Matching Items (147)
Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
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
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
Dissolved organic matter (DOM) can have numerous effects on the water chemistry and the biological life within an aquatic system with its wide variety of chemical structures and properties. The composition of the dissolved carbon can be estimated by utilizing the fluorescent properties of some DOM such as aromatic amino acids and humic material. This experiment was used to observe how organic matter could influence hydrothermal systems, such as Sylvan Springs in Yellowstone National Park, USA. Using optical density at 600 nm (OD 600), excitation-emission matrix spectra (EEMS), and Illumina sequencing methods (16S rRNA gene sequencing), changes in dissolved organic matter (DOM) were observed based on long term incubation at 84ºC and microbial influence. Four media conditions were tested over a two-month duration to assess these changes: inoculated pine needle media, uninoculated pine needle media, inoculated yeast extract media, and uninoculated yeast extract media. The inoculated samples contained microbes from a fluid and sediment sample of Sylvan Spring collected July 23, 2018. Absorbance indicated that media containing pine needle broth poorly support life, whereas media containing yeast extract revealed a positive increase in growth. Excitation-Emission Matrix Spectra of the all media conditions indicated changes in DOM composition throughout the trial. There were limited differences between the inoculated and uninoculated samples suggesting that the DOM composition change in this study was dominated by the two-month incubation at 84ºC more than biotic processes. Sequencing performed on a sediment sample collected from Sylvan Spring indicated five main order of prokaryotic phyla: Aquificales, Desulfurococcales, Thermoproteales, Thermodesulfobacteriales, and Crenarchaeota. These organisms are not regarded as heterotrophic microbes, so the lack of significant biotic changes in DOM could be a result of these microorganisms not being able to utilize these enrichments as their main metabolic energy supply.
ContributorsKnott, Nicholas Joseph (Author) / Shock, Everett (Thesis director) / Hartnett, Hilairy (Committee member) / Till, Christy (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Background
The transmission dynamics of Tuberculosis (TB) involve complex epidemiological and socio-economical interactions between individuals living in highly distinct regional conditions. The level of exogenous reinfection and first time infection rates within high-incidence settings may influence the impact of control programs on TB prevalence. The impact that effective population size and the distribution of individuals’ residence times in different patches have on TB transmission and control are studied using selected scenarios where risk is defined by the estimated or perceive first time infection and/or exogenous re-infection rates.
Methods
This study aims at enhancing the understanding of TB dynamics, within simplified, two patch, risk-defined environments, in the presence of short term mobility and variations in reinfection and infection rates via a mathematical model. The modeling framework captures the role of individuals’ ‘daily’ dynamics within and between places of residency, work or business via the average proportion of time spent in residence and as visitors to TB-risk environments (patches). As a result, the effective population size of Patch i (home of i-residents) at time t must account for visitors and residents of Patch i, at time t.
Results
The study identifies critical social behaviors mechanisms that can facilitate or eliminate TB infection in vulnerable populations. The results suggest that short-term mobility between heterogeneous patches contributes to significant overall increases in TB prevalence when risk is considered only in terms of direct new infection transmission, compared to the effect of exogenous reinfection. Although, the role of exogenous reinfection increases the risk that come from large movement of individuals, due to catastrophes or conflict, to TB-free areas.
Conclusions
The study highlights that allowing infected individuals to move from high to low TB prevalence areas (for example via the sharing of treatment and isolation facilities) may lead to a reduction in the total TB prevalence in the overall population. The higher the population size heterogeneity between distinct risk patches, the larger the benefit (low overall prevalence) under the same “traveling” patterns. Policies need to account for population specific factors (such as risks that are inherent with high levels of migration, local and regional mobility patterns, and first time infection rates) in order to be long lasting, effective and results in low number of drug resistant cases.
The transmission dynamics of Tuberculosis (TB) involve complex epidemiological and socio-economical interactions between individuals living in highly distinct regional conditions. The level of exogenous reinfection and first time infection rates within high-incidence settings may influence the impact of control programs on TB prevalence. The impact that effective population size and the distribution of individuals’ residence times in different patches have on TB transmission and control are studied using selected scenarios where risk is defined by the estimated or perceive first time infection and/or exogenous re-infection rates.
Methods
This study aims at enhancing the understanding of TB dynamics, within simplified, two patch, risk-defined environments, in the presence of short term mobility and variations in reinfection and infection rates via a mathematical model. The modeling framework captures the role of individuals’ ‘daily’ dynamics within and between places of residency, work or business via the average proportion of time spent in residence and as visitors to TB-risk environments (patches). As a result, the effective population size of Patch i (home of i-residents) at time t must account for visitors and residents of Patch i, at time t.
Results
The study identifies critical social behaviors mechanisms that can facilitate or eliminate TB infection in vulnerable populations. The results suggest that short-term mobility between heterogeneous patches contributes to significant overall increases in TB prevalence when risk is considered only in terms of direct new infection transmission, compared to the effect of exogenous reinfection. Although, the role of exogenous reinfection increases the risk that come from large movement of individuals, due to catastrophes or conflict, to TB-free areas.
Conclusions
The study highlights that allowing infected individuals to move from high to low TB prevalence areas (for example via the sharing of treatment and isolation facilities) may lead to a reduction in the total TB prevalence in the overall population. The higher the population size heterogeneity between distinct risk patches, the larger the benefit (low overall prevalence) under the same “traveling” patterns. Policies need to account for population specific factors (such as risks that are inherent with high levels of migration, local and regional mobility patterns, and first time infection rates) in order to be long lasting, effective and results in low number of drug resistant cases.
ContributorsMoreno Martinez, Victor (Author) / Espinoza Cortes, Baltazar (Author) / Barley, Kamal (Author) / Paredes Gutierrez, Marlio (Author) / Bichara, Derdei (Author) / Mubayi, Anuj (Author) / Castillo-Chavez, Carlos (Author) / Simon M. Levin Mathematical, Computational and Modeling Sciences Center (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2017-01-11
Description
Finding life beyond Earth could change our understanding of life and habitability. The best place to look for life beyond Earth is Jupiter's moon, Europa. It has been estimated Europa may have a liquid, salt-water subsurface with 2 to 3 times the volume of all Earth's oceans. Knowing that all life requires water, it is in our best interest to explore Europa. This thesis explored the plausibility of life on Europa in four of its environments: on the surface, under the ice shell, in the liquid subsurface, and at the bottom of the liquid subsurface. Each of these environments were defined from science literature and compared to known Earth analogs. Europa's surface is not likely to support life, as there is not liquid water present. There is also extremely high radiation bombardment and extremely low surface temperatures that are estimated to be well out of the range for supporting life. It is more plausible that life could be under Europa's ice shell than on the surface. Under the surface, radiation exposure dramatically reduces. Researchers have found organisms on Earth that can live in similar environments as Europa's ice as well. These organisms require some interaction with liquid water though. Uncertainties about Europa's ice shell thickness and radiation load per depth it experiences, as well as there being limited research on organisms in ice environments, hinder us from definitively assessing the plausibility of life under the surface. The best environment on Europa to look for life on Europa is the subsurface. There remain a lot of uncertainties about the subsurface, however, that make it difficult to assess the plausibility of finding life. These uncertainties include its depth, water activity, salinity, temperature, pressure, and structure. This subsurface may be suitable for life, but until we can further understand the environment of the subsurface, we cannot make definite conclusions. As for assessing the plausibility of life at the bottom of Europa's subsurface, there is not much we know about this environment either. It has been suggested there may be hydrothermal vents, but no evidence has either supported or rejected this idea. Without a clear understanding of the environment at the bottom of the subsurface, the plausibility of life here cannot be definitively answered. It is apparent we need to further study Europa. In particular, we need to focus on understanding the subsurface. When the subsurface is better defined, we can better assess the plausibility of life being present. Fortunately, both NASA and the ESA are currently planning missions to Europa that are scheduled to launch in the 2020s.
ContributorsHoward, Cheyenne Whiffen (Author) / Farmer, Jack (Thesis director) / Shock, Everett (Committee member) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Yellowstone National Park has a vibrant variety of flora, fauna, and hydrothermal systems all collected together in one large and complex system. Studies have been conducted for at least several decades in order to make sense of this system in ways that may be relevant to other similar geologies around the world. The latest update in this ever-ongoing study involves the collection and analysis of water samples from 2016. These samples have been analyzed for conductivity, pH, temperature, dissolved organic carbon, dissolved inorganic carbon, carbon isotopes, dissolved oxygen, ferrous iron, sulfide, silica, and more. While not many trends were found in this data in regards to dissolved organic carbon values, this is a substantial addition to a growing body of information that could yield more impressive information in times to come. In addition, factors that have yet to analyzed for this 2016 data, such as concentrations of metals and metalloids, may provide some insights when put through a chloride vs sulfate framework to separate out different reaction regions.
ContributorsDoan, Cuong Le (Author) / Shock, Everett (Thesis director) / Gould, Ian (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The ability to find evidence of life on early Earth and other planets is constrained by the current understanding of biosignatures and our ability to differentiate fossils from abiotic mimics. When organisms transition from the living realm to the fossil record, their morphological and chemical characteristics are modified, usually resulting in the loss of information. These modifications can happen during early and late diagenesis and differ depending on local geochemical properties. These post-depositional modifications need to be understood to better interpret the fossil record. Siliceous hot spring deposits (sinters) are of particular interest for biosignature research as they are early Earth analog environments and targets for investigating the presence of fossil life on Mars. As silica-supersaturated fluids flow from the vent to the distal apron, they precipitate non-crystalline opal-A that fossilizes microbial communities at a range in scales (μm-cm). Therefore, many studies have documented the ties between the active microbial communities and the morphological and chemical biosignatures in hot springs. However, far less attention has been placed on understanding preservation in systems with complex mineralogy or how post-depositional alteration affects the retention of biosignatures. Without this context, it can be challenging to recognize biosignatures in ancient rocks. This dissertation research aims to refine our current understanding of biosignature preservation and retention in sinters. Biosignatures of interest include organic matter, microfossils, and biofabrics. The complex nature of hot springs requires a comprehensive understanding of biosignature preservation that is representative of variable chemistries and post-depositional alterations. For this reason, this dissertation research chapters are field site-based. Chapter 2 investigates biosignature preservation in an unusual spring with mixed opal-A-calcite mineralogy at Lýsuhóll, Iceland. Chapter 3 tracks how silica diagenesis modifies microfossil morphology and associated organic matter at Puchuldiza, Chile. Chapter 4 studies the effects of acid fumarolic overprinting on biosignatures in Gunnuhver, Iceland. To accomplish this, traditional geologic methods (mapping, petrography, X-ray diffraction, bulk elemental analyses) were combined with high-spatial-resolution elemental mapping to better understand diagenetic effects in these systems. Preservation models were developed to predict the types and styles of biosignatures that can be present depending on the depositional and geochemical context. Recommendations are also made for the types of deposits that are most likely to preserve biosignatures.
ContributorsJuarez Rivera, Marisol (Author) / Farmer, Jack D (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Shock, Everett (Committee member) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2021
Description
Interdigitated back contact (IBC) solar cells have achieved the highest single junction silicon wafer-based solar cell power conversion efficiencies reported to date. This thesis is about the fabrication of a high-efficiency silicon heterojunction IBC solar cell for potential use as the bottom cell for a 3-terminal lattice-matched dilute-nitride Ga (In)NP(As)/Si monolithic tandem solar cell. An effective fabrication process has been developed and the process challenges related to open circuit voltage (Voc), series resistance (Rs), and fill factor (FF) are experimentally analyzed. While wet etching, the sample lost the initial passivation, and by changing the etchant solution and passivation process, the voltage at maximum power recovered to an initial value of over 710 mV before metallization. The factors reducing the series resistance loss in IBC cells were also studied. One of these factors was the Indium Tin Oxide (ITO) sputtering parameters, which impact the conductivity of the ITO layer and transport across the a-Si:H/ITO interface. For the standard recipe, the chamber pressure was 3.5 mTorr with no oxygen partial pressure, and the thickness of the ITO layer in contact with the a-Si:H layers, was optimized to 150 nm. The patterning method for the metal contacts and final annealing also change the contact resistance of the base and emitter stack layers. The final annealing step is necessary to recover the sputtering damage; however, the higher the annealing time the higher the final IBC series resistance. The best efficiency achieved was 19.3% (Jsc = 37 mA/cm2, Voc = 691 mV, FF = 71.7%) on 200 µm thick 1-15 Ω-cm n-type CZ C-Si with a designated area of 4 cm2.
ContributorsMoeini Rizi, Mansoure (Author) / Goodnick, Stephen (Thesis advisor) / Honsberg, Christina (Committee member) / Goryll, Michael (Committee member) / Smith, David (Committee member) / Bowden, Stuart (Committee member) / Arizona State University (Publisher)
Created2022
Description
I present results of field and laboratory experiments investigating the habitability of one of Earth’s driest environments: the Atacama Desert. This Desert, along the west coast of South America spanning Perú and Chile, is one of the driest places on Earth and has been exceedingly arid for millions of years. These conditions create the perfect natural laboratory for assessing life at the extremes of habitability. All known life needs water; however, the extraordinarily dry Atacama Desert is inhabited by well-adapted microorganisms capable of colonizing this hostile environment. I show field and laboratory evidence of an environmental process, water vapor adsorption, that provides a daily, sustainable input of water into the near (3 - 5 cm) subsurface through water vapor-soil particle interactions. I estimate that this water input may rival the yearly average input of rain in these soils (~2 mm).
I also demonstrate, for the first time, that water vapor adsorption is dependent on mineral composition via a series of laboratory water vapor adsorption experiments. The results of these experiments provide evidence that mineral composition, and ultimately soil composition, measurably and significantly affect the equilibrium soil water content. This suggests that soil microbial communities may be extremely heterogeneous in distribution depending on the distribution of adsorbent minerals.
Finally, I present changes in biologically relevant gasses (i.e., H2, CH4, CO, and CO2) over long-duration incubation experiments designed to assess the potential for biological activity in soils collected from a hyperarid region in the Atacama Desert. These long-duration experiments mimicked typical water availability conditions in the Atacama Desert; in other words, the incubations were performed without condensed water addition. The results suggest a potential for methane-production in the live experiments relative to the sterile controls, and thus, for biological activity in hyperarid soils. However, due to the extremely low biomass and extremely low rates of activity in these soils, the methods employed here were unable to provide robust evidence for activity. Overall, the hyperarid regions of the Atacama Desert are an important resource for researchers by providing a window into the environmental dynamics and subsequent microbial responses near the limit of habitability.
ContributorsGlaser, Donald M (Author) / Hartnett, Hilairy E (Thesis advisor) / Anbar, Ariel (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2022