenging and further clarification of species boundaries is needed. There is also a lack of cytogenetic information. Some of the relatively few published chromosome numbers, e.g. 2n=28, and 44, differ from those of the rest of the genus, which are mostly 2n=16 or multiples thereof, although seven species are 2n=14. As part of a larger study of the genome and chromosome number evolution in the genus Medicago, we obtained genome size data using flow cytometry for 44 accessions of 14 currently recognized early diverging species, with a focus on Medicago monantha. Chromosome numbers were obtained using standard cytological methods. Our chromosome number data confirm a chromosome number of 2n=16 for M. brachycarpa (genome size of 1.33 pg), and M. monspeliaca (1.88 pg), and 2n=28 for M. polyceratia (2.77 pg) and give new numbers for some species; 2n=16 for M. biflora (2.7 pg), and a previously unknown chromosome number for these early diverging species of 2n=14 for Medicago fischeriana (~1.35 pg). Interestingly, our data support the hypothesis that there are at least two entities within M. monantha as currently recognized that differ in chromosome number and genome size; two accessions had chromosome numbers of 2n=26 and 30 with corresponding genome sizes of 2.68 and 2.85 pg and three other accessions had chromosome numbers 2n=36,44, and another 44 with genome sizes of 3.94, 3.89, and 4.04 pg. There are also some significant morphological differences between these two entities, such as fruit length and areole area. These data lead to both further clarification of the relationships of early diverging Medicago and help build a platform for more in-depth research concerning the evolution of chromosome number and genome size within Medicago.

Contributors

Agent

Created

Date Created
  • 2016-05

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Toward an Ideal Typology of the Search and Rescue Dog

Description

The purpose of this thesis is to develop an aptitude test to administer to shelter dogs in order to determine which dogs could be adopted and trained for Search and

The purpose of this thesis is to develop an aptitude test to administer to shelter dogs in order to determine which dogs could be adopted and trained for Search and Rescue (SAR) work. SAR is an essential field made up primarily of volunteers that search for people who have gotten lost. Many SAR teams work with the police force to locate missing persons. There are various types of SAR work, such as urban SAR, ground SAR, mountain rescue, and cadaver SAR, among others. The tasks of hiking, climbing, crawling, and various other methods of maneuvering are required from the SAR dogs and their handlers, so physical fitness is necessary in all SAR dogs. A stable, confident demeanor is also crucial for the overall effectiveness of the canine. The availability of a standardized aptitude test could prove beneficial for SAR dog handlers seeking dogs to train for work in the SAR field. This also presents the opportunity for increased adoption of shelter dogs, provided SAR dog handlers decide to work with homeless adult dogs. The aptitude test encompasses the critical qualities necessary for SAR dogs to possess. Physical suitability, temperament, aptitude, object focus, and emotional suitability have been implemented and defined in the test, based on the desired traits described by various SAR organizations and evaluations for puppies and working dogs. Though there are multiple variations of aptitude and temperament tests, these evaluations do not incorporate the administration to shelter dogs in order to determine their potential for working in a special field particularly the field of Search and Rescue. The qualities for SAR dogs described in this thesis were utilized to create ideal typologies of SAR dogs. This provides a theoretical idea of realistic dogs suitable for SAR work. These ideal typologies were scored against the aptitude test based on their characteristics described in order to determine consistent implementation of the test by multiple users. The aptitude test was also implemented on two real dogs to discern the effectiveness of the test. Although neither dog displayed the proper characteristics to become SAR dogs, the results from the trials demonstrated an overall efficacy of the test.

Contributors

Agent

Created

Date Created
  • 2017-05

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Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

Description

Premise of the study: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of

Premise of the study: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.
Methods: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).
Key results: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.
Conclusions: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.

Contributors

Created

Date Created
  • 2015-07-01

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The influence of soil characteristics on Saguaro (Carnegiea gigantea) post wild fire restoration efforts

Description

The Cave Creek Complex fires of June and July of 2005 north of Phoenix, Arizona, U.S.A. burned 248,310 acres of Sonoran desert, primarily on the Tonto National Forest, USFS. The

The Cave Creek Complex fires of June and July of 2005 north of Phoenix, Arizona, U.S.A. burned 248,310 acres of Sonoran desert, primarily on the Tonto National Forest, USFS. The fires consumed multiple stands of the keystone species Carnegiea gigantea, the saguaro cactus. Restoration efforts in late spring 2007 involved the monitoring of 200 transplanted saguaro cacti over a two year period for overall establishment and success. Observation of local saguaro distribution suggests that soil factors might influence saguaro growth. Therefore, soil samples were collected from each transplant location and analyzed for percentage coarse fragments, texture, pH and electrical conductivity as soil collection and analysis of these variables are relatively inexpensive and expedient. Regression analysis was used to determine which, if any of these soil characteristics significantly correlated with plant growth. The results of this study found significant correlation between saguaro transplant growth and the soil variables of clay content and pH, but no correlation between saguaro growth and coarse fragment percentages or electrical conductivity.

Contributors

Agent

Created

Date Created
  • 2013