bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19
Authors: Unterman Avraham , Sumida Tomokazu S. , Nouri Nima , Yan Xiting , Zhao Amy Y. , Gasque Victor , Schupp Jonas C. , Asashima Hiromitsu , Liu Yunqing , Cosme Carlos , Deng Wenxuan , Chen Ming , Raredon Micha Sam Brickman , Hoehn Kenneth , Wang Guilin , Wang Zuoheng , DeIuliis Giuseppe , Ravindra Neal G. , Li Ningshan , Castaldi Christopher , Wong Patrick , Fournier John , Bermejo Santos , Sharma Lokesh , Casanovas-Massana Arnau , Vogels Chantal B.F. , Wyllie Anne L. , Grubaugh Nathan D. , Melillo Anthony , Meng Hailong , Minasyan Maksym ,   the Yale IMPACT research team, Niklason Laura E. , Ko Albert I. , Montgomery Ruth R. , Farhadian Shelli F. , Iwasaki Akiko , Shaw Albert C. , van Dijk David , Zhao Hongyu , Kleinstein Steven H. , Hafler David A. , Kaminski Naftali , Dela Cruz Charles S.
Published: July 2020

A dysregulated immune response against the SARS-CoV-2 virus plays a critical role in severe COVID-19. However, the molecular and cellular mechanisms by which the virus causes lethal immunopathology are poorly understood. Here, we utilize multiomics single-cell analysis to probe dynamic immune responses in patients with stable or progressive manifestations of COVID-19, and assess the effects of tocilizumab, an anti-IL-6 receptor monoclonal antibody. Coordinated profiling of gene expression and cell lineage protein markers reveals a prominent type-1 interferon response across all immune cells, especially in progressive patients. An anti-inflammatory innate immune response and a pre-exhaustion phenotype in activated T cells are hallmarks of progressive disease. Skewed T cell receptor repertoires in CD8+ T cells and uniquely enriched V(D)J sequences are also identified in COVID-19 patients. B cell repertoire and somatic hypermutation analysis are consistent with a primary immune response, with possible contribution from memory B cells. Our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19, which may contribute to delayed virus clearance and has implications for therapeutic intervention.
Hospital mortality and resource implications of hospitalisation with COVID-19 in London, UK: a prospective cohort study
Authors: Vlachos Savvas , Wong Adrian , Metaxa Victoria , Canestrini Sergio , Soto Carmen Lopez , Periselneris Jimstan , Lee Kai , Patrick Tanya , Stovin Christopher , Abernethy Katrina , Albudoor Budoor , Banerjee Rishi , Juma Fatima , Al-Hashimi Sara , Bernal William , Maharaj Ritesh
Published: July 2020

Background

Coronavirus disease 2019 (COVID-19) had a significant impact on the National Health Service in the United Kingdom (UK), with over 33 000 cases reported in London by July 6, 2020. Detailed hospital-level information on patient characteristics, outcomes and capacity strain are currently scarce but would guide clinical decision-making and inform prioritisation and planning.

Methods

We aimed to determine factors associated with hospital mortality and describe hospital and ICU strain by conducting a prospective cohort study at a tertiary academic centre in London, UK. We included adult patients admitted to hospital with laboratory-confirmed COVID-19 and followed them up until hospital discharge or 30 days. Baseline factors that are associated with hospital mortality were identified via semi-parametric and parametric survival analyses.

Results

Our study included 429 patients; 18% of them were admitted to ICU, 52% met criteria for ICU outreach team activation and 61% had treatment limitations placed during their admission. Hospital mortality was 26% and ICU mortality was 34%. Hospital mortality was independently associated with increasing age, male sex, history of chronic kidney disease, increasing baseline C-reactive protein level and dyspnoea at presentation. COVID-19 resulted in substantial ICU and hospital strain, with up to 9 daily ICU admissions and 41 daily hospital admissions, to a peak census of 80 infected patients admitted in ICU and 250 in the hospital. Management of such a surge required extensive reorganisation of critical care services with expansion of ICU capacity from 69 to 129 beds, redeployment of staff from other hospital areas and coordinated hospital-level effort.

Conclusions

COVID-19 is associated with a high burden of mortality for patients treated on the ward and the ICU and required substantial reconfiguration of critical care services. This has significant implications for planning and resource utilization.
Computer-aided covid-19 patient screening using chest images (X-Ray and CT scans)
Authors: Burgos-Artizzu Xavier P.
Published: July 2020

Objectives

to evaluate the performance of Artificial Intelligence (AI) methods to detect covid-19 from chest images (X-Ray and CT scans).

Methods

Chest CT scans and X-Ray images collected from different centers and institutions were downloaded and combined together. Images were separated by patient and 66% of the patients were used to develop and train AI image-based classifiers. Then, the AI automated classifiers were evaluated on a separate set of patients (the remaining 33% patients).

Results (Chest X-Ray)

Five different data sources were combined for a total of N=9,841 patients (1,733 with covid-19, 810 with bacterial tuberculosis and 7,298 healthy patients). The test sample size was N=3,528 patients. The best AI method reached an Area Under the Curve (AUC) for covid-19 detection of 99%, with a detection rate of 96.4% at 1.0% false positive rate.

Results (Chest CT scans)

Two different data sources were combined for a total of N=363 patients (191 having covid-19 and 172 healthy patients). The test sample size was N=121 patients. The best AI method reached an AUC for covid-19 detection of 90.9%, with a detection rate of 90.6% at 24.6% false positive rate.

Conclusions

Computer aided automatic covid-19 detection from chest X-ray images showed promising results to be used as screening tool during the covid-19 outbreak. The developed method may help to manage patients better in case access to PCR testing is not possible or to detect patients with symptoms missed in a first round of PCR testing. The method will be made available online (www.quantuscovid19.org). These results merit further evaluation collecting more images. We hope this study will allow us to start such collaborations.
Reduced Mortality During Holidays and the COVID-19 Pandemic in Israel
Authors: Rasnic Roni , Klinger Danielle , Ofer Dan , Comay Yoav , Linial Michal , Bachmat Eitan
Published: July 2020

Evidence suggests varied trends in mortality surrounding the holiday period. Most studies support an association between increased mortality rates and holidays. We compare the effect of the number of holiday days per week on the overall mortality rate in the Israeli population. Between 2000-2020, we see significantly reduced mortality rates in weeks containing national holidays. We observed the same trend in all-cause mortality during the 3-weeks COVID-19 pandemic lockdown. As the Israeli health care system, and hospitals especially, function near peak capacity year-round, we propose that reduced medical service utilization during holidays and the COVID-19 lockdown period might underlie the lower mortality rates.
Molecular signatures of cognition and affect
Authors: Hansen Justine Y. , Markello Ross D. , Vogel Jacob W. , Seidlitz Jakob , Bzdok Danilo , Misic Bratislav
Published: July 2020

Regulation of gene expression drives protein interactions that govern synaptic wiring and neuronal activity. The resulting coordinated activity among neuronal populations supports complex psychological processes, yet how gene expression shapes cognition and emotion remains unknown. Here we directly bridge the microscale and macroscale by mapping gene expression patterns to functional activation patterns across the cortical sheet. Applying unsupervised learning to the Allen Human Brain Atlas and Neurosynth databases, we identify a ventromedial-dorsolateral gradient of gene assemblies that separate affective and cognitive domains. This topographic molecular-psychological signature reflects the hierarchical organization of the neocortex, including systematic variations in cell type, myeloarchitecture, laminar differentiation, and intrinsic network affiliation. In addition, this molecular-psychological signature is related to individual differences in cognitive performance, strengthens over neurodevelopment, and can be replicated in two independent repositories. Collectively, our results reveal spatially covarying transcriptomic and cognitive architectures, highlighting the influence that molecular mechanisms exert on psychological processes.
Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenicEscherichia coli(ETEC) circulating in modern time
Authors: von Mentzer Astrid , Blackwell Grace A. , Pickard Derek , Boinett Christine J. , Joffré Enrique , Page Andrew J , Svennerholm Ann-Mari , Dougan Gordon , Sjöling Åsa
Published: July 2020

Background

EnterotoxigenicEscherichia coli(ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 fatalities per year, with the highest rates of burden, ca 75 million cases per year, amongst children under five years of age in resource-poor countries. It is also the leading cause of diarrhoea in travellers. Previous large-scale sequencing studies have found seven major ETEC lineages currently in circulation worldwide.

Results

We used PacBio long-read sequencing combined with Illumina sequencing to create high-quality complete reference genomes for each of the major lineages with manually curated chromosomes and plasmids. The plasmids carrying ETEC virulence genes were compared to other available long-read sequenced ETEC strains using blastn. The ETEC reference strains harbour between two and five plasmids, including virulence, antibiotic resistance and phage-plasmids. The virulence plasmids carrying the colonisation factors are highly conserved as shown by comparison with plasmids with other ETEC strains and confirm that the plasmids and chromosomes of ETEC are both crucial for ETEC virulence and success as pathogens.

Conclusion

We confirm that the major ETEC lineages all harbour conserved plasmids that have been associated with their respective background genomes for decades. The in-depth analysis of gene content, synteny and correct annotations of plasmids will elucidate other plasmids with and without virulence factors in related bacterial species. These reference genomes allow for fast and accurate comparison between different ETEC strains, and these data will form the foundation of ETEC genomics research for years to come.
Immature dendritic cells promote high-avidity tuning of vaccine T cell response
Authors: Kumbhari Adarsh , Egelston Colt A. , Lee Peter P. , Kim Peter S.
Published: July 2020

Therapeutic vaccines can elicit tumor-specific cytotoxic T lymphocytes (CTLs), but durable reductions in tumor burden require vaccines that stimulate high-avidity CTLs. Recent advances in immunotherapy responses have led to renewed interest in vaccine approaches, including dendritic cell vaccine strategies. However, dendritic cell requirements for vaccines that generate potent anti-tumor T-cell responses are unclear. Here we use mathematical modeling to show that counterintuitively, increasing levels of immature dendritic cells may lead to selective expansion of high-avidity CTLs. This finding contrasts with traditional dendritic cell vaccine approaches that have sought to harness ex vivo generated mature dendritic cells. We show that the injection of vaccine antigens in the context of increased numbers of immature dendritic cells results in a decreased overall peptide:MHC complex load that favors high-avidity CTL activation and expansion. Overall, our results provide a firm basis for further development of this approach, both alone and in combination with other immunotherapies such as checkpoint blockade.
Characterizing the diverse cells that associate with the developing commissures of the zebrafish forebrain
Authors: Schnabl J. , Litz M.P.H. , Schneider C. , PenkoffLidbeck N. , Bashiruddin S. , Schwartz M.S. , Alligood K. , Barresi M.J.F.
Published: July 2020

During embryonic development of bilateral organisms, neurons send axons across the midline at specific points to connect the two halves of the nervous system with a commissure. Little is known about the cells at the midline that facilitate this tightly regulated process. We exploit the con served process of vertebrate embryonic development in the zebrafish model system to elucidate the identity of cells at the midline that may facilitate postoptic (POC) and anterior commissure (AC) development. We have discovered that three differentgfap+ astroglialcell morphologies persist in contact with pathfinding axons throughout commissure formation. Similarly,olig2+progenitor cells occupy delineated portions of the postoptic and anterior commissures. These earlyolig2+progenitors demonstrate glial-like morphologies despite the lack of a myelination marker. Moreover, we conclude that both thegfap+andolig2+progenitor cells give rise to neuronal populations in both the telencephalon and diencephalon. Interestingly, these varied cell populations showed significant developmental heterochrony between the telencephalon and diencephalon. Lastly, we also showed thatfli1a+mesenchymal cells migrate along the presumptive commissure regions before and during midline axon crossing. Furthermore, following commissure maturation, specific blood vessels formed at the midline of the POC and immediately ventral and parallel to the AC. This comprehensive account of the cellular populations that correlate with the timing and position of commissural axon pathfinding has supported the conceptual modeling and identification of the early forebrain architecture that may be necessary for proper commissure development.
Cytoplasmic aggregation of uranium in human dopaminergic cells after continuous exposure to soluble uranyl at non-cytotoxic concentrations
Authors: Carmona Asuncion , Porcaro Francesco , Somogyi Andrea , Roudeau Stéphane , Domart Florelle , Medjoubi Kadda , Aubert Michel , Isnard Hélène , Nonell Anthony , Rincel Anaïs , Paredes Eduardo , Vidaud Claude , Malard Véronique , Bresson Carole , Ortega Richard
Published: July 2020

Uranium exposure can lead to neurobehavioral alterations in particular of the monoaminergic system, even at non-cytotoxic concentrations. However, the mechanisms of uranium neurotoxicity after non-cytotoxic exposure are still poorly understood. In particular, imaging uranium in neurons at low intracellular concentration is still very challenging. We investigated uranium intracellular localization by means of synchrotron X-ray fluorescence imaging with high spatial resolution (< 300 nm) and high analytical sensitivity (< 1 μg.g-1per 300 nm pixel). Neuron-like SH-SY5Y human cells differentiated into a dopaminergic phenotype were continuously exposed, for seven days, to a non-cytotoxic concentration (10 μM) of soluble natural uranyl. Cytoplasmic submicron uranium aggregates were observed accounting on average for 62% of the intracellular uranium content. In some aggregates, uranium and iron were co-localized suggesting common metabolic pathways between uranium and iron storage. Uranium aggregates contained no calcium or phosphorous indicating that detoxification mechanisms in neuron-like cells are different from those described in bone or kidney cells. Uranium intracellular distribution was compared to fluorescently labeled organelles (lysosomes, early and late endosomes) and to fetuin-A, a high affinity uranium-binding protein. A strict correlation could not be evidenced between uranium and the labelled organelles, or with vesicles containing fetuin-A. Our results indicate a new mechanism of uranium cytoplasmic aggregation after non-cytotoxic uranyl exposure that could be involved in neuronal defense through uranium sequestration into less reactive species. The remaining soluble fraction of uranium would be responsible for protein binding and the resulting neurotoxic effects.
Targeted intragenic demethylation initiates chromatin rewiring for gene activation
Authors: Liu Yanjing V. , Bassal Mahmoud A. , Jayasinghe Migara Kavishka , Lin Quy Xiao Xuan , Wu Chan-Shuo , Tang Jing Ping , Kwon Junsu , Zhou Qiling , Tan Hong Kee , Ebralidze Alexander K. , Le Minh T.N. , Chai Li , Benoukraf Touati , Ruscio Annalisa Di , Tenen Daniel G.
Published: July 2020

Aberrant DNA methylation in the region surrounding the transcription start site is a hallmark of gene silencing in cancer. Currently approved demethylating agents lack specificity and exhibit high toxicity. Herein we show, using thep16gene as an example, that targeted demethylation of the promoter-exon 1-intron 1 (PrExI) region initiates an epigenetic wave of local chromatin remodeling and distal long-range interactions, culminating in gene-locus specific activation. Through development of CRISPR-DiR (DNMT1-interacting RNA), in which ad hoc edited guides block methyltransferase activity in a locus-specific fashion, we demonstrate that demethylation is coupled to epigenetic and topological changes. These results suggest the existence of a specialized “demethylation firing center (DFC)” which can be switched on by an adaptable and selective RNA-mediated approach for locus-specific transcriptional activation.

One Sentence Summary

Locus demethylation via CRISPR-DiR reshapes chromatin structure and specifically reactivates its cognate gene.
Query to reference single-cell integration with transfer learning
Authors: Lotfollahi Mohammad , Naghipourfar Mohsen , Luecken Malte D. , Khajavi Matin , Büttner Maren , Avsec Ziga , Misharin Alexander V. , Theis Fabian J.
Published: July 2020

Large single-cell atlases are now routinely generated with the aim of serving as reference to analyse future smaller-scale studies. Yet, learning from reference data is complicated by batch effects between datasets, limited availability of computational resources, and sharing restrictions on raw data. Leveraging advances in machine learning, we propose a deep learning strategy to map query datasets on top of a reference calledsingle-cell architectural surgery(scArches,https://github.com/theislab/scarches). It uses transfer learning and parameter optimization to enable efficient, decentralized, iterative reference building, and the contextualization of new datasets with existing references without sharing raw data. Using examples from mouse brain, pancreas, and whole organism atlases, we showcase that scArches preserves nuanced biological state information while removing batch effects in the data, despite using four orders of magnitude fewer parameters compared tode novointegration. To demonstrate mapping disease variation, we show that scArches preserves detailed COVID-19 disease variation upon reference mapping, enabling discovery of new cell identities that are unseen during training. We envision our method to facilitate collaborative projects by enabling the iterative construction, updating, sharing, and efficient use of reference atlases.
Flavoceraceomyces(NOM. PROV.) (Irpicaceae, Basidiomycota), encompassingCeraceomyces serpensandCeriporia sulphuricola, and a new resupinate species,F. damiettense, found onPhoenix dactylifera(date palm) trunks in the Nile Delta of Egypt
Authors: El-Gharabawy Hoda M. , Leal-Dutra Caio A. , Griffith Gareth W.
Published: July 2020

The taxonomy of Polyporales is complicated by the variability in key morphological characters across families and genera, now being gradually resolved through molecular phylogenetic analyses. Here a new resupinate species,Flavoceraceomyces damiettense(NOM. PROV.) found on the decayed trunks of date palm (Phoenix dactylifera) trees in the fruit orchards of the Nile Delta region of Egypt is reported. Multigene phylogenetic analyses based on ITS, LSU, EF1α, RPB1 and RPB2 loci place this species in Irpicaceae, and forming a distinct clade withCeraceomyces serpensandCeriporia sulphuricolor, which we also incorporate into a new genusFlavoceraceomyces(NOM. PROV.). The honey-yellow basidiomes with white margins and presence of crystal-encrusted hyphae in the hymenium and subiculum are distinctive features ofFlavoceraceomyces(NOM. PROV.), despite variability in hymenium morphology and presence of clamp connections and cystidia, as noted for other genera within Irpicacae.F. damiettenseis hitherto consistently associated with date palms killed by the red palm weevilRhynchophorus ferrugineus, a highly damaging and invasive pest, recently spread to the Mediterranean region.F. damiettensecauses rapid wood decay by a potentially unusual white-rot mechanism and may play a role in the damage caused byR. ferrugineus.
Automatic Integration of Gender Information during Phrase Processing: ERP Evidence
Authors: Alekseeva Maria , Myachykov Andriy , Margaretto Beatriz Bermudez , Shtyrov Yury
Published: July 2020

Both linguistic (e.g., words, syntax) and extralinguistic (e.g., voice quality) information needs to be considered by interlocutors during linguistic communication. The effects of extralinguistic information on neural sentence processing are particularly poorly understood. Here, we used EEG and passive non-attend design with visual distraction in order to investigate how extralinguistic information affects brain activity during syntactic processing. We collected ERPs while participants listened to Russian pronoun-verb phrases recorded in either male or female voice. We manipulated congruency between the grammatical gender signaled by the verb’s ending and the speaker’s apparent gender. We registered both early and late phrase processing signatures in the incongruent conditions including ELAN (peaking at ∼150 ms) and N400. Our data suggest a high degree of automaticity in integrating extralinguistic information during syntactic processing indicating existence of a rapid automatic syntactic integration mechanism sensitive to both linguistic and extralinguistic information.
New genes involved in Angelman syndrome-like: expanding the genetic spectrum
Authors: Aguilera Cinthia , Gabau Elisabeth , Ramirez-Mallafré Ariadna , Brun-Gasca Carme , Dominguez-Carral Jana , Delgadillo Veronica , Laurie Steve , Derdak Sophia , Padilla Natàlia , de la Cruz Xavier , Capdevila Núria , Spataro Nino , Baena Neus , Guitart Miriam , Ruiz Anna
Published: July 2020

Angelman syndrome (AS) is a neurogenetic disorder characterized by severe developmental delay with absence of speech, happy disposition, frequent laughter, hyperactivity, stereotypies, ataxia and seizures with specific EEG abnormalities. There is a 10-15% of patients with an AS phenotype whose genetic cause remains unknown (Angelman-like syndrome, AS-like). Whole-exome sequencing (WES) was performed on a cohort of 14 patients with clinical features of AS and no molecular diagnosis. As a result, we identified 10de novoand 1 X-linked pathogenic/likely pathogenic variants in 10 neurodevelopmental genes (SYNGAP1, VAMP2, TBL1XR1, ASXL3, SATB2, SMARCE1, SPTAN1, KCNQ3, SLC6A1andLAS1L) and one deleteriousde novovariant in a candidate gene (HSF2). Our results highlight the wide genetic heterogeneity in AS-like patients and expands the differential diagnosis. New AS-like genes do not interact directly withUBE3Agene product but are involved in synapsis and neuron system development.
Sample pooling methods for efficient pathogen screening: Practical implications
Authors: Furstenau Tara N. , Cocking Jill H. , Hepp Crystal M. , Fofanov Viacheslav Y.
Published: July 2020

Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.
Selected reaction monitoring for the quantification ofEscherichia coliribosomal proteins
Authors: Kosaka Yuishin , Aoki Wataru , Mori Megumi , Aburaya Shunsuke , Ohtani Yuta , Minakuchi Hiroyoshi , Ueda Mitsuyoshi
Published: July 2020

Ribosomes are the sophisticated machinery that is responsible for protein synthesis in a cell. Recently, quantitative mass spectrometry (qMS) based on data-dependent acquisition (DDA) have been widely used to understand the biogenesis and function of ribosomes. However, DDA-based qMS sometimes does not provide the reproducible and quantitatively reliable analysis that is needed for high-throughput hypothesis testing. To overcome this problem, we developed a highly sensitive, specific, and accurate method to quantify all ribosomal proteins (r-proteins) by combining selected reaction monitoring (SRM) and isotope labeling. We optimized the SRM methods using purified ribosomes andEscherichia colilysates, and verified this approach as a high-throughput analytical tool by detecting 41 of the 54 r-proteins separately synthesized inE. coliS30 extracts. The SRM methods will enable us to utilize qMS as a high-throughput hypothesis testing tool in the research ofE. coliribosomes, and they have potential to accelerate the understanding of ribosome biogenesis, function, and the development of engineered ribosomes with additional functions.
Inhibition of p-glycoprotein does not increase the efficacy of proteasome inhibitors in multiple myeloma cells
Authors: Mynott Rachel L. , Wallington-Beddoe Craig T.
Published: July 2020

The aim of this study is to determine whether manipulation of the drug transporter P-glycoprotein improves the efficacy of proteasome inhibitors in multiple myeloma cells. P-glycoprotein is a well-known drug transporter that is associated with chemotherapy resistance in a number of cancers but its role in modulating the efficacy of proteasome inhibitors in multiple myeloma is not well understood. Research has shown that the second generation proteasome inhibitor carfilzomib is a substrate of P-glycoprotein and as such its efficacy may correlate with P-glycoprotein activity. In contrast to carfilzomib, research concerning the first-in-class proteasome inhibitor bortezomib is inconsistent with some reports suggesting that inhibition of P-glycoprotein increases bortezomib cytotoxicity in multiple myeloma cells whereas others have shown no effect. Through the mining of publicly available gene expression microarrays of patient bone marrow, we show that P-glycoprotein gene expression increases with the disease stages leading to multiple myeloma. However, RNA-seq on LP-1 cells treated with bortezomib or carfilzomib demonstrated minimal basal P-glycoprotein expression which did not increase with treatment. Moreover, only one (KMS-18) of nine multiple myeloma cell lines expressed P-glycoprotein, including RPMI-8226 cells that are resistant to bortezomib or carfilzomib. We hypothesised that by inhibiting P-glycoprotein, multiple myeloma cell sensitivity to proteasome inhibitors would increase, thus providing a potential approach to improving responses and reversing resistance to these agents. However, the sensitivity of multiple myeloma cells lines to proteasome inhibition was not enhanced by inhibition of P-glycoprotein with the specific inhibitor tariquidar. In addition, targeting glucosylceramide synthase with eliglustat did not inhibit P-glycoprotein activity and also did not improve proteasome inhibitor efficacy except at a high concentration. We conclude that P-glycoprotein is poorly expressed in multiple myeloma cells, its inhibition does not enhance the efficacy of proteasome inhibitors, and it is unlikely to be a useful avenue for further translational research.
Chemical and technological characteristics of sugarcane as a function of pelletized organomineral fertilizer with filter cake or sewage sludge sources
Authors: Gonçalves Carlos André , de Camargo Reginaldo , de Sousa Robson Thiago Xavier , Soares Narcisa Silva , de Oliveira Roberta Camargos , Stanger Mayara Cristina , Quintão Lana Regina Maria , Lemes Ernane Miranda
Published: July 2020

Sugarcane is one of the major alternatives for the biofuel sector and its large production has considerable environmental impacts. Organomineral fertilizers formulated with environmental liabilities such as filter cake and sewage sludge positively affect parameters of plant growth and development. The objective of this study was to evaluate the chemical and technological characteristics of sugarcane fertilized with pelletized organomineral fertilizers based on filter cake and sewage sludge. Eight field treatments were studied, being three levels of organomineral (50, 100, 150%) of two organic matter sources (filter cake, sewage sludge), plus a control with 100% of the recommended fertilization via mineral fertilizer and no fertilization control (0%). Sugarcane was evaluated during two consecutive harvest, and the amount of stalks per hectare (ton ha−1), the sugarcane productivity (ton ha−1), the quantity of sugar per hectare (TSH, ton ha−1), and the chemical and technological analysis of the sugarcane juice: pol (%), brix (%), purity (%) and fiber (%) were evaluated. None of the organomineral sources or doses differed from the exclusive mineral fertilization. The analysis of both harvests indicated that the first cut was the most productive since the responses of the first harvest were superior or similar to the second harvest. The recommended organomineral dose to obtaining maximum quantitative and qualitative sugarcane results was between 102 and 109% of the regular recommendation for mineral fertilization, regardless of the organic source in the first sugarcane harvest. In the second sugarcane harvest, sewage sludge source increase by 4.68 and 4.19% the total amount of sugar per hectare and the quantity of sugarcane compared to the sugarcane filter cake source. Sewage sludge and sugarcane filter cake as sources for organominerals are viable alternatives and advantageous in economic and environmental terms for the cultivation of sugarcane.
The essentialPorphyromonas gingivalistype IX secretion system component PorZ delivers anionic-lipopolysaccharide to the PorU sortase for transpeptidase processing of cargos
Authors: Madej Mariusz , Nowakowska Zuzanna , Ksiazek Miroslaw , Lasica Anna M. , Mizgalska Danuta , Nowak Magdalena , Jacula Anna , Scavenius Carsten , Enghild Jan J. , Aduse-Opoku Joseph , Curtis Michael A. , Gomis-Rüth F. Xavier , Potempa Jan
Published: July 2020

Cargo proteins of the type IX secretion system (T9SS) in human pathogens from phylum Bacteroidetes invariably possess a conserved C-terminal domain (CTD) that functions as a signal for outer membrane (OM) translocation. InPorphyromonas gingivalis, the CTD of selected cargos is cleaved off after translocation, and anionic lipopolysaccharide (A-LPS) is attached. This transpeptidase reaction anchors secreted proteins to the OM. PorZ, a cell surface-associated protein, is an essential component of the T9SS whose function was previously unknown. We recently solved the crystal structure of PorZ, and found that it consists of two β-propeller moieties followed by a CTD. In this study, we performed structure-based modelling suggesting that PorZ is a carbohydrate-binding protein. We found that recombinant PorZ specifically binds A-LPS. Binding was blocked by monoclonal antibodies that specifically react with a phosphorylated branched mannan in the anionic polysaccharide (A-PS) component of the A-LPS, but not with the core oligosaccharide or the lipid A endotoxin. Examination of A-LPS derived from a cohort of mutants producing various truncations of A-PS confirmed that the phosphorylated branched mannan is indeed the PorZ ligand. Moreover, purified recombinant PorZ interacted with the PorU sortase in an A-LPS–dependent manner. This interaction on the cell surface is crucial for the function of the attachment complex composed of PorU, PorZ, and the integral OM β-barrel proteins PorV and PorQ, which is involved in post-translational modification and retention of T9SS cargos on the bacterial surface.

Author summary

Bacteria have evolved multiple systems to transport effector proteins to their surface or into the surrounding milieu. These proteins have a wide range of functions, including attachment, motility, nutrient acquisition, and toxicity in the host.Porphyromonas gingivalis, the human pathogen responsible for severe gum diseases (periodontitis), uses a recently characterized type IX secretion system (T9SS) to translocate and anchor secreted virulence effectors to the cell surface. Anchorage is facilitated by sortase, an enzyme that covalently attaches T9SS cargo proteins to a unique anionic lipopolysaccharide (A-LPS) moiety ofP. gingivalis. Here, we show that the T9SS component PorZ interacts with sortase and specifically binds A-LPS. Binding is mediated by a phosphorylated branched mannan repeat in A-LPS polysaccharide. A-LPS– bound PorZ interacts with sortase with significantly greater affinity, facilitating modification of cargo proteins by the cell-surface attachment complex of the T9SS.
Macroscopic digestive anatomy of ring-tailed lemurs (Lemur catta), including a comparison of frozen and formalin-stored specimens
Authors: Clauss Marcus , Trümpler Jelscha , Ackermans Nicole L. , Kitchener Andrew C. , Hantke Georg , Stagegaard Julia , Takano Tomo , Shintaku Yuta , Matsuda Ikki
Published: July 2020

Digestive tract measurements are often considered species-specific, but little information exists on the degree to which they change during ontogeny within species. Additionally, access to anatomical material from nondomestic species is often limited, with fixed tissues possibly representing the only available source, though the degree at which this material is representative in terms of dimensions and weight is debatable. In the present study, the macroscopic digestive tract anatomy (length of intestinal portions, and tissue weights of stomach and intestines) ofn=58 Lemur catta(from neonates to 25 years of age) was quantified, of which 27 had been stored frozen and 31 fixed in formalin. Particular attention was paid to the caecum and the possible presence of an appendix. The intraspecific allometric scaling of body mass (BM)0.46[0.40;0.51]for total intestine length and BM0.48[0.41;0.54]for small intestine length was higher than the expected geometric scaling of BM0.33, similar to literature results on interspecific scaling. This difference in scaling is usually explained by the hypothesis that the diameter of the intestinal tube cannot increase geometrically, to maintain optimal absorption. Therefore, geometric volume gain of increasing body mass is accommodated by more-than-geometric length scaling. Literature describesL. cattaas being variable with respect to the presence of an appendix. No appendix was found in specimens of the present study. The proportions of length measurements did not change markedly during ontogeny, indicating that proportions developed in the foetus are already representative for the adult animal. By contrast, width and tissue-mass scaling of the caecum indicated a disproportionate growth of this organ during ontogeny that was not reflected in its length. Compared to overall intraspecific variation, the method of storage (frozen vs. formalin) had no relevant impact on length or weight measurements.
Spelling changes and fluorescent tagging with prime editing vectors for plants
Authors: Wang Li , Kaya Hilal Betul , Zhang Ning , Rai Rhitu , Willmann Matthew R. , Carpenter Sara C. D. , Read Andrew C. , Martin Federico , Fei Zhangjun , Leach Jan E. , Martin Gregory B. , Bogdanove Adam J.
Published: July 2020

Prime editing (PE) is a recent adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase (RT) fusion and a guide RNA (pegRNA) amended with template and primer binding site (PBS) sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of PE in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for PE in dicots and monocots, their validation inNicotiana benthamiana, rice and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.
Cryo-EM reveals the complex architecture of dynactin’s shoulder and pointed end
Authors: Lau Clinton K. , O’Reilly Francis J. , Santhanam Balaji , Lacey Samuel E. , Rappsilber Juri , Carter Andrew P.
Published: July 2020

Dynactin is a 1.1 MDa complex that activates the molecular motor, dynein, for ultra-processive transport along microtubules. In order to do this it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder positions the four identical p50 subunits in different conformations to bind dynactin’s filament and securely houses the p150 subunit. The pointed end map allows us to build the first structure of p62, and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.
Visual Search P300 Source Analysis Based On ERP-fMRI Integration
Authors: Zhang Qiuzhu , Luo Cimei , Zhang Junjun , Jin Zhenlan , Li Ling
Published: July 2020

Attention control can be achieved in two ways, stimulus-driven bottom-up attention and goal-driven top-down attention. Different visual search tasks involve different attention control. The pop-out task requires more bottom-up attention, whereas the search task involves more top-down attention. P300 which is the positive potential generated by the brain in the latency of 300-600 ms after the stimulus, reflects the processing of cognitive process and is an important component in visual attention. The P300 source is not consistent in the previous researches, our aim therefore, is to study the source location of P300 component based on visual search attention process. Here we use pop-out and search paradigm to get the ERP data of 13 subjects and the fMRI data of 25 subjects, and analyze the source location of P300 using the ERP-fMRI integration technology with high temporal resolution and high spatial resolution. The target differs from the distractor in color and orientation in the pop-out task, whereas the target and the distractor have different orientation and the same color in the search task. ERP results indicate that pop-out induces larger P300 concentrated in the parietal lobe, whereas search induced P300 is more distributed in the frontal lobe. Further ERP and fMRI integration analyses reveal that the left angular gyrus, right postcentral gyrus of parietal lobe and the left superior frontal gyrus (medial orbital) are the source of P300. Our study suggests the contribution of the frontal and parietal lobes to the P300 component.
An in-vivo study of BOLD laminar responses as a function of echo time and static magnetic field strength
Authors: Markuerkiaga Irati , Marques José P. , Bains Lauren J. , Norris David G.
Published: July 2020

Layer specific functional MRI requires high spatial resolution data. An approach often used for compensating for the poor signal to noise ratio (SNR) associated with small voxel sizes consists of integrating the signal from voxels at a given cortical depth over a patch of cortex. After this integration, physiological noise is expected to be the dominant noise source in the signal. In this context, the sensitivity gain in moving to higher static field strengths is expected to be lower than when thermal noise dominates. In this work, activation profiles in response to the same visual stimulus are compared at 1.5 T, 3 T and 7 T using a multi-echo, gradient echo (GE) FLASH sequence, with a 0.75 mm isotropic voxel size and the cortical integration approach. The results show that after integrating over a patch of cortex between 40 and 100 mm3(at 7 T and 1.5 T, respectively), the signal is in the physiological noise dominated regime, and that the obtained activation profiles are similar at the three different field strengths for equivalent echo times. The evolution of the resting-state signal over echo time indicates that BOLD-like noise is the dominant source of physiological noise. Consequently, the functional contrast to noise ratio is not strongly echo-time or field-strength dependent. The results show that compared to 7T, the gold standard, laminar GE-BOLD fMRI at lower field strengths is feasible at the cost of poorer spatial resolution (larger cortical integration extensions) and lower efficiency.
ESRP1-Mediated Alternative Splicing During Oocyte Development is Required for Mouse Fertility
Authors: Yu Luping , Zhang Huiru , Guan Xuebing , Qin Dongdong , Zhou Jian , Wu Xin
Published: July 2020

Alternative splicing (AS) contributes to gene diversification in cells, but the importance of AS during germline development remains largely undefined. Here, we interrupted pre-mRNA splicing events controlled by epithelial splicing regulatory protein 1 (ESRP1) and found that it induced female infertility in mice. Germline-specific knockout ofEsrp1perturbed spindle organization, chromosome alignment, and metaphase-to-anaphase transformation in oocytes. The first polar body extrusion (PBE) was blocked during oocyte meiosis and was found to be due to abnormal activation of spindle assembly checkpoint (SAC) and insufficiency of anaphase-promoting complex/cyclosome (APC/C) inEsrp1-knockout oocytes.Esrp1-knockout in oocytes hampered follicular development and ovulation; eventually, premature ovarian failure (POF) occurred in six-month-oldEsrp1-knockout mouse. Using single-cell RNA sequencing analysis, 528 aberrant AS events of maternal mRNA transcripts were revealed and were preferentially associated with microtubule cytoskeletal organization inEsrp1-knockout oocytes. Notably, we found that loss of ESRP1 disturbed a comprehensive set of gene-splicing sites—including those withinTrb53bp1, Rac1, Bora, Kif2c, Kif23, Ndel1, Kif3a, Cenpa, andLsm14b—that ultimately caused abnormal spindle organization. Taken together, our findings provide the first report elucidating the AS program of maternal mRNA transcripts, mediated by the splicing factor, ESRP1, that is required for oocyte meiosis and female fertility in mice.
The half-life of the bone-derived hormone osteocalcin is regulated throughO-glycosylation in mice, but not in humans
Authors: Rifai Omar Al , Julien Catherine , Faubert Denis , Lira-Navarrete Erandi , Narimatsu Yoshiki , Lacombe Julie , Clausen Henrik , Ferron Mathieu
Published: July 2020

Osteocalcin (OCN) is an osteoblast-derived hormone with pleiotropic physiological functions. Like many peptide hormones, OCN is subjected to post-translational modifications (PTMs) which control its activity. Here, we uncoverO-glycosylation as a novel PTM present on mouse OCN and occurring on a single serine (S8) independently of its carboxylation and endoproteolysis, two other PTMs regulating this hormone. We also show thatO-glycosylation increases OCN half-life in plasma ex vivo and in the circulation in vivo. Remarkably, in human OCN (hOCN), the residue corresponding to S8 is a tyrosine (Y12), which is notO-glycosylated. Yet, the Y12S mutation is sufficient toO-glycosylate hOCN and to increase its half-life in plasma compared to wildtype hOCN. These findings reveal an important species difference in OCN regulation, which may explain why serum concentrations of OCN are higher in mouse than in human.

The authors have nothing to disclose
Single cell characterization of a synthetic bacterial clock with a hybrid feedback loop containing dCas9-sgRNA
Authors: Henningsen John , Schwarz-Schilling Matthaeus , Leibl Andreas , Guttierez Joaquin A. M. , Sagredo Sandra , Simmel Friedrich C.
Published: July 2020

Genetic networks that generate oscillations in gene expression activity are found in a wide range of organisms throughout all kingdoms of life. Oscillatory dynamics facilitates the temporal orchestration of metabolic and growth processes inside cells and organisms, as well as the synchronization of such processes with periodically occurring changes in the environment. Synthetic oscillator gene circuits such as the ‘repressilator’ can perform similar functions in bacteria. Until recently, such circuits were mainly based on a relatively small set of well-characterized transcriptional repressors and activators. A promising, sequence-programmable alternative for gene regulation is given by CRISPR interference (CRISPRi), which enables transcriptional repression of nearly arbitrary gene targets directed by short guide RNA molecules. In order to demonstrate the use of CRISPRi in the context of dynamic gene circuits, we here replaced one of the nodes of a repressilator circuit by the RNA-guided dCas9 protein. Using single cell experiments in microfluidic reactors we show that this system displays robust relaxation oscillations over multiple periods and over the time course of several days. Through statistical analysis of the single cell data, the potential for the circuit to act as a synthetic pacemaker for cellular processes is evaluated. The use of CRISPRi in the context of an oscillator circuit is found to have profound effects on its dynamics. Specifically, irreversible binding of dCas9-sgRNA appears to prolong the period of the oscillator. Further, we demonstrate that the oscillator affects cellular growth, leading to variations in growth rate with the oscillator’s frequency.
Keratin 17 regulates nuclear morphology and chromatin organization
Authors: Jacob Justin T. , Nair Raji R. , Poll Brian G. , Pineda Christopher M. , Hobbs Ryan P. , Matunis Michael J. , Coulombe Pierre A.
Published: July 2020

Keratin 17 (KRT17; K17), a non-lamin intermediate filament protein, was recently found to occur in the nucleus. We report here on K17-dependent differences in nuclear morphology, chromatin organization, and cell proliferation. Human tumor keratinocyte cell lines lacking K17 exhibit flatter nuclei relative to normal. Re-expression of wildtype K17, but not a mutant form lacking an intact nuclear localization signal (NLS), rescues nuclear morphology inKRT17null cells. Analyses of primary cultures of skin keratinocytes from a mouse strain expressing K17 with a mutated NLS corroborated these findings. Proteomics screens identified K17-interacting nuclear proteins with known roles in gene expression, chromatin organization, and RNA processing. Key histone modifications and LAP2β localization within the nucleus are altered in the absence of K17, correlating with decreased cell proliferation and suppression of GLI1 target genes. Nuclear K17 thus impacts nuclear morphology with an associated impact on chromatin organization, gene expression, and proliferation in epithelial cells.

Keratin 17 (K17) is one of two non-lamin intermediate filament proteins recently identified to localize to and function in the cell nucleus. K17 is here shown to regulate nuclear morphology, chromatin organization, LAP2 localization, and cell proliferation.