Matching Items (18)
Description
Background
The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected that DNA repair proteins would be evolutionarily conserved, exhibiting very minimal sequence change over time. However, BRCA1, an essential gene involved in DNA repair, has been reported to be evolving rapidly despite the fact that many protein-altering mutations within this gene convey a significantly elevated risk for breast and ovarian cancers.
Results
To obtain a deeper understanding of the evolutionary trajectory of BRCA1, we analyzed complete BRCA1 gene sequences from 23 primate species. We show that specific amino acid sites have experienced repeated selection for amino acid replacement over primate evolution. This selection has been focused specifically on humans and our closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). After examining BRCA1 polymorphisms in 7 bonobo, 44 chimpanzee, and 44 rhesus macaque (Macaca mulatta) individuals, we find considerable variation within each of these species and evidence for recent selection in chimpanzee populations. Finally, we also sequenced and analyzed BRCA2 from 24 primate species and find that this gene has also evolved under positive selection.
Conclusions
While mutations leading to truncated forms of BRCA1 are clearly linked to cancer phenotypes in humans, there is also an underlying selective pressure in favor of amino acid-altering substitutions in this gene. A hypothesis where viruses are the drivers of this natural selection is discussed.
The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected that DNA repair proteins would be evolutionarily conserved, exhibiting very minimal sequence change over time. However, BRCA1, an essential gene involved in DNA repair, has been reported to be evolving rapidly despite the fact that many protein-altering mutations within this gene convey a significantly elevated risk for breast and ovarian cancers.
Results
To obtain a deeper understanding of the evolutionary trajectory of BRCA1, we analyzed complete BRCA1 gene sequences from 23 primate species. We show that specific amino acid sites have experienced repeated selection for amino acid replacement over primate evolution. This selection has been focused specifically on humans and our closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). After examining BRCA1 polymorphisms in 7 bonobo, 44 chimpanzee, and 44 rhesus macaque (Macaca mulatta) individuals, we find considerable variation within each of these species and evidence for recent selection in chimpanzee populations. Finally, we also sequenced and analyzed BRCA2 from 24 primate species and find that this gene has also evolved under positive selection.
Conclusions
While mutations leading to truncated forms of BRCA1 are clearly linked to cancer phenotypes in humans, there is also an underlying selective pressure in favor of amino acid-altering substitutions in this gene. A hypothesis where viruses are the drivers of this natural selection is discussed.
ContributorsLou, Dianne I. (Author) / McBee, Ross M. (Author) / Le, Uyen Q. (Author) / Stone, Anne (Author) / Wilkerson, Gregory K. (Author) / Demogines, Ann M. (Author) / Sawyer, Sara L. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2014-07-11
Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
Description
Bermuda Land Snails make up a genus called Poecilozonites that is endemic to Bermuda and is extensively present in its fossil record. These snails were also integral to the creation of the theory of punctuated equilibrium. The DNA of mollusks is difficult to sequence because of a class of proteins called mucopolysaccharides that are present in high concentrations in mollusk tissue, and are not removed with standard DNA extraction methods. They inhibit Polymerase Chain Reactions (PCRs) and interfere with Next Generation Sequencing methods. This paper will discuss the DNA extraction methods that were designed to remove the inhibitory proteins that were tested on another gastropod species (Pomacea canaliculata). These were chosen because they are invasive and while they are not pulmonates, they are similar enough to Bermuda Land Snails to reliably test extraction methods. The methods that were tested included two commercially available kits: the Qiagen Blood and Tissue Kit and the Omega Biotek Mollusc Extraction Kit, and one Hexadecyltrimethylammonium Bromide (CTAB) Extraction method that was modified for use on mollusk tissue. The Blood and Tissue kit produced some DNA, the mollusk kit produced almost none, and the CTAB Extraction Method produced the highest concentrations on average, and may prove to be the most viable option for future extractions. PCRs attempted with the extracted DNA have all failed, though it is likely due to an issue with reagents. Further spectrographic analysis of the DNA from the test extractions has shown that they were successful at removing mucopolysaccharides. When the protocol is optimized, it will be used to extract DNA from the tissue from six individuals from each of the two extant species of Bermuda Land Snails. This DNA will be used in several experiments involving Next Generation Sequencing, with the goal of assembling a variety of genome data. These data will then be used to a construct reference genome for Bermuda Land Snails. The genomes generated by this project will be used in population genetic analyses between individuals of the same species, and between individuals of different species. These analyses will then be used to aid in conservation efforts for the species.
ContributorsClark, Patrick Louis (Author) / Stone, Anne (Thesis director) / Winingear, Stevie (Committee member) / School of Life Sciences (Contributor, Contributor) / School of Human Evolution & Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
In biology and medicine today, Next Generation Sequencing (NGS) is used to quantify entire genomes and has changed genomics research by providing a low cost, streamlined approach to producing large amounts of genetic data. One of the main steps of NGS is library preparation and these libraries can be double or single stranded. When DNA is degraded or damaged, it can be difficult to create into double stranded libraries and analyze. In this case, single stranded libraries can be prepared when DNA input is low. However, most research on comparing single and double stranded libraries for degraded DNA is limited to ancient DNA. Here we compare SRSLY single stranded DNA libraries with Illumina double stranded DNA libraries using modern degraded DNA samples from deceased unidentified individuals. Our results potentially show that single stranded libraries had a greater concentration of degraded DNA. However, further research must be conducted using qPCR to definitively state that single stranded library preparation was more effective in capturing the modern degraded DNA.
ContributorsMehta, Rishika (Author) / Stone, Anne (Thesis director) / Parker, Cody (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2023-05
Description
This project studies two single nucleotide polymorphisms (SNPs) within the HBS1L-MYB loci. Both SNPs are associated with a heightened expression of fetal hemoglobin. DNA samples of NCAA athletes who have sickle cell trait were genotyped to find the allele frequency of each SNP. When comparing all populations using information provided from the Human Genome Project on Ensembl, the minor A allele has a frequency of 22% and the major, G, allele has a frequency of 78%. The frequency distribution of the minor allele in the population data was higher than the frequency obtained from the sampled data by 15%. This means that the samples, which are heterozygous for sickle cell, display a lower frequency for the mutation than the global population.
ContributorsCiambella, Michelle Lynn (Author) / Stone, Anne (Thesis director) / Foy, Joseph (Committee member) / Madrigal, Lorena (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Treponemal disease in primates is caused by the spirochaete bacteria Treponema pallidum. Three subspecies of T. pallidum are currently recognized; pallidum, pertenue, and endemicum. In humans, these are generally associated with the diseases syphilis, yaws, and bejel, respectively. Syphilis is located worldwide and spreads through sexual contact, while yaws and bejel are geographically limited and spread by skin-to-skin contact. Despite different clinical presentations, these subspecies are very similar genetically and are unable to be serologically distinguished. Reports of symptoms resembling treponemal disease in non-human primates (NHPs) date to the 1960s, though few studies have been executed to isolate and study T. pallidum from NHPs on a molecular level. Obtaining whole-genome sequences of T. pallidum from a variety of NHPs will help efforts to determine evolutionary relationships of strains within and between species. Currently, no whole-genome sequences of T. pallidum have been sequenced from chimpanzees or gorillas. In this thesis, I will determine if T. pallidum is detectable in fecal samples from NHP’s with visible signs of treponemal infection using a polymerase chain reaction (PCR) method.
ContributorsChaffee, Elaine (Author) / Stone, Anne (Thesis director) / Winingear, Stevie (Committee member) / Sanz, Crickette (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Music, Dance and Theatre (Contributor)
Created2024-05
Description
Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to have evolved from a Y-specific inversion that suppressed recombination across the boundary. In addition to the two PARs, there is also a human-specific X-transposed region (XTR) that was duplicated from the X to the Y chromosome. Genetic diversity is expected to be higher in recombining than nonrecombining regions, particularly because recombination reduces the effects of linked selection, allowing neutral variation to accumulate. We previously showed that diversity decreases linearly across the previously defined pseudoautosomal boundary (rather than drop suddenly at the boundary), suggesting that the pseudoautosomal boundary may not be as strict as previously thought. In this study, we analyzed data from 1271 genetic females to explore the extent to which the pseudoautosomal boundary varies among human populations (broadly, African, European, South Asian, East Asian, and the Americas). We found that, in all populations, genetic diversity was significantly higher in the PAR1 and XTR than in the non-PAR regions, and that diversity decreased linearly from the PAR1 to finally reach a non-PAR value well past the pseudoautosomal boundary in all populations. However, we also found that the location at which diversity changes from reflecting the higher PAR1 diversity to the lower nonPAR diversity varied by as much as 500 kb among populations. The lack of genetic evidence for a strict pseudoautosomal boundary and the variability in patterns of diversity across the pseudoautosomal boundary are consistent with two potential explanations: (1) the boundary itself may vary across populations, or (2) that population-specific demographic histories have shaped diversity across the pseudoautosomal boundary.
ContributorsCotter, Daniel Juetten (Author) / Wilson Sayres, Melissa (Thesis director) / Stone, Anne (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The health situation of indigenous peoples is comparable to that of the world's poorest populations, but with the additional burdens of social and cultural marginalization, geographic and cultural barriers to accessing health services, and, in some areas, appropriation of land and natural resources. Cultural transmission (the transfer of beliefs, ideas, and behaviors from one culture to another) from outsider health institutions should presumably aid in closing this health gap by transferring knowledge, practices, and infrastructure to prevent and treat disease. This study examines the biosocial construction of the disease ecology of tuberculosis (TB) in indigenous communities of the Paraguayan Chaco with varying degrees of cultural transmission from outside institutions (government, religious, and NGOs), to determine the influence of cultural transmission on local disease ecologies. Using a biocultural epidemiological framework for the analysis of human infectious disease ecology, this study employed an interdisciplinary, mixed methods approach to examine the interactions of host, pathogen, and the environment in the Paraguayan Chaco. Three case studies examining aspects of TB disease ecology in indigenous communities are presented: (1) The effective cultural transmission of biomedical knowledge to isolated communities, (2) Public health infrastructure, hygiene, and the prevalence of intestinal parasites: co-morbidities that promote the progression to active TB disease, and (3) Community-level risk factors for TB and indigenous TB burden. Findings from the case studies suggest that greater influence from outside institutions was not associated with greater adoption of biomedical knowledge of TB. The prevalence of helminthiasis was unexpectedly low, but infection with giardia was common, even in a community with cleaner water sources. Communities with a health post were more likely to report active adult TB, while communities with more education were less likely to report active pediatric TB, suggesting that healthcare access is the major determinant of TB detection. More research is needed on the role of non-indigenous community residents and other measures of acculturation or integration in TB outcomes, especially at the household level. Indigenous TB burden in the Chaco is disproportionately high, and better understanding of the mechanisms that produce higher incidence and prevalence of the disease is needed.
ContributorsVansteelandt, Amanda (Author) / Hurtado, Ana Magdalena (Thesis advisor) / Stone, Anne (Thesis advisor) / Hruschka, Daniel (Committee member) / Rojas de Arias, Antonieta (Committee member) / Arizona State University (Publisher)
Created2014
Description
Leprosy, or Hansen’s disease, is often relegated to antiquity, yet it remains a modern public health concern with around 200,000 new cases reported annually around the world (World Health Organization, 2023). Most leprosy cases in humans are caused by Mycobacterium leprae, but a small number of cases are now known to be caused by Mycobacterium lepromatosis, which is found mostly in Mexico and the Caribbean (Han et al., 2008; 2012). Recent work has improved our understanding of the pattern of genomic variation in M. leprae strains, however certain regions remain understudied. Additionally, ongoing surveillance has identified pockets of hyperendemicity, which could act as hotspots for the spread of drug-resistant strains. Despite increased surveillance, there has been limited genomic research in regions like the Pacific and few surveys incorporating a broad species range in endemic areas. To address this, M. leprae genomes were isolated from clinical formalin-fixed, paraffin-embedded (FFPE) samples from the Pacific Islands and used in phylogenetic and phylogeographic analyses. 21 novel M. leprae strains from these samples were sequenced and dating analyses determined that M. leprae strains have been circulating in the Pacific since the original peopling of the region. Furthermore, recent radiation events among the Pacific Islands, as well as a rise in drug-resistant M. leprae strains, were identified and described. Additionally, a survey of animals in an endemic state in Brazil resulted in the first M. leprae genome isolated from a big cat. This body of research leverages genomic data to characterize novel diversity of M. leprae strains, identify drug-resistant strains in these regions, and determine how this pathogen spreads through space and time. The results of this work will aid in our understanding of the history of leprosy and improve public health responses to this disease.
ContributorsCrane, Adele Elizabeth (Author) / Stone, Anne (Thesis advisor) / Fox, Keolu (Committee member) / Varsani, Arvind (Committee member) / Wilson, Melissa (Committee member) / Arizona State University (Publisher)
Created2024
Description
Within the primate lineage, skeletal traits that contribute to inter-specific anatomical variation and enable varied niche occupations and forms of locomotion are often described as the result of environmental adaptations. However, skeletal phenotypes are more accurately defined as complex traits, and environmental, genetic, and epigenetic mechanisms, such as DNA methylation which regulates gene expression, all contribute to these phenotypes. Nevertheless, skeletal complexity in relation to epigenetic variation has not been assessed across the primate order. In order to gain a complete understanding of the evolution of skeletal phenotypes across primates, it is necessary to study skeletal epigenetics in primates. This study attempts to fill this gap by identifying intra- and inter-specific variation in primate skeletal tissue methylation in order to test whether specific features of skeletal form are related to specific variations in methylation. Specifically, methylation arrays and gene-specific methylation sequencing are used to identify DNA methylation patterns in femoral trabecular bone and cartilage of several nonhuman primate species. Samples include baboons (Papio spp.), macaques (Macaca mulatta), vervets (Chlorocebus aethiops), chimpanzees (Pan troglodytes), and marmosets (Callithrix jacchus), and the efficiencies of these methods are validated in each taxon. Within one nonhuman primate species (baboons), intra-specific variations in methylation patterns are identified across a range of comparative levels, including skeletal tissue differences (bone vs. cartilage), age cohort differences (adults vs. juveniles), and skeletal disease state differences (osteoarthritic vs. healthy), and some of the identified patterns are evolutionarily conserved with those known in humans. Additionally, in all nonhuman primate species, intra-specific methylation variation in association with nonpathological femur morphologies is assessed. Lastly, inter-specific changes in methylation are evaluated among all nonhuman primate taxa and used to provide a phylogenetic framework for methylation changes previously identified in the hominin lineage. Overall, findings from this work reveal how skeletal DNA methylation patterns vary within and among primate species and relate to skeletal phenotypes, and together they inform our understanding of epigenetic regulation and complex skeletal trait evolution in primates.
ContributorsHousman, Genevieve (Author) / Stone, Anne (Thesis advisor) / Quillen, Ellen (Committee member) / Kusumi, Kenro (Committee member) / Stojanowski, Christopher (Committee member) / Arizona State University (Publisher)
Created2017