bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel evolution of mutational fitness effects over 50,000 generations
Authors: Limdi Anurag , Owen Siân V. , Herren Cristina M. , Lenski Richard E. , Baym Michael 
Published: May 2022

AbstractAs evolving populations accumulate mutations, the benefits and costs of subsequent mutations change. As fitness increases, the relative benefit of new mutations typically decreases. However, the question remains whether deleterious mutations tend to have larger or smaller costs as a population adapts; theory and experiments provide support for both conflicting hypotheses. To address this question, we compared the effects of insertion mutations in every gene inEscherichia colibetween ancestral and 12 independently derived strains after 50,000 generations in a uniform environment. We found both increases and decreases in the fitness costs of mutations, leaving the overall distribution of effects largely unchanged. However, at the extreme, more genes became essential over evolution than vice versa. Both changes in fitness effects and essentiality evolved in parallel across the independent populations, and most changes were not explained by structural variation or altered gene expression. Thus, the macroscopic features of the local fitness landscape remained largely unchanged, even as access to particular evolutionary trajectories changed consistently during adaptation to the experimental environment.One Sentence SummaryLimdi et al. report parallel changes in the cost of mutations in replicate lineages of a decades-longE. colievolution experiment.
Structural disruption of BAF chromatin remodeller impairs neuroblastoma metastasis by reverting an invasiveness epigenomic program
Authors: Jiménez Carlos , Antonelli Roberta , Nadal-Ribelles Mariona , Devis-Jauregui Laura , Latorre Pablo , Solé Carme , Masanas Marc , Molero-Valenzuela Adrià , Soriano Aroa , de Toledo Josep Sánchez , Llobet-Navas David , Roma Josep , Posas Francesc , de Nadal Eulàlia , Gallego Soledad , Moreno Lucas , Segura Miguel F. 
Published: May 2022

AbstractBackgroundEpigenetic programming during development is essential for determining cell lineages, and alterations in this programming contribute to the initiation of embryonal tumour development. In neuroblastoma, neural crest progenitors block their course of natural differentiation into sympathoadrenergic cells, leading to the development of aggressive and metastatic paediatric cancer. Research of the epigenetic regulators responsible for oncogenic epigenomic networks is crucial for developing new epigenetic-based therapies against these tumours. Mammalian switch/sucrose non-fermenting (mSWI/SNF) ATP-dependent chromatin remodelling complexes act genome-wide translating epigenetic signals into open chromatin states. The present study aimed to understand the contribution of mSWI/SNF to the oncogenic epigenomes of neuroblastoma and its potential as a therapeutic target.MethodsFunctional characterisation of the mSWI/SNF complexes was performed in neuroblastoma cells using proteomic approaches, loss-of-function experiments, transcriptome and chromatin accessibility analyses, andin vitroandin vivoassays.ResultsNeuroblastoma cells contain three main mSWI/SNF subtypes, but only BRG1-associated factor (BAF) complex disruption through silencing of its key structural subunits, ARID1A and ARID1B, impairs cell proliferation by promoting cell cycle blockade. Genome-wide chromatin remodelling and transcriptomic analyses revealed that BAF disruption results in the epigenetic repression of an extensive invasiveness-related expression program involving integrins, cadherins, and key mesenchymal regulators, thereby reducing adhesion to the extracellular matrix and the subsequent invasionin vitroand drastically inhibiting the initiation and growth of neuroblastoma metastasisin vivo.ConclusionsWe report a novel ATPase-independent role for the BAF complex in maintaining an epigenomic program that allows neuroblastoma invasiveness and metastasis, urging for the development of new BAF pharmacological structural disruptors for therapeutic exploitation in metastatic neuroblastoma.
Homeostatic feedback between lysosomal mTORC1 and mTORC2-AKT signaling controls nutrient uptake in brown adipose tissue
Authors: Liebscher Gudrun , Vujic Nemanja , Schreiber Renate , Heine Markus , Krebiehl Caroline , Duta-Mare Madalina , Lamberti Giorgia , de Smet Cedric H. , Hess Michael W. , Eichmann Thomas O. , Hölzl Sarah , Scheja Ludger , Heeren Joerg , Kratky Dagmar , Huber Lukas A. 
Published: May 2022

AbstractIn brown adipose tissue (iBAT), the balance of lipid/glucose uptake and lipolysis is regulated by insulin signaling. Downstream of the insulin receptor, PDK1 and mTORC2 phosphorylate AKT, which activates glucose uptake and lysosomal mTORC1 signaling. The latter requires the late endosomal/lysosomal adaptor and MAPK and mTOR activator (LAMTOR/Ragulator). Deletion of LAMTOR2 (and thereby loss of the LAMTOR complex) in mouse adipocytes resulted in insulin-independent AKT hyperphosphorylation in iBAT, causing increased glucose and fatty acid uptake as evidenced by massively enlarged lipid droplets. As LAMTOR2 was essential for the upregulation ofde novolipogenesis, LAMTOR2 deficiency triggered exogenous glucose storage as glycogen in iBAT. These effects are cell autonomous, since AKT hyperphosphorylation was reversed by PI3K inhibition or by deletion of the mTORC2 component Rictor in LAMTOR2-deficient mouse embryonic fibroblasts. We identified a homeostatic circuit connecting LAMTOR-mTORC1 signaling with PI3K-mTORC2-AKT signaling downstream of the insulin receptor to maintain iBAT metabolism.
Mammalian D-Cysteine controls insulin secretion in the pancreas
Authors: Roychaudhuri Robin , West Timothy , Bhattacharya Soumyaroop , Saavedra Harry G. , Albacarys Lauren , Gadalla Moataz M. , Amzel Mario , Yang Peixin , Snyder Solomon H. 
Published: May 2022

AbstractD-amino acids are being recognized in mammals as important molecules with function. This is a first identification of endogenous D-cysteine in mammalian pancreas. D-cysteine is synthesized by serine racemase (SR) and SR−/−mice produce 6-10 fold higher levels of insulin in the pancreas and plasma including higher glycogen and ketone bodies in the liver. The excess insulin is stored as amyloid in secretory vesicles and exosomes. In glucose stimulated insulin secretion studies in mouse and human islets, equimolar amount of D-cysteine showed higher inhibition of insulin secretion compared to D-serine, another closely related stereoisomer synthesized by SR. In mouse models of diabetes (STZ and NOD) and human pancreas, the diabetic state showed increased expression of D-cysteine compared to D-serine followed by increased expression of SR. SR−/−mice show decreased cAMP in the pancreas followed by reduced phosphorylation of CREB (S133), lower DNA methyltransferase enzymatic and promoter activities resulting in decreased methylation of theIns1promoter. D-cysteine is efficiently metabolized by D-amino acid oxidase and transported by ASCT2 and Asc1. Dietary supplementation with methyl donors restored the high insulin levels and low DNMT enzymatic activity in SR−/−mice. Our data show that endogenous D-cysteine in the mammalian pancreas is a regulator of insulin secretion.HighlightsSerine Racemase also functions as a cysteine racemase.Lack of Serine Racemase results in significantly high levels of insulin in the pancreas, plasma and larger islets.D-cysteine shows greater inhibition of insulin secretion compared to D-serine.Endogenous D-cysteine signals via cyclic AMP that mediates downstream CREB-DNMT1 interaction.CREB-DNMT1 interaction results in hypomethylation ofIns1promoter that can be rescued by high methyl donor dietary supplementation rescuing high insulin levels.
The vestibular calyceal junction is dismantled following subchronic streptomycin in rats and sensory epithelium stress in humans
Authors: Maroto Alberto F. , Borrajo Mireia , Prades Sílvia , Callejo Àngela , Amilibia Emilio , Pérez-Grau Marta , Roca-Ribas Francesc , Castellanos Elisabeth , Barrallo-Gimeno Alejandro , Llorens Jordi 
Published: May 2022

ABSTRACTHair cell (HC) loss by epithelial extrusion has been described to occur in the rodent vestibular system during chronic 3,3’-iminodipropionitrile (IDPN) ototoxicity. This is preceded by dismantlement of the calyceal junction in the contact between type I HC (HCI) and calyx afferent terminals. Here, we evaluated whether these phenomena have wider significance. First, we studied rats receiving streptomycin for 3 to 8 weeks. Streptomycin caused loss of vestibular function associated with partial loss of HCI and decreased expression of contactin-associated protein (CASPR1), denoting calyceal junction dismantlement, in the calyces encasing the surviving HCI. Additional molecular and ultrastructural data supported the conclusion that HC-calyx detachment precede HCI loss by extrusion. Animals allowed to survive after the treatment showed functional recuperation and rebuilding of the calyceal junction. Second, we evaluated human sensory epithelia obtained during therapeutic labyrinthectomies and trans-labyrinthine tumour excisions. Some samples showed abnormal CASPR1 label strongly suggestive of calyceal junction dismantlement. Therefore, reversible dismantlement of the vestibular calyceal junction may be a common response triggered by chronic stress, including ototoxic stress, before HCI loss. This may partly explain clinical observations of reversion in function loss after aminoglycoside exposure.
Intracellular Calcium links Milk Stasis to Lysosome Dependent Cell Death by Activating a TGFβ3/TFEB/STAT3 Pathway Early during Mammary Gland Involution
Authors: Jeong Jaekwang , Lee Jongwon , Talaia Gabriel , Kim Wonnam , Song Junho , Hong Juhyeon , Yoo Kwangmin , Gonzalez David G. , Athonvarangkul Diana , Shin Jaehun , Dann Pamela , Haberman Ann M , Kim Lark Kyun , Ferguson Shawn M. , Choi Jungmin , Wysolmerski John 
Published: May 2022

AbstractInvolution of the mammary gland after lactation is a dramatic example of coordinated cell death. Weaning causes distension of the alveolar structures due to the accumulation of milk, which, in turn, activates STAT3 and initiates a caspase- independent but lysosome-dependent cell death (LDCD) pathway. Although the importance of STAT3 and LDCD in early mammary involution is well established, it has not been entirely clear how milk stasis activates STAT3. In this report, we demonstrate that protein levels of the PMCA2 calcium pump are significantly downregulated within 2- 4 hours of experimental milk stasis. Reductions in PMCA2 expression correlate with an increase in cytoplasmic calciumin vivoas measured by multiphoton intravital imaging of GCaMP6f fluorescence. These events occur concomitant with the appearance of nuclear pSTAT3 expression but prior to significant activation of LDCD or its previously implicated mediators such as LIF, IL6 and TGFβ3, all of which appear to be upregulated by increased intracellular calcium. We also observed that milk stasis, loss of PMCA2 expression and increased intracellular calcium levels activate TFEB, an important regulator of lysosome biogenesis. This is the result of increased TGFβ signaling and inhibition of cell cycle progression. Finally, we demonstrate that increased intracellular calcium activates STAT3 by inducing degradation of its negative regulator, SOCS3, a process which also appears to be mediated by TGFβ signaling. In summary, these data suggest that intracellular calcium serves as an important proximal biochemical signal linking milk stasis to STAT3 activation, increased lysosomal biogenesis, and lysosome- mediated cell death.
The Nse5/6-like SIMC1-SLF2 Complex Localizes SMC5/6 to Viral Replication Centers
Authors: Oravcová Martina , Nie Minghua , Zilio Nicola , Maeda Shintaro , Jami-Alahmadi Yasaman , Lazzerini-Denchi Eros , Wohlschlegel James A. , Ulrich Helle D. , Otomo Takanori , Boddy Michael N. 
Published: May 2022

AbstractThe human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1’s Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1’s helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions, binds SLF2 analogously to SIMC1 and forms a distinct Nse5/6-like complex. Thus, two Nse5/6-like complexes independently regulate human SMC5/6: SIMC1-SLF2 responding to viral challenge and SLF1/2 recognizing DNA damage.
FliL has a conserved function in diverse microbes to negatively modulate motor output via its N-terminal region
Authors: Liu Xiaolin , Roujeinikova Anna , Ottemann Karen M. 
Published: May 2022

AbstractBacterial surface sensing is often conferred by flagella. The flagellar motor protein FliL plays a key role in this process, but its exact role has been obscured by varying fliL mutant phenotypes. We reanalyzed results from studies on these fliL alleles and found they inadvertently compared mutants with differing length of the retained native N-terminal region, including the transmembrane helix (TM). We find that TM retention in the mutants that lack the native C-terminal domain results in loss of swimming and swarming motility, while alleles that completely lack the TM retain motility. We suggest FliL negatively regulates motor function via its N-terminal region, an observation that may relate to FliL function in mechanosensing.
Efficient querying of genomic reference databases with gget
Authors: Luebbert Laura , Pachter Lior 
Published: May 2022

AbstractMotivationA recurring challenge in interpreting genomic data is the assessment of results in the context of existing reference databases. Currently, there is no tool implementing automated, easy programmatic access to curated reference information stored in a diverse collection of large, public genomic databases.Resultsgget is a free and open-source command-line tool and Python package that enables efficient querying of genomic reference databases, such as Ensembl. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying required for genomic data analysis in a single line of code.AvailabilityThe manual and source code are available at https://github.com/pachterlab/gget.Contactlpachter@caltech.edu
Persistence of phenotypic responses to short-term heat stress in the tabletop coral Acropora hyacinthus
Authors: Walker Nia S. , Cornwell Brendan H. , Nestor Victor , Armstrong Katrina C. , Golbuu Yimnang , Palumbi Stephen R. 
Published: May 2022

AbstractWidespread mapping of coral thermal resilience is essential for developing effective management strategies and requires replicable and rapid multi-location assays of heat resistance and recovery. One- or two-day short-term heat stress experiments have been previously employed to assess heat resistance, followed by single assays of bleaching condition. We tested the reliability of short-term heat stress resistance, and linked resistance and recovery assays, by monitoring the post short-term heat stress phenotypic response of fragments from 101 Acropora hyacinthus colonies located in Palau (Micronesia). Following short-term heat stress, bleaching and mortality were recorded after 16 hours, daily for seven days, and after months one and two into recovery. To follow corals over time, we utilized a qualitative, non-destructive visual bleaching score metric that correlated with standard symbiont retention assays. The bleaching state of coral nubbins 16 hours post-heat stress was highly indicative of their state over the next 7 days, suggesting that symbiont population sizes within corals may quickly stabilize post-heat stress. Bleaching 16 hours post-heat stress predicted likelihood of mortality over the subsequent 3-5 days, after which there was little additional mortality. Together, bleaching and mortality suggested that rapid assays of the phenotypic response following short-term heat stress were good metrics of the total heat treatment effect. Additionally, our data confirm geographic patterns of intraspecific variation in Palau and show that bleaching severity among colonies was highly correlated with mortality over the first week post-stress. We found high survival (98%) and visible recoverability (100%) two months after heat stress among coral nubbins that survived the first week post-stress. These findings help simplify rapid, widespread surveys of heat sensitivity in Acropora hyacinthus by showing that standardized short-term experiments can be confidently assayed after 16 hours, and that bleaching sensitivity may be linked to subsequent survival using experimental assessments.
Analysis of the Drosophila Ajuba LIM protein defines functions for distinct LIM domains
Authors: Rauskolb Cordelia , Han Ahri , Kirichenko Elmira , Ibar Consuelo , Irvine Kenneth D. 
Published: May 2022

ABSTRACTThe Ajuba LIM protein Jub mediates regulation of Hippo signaling by cytoskeletal tension through interaction with the kinase Warts, and also participates in feedback regulation of junctional tension through regulation of the cytohesin Steppke. To investigate how Jub interacts with and regulates its distinct partners, we investigated the ability of Jub proteins missing different combinations of its three LIM domains to rescue jub phenotypes and to interact with α-catenin, Warts and Steppke. Multiple regions of Jub contribute to its ability to bind α-catenin and to localize to adherens junctions in Drosophila wing imaginal discs. Co-immunoprecipitation experiments in cultured cells identified a specific requirement for LIM2 for binding to Warts. However, in vivo, both LIM1 and LIM2, but not LIM3, were required for regulation of wing growth, Yorkie activity, and Warts localization. Conversely, LIM2 and LIM3, but not LIM1, were required for regulation of cell shape and Steppke localization in vivo, and for maximal Steppke binding in co-immunoprecipitation experiments. These observations identify distinct functions for the different LIM domains of Jub.
ER translocation of suboptimal targeting sequences depends on Sec61β/Sbh1 and its phosphorylation
Authors: Barbieri Guido , Simon Julien , Lupusella Cristina R. , Pereira Fabio , Elia Francesco , Meyer Hadar , Schuldiner Maya , Hanes Steven D. , Nguyen Duy , Helms Volkhard , Römisch Karin 
Published: May 2022

ABSTRACTThe endoplasmic reticulum (ER) protein translocation channel subunit Sec61β/Sbh1 is non-essential, but contains multiple phosphorylation sites suggesting a regulatory role in ER protein import. We show here that mutating two N-terminal, proline-flanked, phosphorylation sites in the Sbh1 cytosolic domain phenocopies the temperature-sensitivity of a yeast strain lacking SBH1/SBH2, and results in reduced translocation into the ER of an Sbh1-dependent substrate, Gls1. In a microscopic screen we show that about 12% of GFP-tagged secretory proteins depend on Sbh1 for translocation. Sbh1-dependent proteins have targeting sequences with less pronounced hydrophobicity and often no or an inverse charge bias. A subset of these proteins was dependent on N-terminal phosphorylation of Sbh1 and on the phospho-S/T-specific proline isomerase Ess1 (PIN1 in mammals) for ER import. We conclude that Sbh1 promotes ER translocation of substrates with suboptimal targeting sequences and that its activity is regulated by a conformational change induced by N-terminal phosphorylation.
On the intrinsic curvature of animal whiskers
Authors: Luo Yifu , Hartmann Mitra J.Z. 
Published: May 2022

AbstractFacial vibrissae (whiskers) are thin, tapered, and flexible hair-like structures that are an important source of tactile sensory information for many species of animals. In contrast to insect antennae, whiskers have no sensors along their lengths. Instead, when a whisker touches an object, the resulting deformation is transmitted to mechanoreceptors in a follicle at the whisker base. Previous work has shown that the mechanical signals transmitted along the whisker will depend strongly on the whisker’s geometric parameters, in particular on its taper (how diameter varies with arc length) and on its intrinsic curvature. Although previous studies have largely agreed on how to define taper, multiple approaches have been used to quantify intrinsic curvature. The present work, compares and contrasts different mathematical methods to quantify intrinsic curvature, including polynomial, fractional exponent, elliptical, and Cesàro. Comparisons are performed across ten species of whiskered animals, ranging from rodents to pinnipeds. The fractional exponent model is shown to be a particularly promising approach for distinguishing between whiskers of different species. We conclude with a discussion of the advantages and disadvantages of using the different models for different modeling situations.
The Indirect Pathway of the Basal Ganglia Promotes Negative Reinforcement, But Not Motor Suppression
Authors: Isett Brian R. , Nguyen Katrina P. , Schwenk Jenna C. , Snyder Christen N. , Adegbesan Kendra A. , Ziausyte Ugne , Gittis Aryn H. 
Published: May 2022

SummaryOptogenetic stimulation of Adora2a receptor expressing spiny projection neurons (A2A-SPN) in the striatum drives locomotor suppression and negative reinforcement, results attributed to activation of the indirect pathway. The sole long-range projection target of A2A-SPNs is the external globus pallidus (GPe). Unexpectedly, we found that inhibition of the GPe did not suppress movement, but did drive robust negative reinforcement in a real-time place preference assay. Within the striatum, A2A-SPNs inhibit other SPNs through a short-range inhibitory collateral network, and we found that optogenetic stimuli that drove motor suppression shared a common mechanism of recruiting this inhibitory collateral network. Our results suggest that the indirect pathway plays a more prominent role in negative reinforcement than in motor control and challenges the assumption that activity of A2A-SPNs is synonymous with indirect pathway activity.