bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tau tubulin kinase 1 and 2 regulate ciliogenesis and human pluripotent stem cells–derived neural rosettes
Authors: Binó Lucia , Čajánek Lukáš 
Published: January 2023

AbstractPrimary cilia are key regulators of embryo development and tissue homeostasis. However, their mechanisms and functions, particularly in the context of human cells, are still unclear. Here, we analyzed the consequences of primary cilia modulation for human pluripotent stem cells (hPSCs) proliferation and differentiation. We show that neither activation of the cilia-associated Hedgehog signaling pathway nor ablation of primary cilia by CRISPR gene editing to knockout Tau Tubulin Kinase 2 (TTBK2), a crucial ciliogenesis regulator, affects the selfrenewal of hPSCs. In addition, we demonstrate that TTBK1, a closely related kinase without previous links to ciliogenesis, is upregulated during hPSCs-derived neural rosette differentiation to regulate primary cilia formation together with TTBK2. Finally, we show that TTBK1/2 and primary cilia are implicated in the regulation of the size of hPSCs-derived neural rosettes.
The Shot CH1 domain recognises a distinct form of F-actin duringDrosophilaoocyte determination
Authors: Nashchekin D. , Squires I. , Prokop A. , St Johnston D. 
Published: January 2023

AbstractAs in mammals, only one cell in aDrosophilamulticellular female germline cyst is specified as an oocyte. The symmetry-breaking cue for oocyte selection is provided by the fusome, a tubular structure connecting all cells in the cyst. TheDrosophilaspectraplakin Shot localises to the fusome and translates its asymmetry into a polarised microtubule network that is essential for oocyte specification, but how Shot recognises the fusome is unclear. Here we demonstrate that Shot’s actin-binding domain (ABD) is necessary and sufficient to localise Shot to the fusome and mediates Shot function in oocyte specification together with the microtubule-binding domains. The calponin homology domain 1 (CH1) of Shot’s ABD recognises fusomal F-actin and requires CH2 to distinguish it from other forms of F-actin in the cyst. By contrast, the ABDs of Utrophin, Fimbrin, Filamin, Lifeact and F-tractin do not recognise fusomal F-actin. We therefore propose that Shot propagates fusome asymmetry by recognising a specific conformational state of F-actin on the fusome.
High-throughput sequencing of macaque basolateral amygdala projections reveals dissociable connectional motifs with frontal cortex
Authors: Zeisler Zachary R , London Liza , Janssen William G , Fredericks J Megan , Elorette Catherine , Fujimoto Atsushi , Zhan Huiqing , Russ Brian E , Clem Roger L , Hof Patrick R , Stoll Frederic M , Rudebeck Peter H 
Published: January 2023

AbstractThe basolateral amygdala (BLA) projects widely across the macaque frontal cortex1–4, and amygdalo-frontal projections are critical for optimal emotional responding5and decision- making6. Yet, little is known about the single-neuron architecture of these projections: namely, whether single BLA neurons project to multiple parts of the frontal cortex. Here, we use MAPseq7to determine the projection patterns of over 3000 macaque BLA neurons. We found that one-third of BLA neurons have two or more distinct targets in parts of frontal cortex and of subcortical structures. Further, we reveal non-random structure within these branching patterns such that neurons with four targets are more frequently observed than those with two or three, indicative of widespread networks. Consequently, these multi-target single neurons form distinct networks within medial and ventral frontal cortex consistent with their known functions in regulating mood and decision-making. Additionally, we show that branching patterns of single neurons shape functional networks in the brain as assessed by fMRI-based functional connectivity. These results provide a neuroanatomical basis for the role of the BLA in coordinating brain-wide responses to valent stimuli8and highlight the importance of high- resolution neuroanatomical data for understanding functional networks in the brain.
Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research
Authors: Coleman-Gosser Nikki , Raghuvanshi Shiva , Stitzinger Shane , Hu Yanhui , Chen Weihang , Luhur Arthur , Mariyappa Daniel , Josifov Molly , Zelhof Andrew , Mohr Stephanie E. , Perrimon Norbert , Simcox Amanda 
Published: January 2023

ABSTRACTExpression of activated Ras, RasV12, provides Drosophila cultured cells with a proliferation and survival advantage that simplifies the generation of continuous cell lines. Here we used lineage restricted RasV12expression to generate continuous cell lines of muscle, glial, and epithelial cell type. Additionally, cell lines with neuronal and hemocyte characteristics were isolated by cloning from cell cultures established with broad RasV12expression. Differentiation with the hormone ecdysone caused maturation of cells from mesoderm lines into active muscle tissue and enhanced dendritic features in neuronal-like lines. Transcriptome analysis showed expression of key cell-type specific genes and the expected alignment with single cell sequencing data in several cases. Overall, the technique has produced in vitro cell models with characteristics of glia, epithelium, muscle, nerve, and hemocyte. The cells and associated data are available from the Drosophila Genomic Resource Center.
L-type Ca2+channels mediate regulation of glutamate release by subthreshold potential changes
Authors: Lee Byoung Ju , Lee Unghwi , Ryu Seung Hyun , Han Sukmin , Lee Seung Yeon , Lee Jae Sung , Ju Anes , Chang Sunghoe , Lee Suk-Ho , Kim Sung Hyun , Ho Won-Kyung 
Published: January 2023

ABSTRACTSubthreshold depolarization enhances neurotransmitter release evoked by action potentials and plays a key role in modulating synaptic transmission by combining analog and digital signals. This process is known to be Ca2+-dependent. However, the underlying mechanism of how small changes in basal Ca2+caused by subthreshold depolarization can regulate transmitter release triggered by a large increase in local Ca2+is not well understood. This study aimed to investigate the source and signaling mechanisms of Ca2+that couple subthreshold depolarization with the enhancement of glutamate release in hippocampal cultures and CA3 pyramidal neurons. Subthreshold depolarization increased presynaptic Ca2+levels, the frequency of spontaneous release, and the amplitude of evoked release, all of which were abolished by blocking L-type Ca2+channels. A high concentration of intracellular Ca2+buffer or blockade of calmodulin and phospholipase C abolished depolarization induced increases in transmitter release. Estimation of the readily releasable pool size using hypertonic sucrose showed depolarization induced increases in readily releasable pool size, and this increase was abolished by blockade of calmodulin or phospholipase C. Our results provide mechanistic insights into the modulation of transmitter release by subthreshold potential change and highlight the role of L-type Ca2+channels in coupling subthreshold depolarization to the activation of Ca2+-dependent signaling molecules that regulate transmitter release.SIGNIFICANCENeuronal activities are encoded by action potentials, but subthreshold changes in resting membrane potentials also play important roles in regulating neuronal functions including synaptic transmission. It is, however, poorly understood how small changes in basal Ca2+induced by subthreshold depolarization regulate transmitter release triggered by a large increase in local Ca2+in presynaptic terminals. We demonstrate that L-type Ca2+channels are the major source of presynaptic Ca2+influx at basal state and during subthreshold depolarization, resulting in the activation of signaling molecules such as calmodulin and phospholipase C, which facilitate transmitter release by increasing both release probability and the readily releasable pool size. Our results provide mechanistic insight into how subthreshold potential changes contribute to regulating transmitter release.
Role of cytoneme-like structures and extracellular vesicles inTrichomonas vaginalisparasite: parasite communication
Authors: Salas Nehuén , Pedreros Manuela Blasco , Santos Melo Tuanne dos , Maguire Vanina G. , Sha Jihui , Wohlschlegel James A. , Pereira-Neves Antonio , de Miguel Natalia 
Published: January 2023

AbstractTrichomonas vaginalis, the etiologic agent of the most common non-viral sexually transmitted infection worldwide, colonizes the human urogenital tract where it remains extracellular and adheres to epithelial cells. With an estimated prevalence of 276 million new cases annually, mixed infections with different parasite strains are expected. Although it is considered as obvious that parasites interact with their host to enhance their own survival and transmission, evidence of mixed infection call into question the extent to which unicellular parasites communicate with each other. Here, we demonstrated that differentT. vaginalisstrains are able to communicate through the formation of cytoneme-like membranous cell connections. We showed thatT. vaginalisadherent strains form abundant membrane protrusions and cytonemes formation of an adherent parasite strain (CDC1132) is affected in the presence of a different strain (G3 or B7RC2). Using a cell culture inserts assays, we demonstrated that the effect in cytoneme formation is contact independent and that extracellular vesicles (EVs) are responsible, at least in part, of the communication among strains. In this sense, we found that EVs isolated from G3, B7RC2 and CDC1132 strains contain a highly distinct repertoire of proteins, some of them involved in signaling and communication, among other functions. Finally, we showed that parasite adherence to host cells is affected by this communication between strains as binding of adherentT. vaginalisCDC1132 strain to prostate cells is significantly higher in the presence of G3 or B7RC2 strains. Demonstrating that interaction of isolates with distinct phenotypic characteristics may have significant clinical repercussions, we also observed that a poorly adherent parasite strain (G3) adheres more strongly to prostate cells in the presence of an adherent strain. The study of signaling, sensing and cell communication in parasitic organisms will surely enhance our understanding of the basic biological characteristics of parasites that might have important consequences in pathogenesis.
Excitation and inhibition delays within a feedforward inhibitory pathway modulate cerebellar Purkinje cell output in mice
Authors: Binda Francesca , Spaeth Ludovic , Kumar Arvind , Isope Philippe 
Published: January 2023

AbstractThe cerebellar cortex computes sensorimotor information from many brain areas through a feedforward inhibitory (FFI) microcircuit between the input stage, the granule cell layer, and the output stage, the Purkinje cells. While in other brain areas FFI underlies a precise excitation vs inhibition temporal correlation, recent findings in the cerebellum highlighted more complex behaviors at the granule cell (GC) – molecular layer interneuron (MLI) – Purkinje cell (PC) FFI pathway. To dissect the temporal organization of the cerebellar FFI pathway, we combined exvivo patch clamp recordings of PCs with a viral-based strategy to express Channelrhodopsin2 in a subset of mossy fibers (MFs), a major excitatory input to GCs. We show that light-mediated MF activation elicits excitatory and inhibitory currents in PCs with a wide range of temporal delays. Furthermore, in many recordings, excitation and inhibition were initiated by different groups of GCs, expanding PCs synaptic temporal integration. Using a computational model of the FFI pathway we demonstrated that this temporal expansion could strongly influence how PCs integrate MF inputs. Our findings suggest that MF inputs are also encoded by specific delays between excitation and inhibition in PCs.
Bioengineering of aLactococcus lactissubsp.lactisstrain enhances nisin production and bioactivity
Authors: Portieles Roxana , Xu Hongli , Chen Feng , Gao Jingyao , Du Lihua , Gao Xiangyou , Nordelo Carlos Borroto , Yue Qiulin , Zhao Lin , Gonzalez Nayanci Portal , Bermudez Ramon Santos , Borrás-Hidalgo Orlando 
Published: January 2023

AbstractLactococcus lactissubsp.lactisis a food bacterium that has been utilized for decades in food fermentation and the development of high-value industrial goods. Among these, nisin is produced by several strains ofL. lactissubsp.lactisplays a crucial role as a food bio-preservative. The relative expression of the gene cluster involved in nisin production was evaluated using qPCR analysis. Additionally, a series of re-transformations of the strain introducing multi copies of thenisAandnisRKgenes involved in nisin biosynthesis were developed. The simultaneous expression ofnisAandnisZgenes was used to potentiate the effective inhibition of foodborne pathogens. Further, qPCR analysis revealed a low expression of thenisAandnisRKgenes in wild-typeL. lactissubsp.lactis. After several re-transformations of the strain with thenisAandnisRKgenes, a high expression of these genes was obtained, contributing to improved nisin production. Also, the co-expression ofnisAandnisZgenes results in highly efficient antimicrobial activity. Hence, this study would supply an approach to enhancing nisin production during industrial processes and antimicrobial activity.
Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors
Authors: Pöll Gisela , Griesenbeck Joachim , Tschochner Herbert , Milkereit Philipp 
Published: January 2023

AbstractRpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required for the stabilisation and maturation of SSU precursors at specific post-nucleolar stages.Here, we analysed the role of S0-cluster formation for rRNA folding. Structures of SSU precursors isolated from yeast S0-cluster expression mutants or control strains were analysed by cryogenic electron microscopy. The obtained resolution was sufficient to detect individual 2’-O-methyl RNA modifications using an unbiased scoring approach.The data show how S0-cluster formation enables the initial recruitment of the pre-rRNA processing factor Nob1 in yeast. Furthermore, they reveal hierarchical effects on the pre-rRNA folding pathway, including the final maturation of the central pseudoknot.Based on these structural insights we discuss how formation of the S0-cluster determines at this early cytoplasmic assembly checkpoint if SSU precursors further mature or are degraded.
Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature
Authors: Knafou Julien , Haas Quentin , Borissov Nikolay , Counotte Michel , Low Nicola , Imeri Hira , Ipekci Aziz Mert , Buitrago-Garcia Diana , Heron Leonie , Amini Poorya , Teodoro Douglas 
Published: January 2023

AbstractBackgroundThe COVID-19 pandemic has led to an unprecedented amount of scientific publications, growing at a pace never seen before. Multiple living systematic reviews have been developed to assist professionals with up-to-date and trustworthy health information, but it is increasingly challenging for systematic reviewers to keep up with the evidence in electronic databases. We aimed to investigate deep learning-based machine learning algorithms to classify COVID-19 related publications to help scale-up the epidemiological curation process.MethodsIn this retrospective study, five different pre-trained deep learning-based language models were fine-tuned on a dataset of 6,365 publications manually classified into two classes, three subclasses and 22 sub-subclasses relevant for epidemiological triage purposes. In ak-fold cross-validation setting, each standalone model was assessed on a classification task and compared against an ensemble, which takes the standalone model predictions as input and uses different strategies to infer the optimal article class. A ranking task was also considered, in which the model outputs a ranked list of sub-subclasses associated with the article.ResultsThe ensemble model significantly outperformed the standalone classifiers, achieving a F1-score of 89.2 at the class level of the classification task. The difference between the standalone and ensemble models increases at the sub-subclass level, where the ensemble reaches a micro F1-score of 70% against 67% for the best performing standalone model. For the ranking task, the ensemble obtained the highest recall@3, with a performance of 89%. Using an unanimity voting rule, the ensemble can provide predictions with higher confidence on a subset of the data, achieving detection of original papers with a F1-score up to 97% on a subset of 80% of the collection instead of 93% on the whole dataset.ConclusionThis study shows the potential of using deep learning language models to perform triage of COVID-19 references efficiently and support epidemiological curation and review. The ensemble consistently and significantly outperforms any standalone model. Fine-tuning the voting strategy thresholds is an interesting alternative to annotate a subset with higher predictive confidence.
Medial entorhinal cortex plays a specialized role in learning of flexible, context-dependent interval timing behavior
Authors: Bigus Erin R. , Lee Hyun-Woo , Bowler John C. , Shi Jiani , Heys James G. 
Published: January 2023

SummaryEpisodic memory requires encoding the temporal structure of experience and relies on brain circuits in the medial temporal lobe, including the medial entorhinal cortex (MEC). Recent studies have identified MEC ’time cells’, which fire at specific moments during interval timing tasks, collectively tiling the entire timing period. It has been hypothesized that MEC time cells could provide temporal information necessary for episodic memories, yet it remains unknown whether MEC time cells display learning dynamics required for encoding different temporal contexts. To explore this, we developed a novel behavioral paradigm that requires distinguishing temporal contexts. Combined with methods for cellular resolution calcium imaging, we find that MEC time cells display context-dependent neural activity that emerges with task learning. Through chemogenetic inactivation we find that MEC activity is necessary for learning of context-dependent interval timing behavior. Finally, we find evidence of a common circuit mechanism that could drive sequential activity of both time cells and spatially selective neurons in MEC. Our work suggests that the clock-like firing of MEC time cells can be modulated by learning, allowing the tracking of various temporal structures that emerge through experience.
Lysine-deficient proteome can be regulated through non-canonical ubiquitination and ubiquitin-independent proteasomal degradation
Authors: Szulc Natalia A. , Piechota Małgorzata , Thapa Pankaj , Pokrzywa Wojciech 
Published: January 2023

SummaryThe ubiquitin-proteasome system (UPS) removes damaged and unwanted proteins by attaching ubiquitin to lysines in a process termed ubiquitination. Little is known how functional components of the UPS, often exposed to erroneous labeling by ubiquitin during functioning, avoid premature proteolysis. An extensive lysine-less region (lysine desert) in the yeast E3 ligase Slx5 was shown to counteract its ubiquitin-dependent turnover. We conducted bioinformatic screens among prokaryotes and eukaryotes to describe the scope and conservation of this phenomenon. We found that lysine deserts are widespread among bacteria using pupylation-dependent proteasomal degradation, an analog of the UPS. In eukaryotes, lysine deserts appear with increasing organismal complexity, and the most evolutionarily conserved are enriched in the UPS members. Using VHL and SOCS1 E3 ligases, which elongate their lysine desert in the course of evolution, we established that they are non-lysine ubiquitinated, which does not influence their stability, and can be subject to proteasome turnover irrespective of ubiquitination. Our data suggest that a combination of non-lysine ubiquitination and ubiquitin-independent degradation may control the function and fate of the lysine-deficient proteome, as the presence of lysine deserts does not correlate with the half-life.
The N-coil and the globular N-terminal domain of plant ARGONAUTE1 are interaction hubs for regulatory factors
Authors: Bressendorff Simon , Kausika Swathi , Sjøgaard Ida Marie Zobbe , Oksbjerg Emilie Duus , Michels Alec , Poulsen Christian , Brodersen Peter 
Published: January 2023

ABSTRACTThe effector complex of RNA interference (RNAi) contains at its core an ARGONAUTE (AGO) protein bound to a small guide RNA. AGO proteins adopt a two-lobed structure in which the N-terminal (N) and Piwi-Argonaute-Zwille (PAZ) domains make up one lobe, while the middle (MID) and Piwi domains make up the other. Specific biochemical functions of PAZ, MID and Piwi domains of eukaryotic AGO proteins have been described, but the functions of the N-terminal domain remain less clear. Here, we use yeast two-hybrid screening with the N-terminal domain of the founding member of the AGO protein family, arabidopsis AGO1, to reveal that it interacts with many factors involved in regulated proteolysis. Interaction with a large group of proteins, including the autophagy cargo receptors ATI1 and ATI2, requires residues in a short, linear region, the N-coil, that joins the MID-Piwi lobe in the three-dimensional structure of AGO. In contrast, the F-box protein AUF1 interacts with AGO1 independently of the N-coil and requires distinct residues in the globular N domain itself. Mutation of AGO1 residues necessary for interaction with protein degradation factors in yeast stabilizes reporters fused to the AGO1 N-terminal domain in plants, supporting theirin vivorelevance. Our results define distinct regions of the N domain implicated in protein-protein interaction, and point to a particular importance of the AGO1 N-coil as a site of interaction with regulatory factors.
Engineering a Scalable and Orthogonal Platform for Synthetic Communication in Mammalian Cells
Authors: Pistikou Anna-Maria Makri , Cremers Glenn A.O. , Nathalia Bryan L. , Bögels Bas W.A. , Eijkens Bruno V. , de Dreu Anne , Bezembinder Maarten T.H. , Stassen Oscar M.J.A. , Bouten Carlijn C.V. , Merkx Maarten , Jerala Roman , de Greef Tom F. A. 
Published: January 2023

AbstractThe rational design and implementation of synthetic, orthogonal mammalian communication systems has the potential to unravel fundamental design principles of mammalian cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics and artificial tissue engineering. We lay here the foundations for the engineering of an orthogonal, and scalable mammalian synthetic intercellular communication platform that exploits the programmability of synthetic receptors and selective affinity and tunability of diffusing coiled-coil (CC) peptide heterodimers. Leveraging the ability of CCs to exclusively bind to a selected cognate receptor, we demonstrate orthogonal receptor activation, as well as Boolean logic computations. Next, we reveal synthetic intercellular communication based on synthetic receptors and secreted multidomain CC ligands and demonstrate a minimal, three-cell population system that can perform distributed AND gate logic. Our work provides a modular and scalable framework for the engineering of complex cell consortia, with the potential to expand the aptitude of cell therapeutics and diagnostics.