bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries
Authors: Weile Jochen , Ferra Gabrielle , Boyle Gabriel , Pendyala Sriram , Amorosi Clara , Yeh Chiann-Ling , Cote Atina G. , Kishore Nishka , Tabet Daniel , van Loggerenberg Warren , Rayhan Ashyad , Fowler Douglas M , Dunham Maitreya J. , Roth Frederick P 
Published: February 2023

AbstractSummaryLong read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or non-unique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.Availability and ImplementationPacybara, freely available athttps://github.com/rothlab/pacybara, is implemented using R, Python and bash for Linux. It has both a single-threaded implementation and, for GNU/Linux clusters that use Slurm, PBS, or GridEngine schedulers, a multi-node version.Supplementary MaterialSupplementary materials are available at Bioinformatics online.
Single neurons in the human medial temporal lobe flexibly shift representations across spatial and memory tasks
Authors: Donoghue Thomas , Cao Runnan , Han Claire Z , Holman Cameron M , Brandmeir Nicholas J , Wang Shuo , Jacobs Joshua 
Published: February 2023

AbstractInvestigations into how individual neurons encode behavioral variables of interest have revealed specific representations in single neurons, such as place and object cells, as well as a wide range of cells with conjunctive encodings or mixed selectivity. However, as most experiments examine neural activity within individual tasks, it is currently unclear if and how neural representations change across different task contexts. Within this discussion, the medial temporal lobe is particularly salient, as it is known to be important for multiple behaviors including spatial navigation and memory, however the relationship between these functions is currently unclear. Here, to investigate how representations in single neurons vary across different task contexts in the MTL, we collected and analyzed single-neuron activity from human participants as they completed a paired-task session consisting of a passive-viewing visual working memory and a spatial navigation and memory task. Five patients contributed 22 paired-task sessions, which were spike sorted together to allow for the same putative single neurons to be compared between the different tasks. Within each task, we replicated concept-related activations in the working memory task, as well as target-location and serial-position responsive cells in the navigation task. When comparing neuronal activity between tasks, we first established that a significant number of neurons maintained the same kind of representation, responding to stimuli presentations across tasks. Further, we found cells that changed the nature of their representation across tasks, including a significant number of cells that were stimulus responsive in the working memory task that responded to serial position in the spatial task. Overall, our results support a flexible encoding of multiple, distinct aspects of different tasks by single neurons in the human MTL, whereby some individual neurons change the nature of their feature coding between task contexts.
Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions
Authors: Newman Nolan K. , Macovsky Matthew , Rodrigues Richard R. , Bruce Amanda M. , Pederson Jacob W. , Patil Sankalp S , Padiadpu Jyothi , Dzutsev Amiran K. , Shulzhenko Natalia , Trinchieri Giorgio , Brown Kevin , Morgun Andrey 
Published: February 2023

AbstractTechnological advances have generated tremendous amounts of high-throughput omics data. Integrating data from multiple cohorts and diverse omics types from new and previously published studies can offer a holistic view of a biological system and aid in deciphering its critical players and key mechanisms. In this protocol, we describe how to use Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that can perform meta-analysis of cohorts and detect master regulators among measured parameters that govern pathological or physiological responses of host-microbiota (or any multi-omic data) interactions in a particular condition or disease.TkNA first reconstructs the network that represents a statistical model capturing the complex relationships between the different omics of the biological system. Here, it selects differential features and their per-group correlations by identifying robust and reproducible patterns of fold change direction and sign of correlation across several cohorts. Next, a causality-sensitive metric, statistical thresholds, and a set of topological criteria are used to select the final edges that form the transkingdom network. The second part of the analysis involves interrogating the network. Using the network’s local and global topology metrics, it detects nodes that are responsible for control of given subnetwork or control of communication between kingdoms and/or subnetworks.The underlying basis of the TkNA approach involves fundamental principles including laws of causality, graph theory and information theory. Hence, TkNA can be used for causal inference via network analysis of any host and/or microbiota multi-omics data. This quick and easy-to-run protocol requires very basic familiarity with the Unix command-line environment.
Defining Early Steps inB. subtilisBiofilm Biosynthesis
Authors: Arbour Christine A. , Nagar Rupa , Bernstein Hannah M. , Ghosh Soumi , Al-Sammarraie Yusra , Dorfmueller Helge C. , Ferguson Michael A. J. , Stanley-Wall Nicola R. , Imperiali Barbara 
Published: February 2023

ABSTRACTTheBacillus subtilisextracellular biofilm matrix includes an exopolysaccharide that is critical for the architecture and function of the community. To date, our understanding of the biosynthetic machinery and the molecular composition of the exopolysaccharide ofB. subtilisremains unclear and incomplete. This report presents synergistic biochemical and genetic studies built from a foundation of comparative sequence analyses targeted at elucidating the activities of the first two membrane-committed steps in the exopolysaccharide biosynthetic pathway. By taking this approach, we determined the nucleotide sugar donor and lipid-linked acceptor substrates for the first two enzymes in theB. subtilisbiofilm exopolysaccharide biosynthetic pathway. EpsL catalyzes the first phosphoglycosyl transferase step using UDP-di-N-acetyl bacillosamine as phospho-sugar donor. EpsD is a GT-B fold glycosyl transferase that facilitates the second step in the pathway that utilizes the product of EpsL as an acceptor substrate and UDP-N-acetyl glucosamine as the sugar donor. Thus, the study defines the first two monosaccharides at the reducing end of the growing exopolysaccharide unit. In doing so we provide the first evidence of the presence of bacillosamine in an exopolysaccharide synthesized by a Gram-positive bacterium.IMPORTANCEBiofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here we identify the first two essential steps in theBacillus subtilisbiofilm matrix exopolysaccharide synthesis pathway. Together our studies and approaches provide the foundation for the sequential characterization of the steps in exopolysaccharide biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenol diphosphate-linked glycan substrates.
Novel Fas-TNFR chimeras that prevents Fas ligand-mediated kill and signals synergistically to enhance CAR T-cell efficacy
Authors: McKenzie Callum , El-Kholy Mohamed , Parekh Farhaan , Robson Mathew , Lamb Katarina , Allen Christopher , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin 
Published: February 2023

ABSTRACTThe hostile tumour microenvironment limits the efficacy of adoptive cell therapies. Activation of the Fas death receptor initiates apoptosis and disrupting these receptors could be key to increase CAR T-cell efficacy. We screened a library of Fas-TNFR proteins identifying several novel chimeras that not only prevented Fas ligand-mediated kill, but also enhanced CAR T-cell efficacy by signalling synergistically with the CAR. Upon binding Fas ligand, Fas-CD40 activated the NF-κB pathway, inducing greatest proliferation and IFNγ release out of all Fas-TNFRs tested. Fas-CD40 induced profound transcriptional modifications, particularly genes relating to the cell cycle, metabolism, and chemokine signalling. Co-expression of Fas-CD40 with either 4-1BB- or CD28-containing CARs increasedin vitroefficacy by eliciting maximal CAR T-cell proliferation and cancer target cytotoxicity, and enhanced tumour killing and overall mouse survivalin vivo. Functional activity of the Fas-TNFRs were dependent on the co-stimulatory domain within the CAR, highlighting crosstalk between signalling pathways. Furthermore, we show that a major source for Fas-TNFR activation derives from CAR T cells themselves via activation-induced Fas ligand upregulation, highlighting a universal role of Fas-TNFRs in augmenting CAR T-cell responses. We have identified Fas-CD40 as the optimal chimera for overcoming Fas ligand-mediated kill and enhancing CAR T-cell efficacy.
HELZ2: a new, interferon-regulated, human 3’-5’ exoribonuclease of the RNB family is expressed from a non-canonical initiation codon
Authors: Huntzinger Eric , Sinteff Jordan , Morlet Bastien , Seraphin Bertrand 
Published: February 2023

AbstractProteins containing a RNB domain, originally identified inE. coliRNase II, are widely present throughout the tree of life. Many RNB proteins are endowed with 3’-5’ exoribonucleolytic activity but some have lost catalytic function during evolution. Database searches identified a new RNB domain containing protein in human: HELZ2. Analysis of genomic and expression data with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 harbors also two RNA helicase domains and several zinc-fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3’-5’ ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.
Specialized pathogenic cells release Tc toxins using a type 10 secretion system
Authors: Sitsel Oleg , Wang Zhexin , Janning Petra , Kroczek Lara , Wagner Thorsten , Raunser Stefan 
Published: February 2023

AbstractDisease-causing bacteria use a variety of secreted toxins to invade and subjugate their hosts. While the machinery responsible for secretion of many smaller toxins has already been established, it remains enigmatic for larger ones such as Tc toxins from human and insect pathogens, which approach the size of a prokaryotic ribosome. In the present study, we combine targeted genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogenYersinia entomophagato reveal that a specialized subset of bacterial cells produces the Tc toxin YenTc as part of a complex toxin cocktail released into the environment by controlled cell lysis using a transcriptionally-coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the process of Tc toxin export by a T10SS in hitherto unprecedented detail, identifying that T10SSs operate via a previously unknown lytic mode of action, and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major human pathogens such asYersinia pestisandSalmonella enterica, we anticipate our findings to model an important aspect of pathogenesis in bacteria with a significant impact on global human health.
The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid
Authors: Bellegarda Celine , Zavard Guillaume , Moisan Lionel , Gray Ryan S. , Brochard-Wyart Françoise , Joanny Jean-François , Cantaut-Belarif Yasmine , Wyart Claire 
Published: February 2023

AbstractThe Reissner fiber (RF) is an acellular thread positioned in the midline of the central canal that aggregates thanks to the beating of numerous cilia from ependymal radial glial cells (ERGs) generating flow in the central canal of the spinal cord. RF together with cerebrospinal fluid (CSF)-contacting neurons (CSF-cNs) forms an axial sensory system detecting curvature. How RF, CSF-cNs and the multitude of motile cilia from ERGs interactin vivoappears critical for maintenance of RF and sensory functions of CSF-cNs to keep a straight body axis but is not well-understood. Usingin vivoimaging in larval zebrafish, we show that RF is under tension and resonates dorsoventrally. Focal RF ablations trigger retraction and relaxation of the fiber cut ends, with larger retraction speeds for rostral ablations. We built a mechanical model that estimates RF stress diffusion coefficient at 4 mm2/ s and reveals that tension builds up rostrally along the fiber. After RF ablation, CSF-cN spontaneous activity decreased and ciliary motility changed, suggesting physical interactions between RF and cilia projecting into the central canal. We observed that motile cilia were caudally-tilted and frequently interacted with RF. We propose that the numerous ependymal motile monocilia contribute to RF heterogenous tension via weak interactions. Our work demonstrates that under tension, the Reissner fiber dynamically interacts with motile cilia generating CSF flow and spinal sensory neurons.
Capturing and Detecting of Extracellular Vesicles Derived from SingleEscherichia coliMother Cells
Authors: Yokoyama Fumiaki , Kling André , Dittrich Petra S. 
Published: February 2023

AbstractCells have a phenotypic heterogeneity even in isogeneic populations. Differences in secretion of substances have been well-investigated with single mammalian cells. However, studies on the heterogeneity of secreted substances at the single-bacterial-cell level are challenging due to the small size, motility, and rapid proliferation of bacterial cells such asEscherichia coli. Here, we propose a microfluidic device to achieve an isolated culture of single bacterial cells and capture of extracellular vesicles (EVs) secreted from individuals. The device has winding channels to trap single rod-shapedE. colicells at their entrances. Isolated single mother cells grew constantly up to 24 h, while their daughter cells were removed by flow. The flow carried EVs of the trapped cells along the channel, whose surface was rendered positively charged to electrostatically capture negatively charged EVs, followed by staining with a lipophilic dye to detect EVs by microscopy. Our results underline that the amounts of segregated EVs vary among cells. Moreover, individual responses to perturbation using a membrane-perturbing antibiotic were observed in growth dynamics and EV secretion of living-alone bacteria. The proposed method can be applied to detect other secreted substances of interest, possibly paving the way for elucidating unknown heterogeneities in bacteria.
The song does not remain the same: daily singing of adult songbirds prevents passive changes in song structure independently of auditory feedback
Authors: Mizuguchi Daisuke , Sánchez-Valpuesta Miguel , Kim Yunbok , dos Santos Ednei B. , Kang HiJee , Mori Chihiro , Wada Kazuhiro , Kojima Satoshi 
Published: February 2023

AbstractMany songbirds learn to produce songs through vocal practice early in life and continue to sing numerous renditions of their learned songs daily throughout their lifetime. While it is well-known that adult songbirds sing as part of a mating ritual, the functions of singing behavior outside of reproductive contexts are not fully understood. Here, we demonstrate that adult singing outside of reproductive contexts serves to prevent passive changes in song performance. We suppressed the daily singing behavior of adult zebra finches produced in the solo context for two weeks using a reversible behavioral manipulation and examined the effect on song performance. Our results indicated that suppressing daily singing significantly decreased the pitch of song elements and both the amplitude and duration of song motifs. These findings suggest that adult song is not acoustically stable without singing, and that adult birds maintain their song performance by daily singing. Moreover, we found that the changes in song structure caused by singing suppression were substantially recovered within two weeks of free singing, even in deafened birds. Thus, the recovery of song performance does not necessarily require auditory feedback but is predominantly caused by singing behavior per se (i.e., the physical act of singing). Finally, unlike the auditory feedback-dependent song plasticity reported previously, the passive song changes caused by singing suppression were not significantly dependent on age. Taken together, our findings demonstrate that adult songbirds maintain song performance by preventing passive song changes through the physical act of daily singing throughout their life. Such daily singing likely functions as vocal training to maintain the neural and/or muscular system in optimal conditions for song performance in reproductive contexts, similar to how human singers and athletes practice daily to maintain their performance.
Cell-cycle status of male and female gametes during Arabidopsis reproduction
Authors: Voichek Yoav , Hurieva Bohdana , Michaud Caroline , Schmücker Anna , Vergara Zaida , Desvoyes Bénédicte , Gutierrez Crisanto , Nizhynska Viktoria , Jaegle Benjamin , Borg Michael , Berger Frédéric , Nordborg Magnus , Ingouff Mathieu 
Published: February 2023

AbstractFertilization inArabidopsis thalianais a highly coordinated process that begins with a pollen tube delivering the two sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization still remains elusive as DNA quantification and DNA replication assays have given conflicting results1–4. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all the phases of the cell cycle. We show that male and female gametes in Arabidopsis are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.
Dentate Neurogenesis Modulates Dorsal Hippocampal Excitation/Inhibition Balance Crucial for Cognitive Flexibility
Authors: Li Haowei , Tamura Risako , Hayashi Daiki , Asai Hirotaka , Koga Junya , Ando Shota , Yokota Sayumi , Kaneko Jun , Sakurai Keisuke , Sumiyoshi Akira , Yamamoto Tadashi , Hikishima Keigo , Tanaka Kazumasa Z. , McHugh Thomas J. , Hisatsune Tatsuhiro 
Published: February 2023

AbstractAdult neurogenesis endows the hippocampus with unparalleled neural plasticity, essential for intricate cognitive functions. However, the manner in which sparse newborn neurons (NBNs) modulate neural activities and subsequently shape behavior remains enigmatic. Utilizing a newly engineered NBN-Tetanus Toxin mouse model, we non-invasively silenced NBNs and confirmed their crucial role in cognitive flexibility, as demonstrated through reversal learning in the Morris water maze and the Go/Nogo task in operant learning. Pairing task-based functional MRI (tb-fMRI) with operant learning revealed a dorsal hippocampal hyperactivation during Nogo task, implying that hippocampal hyperexcitability might underlie the observed behavioral deficits. Notably, resting-state fMRI (rs-fMRI) revealed enhanced functional connectivity between the dorsal and ventral dentate gyrus following NBN silencing. Further exploration of PV+ interneurons and mossy cells’ activities highlighted NBN’s integral part in preserving the excitation/inhibition balance within the hippocampus. Our findings emphasize how the neural plasticity driven by NBNs extensively modulates the hippocampus, sculpting cognitive flexibility.
Complex chemical signals dictate Ah receptor activation through the gut-lung axis
Authors: Dong Fangcong , Murray Iain A. , Annalora Andrew , Coslo Denise , Desai Dhimant , Gowda Krishne , Yang Jian , Wang Dingbowen , Koo Imhoi , Hao Fuhua , Amin Shantu G. , Patterson Andrew D. , Marcus Craig , Perdew Gary H. 
Published: February 2023

ABSTRACTThe aryl hydrocarbon receptor (AHR) mediates intestinal barrier homeostasis. Many AHR ligands are also CYP1A1/1B1 substrates, which can result in the rapid clearance within the intestinal tract, limiting AHR activation. This led us to the hypothesis that there are dietary substrates of CYP1A1/1B1 that increase the half-life of potent AHR ligands. We examined the potential of urolithin A (UroA) as a CYP1A1/1B1 substrate to enhance AHR activity in vivo. UroA is a competitive substrate for CYP1A1/1B1 in an in vitro competition assay. A broccoli-containing diet promotes the gastric formation of the potent hydrophobic AHR ligand and CYP1A1/1B1 substrate, 5,11-dihydroindolo[3,2-b]carbazole (ICZ). Dietary exposure to UroA in a broccoli diet led to a coordinated increase in duodenal, cardiac, and pulmonary AHR activity, but no increase in activity in liver. Thus, CYP1A1 dietary competitive substrates can lead to intestinal “escape”, likely through the lymphatic system, increasing AHR activation in key barrier tissues.