BioSciences Publications

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BioSciences faculty publications. For works published before Summer 2014, please see the Biochemistry & Cell Biology and Ecology & Evolutionary Biology collections.

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    Trapped-ion quantum simulation of electron transfer models with tunable dissipation
    (AAAS, 2024) So, Visal; Duraisamy Suganthi, Midhuna; Menon, Abhishek; Zhu, Mingjian; Zhuravel, Roman; Pu, Han; Wolynes, Peter G.; Onuchic, José N.; Pagano, Guido; Center for Theoretical Biological Physics
    Electron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. The exact simulation of these reactions is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. Here, we experimentally simulate a paradigmatic model of molecular electron transfer using a multispecies trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently. By manipulating both the ground-state and optical qubits, we observe the real-time dynamics of the spin excitation, measuring the transfer rate in several regimes of adiabaticity and relaxation dynamics. Our results provide a testing ground for increasingly rich models of molecular excitation transfer processes that are relevant for molecular electronics and light-harvesting systems.
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    Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet
    (Springer Nature, 2024) Saliba, Nahima; Gagliano, Gabriella; Gustavsson, Anna-Karin; Smalley-Curl Institute;Center for Nanoscale Imaging Sciences
    Multi-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample. This easily adaptable microfluidic fabrication pipeline allows for the incorporation of reflective optics into microfluidic channels without disrupting efficient and automated solution exchange. We combine these innovations with point spread function engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets. We then demonstrate that this platform, termed soTILT3D, enables whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.
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    A bacterial transcription activator dedicated to the expression of the enzyme catalyzing the first committed step in fatty acid biosynthesis
    (Oxford University Press, 2024) Xu, Yuanyou; Lin, Zihan; Hou, Jiyuan; Ye, Kai; Han, Sirui; Liang, Yuxuan; Liang, Huihui; Wu, Shihua; Tao, Yizhi J; Gao, Haichun
    Acetyl-CoA carboxylase (ACCase) catalyzes the first committed and rate-limiting step of de novo fatty acid synthesis (FAS). Although this step is tightly regulated, regulators that specifically control transcription of the ACCase genes remain elusive. In this study, we identified LysR-type transcriptional regulator AccR as a dedicated activator for the transcription of accS, a gene encoding a multiple-domain ACCase in Shewanella oneidensis. We showed that AccR interacts with the accS promoter in vivo in response to changes in acetyl-CoA levels and in vitro. Analysis of the crystal structure of the effector-binding domain (EBD) of AccR identified two potential ligand-binding pockets, one of which is likely to bind acetyl-CoA as a ligand based on results from molecular docking, direct binding assay and mutational analysis of the residues predicted to interact with acetyl-CoA. Despite this, the interaction between AccR and acetyl-CoA alone appears unstable, implying that an additional yet unknown ligand is required for activation of AccR. Furthermore, we showed that AccR is acetylated, but the modification may not be critical for sensing acetyl-CoA. Overall, our data substantiate the existence of a dedicated transcriptional regulator for ACCases, expanding our current understanding of the regulation of FAS.
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    Electronic relaxation pathways in thio-acridone and thio-coumarin: two heavy-atom-free photosensitizers absorbing visible light
    (Royal Society of Chemistry, 2024) Acquah, Chris; Hoehn, Sean; Krul, Sarah; Jockusch, Steffen; Yang, Shudan; Seth, Sourav Kanti; Lee, Eric; Xiao, Han; Crespo-Hernández, Carlos E.; SynthX Center
    Heavy-atom-free photosensitizers (HAF-PSs) have emerged as a new class of photosensitizers aiming to broaden their applicability and versatility across various fields of the photodynamic therapy of cancers. The strategy involves replacing the exocyclic oxygen atoms of the carbonyl groups of established biocompatible organic fluorophores with sulfur, thereby bathochromically shifting their absorption spectra and enhancing their intersystem crossing efficiencies. Despite these advancements, the photophysical attributes and electronic relaxation mechanisms of many of these HAF-PSs remain inadequately elucidated. In this study, we investigate the excited state dynamics and photochemical properties of two promising HAF-PSs, thio-coumarin and thio-acridone. Employing a combination of steady-state and time-resolved techniques from femtoseconds to microseconds, coupled with quantum chemical calculations, we unravel the electronic relaxation mechanisms that give rise to the efficient population of long-lived and reactive triplet states in these HAF-PSs.
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    Temporal host–symbiont dynamics in community contexts: Impacts of host fitness and vertical transmission efficiency on symbiosis prevalence
    (Wiley, 2024) Gundel, Pedro E.; Ueno, Andrea C.; Casas, Cecilia; Miller, Tom E. X.; Pérez, Luis I.; Cuyeu, Romina; Omacini, Marina
    Symbiotic associations play a role in plant ecology and evolution, but the outcome of the interaction depends on the life-history traits of the partners and the environmental context. Although symbiosis with vertically transmitted microorganisms should result in mutualism, it is not clear how the transmission process aligns with the outcome of the context-dependent symbiosis. For 3 years, we sampled individuals of an annual plant species that forms symbiosis with a vertically transmitted fungal endophyte, in paired stands of two contrasting vegetation communities (humid mesophytic meadows [HMM]: productive/low stress, and humid prairies [HP]: less productive/high stress). We estimated the prevalence of symbiosis at the population level, and the fitness of the plant, the symbiotic status and vertical transmission efficiency at the individual level. Over 3 years, the prevalence of symbiosis was ≈100% in HMM and ≈75% in HP. Plant fitness was very low and high in years with precipitation below and above the yearly mean, respectively. The higher fitness of endophyte-symbiotic plants was evident in the HMM and high precipitation years. Vertical transmission of endophytes was higher in HMM (≈96%) compared to HP (≈93%) and was not related to plant fitness. Despite transmission inefficiencies in HP, changes in prevalence within the growing season (from seeds to the final plant stand) suggest a fitness advantage for symbiotic plants. Vertical transmission is expected to promote mutualism as it aligns partners' fitness. Although symbiotic plants showed higher fitness and the probability of transmission failures was higher among low-fitness plants, the variation in transmission efficiency between plants and vegetation communities was not related to the fitness of the individual host. Our study provides evidence that context-dependent vertical transmission efficiency and endophyte-mediated fitness advantages interact complexly to determine the prevalence of symbiosis in populations that occur in contrasting vegetation communities. Read the free Plain Language Summary for this article on the Journal blog.
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    Defaunation Increases Clustering and Fine-Scale Spatial Genetic Structure in a Small-Seeded Palm Despite Remaining Small-Bodied Frugivores
    (Wiley, 2025) Lamperty, Therese; Diaz-Martin, Zoe; Swamy, Varun; Karubian, Jordan; Choo, Juanita; Dunham, Amy E.
    Anthropogenic pressures such as hunting are increasingly driving the localised functional extinctions of large- and medium-sized wildlife in tropical forests, a phenomenon broadly termed ‘defaunation’. Concurrently in these areas, smaller-bodied species benefit from factors such as competitive release and increase in numbers. This transformation of the wildlife community can impact species interactions and ecosystem services such as seed dispersal and seed-mediated geneflow with far-reaching consequences. Evidence for negative genetic effects following defaunation is well-documented in large-seeded plants that require large frugivores for long-distance seed dispersal. However, how defaunation affects plants with small or medium-small seeds (< 1.5 cm), which tend to be consumed and dispersed by frugivorous mutualists of a range of body sizes and responses to anthropogenic threats, is not well understood. To better understand defaunation's impacts on tropical plant communities, we investigated spatial and genetic patterns in a hyperabundant medium-to-small-seeded palm, Euterpe precatoria in three sites with different defaunation levels. Results indicate that defaunation is associated with higher fine-scale spatial genetic structure among seedlings and increased spatial clustering within seedling cohorts and between seedlings and conspecific adults, as well as a reduction in nearest-neighbour distances between seedlings and conspecific adults. There were no clear effects on inbreeding or genetic diversity. However, we caution these trends may indicate that defaunation reduces seed dispersal services for species previously presumed to be robust to deleterious effects of losing large frugivores by virtue of having smaller seeds and broad suites of dispersal agents, and negative downstream effects on genetic diversity could occur.
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    Ecological shifts underlie parallels between ontogenetic and evolutionary allometries in parrotfishes
    (Royal Society, 2024) Neves, Mayara P.; Hugi, April; Chan, Howan; Arnold, Kaleigh; Titus, Kara; Westneat, Mark W.; Zelditch, Miriam L.; Brandl, Simon; Evans, Kory M.
    During ontogeny, animals often undergo significant shape and size changes, coinciding with ecological shifts. This is evident in parrotfishes (Eupercaria: Labridae), which experience notable ecological shifts during development, transitioning from carnivorous diets as larvae and juveniles to herbivorous and omnivorous diets as adults, using robust beaks and skulls for feeding on coral skeletons and other hard substrates. These ontogenetic shifts mirror their evolutionary history, as parrotfishes are known to have evolved from carnivorous wrasse ancestors. Parallel shifts at ontogenetic and phylogenetic levels may have resulted in similar evolutionary and ontogenetic allometric trajectories within parrotfishes. To test this hypothesis, using micro-computed tomography (μCT) scanning and three-dimensional geometric morphometrics, we analyse the effects of size on the skull shape of the striped parrotfish Scarus iseri and compare its ontogenetic allometry to the evolutionary allometries of 57 parrotfishes and 162 non-parrotfish wrasses. The young S. iseri have skull shapes resembling non-parrotfish wrasses and grow towards typical adult parrotfish forms as they mature. There was a significant relationship between size and skull shapes and strong evidence for parallel ontogenetic and evolutionary slopes in parrotfishes. Our findings suggest that morphological changes associated with the ecological shift characterizing interspecific parrotfish evolution are conserved in their intraspecific ontogenies.
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    Invasive plants and their root traits are linked to the homogenization of soil microbial communities across the United States
    (National Academy of Sciences, 2024) Nunez-Mir, Gabriela C.; McCary, Matthew A.
    Although the impacts of invasive plants on soil ecosystems are widespread, the role and impacts of invader root traits in structuring microbial communities remain poorly understood. Here, we present a macroecological study investigating how plant invaders and their root traits affect soil microbial communities, spanning data from 377 unique plots across the United States sampled multiple times, totaling 632 sampling events and 94 invasive plant species. We found that native and invasive plants harbor different root traits on average, with invasive plants possessing higher specific root lengths and native plants having higher root tissue density. We also show that soil microbial communities experiencing heavy plant invasions were more similar to each other in composition across ecosystem types and geographical regions than plots with higher proportions of native plants, which displayed highly variable microbial communities across the continent. Root traits of invasive plants in highly invaded plots explained two times more variation in microbial composition than native plants. This work represents an important step toward understanding macroscale and cross-scale patterns of the relationship between plant invasions, root traits, and soil microbial composition. Our findings provide insights into how invasive plants may impact ecosystem functioning at the macroscale via their homogenizing influence on microbial communities.
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    Evolutionary innovation accelerates morphological diversification in pufferfishes and their relatives
    (Oxford University Press, 2024) Troyer, Emily M; Evans, Kory M; Goatley, Christopher H R; Friedman, Matt; Carnevale, Giorgio; Nicholas, Benjamin; Kolmann, Matthew; Bemis, Katherine E; Arcila, Dahiana
    Evolutionary innovations have played an important role in shaping the diversity of life on Earth. However, how these innovations arise and their downstream effects on patterns of morphological diversification remain poorly understood. Here, we examine the impact of evolutionary innovation on trait diversification in tetraodontiform fishes (pufferfishes, boxfishes, ocean sunfishes, and allies). This order provides an ideal model system for studying morphological diversification owing to their range of habitats and divergent morphologies, including the fusion of the teeth into a beak in several families. Using three-dimensional geometric morphometric data for 176 extant and fossil species, we examine the effect of skull integration and novel habitat association on the evolution of innovation. Strong integration may be a requirement for rapid trait evolution and facilitating the evolution of innovative structures, like the tetraodontiform beak. Our results show that the beak arose in the presence of highly conserved patterns of integration across the skull, suggesting that integration did not limit the range of available phenotypes to tetraodontiforms. Furthermore, we find that beaks have allowed tetraodontiforms to diversify into novel ecological niches, irrespective of habitat. Our results suggest that general rules pertaining to evolutionary innovation may be more nuanced than previously thought.
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    The Drosophila Nesprin-1 homolog MSP300 is required for muscle autophagy and proteostasis
    (The Company of Biologists, 2024) van der Graaf, Kevin; Srivastav, Saurabh; Nishad, Rajkishor; Stern, Michael; McNew, James A.
    Nesprin proteins, which are components of the linker of nucleoskeleton and cytoskeleton (LINC) complex, are located within the nuclear envelope and play prominent roles in nuclear architecture. For example, LINC complex proteins interact with both chromatin and the cytoskeleton. Here, we report that the Drosophila Nesprin MSP300 has an additional function in autophagy within larval body wall muscles. RNAi-mediated MSP300 knockdown in larval body wall muscles resulted in defects in the contractile apparatus, muscle degeneration and defective autophagy. In particular, MSP300 knockdown caused accumulation of cytoplasmic aggregates that contained poly-ubiquitylated cargo, as well as the autophagy receptor ref(2)P (the fly homolog of p62 or SQSTM) and Atg8a. Furthermore, MSP300 knockdown larvae expressing an mCherry–GFP-tagged Atg8a transgene exhibited aberrant persistence of the GFP signal within these aggregates, indicating failure of autophagosome maturation. These autophagy deficits were similar to those exhibited by loss of the endoplasmic reticulum (ER) fusion protein Atlastin (Atl), raising the possibility that Atl and MSP300 might function in the same pathway. In support of this possibility, we found that a GFP-tagged MSP300 protein trap exhibited extensive localization to the ER. Alteration of ER-directed MSP300 might abrogate important cytoskeletal contacts necessary for autophagosome completion.
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    The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes
    (National Academy of Sciences, 2024) Jaafari, Hana; Bueno, Carlos; Schafer, Nicholas P.; Martin, Jonathan; Morcos, Faruck; Wolynes, Peter G.; Center for Theoretical Biophysics
    Protein evolution is guided by structural, functional, and dynamical constraints ensuring organismal viability. Pseudogenes are genomic sequences identified in many eukaryotes that lack translational activity due to sequence degradation and thus over time have undergone “devolution.” Previously pseudogenized genes sometimes regain their protein-coding function, suggesting they may still encode robust folding energy landscapes despite multiple mutations. We study both the physical folding landscapes of protein sequences corresponding to human pseudogenes using the Associative Memory, Water Mediated, Structure and Energy Model, and the evolutionary energy landscapes obtained using direct coupling analysis (DCA) on their parent protein families. We found that generally mutations that have occurred in pseudogene sequences have disrupted their native global network of stabilizing residue interactions, making it harder for them to fold if they were translated. In some cases, however, energetic frustration has apparently decreased when the functional constraints were removed. We analyzed this unexpected situation for Cyclophilin A, Profilin-1, and Small Ubiquitin-like Modifier 2 Protein. Our analysis reveals that when such mutations in the pseudogene ultimately stabilize folding, at the same time, they likely alter the pseudogenes’ former biological activity, as estimated by DCA. We localize most of these stabilizing mutations generally to normally frustrated regions required for binding to other partners.
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    Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory
    (American Chemical Society, 2024) Haynes, Karmella A.; Andrews, Lauren B.; Beisel, Chase L.; Chappell, James; Cuba Samaniego, Christian E.; Dueber, John E.; Dunlop, Mary J.; Franco, Elisa; Lucks, Julius B.; Noireaux, Vincent; Savage, David F.; Silver, Pamela A.; Smanski, Michael; Young, Eric
    The Cold Spring Harbor Laboratory (CSHL) Summer Course on Synthetic Biology, established in 2013, has emerged as a premier platform for immersive education and research in this dynamic field. Rooted in CSHL’s rich legacy of biological discovery, the course offers a comprehensive exploration of synthetic biology’s fundamentals and applications. Led by a consortium of faculty from diverse institutions, the course structure seamlessly integrates practical laboratory sessions, exploratory research rotations, and enriching seminars by leaders in the field. Over the years, the curriculum has evolved to cover essential topics such as cell-free transcription–translation, DNA construction, computational modeling of gene circuits, engineered gene regulation, and CRISPR technologies. In this review, we describe the history, development, and structure of the course, and discuss how elements of the course might inform the development of other short courses in synthetic biology. We also demonstrate the course’s impact beyond the lab with a summary of alumni contributions to research, education, and entrepreneurship. Through these efforts, the CSHL Summer Course on Synthetic Biology remains at the forefront of shaping the next generation of synthetic biologists.
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    Native Plant Diversity Generates Microbial Legacies That Either Promote or Suppress Non-Natives, Depending on Drought History
    (Wiley, 2024) Tao, Zhibin; Zhang, Kaoping; Callaway, Ragan M.; Siemann, Evan; Liu, Yanjie; Huang, Wei
    Diverse native plant communities resist non-native plants more than species-poor communities, in part through resource competition. The role of soil biota in diversity–invasibility relationships is poorly understood, although non-native plants interact with soil biota during invasions. We tested the responses of non-native plants to soil biota generated by different native plant diversities. We applied well-watered and drought treatments in both conditioning and response phases to explore the effects of ‘historical’ and ‘contemporary’ environmental stresses. When generated in well-watered soils, the microbial legacies from higher native diversity inhibited non-native growth in well-watered conditions. In contrast, when generated in drought-treated soils, the microbial legacies from higher native diversity facilitated non-native growth in well-watered conditions. Contemporary drought eliminated microbial legacy effects on non-native growth. We provide a new understanding of mechanisms behind diversity–invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota and non-native plants.
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    Expansion of a neural crest gene signature following ectopic MYCN expression in sympathoadrenal lineage cells in vivo
    (Public Library of Science, 2024) Ibarra-García-Padilla, Rodrigo; Nambiar, Annika; Hamre, Thomas A.; Singleton, Eileen W.; Uribe, Rosa A.
    Neural crest cells (NCC) are multipotent migratory stem cells that originate from the neural tube during early vertebrate embryogenesis. NCCs give rise to a variety of cell types within the developing organism, including neurons and glia of the sympathetic nervous system. It has been suggested that failure in correct NCC differentiation leads to several diseases, including neuroblastoma (NB). During normal NCC development, MYCN is transiently expressed to promote NCC migration, and its downregulation precedes neuronal differentiation. Overexpression of MYCN has been linked to high-risk and aggressive NB progression. For this reason, understanding the effect overexpression of this oncogene has on the development of NCC-derived sympathoadrenal progenitors (SAP), which later give rise to sympathetic nerves, will help elucidate the developmental mechanisms that may prime the onset of NB. Here, we found that overexpressing human EGFP-MYCN within SAP lineage cells in zebrafish led to the transient formation of an abnormal SAP population, which displayed expanded and elevated expression of NCC markers while paradoxically also co-expressing SAP and neuronal differentiation markers. The aberrant NCC signature was corroborated with in vivo time-lapse confocal imaging in zebrafish larvae, which revealed transient expansion of sox10 reporter expression in MYCN overexpressing SAPs during the early stages of SAP development. In these aberrant MYCN overexpressing SAP cells, we also found evidence of dampened BMP signaling activity, indicating that BMP signaling disruption occurs following elevated MYCN expression. Furthermore, we discovered that pharmacological inhibition of BMP signaling was sufficient to create an aberrant NCC gene signature in SAP cells, phenocopying MYCN overexpression. Together, our results suggest that MYCN overexpression in SAPs disrupts their differentiation by eliciting abnormal NCC gene expression programs, and dampening BMP signaling response, having developmental implications for the priming of NB in vivo.
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    Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA synthesis
    (Elsevier, 2024) Chang, Caleb; Zhou, Grace; Lee Luo, Christie; Eleraky, Sarah; Moradi, Madeline; Gao, Yang
    Nucleoside analogue drugs are pervasively used as antiviral and chemotherapy agents. Cytarabine and gemcitabine are anti-cancer nucleoside analogue drugs that contain C2′ modifications on the sugar ring. Despite carrying all the required functional groups for DNA synthesis, these two compounds inhibit DNA extension once incorporated into DNA. It remains unclear how the C2′ modifications on cytarabine and gemcitabine affect the polymerase active site during substrate binding and DNA extension. Using steady-state kinetics, static and time-resolved X-ray crystallography with DNA polymerase η (Pol η) as a model system, we showed that the sugar ring C2′ chemical groups on cytarabine and gemcitabine snugly fit within the Pol η active site without occluding the steric gate. During DNA extension, Pol η can extend past gemcitabine but with much lower efficiency past cytarabine. The Pol η crystal structures show that the -OH modification in the β direction on cytarabine locks the sugar ring in an unfavorable C2′-endo geometry for product formation. On the other hand, the addition of fluorine atoms on gemcitabine alters the proper conformational transition of the sugar ring for DNA synthesis. Our study illustrates mechanistic insights into chemotherapeutic drug inhibition and resistance and guides future optimization of nucleoside analogue drugs.
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    Polyphest: fast polyploid phylogeny estimation
    (Oxford University Press, 2024) Yan, Zhi; Cao, Zhen; Nakhleh, Luay
    Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies.We introduce Polyphest (POLYploid PHylogeny ESTimation), a new method for efficiently and accurately inferring species phylogenies in the presence of both polyploidy and ILS. Polyphest bypasses the need for extensive network space searches by first generating a multilabeled tree based on gene trees, which is then converted into a (uniquely labeled) species phylogeny. We compare the performance of Polyphest to that of two polyploid phylogeny estimation methods, one of which does not account for ILS, namely PADRE, and another that accounts for ILS, namely MPAllopp. Polyphest is more accurate than PADRE and achieves comparable accuracy to MPAllopp, while being significantly faster. We also demonstrate the application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes.Polyphest is available at https://github.com/NakhlehLab/Polyphest.
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    RACER-m leverages structural features for sparse T cell specificity prediction
    (AAAS, 2024) Wang, Ailun; Lin, Xingcheng; Chau, Kevin Ng; Onuchic, José N.; Levine, Herbert; George, Jason T.; Center for Theoretical Biological Physics
    Reliable prediction of T cell specificity against antigenic signatures is a formidable task, complicated by the immense diversity of T cell receptor and antigen sequence space and the resulting limited availability of training sets for inferential models. Recent modeling efforts have demonstrated the advantage of incorporating structural information to overcome the need for extensive training sequence data, yet disentangling the heterogeneous TCR-antigen interface to accurately predict MHC-allele-restricted TCR-peptide interactions has remained challenging. Here, we present RACER-m, a coarse-grained structural model leveraging key biophysical information from the diversity of publicly available TCR-antigen crystal structures. Explicit inclusion of structural content substantially reduces the required number of training examples and maintains reliable predictions of TCR-recognition specificity and sensitivity across diverse biological contexts. Our model capably identifies biophysically meaningful point-mutant peptides that affect binding affinity, distinguishing its ability in predicting TCR specificity of point-mutants from alternative sequence-based methods. Its application is broadly applicable to studies involving both closely related and structurally diverse TCR-peptide pairs.
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    CrysFormer: Protein structure determination via Patterson maps, deep learning, and partial structure attention
    (AIP Publishing LLC, 2024) Pan, Tom; Dun, Chen; Jin, Shikai; Miller, Mitchell D.; Kyrillidis, Anastasios; Phillips, George N., Jr.
    Determining the atomic-level structure of a protein has been a decades-long challenge. However, recent advances in transformers and related neural network architectures have enabled researchers to significantly improve solutions to this problem. These methods use large datasets of sequence information and corresponding known protein template structures, if available. Yet, such methods only focus on sequence information. Other available prior knowledge could also be utilized, such as constructs derived from x-ray crystallography experiments and the known structures of the most common conformations of amino acid residues, which we refer to as partial structures. To the best of our knowledge, we propose the first transformer-based model that directly utilizes experimental protein crystallographic data and partial structure information to calculate electron density maps of proteins. In particular, we use Patterson maps, which can be directly obtained from x-ray crystallography experimental data, thus bypassing the well-known crystallographic phase problem. We demonstrate that our method, CrysFormer, achieves precise predictions on two synthetic datasets of peptide fragments in crystalline forms, one with two residues per unit cell and the other with fifteen. These predictions can then be used to generate accurate atomic models using established crystallographic refinement programs.
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    Breakdown of Boltzmann-type models for the alignment of self-propelled rods
    (Elsevier, 2024) Murphy, Patrick; Perepelitsa, Misha; Timofeyev, Ilya; Lieber-Kotz, Matan; Islas, Brandon; Igoshin, Oleg A.; Center for Theoretical Biological Physics
    Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann’s “molecular chaos” hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore the agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.
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    Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo
    (eLife Sciences Publications Ltd, 2024) Chang, Caleb; Zhou, Grace; Gao, Yang
    Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.