ASU Regents' Professors Open Access Works
The title “Regents’ Professor” is the highest faculty honor awarded at Arizona State University. It is conferred on ASU faculty who have made pioneering contributions in their areas of expertise, who have achieved a sustained level of distinction, and who enjoy national and international recognition for these accomplishments. This collection contains primarily open access works by ASU Regents' Professors.
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- Creators: Nemanich, Robert
- Creators: Stone, Anne
- Creators: Ferry, David
Description
Background
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.
Results
For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.
Conclusions
SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.
ContributorsSchwartz, Rachel (Author) / Harkins, Kelly (Author) / Stone, Anne (Author) / Cartwright, Reed (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-06-11
Description
Animal hybridization is well documented, but evolutionary outcomes and conservation priorities often differ for natural and anthropogenic hybrids. Among primates, an order with many endangered species, the two contexts can be hard to disentangle from one another, which carries important conservation implications. Callithrix marmosets give us a unique glimpse of genetic hybridization effects under distinct natural and human-induced contexts. Here, we use a 44 autosomal microsatellite marker panel to examine genome-wide admixture levels and introgression at a natural C. jacchus and C. penicillata species border along the Sao Francisco River in NE Brazil and in an area of Rio de Janeiro state where humans introduced these species exotically. Additionally, we describe for the first time autosomal genetic diversity in wild C. penicillata and expand previous C. jacchus genetic data. We characterize admixture within the natural zone as bimodal where hybrid ancestry is biased toward one parental species or the other. We also show evidence that Sao Francisco River islands are gateways for bidirectional gene flow across the species border. In the anthropogenic zone, marmosets essentially form a hybrid swarm with intermediate levels of admixture, likely from the absence of strong physical barriers to interspecific breeding. Our data show that while hybridization can occur naturally, the presence of physical, even if leaky, barriers to hybridization is important for maintaining species genetic integrity. Thus, we suggest further study of hybridization under different contexts to set well informed conservation guidelines for hybrid populations that often fit somewhere between "natural" and "man-made."
ContributorsMalukiewicz, Joanna (Author) / Boere, Vanner (Author) / Fuzessy, Lisieux F. (Author) / Grativol, Adriana D. (Author) / de Oliveira e Silva, Ita (Author) / Pereira, Luiz C. M. (Author) / Ruiz-Miranda, Carlos R. (Author) / Valenca, Yuri M. (Author) / Stone, Anne (Author) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2015-06-10
Description
We have fabricated a high mobility device, composed of a monolayer graphene flake sandwiched between two sheets of hexagonal boron nitride. Conductance fluctuations as functions of a back gate voltage and magnetic field were obtained to check for ergodicity. Non-linear dynamics concepts were used to study the nature of these fluctuations. The distribution of eigenvalues was estimated from the conductance fluctuations with Gaussian kernels and it indicates that the carrier motion is chaotic at low temperatures. We argue that a two-phase dynamical fluid model best describes the transport in this system and can be used to explain the violation of the so-called ergodic hypothesis found in graphene.
Contributorsda Cunha, C. R. (Author) / Mineharu, M. (Author) / Matsunaga, M. (Author) / Matsumoto, N. (Author) / Chuang, C. (Author) / Ochiai, Y. (Author) / Kim, G.-H. (Author) / Watanabe, K. (Author) / Taniguchi, T. (Author) / Ferry, David (Author) / Aoki, N. (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor)
Created2016-09-09
Description
Zoonotic pathogens that cause leprosy (Mycobacterium leprae) and tuberculosis (Mycobacterium tuberculosis complex, MTBC) continue to impact modern human populations. Therefore, methods able to survey mycobacterial infection in potential animal hosts are necessary for proper evaluation of human exposure threats. Here we tested for mycobacterial-specific single- and multi-copy loci using qPCR. In a trial study in which armadillos were artificially infected with M. leprae, these techniques were specific and sensitive to pathogen detection, while more traditional ELISAs were only specific. These assays were then employed in a case study to detect M. leprae as well as MTBC in wild marmosets. All marmosets were negative for M. leprae DNA, but 14 were positive for the mycobacterial rpoB gene assay. Targeted capture and sequencing of rpoB and other MTBC genes validated the presence of mycobacterial DNA in these samples and revealed that qPCR is useful for identifying mycobacterial-infected animal hosts.
ContributorsHousman, Genevieve (Author) / Malukiewicz, Joanna (Author) / Boere, Vanner (Author) / Grativol, Adriana D. (Author) / Pereira, Luiz Cezar M. (Author) / de Oliveira e Silva, Ita (Author) / Ruiz-Miranda, Carlos R. (Author) / Truman, Richard (Author) / Stone, Anne (Author) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor) / Biodesign Institute (Contributor) / Personalized Diagnostics (Contributor)
Created2015-11-16
Description
GaN-based devices are currently limited by reliability issues such as gate leakage and current collapse, where the mechanisms responsible for degradation are closely related to the electronic surface state configuration. Therefore, understanding the electronic surface state configuration of GaN-based materials will help improve device performance. Since GaN has an inherent polarization, these materials are also subject to a bound polarization charge, which influences the electronic state configuration. In this study, the surface band bending of N-face GaN, Ga-face GaN, and Ga-face AlGaN was measured with x-ray photoemission spectroscopy after various cleaning steps to investigate the effects of the polarization. Despite the different surface bound charge on these materials, similar band bending was observed regardless of the magnitude or direction of the charge. Specifically, the band bending varied from −0.1 eV to 0.9 eV on these samples, which supported the models of a Fermi level pinning state at ∼0.4 eV to 0.8 eV below the conduction band. Based on available literature, we suggest this pinning state is indirectly evident of a nitrogen vacancy or gallium-dangling bond.
ContributorsEller, Brianna S. (Author) / Yang, Jialing (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-12-01
Description
This work presents a spectroscopic study of the thermally enhanced photoinduced electron emission from nitrogen-doped diamond films prepared on p-type silicon substrates. It has been shown that photon-enhanced thermionic emission (PETE) can substantially enhance thermionic emission intensity from a p-type semiconductor. An n-type diamond/p-type silicon structure was illuminated with 400–450 nm light, and the spectra of the emitted electrons showed a work function less than 2 eV and nearly an order of magnitude increase in emission intensity as the temperature was increased from ambient to ∼400 °C. Thermionic emission was negligible in this temperature range. The results are modeled in terms of contributions from PETE and direct photoelectron emission, and the large increase is consistent with a PETE component. The results indicate possible application in combined solar/thermal energy conversion devices.
ContributorsSun, Tianyin (Author) / Koeck, Franz (Author) / Rezikyan, Aram (Author) / Treacy, Michael (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-09-15
Description
The effects of surface pretreatment, dielectric growth, and post deposition annealing on interface electronic structure and polarization charge compensation of Ga- and N-face bulk GaN were investigated. The cleaning process consisted of an ex-situ wet chemical NH[subscript 4]OH treatment and an in-situ elevated temperature NH[subscript 3] plasma process to remove carbon contamination, reduce oxygen coverage, and potentially passivate N-vacancy related defects. After the cleaning process, carbon contamination decreased below the x-ray photoemission spectroscopy detection limit, and the oxygen coverage stabilized at ∼1 monolayer on both Ga- and N-face GaN. In addition, Ga- and N-face GaN had an upward band bending of 0.8 ± 0.1 eV and 0.6 ± 0.1 eV, respectively, which suggested the net charge of the surface states and polarization bound charge was similar on Ga- and N-face GaN. Furthermore, three dielectrics (HfO[subscript 2], Al[subscript 2]O[subscript 3], and SiO[subscript 2]) were prepared by plasma-enhanced atomic layer deposition on Ga- or N-face GaN and annealed in N[subscript 2] ambient to investigate the effect of the polarization charge on the interface electronic structure and band offsets. The respective valence band offsets of HfO[subscript 2], Al[subscript 2]O[subscript 3], and SiO[subscript 2] with respect to Ga- and N-face GaN were 1.4 ± 0.1, 2.0 ± 0.1, and 3.2 ± 0.1 eV, regardless of dielectric thickness. The corresponding conduction band offsets were 1.0 ± 0.1, 1.3 ± 0.1, and 2.3 ± 0.1 eV, respectively. Experimental band offset results were consistent with theoretical calculations based on the charge neutrality level model. The trend of band offsets for dielectric/GaN interfaces was related to the band gap and/or the electronic part of the dielectric constant. The effect of polarization charge on band offset was apparently screened by the dielectric-GaN interface states.
ContributorsYang, Jialing (Author) / Eller, Brianna S. (Author) / Nemanich, Robert (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-09-28
Description
The Physics and Chemistry of Surfaces and Interfaces conference has maintained a focus on the interfacial and surface properties of materials since its initiation in 1974. The conference continues to be a major force in this field, bringing together scientists from a variety of disciplines to focus upon the science of interfaces and surfaces. Here, a historical view of the development of the conference and a discussion of some of the themes that have been focal points for many years are presented.
ContributorsFerry, David (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor)
Created2013
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
Electricity plays a special role in our lives and life. The dynamics of electrons allow light to flow through a vacuum. The equations of electron dynamics are nearly exact and apply from nuclear particles to stars. These Maxwell equations include a special term, the displacement current (of a vacuum). The displacement current allows electrical signals to propagate through space. Displacement current guarantees that current is exactly conserved from inside atoms to between stars, as long as current is defined as the entire source of the curl of the magnetic field, as Maxwell did.We show that the Bohm formulation of quantum mechanics allows the easy definition of the total current, and its conservation, without the dificulties implicit in the orthodox quantum theory. The orthodox theory neglects the reality of magnitudes, like the currents, during times that they are not being explicitly measured.We show how conservation of current can be derived without mention of the polarization or dielectric properties of matter. We point out that displacement current is handled correctly in electrical engineering by ‘stray capacitances’, although it is rarely discussed explicitly. Matter does not behave as physicists of the 1800’s thought it did. They could only measure on a time scale of seconds and tried to explain dielectric properties and polarization with a single dielectric constant, a real positive number independent of everything. Matter and thus charge moves in enormously complicated ways that cannot be described by a single dielectric constant,when studied on time scales important today for electronic technology and molecular biology. When classical theories could not explain complex charge movements, constants in equations were allowed to vary in solutions of those equations, in a way not justified by mathematics, with predictable consequences. Life occurs in ionic solutions where charge is moved by forces not mentioned or described in the Maxwell equations, like convection and diffusion. These movements and forces produce crucial currents that cannot be described as classical conduction or classical polarization. Derivations of conservation of current involve oversimplified treatments of dielectrics and polarization in nearly every textbook. Because real dielectrics do not behave in that simple way-not even approximately-classical derivations of conservation of current are often distrusted or even ignored. We show that current is conserved inside atoms. We show that current is conserved exactly in any material no matter how complex are the properties of dielectric, polarization, or conduction currents. Electricity has a special role because conservation of current is a universal law.Most models of chemical reactions do not conserve current and need to be changed to do so. On the macroscopic scale of life, conservation of current necessarily links far spread boundaries to each other, correlating inputs and outputs, and thereby creating devices.We suspect that correlations created by displacement current link all scales and allow atoms to control the machines and organisms of life. Conservation of current has a special role in our lives and life, as well as in physics. We believe models, simulations, and computations should conserve current on all scales, as accurately as possible, because physics conserves current that way. We believe models will be much more successful if they conserve current at every level of resolution, the way physics does.We surely need successful models as we try to control macroscopic functions by atomic interventions, in technology, life, and medicine. Maxwell’s displacement current lets us see stars. We hope it will help us see how atoms control life.
ContributorsEisenberg, Bob (Author) / Oriols, Xavier (Author) / Ferry, David (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor)
Created2017-10-28