bluuebunny/crossref_metadata_2025_split huggingface dataset:
TomoTwin: Generalized 3D Localization of Macromolecules in Cryo-electron Tomograms with Structural Data Mining
Authors: Rice Gavin , Wagner Thorsten , Stabrin Markus , Raunser Stefan 
Published: June 2022

AbstractCryoelectron tomography enables the visualization of cellular environments in extreme detail through the lens of a benign observer; what remains lacking however are tools to analyze the full amount of information contained within these densely packed volumes. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: a robust, first in class general picking model for cryo-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space which separates macromolecules according to their 3-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network each time a new protein is to be located. TomoTwin is open source and available at https://github.com/MPI-Dortmund/tomotwin-cryoet.
An Atlas of Cells in the Human Tonsil
Authors: Massoni-Badosa Ramon , Soler-Vila Paula , Aguilar-Fernández Sergio , Nieto Juan C. , Elosua-Bayes Marc , Marchese Domenica , Kulis Marta , Vilas-Zornoza Amaia , Bühler Marco Matteo , Rashmi Sonal , Alsinet Clara , Caratù Ginevra , Moutinho Catia , Ruiz Sara , Lorden Patricia , Lunazzi Giulia , Colomer Dolors , Frigola Gerard , Blevins Will , Palomino Sara , Gomez-Cabrero David , Agirre Xabier , Weniger Marc A. , Marini Federico , Cervera-Paz Francisco Javier , Baptista Peter M. , Vilaseca Isabel , Prosper Felipe , Küppers Ralf , Gut Ivo Glynne , Campo Elias , Martin-Subero José Ignacio , Heyn Holger 
Published: June 2022

AbstractPalatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census of cell types forming the human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well as spatial transcriptomics, resulting in an atlas of >357,000 cells. We provide a glossary of 121 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease. Here, we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.
Yeast U6 snRNA made by RNA polymerase II is less stable but functional
Authors: Lipinski Karli A. , Chi Jing , Chen Xin , Hoskins Aaron A. , Brow David A. 
Published: June 2022

ABSTRACTU6 small nuclear (sn)RNA is the shortest and most conserved snRNA in the spliceosome and forms a substantial portion of its active site. Unlike the other four spliceosomal snRNAs, which are synthesized by RNA polymerase (RNAP) II, U6 is made by RNAP III. To determine if some aspect of U6 function is incompatible with synthesis by RNAP II, we created a U6 snRNA gene with RNAP II promoter and terminator sequences. This “U6-II” gene is functional as the sole source of U6 snRNA in yeast, but its transcript is much less stable than U6 snRNA made by RNAP III. Addition of the U4 snRNA Sm protein binding site to U6-II increased its stability and led to formation of U6-II•Sm complexes. We conclude that synthesis of U6 snRNA by RNAP III is not required for its function and that U6 snRNPs containing the Sm complex can form in vivo. The ability to synthesize U6 snRNA with RNAP II relaxes sequence restraints imposed by intragenic RNAP III promoter and terminator elements and allows facile control of U6 levels via regulators of RNAP II transcription.
The wheat head blight pathogen Fusarium graminearum recruits facultative endohyphal bacteria from the soil, making the fungal-bacterial holobiont nitrogen-fixing and increasing the fungal pathogenicity
Authors: Ali Hina , Pei Mengtian , Li Hongchen , Fang Wenqin , Khan Hamid Ali , Nadeem Tariq , Olsson Stefan 
Published: June 2022

AbstractIn nature, fungal endophytes often have facultative endohyphal bacteria. Can a fungal pathogen such as Fusarium graminearum, pathogenic on wheat, get facultative endohyphal bacteria from soil (FEB) and how does the FEB affect the fungal phenotype? We constructed a growth system/microcosm that allowed a molecularly well-studied F. graminearum isolate, PH-1, to grow through natural soil and then be re-isolated on a gentamicin-containing medium, allowing endohyphal growth of the bacteria while killing eventual bacteria growing on the agar medium. We had labelled the F. graminearum PH-1 with a His1mCherry gene staining the fungal nuclei fluorescent red to confirm re-isolation of the same isolate we sent through the soil. Through qPCR of the 16SrRNA gene in the bacteria using universal primers combined with qPCR of the mCherry gene of DNA from the re-isolated cultures of the Fg-FEB holobionts growing on gentamicin-containing media, it was found that most of the holobiont isolates contained about 10 16SrRNA genes per fungal mCherry gene. The Fg-FEB holobiont isolates were sub-cultured several times, and the FEB content on lab media was stable. Sequencing the 16SrRNA gene from several Fg-FEB holobiont isolates revealed known endophytic bacteria capable of nitrogen fixation. We compared the pathogenicity of one of the Fg-FEB holobionts Fg-S.maltophilia, with the background without FEB and found that it was more pathogenic than without FEB. We could also show that the bacterial 16SrRNA load per fungal His1mCherry gene inside the wheat stayed the same as in culture. Finally, we tested if the Fg-S.maltophilia was capable of nitrogen fixation and could show that it, on a nitrogen-free medium, formed a dense mycelium containing proteins at similar levels as on regular nitrogen-containing media. Our results could indicate that naturally occurring fungal pathogens outside lab conditions might contain facultative endohyphal bacteria, positively affecting their pathogenicity and ecological fitness.
Myeloid reprogramming by JAK inhibition enhances checkpoint blockade therapy
Authors: Zak Jaroslav , Pratumchai Isaraphorn , Marro Brett S. , Marquardt Kristi L. , Zavareh Reza Beheshti , Lairson Luke L. , Oldstone Michael B. A. , Varner Judith A. , Bachanova Veronika , Teijaro John R. 
Published: June 2022

AbstractUnleashing anti-tumor T cell activity by checkpoint inhibition is effective in many cancer patients but clinical response rates remain limited. Myeloid derived suppressor cells erode antitumor lymphocyte numbers and function, and correlate with resistance to checkpoint inhibitors. By screening small molecule libraries, we identified JAK inhibitors’ ability to rescue T cell function. Despite its documented immune suppressive properties, the prototypical JAK inhibitor ruxolitinib enhanced the efficacy of immune checkpoint blockade in cancer. This effect correlated with loss of suppressive gene expression, and acquisition of immunostimulatory molecular markers and T cell stimulatory activity in myeloid cells. In preclinical models, ruxolitinib significantly improved the function and increased the total numbers of activated tumor-infiltrating NK and CD4 T cells compared to checkpoint blockade alone and the efficacy was conditional on granulocytic cells. In addition to myeloid reprogramming in the tumor, ruxolitinib blunts G-CSF signaling in the bone marrow to prevent expression of suppressive and chemotaxis genes in neutrophils. In a clinical trial of Hodgkin lymphoma patients resistant to checkpoint inhibitors, treatment with ruxolitinib significantly reduced neutrophil-to-lymphocyte ratios and levels of suppressive markers in myeloid cells but increased numbers of cytokine-producing T cells. These results support the therapeutic potential of JAK inhibition in combination with checkpoint inhibitors in cancer and highlight the potential of reshaped myeloid immunity to improve immunotherapy.One sentence summary: Ruxolitinib reshapes myeloid immunity to synergize with checkpoint inhibitors
The tau oligomer antibody APNmAb005 detects early-stage pathological tau enriched at synapses and rescues neuronal loss in long-term treatments
Authors: Tai Hwan-Ching , Ma Haou-Tzong , Huang Shien-Chieh , Wu Meng-Fang , Wu Chia-Lin , Lai Yen-Ting , Li Zhong-Lin , Margolin Richard , Intorcia Anthony J. , Serrano Geidy E. , Beach Thomas G. , Nallani Madhaven , Navia Bradford , Jang Ming-Kuei , Tai Chin-Yin 
Published: June 2022

ABSTRACTNumerous tau immunotherapies are being developed against Alzheimer’s disease (AD), but it has been challenging to specifically target early-stage tau aggregates using conformation-dependent antibodies. Here, we report a monoclonal antibody, APNmAb005, that recognized a conformational epitope associated with tau oligomers. In AD brain extracts, mAb005 preferentially recognized oligomeric tau in the synapse over monomeric tau in the cytosol. In the prefrontal cortex and hippocampus, mAb005 immunoreactivity was strongly present in early-stage AD but surprisingly diminished in late-stage AD (Braak stage VI). mAb005 also recognized aggregates in 3R tauopathies (Pick’s disease) and 4R tauopathies (corticobasal degeneration and progressive supranuclear palsy), including those in astrocytes and oligodendrocytes. In rTg4510 mice (P301L tau), mAb005 immunoreactivity first appeared in distal neurites but much later in neuronal somas. Thus, the mAb005 epitope appears to be associated with early-stage oligomers of tau (esoTau) that accumulate around synapses in AD, which is also detectable in both 3R and 4R tauopathies. In cellular uptake models of tauopathy transmission, mAb005 blocked the formation of intracellular inclusions induced by incubation with rTg4510 mouse brain extracts. Long-term treatments with mAb005 in rTg4510 mice partially rescued synaptic and neuronal loss in the hippocampus without promoting overall tau clearance. Our data suggest that immunotherapies targeting esoTau enriched around synaptic sites may alleviate tau toxicity against synapses and neurons, which may be a promising treatment strategy against AD.One Sentence SummaryA tau-conformer antibody recognizing synaptic oligomers and 3R, 4R, and mixed aggregates in humans rescues neuronal loss in mouse tauopathy models.
Deep brain cancer metastasis detection with wide-volume Raman spectroscopy through a single tapered fiber
Authors: Pisano Filippo , Masmudi-Martín Mariam , Andriani Maria Samuela , Cid Elena , Pisanello Marco , Balena Antonio , Collard Liam , Tantussi Francesco , Grande Marco , Sileo Leonardo , Gentile Francesco , De Angelis Francesco , De Vittorio Massimo , de La Prida Liset Menendez , Valiente Manuel , Pisanello Ferruccio 
Published: June 2022

AbstractWe propose a low-invasive method to enable implantable, large volume Raman spectroscopy in arbitrarily deep brain regions of the mouse brain. Using a single tapered fiber as thin as 1 μm at the tip, we identified diagnostic markers of brain metastasis - the most frequent brain tumor in human adults - with overall accuracy ≥ 90%. We view our approach as a promising complement to the existing palette of tools for optical interrogation of the brain.
Structural basis of ubiquitin-independent PP1 complex disassembly by p97
Authors: van den Boom Johannes , Meyer Hemmo , Saibil Helen 
Published: June 2022

AbstractThe AAA+ ATPase p97 (also called VCP, or Cdc48 in yeast) unfolds proteins and disassembles protein complexes in a myriad of cellular processes, but how a substrate complex needs to be loaded onto p97 by a dedicated substrate adapter and then disassembled by p97 has not been structurally visualized so far. Here we present cryo-EM structures of p97 in the process of disassembling a protein phosphatase-1 (PP1) complex by stripping off an inhibitory subunit. We show that PP1 and its partners SDS22 and inhibitor-3 (I3) bind to a peripheral N-domain of p97 via a direct contact between SDS22 and a groove in the N-domain. A density consistent with the SHP box of the p37 adapter binds to the same N-domain underneath the PP1 complex, while the p37-UBX domain is found on the adjacent N-domain. I3 is likely represented by three densities. One covers the PP1 catalytic site adjacent to SDS22, another is at the PP1 binding site for the RVXF motif in I3 pointing towards the p97 pore, and the third is a peptide threaded through the central channel of the spiral-shaped p97 hexamer. Our data show how p97 arranges a substrate complex between the N-domain and central channel, and then extracts one component by threading it through the channel to disassemble the complex.
PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period
Authors: Philpott Jonathan M. , Freeberg Alfred M. , Park Jiyoung , Lee Kwangjun , Ricci Clarisse G. , Hunt Sabrina R. , Narasimamurthy Rajesh , Segal David H. , Robles Rafael , Cai Yao D. , Tripathi Sarvind , McCammon J. Andrew , Virshup David M. , Chiu Joanna C. , Lee Choogon , Partch Carrie L. 
Published: June 2022

SummaryPERIOD (PER) and Casein Kinase 1δ regulate circadian rhythms through a phosphoswitch that controls PER stability and repressive activity in the molecular clock. CK1δ phosphorylation of the Familial Advanced Sleep Phase (FASP) serine cluster embedded within the Casein Kinase 1 binding domain (CK1BD) of mammalian PER1/2 inhibits its activity on phosphodegrons to stabilize PER and extend circadian period. Here, we show that the phosphorylated FASP region (pFASP) of PER2 directly interacts with and inhibits CK1δ. Co-crystal structures in conjunction with accelerated molecular dynamics simulations reveal how pFASP phosphoserines dock into conserved anion binding sites near the active site of CK1δ. Limiting phosphorylation of the FASP serine cluster reduces product inhibition, decreasing PER2 stability and shortens circadian period in human cells. We found that Drosophila PER also regulates CK1δ via feedback inhibition through the phosphorylated PER-Short domain, revealing a conserved mechanism by which PER phosphorylation near the CK1BD regulates CK1 kinase activity.
Humanized antibody potently neutralizes all SARS-CoV-2 variants by a novel mechanism
Authors: Luo Sai , Zhang Jun , Kreutzberger Alex J.B. , Eaton Amanda , Edwards Robert J. , Jing Changbin , Dai Hai-Qiang , Sempowski Gregory D. , Cronin Kenneth , Parks Robert , Ye Adam Yongxin , Mansouri Katayoun , Barr Maggie , Pishesha Novalia , Williams Aimee Chapdelaine , Francisco Lucas Vieira , Saminathan Anand , Peng Hanqin , Batra Himanshu , Bellusci Lorenza , Khurana Surender , Alam S. Munir , Montefiori David C. , Saunders Kevin O. , Tian Ming , Ploegh Hidde , Kirchhausen Tom , Chen Bing , Haynes Barton F. , Alt Frederick W. 
Published: June 2022

AbstractSARS-CoV-2 Omicron variants have generated a world-wide health crisis due to resistance to most approved SARS-CoV-2 neutralizing antibodies and evasion of antibodies induced by vaccination. Here, we describe the SARS-CoV-2 neutralizing SP1-77 antibody that was generated from a humanized mouse model with a single human VH1-2 and Vκ1-33-associated with immensely diverse complementarity-determining-region-3 (CDR3) sequences. SP1-77 potently and broadly neutralizes SARS-CoV-2 variants of concern and binds the SARS-CoV-2 spike protein receptor-binding-domain (RBD) via a novel-CDR3-based mode. SP1-77 does not block RBD-binding to the ACE2-receptor or endocytosis step of viral entry, but rather blocks membrane fusion. Our findings provide the first mechanistic insight into how a non-ACE2 blocking antibody potently neutralizes SARS-CoV-2, which may inform strategies for designing vaccines that robustly neutralize current and future SARS-CoV-2 variants.
Cross-Protective Antibodies Against Common Endemic Respiratory Viruses
Authors: Cabán Madelyn , Rodarte Justas V. , Bibby Madeleine , Gray Matthew D. , Taylor Justin J. , Pancera Marie , Boonyaratanakornkit Jim 
Published: June 2022

ABSTRACTRespiratory syncytial virus (RSV), human metapneumovirus (HMPV), and human parainfluenza virus types one (HPIV1) and three (HPIV3) are a major cause of death, morbidity, and health care costs worldwide, and they can exact a significant toll on immunocompromised patients, the elderly, and those with underlying lung disease. There is an unmet medical need for safe and effective medications for many of the viruses responsible for common respiratory viral infections in vulnerable patient populations. While a protective monoclonal antibody exists for RSV, clinical use is limited to high-risk infant populations. Here, we present the discovery, in vitro characterization, and in vivo efficacy testing of two cross-neutralizing monoclonal antibodies, one targeting both HPIV3 and HPIV1 and the other targeting both RSV and HMPV. The 3×1 antibody is capable of targeting multiple parainfluenza viruses; the MxR antibody shares features with other previously reported monoclonal antibodies that are capable of neutralizing both RSV and HMPV. We obtained structures using cryo-electron microscopy of these antibodies in complex with their antigens to 3.62 Å resolution for 3×1:HPIV3 and to 2.24 Å for MxR:RSV, providing a structural basis to corroborate our in vitro characterization of binding and neutralization. Together, a cocktail of 3×1 and MxR could have clinical utility in providing broad protection against four of the respiratory viruses that cause significant morbidity and mortality in at-risk individuals.
Human RAD52 stimulates the RAD51-mediated homology search
Authors: Muhammad Ali Akbar , Peterlini Thibault , Guirouilh-Barbat José , Veaute Xavier , Busso Didier , Lopez Bernard , Masson Jean-Yves , Mazon Gérard , Le Cam Eric , Dupaigne Pauline 
Published: June 2022

AbstractHomologous recombination (HR) is a DNA repair mechanism of double strand breaks and blocked replication forks that involves a process of homology search and homologous pairing leading to the formation of synaptic intermediates whose architecture and dynamics are tightly regulated to ensure genome integrity. In this mechanism, RAD51 recombinase plays a central role and is supported by many partner including BRCA2 and RAD52. If the mediator function of BRCA2 to load RAD51 on RPA-covered ssDNA is well established, the role of RAD52 in HR, more precisely its interplay with BRCA2 is still far from understood. We have used Transmission Electron Microscopy combined with biochemistry to characterize the sequential participation of RPA, RAD52 and BRCA2 in the assembly of the RAD51 filament, its architecture and its activity. Despite our results confirm that RAD52 lacks a mediator activity, we observed that RAD52 can tightly bind to RPA-coated ssDNA, inhibit the mediator role of BRCA2 and form shorter RAD52- and RAD51-containing mixed filaments that are more efficient in subsequent homology search and formation of synaptic complexes and D-loops, resulting in more frequent multi-invasions as well. Through the characterization of the behavior of RAD52 and BRCA2, these results provide new molecular insights on the formation and regulation of presynaptic and synaptic intermediates during human HR.
Three-dimensional mitochondrial fission, fusion and depolarisation event location prediction for a high throughput analysis of fluorescence microscopy images
Authors: de Villiers James Garrett , Theart Rensu Petrus 
Published: June 2022

AbstractThis paper documents the development of a novel method to predict the occurrence and exact locations of mitochondrial fission, fusion and depolarisation events in three dimensions. These occurrence and location of these events were successfully predicted with a three-dimensional version of the Pix2Pix generative adversarial network (GAN) as well as a three-dimensional adversarial segmentation network called the Vox2Vox GAN. The Pix2Pix GAN predicted the locations of mitochondrial fission, fusion and depolarisation events with accuracies of 35.9%, 33.2% and 4.90%, respectively. Similarly, the Vox2Vox GAN achieved accuracies of 37.1%, 37.3% and 7.43%. The accuracies achieved by the networks in this paper are too low for the immediate implementation of these tools in life science research. They do however indicate that the networks have modelled the mitochondrial dynamics to some degree of accuracy and may therefore still be helpful as an indication of where events might occur if time lapse sequences are not available. The prediction of these morphological mitochondrial events have, to our knowledge, never been achieved before in literature. The results from this paper can be used as a baseline for the results obtained by future work.
Jouska: a lesson on financial (il)literacy of Indonesian millennials?
Authors: Soepriyanto Gatot , Limijaya Amelia 
Published: June 2022

Learning outcomesThe learning outcomes are as follows: Students/participants can understand the type of financial fraud pertaining to the case; Students/participants can analyse the case using the fraud triangle perspective; students/participants can describe detection/anticipation strategies to prevent such acts from taking place in the future; students/participants can evaluate the case using the ethical decision-making framework; and students/participants can comprehend the importance of financial literacy when investing, especially in this digital era.Case overview/synopsisThis case discusses the investment funds mismanagement accusations addressed to PT Jouska Finansial Indonesia (Jouska). Jouska is a financial planner business that was immensely popular among Indonesian young investors. It actively posted interesting content on its social media accounts, gaining attention from the millennial and Gen Z generations. However, in 2020, many of its clients reported and filed complaints that their portfolio values decreased significantly because of Jouska’s decision to invest their funds in low-quality stocks. Jouska was also alleged to violate its role as a financial planner by being able to perform several activities that fell under the authority of investment managers. This case attracted the attention of authorities so that the Investment Alert Task Force (SWI) stopped Jouska’s operational activities and initiated an investigation into the case. SWI also blocked Jouska’s websites, applications and social media accounts, in cooperation with the Ministry of Communication and Information. Despite settlement agreements that Jouska claimed had been offered to several clients, at the end of 2020 some of its clients and former clients filed a formal lawsuit. As of January 2021, several alleged criminal actions attributed to Jouska were still under investigation, comprised of money laundering, clients’ funds embezzlement, fraud, and insider trading. In October 2021, Aakar’s status was a suspect in the allegations. This case is another example of investment misconduct or fraud; to put it another way, it is the effect. It is expected that the participants can deliberate other perspectives during the discussion that could be the cause of such a case, hence viewing it holistically.Complexity academic levelUndergraduate level.Supplementary materialsTeaching notes are available for educators only.Subject codeCSS 1: Accounting and Finance.