bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial genomics maps the structure, character and evolution of cancer clones
Authors: Lomakin Artem , Svedlund Jessica , Strell Carina , Gataric Milana , Shmatko Artem , Park Jun Sung , Ju Young Seok , Dentro Stefan , Kleshchevnikov Vitalii , Vaskivskyi Vasyl , Li Tong , Bayraktar Omer Ali , Moore Luiza , Pinder Sarah , Richardson Andrea L , Campbell Peter J , Gerstung Moritz , Nilsson Mats , Yates Lucy R 
Published: April 2021

AbstractSubclonality is a universal feature of cancers yet how clones grow, are spatially organised, differ phenotypically or influence clinical outcome is unclear. To address this, we developed base specific in situ sequencing (BaSISS). In fixed tissues, transcripts harbouring clone-defining mutations are detected, converted into quantitative clone maps and characterised through multi-layered data integration. Applied to 8 samples from key stages of breast cancer progression BaSISS localised 1.42 million genotype informative transcripts across 4.9cm2of tissue. Microscopic clonal topographies are shaped by resident tissue architectures. Distinct transcriptional, histological and immunological features distinguish coexistent genetic clones. Spatial lineage tracing temporally orders clone features associated with the emergence of aggressive clinical traits. These results highlight the pivotal role of spatial genomics in deciphering the mechanisms underlying cancer progression.
Extended frontal networks for visual and auditory working memory
Authors: Noyce Abigail L. , Lefco Ray W. , Brissenden James A. , Tobyne Sean M. , Shinn-Cunningham Barbara G. , Somers David C. 
Published: April 2021

AbstractWorking memory (WM) supports the persistent representation of transient sensory information. Visual and auditory stimuli place different demands on WM and recruit different brain networks. Separate auditory- and visual-biased WM networks extend into the frontal lobes, but several challenges confront attempts to parcellate human frontal cortex, including fine-grained organization and between-subject variability. Here, we use differential intrinsic functional connectivity from two visual-biased and two auditory-biased frontal structures to identify additional candidate sensory-biased regions in frontal cortex. We then examine direct contrasts of task fMRI during visual vs. auditory 2-back WM to validate those candidate regions. Three visual-biased and five auditory-biased regions are robustly activated bilaterally in the frontal lobes of individual subjects (N=14, 7 women). These regions exhibit a sensory preference during passive exposure to task stimuli, and that preference is stronger during WM. Hierarchical clustering analysis of intrinsic connectivity among novel and previously identified bilateral sensory-biased regions confirms that they functionally segregate into visual and auditory networks, even though the networks are anatomically interdigitated. We also observe that the fronto-temporal auditory WM network is highly selective and exhibits strong functional connectivity to structures serving non-WM functions, while the fronto-parietal visual WM network hierarchically merges into the multiple-demand cognitive system.
Role of African swine fever virus (ASFV) proteins EP153R and EP402R in reducing viral persistence and virulence from attenuated BeninΔDP148R
Authors: Petrovan Vlad , Rathakrishnan Anusyah , Islam Muneeb , Goatley Lynnette C. , Moffat Katy , Sanchez-Cordon Pedro J. , Reis Ana L. , Dixon Linda K. 
Published: April 2021

AbstractThe limited knowledge on the role of many of the approximately 170 proteins encoded by African swine fever virus restricts progress towards vaccine development. In this study we investigated the effect of deleting combinations of different genes from a previously attenuated virus, BeninΔDP148R on: virus replication in macrophages, virus persistence and clinical signs post immunization, and induction of protection against challenge. Deletion of either EP402R or EP153R genes individually or in combination from BeninΔDP148R did not reduce virus replicationin vitro. However, deletion of EP402R dramatically reduced viral persistencein vivo, whilst maintaining high levels of protection against challenge. The additional deletion of EP153R (BeninΔDP148RΔEP153RΔEP402R) further attenuated the virus and no viremia or clinical signs were observed post immunization. This was associated with decreased protection and detection of moderate levels of challenge virus in blood. Interestingly, the deletion of EP153R alone from BeninΔDP148R did not result in further virus attenuation and a slight increase in virus genome copies in blood was observed at different times post immunization when compared with BeninΔDP148R. These results show that EP402R and EP153R have a synergistic role in promoting viremia, however EP153R alone does not seem to have a major impact on virus levels in blood.
Structural brain connectivity in children with developmental dyscalculia
Authors: Ayyıldız Nazife , Beyer Frauke , Üstün Sertaç , Kale Emre H. , Mançe Çalışır Öykü , Uran Pınar , Öner Özgür , Olkun Sinan , Anwander Alfred , Witte A. Veronica , Villringer Arno , Çiçek Metehan 
Published: April 2021

ABSTRACTDevelopmental dyscalculia (DD) is a neurodevelopmental disorder specific to arithmetic learning even with normal intelligence and age-appropriate education. Difficulties often persist from childhood through adulthood. Underlying neurobiological mechanisms of DD, however, are poorly understood. This study aimed to identify possible structural connectivity alterations in DD. We evaluated 10 children withpureDD (11.3 ± 0.7 years) and 16 typically developing (TD) peers (11.2 ± 0.6 years) using diffusion tensor imaging. We first assessed white matter microstructure with tract-based spatial statistics. Then we used probabilistic tractography to evaluate tract lengths and probabilistic connectivity maps in specific regions. At whole brain level, we found no significant microstructural differences in white matter between children with DD and TD peers. Also, seed-based connectivity probabilities did not differ between groups. However, we did find significant differences in regions-of-interest tracts which had previously been related to math ability in children. The major findings of our study were reduced white matter coherence and shorter tract lengths of the left superior longitudinal/arcuate fasciculus and left anterior thalamic radiation in the DD group. Furthermore, lower white matter coherence and shorter pathways corresponded with the lower math performance as a result of the correlation analyses. These results from regional analyses indicate that learning, memory and language-related pathways in the left hemisphere might underlie DD.
Mycobacterial infection of precision cut lung slices reveals that the type 1 interferon pathway is locally induced by Mycobacterium bovis but not M. tuberculosis in different cattle breeds
Authors: Remot Aude , Carreras Florence , Coupé Anthony , Doz-Deblauwe Émilie , Boschiroli ML , Browne John A. , Marquant Quentin , Descamps Delphyne , Archer Fabienne , Aseffa Abrahma , Germon Pierre , Gordon Stephen V. , Winter Nathalie 
Published: April 2021

ABSTRACTTuberculosis exacts a terrible toll on human and animal health. WhileMycobacterium tuberculosis(Mtb) is restricted to humans,Mycobacterium bovis(Mb) is present in a large range of mammalian hosts. In cattle, bovine TB (bTB) is a notifiable disease responsible for important economic losses in developed countries and underestimated zoonosis in the developing world. Early interactions that take place between mycobacteria and the lung tissue early after aerosol infection govern the outcome of the disease. In cattle, these early steps remain poorly characterized. The precision-cut lung slice (PCLS) model preserves the structure and cell diversity of the lung. We developed this model in cattle in order to study the early lung response to mycobacterial infection.In situimaging of PCLS infected with fluorescent Mb revealed bacilli in the alveolar compartment, adjacent or inside alveolar macrophages (AMPs) and in close contact with pneumocytes. We analyzed the global transcriptional lung inflammation signature following infection of PCLS with Mb and Mtb in two French beef breeds: Blonde d’Aquitaine and Charolaise. Whereas lungs from the Blonde d’Aquitaine produced high levels of mediators of neutrophil and monocyte recruitment in response to infection, such signatures were not observed in the Charolaise in our study. In the Blonde d’Aquitaine lung, whereas the inflammatory response was highly induced by two Mb strains, AF2122 isolated from cattle in the UK and Mb3601 circulating in France, the response against two Mtb strains, H37Rv the reference laboratory strain and BTB1558 isolated from zebu in Ethiopia, was very low. Strikingly, the type I interferon pathway was only induced by Mb but not Mtb strains indicating that this pathway may be involved in mycobacterial virulence and host tropism. Hence, the PCLS model in cattle is a valuable tool to deepen our understanding of early interactions between lung host cells and mycobacteria. It revealed striking differences between cattle breeds and mycobacterial strains. This model could help deciphering biomarkers of resistanceversussusceptibility to bTB in cattle as such information is still critically needed for bovine genetic selection programs and would greatly help the global effort to eradicate bTB.
Antibody Cocktail Exhibits Broad Neutralization against SARS-CoV-2 and SARS-CoV-2 variants
Authors: Qu Yuanyuan , Zhang Xueyan , Wang Meiyu , Sun Lina , Jiang Yongzhong , Li Cheng , Wu Wei , Chen Zhen , Yin Qiangling , Jiang Xiaolin , Liu Yang , Li Chuan , Li Jiandong , Ying Tianlei , Li Dexin , Zhan Faxian , Wang Youchun , Guan Wuxiang , Wang Shiwen , Liang Mifang 
Published: April 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446 -S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, F61 and H121 exhibited efficient neutralizing activity against variants B.1.1.7 and B.1.351, those showed immune escape. Efficient neutralization of F61 and H121 against multiple mutations within RBD revealed a broad neutralizing activity against SARS-CoV-2 variants, which mitigated the risk of viral escape. Our findings defined the basis of therapeutic cocktails of F61 and H121 with broad neutralization and delivered a guideline for the current and future vaccine design, therapeutic antibody development, and antigen diagnosis of SARS-CoV-2 and its novel variants.
Image-based phenotypic profiling of a chemogenomic screening library identifies novel druggable targets in the EGFR-pathway
Authors: Tanabe Kenji 
Published: April 2021

SummaryThe gene encoding epidermal growth factor receptor (EGFR) is a major driver gene in cancer. Many drugs targeting EGFR-associated molecules have been developed, yet many have failed in clinical trials due to a lack of efficacy and/or unexpected side effects. In this study, I used image-based phenotypic profiling to screen a pharmacologically active compound library with the aim of identifying new druggable targets in the EGFR pathway. As anticipated, the phenotypic screen identified compounds that produce phenotypes resulting from targeting a known specific molecule or pathway. The assay also showed that compounds with diverse known mechanisms of action produced similar, EGFR-related cellular phenotypes. Biochemical assays revealed that those compounds share a previously unappreciated common target/pathway, showing that the image-based assay can identify new target molecules that are independent of the compound’s known target. Further experiments showed that ROCK1 and PSMD2 are novel druggable targets within the EGFR pathway.
A programmable system to methylate and demethylate m6A on specific mRNAs
Authors: Chang Chen , Ma Gang , Cheung Edwin , Hutchins Andrew P. 
Published: April 2021

AbstractRNA N6-Methyladenosine (m6A) is the most abundant mRNA modification, and forms part of an epitranscriptomic system that modulates RNA function. RNA modifications can be reversibly catalyzed by several specific enzymes, and those modifications can be recognized by RNA binding proteins that in turn regulate biological processes. Although there are many reports demonstrating m6A participation in critical biological functions, this exploration has mainly been conducted through the global knockout or knockdown of the writers, erasers, or readers of m6A. Consequently, there is a lack of information about the role of m6A on single transcripts in biological processes, posing a challenge in understanding the biological functions of m6A. Here, we demonstrate a CRISPR/dCas13a-based RNA m6A-editor which can target mRNAs using single crRNA or multiple crRNAs array to methylate or demethylate m6A. We systematically assay its capabilities to enable the targeted rewriting of m6A dynamics, including modulation of circular RNA translation and transcript half-life. Finally, we demonstrate the utility of the system by specifically modulating XIST m6A levels, which can control X chromosome silencing and activation. Based on our editors, m6A on single and multiple transcripts can be modified to allow the exploration of the role of m6A on in biological processes.
Homo-harringtonine (HHT) – A highly effective drug against coronaviruses and the potential for large-scale clinical applications
Authors: Wen Hai-Jun , Lin Pei , Zhong Gong-Xun , Xu Zhi-Chao , Shuai Lei , Wen Zhi-Yuan , Wang Chong , Cao Xue , He Wen-Bin , Feng Jing , Cai Qi-Chun , Ma Hua-Juan , Wu Si-Jin , Wang Guo-Dong , Lyu Xue-Mei , Liu Feng-Liang , Zheng Yong-Tang , Zeng Hui , He Xiong-Lei , Chen Hualan , Zhang Fu-Jie , Wu Chung-I 
Published: April 2021

AbstractIn the search for treatment schemes of COVID-19, we start by examining the general weakness of coronaviruses and then identify approved drugs attacking that weakness. The approach, if successful, should identify drugs with a specific mechanism that is at least as effective as the best drugs proposed and are ready for clinical trials. All coronaviruses translate their non-structural proteins (∼16) in concatenation, resulting in a very large super-protein. Homo-harringtonine (HHT), which has been approved for the treatment of leukemia, blocks protein elongation very effectively. Hence, HHT can repress the replication of many coronaviruses at the nano-molar concentration. In two mouse models, HHT clears SARS-CoV-2 in 3 days, especially by nasal dripping of 40 ug per day. We also use dogs to confirm the safety of HHT delivered by nebulization. The nebulization scheme could be ready for large-scale applications at the onset of the next epidemics. For the current COVID-19, a clinical trial has been approved by the Ditan hospital of Beijing but could not be implemented for want of patients. The protocol is available to qualified medical facilities.
Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision
Authors: Watson James A , Ndila Carolyne M , Uyoga Sophie , Macharia Alexander W , Nyutu Gideon , Shebe Mohammed , Ngetsa Caroline , Mturi Neema , Peshu Norbert , Tsofa Benjamin , Rockett Kirk , Leopold Stije , Kingston Hugh , George Elizabeth C , Maitland Kathryn , Day Nicholas PJ , Dondorp Arjen , Bejon Philip , Williams Thomas N , Holmes Chris C , White Nicholas J 
Published: April 2021

AbstractSevere falciparum malaria has substantially affected human evolution. Genetic association studies of patients with clinically defined severe malaria and matched population controls have helped characterise human genetic susceptibility to severe malaria, but phenotypic imprecision compromises discovered associations. In areas of high malaria transmission the diagnosis of severe malaria in young children and, in particular, the distinction from bacterial sepsis, is imprecise. We developed a probabilistic diagnostic model of severe malaria using platelet and white count data. Under this model we re-analysed clinical and genetic data from 2,220 Kenyan children with clinically defined severe malaria and 3,940 population controls, adjusting for phenotype mis-labelling. Our model, validated by the distribution of sickle trait, estimated that approximately one third of cases did not have severe malaria. We propose a data-tilting approach for case-control studies with phenotype mis-labelling and show that this reduces false discovery rates and improves statistical power in genome-wide association studies.
Protein content and lipid profiling of isolated native autophagosomes
Authors: Schmitt Daniel , Bozkurt Süleyman , Henning-Domres Pascale , Huesmann Heike , Eimer Stefan , Bindila Laura , Tascher Georg , Münch Christian , Behl Christian , Kern Andreas 
Published: April 2021

AbstractAutophagy is a central eukaryotic catabolic pathway responsible for clearance and recycling of an extensive portfolio of cargoes, which are packed in vesicles, called autophagosomes, and are delivered to lysosomes for degradation. Besides basal autophagy, which constantly degrades cellular material, the pathway is highly responsive to several stress conditions. However, the exact protein content and phospholipid composition of autophagosomes under changing autophagy conditions remain elusive so far. Here, we introduce a FACS-based approach for isolation of native unmanipulated autophagosomes and ensure the quality of the preparations. Employing quantitative proteomics and phospholipidomics, we obtained a profound cargo and lipid profile of autophagosomes purified upon basal autophagy conditions, nutrient deprivation, and proteasome inhibition. Indeed, starvation only mildly affected the content profile, while interference with proteasome activity showed stronger effects and specifically altered autophagosome cargoes. Interestingly, the phospholipid composition of autophagosomes was unaffected by the different treatments. Thus, the novel isolation method enables purification of intact autophagosomes in large quantities and allows protein content and phospholipid profiling without the requirement of exhaustive cellular fractionation or genetic manipulation.
Innate immunity mediator STING modulates nascent DNA metabolism at stalled forks in human cells
Authors: Nguyen Vy N. , Brunon Salomé , Pavlova Maria N. , Lazarchuk Pavlo , Sharifian Roya D. , Sidorova Julia M. 
Published: April 2021

AbstractThe cGAS/STING pathway, part of the innate immune response to foreign DNA, is known to be activated by cell’s own DNA arising from the processing of the genome, including the excision of nascent DNA at arrested replication forks. We found STING activation to affect nascent DNA processing, suggesting a novel, unexpected feedback connection between the two events. Depletion of STING suppressed and re-expression of the protein in STING-deficient cells upregulated degradation of nascent DNA. Fork arrest was accompanied by the STING pathway activation, and a STING mutant that does not activate the pathway failed to upregulate nascent strand degradation. Consistent with this, cells expressing the STING mutant had a reduced level of RPA on parental and nascent DNA of arrested forks as well as a reduced CHK1 activation compared to the cells with wild type STING. Together our findings reveal a novel connection between replication stress and innate immunity.
Decellularized Articular Cartilage Microparticles for Expansion of Mesenchymal Stem Cells and Zonal Regeneration of Articular Cartilage
Authors: Sepahvandi Azadeh , Kader Safaa Ibrahim , Monavarian Mehri , Madormo Victor Anthony , Jabbari Esmaiel 
Published: April 2021

AbstractIntroductionThe objective was to create multilayer cellular constructs using fetal or adult, decellularized articular cartilage in particulate form as microcarriers for expansion and fusion of mesenchymal stem cells (MSCs) to regenerate the stratified structure of articular cartilage.MethodsPorous microparticles (CMPs) generated from decellularized fetal or adult bovine articular cartilage were used as microcarriers for expansion of human MSCs. The CMP expanded MSCs (CMP-MSCs) were used to generate injectable hydrogels or preformed multilayer constructs for articular cartilage regeneration. In the injectable approach, CMP-MSCs were suspended in alginate gel, crosslinked with calcium chloride, and incubated in chondrogenic medium to generate an injectable regenerative construct. In the preformed approach, fetal or adult CMP-MSCs were suspended in a culture medium, allowed to settle sequentially by the force of gravity, and fused by incubation in chondrogenic medium to generate multilayer cell sheets. The constructs were characterized with respect to compressive modulus, cellularity, and expression of chondrogenic markers.ResultsHuman MSCs expanded on fetal or adult CMPs in basal medium maintained the expression of mesenchymal markers. The injectable CMP-MSCs hydrogels had significantly higher expression of chondrogenic markers and compressive modulus after four weeks incubation in chondrogenic medium compared to MSCs directly encapsulated in alginate gel; preformed CMP-MSCs cell sheets had significantly higher compressive modulus and expression of chondrogenic markers compared to MSCs in the pellet culture.ConclusionThe preformed cell sheet approach is potentially useful for creating multilayer constructs by sequential gravitational settling of CMP-MSCs to mimic the stratified structure of articular cartilage.Insight, Innovation, IntegrationThis work described a novel approach to recreate the zonal structure of articular cartilage. Human MSCs were expanded on porous microcarrier beads generated from decellularized fetal or adult bovine articular cartilage. The cell-seeded microbeads were fused by gravitational settling to form mono- or bi-layer cell sheets. The cell sheets were cultured in chondrogenic medium to regenerate the articular cartilage tissue. Thein vitroregenerated tissue had higher compressive modulus and expression of chondrogenic markers compared to the MSC pellet culture.