bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiosynthesis and Preclinical Evaluation of [68Ga]Ga-NOTA-Folate for PET Imaging of Folate Receptor β Positive Macrophages
Authors: Moisio Olli , Palani Senthil , Virta Jenni , Elo Petri , Liljenbäck Heidi , Tolvanen Tuula , Käkelä Meeri , Miner Maxwell G. , Herre Erika Atencio , Marjamäki Päivi , Örd Tiit , Heinäniemi Merja , Kaikkonen-Määttä Minna , Zhang Fenghua , Srinivasarao Madduri , Knuuti Juhani , Low Philip S. , Saraste Antti , Li Xiang-Guo , Roivainen Anne
Published: May 2020

Folate receptor β (FR-β) is one of the markers expressed on macrophages and a promising target for imaging of inflammation. Here, we report the radiosynthesis and preclinical evaluation of [68Ga]Ga-NOTA-folate (68Ga-FOL). First, we determined the affinity of68Ga-FOL using human FR-β expressing cells. Then, we studied atherosclerotic mice with68Ga-FOL and18F-FDG PET/CT. After sacrifice, the tissues excised were measured with a γ-counter forex vivobiodistribution. Further, the tracer distribution and co-localization with macrophages in aorta cryosections were studied using autoradiography, hematoxylin-eosin staining and immunostaining with anti-Mac-3 antibody. Specificity of68Ga-FOL was assessed in a blocking study with excess of folate glucosamine. As a last step, human radiation doses were extrapolated from rat PET data. We were able to produce68Ga-FOL at high radioactivity concentration, with high molar activity and radiochemical purity. The cell binding studies showed high (5.1 ± 1.1 nM) affinity of68Ga-FOL to FR-β. The myocardial uptake of68Ga-FOL (SUV 0.43 ± 0.06) was 20-folds lower compared to18F-FDG (SUV 10.6 ± 1.8,P= 0.001). The autoradiography and immunohistochemistry of aorta revealed that68Ga-FOL radioactivity co-localized with Mac-3-positive macrophage-rich atherosclerotic plaques. The plaque-to-healthy vessel wall ratio of68Ga-FOL (2.44 ± 0.15) was significantly higher than that of18F-FDG (1.93 ± 0.22,P= 0.005). Blocking studies verified68Ga-FOL specificity to FR. As estimated from rat data the human effective dose was 0.0105 mSv/MBq. The organ with highest absorbed dose was kidney (0.1420 mSv/MBq). In conclusion,68Ga-FOL is a promising new FR-β-targeted tracer for imaging macrophage-associated inflammation.

TABLE OF CONTENT/ABSTRACT GRAPHIC
Integrated multi-omics reveals common properties underlying stress granule and P-body formation
Authors: Kershaw Christopher J. , Nelson Michael G. , Lui Jennifer , Bates Christian P. , Jennings Martin D. , Hubbard Simon J. , Ashe Mark P. , Grant Chris M.
Published: May 2020

Non-membrane-bound compartments such as P-bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common stress condition imposed by glucose depletion. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that may act as seeds for the further condensation of proteins forming mature PBs and SGs. Both before and after glucose depletion, these HMW complexes are enriched for proteins containing low complexity and RNA binding domains. The mRNA content of these HMW complexes is enriched for long, structured mRNAs that become more poorly translated following glucose depletion. Many proteins and mRNAs are shared between PBs and SGs including several multivalent RNA binding proteins that may promote condensate interactions during liquid-liquid phase separation. Even where the precise identity of mRNAs and proteins localizing to PBs and SGs is distinct, the mRNAs and proteins share common biophysical and chemical features that likely trigger their phase separation.
Empirical field mapping for gradient nonlinearity correction of multi-site diffusion weighted MRI
Authors: Hansen Colin B. , Rogers Baxter P. , Schilling Kurt G. , Nath Vishwesh , Blaber Justin A. , Irfanoglu Okan , Barnett Alan , Pierpaoli Carlo , Anderson Adam W. , Landman Bennett A.
Published: May 2020

Background

Achieving inter-site / inter-scanner reproducibility of diffusion weighted magnetic resonance imaging (DW-MRI) metrics has been challenging given differences in acquisition protocols, analysis models, and hardware factors.

Purpose

Magnetic field gradients impart scanner-dependent spatial variations in the applied diffusion weighting that can be corrected if the gradient nonlinearities are known. However, retrieving manufacturer nonlinearity specifications is not well supported and may introduce errors in interpretation of units or coordinate systems. We propose an empirical approach to mapping the gradient nonlinearities with sequences that are supported across the major scanner vendors.

Study Type

Prospective observational study

Subjects

A spherical isotropic diffusion phantom, and a single human control volunteer

Field Strength/Sequence

3T (two scanners). Stejskal-Tanner spin echo sequence with b-values of 1000, 2000 s/mm2with 12, 32, and 384 diffusion gradient directions per shell.

Assessment

We compare the proposed correction with the prior approach using manufacturer specifications against typical diffusion pre-processing pipelines (i.e., ignoring spatial gradient nonlinearities). In phantom data, we evaluate metrics against the ground truth. In human and phantom data, we evaluate reproducibility across scans, sessions, and hardware.

Statistical Tests

Wilcoxon rank-sum test between uncorrected and corrected data.

Results

In phantom data, our correction method reduces variation in mean diffusivity across sessions over uncorrected data (p<0.05). In human data, we show that this method can also reduce variation in mean diffusivity across scanners (p<0.05).

Conclusion

Our method is relatively simple, fast, and can be applied retroactively. We advocate incorporating voxel-specific b-value and b-vector maps should be incorporated in DW-MRI harmonization preprocessing pipelines to improve quantitative accuracy of measured diffusion parameters.
Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI
Authors: Thompson WH , Nair R , Oya H , Esteban O , Shine JM , Petkov CI , Poldrack RA , Howard M , Adolphs R
Published: May 2020

Mapping the causal effects of one brain region on another (effective connectivity) is a challenging problem in neuroscience, since it requires invasive direct manipulation of brain function, together with whole-brain measurement of the effects produced. Here we establish a unique resource and present data from 26 human patients who underwent electrical stimulation during functional magnetic resonance imaging (es-fMRI). The patients had medically refractory epilepsy requiring surgically implanted intracranial electrodes in cortical and subcortical locations. One or multiple contacts on these electrodes were stimulated while simultaneously recording BOLD-fMRI activity in a block design. Multiple runs exist for patients with different stimulation sites. We describe the resource, data collection process, preprocessing using the fMRIPrep analysis pipeline and management of artifacts, and provide end-user analyses to visualize distal brain activation produced by site-specific electrical stimulation. The data are organized according to the brain imaging data structure (BIDS) specification, and are available for analysis or future dataset contributions on openneuro.org including both raw and preprocessed data.
Fast and Comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco
Authors: Polasky Daniel A. , Yu Fengchao , Teo Guo Ci , Nesvizhskii Alexey I.
Published: May 2020

Glycosylation is a ubiquitous and heterogeneous post-translational modification (PTM) used to accomplish a wide variety of critical cellular tasks. Recent advances in methods for enrichment and mass spectrometric analysis of intact glycopeptides have produced large-scale, high-quality glycoproteomics datasets, but interpreting this data remains challenging. In addition to being large, complex, and heterogeneous, glycans undergo fragmentation during vibrational activation, making common PTM search strategies ineffective for their identification. We present a computational tool called MSFragger-Glyco for fast and highly sensitive identification of N- and O-linked glycopeptides using open and glycan mass offset search strategies. Reanalysis of recently published N-glycoproteomics data resulted in annotation of 83% more glycopeptide-spectrum matches (glycoPSMs) than in previous results, which translated to substantial increases in the numbers of glycoproteins and glycosites that could be identified. In published O-glycoproteomics data, our method more than doubled the number of glycoPSMs annotated when searching the same peptides as the original search and resulted in up to a 6-fold increase when expanding searches to include large numbers of possible glycan compositions and other modifications. Expanded searches revealed trends in glycan composition and crosstalk with phosphorylation that remained hidden to the original search. With greatly improved spectral annotation, coupled with the fast speed of fragment ion index-based scoring, MSFragger-Glyco makes it possible to comprehensively interrogate glycoproteomics data and illuminate the many roles of glycosylation.
Reads2Resistome: An adaptable and high-throughput whole-genome sequencing pipeline for bacterial resistome characterization
Authors: Woyda Reed , Oladeinde Adelumola , Abdo Zaid
Published: May 2020

The bacterial resistome is the collection of all the antibiotic resistance genes, virulence genes, and other resistance elements within a bacterial isolate genome including plasmids and bacteriophage regions. Accurately characterizing the resistome is crucial for prevention and mitigation of emerging antibiotic resistance threats to animal and human health. Reads2Resistome is a tool which allows researchers to assemble and annotate bacterial genomes using long or short read sequencing technologies or both in a hybrid approach. Using a massively parallel analysis pipeline, Reads2Resistome performs assembly, annotation and resistome characterization with the goal of producing an accurate and comprehensive description of a bacterial genome and resistome contents. Key features of the Reads2Resistome pipeline include quality control of input sequencing reads, genome assembly, genome annotation, resistome characterization and alignment. All prerequisite dependencies come packaged together in a single suit which can easily be downloaded and run on Linux and Mac operating systems.

Availability

Reads2Resistome is freely available as an open-source package under the MIT license, and can be downloaded via GitHub (https://github.com/BioRRW/Reads2Resistome).
Netome: The Molecular Characterization of Neutrophil Extracellular Traps (NETs)
Authors: Scieszka David , Lin Yi-Han , Li Weizhong , Choudhury Saibyasachi , Yu Yanbao , Freire Marcelo
Published: May 2020

Neutrophils are the most abundant type of white blood cells in humans with biological roles relevant to inflammation and fighting infections. The release of neutrophil extracellular DNA aims to control invasion by bacteria, viruses, fungi, and tissue damage. Neutrophil Extracellular Traps (NETs) act as antimicrobial agents triggering immune signaling through the release of the nuclear content into the extracellular space. Although intense investigations have elucidated the pathways preceding NET formation, the exact molecular composition of released NETs has not been mapped. We aimed to decode the sequences of DNA and proteins from NETs. With emerging needs to understand neutrophil functions precisely, we open the field of NETOMIC studies through isolation of NETs in combination with omics approaches including shotgun genomics and proteomics. Our in vitro NET isolation methodology allowed for unprecedented replicability with induction in a sterile inflammation model system. Enrichment of mitochondrial DNA and telomere sequences are significantly expressed in NET genomes. This study revealed that the genomic sequence released in the extracellular milieu is not stochastically serving as a scaffold for a repertoire of proteins involved in neutrophil protective functions. Collectively, we established the gene and protein signatures exclusive to the extracellular NETs in comparison to undifferentiated and differentiated neutrophil states, further guiding future detection of specific regions needed for diagnostics and targeted therapies of NET related conditions.
Effects of age on pre-stimulus neural activity predictive of successful memory encoding: an fMRI study
Authors: Liu E. Song , Koen Joshua D. , Rugg Michael D.
Published: May 2020

Pre-stimulus subsequent memory effects (SMEs) – differences in neural activity preceding the onset of study items that are predictive of later memory performance – have consistently been reported in young adults. The present fMRI experiment investigated potential age-related differences in pre-stimulus SMEs. During study, healthy young and older participants made one of two semantic judgments on images, with the judgment signaled by a preceding cue. In the test phase, participants first made an item recognition judgment and, for each item judged old, a source memory judgment. Age-invariant pre-stimulus SMEs were observed in left dorsomedial prefrontal cortex, left hippocampus, and right subgenual cortex. In each case, the effects reflected lower BOLD signal for later recognized items, regardless of source accuracy, than unrecognized items. A similar age-invariant pattern was observed in left orbitofrontal cortex, but the effect in this region was specific to items attracting a correct source response compared to unrecognized items. In contrast, the left angular gyrus and fusiform cortex demonstrated negative pre-stimulus SMEs that were exclusive to young participants. The findings indicate that age differences in pre-stimulus SMEs are regionally specific and suggest that pre-stimulus SMEs reflect multiple cognitive processes, only some of which are vulnerable to advancing age.
Ant community potential for pest control in olive groves: management and landscape effects
Authors: Martínez-Núñez Carlos , Rey Pedro J. , Salido Teresa , Manzaneda Antonio J. , Camacho Francisco M. , Isla Jorge
Published: May 2020

Ants are important pest control agents in many agroecosystems worldwide. However, little is known about how management, ecological contrast generated by different agricultural practices, and landscape complexity affect their communities and the potential pest control that they can provide.

Here, we surveyed ant communities in 40 paired olive groves with different ground-herb cover management across 20 localities spanning a wide range of landscape complexity at the regional scale. We also conducted experiments with dummy plasticine models in 18 of these groves to explore the ant potential to control the two main pests of the olive tree (olive moth and olive fly). In addition, we calculated an index, the Ant-community Predation Function (APF), which informs about the predation pressure exerted by ant communities over these pests.

Results show that: a) extensive management at intermediate landscape complexity maximizes the abundance and pest control by ants; b) the ecological contrast affects ant abundance and ant richness but does not impact the predation function; c) APF is a good measure of pest control potential at the community level; and, d)Tapinoma nigerrimumis an important ant species for pest control in our system, which seems little affected by local or landscape heterogeneity.

This study advances our knowledge about local management and landscape effects on ants and their potential contribution to pest control in olive groves. Extensive herb cover management and landscape heterogeneity increased ant predation pressure in olive groves.
Cell cycle-gated feedback control mediates desensitization to interferon stimulation
Authors: Mudla Anusorn , Jiang Yanfei , Arimoto Kei-ichiro , Xu Bingxian , Rajesh Adarsh , Ryan Andy P , Wang Wei , Daugherty Matthew D , Zhang Dong-Er , Hao Nan
Published: May 2020

Cells use sophisticated molecular circuits to interpret and respond to extracellular signal factors, such as hormones and cytokines, which are often released in a temporally varying fashion. In this study, we focus on type I interferon (IFN) signaling in human epithelial cells and combine microfluidics, time-lapse microscopy, and computational modeling to investigate how the IFN-responsive regulatory network operates in single cells to process repetitive IFN stimulation. We found that IFN-α pretreatments lead to opposite effects, priming versus desensitization, depending on the input durations. These effects are governed by a regulatory network composed of a fast-acting positive feedback loop and a delayed negative feedback loop, mediated by upregulation of ubiquitin-specific peptidase 18 (USP18). We further revealed that USP18 upregulation can only be initiated at the G1 and early S phases of cell cycle upon the treatment onset, resulting in heterogeneous and delayed induction kinetics in single cells. This cell cycle gating provides a temporal compartmentalization of feedback control processes, enabling duration-dependent desensitization to repetitive stimulations. Moreover, our results, highlighting the importance of IFN dynamics, may suggest time-based strategies for enhancing the effectiveness of IFN pretreatment in clinical applications against viruses, such as SARS-CoV-2.
In-VivoToxicity Studies andIn-VitroInactivation of SARS-CoV-2 by Povidone-iodineIn-situGel Forming Formulations
Authors: Liang Bo , Yuan Xudong , Wei Gang , Wang Wei , Zhang Ming , Peng Haizhou , Javer Amin , Mendenhall Michelle , Julander Justin , Huang Sammi , Michail Hany , Lu Yong , Zhu Qi , Baldwin John
Published: May 2020

To curb the spread of SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, we characterize the virucidal activity of long-acting Povidone Iodine (PVP-I) compositions developed using anin-situgel forming technology. The PVP-I gel forming nasal spray (IVIEW-1503) and PVP-I gel forming ophthalmic eye drop (IVIEW-1201) rapidly inactivated SARS-CoV-2, inhibiting the viral infection of VERO76 cells. No toxicity was observed for the PVP-I formulations. Significant inactivation was noted with preincubation of the virus with these PVP-I formulations at the lowest concentrations tested. It has been demonstrated that both PVP-I formulations can inactivate SARS-CoV-2 virus efficiently in both a dose-dependent and a time-dependent manner. These results suggest IVIEW-1503 and IVIEW-1201 could be potential agents to reduce or prevent the transmission of the virus through the nasal cavity and the eye, respectively. Further studies are needed to clinically evaluate these formulations in early-stage COVID-19 patients.
The H-NS regulator plays a role in the stress induced by carbapenemase expression inAcinetobacter baumannii
Authors: Huang Fanny , Fitchett Noelle , Razo-Gutierrez Chelsea , Le Casin , Ra Grace , Lopez Carolina , Gonzalez Lisandro J. , Sieira Rodrigo , Vila Alejandro J. , Bonomo Robert A. , Ramirez Maria Soledad
Published: May 2020

Disruption of the histone-like nucleoid structuring protein (H-NS) was shown to affect the ability for Gram-negative bacteria to regulate genes associated with virulence, persistence, stress response, quorum sensing, biosynthesis pathways and cell adhesion. Here, we used the expression of metallo-β-lactamases (MBLs) known to elicit envelope stress by the accumulation of toxic species in the periplasm to interrogate the role of H-NS inAcinetobacter baumannii, together with other stressors. Using a multidrug-resistantA. baumannii, we observed that H-NS plays a role in alleviating the stress triggered by MBL toxic precursors and counteract the effect of DNA-damaging agents, supporting its role in stress response.

Importance

Carbapenem-resistantA. baumannii(CRAB) is recognized as one of the most threatening gram-negative bacilli. H-NS is known to play a role in controlling the transcription of a variety of different genes, including those associated with stress response, persistence and virulence. In the present work, we uncovered a link between the role of H-NS in theA. baumanniistress response and its relationship with the envelope stress response and resistance to DNA-damaging agents. Overall, we posit a new role of H-NS, showing that H-NS serves to endure envelope stress that could also be a mechanism that alleviates the stress induced by MBL expression inA. baumannii. This could be an evolutionary advantage to further resist the action of carbapenems.
Risk factors associated with mortality of COVID-19 in 3125 counties of the United States
Authors: Tian Ting , Zhang Jingwen , Hu Liyuan , Jiang Yukang , Duan Congyuan , Li Zhongfei , Wang Xueqin , Zhang Heping
Published: May 2020

Background

The number of cumulative confirmed cases of COVID-19 in the United States has risen sharply since March 2020. A county health ranking and roadmaps program has been established to identify factors associated with disparity in mobility and mortality of COVID-19 in all counties in the United States.

Methods

To find out the risk factors associated with county-level mortality of COVID-19 with various levels of prevalence, a negative binomial design was applied to the county-level mortality counts of COVID-19 as of August 27, 2020 in the United States. In this design, the infected counties were categorized into three levels of infections using clustering analysis based on time-varying cumulative confirmed cases from March 1 to August 27, 2020. COVID-19 patients were not analyzed individually but were aggregated at the county-level, where the county-level deaths of COVID-19 confirmed by the local health agencies.

Results

3125 infected counties were assigned into three classes corresponding to low, median, and high prevalence levels of infection. Several risk factors were significantly associated with the mortality counts of COVID-19, where higher level of air pollution (0.153,P<0.001) increased the mortality in the low prevalence counties and elder individuals were more vulnerable in both the median and high prevalence counties. The segregation between non-Whites and Whites and higher Hispanic population had higher likelihood of risk of the deaths in all infected counties.

Conclusions

The mortality of COVID-19 depended on sex, race/ethnicity, and outdoor environment. The increasing awareness of the impact of these significant factors may lead to the reduction in the mortality of COVID-19.
A Novel Smart City Based Framework on Perspectives for application of Machine Learning in combatting COVID-19
Authors: Ezugwu Absalom E. , Hashem Ibrahim A.T. , Oyelade Olaide N. , Chiroma Haruna , Al-Garadi Mohammed A. , Abdullahi Idris N. , Otegbeye Olumuyiwa , Shukla Amit K. , Almutari Mubarak
Published: May 2020

The spread of COVID-19 across the world continues as efforts are being made from multi-dimension to curtail its spread and provide treatment. The COVID-19 triggered partial and full lockdown across the globe in an effort to prevent its spread. COVID-19 causes serious fatalities with United States of America recording over 3,000 deaths within 24 hours, the highest in the world for a single day and as of October 2020 has recorded a total of 270,642 death toll. In this paper, we present a novel framework which intelligently combines machine learning models and internet of things (IoT) technology specific in combatting COVID-19 in smart cities. The purpose of the study is to promote the interoperability of machine learning algorithms with IoT technology in interacting with a population and its environment with the aim of curtailing COVID-19. Furthermore, the study also investigates and discusses some solution frameworks, which can generate, capture, store and analyze data using machine learning algorithms. These algorithms are able to detect, prevent, and trace the spread of COVID-19, and provide better understanding of the virus in smart cities. Similarly, the study outlined case studies on the application of machine learning to help in the fight against COVID-19 in hospitals across the world. The framework proposed in the study is a comprehensive presentation on the major components needed for an integration of machine learning approach with other AI-based solutions. Finally, the machine learning framework presented in this study has the potential to help national healthcare systems in curtailing the COVID-19 pandemic in smart cities. In addition, the proposed framework is poised as a point for generating research interests which will yield outcomes capable of been integrated to form an improved framework.
Dynamic Mechanical Cue Facilitate Collective Responses of Crowded Cell Population
Authors: Che Bingchen , Zhao Wei , Jing Guangyin , Bai Jintao , Zhang Ce
Published: May 2020

Collective cell behavior is essential for tissue growth, development and function, e.g. heartbeat1, immune responses2and cerebral consciousness3. In recent years, studies on population cells uncover that collective behavior emerges in both inter- and intra-cellular activities, e.g. synchronized signal cascade4, and collective migration5. As the movement and shape transition of cells within the crowded environment of biological tissue can generate mechanical cues at the cell-cell interface, which may affect the signaling cascade6,7, we suspect that the inter- and intra-cellular collective behavior interplay with one another and cooperatively regulate life machinery. To verify our hypothesis, we study the collective responses of fibroblasts in a confluent cell monolayer (CCM). Our results demonstrate that cells in CCM show distinctive behavior as compared to the stand-alone (SA) cells, suggesting effect of inter-cellular interactions. Upon periodic TNF-α stimulation, collective behavior emerges simultaneously in NF-κB signaling cascade and nuclear shape fluctuations in CCM but not SA cells. We then model the inter-cellular interactions in CCM using a customized microfluidic device, and discover a feedback loop intrinsic to CCM, in which dynamic mechanical cues and mechano-signaling act as link connecting the inter- and intra-cellular collective activities. We found that mechano-signaling triggered by the dynamic mechanical cues causes collective nuclear shape fluctuation (NSF), which subsequently facilitates the collective behavior in NF-κB dynamics. Furthermore, our studies reveal that regardless of the input TNF-α periodicity, cellular responses of single fibroblasts are elevated when the dynamic mechanical cues synergize with the chemical inputs, and inhibited when there is phase-mismatching. We, therefore, postulate that besides the biological significance of mechano-signaling in regulating collective cell responses, the induction of dynamic mechanical cues to human body may be a potential therapeutic approach, allowing us to regulate the action of single cells to achieve optimal tissue performance.
Evidence for motility in 3.4 Gyr-old organic-walled microfossils ?
Authors: Delarue F. , Bernard S. , Sugitani K. , Robert F. , Tartèse R. , Albers S.-V. , Duhamel R. , Pont S. , Derenne S.
Published: May 2020

The oldest traces for planktonic lifestyle have been reported in ca. 3.4 billion years old silicified sediments from the Strelley Pool Formation in Western Australia. Observation of flange appendages suggests that Archean life motility was passive and driven by drifting of microorganisms in their surrounding environment. Until now, the oldest traces for active motility are ca. 2.1 billion years old. Whether or not active motility already existed during the Archean eon remains an open question. Here we report the discovery of new 3.4 billion years old tailed microfossils. These microfossils exhibit a lash-like appendage that likely provided them with movement capabilities. This suggests that these microfossils are the oldest remains of active motile life forms. With the ability to move in liquids and on organic and/or mineral surfaces, these microorganisms were capable of escaping from harsh environments and/or colonizing new ecological niches as early as 3.4 billion years ago. The existence of these deep-rooted Archean motile life forms offers a new picture of the Archean biodiversity, with unanticipated evolutionary innovative morphological complexities.
Prediction of the virus incubation period for COVID-19 and future outbreaks
Authors: Gussow Ayal B. , Auslander Noam , Wolf Yuri I. , Koonin Eugene V.
Published: May 2020

A crucial factor in mitigating respiratory viral outbreaks is early determination of the duration of the incubation period and, accordingly, the required quarantine time for potentially exposed individuals. Here, we explore different genomic features of RNA viruses that correlate with the incubation times and provide a predictive model that accurately estimates the upper limit incubation time for diverse viruses including SARS-CoV-2, and thus, could help control future outbreaks.
GWAS of serum ALT and AST reveals an association ofSLC30A10Thr95Ile with hypermanganesemia symptoms
Authors: Ward Lucas D. , Tu Ho-Chou , Quenneville Chelsea B. , Tsour Shira , Flynn-Carroll Alexander O. , Parker Margaret M. , Deaton Aimee M. , Haslett Patrick A. J. , Lotta Luca A. , Verweij Niek , Ferreira Manuel A. R. ,   Regeneron Genetics Center, Geisinger-Regeneron DiscovEHR Collaboration, Baras Aris , Hinkle Gregory , Nioi Paul
Published: May 2020

To investigate mechanisms of hepatocellular damage, we performed genome-wide association studies (GWAS) on alanine aminotransferase (ALT) and aspartate aminotransferase (AST) serum activities across 411,048 subjects from four ancestry groups in the UK Biobank, and found 100 loci associating with both enzymes. The rare missense variantSLC30A10Thr95Ile (rs188273166) associates with a larger elevation in ALT and AST than any other variant tested and this association also replicates in the DiscovEHR study. SLC30A10 excretes manganese from the liver to the bile duct, and rare homozygous loss of function causes the syndrome hypermanganesemia with dystonia-1 (HMNDYT1) which involves cirrhosis. Consistent with hematological symptoms of hypermanganesemia,SLC30A10Thr95Ile carriers have increased hematocrit and risk of iron deficiency anemia. Carriers also have increased risk of extrahepatic bile duct cancer. These associations suggest that genetic variation inSLC30A10adversely affects more individuals than patients with diagnosed HMNDYT1.
Rapid Tilt-Series Method for Cryo-Electron Tomography: Characterizing Stage Behavior During FISE Acquisition
Authors: Chreifi Georges , Chen Songye , Jensen Grant J.
Published: May 2020

We and others recently developed rapid tilt-series acquisition methods for cryo-electron tomography on a Titan Krios G3i equipped with a single axis holder and a K-series direct electron detector and showed that one of these, the fast-incremental single exposure (FISE) method, significantly accelerates tilt-series acquisition when compared to traditional methods while preserving the quality of the images. Here, we characterize the behavior of our single axis holder in detail during a FISE experiment to optimally balance data quality with speed. We explain our methodology in detail so others can characterize their own stages, and conclude with recommendations for projects with different resolution goals.
Selective role of the translin/trax RNase complex in hippocampal synaptic plasticity
Authors: Park Alan Jung , Shetty Mahesh Shivarama , Baraban Jay M. , Abel Ted
Published: May 2020

Activity-dependent local protein synthesis is critical for synapse-specific, persistent plasticity. Abnormalities in local protein synthesis have been implicated in psychiatric disorders. We have recently identified the translin/trax microRNA-degrading enzyme as a novel mediator of protein synthesis at activated synapses. Additionally, mice lacking translin/trax exhibit some of the behavioral abnormalities found in a mouse model of fragile X syndrome. Therefore, identifying signaling pathways interacting with translin/trax to support persistent synaptic plasticity is a translationally relevant goal. Here, as a first step to achieve this goal, we have assessed the requirement of translin/trax for multiple hippocampal synaptic plasticity paradigms that rely on distinct molecular mechanisms. We found that mice lacking translin/trax exhibited selective impairment in a form of persistent hippocampal plasticity, which requires postsynaptic PKA activity. In contrast, enduring forms of plasticity that are dependent on presynaptic PKA were unaffected. Furthermore, these mice did not display exaggerated metabotropic glutamate receptor-mediated long-term synaptic depression, a hallmark of the mouse model of fragile X syndrome. Taken together, these findings demonstrate that translin/trax mediates long-term synaptic plasticity that is dependent on postsynaptic PKA signaling.
The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment
Authors: Minich Jeremiah J , Power Cecilia , Melanson Michaela , Knight Rob , Webber Claire , Rough Kirsten , Bott Nathan J. , Nowak Barbara , Allen Eric E
Published: May 2020

Aquaculture is the fastest growing primary industry worldwide. Marine finfish culture in open ocean net pens, or pontoons, is one of the largest growth areas and is currently the only way to rear high value fish such as bluefin tuna. Ranching involves catching wild juveniles, stocking in floating net pens and fattening for four to eight months. Tuna experience several parasite-induced disease challenges in culture that can be mitigated by application of praziquantel (PZQ) as a therapeutic. In this study, we characterized the microbiome of ranched southern Bluefin Tuna,Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. Southern bluefin tuna gill, skin, and digesta microbiome communities are unique and potentially influenced by husbandry practices, location of pontoon growout pens, and treatment with the antiparasitic PZQ. There was no significant relationship between the fish mucosal microbiome and incidence or abundance of adult blood fluke in the heart or fluke egg density in the gill. An enhanced understanding of microbiome diversity and function in high-value farmed fish species such as bluefin tuna is needed to optimize fish health and improve aquaculture yield. Comparison of the bluefin tuna microbiome to other fish species, includingSeriola lalandi(yellowtail kingfish), a common farmed species from Australia, andScomber japonicus(Pacific mackerel), a wild caught Scombrid relative of tuna, showed the two Scombrids had more similar microbial communities compared to other families. The finding that mucosal microbial communities are more similar in phylogenetically related fish species exposes an opportunity to develop mackerel as a model for tuna microbiome and parasite research.
DNA from dried blood spots yields high quality sequences for exome analysis
Authors: Sunderam Uma , Adhikari Aashish N. , Kundu Kunal , Puck Jennifer M. , Currier Robert , Kwok Pui-Yan , Brenner Steven E. , Srinivasan Rajgopal
Published: May 2020

Background

DNA sequencing of archived dried blood spots (DBS) collected by newborn screening programs constitutes a potential health resource to study newborn disorders and understand genotype-phenotype relationships. However, its essential to verify that sequencing reads from DBS derived DNA are suitable for variant discovery.

Results

We explored 16 metrics to comprehensively assess the quality of sequencing reads from 180 DBS and 35 whole blood (WB) samples. These metrics were used to assess a) mapping of reads to the reference genome, b) degree of DNA damage, and c) variant calling. Reads from both sets mapped with similar efficiencies, had similar overall DNA damage rates, measured by the mismatch rate with the reference genome, and produced variant calls sets with similar Transition-Transversion ratios. While evaluating single nucleotide changes that may have arisen from DNA damage, we observed that the A>T and T>A changes were more frequent in DNA from DBS than from WB. However, this did not affect the accuracy of variant calling, with DBS samples yielding a comparable count of high quality SNVs and indels in samples with at least 50x coverage.

Conclusions

Overall, DBS DNA provided exome sequencing data of sufficient quality for clinical interpretation.
Reproducible and accessible analysis of transposon insertion data at scale
Authors: Larivière Delphine , Wickham Laura , Keiler Kenneth C. , Nekrutenko Anton
Published: May 2020

Significant progress has been made in advancing and standardizing tools for human genomic and biomedical research, yet the field of next generation sequencing (NGS) analysis for microorganisms (including multiple pathogens) remains fragmented, lacks accessible and reusable tools, is hindered by local computational resource limitations, and does not offer widely accepted standards. One of such “problem areas” is the analysis of Transposon Insertion Sequencing (TIS) data. TIS allows perturbing the entire genome of a microorganism by introducing random insertions of transposon-derived constructs. The impact of the insertions on the survival and growth provides precise information about genes affecting specific phenotypic characteristics. A wide array of tools has been developed to analyze TIS data and among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis. Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures such as the determination of the optimal tool parameters for the analysis and removal of contamination. Our work provides an assessment of the currently available tools for TIS data analysis and offers ready to use workflows that can be invoked by anyone in the world using our public Galaxy platform (https://usegalaxy.org). To lower the entry barriers we have also developed interactive tutorials explaining details of TIS data analysis procedures athttps://bit.ly/gxy-tis.

Importance

A wide array of tools has been developed to analyze TIS data and among the variety of options available, it is often difficult to identify which one can provide a reliable and reproducible analysis. Here we sought to understand the challenges and propose reliable practices for the analysis of TIS experiments. Using data from two recent TIS studies we have developed a series of workflows that include multiple tools for data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome. Particular attention was paid to quality control procedures such as the determination of the optimal tool parameters for the analysis and removal of contamination. Our work democratizes the TIS data analysis by providing open workflows supported by public computational infrastructure.
Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures
Authors: Vanderheiden Abigail , Ralfs Philipp , Chirkova Tatiana , Upadhyay Amit A. , Zimmerman Matthew G. , Bedoya Shamika , Aoued Hadj , Tharp Gregory M. , Pellegrini Kathryn L. , Lowen Anice C. , Menachery Vineet D. , Anderson Larry J. , Grakoui Arash , Bosinger Steven E. , Suthar Mehul S.
Published: May 2020

The newly emerged human coronavirus, SARS-CoV-2, has caused a pandemic of respiratory illness. The innate immune response is critical for protection against Coronaviruses. However, little is known about the interplay between the innate immune system and SARS-CoV-2. Here, we modeled SARS-CoV-2 infection using primary human airway epithelial (pHAE) cultures, which are maintained in an air-liquid interface. We found that SARS-CoV-2 infects and replicates in pHAE cultures and is directionally released on the apical, but not basolateral surface. Transcriptional profiling studies found that infected pHAE cultures had a molecular signature dominated by pro-inflammatory cytokines and chemokine induction, including IL-6, TNFα, CXCL8. We also identified NF-κB and ATF4 transcription factors as key drivers of this pro-inflammatory cytokine response. Surprisingly, we observed a complete lack of a type I or III IFN induction during SARS-CoV-2 infection. Pre-treatment or post-treatment with type I and III IFNs dramatically reduced virus replication in pHAE cultures and this corresponded with an upregulation of antiviral effector genes. Our findings demonstrate that SARS-CoV-2 induces a strong pro-inflammatory cytokine response yet blocks the production of type I and III IFNs. Further, SARS-CoV-2 is sensitive to the effects of type I and III IFNs, demonstrating their potential utility as therapeutic options to treat COVID-19 patients.

IMPORTANCE

The current pandemic of respiratory illness, COVID-19, is caused by a recently emerged coronavirus named SARS-CoV-2. This virus infects airway and lung cells causing fever, dry cough, and shortness of breath. Severe cases of COVID-19 can result in lung damage, low blood oxygen levels, and even death. As there are currently no vaccines or antivirals approved for use in humans, studies of the mechanisms of SARS-CoV-2 infection are urgently needed. SARS-CoV-2 infection of primary human airway epithelial cultures induces a strong pro-inflammatory cytokine response yet blocks the production of type I and III IFNs. Further, SARS-CoV-2 is sensitive to the effects of type I and III IFNs, demonstrating their potential utility as therapeutic options to treat COVID-19 patients.
Loss of PKCα increases arterial medial calcification in a uremic mouse model of chronic kidney disease
Authors: Borland Samantha J , Facchi Cecilia , Behnsen Julia , Adamson Antony , Humphreys Neil E , Withers Philip J , Sherratt Michael J , Francis Sheila E , Brennan Keith , Ashton Nick , Canfield Ann E
Published: May 2020

Arterial medial calcification is an independent risk factor for mortality in chronic kidney disease. We previously reported that knock-down of PKCα expression increases high phosphate-induced mineral deposition by vascular smooth muscle cellsin vitro. This new study tests the hypothesis that PKCα regulates uremia-induced medial calcificationin vivo. Female wild-type and PKCα−/−mice underwent a two-stage subtotal nephrectomy and were fed a high phosphate diet for 8 weeks. X-ray micro computed tomography demonstrated that uremia-induced medial calcification was increased in the abdominal aorta and aortic arch of PKCα−/−mice compared to wild-types. Blood urea nitrogen was also increased in PKCα−/−mice compared to wild-types; there was no correlation between blood urea nitrogen and calcification in PKCα−/−mice. Phosphorylated SMAD2 immunostaining was detected in calcified aortic arches from uremic PKCα−/−mice; the osteogenic marker Runx2 was also detected in these areas. No phosphorylated SMAD2 staining were detected in calcified arches from uremic wild-types. PKCα knock-down increased TGF-β1-induced SMAD2 phosphorylation in vascular smooth muscle cellsin vitro, whereas the PKCα activator prostratin decreased SMAD2 phosphorylation. In conclusion, loss of PKCα increases uremia-induced medial calcification. The PKCα/TGF-β signaling axis could therefore represent a new therapeutic target for arterial medial calcification in chronic kidney disease.
Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients
Authors: Wang Yanqun , Wang Daxi , Zhang Lu , Sun Wanying , Zhang Zhaoyong , Chen Weijun , Zhu Airu , Huang Yongbo , Xiao Fei , Yao Jinxiu , Gan Mian , Li Fang , luo Ling , Huang Xiaofang , Zhang Yanjun , Wong Sook-san , Cheng Xinyi , Ji Jingkai , Ou Zhihua , Xiao Minfeng , Li Min , Li Jiandong , Ren Peidi , Deng Ziqing , Zhong Huanzi , Yang Huanming , Wang Jian , Xu Xun , Song Tie , Mok Chris Ka Pun , Peiris Malik , Zhong Nanshan , Zhao Jingxian , Li Yimin , Li Junhua , Zhao Jincun
Published: May 2020

As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.
Algorithmic Assessment of Missense Mutation Severity in the Von-Hippel Lindau Protein
Authors: Fields Francisco R. , Suresh Niraja , Hiller Morgan , Freed Stefan D. , Haldar Kasturi , Lee Shaun W.
Published: May 2020

Von Hippel-Lindau disease (VHL) is an autosomal dominant rare disease that causes the formation of angiogenic tumors. When functional, pVHL acts as an E3 ubiquitin ligase that negatively regulates hypoxia inducible factor (HIF). Genetic mutations that perturb the structure of pVHL result in dysregulation of HIF, causing a wide array of tumor pathologies including retinal angioma, pheochromocytoma, central nervous system hemangioblastoma, and clear cell renal carcinoma. These VHL-related cancers occur throughout the lifetime of the patient, requiring frequent intervention procedures, such as surgery, to remove the tumors. Although VHL is classified as a rare disease (1 in 39,000 to 1 in 91,000 affected) there is a large heterogeneity in genetic mutations listed for observed pathologies. Understanding how these specific mutations correlate with the myriad of observed pathologies for VHL could provide clinicians insight into the potential severity and onset of disease. Using a set of 285 ClinVar mutations in VHL, we developed a multiparametric scoring algorithm to evaluate the overall clinical severity of missense mutations in pVHL. The mutations were assessed according to eight weighted parameters as a comprehensive evaluation of protein misfolding and malfunction. Higher mutation scores were strongly associated with pathogenicity. Our approach establishes a novelin silicomethod by which VHL-specific mutations can be assessed for their severity and effect on the biophysical functions of the VHL protein.