bluuebunny/crossref_metadata_2025_split huggingface dataset:
The characteristics of intracellular Ca2+signalsin vivonecessitate a new model for salivary fluid secretion
Authors: Takano Takahiro , Wahl Amanda M. , Huang Kai-Ting , Rugis John , Sneyd James , Yule David I. 
Published: January 2021

AbstractSalivary fluid secretion involves an intricate choreography to result in the trans-epithelial movement of NaCl and water into the acinus lumen. Current models are based on experimental observations in enzymatically isolated cells where the Ca2+signal invariably propagates globally and thus appears ideally suited to activate spatially separated Cl and K channels. We monitored Ca2+signals and salivary secretion in live mice expressing GCamp6F, following stimulation of the nerves innervating the submandibular gland. Consistent within vitrostudies, Ca2+signals were initiated in the apical endoplasmic reticulum. In marked contrast toin vitrodata, highly localized trains of Ca2+transients that failed to propagate from the apical region were observed. Following stimuli optimum for secretion, large apical-basal gradients were elicited. Given this incompatibility to the previous model, a new mathematical model was constructed to explain how salivary secretion can be efficiently stimulated by apically localized Ca2+signals.
Pan-cancer analysis of mRNA stability for decoding tumour post-transcriptional programs
Authors: Perron Gabrielle , Jandaghi Pouria , Rajaee Maryam , Alkallas Rached , Riazalhosseini Yasser , Najafabadi Hamed S. 
Published: January 2021

AbstractRNA stability is a crucial and often overlooked determinant of gene expression. Some of the regulators of mRNA stability are long known as key oncogenic or tumour suppressor factors. Nonetheless, the extent to which mRNA stability contributes to transcriptome remodeling in cancer is unknown, and the factors that modulate mRNA stability during cancer development and progression are largely uncharacterized. Here, by decoupling transcriptional and post-transcriptional effects in RNA-seq data of 7760 samples from 18 cancer types, we present a pan-cancer view of the mRNA stability changes that accompany tumour development and progression. We show that thousands of genes are dysregulated at the mRNA stability level, and identify the potential factors that drive these changes, including >80 RNA-binding proteins (RBPs) and microRNAs (miRNAs). Most RBPs and miRNAs have cancer type-specific activities, but a few show recurrent inactivation across multiple cancers, including the RBFOX family of RBPs and miR-29. Analysis of cell lines with phenotypic activation or inhibition of RBFOX1 and miR-29 confirms their role in modulation of genes that are dysregulated across multiple cancers, with functions in calcium signaling, extracellular matrix organization, and stemness. Overall, our study highlights the critical role of mRNA stability in shaping the tumour transcriptome, with recurrent post-transcriptional changes that are ~30% as frequent as transcriptional events. These results provide a resource for systematic interrogation of cancer-associated stability drivers and pathways.
Allosteric communication in Class A β-lactamases occurs via Cooperative Coupling of Loop Dynamics
Authors: Galdadas Ioannis , Qu Shen , F Oliveria Ana Sofia , Olehnovics Edgar , Mack Andrew R , Mojica Maria F , Agarwal Pratul K , Tooke Catherine L , Gervasio Francesco L , Spencer James , Bonomo Robert A , Mulholland Adrian J , Haider Shozeb 
Published: January 2021

AbstractAllosteric effects control protein (e.g. enzyme) activity in ways that are not fully understood. Better understanding of allosteric effects, and tools to identify them, would offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways from two distant ligand binding sites to important active site structural elements that control enzymatic activity in two prototypical class A β-lactamases, TEM-1 and KPC-2. Both of these enzymes are important determinants of antibiotic resistance in widespread bacterial pathogens. The simulations show that the allosteric sites are connected to the active site in both enzymes, (e.g. affecting the conformation of the Ω-loop) highlighting how allosteric inhibitors may exert their effects. Nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. In these identified signaling pathways, the propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more clinically relevant amino acid substitutions in each enzyme map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.
Integrative analysis reveals unique features of the Smc5/6 complex
Authors: Yu You , Li Shibai , Ser Zheng , Sanyal Tanmoy , Choi Koyi , Wan Bingbing , Sali Andrej , Kentsis Alex , Patel Dinshaw J. , Zhao Xiaolan 
Published: January 2021

AbstractStructural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly regulates DNA replication and repair. The molecular basis for Smc5/6’s distinct functions is currently poorly understood. Here, we report an integrative structural study of the budding yeast Smc5/6 complex using electron microscopy, cross-linking mass spectrometry, and computational modeling. We show that while the complex shares a similar overall organization with other SMC complexes, it possesses several unique features. In contrast to the reported folded-arm structures of cohesin and condensin, our data suggest that Smc5 and Smc6 arm regions do not fold back on themselves. Instead, these long filamentous regions interact with subunits uniquely acquired by the Smc5/6 complex, namely the Nse2 SUMO ligase and the Nse5-Nse6 subcomplex. Further, we show that Nse5-Nse6 subcomplex adopts a novel structure with an extensive dimerization interface and multiple domains contacting other subunits of the Smc5/6 complex. We also provide evidence that the Nse5-Nse6 module uses its SUMO-binding motifs to contribute to Nse2-mediated sumoylation. Collectively, our integrative multi-scale study identifies distinct structural features of the Smc5/6 complex and functional cooperation amongst its co-evolved unique subunits.
Olfactory coding in the bumble bee antennal lobe
Authors: Mertes Marcel , Carcaud Julie , Sandoz Jean-Christophe 
Published: January 2021

AbstractSociality is classified as one of the major transitions in evolution, with the largest number of eusocial species found in the insect order Hymenoptera, including the Apini (honey bees) and the Bombini (bumble bees). Bumble bees and honey bees not only differ in their social organization and foraging strategies, but comparative analyses of their genomes demonstrated that bumble bees have a slightly less diverse family of olfactory receptors than honeybees, suggesting that their olfactory abilities have adapted to different social and/or ecological conditions. However, unfortunately, no precise comparison of olfactory coding has been performed so far between honey bees and bumble bees, and little is known about the rules underlying olfactory coding in the bumble bee brain. In this study, we usedin vivocalcium imaging to study olfactory coding of a panel of floral odorants in the antennal lobe (AL) of the bumble beeBombus terrestris. Our results show that odorants evoke consistent neuronal activity in the bumble bee antennal lobe. Each odorant evokes a different glomerular activity pattern revealing this molecule’s chemical structure, i.e. its carbon chain length and functional group. Response intensity as well as odor-similarity relationships were highly correlated to those measured in honey bees. This study thus suggests that bumble bees, like honey bees, are equipped to respond to odorants according to their chemical features.
Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses
Authors: Banchenko Sofia , Krupp Ferdinand , Gotthold Christine , Bürger Jörg , Graziadei Andrea , O’Reilly Francis , Sinn Ludwig , Ruda Olga , Rappsilber Juri , Spahn Christian M. T. , Mielke Thorsten , Taylor Ian A. , Schwefel David 
Published: January 2021

AbstractViruses have evolved means to manipulate the host’s ubiquitin-proteasome system, in order to down-regulate antiviral host factors. The Vpx/Vpr family of lentiviral accessory proteins usurp the substrate receptor DCAF1 of host Cullin4-RING ligases (CRL4), a family of modular ubiquitin ligases involved in DNA replication, DNA repair and cell cycle regulation. CRL4DCAF1specificity modulation by Vpx and Vpr from certain simian immunodeficiency viruses (SIV) leads to recruitment, poly-ubiquitylation and subsequent proteasomal degradation of the host restriction factor SAMHD1, resulting in enhanced virus replication in differentiated cells. To unravel the mechanism of SIV Vpr-induced SAMHD1 ubiquitylation, we conducted integrative biochemical and structural analyses of the Vpr protein from SIVs infectingCercopithecus cephus(SIVmus). X-ray crystallography reveals commonalities between SIVmusVpr and other members of the Vpx/Vpr family with regard to DCAF1 interaction, while cryo-electron microscopy and cross-linking mass spectrometry highlight a divergent molecular mechanism of SAMHD1 recruitment. In addition, these studies demonstrate how SIVmusVpr exploits the dynamic architecture of the multi-subunit CRL4DCAF1assembly to optimise SAMHD1 ubiquitylation. Together, the present work provides detailed molecular insight into variability and species-specificity of the evolutionary arms race between host SAMHD1 restriction and lentiviral counteraction through Vpx/Vpr proteins.Author summaryDue to the limited size of virus genomes, virus replication critically relies on host cell components. In addition to the host cell’s energy metabolism and its DNA replication and protein synthesis apparatus, the protein degradation machinery is an attractive target for viral re-appropriation. Certain viral factors divert the specificity of host ubiquitin ligases to antiviral host factors, in order to mark them for destruction by the proteasome, to lift intracellular barriers to virus replication. Here, we present molecular details of how the simian immunodeficiency virus accessory protein Vpr interacts with a substrate receptor of host Cullin4-RING ubiquitin ligases, and how this interaction redirects the specificity of Cullin4-RING to the antiviral host factor SAMHD1. The studies uncover the mechanism of Vpr-induced SAMHD1 recruitment and subsequent ubiquitylation. Moreover, by comparison to related accessory proteins from other immunodeficiency virus species, we illustrate the surprising variability in the molecular strategies of SAMHD1 counteraction, which these viruses adopted during evolutionary adaptation to their hosts. Lastly, our work also provides deeper insight into the inner workings of the host’s Cullin4-RING ubiquitylation machinery.
Manipulating the murineLgr5locus using a rapid, efficient and flexible CRISPR/Cas9 pipeline
Authors: Reichmuth Jan , vom Berg Johannes , Brügger Michael , Hausmann George , Valenta Tomas , Basler Konrad 
Published: January 2021

AbstractThe maintenance of adult epithelial tissues, such as the lining of the intestine, depends on their periodical renewal. This is achieved through small populations of adult stem cells. Lgr5 serves as a marker for these cells. Here we report a novel non-variegated Lgr5 mouse model, which was generated via the CRISPR/Cas9 system. We show that thisLgr5-2A-CreERT2-2A-mOrange2mouse line can be used for lineage tracing, as well as for directing gene expression to Lgr5+cells. The introduction of the transgene affects neither the expression, nor the function of endogenousLgr5. Therefore, this new tool will serve to mark and manipulate intestinal stem cells to gain new biological insights.
Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads
Authors: Belicova Lenka , Repnik Urska , Delpierre Julien , Gralinska Elzbieta , Seifert Sarah , Ignacio Valenzuela José , Morales-Navarrete Hernán Andrés , Franke Christian , Räägel Helin , Shcherbinina Evgeniya , Prikazchikova Tatiana , Koteliansky Victor , Vingron Martin , Kalaidzidis Yannis , Zatsepin Timofei , Zerial Marino 
Published: January 2021

AbstractLumen morphogenesis is key to the function of organs and results from the integration of molecular pathways and mechanical forces1–3. The mechanisms governing anisotropic lumen expansion remain elusive4–6. In contrast to epithelial cells which have simple apico-basal polarity and form tubes, hepatocytes are multi-polar and form narrow lumina that grow anisotropically between adjacent cells, collectively generating a complex 3D network of bile canaliculi (BC)7,8. Here, we studied lumen elongation and BC morphogenesis in differentiating primary mouse hepatoblastsin vitro. Remarkably, we discovered a pattern of specific extensions of the apical membrane traversing the lumen between adjacent hepatocytes and sealed by tight junctions, reminiscent of the bulkheads of boats. These structures were also present in the developing liver. A targeted screen revealed that silencing of Rab35 caused loss of the bulkheads, conversion of hepatocyte into simple epithelial polarity and formation of spherical luminain vitro. Strikingly, we could re-engineer hepatocyte polarity and tissue morphogenesisin vivoin the embryonic liver, converting BC into simple epithelial tubes. Our results suggest that the apical bulkheads of hepatocytes are cell-intrinsic anisotropic mechanical elements that ensure stability of the elongating lumen between two cells, thus determining the structure of BC during liver tissue morphogenesis.
The growing topology of theC. elegansconnectome
Authors: Helm Alec , Blevins Ann S. , Bassett Danielle S. 
Published: January 2021

AbstractProbing the developing neural circuitry inCaenorhabditis eleganshas enhanced our understanding of nervous systems. TheC. elegansconnectome, like those of other species, is characterized by a rich club of densely connected neurons embedded within a small-world architecture. This organization of neuronal connections, captured by quantitative network statistics, provides insight into the system’s capacity to perform integrative computations. Yet these network measures are limited in their ability to detect weakly connected motifs, such as topological cavities, that may support the system’s capacity to perform segregated computations. We address this limitation by using persistent homology to track the evolution of topological cavities in the growingC. elegansconnectome throughout neural development, and assess the degree to which the growing connec-tome’s topology is resistant to biological noise. We show that the developing connectome topology is both relatively robust to changes in neuron birth times and not captured by similar growth models. Additionally, we quantify the consequence of a neuron’s specific birth time and ask if this metric tracks other biological properties of neurons. Our results suggest that the connectome’s growing topology is a robust feature of the developing con-nectome that is distinct from other network properties, and that the growing topology is particularly sensitive to the exact birth times of a small set of predominantly motor neurons. By utilizing novel measurements that track biological features, we anticipate that our study will be helpful in the construction of more accurate models of neuronal development inC. elegans.Author SummaryNetwork analyses have identified several local and global properties of theC. elegansconnectome that are relevant to the organism’s function and its capacity for information processing. Recent work has extended those investigations by focusing on the connectome’s growth, in an effort to uncover potential drivers of connectome formation. Here we investigate connectome growth from the perspective of applied algebraic topology, by tracking both changing and persistent homology. In doing so, we are able to measure the resilience of the growth process to perturbations, and assess spatial variations in that resilience throughout the organism’s body. Our findings provide new insights regarding the development of this simple natural connectome, as we have determined the existence of a robust and topologically simple network feature that is unexplained by the presence of other notable features of the connectome.
Widespread inhibitory projections from the cerebellar interposed nucleus
Authors: Judd Elena N. , Lewis Samantha M. , Person Abigail L. 
Published: January 2021

AbstractThe cerebellum consists of parallel parasagittal modules that contribute to diverse behaviors, spanning motor to cognitive. Recent work employing cell-type specific tracing has identified circumscribed output channels of the cerebellar nuclei that could confer tight functional specificity. These studies have largely focused on excitatory projections of the cerebellar nuclei, however, leaving open the question of whether inhibitory neurons also constitute multiple output modules. We mapped output and input patterns to intersectionally restricted cell types of the interposed and adjacent interstitial nuclei. In contrast to the widespread assumption of primarily excitatory outputs and restricted inferior olive-targeting inhibitory output, we found that inhibitory neurons from this region ramified widely within the brainstem, targeting both motor- and sensory-related nuclei, distinct from excitatory output targets. Despite differences in output targeting, monosynaptic rabies tracing revealed largely shared afferents to both cell classes. We discuss the potential novel functional roles for inhibitory outputs in the context of cerebellar theory.
Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing
Authors: Anderson Donovan J. , Pauler Florian M. , McKenna Aaron , Shendure Jay , Hippenmeyer Simon , Horwitz Marshall S. 
Published: January 2021

ABSTRACTAcquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans.
A Constitutively Closed Pannexin1 Channel in Lipid Bilayer Nanodiscs Assembles as a Large-Pore Heptamer
Authors: Jin Xueyao , Leonhardt Susan A. , Chiu Yu-Hsin , Purdy Michael D. , McIntire William E. , Bennett Brad C. , Bayliss Douglas A. , Yeager Mark 
Published: January 2021

SUMMARYPannexin 1 (Panx1) channels are widely expressed and play important roles in apoptotic cell clearance, inflammation, blood pressure regulation, neurological disorders, opiate withdrawal, and cancer progression and metastasis. We performed (1) physicochemical analysis on a constitutively closed Panx1 channel (designated fPanx1ΔC) to examine the entire population of particles to detect multiple oligomeric states and (2) cryoEM in the membrane mimetics amphipol A8-35 and lipid bilayer nanodiscs. Our results reveal that the dominant if not exclusive oligomeric state of fPanx1ΔC is a heptamer, in solution and by cryoEM. The Panx1 heptamer provides further structural diversity within the family of large-pore channels, including hexameric LRRC8 (SWELL1) channels and connexin hemichannels, octameric CALHM1 channels and innexin hemichannels, and undecameric CALHM2 channels. Conserved structural themes are a large cytoplasmic vestibule with a diameter that corresponds roughly with the oligomeric state and a 4-helix bundle protomer, albeit with noncanonical helical packing for CALHM1 and CALHM2.In BriefThe 4-helix bundle protomer of a constitutively closed pannexin1 channel assembles as a heptamer in solution and by cryoEM.
Cyclic AMP signalling and glucose metabolism mediate pH taxis by African trypanosomes
Authors: Shaw Sebastian , Knüsel Sebastian , Abbühl Daniel , Naguleswaran Arunasalam , Etzensperger Ruth , Benninger Mattias , Roditi Isabel 
Published: January 2021

AbstractThe collective movement of African trypanosomes on semi-solid surfaces, known as social motility, is presumed to be due to migration factors and repellents released by the parasites. Here we show that procyclic (insect midgut) forms acidify their environment as a consequence of glucose metabolism, generating pH gradients by diffusion. Early and late procyclic forms exhibit self-organising properties on agarose plates. While early procyclic forms are repelled by acid and migrate outwards, late procyclic forms remain at the inoculation site. Furthermore, trypanosomes respond to exogenously formed pH gradients, with both early and late procyclic forms being attracted to alkali. pH taxis is mediated by multiple cyclic AMP effectors: deletion of one copy of adenylate cyclase ACP5, or both copies of the cyclic AMP response protein CARP3, abrogates the response to acid, while deletion of phosphodiesterase PDEB1 completely abolishes pH taxis. The ability to sense pH is biologically relevant as trypanosomes experience large changes as they migrate through their tsetse host. Supporting this, a CARP3 null mutant is severely compromised in its ability to establish infections in flies. Based on these findings, we propose that the expanded family of adenylate cyclases in trypanosomes might govern other chemotactic responses in their two hosts.