Wiess School of Natural Sciences

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1D to 3D Crossover of a Spin-Imbalanced Fermi Gas
(American Physical Society, 2016) Revelle, Melissa C.; Fry, Jacob A.; Olsen, Ben A.; Hulet, Randall G.; Rice Center for Quantum Materials
We have characterized the one-dimensional (1D) to three-dimensional (3D) crossover of a two-component spin-imbalanced Fermi gas of 6Li atoms in a 2D optical lattice by varying the lattice tunneling and the interactions. The gas phase separates, and we detect the phase boundaries using in situ imaging of the inhomogeneous density profiles. The locations of the phases are inverted in 1D as compared to 3D, thus providing a clear signature of the crossover. By scaling the tunneling rate t with respect to the pair binding energy εB, we observe a collapse of the data to a universal crossover point at a scaled tunneling value of ˜tc=0.025(7).
222Rn emanation measurements for the XENON1T experiment
(Springer Nature, 2021) XENON Collaboration
The selection of low-radioactive construction materials is of utmost importance for the success of low-energy rare event search experiments. Besides radioactive contaminants in the bulk, the emanation of radioactive radon atoms from material surfaces attains increasing relevance in the effort to further reduce the background of such experiments. In this work, we present the 222Rn emanation measurements performed for the XENON1T dark matter experiment. Together with the bulk impurity screening campaign, the results enabled us to select the radio-purest construction materials, targeting a 222Rn activity concentration of 10μBq/kg in 3.2t of xenon. The knowledge of the distribution of the 222Rn sources allowed us to selectively eliminate problematic components in the course of the experiment. The predictions from the emanation measurements were compared to data of the 222Rn activity concentration in XENON1T. The final 222Rn activity concentration of (4.5±0.1)μBq/kg in the target of XENON1T is the lowest ever achieved in a xenon dark matter experiment.
3D Shear Velocity Structure of the Caribbean—Northwestern South America Subduction Zone From Ambient Noise and Ballistic Rayleigh Wave Tomography
(Wiley, 2024) Miao, Wenpei; Cornthwaite, John; Levander, Alan; Niu, Fenglin; Schmitz, Michael; Li, Guoliang; Dionicio, Viviana; Prieto, German
The Caribbean-South America subduction zone is a flat subduction zone, with Laramide-style thick-skinned uplifts occurring in the Merida Andes, Sierra de Perija Range, and Santa Marta Massif. Geodetic measurements and historical seismicity show this region is storing strain energy and is capable of a mega-thrust earthquake (M ≥ 8.0). Previous seismic investigations of the lithosphere and upper mantle in this area are either very large scale, very local, or only peripheral to this area; therefore, details of the Caribbean plate subduction geometry beneath the Maracaibo block remain unclear. In this study, we used a new data set acquired by the Caribbean-Merida Andes seismic experiment (CARMA), which comprised 65 temporary broadband stations and 44 permanent stations from the Colombian and Venezuelan national seismic networks. We jointly inverted ambient noise Rayleigh wave Z/H ratios, phase velocities in the 8–30 s band and ballistic Rayleigh wave phase velocities in 30–80 s band to construct a 3-D S-wave velocity model in the area between 75°–65°W and 5°–12°N. The 3-D model reveals a general increase in crust thickness from the trench to the southeast. An anomalous area is the Lake Maracaibo, which is underlaid by the thinnest crystalline crust in the region. This observation may indicate that the Maracaibo block is experiencing a contortion deformation within the crust. We also identified a high velocity anomaly above the subducting Caribbean slab, likely representing a detached piece of eclogitized Caribbean large igneous province from the base of the Maracaibo block. Additionally, our Vs model clearly indicates a slab tear within the subducted Caribbean slab, approximately beneath the Oca-Ancon Fault.
4500-year paleohurricane record from the Western Gulf of Mexico, Coastal Central TX, USA
(Elsevier, 2024) Monica, Sarah B.; Wallace, Davin J.; Wallace, Elizabeth J.; Du, Xiaojing; Dee, Sylvia G.; Anderson, John B.
Texas receives the second-highest number of tropical cyclone (TC) landfalls per year in the United States. At present, long-term TC projections from climate models remain uncertain due to the short and biased nature of Atlantic TC observations. Sediment archives of past storms can help extend the observational record of TC strikes over the past few millennia. When a TC makes landfall along the central Texas coast, coastal downwelling channels and storm currents transport and deposit coarse sediment to a zone of rapid accumulation along the shelf, known as the Texas Mud Blanket (TMB). This “backwash” process results in expansive storm deposits along the shelf, making this region ideal for paleotempestological reconstructions. Here, we present two sediment cores, located approximately 6 km southeast of Matagorda Island (TX), that collectively yield a ∼4500-year paleohurricane record. 210Pb and 137Cs are utilized in conjunction with radiocarbon ages to produce high-resolution Bayesian age models. One-centimeter interval grain size analyses are used to identify TC deposits. Two-centimeter interval X-Ray Fluorescence (XRF) is used as an additional measure to verify depositional mechanisms in this shelf environment. We define an intense paleohurricane event threshold through statistical analysis of mean grain size data. The sediment-derived TC record is correlated to Palmer Drought Severity Index (PDSI) data from Paleo Hydrodynamics Data Assimilation (PHYDA) to bolster our interpretation of the TC record, revealing a coupled relationship between PDSI and TCs since ∼300 yr BP. Over the ∼4500-year period, 24 intense TCs were recorded in the sediment record, yielding a long-term annual landfall probability of ∼0.53%. Additionally, comparisons between other TC records within the Atlantic establish a relationship between enhanced TC activity in the Western Gulf of Mexico (GOM) and TCs formed in the Caribbean Sea.
A 3D inﾠvitro model of patient-derived prostate cancer xenograft for controlled interrogation of inﾠvivo tumor-stromal interactions
(Elsevier, 2016) Fong, Eliza L.S.; Wan, Xinhai; Yang, Jun; Morgado, Micaela; Mikos, Antonios G.; Harrington, Daniel Anton; Navone, Nora M.; Farach-Carson, Mary C.
Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel system capable of supporting the co-culture of PCa PDX cells and osteoblastic cells to recapitulate the PCa-osteoblast unit within the bone metastatic microenvironment in vitro. Our 3D model not only maintained cell viability but also preserved the typical osteogenic phenotype of PCa PDX cells. Additionally, co-culture cellularity was maintained over that of either cell type cultured alone, suggesting that the PCa-osteoblast cross-talk supports PCa progression in bone, as is hypothesized to occur in patients with prostatic bone metastasis. Strikingly, osteoblastic cells co-cultured with PCa PDX tumoroids organized around the tumoroids, closely mimicking the architecture of PCa metastases in bone. Finally, tumor-stromal signaling mediated by the fibroblast growth factor axis tightly paralleled that in the in vivo counterpart. Together, these findings indicate that this 3D PCa PDX model recapitulates important pathological properties of PCa bone metastasis, and validate the use of this model for controlled and systematic interrogation of complex in vivo tumor-stromal interactions.
A 5-km-thick reservoir with > 380,000 km3 of magma within the ancient Earth's crust
(Springer Nature, 2022) Latypov, Rais; Chistyakova, Sofya; Hornsey, Richard A.; Costin, Gelu; van der Merwe, Mauritz
Several recent studies have argued that large, long-lived and molten magma chambers may not occur in the shallow Earth’s crust. Here we present, however, field-based observations from the Bushveld Complex that provide evidence to the contrary. In the eastern part of the complex, the magmatic layering continuously drapes across a ~ 4-km-high sloping step in the chamber floor. Such deposition of magmatic layering implies that the resident melt column was thicker than the stepped relief of the chamber floor. Prolonged internal differentiation within this thick magma column is further supported by evolutionary trends in crystallization sequence and mineral compositions through the sequence. The resident melt column in the Bushveld chamber during this period is estimated at > 5-km in thickness and > 380,000 km3 in volume. This volume of magma is three orders of magnitude larger than any known super-eruption in the Earth’s history and is only comparable to the extrusive volumes of some of Earth’s large igneous provinces. This suggests that super-large, entirely molten, and long-lived magma chambers occur, at least occasionally, in the geological history of our planet. Therefore, the classical view of magma chambers as ‘big magma tanks’ remains a viable research concept for some of Earth’s magmatic provinces.
A Bayesian Approach to Social Structure Uncovers Cryptic Regulation of Group Dynamics in Drosophila melanogaster
(The University of Chicago Press for The American Society of Naturalists, 2015) Foley, Brad R.; Saltz, Julia Barbara; Nuzhdin, Sergey V.; Marjoram, Paul
Understanding the mechanisms that give rise to social structure is central to predicting the evolutionary and ecological outcomes of social interactions. Modeling this process is challenging, because all individuals simultaneously behave in ways that shape their social environments—a process called social niche construction (SNC). In earlier work, we demonstrated that aggression acts as an SNC trait in fruit flies (Drosophila melanogaster), but the mechanisms of that process remained cryptic. Here, we analyze how individual social group preferences generate overall social structure. We use a combination of agent-based simulation and approximate Bayesian computation to fit models to empirical data. We confirm that genetic variation in aggressive behavior influences social group structure. Furthermore, we find that female decamping due to male behavior may play an underappreciated role in structuring social groups. Male-male aggression may sometimes destabilize groups, but it may also be an SNC behavior for shaping desirable groups for females. Density intensifies female social preferences; thus, the role of female behavior in shaping group structure may become more important at high densities. Our ability to model the ontogeny of group structure demonstrates the utility of the Bayesian model–based approach in social behavioral studies.
A Burrowing/Tunneling Assay for Detection of Hypoxia in Drosophila melanogaster Larvae
(JoVE, 2018) Qiang, Karen M.; Zhou, Fanli; Beckingham, Kathleen M.
Oxygen deprivation in animals can result from exposure to low atmospheric oxygen levels or from internal tissue damage that interferes with oxygen distribution. It is also possible that aberrant behavior of oxygen-sensing neurons could induce hypoxia-like behavior in the presence of normal oxygen levels. In D. melanogaster, development at low oxygen levels results in inhibition of growth and sluggish behavior during the larval phases. However, these established manifestations of oxygen deficit overlap considerably with the phenotypes of many mutations that regulate growth, stress responses or locomotion. As result, there is currently no assay available to identify i) cellular hypoxia induced by a mutation or ii) hypoxia-like behavior when induced by abnormal neuronal behavior. We have recently identified two distinctive behaviors in D. melanogaster larvae that occur at normal oxygen levels in response to internal detection of hypoxia. First, at all stages, such larvae avoid burrowing into food, often straying far away from a food source. Second, tunneling into a soft substratum, which normally occurs during the wandering third instar stage is completely abolished if larvae are hypoxic. The assay described here is designed to detect and quantitate these behaviors and thus to provide a way to detect hypoxia induced by internal damage rather than low external oxygen. Assay plates with an agar substratum and a central plug of yeast paste are used to support animals through larval life. The positions and state of the larvae are tracked daily as they proceed from first to third instar. The extent of tunneling into the agar substratum during wandering phase is quantitated after pupation using NIH ImageJ. The assay will be of value in determining when hypoxia is a component of a mutant phenotype and thus provide insight into possible sites of action of the gene in question.
A Choose-Your-Own-Adventure-Style Virtual Lab Activity
(American Chemical Society, 2021) Warning, Lauren A.; Kobylianskii, Krista
Especially in the wake of the recent COVID-19 pandemic, which has caused universities across the globe to suspend in-person classes, online alternatives for laboratory activities are needed. Here, we report a choose-your-own-adventure (CYOA)-style activity, in which undergraduate general chemistry students influence the observed outcome of a prerecorded electrochemistry lab experiment. During the activity, students decide how to build an electrochemical cell by varying experimental parameters including electrode charge, power source voltage, and salt addition. We show evidence that students’ understanding of electrochemistry concepts improved after completing the CYOA-style activity. We propose that CYOA-style activities strike a good balance between the demand for instructor time and student opportunity to develop laboratory decision-making skills. We suggest the use of CYOA-style activities as a better alternative to simply having students watch prerecorded videos of laboratory experiments when a traditional in-laboratory activity is impossible.
A collagen glucosyltransferase drives lung adenocarcinoma progression in mice
(Springer Nature, 2021) Guo, Hou-Fu; Bota-Rabassedas, Neus; Terajima, Masahiko; Leticia Rodriguez, B.; Gibbons, Don L.; Chen, Yulong; Banerjee, Priyam; Tsai, Chi-Lin; Tan, Xiaochao; Liu, Xin; Yu, Jiang; Tokmina-Roszyk, Michal; Stawikowska, Roma; Fields, Gregg B.; Miller, Mitchell D.; Wang, Xiaoyan; Lee, Juhoon; Dalby, Kevin N.; Creighton, Chad J.; Phillips, George N.Jr.; Tainer, John A.; Yamauchi, Mitsuo; Kurie, Jonathan M.
Cancer cells are a major source of enzymes that modify collagen to create a stiff, fibrotic tumor stroma. High collagen lysyl hydroxylase 2 (LH2) expression promotes metastasis and is correlated with shorter survival in lung adenocarcinoma (LUAD) and other tumor types. LH2 hydroxylates lysine (Lys) residues on fibrillar collagen’s amino- and carboxy-terminal telopeptides to create stable collagen cross-links. Here, we show that electrostatic interactions between the LH domain active site and collagen determine the unique telopeptidyl lysyl hydroxylase (tLH) activity of LH2. However, CRISPR/Cas-9-mediated inactivation of tLH activity does not fully recapitulate the inhibitory effect of LH2 knock out on LUAD growth and metastasis in mice, suggesting that LH2 drives LUAD progression, in part, through a tLH-independent mechanism. Protein homology modeling and biochemical studies identify an LH2 isoform (LH2b) that has previously undetected collagen galactosylhydroxylysyl glucosyltransferase (GGT) activity determined by a loop that enhances UDP-glucose-binding in the GLT active site and is encoded by alternatively spliced exon 13 A. CRISPR/Cas-9-mediated deletion of exon 13 A sharply reduces the growth and metastasis of LH2b-expressing LUADs in mice. These findings identify a previously unrecognized collagen GGT activity that drives LUAD progression.
A community-based geological reconstruction of Antarctic Ice Sheet deglaciation since the Last Glacial Maximum
(Elsevier, 2014) The RAISED Consortium; Bentley, Michael J.; Ó Cofaigh, Colm; Anderson, John B.; Conway, Howard; Davies, Bethan; Graham, Alastair G.C.; Hillenbrand, Claus-Dieter; Hodgson, Dominic A.; Jamieson, Stewart S.R.; Larter, Robert D.; Mackintosh, Andrew; Smith, James A.; Verleyen, Elie; Ackert, Robert P.; Bart, Philip J.; Berg, Sonja; Brunstein, Daniel; Canals, Miquel; Colhoun, Eric A.; Crosta, Xavier; Dickens, William A.; Domack, Eugene; Dowdeswell, Julian A.; Dunbar, Robert; Ehrmann, Werner; Evans, Jeffrey; Favier, Vincent; Fink, David; Fogwill, Christopher J.; Glasser, Neil F.; Gohl, Karsten; Golledge, Nicholas R.; Goodwin, Ian; Gore, Damian B.; Greenwood, Sarah L.; Hall, Brenda L.; Hall, Kevin; Hedding, David W.; Hein, Andrew S.; Hocking, Emma P.; Jakobsson, Martin; Johnson, Joanne S.; Jomelli, Vincent; Jones, R. Selwyn; Klages, Johann P.; Kristoffersen, Yngve; Kuhn, Gerhard; Leventer, Amy; Licht, Kathy; Lilly, Katherine; Lindow, Julia; Livingstone, Stephen J.; Massé, Guillaume; McGlone, Matt S.; McKay, Robert M.; Melles, Martin; Miura, Hideki; Mulvaney, Robert; Nel, Werner; Nitsche, Frank O.; O'Brien, Philip E.; Post, Alexandra L.; Roberts, Stephen J.; Saunders, Krystyna M.; Selkirk, Patricia M.; Simms, Alexander R.; Spiegel, Cornelia; Stolldorf, Travis D.; Sugden, David E.; van der Putten, Nathalie; van Ommen, Tas; Verfaillie, Deborah; Vyverman, Wim; Wagner, Bernd; White, Duanne A.; Witus, Alexandra E.; Zwartz, Dan
A robust understanding of Antarctic Ice Sheet deglacial history since the Last Glacial Maximum is important in order to constrain ice sheet and glacial-isostatic adjustment models, and to explore the forcing mechanisms responsible for ice sheet retreat. Such understanding can be derived from a broad range of geological and glaciological datasets and recent decades have seen an upsurge in such data gathering around the continent and Sub-Antarctic islands. Here, we report a new synthesis of those datasets, based on an accompanying series of reviews of the geological data, organised by sector. We present a series of timeslice maps for 20 ka, 15 ka, 10 ka and 5 ka, including grounding line position and ice sheet thickness changes, along with a clear assessment of levels of confidence. The reconstruction shows that the Antarctic Ice sheet did not everywhere reach the continental shelf edge at its maximum, that initial retreat was asynchronous, and that the spatial pattern of deglaciation was highly variable, particularly on the inner shelf. The deglacial reconstruction is consistent with a moderate overall excess ice volume and with a relatively small Antarctic contribution to meltwater pulse 1a. We discuss key areas of uncertainty both around the continent and by time interval, and we highlight potential priorities for future work. The synthesis is intended to be a resource for the modelling and glacial geological community.
A comparative approach to testing hypotheses for the evolution of sex-biased dispersal in bean beetles
(Wiley, 2015) Downey, Michelle H.; Searle, Rebecca; Bellur, Sunil; Geiger, Adam; Maitner, Brian S.; Ohm, Johanna R.; Tuda, Midori; Miller, Tom E.X.
Understanding the selective forces that shape dispersal strategies is a fundamental goal of evolutionary ecology and is increasingly important in changing, human-altered environments. Sex-biased dispersal (SBD) is common in dioecious taxa, and understanding variation in the direction and magnitude of SBD across taxa has been a persistent challenge. We took a comparative, laboratory-based approach using 16 groups (species or strains) of bean beetles (generaﾠAcanthoscelides,ﾠCallosobruchus, andﾠZabrotes, including 10 strains of one species) to test two predictions that emerge from dominant hypotheses for the evolution of SBD: (1) groups that suffer greater costs of inbreeding should exhibit greater SBD in favor of either sex (inbreeding avoidance hypothesis) and (2) groups with stronger local mate competition should exhibit greater male bias in dispersal (kin competition avoidance hypothesis). We used laboratory experiments to quantify SBD in crawling dispersal, the fitness effects of inbreeding, and the degree of polygyny (number of female mates per male), a proxy for local mate competition. While we found that both polygyny and male-biased dispersal were common across bean beetle groups, consistent with the kin competition avoidance hypothesis, quantitative relationships between trait values did not support the predictions. Across groups, there was no significant association between SBD and effects of inbreeding nor SBD and degree of polygyny, using either raw values or phylogenetically independent contrasts. We discuss possible limitations of our experimental approach for detecting the predicted relationships, as well as reasons why single-factor hypotheses may be too simplistic to explain the evolution of SBD.
A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures
(American Chemical Society, 2018) Boninsegna, Lorenzo; Banisch, Ralf; Clementi, Cecilia; Center for Theoretical Biological Physics
Macromolecular systems are composed of a very large number of atomic degrees of freedom. There is strong evidence suggesting that structural changes occurring in large biomolecular systems at long time scale dynamics may be captured by models coarser than atomistic, although a suitable or optimal coarse-graining is a priori unknown. Here we propose a systematic approach to learning a coarse representation of a macromolecule from microscopic simulation data. In particular, the definition of effective coarse variables is achieved by partitioning the degrees of freedom both in the structural (physical) space and in the conformational space. The identification of groups of microscopic particles forming dynamical coherent states in different metastable states leads to a multiscale description of the system, in space and time. The application of this approach to the folding dynamics of two proteins provides a revised view of the classical idea of prestructured regions (foldons) that combine during a protein-folding process and suggests a hierarchical characterization of the assembly process of folded structures.
A de novo matrix for macroscopic living materials from bacteria
(Springer Nature, 2022) Molinari, Sara; Tesoriero, Robert F.; Li, Dong; Sridhar, Swetha; Cai, Rong; Soman, Jayashree; Ryan, Kathleen R.; Ashby, Paul D.; Ajo-Franklin, Caroline M.
Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create materials with tailored functions. While bottom-up assembly of macroscopic ELMs with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. Here we report growth of ELMs from Caulobacter crescentus cells that display and secrete a self-interacting protein. This protein formed a de novo matrix and assembled cells into centimeter-scale ELMs. Discovery of design and assembly principles allowed us to tune the composition, mechanical properties, and catalytic function of these ELMs. This work provides genetic tools, design and assembly rules, and a platform for growing ELMs with control over both matrix and cellular structure and function.
A deep learning solution for crystallographic structure determination
(International Union of Crystallography, 2023) Pan, T.; Jin, S.; Miller, M. D.; Kyrillidis, A.; Phillips, G. N.
The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallography, based on a synthetic dataset of small fragments derived from a large well curated subset of solved structures in the Protein Data Bank (PDB). In particular, electron-density estimates of simple artificial systems are produced directly from corresponding Patterson maps using a convolutional neural network architecture as a proof of concept.
A Detailed Clinical Case of Localized Prostate Tumors Treated with Nanoparticle-Assisted Sub-Ablative Laser Ablation
(MDPI, 2024) Kadria-Vili, Yara; Schwartz, Jon A.; Polascik, Thomas J.; Goodrich, Glenn P.; Jorden, David; Pinder, Diane; Halas, Naomi J.; Rastinehad, Ardeshir R.; Laboratory for Nanophotonics
AuroLase® Therapy—a nanoparticle-enabled focal therapy—has the potential to safely and effectively treat localized prostate cancer (PCa), preserving baseline functionality. This article presents a detailed case of localized PCa treated with AuroLase, providing insight on expectations from the diagnosis of PCa to one year post-treatment. AuroLase Therapy is a two-day treatment consisting of a systemic infusion of gold nanoshells (~150-nm hydrodynamic diameter) on Day 1, and sub-ablative laser treatment on Day 2. Multiparametric MRI (mpMRI) was used for tumor visualization, treatment planning, and therapy response assessment. The PCa was targeted with a MR/Ultrasound-fusion (MR/US) transperineal approach. Successful treatment was confirmed at 6 and 12 months post-treatment by the absence of disease in MR/US targeted biopsies. On the mpMRI, confined void space was evident, an indication of necrotic tissues encompassing the treated lesion, which was completely resolved at 12 months, forming a band-like scar with no evidence of recurrent tumor. The patient’s urinary and sexual functions were unchanged. During the one-year follow-up, changes on the DCE sequence and in the Ktrans and ADC values assist in qualitatively and quantitatively evaluating tissue changes. The results highlight the potential of gold-nanoparticle-enabled sub-ablative laser treatment to target and control localized PCa, maintain quality of life, and preserve baseline functionality.
A deterministic model for one-dimensional excluded flow with local interactions
(Public Library of Science, 2017) Zarai, Yoram; Margaliot, Michael; Kolomeisky, Anatoly B.
Natural phenomena frequently involve a very large number of interacting molecules moving in confined regions of space. Cellular transport by motor proteins is an example of such collective behavior. We derive a deterministic compartmental model for the unidirectional flow of particles along a one-dimensional lattice of sites with nearest-neighbor interactions between the particles. The flow between consecutive sites is governed by a “soft” simple exclusion principle and by attracting or repelling forces between neighboring particles. Using tools from contraction theory, we prove that the model admits a unique steady-state and that every trajectory converges to this steady-state. Analysis and simulations of the effect of the attracting and repelling forces on this steady-state highlight the crucial role that these forces may play in increasing the steady-state flow, and reveal that this increase stems from the alleviation of traffic jams along the lattice. Our theoretical analysis clarifies microscopic aspects of complex multi-particle dynamic processes.
A discrete intermediate for the biosynthesis of both the enediyne core and the anthraquinone moiety of enediyne natural products
(PNAS, 2023) Bhardwaj, Minakshi; Cui, Zheng; Daniel Hankore, Erome; Moonschi, Faruk H.; Saghaeiannejad Esfahani, Hoda; Kalkreuter, Edward; Gui, Chun; Yang, Dong; Phillips, George N.; Thorson, Jon S.; Shen, Ben; Van Lanen, Steven G.
The enediynes are structurally characterized by a 1,5-diyne-3-ene motif within a 9- or 10-membered enediyne core. The anthraquinone-fused enediynes (AFEs) are a subclass of 10-membered enediynes that contain an anthraquinone moiety fused to the enediyne core as exemplified by dynemicins and tiancimycins. A conserved iterative type I polyketide synthase (PKSE) is known to initiate the biosynthesis of all enediyne cores, and evidence has recently been reported to suggest that the anthraquinone moiety also originates from the PKSE product. However, the identity of the PKSE product that is converted to the enediyne core or anthraquinone moiety has not been established. Here, we report the utilization of recombinant E. coli coexpressing various combinations of genes that encode a PKSE and a thioesterase (TE) from either 9- or 10-membered enediyne biosynthetic gene clusters to chemically complement ΔPKSE mutant strains of the producers of dynemicins and tiancimycins. Additionally, 13C-labeling experiments were performed to track the fate of the PKSE/TE product in the ΔPKSE mutants. These studies reveal that 1,3,5,7,9,11,13-pentadecaheptaene is the nascent, discrete product of the PKSE/TE that is converted to the enediyne core. Furthermore, a second molecule of 1,3,5,7,9,11,13-pentadecaheptaene is demonstrated to serve as the precursor of the anthraquinone moiety. The results establish a unified biosynthetic paradigm for AFEs, solidify an unprecedented biosynthetic logic for aromatic polyketides, and have implications for the biosynthesis of not only AFEs but all enediynes.
A Displaced Lower Mantle Source of the Hainan Plume in South China Revealed by Receiver Function Imaging of the CEArray
(Wiley, 2024) Zhang, Yan; Niu, Fenglin; Ning, Jieyuan; Yu, Chunquan
We analyzed 49,592 teleseismic receiver functions (RFs) recorded by 278 CEArray stations to image the mantle transition zone (MTZ) beneath the South China Block to understand the origins of deep velocity anomalies and their potential links to subduction and intraplate volcanism. We employed a fast-marching method and a high-resolution 3-D velocity model (FWEA18) derived from full waveform inversion in computing P-to-S conversion times to better image the 410- and 660-km discontinuities. Our results indicate that the common-conversion-point stacking of RFs using 3-D conversion times yielded better migration images of the two discontinuities. The images revealed a slightly depressed 410-km with a few small uplifted patches, and showed that the 660-km beneath the western Yangtze Craton is depressed by 10–25 km, which is likely caused by the stagnant Paleo-Pacific slab. The 660-km beneath the southern Cathaysia Block has a 5–15 km high plateau with a topographic low at its central part. The lateral dimension of the topographic low is ∼150 km and is located beneath the central Pearl River Mount Basin near Hong Kong. We speculate that the topographic low occurs within the Hainan plume with a temperature excess of ∼300–400 K and is caused by the garnet phase transition. The displaced deep plume enters the MTZ and spreads nearly horizontally at the base. The plume evolves into two channels with a minor one toward the northeast and a major one toward the southwest, which keep moving upward to the 410-km. The southwest channel is likely the source that feeds the Hainan volcanoes.
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data
(Oxford University Press, 2019) Zhu, Jiafan; Liu, Xinhao; Ogilvie, Huw A.; Nakhleh, Luay K.
Motivation: Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting. However, these methods can only handle a small number of loci from a handful of genomes. Results: In this article, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks on subproblems and then merges them into a network on the full set of taxa. To reduce the number of trinets to infer, we formulate a Hitting Set version of the problem of finding a small number of subsets, and implement a simple heuristic to solve it. We studied their performance, in terms of both running time and accuracy, on simulated as well as on biological datasets. The two-step method accurately infers phylogenetic networks at a scale that is infeasible with existing methods. The results are a significant and promising step towards accurate, large-scale phylogenetic network inference.

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