bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioorthogonal caging-group-free photoactivatable probes for minimal-linkage-error nanoscopy
Authors: Aktalay Ayse , Lincoln Richard , Heynck Lukas , Lima Maria Augusta do R. B. F. , Butkevich Alexey N. , Bossi Mariano L. , Hell Stefan W. 
Published: June 2023

ABSTRACTHere we describe highly compact, click compatible, and photoactivatable dyes for super-resolution fluorescence microscopy (nanoscopy). By combining the photoactivatable xanthone (PaX) core with a tetrazine group, we achieve minimally sized and highly sensitive molecular dyads for selective labeling of unnatural amino acids introduced by genetic code expansion. We exploit the excited state quenching properties of the tetrazine group to attenuate the photoactivation rates of the PaX, and further reduce the overall fluorescence emission of the photogenerated fluorophore, providing two mechanisms of selectivity to reduce off-target signal. Coupled with MINFLUX nanoscopy, we demonstrate our dyads in the minimal-linkage-error imaging of vimentin filaments, demonstrating the molecular scale precision in fluorophore positioning.
Zona incerta distributes a broad movement signal that modulates behavior
Authors: Hormigo Sebastian , Zhou Ji , Chabbert Dorian , Sajid Muhammad S. , Busel Natan , Castro-Alamancos Manuel A. 
Published: June 2023

AbstractThe zona incerta is a subthalamic nucleus made up mostly of GABAergic neurons. It has wide- ranging inputs and outputs and is believed to have many integrative functions that link sensory stimuli with motor responses to guide behavior. However, its role is not well established perhaps because few studies have measured the activity of zona incerta neurons in behaving animals under different conditions. To record the activity of zona incerta neurons during exploratory and cue-driven goal-directed behaviors, we used electrophysiology in head-fixed mice moving on a spherical treadmill and fiber photometry in freely moving mice. We found two groups of neurons based on their sensitivity to movement, with a minority of neurons responding to whisker stimuli. Furthermore, zona incerta GABAergic neurons robustly code the occurrence of exploratory and goal-directed movements, but not their direction. To understand the function of these activations, we performed genetically targeted lesions and optogenetic manipulations of zona incerta GABAergic neurons during exploratory and goal-directed behaviors. The results showed that the zona incerta has a role in modulating the movement associated with these behaviors, but this has little impact on overall performance. Zona incerta neurons distribute a broad corollary signal of movement occurrence to their diverse projection sites, which regulates behavior.
Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
Authors: Rouzé Timothé , Martayan Igor , Marchet Camille , Limasset Antoine 
Published: June 2023

AbstractThe exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashing techniques have successfully transformed large datasets into smaller, more manageable sketches while maintaining comparability using metrics such as Jaccard and containment indices. However, fixed-size sketches encounter difficulties when applied to divergent datasets.Scalable sketching methods, such as Sourmash, provide valuable solutions but still lack resourceefficient, tailored indexing. Our objective is to create lighter sketches with comparable results while enhancing efficiency. We introduce the concept of Fractional Hitting Sets, a generalization of Universal Hitting Sets, which uniformly cover a specified fraction of thek-mer space. In theory and practice, we demonstrate the feasibility of achieving such coverage with simple but highly efficient schemes.By encoding the coveredk-mers as super-k-mers, we provide a space-efficient exact representation that also enables optimized comparisons. Our novel tool, SuperSampler, implements this scheme, and experimental results with real bacterial collections closely match our theoretical findings.In comparison to Sourmash, SuperSampler achieves similar outcomes while utilizing an order of magnitude less space and memory and operating several times faster. This highlights the potential of our approach in addressing the challenges presented by the ever-expanding landscape of genomic data.SuperSampler is an open-source software and can be accessed atgithub.com/TimRouze/supersampler. The data required to reproduce the results presented in this manuscript is available atgithub.com/TimRouze/Expe_SPSP.
FLOP: Tasks for Fitness Landscapes Of Protein wildtypes
Authors: Groth Peter Mørch , Michael Richard , Salomon Jesper , Tian Pengfei , Boomsma Wouter 
Published: June 2023

AbstractProtein engineering has the potential to create optimized protein variants with improved properties and function. An initial step in the protein optimization process typically consists of a search among natural (wildtype) sequences to find the naturally occurring proteins with the most desirable properties. Promising candidates from this initial discovery phase then form the basis of the second step: a more local optimization procedure, exploring the space of variants separated from this candidate by a number of mutations. While considerable progress has been made on evaluating machine learning methods on single protein datasets, benchmarks of data-driven approaches for global fitness landscape exploration are still lacking. In this paper, we have carefully curated a representative benchmark dataset, which reflects industrially relevant scenarios for the initial wildtype discovery phase of protein engineering. We focus on exploration within a protein family, and investigate the downstream predictive power of various protein representation paradigms, i.e., protein language model-based representations, structure-based representations, and evolution-based representations. Our benchmark highlights the importance of coherent split strategies, and how we can be misled into overly optimistic estimates of the state of the field. The codebase and data can be accessed viahttps://github.com/petergroth/FLOP.
Missense mutations in the calcium-activated chloride channel TMEM16A promote tumor growth by activating oncogenic signaling in Human Cancer
Authors: Cruz-Rangel Silvia , De Jesus-Perez Jose Juan , Gopalkrishnan Avani , Gomez-Casal Roberto , Pacheco Jonathan , Brown Maya R , Yassin-Kassab Abdulkader , Hammond Gerald RV , Bertrand Carol A , Arreola Jorge , Kiselyov Kirill , Umamaheswar Duvvuri 
Published: June 2023

ABSTRACTThe calcium-activated chloride channel TMEM16A is overexpressed in several tumors. This condition is associated with a poor survival prognosis but highlights TMEM16A’s potential as a biomarker and target for anti-cancer therapies. Numerous somatic mutations of TMEM16A have been reported; however, their potential and molecular mechanism of oncogenesis are unknown. Here, we investigate the function and oncogenicity of nine-point mutations found in human cancerous tissues (R451P, R455Q, M546I, R557W, F604L, D902N, K913E, D914H, and Q917K). These mutations are located on the extracellular side and near the third Ca2+-binding site, near a PtdIns(4,5)P2 site in the human TMEM16A channel. Our findings reveal that these mutations affected gating, Ca2+sensitivity, phosphorylation of essential signaling proteins, cell proliferation, and tumor growth. Notably, R451P and D902N exhibit low Ca2+sensitivity, yet their overexpression promotes phosphorylation of EGFR and AKT, as well asin vivotumorigenesis, without Ca2+-enhancing stimuli. Conversely, the charged-neutralizing mutation R451Q and the conservative mutation D902E restored Ca2+sensitivity and altered cell proliferation and tumor growth as wild-type did. Thus, we conclude that the oncogenic phenotype of TMEM16A missense mutations is independent of chloride flux but involves the differential activation of cell signaling components associated with cell proliferation.
Genome-wide identification of notochord enhancers comprising the regulatory landscape of theBrachyury(T) locus in mouse
Authors: Schifferl Dennis , Scholze-Wittler Manuela , Luque Alba Villaronga , Pustet Milena , Wittler Lars , Veenvliet Jesse V. , Koch Frederic , Herrmann Bernhard G. 
Published: June 2023

AbstractThe node and notochord are important signaling centers organizing dorso-ventral patterning of cells arising from neuro-mesodermal progenitors forming the embryonic body anlage. Due to the scarcity of notochordal progenitors and notochord cells, a comprehensive identification of regulatory elements driving notochord-specific gene expression has been lacking. Here we have used ATAC-seq analysis of FACS-purified notochordal cells from TS12-13 mouse embryos to identify 8921 putative notochord enhancers. In addition, we established a new model for generating notochordal cells in culture, and found 3728 of these enhancers occupied by the essential notochordal regulators Brachyury (T) and/or Foxa2. We describe the regulatory landscape of the T locus comprising 10 putative enhancers occupied by these factors and confirmed the regulatory activity of 3 of these elements. Moreover, we characterized one new notochord enhancer, termedTNE2, in embryos.TNE2complements the loss ofTNEin the trunk notochord, and is essential for notochordal cell proliferation and differentiation in the tail. Our data demonstrate the essential role of Foxa2 in switching T expressing cells from a NMP/mesodermal trajectory to the notochordal fate.Summary statementCombining multi-omics assays of purified embryonic and in vitro generated cells we identified thousands of notochord enhancers comprisingTNE2essential forTexpression and tail development of the mouse embryo.
Model-free Identification of Phenotype-Relevant Variables From Dose Response Data
Authors: Veliz-Cuba Alan , Murrugarra David , Voss Randal 
Published: June 2023

AbstractComplex phenotypic changes occur during development and in response to injury and disease. Identifying key regulators of phenotypic change is a shared aim of many different fields of research, including life history, tissue regeneration, and cancer. These examples of phenotypic change involve coordinated changes in cellular behaviors and associated changes in gene expression which if disrupted, can alter and even block completion of the phenotypic transition. Experimental treatments that effectively block the completion of a phenotypic transition can be quantitatively manipulated to identify key regulatory genes through changes in transcriptional dose response. In this paper, we present a “model free” approach to identify “bifurcation-like” behaviors of key regulatory genes by tracking spikes in their transcriptional sensitivities. Genes that exhibit such behavior are predicted to comprise nodes in subnetworks or modules that regulate the phenotypic transition. We applied our method to an in-silico data set where we also studied the impact of noise in the predictions. We also applied the method to a gene expression data that were collected during tail regeneration in axolotls. Our code for gene identification, which can be extended more generally to other component variables of complex phenotypic change, is freely available via the following GitHub sitegithub.com/alanavc/id-vars-from-resp-data.
Neural Circuits for Fast Poisson Compressed Sensing in the Olfactory Bulb
Authors: Zavatone-Veth Jacob A. , Masset Paul , Tong William L. , Zak Joseph D. , Murthy Venkatesh N. , Pehlevan Cengiz 
Published: June 2023

AbstractWithin a single sniff, the mammalian olfactory system can decode the identity and concentration of odorants wafted on turbulent plumes of air. Yet, it must do so given access only to the noisy, dimensionally-reduced representation of the odor world provided by olfactory receptor neurons. As a result, the olfactory system must solve a compressed sensing problem, relying on the fact that only a handful of the millions of possible odorants are present in a given scene. Inspired by this principle, past works have proposed normative compressed sensing models for olfactory decoding. However, these models have not captured the unique anatomy and physiology of the olfactory bulb, nor have they shown that sensing can be achieved within the 100-millisecond timescale of a single sniff. Here, we propose a rate-based Poisson compressed sensing circuit model for the olfactory bulb. This model maps onto the neuron classes of the olfactory bulb, and recapitulates salient features of their connectivity and physiology. For circuit sizes comparable to the human olfactory bulb, we show that this model can accurately detect tens of odors within the timescale of a single sniff. We also show that this model can perform Bayesian posterior sampling for accurate uncertainty estimation. Fast inference is possible only if the geometry of the neural code is chosen to match receptor properties, yielding a distributed neural code that is not axis-aligned to individual odor identities. Our results illustrate how normative modeling can help us map function onto specific neural circuits to generate new hypotheses.
Strong epistasis constrains the evolution of strict substrate specificity in apicomplexan lactate dehydrogenases
Authors: Wirth Jacob D. , Boucher Jeffrey I. , Xu Changhan , Classen Scott , Theobald Douglas L. 
Published: June 2023

AbstractThe homologous enzymes lactate and malate dehydrogenase (L/MDH) are structurally similar but are specific for different substrates. LDH vs MDH specificity is canonically governed by the identity of a single “specificity residue” at position 102. However, LDH function has convergently evolved from a specific MDH at least four times, and the catalytic role of residue 102 is not conserved between different phyla. The apicomplexa are a phylum of obligate, intracellular eukaryotic parasites responsible for wide-spread disease such asPlasmodium falciparum(malaria),Cryptosporidium parvum(cryptosporidiosis),Toxoplasma gondii(toxoplasmosis), andEimeria maxima(eimeriosis). The apicomplexan LDH evolved via a five-residue insertion that produced a novel specificity residue, W107f. The commonly accepted mechanism of LDH specificity involves charge balance and steric occlusion, but our data shows that the general mechanism of apicomplexan LDHs does not use W107f as a steric block. OnlyPlasmodiumLDHs evolved substantial steric specificity, making them exceptional among Apicomplexa. Strong protein epistasis constrained this evolution, making it difficult to revert to ancestral phenotypes. Here, we use ancestral sequence reconstruction (ASR), steady-state kinetics, and x-ray crystallography to characterize apicomplexan LDHs which challenge current assumptions about the evolution of L/MDH activity. We demonstrate the unique specificity ofPlasmodiumLDHs and identify the active site residues controlling their substrate recognition. The extraordinarily high specificity ofPlasmodiumLDHs presents difficulties for small-molecule inhibitor development, and successful drugs against Plasmodium LDH may not be efficacious against other Apicomplexa LDHs and their diseases.
Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex
Authors: Zhou Xueyin , Yang Yuqi , Wang Guopeng , Wang Shanshan , Sun Dongjie , Ou Xiaomin , Lian Yuke , Li Long 
Published: June 2023

AbstractMost mitochondrial proteins need to be imported from the cytosol. Over half of mitochondrial proteins are imported through the pre-sequence pathway that is controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. It is unclear on the molecular level how proteins cross the mitochondrial double membranes through the TOM and TIM23 complexes. Here, we report the assembly of the active TOM-TIM23 supercomplex with translocating polypeptide substrates captured in the import pathway. Electron cryo-microscopy (Cryo-EM) analyses reveal that during translocation across the outer membrane, the polypeptide substrates pass through the center of the Tom40 channel while interacting with a glutamine-rich patch in the inner wall of Tom40. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17, and Mgr2 in the inner membrane. Tim17 and Mgr2 shield the polypeptide substrates from the lipid environment. The import pathway consists of two highly conserved residue patches of Tim17, one negatively charged patch at the entrance and one hydrophobic patch in the middle of the pathway. These data reveal an unexpected pre-sequence pathway mediated by the TOM-TIM23 supercomplex for facilitating protein import across the double membranes of mitochondria.
Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment
Authors: Rowdo Florencia P. Madorsky , Xiao Gu , Khramtsova Galina F , Nguyen John , Olopade Olufunmilayo I , Martini Rachel , Stonaker Brian , Boateng Richard , Oppong Joseph K. , Adjei Ernest K. , Awuah Baffour , Kyei Ishmael , Aitpillah Frances S. , Adinku Michael O. , Ankomah Kwasi , Osei-Bonsu Ernest B. , Gyan Kofi K. , Altorki Nasser K. , Cheng Esther , Ginter Paula S. , Hoda Syed , Newman Lisa , Elemento Olivier , Davis Melissa B. , Martin M. Laura , Bargonetti Jill 
Published: June 2023

AbstractPoly (ADP-ribose) polymerase inhibitors (PARPi) are used for patients withBRCA1/2mutations, but patients with other mutations may benefit from PARPi treatment. Another mutation that is present in more cancers thanBRCA1/2is mutation to theTP53gene. In 2D breast cancer cell lines, mutant p53 (mtp53) proteins tightly associate with replicating DNA and Poly (ADP-ribose) polymerase (PARP) protein. Combination drug treatment with the alkylating agent temozolomide and the PARPi talazoparib kills mtp53 expressing 2D grown breast cancer cell lines. We evaluated the sensitivity to the combination of temozolomide plus PARPi talazoparib treatment to breast and lung cancer patient-derived tumor organoids (PDTOs). The combination of the two drugs was synergistic for a cytotoxic response in PDTOs with mtp53 but not for PDTOs with wtp53. The combination of talazoparib and temozolomide induced more DNA double-strand breaks in mtp53 expressing organoids than in wild-type p53 expressing organoids as shown by increased ψ-H2AX protein expression. Moreover, breast cancer tissue microarrays (TMAs) showed a positive correlation between stable p53 and high PARP1 expression in sub-groups of breast cancers, which may indicate sub-classes of breast cancers sensitive to PARPi therapy. These results suggest that mtp53 could be a biomarker to predict response to the combination of PARPi talazoparib-temozolomide treatment.
Machine learning prediction of enzyme optimum pH
Authors: Gado Japheth E. , Knotts Matthew , Shaw Ada Y. , Marks Debora , Gauthier Nicholas P. , Sander Chris , Beckham Gregg T. 
Published: June 2023

AbstractThe relationship between pH and enzyme catalytic activity, especially the optimal pH (pHopt) at which enzymes function, is critical for biotechnological applications. Hence, computational methods to predict pHopt will enhance enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at specific pH levels, and by elucidating sequence-function relationships. In this study, we proposed and evaluated various machine-learning methods for predicting pHopt, conducting extensive hyperparameter optimization, and training over 11,000 model instances. Our results demonstrate that models utilizing language model embeddings markedly outperform other methods in predicting pHopt. We present EpHod, the best-performing model, to predict pHopt, making it publicly available to researchers. From sequence data, EpHod directly learns structural and biophysical features that relate to pHopt, including proximity of residues to the catalytic center and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pHopt prediction and will potentially speed up the development of enzyme technologies.
The Arabidopsis BUB1/MAD3 family protein BMF3 requires BUB3.3 to recruit CDC20 to kinetochores in spindle assembly checkpoint signaling
Authors: Deng Xingguang , Peng Felicia , Tang Xiaoya , Lee Yuh-Ru Julie , Lin Hong-Hui , Liu Bo 
Published: June 2023

ABSTRACTMitosis is monitored by the spindle assembly checkpoint (SAC) which remains active until all chromosomes have their kinetochores attached to microtubules originated from opposite spindle poles. Plants produce both highly conserved and sequence-diverged SAC components, so it has been largely unknown how SAC activation leads to the assembly of these proteins at the unattached kinetochores to prevent anaphase onset in plants. InArabidopsis thaliana, the noncanonical BUB3.3 protein was detected at kinetochores throughout mitosis, unlike MAD1 and the plant specific BUB1/MAD3 family protein BMF3 that associated with unattached chromosomes only. However, BUB3.3 was required to arrest mitotic progression when one or more chromosomes did not congress at the metaphase plate. Nevertheless, BUB3.3 was not required for the kinetochore localization of other SAC components andvice versa. BUB3.3 specifically interacted with BMF3 in a novel region containing two internal repeats that were not required for the kinetochore localization of BMF3. This interaction was important for BMF3 to recruit the CDC20 protein to the unattached kinetochores. Our results showed that the Arabidopsis BUB3.3 protein functioned in the activation of BMF3 for CDC20 recruitment, rather than the recruitment of BMF proteins as what has been found in fungi and animals, in order to arrest mitosis at prometaphase. Therefore, activated SAC resulted in BUB3.3-independent localization of BMF3 and MAD1 to kinetochores and BUB3.3-dependent licensing of BMF3 for CDC20 recruitment inA.thaliana.SIGNIFICANCE STATEMENTMitotic progression into anaphase is monitored by spindle assembly checkpoint that is poorly understood in plants. UsingArabidopsis thalianaas a reference system, we discovered a novel interaction pattern centered at the BUB1 and MAD3 protein BMF3 at kinetochores. A noncanonical isoform of the evolutionarily conserved BUB3 family protein BUB3.3 interacted with two novel internal repeats in BMF3 for recruiting the CDC20 protein to unattached kinetochores in order to inhibit its function in anaphase onset. Hence, our work sheds light on how spindle assembly checkpoint operates in flowering plants that produce the highly conserved BUB3.3 protein but highly divergent BMF proteins.
Development of a computational model to inform environmental surveillance sampling plans forSalmonella entericaserovar Typhi in wastewater
Authors: Burnor Elisabeth , Morin Cory W. , Shirai Jeffry H. , Zhou Nicolette A. , Meschke John Scott 
Published: June 2023

AbstractTyphoid fever – an acute febrile disease caused by infection with the bacteriumSalmonella entericaserotype Typhi (S.Typhi) – continues to be a leading cause of global morbidity and mortality, especially in developing countries with limited access to safe drinking water and adequate sanitation. Environmental surveillance, the process of detecting and enumerating disease-causing agents in wastewater, enables estimating disease prevalence and trends within a community and is a useful tool to monitor the circulation of typhoid fever in endemic regions. This study presents a computational model, which combines dynamic and probabilistic modeling techniques, to predict – on a spatial and temporal scale – the probability of detectingS.Typhi in a wastewater system. This model may be utilized in communities to inform environmental surveillance sampling plans and may provide useful insight into selecting appropriate sampling locations and times.