bluuebunny/crossref_metadata_2025_split huggingface dataset:
BamQuery: a proteogenomic tool for the genome-wide exploration of the immunopeptidome
Authors: Ruiz Cuevas Maria Virginia , Hardy Marie-Pierre , Larouche Jean-David , Apavaloaei Anca , Kina Eralda , Vincent Krystel , Gendron Patrick , Laverdure Jean-Philippe , Durette Chantal , Thibault Pierre , Lemieux Sébastien , Perreault Claude , Ehx Grégory 
Published: October 2022

ABSTRACTMHC-I-associated peptides (MAPs) derive from selective yet highly diverse genomic regions, including allegedly non-protein-coding sequences, such as endogenous retroelements (EREs). Quantifying canonical (exonic) and non-canonical MAPs-encoding RNA expression in malignant and benign cells is critical for identifying tumor antigens (TAs) but represents a challenge for immunologists. We present BamQuery, a computational tool attributing an exhaustive RNA expression to MAPs of any origin (exon, intron, UTR, intergenic) from bulk and single-cell RNA-sequencing data. We show that non-canonical MAPs (including TAs) can derive from multiple different genomic regions (up to 35,343 for EREs), abundantly expressed in normal tissues. We also show that supposedly tumor-specific mutated MAPs, viral MAPs, and MAPs derived from proteasomal splicing can arise from different unmutated non-canonical genomic regions. The genome-wide approach of BamQuery allows comprehensive mapping of all MAPs in healthy and cancer tissues. BamQuery can also help predict MAP immunogenicity and identify safe and actionable TAs.
Pixelated microfluidics for drug screening on tumour spheroids and ex vivo microdissected primary tissue
Authors: Dorrigiv Dina , Goyette Pierre-Alexandre , St-Georges-Robillard Amélie , Mes-Masson Anne-Marie , Gervais Thomas 
Published: October 2022

AbstractAnti-cancer drugs have the lowest success rate of approval in drug development programs. Thus, preclinical assays that closely predict the clinical responses to drugs are of utmost importance in both clinical oncology and pharmaceutical research. 3D tumour models preserve the tumoural architecture and are cost-, labour-, and time-efficient. However, the short-term longevity, limited throughput, and limitations to live imaging of these models have so far driven researchers towards simpler, less realistic tumour models such as monolayer cell cultures. Here, we present a static open-space microfluidic drug screening platform that enables the formation, culture, and multiplexed delivery of several reagents to various 3D tumour models, namely cancer cell line spheroids and ex vivo primary tumour fragments. Our platform utilizes an open-space microfluidic technology, a pixelated chemical display, which creates fluidic “pixels” of biochemical reagents that stream over tumour models in a contact-free fashion. Up to 9 different treatment conditions can be tested over 144 samples in a single experiment. We provide a proof-of-concept application by staining fixed and live tumour models with multiple cellular dyes. Furthermore, we demonstrate that the various responses of the tumour models to biological stimuli can be assessed using the proposed drug screening platform. The platform is amenable to various 3D tumour models, such as tumour organoids. Upscaling of the microfluidic platform to larger areas can lead to higher throughputs, and thus will have a significant impact on developing treatments for cancer.
Widespread chromatin context-dependencies of DNA double-strand break repair proteins
Authors: Vergara Xabier , Manjón Anna G. , Morris Ben , Schep Ruben , Leemans Christ , Sanders Mathijs A. , Beijersbergen Roderick L. , Medema René H. , van Steensel Bas 
Published: October 2022

ABSTRACTDNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ). The balance of these pathways is dependent on the local chromatin context, but the underlying mechanisms are poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different chromatin environments, we identified dozens of DNA repair proteins that modulate pathway balance dependent on the local chromatin state. Proteins that favor NHEJ mostly synergize with euchromatin, while proteins that favor MMEJ generally synergize with distinct types of heterochromatin. BRCA2 is an example of the former, which is corroborated by chromatin-dependent shifts in mutation patterns of BRCA2-/- cancer genomes. These results uncover a complex network of proteins that regulate MMEJ:NHEJ balance in a chromatin context-dependent manner.ONE SENTENCE SUMMARYA multiplexed screen reveals how dozens of proteins sense the local chromatin context to tune the balance between two DNA repair pathways.
Nitrate leaching and its implication for Fe and As mobility in a Southeast Asian aquifer
Authors: Glodowska Martyna , Ma Yinxiao , Smith Garrett , Kappler Andreas , Jetten Mike , Welte Cornelia U. 
Published: October 2022

AbstractThe drinking water quality of millions of people in South and Southeast Asia is at risk due to arsenic (As) contamination of groundwater and insufficient access to water treatment facilities. Intensive use of nitrogen (N) fertilizer increases the possibility of nitrate (NO3-) leaching into aquifers, yet very little is known about how the N cycle will interact with and affect the iron (Fe) and As mobility in aquifers. We hypothesized that input of NO3- into highly methanogenic aquifers can stimulate nitrate-dependent anaerobic methane oxidation (N-DAMO) and subsequently help to remove NO3- and decrease CH4 emission. We, therefore, investigated the effects of N input into aquifers and its effect on Fe and As mobility, by running a set of microcosm experiments using aquifer sediment from Van Phuc, Vietnam supplemented with 15NO3- and 13CH4. Additionally, we assessed the effect of N-DAMO by inoculating the sediment with two different N-DAMO enrichment cultures (N-DAMO(O) and N-DAMO(V)). We found that native microbial communities and both N-DAMO enrichments could efficiently consume nearly 5 mM NO3- in 5 days. In an uninoculated setup, NO3- was preferentially used over Fe(III) as electron acceptor and consequently inhibited Fe(III) reduction and As mobilization. The addition of N-DAMO(O) and N-DAMO(V) enrichment cultures led to substantial Fe(III) reduction followed by the release of Fe2+ (0.190±0.002 mM and 0.350±0.007 mM, respectively) and buildup of sedimentary Fe(II) (11.20±0.20 mM and 10.91±0.47 mM, respectively) at the end of the experiment (day 64). Only in the N-DAMO(O) inoculated setup, As was mobilized (27.1±10.8 μg/L), while in the setup inoculated with N-DAMO(V) a significant amount of Mn (24.15±0.41 mg/L) was released to the water. Methane oxidation and 13CO2 formation were observed only in the inoculated setups, suggesting that the native microbial community did not have sufficient potential for N-DAMO. An increase of NH4+ implied that dissimilatory nitrate reduction to ammonium (DNRA) took place in both inoculated setups. The archaeal community in all treatments was dominated by Ca. Methanoperedens while the bacterial community consisted largely of various denitrifiers. Overall, our results suggest that input of N fertilizers to the aquifer decreases As mobility and that CH4 cannot serve as an electron donor for the native NO3- reducing community.Graphical abstract
A general theory for the dynamics of social populations: Within-group density dependence and between-group processes
Authors: Lerch Brian A. , Abbott Karen C. 
Published: October 2022

AbstractDespite the importance of population structures throughout ecology, relatively little theoretical attention has been paid to understanding the implications of social groups for population dynamics. The dynamics of socially structured populations differ substantially from those of unstructured or metapopulation-structured populations, because social groups themselves may split, fuse, and compete. These “between-group processes” have been suggested to be important drivers of the dynamics of socially-structured populations, but no general theoretical framework exists that can handle various density-dependent between-group processes within a single model. Here, we develop a general framework for the dynamics of socially-structured populations that considers births, deaths, migration, group extinction, fissions, fusions, and between-group competition within a single model. Both logistic growth and an Allee effect are considered for within-group density dependence. We show that the effect of various between-group processes is mediated by their influence on the stable distribution of group sizes, with the ultimate impact on the population determined by the interaction between the altered group size distribution and within-group density dependence. The group level is important to the dynamics of the entire population, since it drives extinction risk, impacts population growth rates, and leads to the emergence of population-level density dependence (even if birth and death rates depend only on group size and not population size). We conclude with a series of case studies that illustrate different ways that age, sex, and class structure impact the dynamics of social populations. In sum, our results make clear the importance of within-group density dependence, between-group dynamics, and the interactions between them for the population dynamics of social species and provide a general, flexible framework for modeling social populations.
Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis
Authors: Bajaj Teena , Kuriyan John , Gee Christine L. 
Published: October 2022

AbstractGenomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M. brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (∼ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. We show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment.
Single-cell profiling of complex plant responses toPseudomonas syringaeinfection
Authors: Zhu Jie , Lolle Signe , Tang Andrea , Guel Bella , Kvikto Brian , Cole Benjamin , Coaker Gitta 
Published: October 2022

SUMMARYPlant response to pathogen infection varies within a leaf, yet this heterogeneity is not well resolved. We exposedArabidopsistoPseudomonas syringaeor mock treatment and profiled >11,000 individual cells using single-cell RNA sequencing. Integrative analysis of cell populations from both treatments identified distinct pathogen responsive cell clusters exhibiting transcriptional responses ranging from immunity to susceptibility. Pseudotime analyses through pathogen infection revealed a continuum of disease progression from an immune to susceptible state. Confocal imaging of promoter reporter lines for transcripts enriched in immune cell clusters expressed surrounding substomatal cavities colonized or in close proximity to bacterial colonies, suggesting cells within immune clusters represent sites of early pathogen invasion. Susceptibility clusters exhibited more general localization and were highly induced at later stages of infection. Overall, our work uncovers cellular heterogeneity within an infected leaf and provides unique insight into plant differential response to infection at a single-cell level.
Dissecting infant leukemia developmental origins with a hemogenic gastruloid model
Authors: Ragusa Denise , Suen Chun-Wai , Torregrosa-Cortés Gabriel , Pastorino Fabio , Johns Ayona , Cicirò Ylenia , Dijkhuis Liza , van den Brink Susanne , Cilli Michele , Byrne Connor , Ionescu Giulia-Andreea , Cerveira Joana , Kranc Kamil R. , Hernandez-Hernandez Victor , Ponzoni Mirco , Bigas Anna , Garcia-Ojalvo Jordi , Martinez Arias Alfonso , Pina Cristina 
Published: October 2022

ABSTRACTCurrent in vitro models of developmental blood formation lack spatio-temporal accuracy and weakly replicate successive waves of hematopoiesis. Herein, we describe a mouse embryonic stem cell (SC)-derived 3D hemogenic gastruloid (hGx) that captures multi-wave blood formation, progenitor specification from hemogenic endothelium (HE), and generates hematopoietic SC precursors capable of short-term engraftment of immunodeficient mice upon maturation in an adrenal niche. We took advantage of the hGx model to interrogate the origins of infant acute myeloid leukemia (infAML). We focused on MNX1-driven leukemia, representing the commonest genetic abnormality unique to the infant group. Enforced MNX1 expression in hGx promotes the expansion and in vitro transformation of yolk sac-like erythroid-myeloid progenitors (EMP) at the HE-to-hematopoietic transition to faithfully recapitulate patient transcriptional signatures. By combining phenotypic, functional and transcriptional profiling, including at the single-cell level, we establish the hGx as a useful new model for the study of normal and leukemic embryonic hematopoiesis.
A data-driven approach for predicting the impact of drugs on the human microbiome
Authors: Algavi Yadid M. , Borenstein Elhanan 
Published: October 2022

AbstractMany medications can negatively impact the bacteria residing in our gut, depleting beneficial species and causing adverse effects. To determine individualized response to pharmaceutical treatment, a comprehensive understanding of the impact of various drugs on the gut microbiome is needed, yet, to date, experimentally challenging to obtain. Towards this end, we developed a data-driven approach, integrating information about the chemical properties of each drug and the genomic content of each microbe, to systematically predicts drug-microbiome interactions. We show that this framework successfully predicts outcomes of in-vitro pairwise drug-microbe experiments, as well as drug-induced microbiome dysbiosis in both animal models and clinical trials. Applying this methodology, we systematically map all interactions between pharmaceuticals and bacteria and demonstrate that medications’ anti-microbial properties are tightly linked to their adverse effects. This computational framework has the potential to unlock the development of personalized medicine and microbiome-based therapeutic approaches, improving outcomes and minimizing side effects.
Dynamic matrices with DNA-encoded viscoelasticity for advanced cell and organoid culture
Authors: Peng Y.-H. , Hsiao S. K. , Gupta K. , Ruland A. , Auernhammer G. K. , Maitz M. F. , Boye S. , Lattner J. , Gerri C. , Honigmann A. , Werner C. , Krieg E. 
Published: October 2022

Abstract3D cell and organoid cultures, which allow in vitro studies of organogenesis and carcinogenesis, rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack rational design and control over key cell-instructive properties. Herein, we report a class of fully synthetic hydrogels based on novel DNA libraries that self-assemble with ultra-high molecular weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables, for the first time, computationally predictable, systematic, and independent control over critical viscoelasticity parameters by merely changing DNA sequence information without affecting the compositional features of the system. This approach enables: (1) thermodynamic and kinetic control over network formation; (2) adjustable heat-activation for the homogeneous embedding of mammalian cells; and (3) dynamic tuning of stress relaxation times over several orders of magnitude, recapitulating the mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto-and hemocompatibility, and controllable degradation. DyNAtrix-based 3D cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts, and human placental organoids exhibit high viability (on par or superior to reference matrices), proliferation, and morphogenesis over several days to weeks. DyNAtrix thus represents a programmable and versatile precision matrix, paving the way for advanced approaches to biomechanics, biophysics, and tissue engineering.
AI-guided cryo-EM probes a thermophilic cell-free system with succinyl-coA manufacturing capability
Authors: Skalidis Ioannis , Kyrilis Fotis L. , Tüting Christian , Hamdi Farzad , Träger Toni K. , Belapure Jaydeep , Hause Gerd , Fratini Marta , O’Reilly Francis J. , Heilmann Ingo , Rappsilber Juri , Kastritis Panagiotis L. 
Published: October 2022

AbstractCell-free systems display tremendous potential for biotechnological applications, complementing in vitro reconstituted enzymatic processes and traditional expression systems. However, they often represent “black boxes” without much insight into their components. Here, we characterize a thermophilic cell-free system that produces succinyl-CoA and discern its intrinsic, non-stochastic organization. By employing biochemical, biophysical, and bioinformatic methods we resolve its molecular composition, 3D architecture and molecular function at atomic resolution. We further report the high-resolution cryo-EM structure of the reaction’s main component, the oxoglutarate dehydrogenase complex core (E2o), which displays various structural adaptations. These include hydrogen bonding patterns confining interactions of participating enzymes (E1o-E2o-E3), electrostatic tunneling that drives inter-communication between subunits, and the presence of a flexible subunit, the E3BPo connecting E2o and E3. This multi-scale analysis of a cell-free system provides a blueprint for structure-function studies of complex mixtures of biotechnological value.
Residue-dependent transition temperatures and denaturant midpoints in the folding of a multi-domain protein
Authors: Liu Zhenxing , Thirumalai D. 
Published: October 2022

AbstractAs a consequence of the finite size of globular proteins, it is expected that there should be dispersions in the global melting temperature (Tm) and the denaturation midpoint (Cm). Thermodynamic considerations dictate that the dispersions, ΔTm in Tm and ΔCm in Cm, should decrease with N, the number of residues in the protein. We performed coarse-grained simulations of the Self-Organized Polymer (SOP) model of the multi-domain protein, Adenylate Kinase (ADK) with N = 214, in order to calculate thermal and denaturation unfolding titration curves. The results show that and are non-zero and follow the previously established (Phys. Rev. Lett. 93 268107 (2004)) thermodynamic scaling for proteins accurately. For ADK, the dispersions are small (≈ 0.004), which implies that the melting temperature is more or less unique, which is unlike in BBL (N =40) where .
Skipper analysis of RNA-protein interactions highlights depletion of genetic variation in translation factor binding sites
Authors: Boyle Evan A. , Her Hsuan-Lin , Mueller Jasmine R. , Nguyen Grady G. , Yeo Gene W. 
Published: October 2022

AbstractTechnology for crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using an improved statistical framework. Compared to existing methods, Skipper on average calls 3.1-4.2 times more transcriptomic binding sites and sometimes >10 times more sites, providing deeper insight into post-transcriptional gene regulation. Skipper also calls binding to annotated repetitive elements and identifies bound elements for 99% of enhanced CLIP experiments. We perform nine translation factor enhanced CLIPs and apply Skipper to learn determinants of translation factor occupancy including transcript region, sequence, and subcellular localization. Furthermore, we observe depletion of genetic variation in occupied sites and nominate transcripts subject to selective constraint because of translation factor occupancy. Skipper offers fast, easy, customizable analysis of CLIP-seq data.
Live-Cell Tracking of γ-H2AX Kinetics Reveals the Distinct Modes of ATM and DNA-PK in Immediate Response to DNA Damage
Authors: Trakarnphornsombat Watanya , Kimura Hiroshi 
Published: October 2022

ABSTRACTDNA double-strand break (DSB) is a serious form of DNA damage that can cause genetic mutation. On the induction of DSBs, histone H2AX becomes phosphorylated by kinases, including ataxia telangiectasia-mutated (ATM), ataxia telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK). Phosphorylated H2AX (γ-H2AX) can be a platform to recruit DNA repair machinery. Here we analyzed the immediate early kinetics of γ-H2AX upon laser-induced DNA damage in ATM-proficient and -deficient living cells by using fluorescently labeled antigen-binding fragments specific for γ-H2AX. The accumulation kinetics of γ-H2AX were similar in both ATM-proficient and -deficient cells. However, γ-H2AX accumulation was delayed when the cells were treated with a DNA-PK inhibitor, suggesting that DNA-PK rapidly phosphorylates H2AX at DSB sites. Ku80, a DNA-PK subunit, diffused freely in the nucleus without DNA damage, whereas ATM repeatedly bound to and dissociated from chromatin. The H2AX phosphorylation activity of ATM, but not DNA-PK, depended on a histone H4K16 acetyltransferase, males absent on the first (MOF). These results suggest distinct actions of ATM and DNA-PK that plays a primary role in immediate early γ-H2AX accumulation.
Loss of cytoskeletal proteostasis links dysregulation of cell size and mechanotransduction in mesenchymal stem cell senescence
Authors: Mallikarjun Venkatesh , Dobre Oana , Jackson Mark R. , Kidd Melissa , Llewellyn Jack , Gilbert Hamish T. J. , Richardson Stephen M. , Swift Joe 
Published: October 2022

ABSTRACTTissues are maintained by homeostatic feedback mechanisms where cells respond to, but also modify, the chemical and mechanical properties of the surrounding extracellular matrix. Mesenchymal stem cells (MSCs) resident in the marrow niche experience a diverse mechanical environment, but ageing can affect the composition and quality of bone and marrow tissues. Here we quantified the effect of replication-induced senescence on MSC morphology and their ability to correctly respond to different substrate stiffnesses. The matrix proteome was found to be sensitive to substrate stiffness, but pharmacological inhibition of cellular contractility perturbed this response, decreasing levels of tenascin-C, fibulins and fibronectin. Similar decreases in these mechanosensitive proteins were observed in senescent cells, suggested a decoupling of mechanotransduction pathways. Intracellular proteomic and transcriptomic analyses confirmed a decrease in components of the cytoskeletal chaperone complex CCT/TRiC in senescent MSCs. Finally, pharmacological inhibition of CCT/TRiC was able to partially recapitulate senescence-associated morphological changes in non-senescent MSCs. These results demonstrate a senescence-mediated perturbation to cytoskeletal homeostasis, pathways of mechanotransduction and the secretion of matrix proteins required for tissue maintenance.