bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frataxin deficiency induces lipid accumulation and affects thermogenesis in brown adipose tissue
Authors: Turchi Riccardo , Tortolici Flavia , Guidobaldi Giulio , Iacovelli Federico , Falconi Mattia , Rufini Stefano , Faraonio Raffaella , Casagrande Viviana , De Angelis Lorenzo , Federici Massimo , Carotti Simone , Francesconi Maria , Zingariello Maria , Morini Sergio , Bernardini Roberta , Maurizio Mattei , Lettieri-Barbato Daniele , Aquilano Katia 
Published: June 2019

ABSTRACTDecreased expression of the mitochondrial protein frataxin (FXN) causes Friedreich’s ataxia (FRDA). FRDA is a neurodegenerative disease also characterized by systemic metabolic alterations that increase the risk of developing type 2 diabetes thus aggravating FRDA prognosis. Brown adipose tissue (BAT) is a mitochondria-enriched and anti-diabetic tissue that, in addition to its thermoregulatory role, turns excess energy into heat to maintain energy balance. Here we report that the FXN knock-in/knock-out (KIKO) mouse shows reduced energy expenditure and VO2, hyperlipidemia, decreased insulin sensitivity and enhanced circulating levels of leptin, recapitulating diabetes-like signatures. FXN deficiency leads to alteration of mitochondrial structure and oxygen consumption, decreased lipolysis and lipid accumulation in BAT. Transcriptomic data highlighted a blunted thermogenesis response, as several biological processes related to thermogenesis (e.g. response to temperature stimuli, mitochondrial gene transcription, triglyceride metabolism, adipogenesis) resulted affected in BAT of KIKO mice upon cold exposure. Decreased adaptation to cool temperature in association with limited PKA-mediated lipolysis and downregulation of the expression of the genes controlling mitochondrial metabolism and lipid catabolism were observed in KIKO mice. T37i brown adipocytes and primary adipocytes with FXN deficiency showed reduced thermogenesis and adipogenesis markers respectively recapitulating the molecular signatures detected in KIKO mice.Collectively our data point to BAT dysfunction in FRDA and suggest BAT as a promising target to overcome metabolic complications in FRDA.
Circadian Oscillations Persist in Low Malignancy Breast Cancer Cells
Authors: Lellupitiyage Don Sujeewa S. , Lin Hui-Hsien , Furtado Jessica J. , Qraitem Maan , Taylor Stephanie R. , Farkas Michelle E. 
Published: June 2019

AbstractEpidemiological studies have shown that humans with altered circadian rhythms have higher cancer incidence, with breast cancer being one of the most cited examples. To uncover how circadian disruptions may be correlated with breast cancer and its development, prior studies have assessed the expression of BMAL1 and PER2 core clock genes via RT-qPCR and western blot analyses. These and our own low-resolution data show that BMAL1 and PER2 expression are suppressed and arrhythmic. We hypothesized that oscillations persist in breast cancer cells, but due to limitations of protocols utilized, cannot be observed. This is especially true where dynamic changes may be subtle. In the present work, we generated luciferase reporter cell lines representing high- and low-grade breast cancers to assess circadian rhythms. We tracked signals for BMAL1 and PER2 to determine whether and to what extent oscillations exist and provide initial correlations of circadian rhythm alterations with breast cancer aggression. In contrast to previous studies, where the clock was deemed to be “broken” in breast cancer, our luminometry data reveal that circadian oscillations of BMAL1 and PER2 do in fact exist in the low-grade, luminal A cell line, MCF7 but are not apparent in high-grade, basal MDA-MB-231 cells. To our knowledge, this is the first evidence of core circadian clock oscillations in breast cancer cells. This work also suggests that circadian rhythms are increasingly disrupted with breast cancer tumor grade/aggressiveness, and that use of real time luminometry to study additional representatives of breast and other cancer subtypes is highly merited.
Phosphatidylcholine biosynthesis in Mitis group streptococci via host metabolite scavenging
Authors: Joyce Luke R. , Guan Ziqiang , Palmer Kelli L. 
Published: June 2019

AbstractThe Mitis group streptococci include the major human pathogenStreptococcus pneumoniaeand the opportunistic pathogensS. mitisandS. oraliswhich are human oral cavity colonizers and agents of bacteremia and infective endocarditis in immunocompromised patients. Bacterial membrane lipids play crucial roles in microbe-host interactions, yet for many pathogens, the composition of the membrane is poorly understood. In this study, we characterized the lipidomes of selected species of Mitis group streptococci and investigated the mechanistic basis for biosynthesis of the phospholipid phosphatidylcholine (PC). PC is a major lipid in eukaryotic cellular membranes, but it is considered to be comparatively rare in bacterial taxa. Using liquid chromatography/mass spectrometry (LC/MS) in conjunction with stable isotope tracing, we determined that Mitis group streptococci synthesize PC via the rare host metabolite scavenging pathway, the glycerophosphocholine (GPC) pathway, which is largely uncharacterized in bacteria. Our work demonstrates that Mitis group streptococci includingS. pneumoniaeremodel their membrane in response to the major human metabolites GPC and lysoPC.ImportanceWe lack fundamental information about the composition of the cellular membrane even for the best studied pathogens of critical significance for human health. The Mitis group streptococci are closely linked to humans in health and disease, yet their membrane biology is poorly understood. Here, we demonstrate that these streptococci scavenge major human metabolites and use them to synthesize the membrane phospholipid phosphatidylcholine. Our work is significant because it identifies a mechanism by which the major human pathogenS. pneumoniaeand the primary human oral colonizersS. mitisandS. oralisremodel their membrane in response to host metabolites.
Correction of β3 integrin haplo-insufficiency by CRISPRa normalizes cortical network activity
Authors: Jaudon Fanny , Thalhammer Agnes , Cingolani Lorenzo A. 
Published: June 2019

SUMMARYThe extracellular matrix (ECM) plays an essential role in regulating the function of neuronal networks. In many cell types, the ECM exerts its effects through the transmembrane receptors integrins. Here, we investigate whether neuronal integrins regulate network excitability. Specifically, we focus on β3 integrin, which has been associated to autism spectrum disorder and whose expression in neurons is regulated by activity. We have designed CRISPRa tools to titrate β3 integrin expression in neurons. By using multi-electrode arrays and Ca2+imaging, we show that β3 integrin boosts network excitability and synchrony in primary cortical neurons. Crucially, CRISPRa could compensate precisely for β3 integrin haplo-insufficiency, thereby rebalancing level and correlation of neuronal activity. By contrast, rescue strategies based on exogenous gene expression resulted in hyper-active networks firing in unison. Thus, regulation of β3 integrin by CRISPRa provides a precise and efficient system for modulating neuronal network function.
Heavy Chain CDR 3 and Junctional Length Biases in Human Antibody Repertoires Associated with Heavy and Light Chain Germline Utilization
Authors: Sankar Kannan , Hoi Kam Hon , Hötzel Isidro 
Published: June 2019

AbstractAntibody variable domain sequence diversity is generated by recombination of germline segments. The third complementarity-determining region of the heavy chain (CDR H3) is the region of highest sequence diversity and is formed by the joining of heavy chain VH, DH and JH germline segments combined with random nucleotide trimming and additions between these segments. We show that CDR H3 length distribution is biased in human antibody repertoires as a function of VH, VL and JH germline segment utilization. Most length biases are apparent in the naïve B cell compartment, with a significant bias towards shorter CDR H3 sequences observed in association with a subset of VH and VL germlines in the antigen experienced compartment. Similar biases were not observed in nonproductive heavy chain recombination products, indicating selection of the repertoire during B cell maturation as a major driver of the length biases. Some VH-associated CDR H3 length biases are dependent on utilization of specific JH germline segments in a manner not directly linked to JH segment length in the germline, but are rather associated with selection of differentially trimmed JH segments in the naïve compartment. In addition, DH segment and N-region random nucleotide insertion lengths within CDR H3 in the naïve compartment were also biased by specific VH/JH germline combinations, indicating a complex set of constraints between germline segments selected during repertoire maturation. Our findings reveal biases in the antibody diversity landscape shaped by VH, VL, and JH germline features with implications for mechanisms of naïve and immune repertoire selection.
The observation of explicit and implicit visuomotor cues can drive predictive motor control
Authors: Rens Guy , Davare Marco 
Published: June 2019

AbstractRecent studies have highlighted that the observation of hand-object interactions can influence perceptual weight judgements made by an observer. Moreover, observing explicit motor errors during object lifting allows individuals to update their internal sensorimotor representation about object weight. Embodying observed visuomotor cues for the planning of a motor command further enables individuals to accurately scale their fingertip forces when subsequently lifting the same object. However, it is still unknown whether observation of a skilled lift is equally able to mediate predictive motor control in the observer. Here, we tested this hypothesis by asking participants to grasp and lift a manipulandum after observing an actor’s lift. The object weight changed unpredictably (light or heavy) every third to sixth trial performed by the actor. Participants were informed that they would always lift the same weight as the actor and that, based on the experimental condition, they would have to observe skilled or erroneously performed lifts. Our results revealed that the observation of both skilled and erroneously performed lifts allows participants to update their internal sensorimotor object representation, in turn enabling them to predict force scaling accurately. These findings suggest that the observation of explicit as well as implicit visuomotor cues are embodied in the observer’s motor repertoire and can drive changes in predictive motor control.
The dynamic chromatin architecture of the regenerating liver
Authors: Wang Amber W. , Wang Yue J. , Zahm Adam M. , Morgan Ashleigh R. , Wangensteen Kirk J. , Kaestner Klaus H. 
Published: June 2019

ABSTRACTBackground & AimsThe adult liver is the main detoxification organ and is routinely exposed to environmental insults but retains the ability to restore its mass and function upon tissue damage. However, massive injury can lead to liver failure, and chronic injury causes fibrosis, cirrhosis, and hepatocellular carcinoma. Currently, the transcriptional regulation of organ repair in the adult liver is incompletely understood.MethodsWe isolated nuclei from quiescent as well as repopulating hepatocytes in a mouse model of hereditary tyrosinemia, which recapitulates the injury and repopulation seen in toxic liver injury in humans. We then performed the ‘assay for transposase accessible chromatin with high-throughput sequencing’ (ATAC-seq) specifically in repopulating hepatocytes to identify differentially accessible chromatin regions and nucleosome positioning. Additionally, we employed motif analysis to predict differential transcription factor occupancy and validated the in silico results with chromatin immunoprecipitation followed by sequencing (ChIP-seq) for hepatocyte nuclear factor 4α (HNF4α) and CCCTC-binding factor (CTCF).ResultsChromatin accessibility in repopulating hepatocytes was increased in the regulatory regions of genes promoting proliferation and decreased in the regulatory regions of genes involved in metabolism. The epigenetic changes at promoters and liver enhancers correspond with regulation of gene expression, with enhancers of many liver function genes displaying a less accessible state during the regenerative process. Moreover, increased CTCF occupancy at promoters and decreased HNF4α binding at enhancers implicate these factors as key drivers of the transcriptomic changes in replicating hepatocytes that enable liver repopulation.ConclusionsOur analysis of hepatocyte-specific epigenomic changes during liver repopulation identified CTCF and HNF4α as key regulators of hepatocyte proliferation and regulation of metabolic programs. Thus, liver repopulation in the setting of toxic injury makes use of both general transcription factors (CTCF) for promoter activation, and reduced binding by a hepatocyte-enriched factor (HNF4α) to temporarily limit enhancer activity.Graphical Abstract
Inspiratory rhythmogenic activity is burst-independent and opioid-sensitive
Authors: Sun Xiaolu , Thörn Pérez Carolina , Nagaraj Halemani D , Shao Xuesi M. , Greenwood Morgan , Heath Sarah , Feldman Jack L. , Kam Kaiwen 
Published: June 2019

SummaryHow mammalian neural circuits generate rhythmic activity in motor behaviors, such as breathing, walking, and chewing, remains elusive. For breathing, rhythm generation can be localized to a brainstem nucleus called the preBötzinger Complex (preBötC). Rhythmic preBötC population activity consists of small amplitude burstlets, which we hypothesize are rhythmogenic, and larger inspiratory bursts, which drive motoneuronal activity. If burstlets are rhythmogenic, opioids, analgesics that can cause profound respiratory depression, should similarly reduce burstlet frequency. In conditions where burstlets were separated from bursts in medullary slices from neonatal mice, the μ-opioid receptor (μOR) agonist DAMGO decreased burstlet frequency. DAMGO-mediated depression was abolished by genetic deletion of μORs in a glutamatergic preBötC subpopulation and was reduced by Substance P, but not blockade of inhibitory synaptic transmission. Our findings suggest that rhythmogenesis need not rely on strong bursts of activity associated with motor output and point to strategies for ameliorating opioid-induced depression of breathing.
Pervasive Translation in Mycobacterium tuberculosis
Authors: Smith Carol , Canestrari Jill G. , Wang Archer J. , Champion Matthew M. , Derbyshire Keith M. , Gray Todd A. , Wade Joseph T. 
Published: June 2019

ABSTRACTMost bacterial ORFs are identified by automated prediction algorithms. However, these algorithms often fail to identify ORFs lacking canonical features such as a length of >50 codons or the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. The newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. Codon usage of the newly discovered ORFs suggests that most have not been subject to purifying selection, and hence do not contribute to cell fitness. Nevertheless, we identify 90 new ORFs (median length of 52 codons) that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs in Mycobacterium tuberculosis serves as a rich source for the evolution of new functional proteins.
A systems chemoproteomic analysis of acyl-CoA/protein interaction networks
Authors: Levy Michaella J. , Montgomery David C. , Sardiu Mihaela E. , Bergholtz Sarah E. , Nance Kellie D. , Montano Jose , Thorpe Abigail L. , Fox Stephen D. , Lin Qishan , Andresson Thorkell , Florens Laurence , Washburn Michael P. , Meier Jordan L. 
Published: June 2019

SummaryAcyl-CoA/protein interactions are required for many functions essential to life including membrane synthesis, oxidative metabolism, and macromolecular acetylation. However, despite their importance, the global scope and selectivity of these protein-metabolite interactions remains undefined. Here we describe the development of CATNIP (CoA/AcetylTraNsferase Interaction Profiling), a chemoproteomic platform for the high-throughput analysis of acyl-CoA/protein interactions in endogenous proteomes. First, we apply CATNIP to identify acetyl-CoA-binding proteins through unbiased clustering of competitive dose-response data. Next, we use this method to profile diverse protein-CoA metabolite interactions, identifying biological processes susceptible to altered acetyl-CoA levels. Finally, we apply systems-level analyses to assess the features of novel protein networks that may interact with acyl-CoAs, and demonstrate a strategy for high-confidence proteomic annotation of acetyl-CoA binding proteins. Overall our studies illustrate the power of integrating chemoproteomics and systems biology, and provide a resource for understanding the roles of acyl-CoA metabolites in biology and disease.
Precise implantation of super-paramagnetic iron oxide (SPIO) nanoparticles in hippocampus with external rotating magnetic field (RMF) produces rapid antidepressent effects in mice
Authors: Chi Yao , Wenwen Cai , Mengqin Xia , Jingyi Dai ,   JF Sun Sr.
Published: June 2019

AbstractBackgroundTMS is an effective anti-depression method commonly used in clinical practice, but it also faces the problems of low spatial resolution, treatment parameters to be optimized and limitation in mechanism research.ObjectiveTo develop a precise magnetic stimulation anti-depression method for the scientific research of magnetic stimulation, especially the mechanism research in animal experiments.MethodsThe cytotoxicity test was conducted in advance to ensure the security of intervention from SPIO nanoparticles and RMF. In animal experiments, 300nl SPIO solution was injected into the right hippocampus of the CUMS model mice, and then treated experimental group mice with rotating magnetic field for five days. The Sucrose Preference Test (SPT), the Forced Swim Test (FST) and BDNF expression levels were used to evaluate the antidepressant effect of this method.ResultsNo significant decrease of cell viability was observed when the iron concentration is between 52.2µg/ml and 208.8µg/ml. And the application of RMF with a certain frequency was considered to be safe in the cytotoxicity test. When treated with SPIO+RMF, the sucrose preference of SPIO+RMF group mice increased markedly (n=9, p<0.01 vs. CUMS), the FST immobile time reduced (n=8, P<0.05 vs. CUMS) and the BDNF level in the hippocampus was significantly up-regulated (n=5, P<0.01 vs. CUMS). However, merely SPIO intervention failed to be effective.Conclusionswhen intervened with external rotating magnetic field, the SPIO nanoparticles injected into the right hippocampus could produce rapid antidepressent effects in mice.
Class A PBPs have a distinct and unique role in the construction of the pneumococcal cell wall
Authors: Straume Daniel , Wiaroslawa Piechowiak Katarzyna , Olsen Silje , Stamsås Gro Anita , Berg Kari Helene , Kjos Morten , Heggenhougen Maria Victoria , Alcorlo Martin , Hermoso Juan A. , Håvarstein Leiv Sigve 
Published: June 2019

AbstractIn oval shapedStreptococcus pneumoniae, septal and longitudinal peptidoglycan synthesis is performed by independent functional complexes; the divisome and the elongasome. Penicillin binding proteins (PBPs) were long considered as the key peptidoglycan synthesizing enzymes in these complexes. Among these were the bifunctional class A PBPs, which are both glycosyltransferases and transpeptidases, and monofunctional class B PBPs with only transpeptidase activity. Recently, however, it was established that the monofunctional class B PBPs work together with non-PBP glycosyltransferases (FtsW and RodA) to make up the core peptidoglycan synthesizing machineries within the pneumococcal divisome (FtsW/PBP2x) and elongasome (RodA/PBP2b). The function of class A PBPs is therefore now an open question. Here we utilize the peptidoglycan hydrolase CbpD to show that class A PBPs have an autonomous role during cell wall synthesis inS. pneumoniae. Purified CbpD was shown to target the septum ofS. pneumoniaecells. Using assays to specifically inhibit PBP2x, we demonstrate that CbpD specifically target nascent peptidoglycan synthesized by the divisome. Notably, class A PBPs could process this nascent peptidoglycan from a CbpD-sensitive to a CbpD-resistant form. The class A PBP mediated processing was independent of divisome and elongasome activities. Class A PBPs thus constitute an autonomous functional entity which processes or repairs nascent peptidoglycan synthesized by FtsW/PBP2x. Our results support a model in which pneumococcal peptidoglycan is made by three functional entities, the divisome, the elongasome and a peptidoglycan-repairing or -remodelling complex consisting of bifunctional PBPs. To our knowledge this is the first time a specific function has been identified for class A PBPs in bacterial cell wall synthesis.
Microtubule-dependent transport of arenavirus matrix protein demonstrated using live-cell imaging microscopy
Authors: Takamatsu Yuki , Kajikawa Junichi , Muramoto Yukiko , Nakano Masahiro , Noda Takeshi 
Published: June 2019

AbstractLassa virus (LASV), belonging to the family Arenaviridae, causes severe haemorrhagic manifestations and is associated with a high mortality rate in humans. Thus, it is classified as a biosafety level (BSL)-4 agent. Since counter measures for LASV diseases are yet to be developed, it is important to elucidate the molecular mechanisms underlying the life cycle of the virus, including its viral and host cellular protein interactions. These underlying molecular mechanisms may serve as the key for developing novel therapeutic options. Lymphocytic choriomeningitis virus (LCMV), a close relative of LASV, is usually asymptomatic and is categorised as a BSL-2 agent. In the present study, we visualised the transport of viral matrix Z protein in LCMV-infected cells using live-cell imaging microscopy. We demonstrated that the transport of Z protein is mediated by polymerised microtubules. Interestingly, the transport of LASV Z protein showed characteristics similar to those of Z protein in LCMV-infected cells. The live-cell imaging system using LCMV provides an attractive surrogate measure for studying arenavirus matrix protein transport in BSL-2 laboratories. In addition, it could be also utilised to analyse the interactions between viral matrix proteins and the cellular cytoskeleton, as well as to evaluate the antiviral compounds that target the transport of viral matrix proteins.