bluuebunny/crossref_metadata_2025 huggingface dataset:
A Recharge Oscillator Model for Interannual Variability in Venus’ Clouds
Authors: Kopparla Pushkar , Seshadri Ashwin , Imamura Takeshi , Lee Yeon Joo
Published: October 2020

Sulfur dioxide is a radiatively and chemically important trace gas in the atmosphere of Venus and its abundance at the cloud tops has been observed to vary on interannual to decadal timescales. This variability is thought to come from changes in the strength of convection which transports sulfur dioxide to the cloud tops, although the dynamics behind such convective variability are unknown. Here, we propose a new conceptual model for convective variability that links the radiative effects of water abundance at the cloud‐base to convective strength within the clouds, which in turn affects water transport within the cloud. The model consists of two coupled equations which are identified as a recharge‐discharge oscillator. The solutions of the coupled equations are finite amplitude sustained oscillations in convective strength and cloud‐base water abundance on 3–9 years timescales. The characteristic oscillation timescale is given by the geometric mean of the radiative cooling time and the eddy mixing time near the base of the convective clouds.
Riverine Dissolved Organic Carbon and Freshwater Export in the Eastern Gulf of Alaska
Authors: Edwards Rick T. , D'Amore David V. , Biles Frances E. , Fellman Jason B. , Hood Eran W. , Trubilowicz Joel W. , Floyd William C.
Published: October 2020

The coastal zone of southeast Alaska contains thousands of streams and rivers that drain one of the wettest, carbon‐rich, and most topographically varied regions in North America. Watersheds draining temperate rainforests, peatlands, glaciers, and three large rivers that flow from the drier interior of the Yukon Territory and British Columbia discharge water and dissolved organic carbon (DOC) into southeast Alaskan coastal waters. This area, which we have designated the southeast Alaska drainage basin (SEAKDB), discharges about twice as much water as the Columbia or Yukon Rivers. An understanding of the timing, location, and source of water and DOC guides research to better understand the influence of terrestrial outputs on the adjacent marine systems. Additionally, a spatially extensive understanding of riverine DOC flux will improve our understanding of lateral losses related to terrestrial carbon cycling. We estimate 1.17 Tg C yr−1 of DOC enters the adjacent marine system along with 430 km2 of freshwater that influences estuary, shelf, and Gulf of Alaska hydrology. We estimate that 23% to 66% of the DOC entering coastal waters is bioavailable and may influence metabolism and productivity within the marine system. The combination of the large and spatially distributed water and DOC input, long and complex shoreline, large enclosed estuarine volume, and bounded nearshore coastal currents suggests that the physiographic structure of southeast Alaska may have a significant impact on the metabolism of riverine DOC in coastal marine ecosystems.
Sempervirine inhibits RNA polymerase I transcription independently from p53 in tumor cells
Authors: Caggiano Cinzia , Guida Eugenia , Todaro Federica , Bielli Pamela , Mori Mattia , Ghirga Francesca , Quaglio Deborah , Botta Bruno , Moretti Fabiola , Grimaldi Paola , Rossi Pellegrino , Jannini Emmanuele A. , Barchi Marco , Dolci Susanna
Published: October 2020

In the search of small molecules that can target MDM2/p53 pathway in testicular germ cell tumors (TGCTs), we identified sempervirine (2,3,4,13-tetrahydro-1H-benz[g]indolo[2,3-a]quinolizin-6-ium), an alkaloid of Gelsemium sempervirens, that has been previously proposed as an inhibitor of MDM2 that targets p53-wildtype (wt) tumor cells. We found that sempervirine not only affects cell growth of p53-wt cancer cells, but it is also active in p53-mutated and p53-null cells by triggering p53-dependent and independent pathways without affecting non-transformed cells. To understand which mechanism/s could be activated both in p53-wt and -null cells, we found that sempervirine induced nucleolar remodeling and nucleolar stress by reducing protein stability of RPA194, the catalytic subunit of RNA polymerase I, that led to rRNA synthesis inhibition and to MDM2 block. As shown for other cancer cell models, MDM2 inhibition by nucleolar stress downregulated E2F1 protein levels both in p53-wt and p53-null TGCT cells with the concomitant upregulation of unphosphorylated pRb. Finally, we show that sempervirine is able to enter the nucleus and accumulates within the nucleolus where it binds rRNA without causing DNA damage. Our results identify semperivirine as a novel rRNA synthesis inhibitor and indicate this drug as a non-genotoxic anticancer small molecule.
The caspase-3/GSDME signal pathway as a switch between apoptosis and pyroptosis in cancer
Authors: Jiang Mingxia , Qi Ling , Li Lisha , Li Yanjing
Published: October 2020

Apoptosis has long been recognized as a mechanism that kills the cancer cells by cytotoxic drugs. In recent years, studies have proved that pyroptosis can also shrink tumors and inhibit cells proliferation. Both apoptosis and pyroptosis are caspase-dependent programmed cell death pathways. Cysteinyl aspartate specific proteinase-3 (Caspase-3) is a common key protein in the apoptosis and pyroptosis pathways, and when activated, the expression level of tumor suppressor gene Gasdermin E (GSDME) determines the mechanism of tumor cell death. When GSDME is highly expressed, the active caspase-3 cuts it and releases the N-terminal domain to punch holes in the cell membrane, resulting in cell swelling, rupture, and death. When the expression of GSDME is low, it will lead to the classical mechanism of tumor cell death, which is apoptosis. More interestingly, researchers have found that GSDME can also be located upstream of caspase-3, connecting extrinsic, and intrinsic apoptotic pathways. Then, promoting caspase-3 activation, and forming a self-amplifying feed-forward loop. GSDME-mediated pyroptosis is correlated with the side effects of chemotherapy and anti-tumor immunity. This article mainly reviews the caspase-3/GSDME signal pathway as a switch between apoptosis and pyroptosis in cancer, to provide new strategies and targets for cancer treatment.
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells
Authors: Tarbier Marcel , Mackowiak Sebastian D. , Frade João , Catuara-Solarz Silvina , Biryukova Inna , Gelali Eleni , Menéndez Diego Bárcena , Zapata Luis , Ossowski Stephan , Bienko Magda , Gallant Caroline J. , Friedländer Marc R.
Published: October 2020

Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells.
ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs
Authors: Lee Ivan T. , Nakayama Tsuguhisa , Wu Chien-Ting , Goltsev Yury , Jiang Sizun , Gall Phillip A. , Liao Chun-Kang , Shih Liang-Chun , Schürch Christian M. , McIlwain David R. , Chu Pauline , Borchard Nicole A. , Zarabanda David , Dholakia Sachi S. , Yang Angela , Kim Dayoung , Chen Han , Kanie Tomoharu , Lin Chia-Der , Tsai Ming-Hsui , Phillips Katie M. , Kim Raymond , Overdevest Jonathan B. , Tyler Matthew A. , Yan Carol H. , Lin Chih-Feng , Lin Yi-Tsen , Bau Da-Tian , Tsay Gregory J. , Patel Zara M. , Tsou Yung-An , Tzankov Alexandar , Matter Matthias S. , Tai Chih-Jaan , Yeh Te-Huei , Hwang Peter H. , Nolan Garry P. , Nayak Jayakar V. , Jackson Peter K.
Published: October 2020

The coronavirus SARS-CoV-2 is the causative agent of the ongoing severe acute respiratory disease pandemic COVID-19. Tissue and cellular tropism is one key to understanding the pathogenesis of SARS-CoV-2. We investigate the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of human donors using a diverse panel of banked tissues. Here, we report our discovery that the ACE2 receptor protein robustly localizes within the motile cilia of airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during host respiratory transmission. We further determine whether ciliary ACE2 expression in the upper airway is influenced by patient demographics, clinical characteristics, comorbidities, or medication use, and show the first mechanistic evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) does not increase susceptibility to SARS-CoV-2 infection through enhancing the expression of ciliary ACE2 receptor. These findings are crucial to our understanding of the transmission of SARS-CoV-2 for prevention and control of this virulent pathogen.
The misuse of colour in science communication
Authors: Crameri Fabio , Shephard Grace E. , Heron Philip J.
Published: October 2020

The accurate representation of data is essential in science communication. However, colour maps that visually distort data through uneven colour gradients or are unreadable to those with colour-vision deficiency remain prevalent in science. These include, but are not limited to, rainbow-like and red–green colour maps. Here, we present a simple guide for the scientific use of colour. We show how scientifically derived colour maps report true data variations, reduce complexity, and are accessible for people with colour-vision deficiencies. We highlight ways for the scientific community to identify and prevent the misuse of colour in science, and call for a proactive step away from colour misuse among the community, publishers, and the press.
Efficient separation of xylene isomers by a guest-responsive metal–organic framework with rotational anionic sites
Authors: Cui Xili , Niu Zheng , Shan Chuan , Yang Lifeng , Hu Jianbo , Wang Qingju , Lan Pui Ching , Li Yijian , Wojtas Lukasz , Ma Shengqian , Xing Huabin
Published: October 2020

The separation of xylene isomers (para-, meta-, orth-) remains a great challenge in the petrochemical industry due to their similar molecular structure and physical properties. Porous materials with sensitive nanospace and selective binding sites for discriminating the subtle structural difference of isomers are urgently needed. Here, we demonstrate the adaptively molecular discrimination of xylene isomers by employing a NbOF52−-pillared metal–organic framework (NbOFFIVE-bpy-Ni, also referred to as ZU-61) with rotational anionic sites. Single crystal X-ray diffraction studies indicate that ZU-61 with guest-responsive nanospace/sites can adapt the shape of specific isomers through geometric deformation and/or the rotation of fluorine atoms in anionic sites, thereby enabling ZU-61 to effectively differentiate xylene isomers through multiple C–H···F interactions. ZU-61 exhibited both high meta-xylene uptake capacity (3.4 mmol g−1) and meta-xylene/para-xylene separation selectivity (2.9, obtained from breakthrough curves), as well as a favorable separation sequence as confirmed by breakthrough experiments: para-xylene elute first with high-purity (≥99.9%), then meta-xylene, and orth-xylene. Such a remarkable performance of ZU-61 can be attributed to the type anionic binding sites together with its guest-response properties.
Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants
Authors: Weinmann Jonas , Weis Sabrina , Sippel Josefine , Tulalamba Warut , Remes Anca , El Andari Jihad , Herrmann Anne-Kathrin , Pham Quang H. , Borowski Christopher , Hille Susanne , Schönberger Tanja , Frey Norbert , Lenter Martin , VandenDriessche Thierry , Müller Oliver J. , Chuah Marinee K. , Lamla Thorsten , Grimm Dirk
Published: October 2020

Adeno-associated virus (AAV) forms the basis for several commercial gene therapy products and for countless gene transfer vectors derived from natural or synthetic viral isolates that are under intense preclinical evaluation. Here, we report a versatile pipeline that enables the direct side-by-side comparison of pre-selected AAV capsids in high-throughput and in the same animal, by combining DNA/RNA barcoding with multiplexed next-generation sequencing. For validation, we create three independent libraries comprising 183 different AAV variants including widely used benchmarks and screened them in all major tissues in adult mice. Thereby, we discover a peptide-displaying AAV9 mutant called AAVMYO that exhibits superior efficiency and specificity in the musculature including skeletal muscle, heart and diaphragm following peripheral delivery, and that holds great potential for muscle gene therapy. Our comprehensive methodology is compatible with any capsids, targets and species, and will thus facilitate and accelerate the stratification of optimal AAV vectors for human gene therapy.
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states
Authors: Lin Ziguang , Jin Suoqin , Chen Jefferson , Li Zhuorui , Lin Zhongqi , Tang Li , Nie Qing , Andersen Bogi
Published: October 2020

The interfollicular epidermis (IFE) forms a water-tight barrier that is often disrupted in inflammatory skin diseases. During homeostasis, the IFE is replenished by stem cells in the basal layer that differentiate as they migrate toward the skin surface. Conventionally, IFE differentiation is thought to be stepwise as reflected in sharp boundaries between its basal, spinous, granular and cornified layers. The transcription factor GRHL3 regulates IFE differentiation by transcriptionally activating terminal differentiation genes. Here we use single cell RNA-seq to show that murine IFE differentiation is best described as a single step gradualistic process with a large number of transition cells between the basal and spinous layer. RNA-velocity analysis identifies a commitment point that separates the plastic basal and transition cell state from unidirectionally differentiating cells. We also show that in addition to promoting IFE terminal differentiation, GRHL3 is essential for suppressing epidermal stem cell expansion and the emergence of an abnormal stem cell state by suppressing Wnt signaling in stem cells.
Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells
Authors: Moroney Justin B. , Vasudev Anusha , Pertsemlidis Alexander , Zan Hong , Casali Paolo
Published: October 2020

Memory B cells (MBCs) are long-lived and produce high-affinity, generally, class-switched antibodies. Here, we use a multiparameter approach involving CD27 to segregate naïve B cells (NBC), IgD+ unswitched (unsw)MBCs and IgG+ or IgA+ class-switched (sw)MBCs from humans of different age, sex and race. Conserved antibody variable gene expression indicates that MBCs emerge through unbiased selection from NBCs. Integrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements uncover a core mRNA-ncRNA transcriptional signature shared by IgG+ and IgA+ swMBCs and distinct from NBCs, while unswMBCs display a transitional transcriptome. Some swMBC transcriptional signature loci are accessible but not expressed in NBCs. Profiling miRNAs reveals downregulated MIR181, and concomitantly upregulated MIR181 target genes such as RASSF6, TOX, TRERF1, TRPV3 and RORα, in swMBCs. Finally, lncRNAs differentially expressed in swMBCs cluster proximal to the IgH chain locus on chromosome 14. Our findings thus provide new insights into MBC transcriptional programs and epigenetic regulation, opening new investigative avenues on these critical cell elements in human health and disease.
Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production
Authors: Li Tianpei , Jiang Qiuyao , Huang Jiafeng , Aitchison Catherine M. , Huang Fang , Yang Mengru , Dykes Gregory F. , He Hai-Lun , Wang Qiang , Sprick Reiner Sebastian , Cooper Andrew I. , Liu Lu-Ning
Published: October 2020

Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.
Auditory information enhances post-sensory visual evidence during rapid multisensory decision-making
Authors: Franzen Léon , Delis Ioannis , De Sousa Gabriela , Kayser Christoph , Philiastides Marios G.
Published: October 2020

Despite recent progress in understanding multisensory decision-making, a conclusive mechanistic account of how the brain translates the relevant evidence into a decision is lacking. Specifically, it remains unclear whether perceptual improvements during rapid multisensory decisions are best explained by sensory (i.e., ‘Early’) processing benefits or post-sensory (i.e., ‘Late’) changes in decision dynamics. Here, we employ a well-established visual object categorisation task in which early sensory and post-sensory decision evidence can be dissociated using multivariate pattern analysis of the electroencephalogram (EEG). We capitalize on these distinct neural components to identify when and how complementary auditory information influences the encoding of decision-relevant visual evidence in a multisensory context. We show that it is primarily the post-sensory, rather than the early sensory, EEG component amplitudes that are being amplified during rapid audiovisual decision-making. Using a neurally informed drift diffusion model we demonstrate that a multisensory behavioral improvement in accuracy arises from an enhanced quality of the relevant decision evidence, as captured by the post-sensory EEG component, consistent with the emergence of multisensory evidence in higher-order brain areas.
Natural variations of SLG1 confer high-temperature tolerance in indica rice
Authors: Xu Yufang , Zhang Li , Ou Shujun , Wang Ruci , Wang Yueming , Chu Chengcai , Yao Shanguo
Published: October 2020

With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification ofSLG1(Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice.SLG1plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction ofSLG1results in plants with thermosensitive phenotype, while overexpression ofSLG1enhances the tolerance of plants to high temperature.SLG1is differentiated between the two Asian cultivated rice subspecies,indicaandjaponica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance ofindicarice varieties. Our results demonstrate that the allelic differentiation ofSLG1confersindicarice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe.
Intestinal release of biofilm-like microcolonies encased in calcium-pectinate beads increases probiotic properties of Lacticaseibacillus paracasei
Authors: Heumann Arnaud , Assifaoui Ali , Da Silva Barreira David , Thomas Charles , Briandet Romain , Laurent Julie , Beney Laurent , Lapaquette Pierre , Guzzo Jean , Rieu Aurélie
Published: October 2020

In this study, we show that calcium pectinate beads (CPB) allow the formation of 20 µm spherical microcolonies of the probiotic bacteria Lacticaseibacillus paracasei (formerly designated as Lactobacillus paracasei) ATCC334 with a high cell density, reaching more than 10 log (CFU/g). The bacteria within these microcolonies are well structured and adhere to a three-dimensional network made of calcium-pectinate through the synthesis of extracellular polymeric substances (EPS) and thus display a biofilm-like phenotype, an attractive property for their use as probiotics. During bacterial development in the CPB, a coalescence phenomenon arises between neighboring microcolonies accompanied by their peripheral spatialization within the bead. Moreover, the cells of L. paracasei ATCC334 encased in these pectinate beads exhibit increased resistance to acidic stress (pH 1.5), osmotic stress (4.5 M NaCl), the freeze-drying process and combined stresses, simulating the harsh conditions encountered in the gastrointestinal (GI) tract. In vivo, the oral administration of CPB-formulated L. paracasei ATCC334 in mice demonstrated that biofilm-like microcolonies are successfully released from the CPB matrix in the colonic environment. In addition, these CPB-formulated probiotic bacteria display the ability to reduce the severity of a DSS-induced colitis mouse model, with a decrease in colonic mucosal injuries, less inflammation, and reduced weight loss compared to DSS control mice. To conclude, this work paves the way for a new form of probiotic administration in the form of biofilm-like microcolonies with enhanced functionalities.
Application of a long short-term memory for deconvoluting conductance contributions at charged ferroelectric domain walls
Authors: Holstad Theodor S. , Ræder Trygve M. , Evans Donald M. , Småbråten Didirk R. , Krohns Stephan , Schaab Jakob , Yan Zewu , Bourret Edith , van Helvoort Antonius T. J. , Grande Tor , Selbach Sverre M. , Agar Joshua C. , Meier Dennis
Published: October 2020

Ferroelectric domain walls are promising quasi-2D structures that can be leveraged for miniaturization of electronics components and new mechanisms to control electronic signals at the nanoscale. Despite the significant progress in experiment and theory, however, most investigations on ferroelectric domain walls are still on a fundamental level, and reliable characterization of emergent transport phenomena remains a challenging task. Here, we apply a neural-network-based approach to regularize local I(V)-spectroscopy measurements and improve the information extraction, using data recorded at charged domain walls in hexagonal (Er0.99,Zr0.01)MnO3 as an instructive example. Using a sparse long short-term memory autoencoder, we disentangle competing conductivity signals both spatially and as a function of voltage, facilitating a less biased, unconstrained and more accurate analysis compared to a standard evaluation of conductance maps. The neural-network-based analysis allows us to isolate extrinsic signals that relate to the tip-sample contact and separating them from the intrinsic transport behavior associated with the ferroelectric domain walls in (Er0.99,Zr0.01)MnO3. Our work expands machine-learning-assisted scanning probe microscopy studies into the realm of local conductance measurements, improving the extraction of physical conduction mechanisms and separation of interfering current signals.
Retraction Note: Alpha-ketoglutarate promotes skeletal muscle hypertrophy and protein synthesis through Akt/mTOR signaling pathways
Authors: Cai Xingcai , Zhu Canjun , Xu Yaqiong , Jing Yuanyuan , Yuan Yexian , Wang Lina , Wang Songbo , Zhu Xiaotong , Gao Ping , Zhang Yongliang , Jiang Qingyan , Shu Gang
Published: October 2020

Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-72330-x
A method for differentiating human induced pluripotent stem cells toward functional cardiomyocytes in 96-well microplates
Authors: Balafkan Novin , Mostafavi Sepideh , Schubert Manja , Siller Richard , Liang Kristina Xiao , Sullivan Gareth , Bindoff Laurence A.
Published: October 2020

The capacity of pluripotent stem cells both for self-renewal and to differentiate into any cell type have made them a powerful tool for studying human disease. Protocols for efficient differentiation towards cardiomyocytes using defined, serum-free culture medium combined with small molecules have been developed, but thus far, limited to larger formats. We adapted protocols for differentiating human pluripotent stem cells to functional human cardiomyocytes in a 96-well microplate format. The resulting cardiomyocytes expressed cardiac specific markers at the transcriptional and protein levels and had the electrophysiological properties that confirmed the presence of functional cardiomyocytes. We suggest that this protocol provides an incremental improvement and one that reduces the impact of heterogeneity by increasing inter-experimental replicates. We believe that this technique will improve the applicability of these cells for use in developmental biology and mechanistic studies of disease.
Magnetic separation of peripheral nerve-resident cells underscores key molecular features of human Schwann cells and fibroblasts: an immunochemical and transcriptomics approach
Authors: Peng Kaiwen , Sant David , Andersen Natalia , Silvera Risset , Camarena Vladimir , Piñero Gonzalo , Graham Regina , Khan Aisha , Xu Xiao-Ming , Wang Gaofeng , Monje Paula V.
Published: October 2020

Nerve-derived human Schwann cell (SC) cultures are irreplaceable models for basic and translational research but their use can be limited due to the risk of fibroblast overgrowth. Fibroblasts are an ill-defined population consisting of highly proliferative cells that, contrary to human SCs, do not undergo senescence in culture. We initiated this study by performing an exhaustive immunological and functional characterization of adult nerve-derived human SCs and fibroblasts to reveal their properties and optimize a protocol of magnetic-activated cell sorting (MACS) to separate them effectively both as viable and biologically competent cells. We next used immunofluorescence microscopy imaging, flow cytometry analysis and next generation RNA sequencing (RNA-seq) to unambiguously characterize the post-MACS cell products. High resolution transcriptome profiling revealed the identity of key lineage-specific transcripts and the clearly distinct neural crest and mesenchymal origin of human SCs and fibroblasts, respectively. Our analysis underscored a progenitor- or stem cell-like molecular phenotype in SCs and fibroblasts and the heterogeneity of the fibroblast populations. In addition, pathway analysis of RNA-seq data highlighted putative bidirectional networks of fibroblast-to-SC signaling that predict a complementary, yet seemingly independent contribution of SCs and fibroblasts to nerve regeneration. In sum, combining MACS with immunochemical and transcriptomics approaches provides an ideal workflow to exhaustively assess the identity, the stage of differentiation and functional features of highly purified cells from human peripheral nerve tissues.
The silk of gorse spider mite Tetranychus lintearius represents a novel natural source of nanoparticles and biomaterials
Authors: Lozano-Pérez Antonio Abel , Pagán Ana , Zhurov Vladimir , Hudson Stephen D. , Hutter Jeffrey L. , Pruneri Valerio , Pérez-Moreno Ignacio , Grbic’ Vojislava , Cenis José Luis , Grbic’ Miodrag , Aznar-Cervantes Salvador
Published: October 2020

Spider mites constitute an assemblage of well-known pests in agriculture, but are less known for their ability to spin silk of nanoscale diameters and high Young’s moduli. Here, we characterize silk of the gorse spider mite Tetranychus lintearius, which produces copious amounts of silk with nano-dimensions. We determined biophysical characteristics of the silk fibres and manufactured nanoparticles and biofilm derived from native silk. We determined silk structure using attenuated total reflectance Fourier transform infrared spectroscopy, and characterized silk nanoparticles using field emission scanning electron microscopy. Comparative studies using T. lintearius and silkworm silk nanoparticles and biofilm demonstrated that spider mite silk supports mammalian cell growth in vitro and that fluorescently labelled nanoparticles can enter cell cytoplasm. The potential for cytocompatibility demonstrated by this study, together with the prospect of recombinant silk production, opens a new avenue for biomedical application of this little-known silk.
Increasing temperatures accentuate negative fitness consequences of a marine parasite
Authors: Godwin Sean C. , Fast Mark D. , Kuparinen Anna , Medcalf Kate E. , Hutchings Jeffrey A.
Published: October 2020

Infectious diseases are key drivers of wildlife populations and agriculture production, but whether and how climate change will influence disease impacts remains controversial. One of the critical knowledge gaps that prevents resolution of this controversy is a lack of high-quality experimental data, especially in marine systems of significant ecological and economic consequence. Here, we performed a manipulative experiment in which we tested the temperature-dependent effects on Atlantic salmon (Salmo salar) of sea lice (Lepeophtheirus salmonis)—a parasite that can depress the productivity of wild-salmon populations and the profits of the salmon-farming industry. We explored sea-louse impacts on their hosts across a range of temperatures (10, 13, 16, 19, and 22 °C) and infestation levels (zero, ‘low’ (mean abundance ± SE = 1.6 ± 0.1 lice per fish), and ‘high’ infestation (6.8 ± 0.4 lice per fish)). We found that the effects of sea lice on the growth rate, condition, and survival of juvenile Atlantic salmon all worsen with increasing temperature. Our results provide a rare empirical example of how climate change may influence the impacts of marine disease in a key social-ecological system. These findings underscore the importance of considering climate-driven changes to disease impacts in wildlife conservation and agriculture.
Modelling early events in Mycobacterium bovis infection using a co-culture model of the bovine alveolus
Authors: Lee Diane Frances , Stewart Graham Roger , Chambers Mark Andrew
Published: October 2020

Bovine tuberculosis (bTB), a zoonosis mainly caused byMycobacterium bovishas severe socio-economic consequences and impact on animal health. Host–pathogen interactions duringM. bovisinfection are poorly understood, especially early events which are difficult to follow in vivo. This study describes the utilisation of an in vitro co-culture model, comprising immortalised bovine alveolar type II (BATII) epithelial cells and bovine pulmonary arterial endothelial cells (BPAECs). When cultured at air–liquid interface, it was possible to follow the migration of liveM. bovisBacille Calmette-Guérin (BCG) and to observe interactions with each cell type, alongside cytokine release. Infection with BCG was shown to exert a detrimental effect primarily upon epithelial cells, with corresponding increases in IL8, TNFα, IL22 and IL17a cytokine release, quantified by ELISA. BCG infection increased expression of CD54, MHC Class I and II molecules in endothelial but not epithelial cells, which exhibited constitutive expression. The effect of peripheral blood mononuclear cell conditioned medium from vaccinated cattle upon apical-basolateral migration of BCG was examined by quantifying recovered BCG from the apical, membrane and basolateral fractions over time. The numbers of recovered BCG in each fraction were unaffected by the presence of PBMC conditioned medium, with no observable differences between vaccinated and naïve animals.
Efficient hybrid 3D system calibration for magnetic particle imaging systems using a dedicated device
Authors: von Gladiss Anselm , Graeser Matthias , Behrends André , Chen Xin , Buzug Thorsten M.
Published: October 2020

Image reconstruction in magnetic particle imaging is often performed using a system matrix based approach. The acquisition of a system matrix is a time-consuming calibration which may take several weeks and thus, is not feasible for a clinical device. Due to hardware characteristics of the receive chain, a system matrix may not even be used in similar devices but has to be acquired for each imager. In this work, a dedicated device is used for measuring a hybrid system matrix. It is shown that the measurement time of a 3D system matrix is reduced by 96%. The transfer function of the receive chains is measured, which allows the use of the same system matrix in multiple devices. Equivalent image reconstruction results are reached using the hybrid system matrix. Furthermore, the inhomogeneous sensitivity profile of receive coils is successfully applied to a hybrid system matrix. It is shown that each aspect of signal acquisition in magnetic particle imaging can be taken into account using hybrid system matrices. It is favourable to use a hybrid system matrix for image reconstruction in terms of measurement time, signal-to-noise ratio and discretisation.
Author Correction: Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis
Authors: Naito Yuichi I. , Meleg Ioana N. , Robu Marius , Vlaicu Marius , Drucker Dorothée G. , Wißing Christoph , Hofreiter Michael , Barlow Axel , Bocherens Hervé
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Ethiopia’s transforming wheat landscape: tracking variety use through DNA fingerprinting
Authors: Hodson D. P. , Jaleta M. , Tesfaye K. , Yirga C. , Beyene H. , Kilian A. , Carling J. , Disasa T. , Alemu S. K. , Daba T. , Misganaw A. , Negisho K. , Alemayehu Y. , Badebo A. , Abeyo B. , Erenstein O.
Published: October 2020

Ethiopia is the largest wheat producer in sub-Saharan Africa yet remains a net importer. Increasing domestic wheat production is a national priority. Improved varieties provide an important pathway to enhancing productivity and stability of production. Reliably tracking varietal use and dynamics is a challenge, and the value of conventional recall surveys is increasingly questioned. We report the first nationally representative, large-scale wheat DNA fingerprinting study undertaken in Ethiopia. Plot level comparison of DNA fingerprinting with farmer recall from nearly 4000 plots in the 2016/17 season indicates that only 28% of farmers correctly named wheat varieties grown. The DNA study reveals that new, rust resistant bread wheat varieties are now widely adopted. Germplasm originating from CGIAR centres has made a significant contribution. Corresponding productivity gains and economic benefits have been substantial, indicating high returns to investments in wheat improvement. The study provides an accurate assessment of wheat varietal status and sets a benchmark for national policy-makers and donors. In recent decades, the Ethiopian wheat landscape has transformed from local tetraploid varieties to widespread adoption of high yielding, rust resistant bread wheat. We demonstrate that DNA fingerprinting can be applied at scale and is likely to transform future crop varietal adoption studies.
Time to first treatment and P53 dysfunction in chronic lymphocytic leukaemia: results of the O-CLL1 study in early stage patients
Authors: Monti Paola , Lionetti Marta , De Luca Giuseppa , Menichini Paola , Recchia Anna Grazia , Matis Serena , Colombo Monica , Fabris Sonia , Speciale Andrea , Barbieri Marzia , Gentile Massimo , Zupo Simonetta , Dono Mariella , Ibatici Adalberto , Neri Antonino , Ferrarini Manlio , Fais Franco , Fronza Gilberto , Cutrona Giovanna , Morabito Fortunato
Published: October 2020

Chronic lymphocytic leukaemia (CLL) is characterised by a heterogeneous clinical course. Such heterogeneity is associated with a number of markers, including TP53 gene inactivation. While TP53 gene alterations determine resistance to chemotherapy, it is not clear whether they can influence early disease progression. To clarify this issue, TP53 mutations and deletions of the corresponding locus [del(17p)] were evaluated in 469 cases from the O-CLL1 observational study that recruited a cohort of clinically and molecularly characterised Binet stage A patients. Twenty-four cases harboured somatic TP53 mutations [accompanied by del(17p) in 9 cases], 2 patients had del(17p) only, and 5 patients had TP53 germ-line variants. While del(17p) with or without TP53 mutations was capable of significantly predicting the time to first treatment, a reliable measure of disease progression, TP53 mutations were not. This was true for cases with high or low variant allele frequency. The lack of predictive ability was independent of the functional features of the mutant P53 protein in terms of transactivation and dominant negative potential. TP53 mutations alone were more frequent in patients with mutated IGHV genes, whereas del(17p) was associated with the presence of adverse prognostic factors, including CD38 positivity, unmutated-IGHV gene status, and NOTCH1 mutations.
A framework to quantify controlled directed interactions in network physiology applied to cognitive function assessment
Authors: Marzbanrad Faezeh , Yaghmaie Negin , Jelinek Herbert F.
Published: October 2020

The complex nature of physiological systems where multiple organs interact to form a network is complicated by direct and indirect interactions, with varying strength and direction of influence. This study proposes a novel framework which quantifies directional and pairwise couplings, while controlling for the effect of indirect interactions. Simulation results confirm the superiority of this framework in uncovering directional primary links compared to previous published methods. In a practical application of cognitive attention and alertness tasks, the method was used to assess controlled directed interactions between the cardiac, respiratory and brain activities (prefrontal cortex). It revealed increased interactions during the alertness task between brain wave activity on the left side of the brain with heart rate and respiration compared to resting phases. During the attention task, an increased number of right brain wave interactions involving respiration was also observed compared to rest, in addition to left brain wave activity with heart rate. The proposed framework potentially assesses directional interactions in complex network physiology and may detect cognitive dysfunctions associated with altered network physiology.
Methylation of MGMT promoter does not predict response to temozolomide in patients with glioblastoma in Donostia Hospital
Authors: Egaña Larraitz , Auzmendi-Iriarte Jaione , Andermatten Joaquin , Villanua Jorge , Ruiz Irune , Elua-Pinin Alejandro , Aldaz Paula , Querejeta Arrate , Sarasqueta Cristina , Zubia Felix , Matheu Ander , Samprón Nicolas
Published: October 2020

O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status has been considered a prognostic factor in newly diagnosed glioblastoma (GBM). In this study, we evaluated the prognostic and predictive value of MGMT promoter methylation in patients with glioblastoma in Donostia Hospital. Surprisingly, methylation of MGMT promoter did not predict response to temozolomide in patients with glioblastoma in Donostia Hospital. Specifically, overall survival (OS) and progression-free survival (PFS) did not differ significantly by MGMT methylation status in our cohort. In contrast, both were longer in patients who received treatment, received more TMZ cycles, had a better general status and perform at least a partial resection. No association was detected between methylation of MGMT promoter and molecular markers such as ATRX, IDH, p53 and Ki67. These results indicate that MGMT methylation did not influence in patient survival in our cohort.
Targeting of the E3 ubiquitin-protein ligase HUWE1 impairs DNA repair capacity and tumor growth in preclinical multiple myeloma models
Authors: Kunz Viktoria , Bommert Kathryn S. , Kruk Jessica , Schwinning Daniel , Chatterjee Manik , Stühmer Thorsten , Bargou Ralf , Bommert Kurt
Published: October 2020

Experimental evidence suggests that ubiquitin-protein ligases regulate a number of cellular processes involved in tumorigenesis. We analysed the role of the E3 ubiquitin-protein ligase HUWE1 for pathobiology of multiple myeloma (MM), a still incurable blood cancer. mRNA expression analysis indicates an increase in HUWE1 expression levels correlated with advanced stages of myeloma. Pharmacologic as well as RNAi-mediated HUWE1 inhibition caused anti-proliferative effects in MM cell lines in vitro and in an MM1.S xenotransplantation mouse model. Cell cycle analysis upon HUWE1 inhibition revealed decreased S phase cell fractions. Analyses of potential HUWE1-dependent molecular functions did not show involvement in MYC-dependent gene regulation. However, HUWE1 depleted MM cells displayed increased DNA tail length by comet assay, as well as changes in the levels of DNA damage response mediators such as pBRCA1, DNA-polymerase β, γH2AX and Mcl-1. Our finding that HUWE1 might thus be involved in endogenous DNA repair is further supported by strongly enhanced apoptotic effects of the DNA-damaging agent melphalan in HUWE1 depleted cells in vitro and in vivo. These data suggest that HUWE1 might contribute to tumour growth by endogenous repair of DNA, and could therefore potentially be exploitable in future treatment developments.
ThicknessTool: automated ImageJ retinal layer thickness and profile in digital images
Authors: Maidana Daniel E. , Notomi Shoji , Ueta Takashi , Zhou Tianna , Joseph Danica , Kosmidou Cassandra , Caminal-Mitjana Josep Maria , Miller Joan W. , Vavvas Demetrios G.
Published: October 2020

To develop an automated retina layer thickness measurement tool for the ImageJ platform, to quantitate nuclear layers following the retina contour. We developed the ThicknessTool (TT), an automated thickness measurement plugin for the ImageJ platform. To calibrate TT, we created a calibration dataset of mock binary skeletonized mask images with increasing thickness masks and different rotations. Following, we created a training dataset and performed an agreement analysis of thickness measurements between TT and two masked manual observers. Finally, we tested the performance of TT measurements in a validation dataset of retinal detachment images. In the calibration dataset, there were no differences in layer thickness between measured and known thickness masks, with an overall coefficient of variation of 0.00%. Training dataset measurements of immunofluorescence retina nuclear layers disclosed no significant differences between TT and any observer’s average outer nuclear layer (ONL) (p = 0.998), inner nuclear layer (INL) (p = 0.807), and ONL/INL ratio (p = 0.944) measurements. Agreement analysis showed that bias between TT vs. observers’ mean was lower than between any observers’ mean against each other in the ONL (0.77 ± 0.34 µm vs 3.25 ± 0.33 µm) and INL (1.59 ± 0.28 µm vs 2.82 ± 0.36 µm). Validation dataset showed that TT can detect significant and true ONL thinning (p = 0.006), more sensitive than manual measurement capabilities (p = 0.069). ThicknessTool can measure retina nuclear layers thickness in a fast, accurate, and precise manner with multi-platform capabilities. In addition, the TT can be customized to user preferences and is freely available to download.
Centrifugal granulation behavior in metallic powder fabrication by plasma rotating electrode process
Authors: Zhao Yufan , Cui Yujie , Numata Haruko , Bian Huakang , Wako Kimio , Yamanaka Kenta , Aoyagi Kenta , Chiba Akihiko
Published: October 2020

In recent years, spherical powders with no or minimal internal pores fabricated by the plasma rotating electrode process (PREP) have been highly recommended for powder-type additive manufacturing. Most research on PREP is aimed at establishing relationship between PREP parameters and powder size. However, almost no dedicated research on granulation behavior has been conducted so far. In the present study, PREP experiments of Ti64 and SUS316 alloys were carried out. Numerical modeling based on computational thermo-fluid dynamics was developed to analyze the granulation behavior. In particular, the roles of the additionally introduced gas blast and the morphology of the electrode end surface in fluid granulation were preliminarily investigated. The study showed that in addition to the electrode's rotating speed and diameter, manipulating the plasma arc current (i.e., the melting rate) could also be an effective way to control the PREP-powder size. According to the simulation, there were competing actions of the gas blast affecting the powder size. The gas blast created disturbance on the fluid and deepened the depression of the electrode end surface, which facilitated powder refinement. However, the cooling effect enhanced the fluid stability and hindered fluid granulation. The conclusions indicated the possibility of using various methods to manipulate PREP-powder size.
Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart
Authors: Dostal Vishantie , Wood Silas D. , Thomas Cody T. , Han Yu , Lau Edward , Lam Maggie P. Y.
Published: October 2020

The heart is sensitive to oxidative damage but a global view on how the cardiac proteome responds to oxidative stressors has yet to fully emerge. Using quantitative tandem mass spectrometry, we assessed the effects of acute exposure of the oxidative stress inducer paraquat on protein expression in mouse hearts. We observed widespread protein expression changes in the paraquat-exposed heart especially in organelle-containing subcellular fractions. During cardiac response to acute oxidative stress, proteome changes are consistent with a rapid reduction of mitochondrial metabolism, coupled with activation of multiple antioxidant proteins, reduction of protein synthesis and remediation of proteostasis. In addition to differential expression, we saw evidence of spatial reorganizations of the cardiac proteome including the translocation of hexokinase 2 to more soluble fractions. Treatment with the antioxidants Tempol and MitoTEMPO reversed many proteomic signatures of paraquat but this reversal was incomplete. We also identified a number of proteins with unknown function in the heart to be triggered by paraquat, suggesting they may have functions in oxidative stress response. Surprisingly, protein expression changes in the heart correlate poorly with those in the lung, consistent with differential sensitivity or stress response in these two organs. The results and data set here could provide insights into oxidative stress responses in the heart and avail the search for new therapeutic targets.