bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains
Authors: Bersaglieri Cristiana , Kresoja-Rakic Jelena , Gupta Shivani , Bär Dominik , Kuzyakiv Rostyslav , Santoro Raffaella 
Published: November 2020

AbstractEukaryotic chromosomes are folded into hierarchical domains, enabling the organization of the genome into functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks thought to contribute to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for genome-wide maps of nucleolar associated domains (NADs). Here we established a method based on a Dam-fused engineered nucleolar histone H2B that marks DNA contacting the nucleolus. NAD-maps of ESCs and neural progenitors revealed layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs showed higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation, chromosomes around the nucleolus acquire a more compact, rigid architecture whereas NADs specific for ESCs decrease their interaction strength within the repressive B-compartment strength, unlocking neural genes from repressive nuclear environment. The methodologies here developed will make possible to include the contribution of the nucleolus in future studies investigating the relationship between nuclear space and genome function.
Consensus molecular subtyping of colorectal cancers is influenced by goblet cell content
Authors: Miller Samuel A. , Ghobashi Ahmed , O’Hagan Heather M. 
Published: November 2020

AbstractA critical obstacle in the field of colorectal cancer (CRC) is the establishment of precise tumor subtypes to facilitate the development of targeted therapeutic regimens. While dysregulated mucin production is a histopathological feature of multiple CRC subtypes, it is not clear how well these pathologies are associated with the proportion of goblet cells in the tumor, or whether or not this proportion is variable across all CRC. This study demonstrates that consensus molecular subtype 3 (CMS3) CRC tumors and cell lines are enriched for the expression of goblet cell marker genes. Further, the proportion of goblet cells in the tumor is associated with the probability of CMS3 subtype assignment and these CMS3 subtype tumors are mutually exclusive from mucinous adenocarcinoma pathologies. This study provides proof of principle for the use of machine learning classification systems to subtype tumors based on cellular content, and provides further context regarding the features weighing CMS3 subtype assignment.
The polarity specific nature of single session high-definition transcranial direct current stimulation to the cerebellum and prefrontal cortex on motor and non-motor task performance
Authors: Maldonado Ted , Bernard Jessica A. 
Published: November 2020

AbstractThe cerebellum has an increasingly recognized role in higher order cognition. Advancements in noninvasive neuromodulation techniques allows one to focally create functional alterations in the cerebellum to investigate its role in cognitive functions. To this point, work in this area has been mixed, in part due to varying methodologies for stimulation, and it is unclear whether or not transcranial direct current stimulation (tDCS) effects on the cerebellum are task or load dependent. Here, we employed a between-subjects design using a high definition tDCS system to apply anodal, cathodal, or sham stimulation to the cerebellum or prefrontal cortex (PFC) to examine the role the cerebellum plays in verbal working memory, inhibition, motor learning, and balance performance, and how this interaction might interact with the cortex (i.e. PFC). We predicted performance decrements following anodal stimulation and performance increases following cathodal stimulation, compared to sham. Broadly, our work provides evidence for cerebellar contributions to cognitive processing, particularly in verbal working memory and sequence learning. Additionally, we found the effect of stimulation might be load specific, particularly when applied to the cerebellum. Critically, anodal simulation negatively impacted performance during effortful processing, but was helpful during less effortful processing. Cathodal stimulation hindered task performance, regardless of simulation region. The current results suggest an effect of stimulation on cognition, perhaps suggesting that the cerebellum is more critical when processing is less effortful but becomes less involved under higher load when processing is more prefrontally-dependent.
Replicating bacterium-vectored vaccine expressing SARS-CoV-2 Membrane and Nucleocapsid proteins protects against severe COVID-19 disease in hamsters
Authors: Jia Qingmei , Bielefeldt-Ohmann Helle , Maison Rachel , Masleša-Galić Saša , Bowen Richard , Horwitz Marcus A. 
Published: November 2020

AbstractAn inexpensive readily manufactured COVID-19 vaccine that protects against severe disease is needed to combat the pandemic. We have employed the LVS ΔcapBvector platform, previously used successfully to generate potent vaccines against the Select Agents of tularemia, anthrax, plague, and melioidosis, to generate a COVID-19 vaccine. The LVS ΔcapBvector, a replicating intracellular bacterium, is a highly attenuated derivative of a tularemia vaccine (LVS) previously administered to millions of people. We generated vaccines expressing SARS-CoV-2 structural proteins and evaluated them for efficacy in the golden Syrian hamster, which develops severe COVID-19 disease. Hamsters immunized intradermally or intranasally with a vaccine co-expressing the Membrane (M) and Nucleocapsid (N) proteins, then challenged 5-weeks later with a high dose of SARS-CoV-2, were protected against severe weight loss and lung pathology and had reduced viral loads in the oropharynx and lungs. Protection by the vaccine, which induces murine N-specific interferon-gamma secreting T cells, was highly correlated with pre-challenge serum anti-N TH1-biased IgG. This potent vaccine against severe COVID-19 should be safe and easily manufactured, stored, and distributed, and given the high homology between MN proteins of SARS-CoV and SARS-CoV-2, has potential as a universal vaccine against the SARS subset of pandemic causing β-coronaviruses.
Evolved increases in hemoglobin-oxygen affinity and Bohr effect coincided with the aquatic specialization of penguins
Authors: Signore Anthony V. , Tift Michael S. , Hoffmann Federico G. , Schmitt Todd. L. , Moriyama Hideaki , Storz Jay F. 
Published: November 2020

AbstractDive capacities of air-breathing vertebrates are dictated by onboard O2stores, suggesting that physiological specializations of diving birds like penguins may have involved adaptive changes in convective O2transport. It has been hypothesized that increased hemoglobin (Hb)-O2affinity improves pulmonary O2extraction and enhance capacities for breath-hold diving. To investigate evolved changes in Hb function associated with the aquatic specialization of penguins, we integrated comparative measurements of whole-blood and purified native Hbs with protein engineering experiments based on site-directed mutagenesis. We reconstructed and resurrected ancestral Hbs representing the common ancestor of penguins and the more ancient ancestor shared by penguins and their closest nondiving relatives (order Procellariiformes, which includes albatrosses, shearwaters, petrels, and storm petrels). These two ancestors bracket the phylogenetic interval in which penguin-specific changes in Hb function would have evolved. The experiments revealed that penguins evolved a derived increase in Hb-O2affinity and a greatly augmented Bohr effect (reduced Hb-O2affinity at low pH). Although an increased Hb-O2affinity reduces the gradient for O2diffusion from systemic capillaries to metabolizing cells, this can be compensated by a concomitant enhancement of the Bohr effect, thereby promoting O2unloading in acidified tissues. We suggest that the evolved increase in Hb-O2affinity in combination with the augmented Bohr effect maximizes both O2extraction from the lungs and O2unloading from the blood, allowing penguins to fully utilize their onboard O2stores and maximize underwater foraging time.
Optimized detection of acute MHV68 infection with a reporter system identifies large peritoneal macrophages as a dominant target of primary infection
Authors: Riggs Julianne B. , Medina Eva M. , Perrenoud Loni J. , Bonilla Diana L. , Clambey Eric T. , van Dyk Linda F. , Berg Leslie J. 
Published: November 2020

AbstractInvestigating the dynamics of virus-host interactions in vivo remains an important challenge, often limited by the ability to directly identify virally-infected cells. Here, we combine detection of a beta-lactamase activated fluorescent substrate with full spectrum flow cytometry to identify primary targets of murine gammaherpesvirus 68 (MHV68) infection in the peritoneal cavity. By optimizing substrate and detection conditions, we were able to achieve multiparameter characterization of infected cells and the ensuing host response. MHV68 infection leads to a pronounced increase in immune cells, with CD8+ T cells increasing by 3 days, and total infiltrate peaking around 8 days post-infection. MHV68 infection results in near elimination of large peritoneal macrophages by 8 days post-infection, and a concordant increase in small peritoneal macrophages and monocytes. Infection is associated with prolonged changes to myeloid cells, with a distinct population of MHC IIhighlarge peritoneal macrophages emerging by 14 days. Targets of MHV68 infection could be readily detected. Between 1 to 3 days post-infection, MHV68 infects ~5-10% of peritoneal cells, with >75% being large peritoneal macrophages. By 8 days post-infection, the frequency of MHV68 infection is reduced at least 10-fold, with infection primarily in small peritoneal macrophages, with few infected dendritic cells and B cells. MHV68 infection at 3 days post-infection contains both lytic and latent infection, consistent with the identification of cells with active reporter gene expression. Our findings demonstrate the utility of the beta-lactamase MHV68 reporter system for high throughput single-cell analysis and identify dynamic changes during primary gammaherpesvirus infection.ImportanceIdentifying virally-infected cells in vivo is key to tracking viral infection and understanding host-pathogen interactions. The ability to further characterize and phenotype virally-infected cells is technically challenging. We use a mouse gammaherpesvirus, MHV68, expressing a reporter gene to identify infected cells during primary infection via flow cytometry. Optimization using this reporter system allowed us to further characterize infected cells via multiparameter full spectrum flow cytometry. Our study provides a technical model for high throughput single-cell immunophenotyping methods in the context of gammaherpesvirus infection. Furthermore, we show that acute MHV68 infection in the peritoneal cavity dramatically changes the immune landscape of this tissue, results in a high number of infected macrophages at early times, and is characterized by both lytic and latent infection within immune cells.
A sense of being needed: an interpretative phenomenological analysis of hospital-based allied health professionals’ experiences during the COVID-19 pandemic
Authors: Oorsouw Roel van , Oerlemans Anke , Klooster Emily , Berg Manon van den , Kalf Johanna , Vermeulen Hester , Graff Maud , Wees Philip van der , Koenders Niek 
Published: November 2020

AbstractBackgroundThe outbreak of COVID-19 has led to many hospitalizations in the Netherlands and worldwide. As a result, the work of hospital-based allied health professionals changed rapidly. In such a healthcare crisis, professionals may not be able to fulfill their own professional values regarding good care, resulting in ethical issues and moral distress. The aim of this study was to explore the lived experiences of allied health professionals working in hospitals during the COVID-19 pandemic, including the ethical issues and moral distress these professionals might have encountered.Methods and findingsLived experiences were collected in semi-structured interviews with 39 allied health professionals including dieticians, occupational therapists, physical therapists, and speech-language therapists, working in four different hospitals in the Netherlands. Interviews were held in June and July 2020, after waning of the first wave of COVID-19 spreading. Interpretative phenomenological analysis revealed four themes: ‘a disease with great impact’, ‘personal health and safety’, ‘staying human in chaotic times’ and ‘solidarity and changing roles’. Participant experiences show that the virus and COVID-19 measures had a significant impact on the in-hospital working environment due to the massive downscaling of regular care, infection prevention measures and unknown risks to allied health professionals’ personal health. At the same time, participants experienced a certain freedom, which made room for authentic motives, connection and solidarity. Participants felt welcomed and appreciated at the COVID-19 wards and intensive care units, and were proud that they were able to fulfill their roles. The themes and accompanying ethical issues reflect a wide range of situations that were morally complex and led to moral distress.ConclusionsTo diminish long-lasting negative impact of the COVID-19 pandemic and moral distress, employers should empathize with experiences of allied health professionals and create conditions for ethical reflection. Our data show that allied health professionals value professional autonomy. Creating room for professional autonomy makes them feel needed, connected and energized. However, the needs of allied health professionals may conflict with organizational rules and structures.
Early impact of school closure and social distancing for COVID-19 on the number of inpatients with childhood non-COVID-19 acute infections in Japan
Authors: Kishimoto Kenji , Bun Seiko , Shin Jung-ho , Takada Daisuke , Morishita Tetsuji , Kunisawa Susumu , Imanaka Yuichi 
Published: November 2020

AbstractMany countries have implemented school closures as part of social distancing measures intended to control the spread of coronavirus disease 2019 (COVID-19). The aim of this study was to assess the early impact of nationwide school closure (March-May 2020) and social distancing for COVID-19 on the number of inpatients with major childhood infectious diseases in Japan. Using data from the Diagnosis Procedure Combination system in Japan, we identified patients aged 15 years or younger with admissions for a diagnosis of upper respiratory tract infection (URTI), lower respiratory tract infection (LRTI), influenza, gastrointestinal infection (GII), appendicitis, urinary tract infection (UTI), or skin and soft tissue infection (SSTI) between July 2018 and June 2020. Two periods were considered in the analysis: a pre- and a post-school-closure period. Changes in the trend of the weekly number of inpatients between the two periods were assessed using interrupted time-series analysis. A total of 75,053 patients in 210 hospitals were included. We found a marked reduction in the number of inpatients in the post-school-closure period, with an estimated reduction of 581 (standard error 42.9) inpatients per week (p < 0.001). The main part of the reduction was for pre-school children. Remarkable decreases in the number of inpatients with URI, LRTI, and GII were observed, while there were relatively mild changes in the influenza, appendicitis, UTI, and SSTI groups. We confirmed a marked reduction in the number of inpatients with childhood non-COVID-19 acute infections in the post-school-closure period.
Isolation of nuclei and downstream processing of cell-type-specific nuclei from micro-dissected mouse brain regions – techniques and caveats
Authors: Chongtham M.C , Todorov H , Wettschereck J.E. , Gerber S. , Winter J. 
Published: November 2020

AbstractThe mammalian brain consists of several structurally and functionally distinct regions equipped with an equally complex cell-type system. Due to its relevance in uncovering disease mechanisms, the study of cell-type-specific molecular signatures of different brain regions has increased. The rapid evolution of newer and cheaper sequencing techniques has also boosted the interest in cell-type-specific epigenetic studies. In fact, the nucleus holds most of the cell’s epigenetic information and is quite resistant to tissue dissociation processes as compared to cells. As such, nuclei are continually preferred over cells for epigenetic studies. However, the isolation of nuclei from cells is still a biochemically complex process, with every step affecting downstream results. Therefore, it is necessary to use protocols that fit the experimental design to yield nuclei of high quality and quantity. However, the current protocols are not suitable for nuclei isolation of small volumes of micro-dissected brain regions from individual mouse brains.Additionally, the caveats associated with centrifugation steps of nuclei extraction and the effects of different buffers have not been thoroughly investigated. Therefore, in this study, we describe an iodixanol based density gradient ultracentrifugation protocol suitable for micro-dissected brain regions from individual mice using ArccreERT2 (TG/WT).R26CAG-Sun1-sfGFP-Myc (M/WT or M/M). This mouse model shows sfGFP expression (sfGFP+) in the nuclear membrane of specific stimulus activated cells, thereby providing a good basis for the study - nuclei isolation and separation of cell-type-specific nuclei. The study also introduces new tools for rapid visualization and assessment of quality and quantity of nascent extracted nuclei. These tools were then used to examine critical morphological features of nuclei derived from different centrifugation methods and the use of different buffers to uncover underlying effects. Finally, to obtain cell-type-specific nuclei (sfGFP+nuclei) from the isolated nuclei pool of high viscosity, an optimized protocol for fluorescence activated nuclei sorting (FANS) was established to speed up sorting. Additionally, we present a 1% PFA protocol for fixation of isolated nuclei for long term microscopic visualization.
The early endosomal protein Rab21 is critical for enterocyte functions and intestinal homeostasis
Authors: Nassari Sonya , Lévesque Dominique , Boisvert François-Michel , Jean Steve 
Published: November 2020

ABSTRACTMembrane trafficking is defined as the vesicular transport of molecules into, out of, and throughout the cell. In intestinal enterocytes, defects in endocytic/recycling pathways result in impaired function and are linked to genetic diseases. However, how these trafficking pathways regulate intestinal tissue homeostasis is poorly understood. Using theDrosophilaintestine as anin vivomodel system, we investigated enterocyte-specific functions for the early endosomal trafficking machinery in gut homeostasis. We focused on the small GTPase Rab21, which regulates specific steps in early endosomal trafficking. Rab21-depleted guts showed severe abnormalities in intestinal morphology, with deregulated homeostasis associated with a gain in mitotic cells and increased cell death. Increases in both apoptosis and yorkie signaling were responsible for compensatory proliferation and tissue inflammation. Using a RNA interference screen, we identified specific regulators of autophagy and membrane trafficking that phenocopied Rab21 loss. We further showed that Rab21-induced hyperplasia was rescued by inhibition of epidermal growth factor receptor signaling, and identified improperly trafficked cargoes in Rab21-depleted enterocytes. Our data shed light on an important role for early endosomal trafficking, and particularly Rab21, in enterocyte-mediated intestinal homeostasis.
A wide-rangingPseudomonas aeruginosaPeptideAtlas build: a useful proteomic resource for a versatile pathogen
Authors: Reales-Calderón J.A. , Sun Z. , Mascaraque V. , Pérez-Navarro E. , Vialás V. , Deutsch E.W. , Moritz RL , Gil C. , Martínez JL , Molero G. 
Published: November 2020

AbstractPseudomonas aeruginosais an important opportunistic pathogen with high prevalence in nosocomial infections. This microorganism is a good model for understanding biological processes such as the quorum-sensing response, the metabolic integration of virulence, the mechanisms of global regulation of bacterial physiology, and the evolution of antibiotic resistance. Till now,P. aeruginosaproteomic data, although available in several on-line repositories, were dispersed and difficult to access. In the present work, proteomes of the PAO1 strain grown under very different conditions and from diverse cellular compartments have been analyzed and joined to build thePseudomonasPeptideAtlas. This resource is a comprehensive mass spectrometry-derived peptide and inferred protein database with 71.3% coverage of the total predicted proteome ofP. aeruginosaPAO1. This is the highest published coverage among the eight bacterial PeptideAtlas datasets currently available. The proteins in thePseudomonasPeptideAtlas cover 84% of metabolic proteins, 71% of proteins involved in genetic information processing, 72% of proteins responsible for environmental information processing, more than 80% of proteins related to quorum sensing and biofilm formation, and 81% of proteins responsible for antimicrobial resistance. It exemplifies a necessary tool for targeted proteomics studies, system-wide observations, and cross-species observational studies. Here we describe how this resource was built and some of the physiologically important proteins of this pathogen.SignificancePseudomonas aeruginosais among the most versatile bacterial pathogens. Studies of its proteome are very important as they can reveal virulence factors and mechanisms of antibiotic resistance. The construction of a proteomic resource such as the PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.
The human cytomegalovirus UL116 glycoprotein is a chaperone to control gH-based complexes levels on virions
Authors: Vezzani Giacomo , Amendola Diego , Yu Dong , Chandramuli Sumana , Frigimelica Elisabetta , Maione Domenico , Merola Marcello 
Published: November 2020

ABSTRACTHuman cytomegalovirus (HCMV) relies in large part upon the viral membrane fusion glycoprotein B (gB) and two alternative gH/gL complexes, gH/gL/gO (Trimer) and the gH/gL/UL128/UL130/UL131A (Pentamer) to enter into cells. The relative amounts of the Trimer and Pentamer vary among HCMV strains and contribute to differences in cell tropism. Although the viral ER resident protein UL148 has been shown to interact with gH to facilitate gO incorporation, the mechanisms that favor the assembly and maturation of one complex over another remain poorly understood. HCMV virions also contain an alternative non-disulfide bound heterodimer comprised of gH and UL116 whose function remains unknown. Here, we show that disruption of HCMV geneUL116causes infectivity defects of ~10-fold relative to wild-type virus and leads to reduced expression of both gH/gL complexes in virions. Furthermore, gH that is not covalently bound to other viral glycoproteins, which are readily detected in wild-type HCMV virions, become undetectable in the absence ofUL116suggesting that the gH/UL116 complex is abundant in virions. We find evidence that UL116 and UL148 interact during infection indicating that the two proteins might cooperate to regulate the abundance of HCMV gH complexes. Altogether, these results are consistent with a role of UL116 as a chaperone for gH during the assembly and maturation of gH complexes in infected cells.