bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold tolerance of mountain stoneflies (Plecoptera: Nemouridae) from the high Rocky Mountains
Authors: Hotaling Scott , Shah Alisha A. , Dillon Michael E. , Giersch J. Joseph , Tronstad Lusha M. , Finn Debra S. , Woods H. Arthur , Kelley Joanna L. 
Published: June 2020

ABSTRACTHow aquatic insects cope with cold temperatures is poorly understood. This is particularly true for high-elevation species that often experience a seasonal risk of freezing. In the Rocky Mountains, nemourid stoneflies (Plecoptera: Nemouridae) are a major component of mountain stream biodiversity and are typically found in streams fed by glaciers and snowfields, which due to climate change, are rapidly receding. Predicting the effects of climate change on mountain stoneflies is difficult because their thermal physiology is largely unknown. We investigated cold tolerance of several alpine stoneflies (Lednia tumana, Lednia tetonica, and Zapada spp.) from the Rocky Mountains, USA. We measured the supercooling point (SCP) and tolerance to ice enclosure of late-instar nymphs collected from a range of thermal regimes. SCPs varied among species and populations, with the lowest SCP measured for nymphs from an alpine pond, which is much more likely to freeze solid in winter than flowing streams. We also show that L. tumana cannot survive being enclosed in ice, even for short periods of time (less than three hours) at relatively mild temperatures (−0.5 °C). Our results indicate that high-elevation stoneflies at greater risk of freezing may have correspondingly lower SCPs, and despite their common association with glacial meltwater, they appear to be living near their lower thermal limits.
Abundance and nuclear antigen reactivity of intestinal and fecal Immunoglobulin A in lupus-prone mice at younger ages correlate with the onset of eventual systemic autoimmunity
Authors: Sun Wei , Gudi Radhika , Johnson Benjamin M. , Vasu Chenthamarakshan 
Published: June 2020

AbstractOur recent studies, using (SWRxNZB)F1 (SNF1) mice, showed a potential contribution of the gut microbiota and pro-inflammatory immune responses of the gut mucosa to systemic autoimmunity in lupus. Here, using this mouse model, we determined the abundance and the nAg reactivity of IgA antibody produced in the intestine under lupus susceptibility. Intestinal lymphoid tissues from SNF1 mice, females particularly, showed significantly higher frequencies of nAg (dsDNA and nucleohistone) reactive IgA producing B cells compared to B6 females. Most importantly, younger age fecal IgA -abundance and - nAg reactivity of lupus-prone mice showed a positive correlation with eventual systemic autoimmunity and proteinuria onset. Depletion of gut microbiota in SNF1 mice resulted in the diminished production of IgA in the intestine and the nAg reactivity of these antibodies. Overall, these observations show that fecal IgA features, nuclear antigen reactivity particularly, at preclinical stages/in at-risk subjects could be predictive of autoimmune progression.
Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism
Authors: Urresti Jorge , Zhang Pan , Moran-Losada Patricia , Yu Nam-Kyung , Negraes Priscilla D. , Trujillo Cleber A. , Antaki Danny , Amar Megha , Chau Kevin , Pramod Akula Bala , Diedrich Jolene , Tejwani Leon , Romero Sarah , Sebat Jonathan , Yates John R. , Muotri Alysson R. , Iakoucheva Lilia M. 
Published: June 2020

AbstractReciprocal deletion and duplication of 16p11.2 region is the most common copy number variation (CNV) associated with Autism Spectrum Disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV has mirror-opposite effect on neuronal maturation, proliferation, and synapse number, in concordance with its effect on brain growth in humans. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with excess of neurons and depletion of neural progenitors observed in deletions, and mirror phenotypes in duplications. Transcriptomic and proteomic profiling revealed multiple dysregulated pathways, including defects in neuron migration. Inhibition of activity of the small GTPase RhoA rescued migration deficits. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.
Using nucleocapsid proteins to investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses
Authors: Schuster Noah 
Published: June 2020

AbstractAn initial outbreak of coronavirus disease 2019 (COVID-19) in China has resulted in a massive global pandemic causing well over 16,500,000 cases and 650,000 deaths worldwide. The virus responsible, SARS-CoV-2, has been found to possess a very close association with Bat-CoV RaTG13 and Pangolin-CoV MP789. The nucleocapsid protein can serve as a decent model for determining phylogenetic, evolutionary, and structural relationships between coronaviruses. Therefore, this study uses the nucleocapsid gene and protein to further investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses. Sequence and phylogenetic analyses have revealed the nucleocapsid gene and protein in SARS-CoV-2 are both closely related to those found in Bat-CoV RaTG13 and Pangolin-CoV MP789. Evidence of recombination was detected within the N gene, along with the presence of a double amino acid insertion found in the N-terminal region. Homology modeling for the N-Terminal Domain revealed similar structures but distinct electrostatic surfaces and topological variations in the β-hairpin that likely reflect specific adaptive functions. In respect to SARS-CoV-2, two amino acids (S37 and A267) were found to exist only in its N protein, along with an extended β-hairpin that bends towards the nucleotide binding site. Collectively, this study strengthens the relationship among SARS-CoV-2, Bat-CoV RaTG13, and Pangolin-CoV MP789, providing additional insights into the structure and adaptive nature of the nucleocapsid protein found in these coronaviruses. Furthermore, these data will enhance our understanding of the complete history behind SARS-CoV-2 and help assist in antiviral and vaccine development.
A PCNA-K164R mutation impinges on origin activation and mitotic DNA synthesis
Authors: Leung Wendy , Baxley Ryan M. , Thakar Tanay , Chang Ya-Chu , Rogers Colette B. , Wang Liangjun , Durrett Wesley , Tella Anika , Moldovan George-Lucian , Shima Naoko , Bielinsky Anja-Katrin 
Published: June 2020

ABSTRACTUbiquitination of the replication clamp proliferating cell nuclear antigen (PCNA) at the conserved residue lysine 164 (K164) occurs during normal S phase progression and increases after DNA damage induced replication stress. PCNA-K164 ubiquitination is critical for Okazaki fragment maturation and the activation of DNA damage tolerance pathways. Moreover, ubiquitinated PCNA operates in a fork protection pathway parallel to BRCA-RAD51. Whether PCNA ubiquitination regulates other genome maintenance mechanisms is unclear. UtilizingPCNAK164Rcells generated by CRISPR-Cas9, we demonstrate that this mutation causes DNA replication defects that impact origin activation.PCNAK164Rcells accumulate single-stranded DNA gaps during replication that persist throughout mitosis due to compromised mitotic DNA synthesis (MiDAS). We uncover a novel role for PCNA-K164 ubiquitination in regulating FANCD2 to initiate MiDAS. Persistent gaps hence interfere with MCM2-7 double hexamer loading in the subsequent G1 phase. Our findings demonstrate that the impact of PCNAK164-Ubis not limited to S/G2 phases but extends to mitosis and G1 phase.SUMMARYPCNA-K164 ubiquitination promotes DNA gap filling during S/G2 phases of the cell cycle. This study identifies a novel role for K164 ubiquitination in replication dynamics and mitotic DNA synthesis and thus provides new insight into the players involved in counteracting under-replication.
Different tertiary interactions create the same important 3-D features in a divergent flavivirus xrRNA
Authors: Jones Rachel A. , Steckelberg Anna-Lena , Szucs Matthew J. , Akiyama Benjamin M. , Vicens Quentin , Kieft Jeffrey S. 
Published: June 2020

ABSTRACTDuring infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3′ untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA for destruction. Previous work on these exoribonuclease-resistant RNAs (xrRNAs) from mosquito-borne FVs revealed a specific 3-dimensional fold with a unique topology in which a ring-like structure protectively encircles the 5′ end of the xrRNA. Conserved nucleotides make specific tertiary interactions that support this fold. Examination of more divergent FVs reveals differences in their 3′ UTR sequences, raising the question of whether they contain xrRNAs and if so, how they fold. To answer this, we demonstrated the presence of an authentic xrRNA in the 3′ UTR of the Tamana Bat Virus (TABV) and solved its structure by x-ray crystallography. The structure reveals conserved features from previously characterized xrRNAs, but in the TABV version these features are created through a novel set of tertiary interactions not previously seen in xrRNAs. This includes two important A-C interactions, four distinct backbone kinks, several ordered Mg2+ ions, and a C+-G-C base triple. The discovery that the same overall architecture can be achieved by very different sequences and interactions in distantly related flaviviruses provides insight into the diversity of this type of RNA and will inform searches for undiscovered xrRNAs in viruses and beyond.
Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Authors: Schlamp Florencia , Delbare Sofie Y. N. , Early Angela M. , Wells Martin T. , Basu Sumanta , Clark Andrew G. 
Published: June 2020

ABSTRACTBackgroundImmune responses need to be initiated rapidly, and maintained as needed, to prevent establishment and growth of infections. At the same time, resources need to be balanced with other physiological processes. On the level of transcription, studies have shown that this balancing act is reflected in tight control of the initiation kinetics and shutdown dynamics of specific immune genes.ResultsTo investigate genome-wide expression dynamics and trade-offs after infection at a high temporal resolution, we performed an RNA-seq time course on D. melanogaster with 20 time points post Imd stimulation. A combination of methods, including spline fitting, cluster analysis, and Granger causality inference, allowed detailed dissection of expression profiles, lead-lag interactions, and functional annotation of genes through guilt-by-association. We identified Imd-responsive genes and co-expressed, less well characterized genes, with an immediate-early response and sustained up-regulation up to five days after stimulation. In contrast, stress response and Toll-responsive genes, among which were Bomanins, demonstrated early and transient responses. We further observed a strong trade-off with metabolic genes, which strikingly recovered to pre-infection levels before the immune response was fully resolved.ConclusionsThis high-dimensional dataset enabled the comprehensive study of immune response dynamics through the parallel application of multiple temporal data analysis methods. The well annotated data set should also serve as a useful resource for further investigation of the D. melanogaster innate immune response, and for the development of methods for analysis of a post-stress transcriptional response time-series at whole-genome scale.
Nanotrap®particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free transport medium methods
Authors: Barclay RA , Akhrymuk I , Patnaik A , Callahan V , Lehman C , Andersen P , Barbero R , Barksdale S , Dunlap R , Goldfarb D , Jones-Roe T , Kelly R , Kim B , Miao S , Munns A , Munns D , Patel S , Porter E , Ramsey R , Sahoo S , Swahn O , Warsh J , Kehn-Hall K , Lepene B 
Published: June 2020

AbstractHere we present a rapid and versatile method for capturing and concentrating SARS-CoV-2 from transport medium and saliva using affinity-capture magnetic hydrogel particles. We demonstrate that the method concentrates virus prior to RNA extraction, thus significantly improving detection of the virus using a real-time RT-PCR assay across a range of viral titers, from 100 to 1,000,000 viral copies/mL; in particular, detection of virus in low viral load samples is enhanced when using the method coupled with the IDT 2019-nCoV CDC EUA Kit. This method is compatible with commercially available nucleic acid extraction kits, as well with a simple heat and detergent method. Using transport medium diagnostic remnant samples that previously had been tested for SARS-CoV-2 using either the Abbott RealTime SARS-CoV-2 EUA Test (n=14) or the Cepheid Xpert Xpress SARS-CoV-2 EUA Test (n=35), we demonstrate that our method not only correctly identifies all positive samples (n = 17) but also significantly improves detection of the virus in low viral load samples. The average improvement in cycle threshold (Ct) value as measured with the IDT 2019-nCoV CDC EUA Kit was 3.1; n = 10. Finally, to demonstrate that the method could potentially be used to enable pooled testing, we spiked infectious virus or a confirmed positive diagnostic remnant sample into 5 mL and 10 mL of negative transport medium and observed significant improvement in the detection of the virus from those larger sample volumes.
Cytoplasmic Microtubule Organizing Centers Regulate Meiotic Spindle Positioning in Mouse Oocyte
Authors: Vasquez Daniela Londono , Rodriguez-Lukey Katherine , Behura Susanta K. , Balboula Ahmed Z. 
Published: June 2020

ABSTRACTDuring oocyte meiosis, migration of the spindle and its positioning must be tightly regulated to ensure elimination of the polar bodies and provide developmentally competent euploid eggs. Although the role of F-actin in regulating these critical processes has been studied extensively, little is known whether microtubules (MTs) participate in regulating these processes. Here, we characterize a pool of MTOCs in the oocyte that does not contribute to spindle assembly but instead remains free in the cytoplasm during metaphase I (metaphase cytoplasmic MTOCs; mcMTOCs). In contrast to spindle pole MTOCs, which primarily originate from the perinuclear region in prophase I, the mcMTOCs are found near the cortex of the oocyte. At nuclear envelope breakdown, they exhibit robust nucleation of MTs, which diminishes during polar body extrusion before returning robustly during metaphase II. The asymmetric positioning of the mcMTOCs provides the spindle with a MT-based anchor line to the cortex opposite the site of polar body extrusion. Depletion of mcMTOCs, by laser ablation, or manipulating their numbers, through autophagy inhibition, revealed that the mcMTOCs are required to regulate the timely migration and positioning of the spindle in meiosis. We discuss how forces exerted by F-actin in mediating movement of the spindle to the oocyte cortex are balanced by MT-mediated forces from the mcMTOCs to ensure spindle positioning and timely spindle migration.
Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19
Authors: Fernández-Pittol Mariana , Hurtado Juan Carlos , Moreno-García Estela , Rubio Elisa , Navarro Mireia , Valiente Marta , Peiró Aida , Capón Alicia , Seijas Nuria , Martínez Miguel J. , Casals-Pascual Climent , Vila Jordi 
Published: June 2020

AbstractThe objective of this study was to assess the performance of direct real time RT-PCR detection of SARS-CoV-2 in heated saliva samples, avoiding the RNA isolation step. Oropharyngeal and nasopharyngeal swabs together with saliva samples were obtained from 51 patients clinically diagnosed as potentially having COVID-19. Two different methods were compared: 1. RNA was extracted from 500 μl of sample using a MagNA Pure Compact Instrument with an elution volume of 50μl and 2. 700µL of saliva were heat-inactivated at 96°C for 15 minutes, and directly subjected to RT-PCR. One step real time RT-PCR was performed using 5 μl of extracted RNA or directly from 5 μl of heated sample. RT-PCR was performed targeting the SARS-CoV-2 envelope (E) gene region. Diagnostic performance was assessed using the results of the RT-PCR from nasopharyngeal and oropharyngeal swabs as the gold standard. The overall sensitivity, specificity, positive and negative predictive values were 81.08%, 92.86%, 96.77% and 65.00%, respectively when RNA extraction was included in the protocol with saliva, whereas sensitivity, specificity, positive and negative predictive values were 83.78%, 92.86%, 68.42% and 96.88%, respectively, for the heat-inactivation protocol. However, when the analysis was performed exclusively on saliva samples with a limited time from the onset of symptoms (<9 days, N=28), these values were 90%, 87.5%, 44% and 98.75% for the heat-inactivation protocol. The study showed that RT-PCR can be performed using saliva in an RNA extraction free protocol, showing good sensitivity and specificity.
Blood parameters measured on admission as predictors of outcome for COVID-19; a prospective UK cohort study
Authors: Arnold DT , Attwood M , Barratt S , Elvers K , Morley A , Noel A , MacGowan A , Maskell NA , Hamilton F 
Published: June 2020

AbstractIntroductionCOVID-19 has an unpredictable clinical course so prognostic biomarkers would be invaluable when triaging patients on admission to hospital. Many biomarkers have been suggested using large observational datasets but sample timing is crucial to ensure prognostic relevance. The DISCOVER study prospectively recruited patients with COVID-19 admitted to a UK hospital and analysed a panel of putative prognostic biomarkers on the admission blood sample to identify markers of poor outcome.MethodsConsecutive patients admitted to hospital with proven or clinicoradiological suspected COVID-19 were recruited. Admission bloods were extracted from the clinical laboratory. A panel of biomarkers (IL-6, suPAR, KL-6, Troponin, Ferritin, LDH, BNP, Procalcitonin) were performed in addition to routinely performed markers (CRP, neutrophils, lymphocytes, neutrophil:lymphocyte ratio). Age, NEWS score and CURB-65 were included as comparators. All biomarkers were tested in logistic regression against a composite outcome of non-invasive ventilation, intensive care admission, or death, with Area Under the Curve (AUC) figures calculated.Results155 patients had 28-day outcomes at the time of analysis. CRP (AUC 0.51, CI:0.40-0.62), lymphocyte count (AUC 0.62, CI:0.51-0.72), and other routine markers did not predict the primary outcome. IL-6 (AUC: 0.78,0.65-0.89) and suPAR (AUC 0.77, CI: 0.66-0.85) showed some promise, but simple clinical features alone such as NEWS score (AUC: 0.74, 0.64-0.83) or age (AUC: 0.70, 0.61-0.78) performed nearly as well.DiscussionAdmission blood biomarkers have only moderate predictive value for predicting COVID-19 outcomes, while simple clinical features such as age and NEWS score outperform many biomarkers. IL-6 and suPAR had the best performance, and further studies should validate these biomarkers in a prospective fashion.
SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring
Authors: La Rosa Giuseppina , Mancini Pamela , Ferraro Giusy Bonanno , Veneri Carolina , Iaconelli Marcello , Bonadonna Lucia , Lucentini Luca , Suffredini Elisabetta 
Published: June 2020

ABSTRACTSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease COVID-19, a public health emergency worldwide, and Italy is among the world’s first and most severely affected countries. The first autochthonous Italian case of COVID-19 was documented on February 21. We investigated the possibility that SARS-CoV-2 emerged in Italy earlier than that date, by analysing 40 composite influent wastewater samples collected - in the framework of other wastewater-based epidemiology projects - between October 2019 and February 2020 from five wastewater treatment plants (WTPs) in three cities and regions in northern Italy (Milan/Lombardy, Turin/Piedmont and Bologna/Emilia Romagna). Twenty-four additional samples collected in the same WTPs between September 2018 and June 2019 were included as blank samples. Viral concentration was performed according to the standard World Health Organization procedure for poliovirus sewage surveillance. Molecular analysis was undertaken with both nested RT-PCR and real-rime RT-PCR assays. A total of 15 positive samples were confirmed by both methods. Of these, 8 were collected before the first autochthonous Italian case. The earliest dates back to 18 December 2019 in Milan and Turin and 29 January 2020 in Bologna. Samples collected in January and February in the three cities were also positive.Our results demonstrate that SARS-CoV-2 was already circulating in northern Italy at the end of 2019. Moreover, it was circulating in different geographic regions simultaneously, which changes our previous understanding of the geographical circulation of the virus in Italy. Our study highlights once again the importance of environmental surveillance as an early warning system, to monitor the levels of virus circulating in the population and identify outbreaks even before cases are notified to the healthcare system.