bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Yield Monocyte, Macrophage, and Dendritic Cell Differentiation from Induced Pluripotent Stem Cells
Authors: Armitage Lucas H. , Khosravi-Maharlooei Mohsen , Meacham Amy , Butfiloski Edward J. , Viola Ryan , Egli Dieter , Sykes Megan , Wallet Mark A. , Mathews Clayton E. 
Published: April 2021

SummaryDifferentiation of induced pluripotent stem cells (iPSC) into monocytes, monocyte-derived macrophages (MDM), and monocyte-derived dendritic cells (moDC) represents a powerful tool for studying human innate immunology and developing novel iPSC-derived immune therapies. Challenges include inefficiencies in iPSC-derived cell cultures, labor-intensive culture conditions, low purity of desired cell types, and feeder cell requirements. Here, a highly efficient method for differentiating monocytes, MDMs, and moDCs that overcomes these challenges is described. The process utilizes commercially-available materials to derive CD34+progenitor cells that are apically released from a hemogenic endothelium. Subsequently, the hemogenic endothelium gives rise to highly pure (>95%), CD34-CD14+monocytes in 19-23 days and yields 13.5-fold more monocytes by day 35 when compared to previous methods. These iPSC-monocytes are analogous to human blood-derived monocytes and readily differentiate into MDM and moDC. The efficient workflow and increase in monocyte output heightens feasibility for high throughput studies and enables clinical-scale iPSC-derived manufacturing processes.
How marine currents and environment shape plankton genomic differentiation: a mosaic view fromTaraOceans metagenomic data
Authors: Laso-Jadart Romuald , O’Malley Michael , Sykulski Adam M. , Ambroise Christophe , Madoui Mohammed-Amin 
Published: April 2021

AbstractPlankton seascape genomics show different trends from large-scale weak differentiation to micro-scale structures. Prior studies underlined the influence of environment and seascape on a few single species differentiation and adaptation. However, these works generally focused on few single species, sparse molecular markers, or local scales. Here, we investigate the genomic differentiation of plankton at macro-scale in a holistic approach usingTaraOceans metagenomic data together with a reference-free computational method to reconstruct theFST-based genomic differentiation of 113 marine planktonic species using metavariant species (MVS). These MVSs, modelling the species only by their polymorphism, include a wide range of taxonomic groups comprising notably 46 Maxillopoda/Copepoda, 24 Bacteria, 5 Dinoflagellates, 4 Haptophytes, 3 Cnidarians, 3 Mamiellales, 2 Ciliates, 1 Collodaria, 1 Echinoidea, 1 Pelagomonadaceae, 1 Cryptophyta and 1 Virus. The analyses showed that differentiation between populations was significantly lower within basins and higher in bacteria and unicellular eukaryotes compared to zooplantkon. By partitioning the variance of pairwise-FSTmatrices, we found that the main drivers of genomic differentiation were Lagrangian travel time, salinity and temperature. Furthermore, we classified MVSs into parameter-driven groups and showed that taxonomy poorly determines which environmental factor drives genomic differentiation. This holistic approach of plankton genomic differentiation for large geographic scales, a wide range of taxa and different oceanic basins, offers a systematic framework to analyse population genomics of non-model and undocumented marine organisms.
ERK3-MK5 signaling regulates myogenic differentiation and muscle regeneration by promoting FoxO3 degradation
Authors: Soulez Mathilde , Tanguay Pierre-Luc , Dô Florence , Crist Colin , Dort Junio , Kotlyarov Alexey , Gaestel Matthias , Dumont Nicolas A. , Meloche Sylvain 
Published: April 2021

ABSTRACTThe physiological functions and downstream effectors of the atypical mitogen-activated protein kinase ERK3 remain to be characterized. We recently reported that mice expressing catalytically-inactive ERK3 (Mapk6KD/KD) exhibit a reduced post-natal growth rate as compared to control mice. Here, we show that genetic inactivation of ERK3 impairs post-natal skeletal muscle growth and adult muscle regeneration after injury. Loss of MK5 phenocopies the muscle phenotypes ofMapk6KD/KDmice. At the cellular level, genetic or pharmacological inactivation of ERK3 or MK5 induces precocious differentiation of C2C12 or primary myoblasts, concomitant with MyoD activation. Reciprocally, ectopic expression of activated MK5 inhibits myogenic differentiation. Mechanistically, we show that MK5 directly phosphorylates FoxO3, promoting its degradation and reducing its association with MyoD. Depletion of FoxO3 rescues in part the premature differentiation of C2C12 myoblasts observed upon inactivation of ERK3 or MK5. Our findings reveal that ERK3 and its substrate MK5 act in a linear signaling pathway to control post-natal myogenic differentiation.
TheTaxus genome provides insights into paclitaxel biosynthesis
Authors: Xiong Xingyao , Gou Junbo , Liao Qinggang , Li Yanlin , Zhou Qian , Bi Guiqi , Li Chong , Du Ran , Wang Xiaotong , Sun Tianshu , Guo Lvjun , Liang Haifei , Lu Pengjun , Wu Yaoyao , Zhang Zhonghua , Ro Dae-Kyun , Shang Yi , Huang Sanwen , Yan Jianbin 
Published: April 2021

AbstractThe ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome ofTaxus chinensisvar.maireiwith a total length of 10.23 Gb. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping ofCYP725As(cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster in the taxadiene biosynthesis, which was mainly formed by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.One Sentence SummaryA chromosome-level genome assembly ofTaxus chinensisvar.maireiuncovers its unique genome evolution process and genetic architectures for the paclitaxel biosynthesis pathway.
A four-point measurement probe for brain tissue conductivity and permittivity characterization
Authors: Poßner Lucas , Seebeck Lydia , Laukner Matthias , Wilhelmy Florian , Lindner Dirk , Pliquett Uwe , Petkovic Bojana , Ziolkowski Marek , Knösche Thomas R. , Weise Konstantin 
Published: April 2021

AbstractWe present a measurement probe consisting of four platinum electrodes fused into soda-lime glass. The probe is based on a four-terminal sensing technique that uses separate pairs of current-carrying and voltage-sensing electrodes and performs more accurate measurements than the simpler and more usual two-terminal sensing technique. The electrodes are aranged within an area of 1 mm2allowing for local characterization of different brain tissues. The operation of the probe is demonstrated in situ on post mortem porcine brain tissue by measuring the impedance spectra of grey and white matter in a frequency range of 1 kHz <f< 1 MHz. The conductivity and relative permittivity are derived from the impedance spectra using the geometry factor of the probe. The geometry factor is obtained experimentally by measuring the impedances of an electrolytical dilution series with known conductivities. The obtained conductivity of grey matter is in the order of 0.11 S/m and of white matter is in the order of 0.07 S/m over the acquired frequency range.
Librator, a platform for optimized sequence editing, design, and expression of influenza virus proteins
Authors: Li Lei , Stovicek Olivia , Guthmiller Jenna J. , Changrob Siriruk , Fu Yanbin , Dugan Haley L. , Stamper Christopher T. , Zheng Nai-Ying , Huang Min , Wilson Patrick C. 
Published: April 2021

AbstractArtificial mutagenesis and chimeric/mosaic protein engineering have laid the foundation for antigenic characterization1and universal vaccine design2–4for influenza viruses. However, many methods used for influenza research and vaccine development require sequence editing and protein expression, limiting their applicability and the progress of related research to specialists. Rapid tools allowing even novice influenza researchers to properly analyze and visualize influenza protein sequences with accurate nomenclature are needed to expand the research field. To address this need, we developed Librator, a system for analyzing and designing protein sequences of influenza virus Hemagglutinin (HA) and Neuraminidase (NA). With Librator’s graphical user interface (GUI) and built-in sequence editing functions, biologists can easily analyze influenza sequences and phylogenies, automatically port sequences to visualize structures, then readily mutate target residues and design sequences for antigen probes and chimeric/mosaic proteins efficiently and accurately. This system provides optimized fragment design for Gibson Assembly5of HA and NA expression constructs based on peptide conservation of all historical HA and NA sequences, ensuring fragments are reusable and compatible, allowing for significant reagent savings. Use of Librator will significantly facilitate influenza research and vaccine antigen design.
Patterns of piRNA regulation inDrosophilarevealed through transposable element clade inference
Authors: Said Iskander , McGurk Michael P. , Clark Andrew G. , Barbash Daniel A. 
Published: April 2021

AbstractTransposable elements (TEs) are self-replicating “genetic parasites” ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their ancestral forms. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85Drosophila melanogastergenomes and found that the genetic variation of several TE families shows significant population structure that arises from the population- specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a pattern whereby new TE variants arise by mutation and then increase in copy number, followed by the host producing antisense piRNAs that may be used to silence these emerging variants.
Simple degradable cyclodextrin polyester with chelator-based crosslinker for stent-based drug delivery
Authors: Young Kathleen , Lord Audrey E. , Burkhart Grace E. , Kozawa Susan K. , Mu Nathan , von Recum Horst A. 
Published: April 2021

ABSTRACTCyclodextrins are a class of molecules which inclusion complexes with small hydrophobic drugs, and has historically been used to improve solubility and bioavailability of labile drugs in pharmaceutical applications. More recently, polymerized cyclodextrin has been applied in various applications as implantable drug delivery depots and as medical device coatings (e.g. polymeric hernia meshes) due to their ability to sustain and control drug delivery as well as prevent biofouling. Cyclodextrin polymers as coatings for metal medical devices, like screws or stents, is less explored; due to the high mechanical property mismatch between polymers and metals, a polymer coating is liable to delaminate easily, especially during device deformation. Novel methods for facilitating attachment to metal substrates have been explored, but coating longevity is still an issue, and these methods typically require the use of multiple reagents and complex methods. We report here the development and characterization of a cyclodextrin polymer with a chelator-based crosslinker with respect to appearance, chemistry, drug release profiles, erosion, pH-dependence. We found that increasing the crosslinking ratio (crosslinker:cyclodextrin) slowed down degradation and decreased drug loading as well. Drug release of the anti-restenotic drug sirolimus proceeded for over 4 weeks. The ability of the polymer to stably coat metal stents was verified, and the coating procedure is a simple, single step protocol.
Data driven phenotyping and COVID-19 case definitions: a pattern recognition approach
Authors: Vavougios George D. , Konstantatos Christoforos , Sinigalias Pavlos-Christoforos , Zarogiannis Sotirios G. , Kolomvatsos Konstantinos , Stamoulis George , Gourgoulianis Konstantinos I. 
Published: May 2021

AbstractIntroductionCOVID-19 has pathological pulmonary as well as several extrapulmonary manifestations and thus many different symptoms may arise in patients. The aim of our study was to determine COVID-19 syndromic phenotypes in a data driven manner using survey results extracted from Carnegie Mellon University’s Delphi Group.MethodsMonthly survey results (>1 million responders per month; 320.326 responders with positive COVID-19 test and disease duration <30 days were included in this study) were used sequentially in identifying and validating COVID-19 syndromic phenotypes. Logistic Regression Weighted Multiple Correspondence Analysis (LRW-MCA) was used as a preprocessing procedure, in order to weight and transform symptoms recorded by the survey to eigenspace coordinates (i.e. object scores per case / dimension), with a goal of capturing a total variance of > 75%. These scores along with symptom duration were subsequently used by the Two Step Clustering algorithm to produce symptom clusters. Post-hoc logistic regression models adjusting for age, gender and comorbidities and confirmatory linear principal components analyses were used to further explore the data. The model created from 66.165 included responders in August, was subsequently validated in data from March – December 2020.ResultsFive validated COVID-19 syndromes were identified in August: 1. Afebrile (0%), Non-Coughing (0%), Oligosymptomatic (ANCOS) 2. Febrile (100%) Multisymptomatic (FMS) 3. Afebrile (0%) Coughing (100%) Oligosymptomatic (ACOS), 4. Oligosymptomatic with additional self-described symptoms (100%; OSDS) and 5. Olfaction / Gustatory Impairment Predominant (100%; OGIP).DiscussionWe present 5 distinct symptom phenotypes within the COVID-19 spectrum that remain stable within 9 – 12 days of first symptom onset. The typical febrile respiratory phenotype is presented as a minority among identified syndromes, a finding that may impact both epidemiological surveillance norms and transmission dynamics.
Age-dependent association between SARS-CoV-2 cases reported by passive surveillance and viral load in wastewater
Authors: Omori Ryosuke , Miura Fuminari , Kitajima Masaaki 
Published: May 2021

AbstractThe true number of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is difficult to estimate using a case-reporting system (i.e., passive surveillance) alone because of asymptomatic infection. While wastewater-based epidemiology has been implemented as an alternative/additional monitoring tool to reduce reporting bias, the relationship between passive and wastewater surveillance data has yet to be explicitly examined. Since there is strong age dependency in the symptomatic ratio of SARS-CoV-2 infections, this study aimed to estimate i) an age-dependent association between the number of reported cases and the viral load in wastewater and ii) the time lag between those time series. The viral load in wastewater was modeled as a combination of contributions from different age groups’ virus shedding, incorporating the delay, and fitted with daily case count data collected from the Massachusetts Department of Public Health and SARS-CoV-2 RNA concentrations in wastewater collected by the Massachusetts Water Resources Authority. The estimated lag between the time series of viral loads in wastewater and of reported cases was 10.8 days (95% confidence interval =[10.2, 11.6]) for wastewater treatment plant’s northern area and 8.8 days [8.4, 9.1] for southern area. The estimated contribution rate of a reported case to the viral load in wastewater in the 0–19 yr age group was 0.38 [0.35, 0.41] for northern area and 0.40 [0.37, 0.43] for southern area, that in the 80+ yr age group was 0.67 [0.65, 0.69] for northern area and 0.51 [0.49, 0.52] for southern area. The estimated lag between those time series suggested the predictability of reported cases ten days later using viral loads in wastewater. The contribution of a reported case in passive surveillance to the viral load in wastewater differed by age, suggesting a large variation in viral shedding kinetics among age groups.
N440K variant of SARS-CoV-2 has Higher Infectious Fitness
Authors: Tandel Dixit , Gupta Divya , Sah Vishal , Harinivas Harshan Krishnan 
Published: May 2021

SUMMARYSeveral variants of SARS-CoV-2 have been emerging across the globe, continuing to threaten the efforts to end COVID-19 pandemic. Recent data indicate the prevalence of variants with N440K Spike substitution in several parts of India, which is under the second wave of the pandemic. Here, we first analyze the prevalence of N440K variants within the sequences submitted from India and identify a rising trend of its spread across various clusters. We then compare the replicative fitness and infectivity of a prototype of this variant with two other previously prevalent strains. The N440K variant produced ten times higher infectious viral titers than a prevalent A2a strain, and over 1000 folds higher titers than a much less prevalent A3i strain prototype in Caco2 cells. Similar results were detected in Calu-3 cells as well, confirming the increased potency of the N440K variant. Interestingly, A3i strain showed the highest viral RNA levels, but the lowest infectious titers in the culture supernatants, indicating the absence of correlation between the RNA content and the infectivity of the sample. N440K mutation has been reported in several viral sequences across India and based on our results, we predict that the higher infectious titers achieved by N440K variant could possibly lead to its higher rate of transmission. Availability of more sequencing data in the immediate future would help understand the potential spread of this variant in more detail.
Induced neural progenitor cells and iPS-neurons from major depressive disorder patients show altered bioenergetics and electrophysiological properties
Authors: Triebelhorn Julian , Cardon Iseline , Kuffner Kerstin , Bader Stefanie , Jahner Tatjana , Meindl Katrin , Rothhammer-Hampl Tanja , Riemenschneider Markus J. , Drexler Konstantin , Berneburg Mark , Nothdurfter Caroline , Manook André , Brochhausen Christoph , Baghai Thomas C. , Hilbert Sven , Rupprecht Rainer , Milenkovic Vladimir M. , Wetzel Christian H. 
Published: April 2021

ABSTRACTThe molecular pathomechanisms of major depressive disorder (MDD) are still not completely understood. Here, we follow the hypothesis, that mitochondria dysfunction which is inevitably associated with bioenergetic disbalance is a risk factor that contributes to the susceptibility of an individual to develop MDD. Thus, we investigated molecular mechanisms related to mitochondrial function in induced neuronal progenitor cells (NPCs) which were reprogrammed from fibroblasts of eight MDD patients and eight non-depressed controls. We found significantly lower maximal respiration rates, altered cytosolic basal calcium levels, and smaller soma size in NPCs derived from MDD patients. These findings are partially consistent with our earlier observations in MDD patient-derived fibroblasts. Furthermore, we differentiated MDD and control NPCs into iPS-neurons and analysed their passive biophysical and active electrophysiological properties to investigate whether neuronal function can be related to altered mitochondrial activity and bioenergetics. Interestingly, MDD patient-derived iPS-neurons showed significantly lower membrane capacitance, a less hyperpolarized membrane potential, increased Na+current density and increased spontaneous electrical activity. Our findings indicate that functional differences evident in fibroblasts derived from MDD patients are partially present after reprogramming to induced-NPCs, might relate to altered function of iPS-neurons and thus might be associated with the aetiology of major depressive disorder.
Low-bias ncRNA Libraries using Ordered Two-Template Relay: Serial Template Jumping by a Modified Retroelement Reverse Transcriptase
Authors: Upton Heather E. , Ferguson Lucas , Temoche-Diaz Morayma M. , Liu Xiaoman , Pimentel Sydney C. , Ingolia Nicholas T. , Schekman Randy , Collins Kathleen 
Published: May 2021

AbstractNon-long terminal repeat (non-LTR) and group II intron retroelements encode reverse transcriptases (RTs) that copy the retroelement transcript directly into host cell DNA, often at specific target sites. Biochemical characterization of these enzymes has been limited by recombinant expression and purification challenges, hampering understanding of their transposition mechanism and their exploitation for research and biotechnology. Properties of retroelement RTs substantiate their application for end-to-end RNA sequence capture. To investigate this utility, we first compared a non-LTR RT fromBombyx moriand a group II intron RT fromEubacterium rectale. Only the non-LTR RT showed processive template jumping, producing one cDNA from discontinuous templates each copied end-to-end. We also discovered an unexpected terminal deoxynucleotidyl transferase activity of the RTs that adds nucleotide(s) of choice to 3’ ends of single-stranded RNA or DNA. Combining these two types of activity with additional insights about non-templated nucleotide additions to duplexed cDNA product, we developed a streamlined protocol for linking Next Generation Sequencing (NGS) adaptors to both cDNA ends in a single RT reaction. When benchmarked using a reference pool of microRNAs (miRNAs), library production using modified non-LTR retroelment RT for Ordered Two-Template Relay (OTTR) outperformed all commercially available kits and rivaled the low bias of technically demanding home-brew protocols. We applied OTTR to inventory RNAs purified from extracellular vesicles (EVs), identifying miRNAs as well as myriad other non-coding (nc) RNAs and ncRNA fragments. Our results establish the utility of OTTR for automation-friendly, low-bias, end-to-end RNA sequence inventories of complex ncRNA samples.SignificanceRetrotransposons are non-infectious mobile genetic elements that proliferate in host genomes via an RNA intermediate that is copied into DNA by a reverse transcriptase (RT) enzyme. RTs are important for biotechnological applications involving information capture from RNA, since RNA is first converted into complementary DNA for detection or sequencing. Here, we biochemically characterize RTs from two retroelements and uncover several activities that allowed us to design a streamlined, efficient workflow for determining the inventory of RNA sequences in processed RNA pools. The unique properties of non-retroviral RT activities obviate many technical issues associated with current methods of RNA sequence analysis, with wide applications in research, biotechnology, and diagnostics.