bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rothmund-Thomson Syndrome-like RECQL4 truncating mutations cause a haploinsufficient low bone mass phenotype in mice
Authors: Castillo-Tandazo Wilson , Frazier Ann E , Sims Natalie A , Smeets Monique F , Walkley Carl R 
Published: November 2020

AbstractRothmund-Thomson Syndrome (RTS) is an autosomal recessive disorder characterized by poikiloderma, sparse or absent hair, and defects in the skeletal system such as bone hypoplasia, short stature, low bone mass, and an increased incidence of osteosarcoma. RTS type 2 patients typically present with germline compound bi-allelic protein-truncating mutations ofRECQL4. As existing murine models predominantly employRecql4null alleles, we have here attempted to more accurately model the mutational spectrum of RTS by generating mice with patient-mimicking truncatingRecql4mutations. We found that truncating mutations impaired stability and subcellular localization of RECQL4, which translated to a homozygous embryonic lethality and haploinsufficient low bone mass and reduced cortical bone thickness phenotypes. Combination of a truncating mutation with a conditionalRecql4null allele demonstrated that these defects were intrinsic to the osteoblast lineage. However, the truncating mutations did not promote tumorigenesis, even after exposure to irradiation. We also utilized murineRecql4null cells to assess the impact of a wider range of humanRECQL4mutations using anin vitrocomplementation assay. We found differential effects of distinct RECQL4 mutations. While some created unstable protein products, others altered subcellular localization of the protein. Interestingly, the severity of the phenotypes correlated with the extent of protein truncation. Collectively, our results reveal that truncating RECQL4 mutations lead to the development of an osteoporosis-like phenotype through defects in early osteoblast progenitors in mice and identify RECQL4 gene dosage as a novel regulator of bone mass.
Biased re-orientation in the chemotaxis of peritrichous bacteria
Authors: Nakai T. , Ando T. , Goto T 
Published: November 2020

AbstractMany kinds of peritrichous bacteria that repeat runs and tumbles by using multiple flagella exhibit chemotaxis by sensing a difference in the concentration of the attractant or repellent between two adjacent time points. If a cell senses that the concentration of an attractant has increased, their flagellar motors decrease the switching frequency from counterclockwise to clockwise direction of rotation, which causes a longer run in swimming up the concentration gradient than swimming down. We investigated the turn angle in tumbles of peritrichous bacteria swimming across the concentration gradient of a chemoattractant because the change in the switching frequency in the rotational direction may affect the way tumbles. We tracked several hundreds of runs and tumbles of singleSalmonella typhimuriumcells in the concentration gradient of L-serine, and found that the turn angle depends on the concentration gradient that the cell senses just before the tumble. The turn angle is biased toward a smaller value when the cells swim up the concentration gradient, whereas the distribution of the angle is almost uniform (random direction) when the cells swim down the gradient. The effect of the observed bias in the turn angle on the degree of chemotaxis was investigated by random walk simulation. In the concentration field where attractants diffuse concentrically from the point source, we found that this angular distribution clearly affects the reduction of the mean square displacement of the cell that has started at the attractant source, that is, the bias in the turn angle distribution contributes to chemotaxis in peritrichous bacteria.Statement of SignificanceWe found another aspect in the chemotactic behavior of peritrichous bacteria. Chemotactic behaviors in peritrichous bacteria were predicted to be observed at the turn angles during tumbles motion as well as at the duration of runs; smaller changes in the swimming direction of cells swimming up the attractant’s gradient can be observed. This behavior is appropriate because the nature of bacterial chemotaxis changes the switching rate of the rotational direction of the flagellar motors according to the environment. Cells swimming upward reduce the turn angle by switching fewer flagellar motors to loosen flagellar filaments from the bundle during tumbles. We have shown that this prediction is correct.
The chemotherapeutic drug methotrexate selects for antibiotic resistance
Authors: Gudmundsdóttir Jónína S. , Fredheim Elizabeth G. A. , Koumans Catharina I. M. , Hegstad Joachim , Tang Po-Cheng , Andersson Dan I. , Samuelsen Ørjan , Johnsen Pål J. 
Published: November 2020

AbstractUnderstanding drivers of antibiotic resistance evolution is fundamental for designing optimal treatment strategies and interventions to reduce the spread of antibiotic resistance. Various cytotoxic drugs used in cancer chemotherapy have antibacterial properties, but how bacterial populations are affected by these selective pressures is unknown. Here we test the hypothesis that the widely used cytotoxic drug methotrexate affects the evolution and selection of antibiotic resistance through the same mechanisms as the antibiotic trimethoprim. We show that methotrexate can select for trimethoprim resistance determinants located on the chromosome or a plasmid in clinical strains ofEscherichia coli. Additionally, methotrexate can co-select for virtually any antibiotic resistance determinant when present together with trimethoprim resistance on a multidrug-resistance clinical plasmid. These selective effects occur at concentrations 40- to >320-fold below the methotrexate minimal inhibitory concentration forE. coli, suggesting a selective role of methotrexate chemotherapy for antibiotic resistance in patients that strongly depend on effective antibiotic treatment.Significance statementThe presented data show that methotrexate has the potential to select for virtually any given antibiotic resistance gene when genetically linked to trimethoprim resistance. This study highlights the need for increased awareness of the presence of acquired antibiotic resistance determinants in the gut of patients with impaired immunity undergoing methotrexate treatment to preserve the effects of downstream antibiotic treatments.
Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies
Authors: Caillat Christophe , Guilligay Delphine , Torralba Johana , Friedrich Nikolas , Nieva Jose L. , Trkola Alexandra , Chipot Christophe , Dehez François , Weissenhorn Winfried 
Published: November 2020

AbstractThe HIV-1 gp120/gp41 trimer undergoes a series of conformational changes in order to catalyze gp41-induced fusion of viral and cellular membranes. Here, we present the crystal structure of gp41 locked in a fusion intermediate state by an MPER-specific neutralizing antibody. The structure illustrates the conformational plasticity of the six membrane anchors arranged asymmetrically with the fusion peptides and the transmembrane regions pointing into different directions. Hinge regions located adjacent to the fusion peptide and the transmembrane region facilitate the conformational flexibility that allows high affinity binding of broadly neutralizing anti-MPER antibodies. Molecular dynamics simulation of the MPER Ab-induced gp41 conformation reveals the transition into the final post-fusion conformation with the central fusion peptides forming a hydrophobic core with flanking transmembrane regions. This, thus, suggests that MPER-specific broadly neutralizing antibodies can block final steps of refolding of the fusion peptide and the transmembrane region, which is required for completing membrane fusion.
Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds
Authors: Buck Moritz , Garcia Sarahi L. , Vidal Leyden Fernandez , Martin Gaëtan , Rodriguez Gustavo A. Martinez , Saarenheimo Jatta , Zopfi Jakob , Bertilsson Stefan , Peura Sari 
Published: November 2020

AbstractStratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems.
A retrospective cluster analysis of COVID-19 cases by county
Authors: Megahed Fadel M. , Jones-Farmer L. Allison , Rigdon Steven E. 
Published: November 2020

AbstractThe COVID-19 pandemic in the U.S. has exhibited distinct waves, the first beginning in March 2020, the second beginning in early June, and additional waves currently emerging. Paradoxically, almost no county has exhibited this multi-wave pattern. We aim to answer three research questions: (1) How many distinct clusters of counties exhibit similar COVID-19 patterns in the time-series of daily confirmed cases?; (2) What is the geographic distribution of the counties within each cluster? and (3) Are county-level demographic, socioeconomic and political variables associated with the COVID-19 case patterns? We analyzed data from counties in the U.S. from March 1 to October 24, 2020. Time series clustering identified clusters in the daily confirmed cases of COVID-19. An explanatory model was used to identify demographic, socioeconomic and political variables associated the cluster patterns. Four patterns were identified from the timing of the outbreaks including counties experiencing a spring, an early summer, a late summer, and a fall outbreak. Several county-level demographic, socioeconomic, and political variables showed significant associations with the identified clusters. The timing of the outbreak is related both to the geographic location within the U.S. and several variables including age, poverty distribution, and political association. These results show that the reported pattern of cases in the U.S. is observed through aggregation of the COVID-19 cases, suggesting that local trends may be more informative. The timing of the outbreak varies by county, and is associated with important demographic, socioeconomic and geographic factors.
The transcription factor Rreb1 regulates epithelial architecture and invasiveness in gastrulating mouse embryos
Authors: Morgani Sophie M. , Su Jie , Nichols Jennifer , Massagué Joan , Hadjantonakis Anna-Katerina 
Published: November 2020

AbstractRas-responsive element-binding protein 1 (Rreb1) is a zinc-finger transcription factor downstream of RAS signaling.Rreb1has been implicated in cancer but little is known about its role in mammalian non-disease states. Here, we found that Rreb1 is essential for mouse embryonic development. Loss ofRreb1led to a reduction in the expression of vasculogenesis factors, cardiovascular defects and embryonic lethality. During gastrulation, the absence ofRreb1also resulted in the upregulation of cytoskeleton-associated genes, a change in the organization of F-ACTIN and adherens junctions within the pluripotent epiblast, and perturbed epithelial architecture characterized by irregular tissue folding and abnormal accumulations of cells. Moreover,Rreb1mutant cells ectopically exited the epiblast epithelium through the underlying basement membrane, paralleling cell behaviors observed during metastasis. Thus, disentangling the function of Rreb1 in development could shed light on its role in cancer and other diseases involving loss of epithelial integrity.
Functional characterization of the cnidarian antiviral immune response reveals ancestral complexity
Authors: Lewandowska Magda , Sharoni Ton , Admoni Yael , Aharoni Reuven , Moran Yehu 
Published: November 2020

ABSTRACTAnimals developed a broad repertoire of innate immune sensors and downstream effector cascades for defense against RNA viruses. Yet, this system highly varies between different bilaterian animals, masking its ancestral state. In this study we aimed to characterize the antiviral immune response of the cnidarianNematostella vectensisand decipher the function of the retinoic acid-inducible gene I-like receptors (RLRs) known to detect viral double-stranded RNA (dsRNA) in bilaterians, but activate different antiviral pathways in vertebrates and nematodes. We show that a mimic of long viral dsRNA triggers a complex antiviral immune response bearing features distinctive for both vertebrate and invertebrate systems. Furthermore, the results of affinity assays and knockdown experiments provide functional evidence for the conserved role of RLRs in initiating immune response to dsRNA that originated before the cnidarian-bilaterian split and lay a strong foundation for future research on the evolution of the immune responses to RNA viruses.
Novel fragile X syndrome 2D and 3D brain models based on human isogenic FMRP-KO iPSCs
Authors: Brighi Carlo , Salaris Federico , Soloperto Alessandro , Cordella Federica , Ghirga Silvia , de Turris Valeria , Rosito Maria , Porceddu Pier Francesca , Reggiani Angelo , Rosa Alessandro , Di Angelantonio Silvia 
Published: November 2020

ABSTRACTFragile X syndrome (FXS) is a neurodevelopmental disorder, characterized by intellectual disability and sensory deficits, caused by epigenetic silencing of theFMR1gene and subsequent loss of its protein product, fragile X mental retardation protein (FMRP). Delays in synaptic and neuronal development in the cortex have been reported in FXS mouse models, however, the main goal of translating lab research into pharmacological treatments in clinical trials has been so far largely unsuccessful, leaving FXS a still incurable disease. Here, we generated 2D and 3D in vitro human FXS model systems based on isogenicFMR1knock-out mutant and wild-type human induced pluripotent stem cell (hiPSC) lines. Phenotypical and functional characterization of cortical neurons derived from FMRP-deficient hiPSCs display altered gene expression and impaired differentiation when compared with the healthy counterpart. FXS cortical cultures show increased proliferation of GFAP positive cells, likely astrocytes, increased spontaneous network activity and depolarizing GABAergic transmission. Cortical brain organoid models show increased proliferation of glial cells, and bigger organoid size. Our findings demonstrate that FMRP is required to correctly support neuronal and glial cell proliferation, and to set the correct excitation/inhibition ratio in human brain development.
Functional correlates of immediate early gene expression in mouse visual cortex
Authors: Mahringer David , Zmarz Pawel , Okuno Hiroyuki , Bito Haruhiko , Keller Georg B. 
Published: November 2020

AbstractDuring visual development, response properties of layer 2/3 neurons in visual cortex are shaped by experience. Both visual and visuomotor experience are necessary to coordinate the integration of bottom-up visual input and top-down motor-related input. Whether visual and visuomotor experience engage different plasticity mechanisms, possibly associated with the two separate input pathways, is still unclear. To begin addressing this, we measured the expression level of three different immediate early genes (IEG) (c-fos, egr1 or Arc) and neuronal activity in layer 2/3 neurons of visual cortex before and after a mouse’s first visual exposure in life, and subsequent visuomotor learning. We found that expression levels of all three IEGs correlated positively with neuronal activity, but that first visual and first visuomotor exposure resulted in differential changes in IEG expression patterns. In addition, IEG expression levels differed depending on whether neurons exhibited primarily visually driven or motor-related activity. Neurons with strong motor-related activity preferentially expressed EGR1, while neurons that developed strong visually driven activity preferentially expressed Arc. Our findings are consistent with the interpretation that bottom-up visual input and top-down motor-related input are associated with different IEG expression patterns and hence possibly also with different plasticity pathways.
Morc3 silences endogenous retroviruses by enabling Daxx-mediated H3.3 incorporation
Authors: Groh Sophia , Milton Anna Viktoria , Marinelli Lisa , Sickinger Cara V. , Bollig Heike , de Almeida Gustavo Pereira , Forné Ignasi , Schmidt Andreas , Imhof Axel , Schotta Gunnar 
Published: November 2020

ABSTRACTEndogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although, specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as top scoring hit. Morc3 knock-out cells display de-repression, reduced H3K9me3 and increased chromatin accessibility of distinct ERV classes. We found that the GHKL ATPase domain of Morc3 is critical for ERV silencing, since mutants which cannot bind ATP, or which are defective in ATP hydrolysis cannot rescue the Morc3 ko phenotype. Proteomic analysis revealed that Morc3 mutant protein which cannot bind ATP fails to interact with the H3.3 chaperone Daxx. This interaction depends on Morc3 SUMOylation, as Daxx lacking the SUMO interaction domain shows reduced association with Morc3. Notably, in Morc3 ko cells, we observed strongly reduced H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as critical regulator of Daxx-mediated H3.3 incorporation to ERV regions.
Nucleosome structural variations in interphase and metaphase chromosomes
Authors: Arimura Yasuhiro , Shih Rochelle M. , Froom Ruby , Funabiki Hironori 
Published: November 2020

SummaryStructural heterogeneity of nucleosomes in functional chromosomes is unknown. Here we report cryo-EM structures of nucleosomes isolated from interphase and metaphase chromosomes at up to 3.4 Å resolution. Averaged chromosomal nucleosome structures are highly similar to canonical left-handed recombinant nucleosome crystal structures, with DNA being selectively stabilized at two defined locations. Compared to free mono-nucleosomes, which exhibit diverse linker DNA angles and large structural variations in H3 and H4, chromosomal nucleosome structures are much more uniform, characterized by a closed linker DNA angle with interactions between the H2A C-terminal tail and DNA. Exclusively for metaphase nucleosomes, structures of the linker histone H1.8 at the on-dyad position of nucleosomes can be reconstituted at 4.4 Å resolution. We also report diverse minor nucleosome structural variants with rearranged core histone configurations, which are more prevalent in metaphase than in interphase chromosomes. This study presents structural characteristics of nucleosomes in interphase and mitotic chromosomes.Highlights3.4~ Å resolution nucleosome structures from interphase and metaphase chromosomesNucleosome structures in chromosomes are more uniform than in free mono-nucleosomesHistone H1.8 binds to the nucleosome dyad axis in metaphase chromosomesNucleosome structural variants are more prevalent in metaphase than in interphaseNOTES TO READERSWe would like to emphasize the importance of supplemental movies S1-S3, which should greatly help readers to understand characteristics of the nucleosome structural variants that we report in this study.
Stenoparib, an inhibitor of cellular poly (ADP-ribose) polymerase (PARP), blocks replication of the SARS-CoV-2 human coronavirusin vitro
Authors: Stone Nathan E. , Jaramillo Sierra A. , Jones Ashley N. , Vazquez Adam J. , Martz Madison , Versluis Lora M. , Raniere Marlee O. , Nunnally Haley E. , Zarn Katherine E. , Nottingham Roxanne , Sahl Jason W. , Wagner David M. , Knudsen Steen , Settles Erik W. , Keim Paul S. , French Christopher T. 
Published: November 2020

ABSTRACTBy late 2020, the coronavirus disease (COVID-19) pandemic, caused by SARS-CoV-2 has caused tens of millions of infections and over 1 million deaths worldwide. A protective vaccine and more effective therapeutics are urgently needed. We evaluated a new PARP inhibitor, stenoparib, which was recently advanced to Stage II clinical trials for treatment of ovarian cancer, for activity against human respiratory coronaviruses, including SARS-CoV-2,in vitro. Stenoparib exhibits dose-dependent suppression of SARS-CoV-2 multiplication and spread in Vero E6 monkey kidney and Calu-3 human lung adenocarcinoma cells. Stenoparib was also strongly inhibitory to the HCoV-NL63 human seasonal respiratory coronavirus. Compared to remdesivir, which inhibits viral replication downstream of cell entry, stenoparib impedes entry and post-entry processes as determined by time-of-addition (TOA) experiments. Moreover, a 10 μM dosage of stenoparib – below the approximated 25.5 μM half-maximally effective concentration (EC50), combined with 0.5 μM remdesivir suppressed coronavirus growth by more than 90%, indicating a potentially synergistic effect for this drug combination. Stenoparib as a standalone or as part of combinatorial therapy with remdesivir should be a valuable addition to the arsenal against COVID-19.ImportanceNew therapeutics are urgently needed in the fight against COVID-19. Repurposing drugs that are either already approved for human use or are in advanced stages of the approval process can facilitate more rapid advances toward this goal. The PARP inhibitor stenoparib may be such a drug, as it is currently in Stage II clinical trials for the treatment of ovarian cancer and its safety and dosage in humans has already been established. Our results indicate that stenoparib possesses strong antiviral activity against SARS-CoV-2 and other coronavirusesin vitro.This activity appears to be based on multiple modes of action, where both pre-entry and post-entry viral replication processes are impeded. This may provide a therapeutic advantage over many current options that have a narrower target range. Moreover, our results suggest that stenoparib and remdesivir in combination may be especially potent against coronavirus infection.