bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid
Authors: Ganda Erika , Beck Kristen L. , Haiminen Niina , Silverman Justin D. , Kawas Ban , Cronk Brittany , Anderson Renee R. , Goodman Laura B. , Wiedmann Martin 
Published: August 2020

ABSTRACTUntargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis could reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in the food industry. However, before these approaches can be applied, it is imperative to verify that the most appropriate methods are used at every step of the process: gathering primary material, laboratory methods, data analysis, and interpretation.The focus of this study is in gathering the primary material, in this case, DNA. We used bovine milk as a model to 1) evaluate commercially available kits for their ability to extract nucleic acids from inoculated bovine milk; 2) evaluate host DNA depletion methods for use with milk, and 3) develop and evaluate a selective lysis-PMA based protocol for host DNA depletion in milk.Our results suggest that magnetic-based nucleic acid extraction methods are best for nucleic acid isolation of bovine milk. Removal of host DNA remains a challenge for untargeted sequencing of milk, highlighting that the individual matrix characteristics should always be considered in food testing. Some reported methods introduce bias against specific types of microbes, which may be particularly problematic in food safety where the detection of Gram-negative pathogens and indicators is essential. Continuous efforts are needed to develop and validate new approaches for untargeted metagenomics in samples with large amounts of DNA from a single host.ImportanceTracking the bacterial communities present in our food has the potential to inform food safety and product origin. To do so, the entire genetic material present in a sample is extracted using chemical methods or commercially available kits and sequenced using next-generation platforms to provide a snapshot of what the relative composition looks like. Because the genetic material of higher organisms present in food (e.g., cow in milk or beef, wheat in flour) is around one thousand times larger than the bacterial content, challenges exist in gathering the information of interest. Additionally, specific bacterial characteristics can make them easier or harder to detect, adding another layer of complexity to this issue. In this study, we demonstrate the impact of using different methods in the ability of detecting specific bacteria and highlight the need to ensure that the most appropriate methods are being used for each particular sample.
Control Strategies against COVID-19 in China: Significance of Effective Testing in the Long Run
Authors: Lin Yatang , Peng Fangyuan 
Published: August 2020

AbstractThe coronavirus disease 2019 (COVID-19) outbreak is reasonably contained in China. In this paper, we evaluated the effectiveness of different containment strategies in halting the pandemic spread in both short- and long-term. We combined a networked metapopulation SEIR model featuring undocumented infections, actual mobility data and Bayesian inference to simulate the counterfactual outbreak scenarios removing each one or a combination of the following three policies in place: i) city lockdowns, ii) intercity travel bans, and iii) testing, detection, and quarantine. Our estimates revealed that 11.4% [95% credible interval (CI): 9.7–13.0%] of the infected cases were unidentified before January 23, 2020. The rate grew to 92.5% [95% credible interval (CI): 85.9–94.5%] in early March, thanks to the boost in coronavirus testing capacity. We show that increasing the detection rate of infections from 11.4% to 92.5% alone would explain 75% of the reduction in infections from a no-policy baseline by March 15, 2020.The most pronounced policy implication is that city lockdowns appeared to be the more effective intervention in the short-run but effective testing is essential in containing the COVID-19 spread in the long run. By March 15, restoring within-city personal contact to its 2019 level would lead to a 678% growth in infections with all the other interventions remaining unaffected. Removing intercity travel restrictions and effective detection measures would lead to 3% and 477% growth, respectively. Extending the time horizon to July 15, the counterfactual increase in infections would become 581%, 3% and 3.0 ∗ 105% had the three classes of interventions been lifted individually.SignificanceThe COVID-19 pandemic has become a long-term crisis that calls for long-term solutions. We combined an augmented SEIR simulation model with real-time human mobility data to decompose the effects of lockdown, travel bans and effective testing measures in the curtailment of COVID-19 spread in China over different time horizons. Our analysis reveals that the significant growth in the detection rate of infectious cases, thanks to the expansion in testing effi-ciency, were as effective as city lockdowns in explaining the reduction in new infections up to mid-March. However, as we extended the analysis to July, increasing the detection rate to at least 50% is the only reliable way to bring the spread under control.
Zoonotic viruses in three species of voles (Microtusspp.) from Poland
Authors: Grzybek Maciej , Tołkacz Katarzyna , Sironen Tarja , Mäki Sanna , Alsarraf Mohammed , Behnke-Borowczyk Jolanta , Biernat Beata , Nowicka Joanna , Vaheri Antti , Henttonen Heikki , Behnke Jerzy M. , Bajer Anna 
Published: August 2020

ABSTRACTRodents are known to be reservoir hosts for a plethora of zoonotic viruses and therefore play a significant role in the dissemination of these pathogens. We trapped three vole species (Microtus arvalis, M. oeconomusandM. agrestis) in N.E. Poland, all of which are widely distributed species in Europe, and, using immunofluorescence assays, we assessed serum samples for the presence of antibodies to hantaviruses, arenaviruses and cowpox viruses (CPXV). We detected antibodies against CPXV and Puumala virus (PUUV), overall seroprevalence of combined viral infections of 18.2% [10.5-29.3] and mostly attributed to CPXV. Antibodies to Tula hantavirus, typical forMicrotusvoles, are known to cross-react strongly with the PUUV antigen used in PUUV screening, but we detected only one PUUV/TULV cross-reaction inMicrotus arvalis(1.3% [0.1-7.9]). We found antibodies against CPXV in all threeMicrotusspp. Seroprevalence was similar in all vole species. There were no significant differences in seroprevalence between the sexes and among host age categories. Our results contribute to the increasing understanding of CPXV abundance in voles in Europe, and confirm that CPXV circulates also inMicrotusspp. voles in NE Poland.
Lipid droplets fuel SARS-CoV-2 replication and production of inflammatory mediators
Authors: da Silva Gomes Dias Suelen , Soares Vinicius Cardoso , Ferreira André C. , Sacramento Carolina Q. , Fintelman-Rodrigues Natalia , Temerozo Jairo R. , Teixeira Lívia , Barreto Ester , Mattos Mayara , de Freitas Caroline S. , Azevedo-Quintanilha Isaclaudia G. , Manso Pedro Paulo A. , Hottz Eugenio D. , Pão Camila R. R. , Bou-Habib Dumith C. , Bozza Fernando A. , Souza Thiago M. L. , Bozza Patrícia T. 
Published: August 2020

AbstractViruses are obligate intracellular parasites that make use of the host metabolic machineries to meet their biosynthetic needs, identifying the host pathways essential for the virus replication may lead to potential targets for therapeutic intervention. The mechanisms and pathways explored by SARS-CoV-2 to support its replication within host cells are not fully known. Lipid droplets (LD) are organelles with major functions in lipid metabolism and energy homeostasis, and have multiple roles in infections and inflammation. Here we described that monocytes from COVID-19 patients have an increased LD accumulation compared to SARS-CoV-2 negative donors.In vitro, SARS-CoV-2 infection modulates pathways of lipid synthesis and uptake, including CD36, SREBP-1, PPARγ and DGAT-1 in monocytes and triggered LD formation in different human cells. LDs were found in close apposition with SARS-CoV-2 proteins and double-stranded (ds)-RNA in infected cells. Pharmacological modulation of LD formation by inhibition of DGAT-1 with A922500 significantly inhibited SARS-CoV-2 replication as well as reduced production of pro-inflammatory mediators. Taken together, we demonstrate the essential role of lipid metabolic reprograming and LD formation in SARS-CoV-2 replication and pathogenesis, opening new opportunities for therapeutic strategies to COVID-19.
Phenotypic plasticity and evolution of thermal tolerance in two lineages of bacteria from temperate and hot environments
Authors: Hurtado-Bautista Enrique , Pérez-Sánchez Laura F. , Islas-Robles África , Santoyo Gustavo , Olmedo-Álvarez Gabriela 
Published: August 2020

AbstractDespite the crucial role of microorganisms to sustain life on Earth, there is little research on the evolution of thermal tolerance of bacteria in the face of the challenge that global warming poses. Phenotypic adaptation to a new environment requires plasticity to allow individuals to respond to selective forces, followed by adaptive evolution. We do not know to what extent phenotypic plasticity allows thermal tolerance evolution in bacteria at the border of their physiological limits. We analyzed growth and thermal reaction norms to temperature of strains of two bacterial lineages,Bacillus cereus sensu latoandBacillus subtilis sensu lato, that evolved in two contrasting environments, a temperate lagoon (T) and a hot spring (H). Our results showed that despite co-occurrence of members of both lineages in the two contrasting environments, norms of reactions to temperature exhibited a similar pattern only within the lineages, suggesting fixed phenotypic plasticity. Additionally, within theB. cereuslineage, strains from the H environment showed only two to three °C more heat tolerance than strains from the T environment. The limited evolutionary changes towards an increase in heat tolerance in bacteria should alert us of the negative impact that climate change can have on all biological cycles in the planet.
EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing
Authors: Csaba Gergely , Berchtold Evi , Hadziahmetovic Armin , Gruber Markus , Ammar Constantin , Zimmer Ralf 
Published: August 2020

ABSTRACTWhile absolute quantification is challenging in high-throughput measurements, changes of features between conditions can often be determined with high precision. Therefore, analysis of fold changes is the standard method, but often, a doubly differential analysis of changes of changes is required. Differential alternative splicing is an example of a doubly differential analysis, i.e. fold changes between conditions for different isoforms of a gene. EmpiRe is a quantitative approach for various kinds of omics data based on fold changes for appropriate features of biological objects. Empirical error distributions for these fold changes are estimated from Replicate measurements and used to quantify feature fold changes and their directions. We assess the performance of EmpiRe to detect differentially expressed genes applied to RNA-Seq using simulated data. It achieved higher precision than established tools at nearly the same recall level. Furthermore, we assess the detection of alternatively Spliced genes via changes of isoform fold changes (EmpiReS) on distribution-free simulations and experimentally validated splicing events. EmpiReS achieves the best precision-recall values for simulations based on different biological datasets. We propose EmpiRe(S) as a general, quantitative and fast approach with high reliability and an excellent trade-off between sensitivity and precision in (doubly) differential analyses.
Hyperpolyploidization of hepatocyte initiates preneoplastic lesion formation in the liver
Authors: Lin Heng , Huang Yen-Sung , Fustin Jean-Michel , Doi Masao , Chen Huatao , Lai Hui-Huang , Lin Shu-Hui , Lee Yen-Lurk , King Pei-Chih , Hou Hsien-San , Chen Hao-Wen , Young Pei-Yun , Chao Hsu-Wen 
Published: August 2020

ABSTRACTHepatocellular carcinoma (HCC) is the most predominant primary malignancy in the liver. Genotoxic and genetic models have revealed that HCC cells are derived from hepatocytes, but where the critical region for tumor foci emergence is and how this transformation occurs are still unclear. Here, hyperpolyploidization of hepatocytes around the centrilobular (CL) region was demonstrated to be closely linked with the development of HCC cells after diethylnitrosamine treatment. We identified the CL region as a dominant lobule for accumulation of hyperpolyploid hepatocytes and preneoplastic tumor foci formation. We also demonstrated that upregulation ofAurkbplays a critical role in promoting hyperpolyploidization. Increase of AURKB phosphorylation was detected on the midbody during cytokinesis, causing abscission failure and hyperpolyploidization. Pharmacological inhibition of AURKB dramatically reduced nucleus size and tumor foci number surrounding the CL region in diethylnitrosamine-treated liver. Our work reveals an intimate molecular link between pathological hyperpolyploidy of CL hepatocytes and transformation into HCC cells.
RUNX1 haploinsufficiency causes a marked deficiency of megakaryocyte-biased hematopoietic progenitor cells: Mechanistic studies and drug correction
Authors: Estevez Brian , Borst Sara , Jarocha Danuta , Sudunagunta Varun , Gonzalez Michael , Garifallou James , Hakonarson Hakon , Gao Peng , Tan Kai , Liu Paul , Bagga Sumedha , Holdreith Nicholas , Tong Wei , Speck Nancy , French Deborah L. , Gadue Paul , Poncz Mortimer 
Published: August 2020

AbstractPatients with familial platelet disorder with a predisposition to myeloid malignancy (FPDMM) harbor germline monoallelic mutations in a key hematopoietic transcription factor RUNX1. Previous studies of FPDMM have focused on megakaryocyte (Mk) differentiation, and platelet production and signaling. However, the effects of RUNX1 haploinsufficiency on hematopoietic progenitor cells (HPCs) and subsequent megakaryopoiesis remains incomplete. To address this issue, we studied induced-pluripotent stem cell (iPSC)-derived HPCs (iHPCs) and Mks (iMks) from both patient-derived lines and a wildtype line modified to be RUNX1 haploinsufficient (RUNX1+/−), each compared to their isogenic wildtype control. All RUNX1+/−lines showed decreased iMk yield and depletion of a Mk-biased iHPC subpopulation. To investigate global and local gene expression changes underlying this iHPC shift, single-cell RNA sequencing was performed on sorted FPDMM and control iHPCs. We defined several cell subpopulations in FPDMM Mk-biased iHPCs. Analyses of gene sets upregulated in FPDMM iHPCs indicated enrichment for response to stress, regulation of signal transduction and response to cytokine gene sets. Immunoblotting studies in FPDMM iMks were consistent with these findings, but also identified augmented baseline c-Jun N-terminal kinase (JNK) phosphorylation, known to be activated by transforming growth factor β1 and cellular stressors. J-IN8 and RepSox, small drugs targeting these pathways, corrected quantitative defects in FPDMM iHPC production. These findings were confirmed in adult human CD34+-derived stem and progenitor cells transduced with lentiviralRUNX1short-hairpin (sh) RNA to mimic RUNX1+/−. These mechanistic studies of the defect in megakaryopoiesis in FPDMM suggest druggable pathways for clinical management of thrombocytopenia in affected patients.Key pointsRUNX1 haploinsufficiency results in a deficiency of megakaryocyte-biased hematopoietic progenitor cells (HPCs).RUNX1 haploinsufficiency elevates druggable proinflammatory and TGFβR1-related pathways in HPCs.
High Cysteinyl Leukotriene Receptor 1 Expression Correlates with Poor Survival of Uveal Melanoma Patients and Cognate Antagonist Drugs Modulate the Growth, Cancer Secretome, and Metabolism of Uveal Melanoma Cells
Authors: Slater Kayleigh , Heeran Aisling B. , Sanz-Pamplona Rebeca , Kalirai Helen , Rahman Arman , Helmi Mays , Garcia-Mulero Sandra , O’Connell Fiona , Bosch Rosa , Portela Anna , Villanueva Alberto , Piulats Josep M. , Gallagher William M. , Jensen Lasse D. , Coupland Sarah E. , O’Sullivan Jacintha , Kennedy Breandán N. 
Published: August 2020

AbstractUveal melanoma (UM) is a rare, but often lethal, form of ocular cancer arising from melanocytes within the uveal tract. UM has a high propensity to spread hematogenously to the liver, with up to 50% of patients developing liver metastases. Unfortunately, once liver metastasis occurs, patient prognosis is extremely poor with as few as 8% of patients surviving beyond two years. There are nostandard-of-caretherapies available for the treatment of metastatic uveal melanoma, hence it is a clinical area of urgent unmet need. Here, the clinical relevance and therapeutic potential of cysteinyl leukotriene receptors (CysLT1and CysLT2) in UM was evaluated. High expression ofCYSLTR1orCYSLTR2transcripts is significantly associated with poor disease-free survival and poor overall survival in UM patients. Digital pathology analysis identified high expression of CysLT1in primary UM is associated with reduced disease-specific survival (p = 0.012) and overall survival (p = 0.011). High CysLT1expression shows a statistically significant (p = 0.041) correlation with ciliary body involvement, a poor prognostic indicator in UM. Small molecule drugs targeting CysLT1were vastly superior at exerting anti-cancer phenotypes in UM cell lines and zebrafish xenografts than drugs targeting CysLT2. Quininib, a selective CysLT1antagonist, significantly inhibits survival (p < 0.0001), long-term proliferation (p < 0.0001), and oxidative phosphorylation (p < 0.001), but not glycolysis, in primary and metastatic UM cell lines. Quininib exerts opposing effects on the secretion of inflammatory markers in primary versus metastatic UM cell lines. Quininib significantly downregulated IL-2 and IL-6 in Mel285 cells (p < 0.05), but significantly upregulated IL-10, IL-1β, IL-2 (p < 0.0001), IL-13, IL-8 (p < 0.001), IL-12p70 and IL-6 (p < 0.05) in OMM2.5 cells. Finally, quininib significantly inhibits tumour growth in orthotopic zebrafish xenograft models of UM. These preclinical data suggest that antagonism of CysLT1, but not CysLT2, may be of therapeutic interest in the treatment of UM.
In-situ observation of mitochondrial biogenesis as the early event of apoptosis
Authors: Shao Chang-Sheng , Zhou Xiu-Hong , Miao Yu-Hui , Wang Peng , Zhang Qian-Qian , Huang Qing 
Published: August 2020

SUMMARYMitochondrial biogenesis is a cell response to external stimuli which is generally believed to suppress apoptosis. However, during the process of apoptosis, whether mitochondrial biogenesis occurs in the early stage of the apoptotic cells remains unclear. To address this question, we constructed the COX8-EGFP-ACTIN-mCherry HeLa cells with recombinant fluorescent proteins respectively tagged on the nucleus and mitochondria, and monitored the mitochondrial changes in living cells exposed to gamma-ray radiation. Besides in situ detection of mitochondrial fluorescence changes, we also examined the cell viability, nuclear DNA damage, reactive oxygen species (ROS), Mitochondrial superoxide, citrate synthase activity, ATP, cytoplasmic and mitochondrial calcium, mitochondrial DNA copy number and expression of transcription genes related to mitochondrial biogenesis as well as the apoptosis biomarkers. As a result, we confirmed that significant mitochondrial biogenesis took place preceding the radiation-induced apoptosis, and the change of mitochondrial biogenesis at early time was closely correlated with the apoptotic cells at late stage. The involved mechanism was also discussed.HighlightsA dual fluorescence reporter system was successfully constructed for in-situ observation of mitochondrial biogenesis in living cells.The whole process of radiation-induced mitochondrial biogenesis and apoptosis was scrutinized.The conception of the relationship between mitochondrial biogenesis and apoptosis was revised.Assessment of the early event of mitochondrial biogenesis is critical for prediction of the late fate of cells.Graphical abstract
Modeling Genetic Epileptic Encephalopathies using Brain Organoids
Authors: Steinberg Daniel J. , Saleem Afifa , Repudi Srinivasa Rao , Banne Ehud , Mahajnah Muhammad , Hanna Jacob H. , Carlen Peter L. , Aqeilan Rami I. 
Published: August 2020

SummaryEpileptic encephalopathies (EEs) are a group of disorders associated with intractable seizures, brain development and functional abnormalities, and in some cases, premature death. Pathogenic human germline biallelic mutations in tumor suppressor WW domain-containing oxidoreductase (WWOX) are associated with a relatively mild autosomal-recessive spinocerebellar ataxia-12 (SCAR12) and a more severe early infantile WWOX-related epileptic encephalopathy (WOREE). In this study, we generated anin-vitromodel for EEs, using the devastating WOREE syndrome as a prototype, by establishing brain organoids from CRISPR-engineered human ES cells and from patient-derived iPSCs. Using these models, we discovered dramatic cellular and molecular CNS abnormalities, including neural population changes, cortical differentiation malfunctions, and Wnt-pathway and DNA-damage response impairment. Furthermore, we provide a proof-of-concept that ectopic WWOX expression could potentially rescue these phenotypes. Our findings underscore the utility of modeling childhood epileptic encephalopathies using brain organoids and their use as a unique platform to test possible therapeutic intervention strategies.
Crowding Effects in an Empirical Predator-Prey System
Authors: Subbey Sam , Frank Anna S. , Kobras Melanie 
Published: August 2020

AbstractThis paper uses a Lotka-Volterra (predator-prey) modeling framework to investigate the dynamical link between the biomass of an empirical predator, and that of its prey. We use a system of ordinary (ODE) differential equations to describe the system dynamics, and derive theoretical conditions for stability, in terms of system parameters. We derive the empirical system parameters by fitting the ODE system to empirical data, using non-constrained optimization.We present results to show that the predator biomass is regulated by that of the prey. Furthermore, that the system dynamics is subject to Hopf bifurcation, conditioned on independent second-order terms in the ODE system. In ecological terms, the findings translate into evidence for existence of population crowding (density) effects.
Conditioned place preference reveals tonic pain in Octopus
Authors: Crook Robyn J 
Published: August 2020

AbstractTonic pain is an ongoing, negative affective state arising from tissue damage or inflammation (1). Because pain is aversive and its relief is innately rewarding, mammals learn to avoid a context in which pain is experienced, and prefer one where pain relief occurs(2, 3). It is generally accepted that vertebrate animals experience pain(4), however, there is currently no compelling evidence that pain occurs in any invertebrate(5). Here we show that octopuses exhibit tonic pain behavior after subcutaneous injection of dilute acetic acid. In conditioned place preference assays, octopuses avoid contexts in which pain was experienced, prefer a location in which they experienced tonic pain relief, and show no conditioned preference in pain’s absence. Octopuses are thus the first invertebrate shown to experience pain.One sentence summaryA cognitive test demonstrating the emotional component of pain in mammals reveals the first example of pain in any invertebrate.