bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
Authors: Amândio Ana Rita , Beccari Leonardo , Lopez-Delisle Lucille , Mascrez Bénédicte , Zakany Jozsef , Gitto Sandra , Duboule Denis 
Published: August 2021

ABSTRACTMammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in-cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the mis-regulation of Hoxd genes in specific structures. Altogether, while most enhancer-promoter interactions can occur in the absence of this series of CTCF sites, it seems that the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer-promoter interactions and some doing both, whereas all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites amongst paralogous Hox clusters or between various vertebrates.
Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape
Authors: Zappia Luke , Theis Fabian J. 
Published: August 2021

AbstractRecent years have seen a revolution in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq). As the number, size and complexity of scRNA-seq datasets continue to increase, so does the number of computational methods and software tools for extracting meaning from them. Since 2016 the scRNA-tools database has catalogued software tools for analysing scRNA-seq data. With the number of tools in the database passing 1000, we take this opportunity to provide an update on the state of the project and the field. Analysis of five years of analysis tool tracking data clearly shows the evolution of the field, and that the focus of developers has moved from ordering cells on continuous trajectories to integrating multiple samples and making use of reference datasets. We also find evidence that open science practices reward developers with increased recognition and help accelerate the field.
Light-controlled elimination of PD-L1+ cells
Authors: Wong Judith Jing Wen , Selbo Pål Kristian 
Published: August 2021

AbstractThe programmed death ligand-1 (PD-L1), also known as CD274 or B7-H1, is mainly expressed on cancer cells and/or immunosuppressive cells in the tumor microenvironment (TME) and plays an essential role in tumor progression and immune escape. Immune checkpoint inhibitors (ICIs) of the PD-1/PD-L1 axis have shown impressive clinical success, however, the majority of the patients do not respond to immune checkpoint therapy (ICT). Thus, to overcome ICT resistance there is a high need for potent and novel strategies that simultaneously target both tumor cells and immunosuppressive cells in the TME. In this study, we show that the intracellular light-controlled drug delivery method photochemical internalization (PCI) induce specific and strongly enhanced cytotoxic effects of the PD-L1-targeting immunotoxin, anti-PD-L1-saporin (Anti-PDL1-SAP), in the PD-L1+ triple-negative breast cancer MDA-MB-231 cell line, while no enhanced efficacy was obtained in the PD-L1 negative control cell line MDA-MB-453. Using fluorescence microscopy, we reveal that the anti-PD-L1 antibody binds to PD-L1 on the surface of the MDA-MD-231 cells and overnight accumulates in late endosomes and lysosomes where it co-localizes with the PCI photosensitizer fimaporfin (TPCS2a). Moreover, light-controlled endosomal/lysosomal escape of the anti-PD-L1 antibody and fimaporfin into the cytosol was obtained. We also confirm that the breast MDA-MB-468 and the prostate PC-3 and DU-145 cancer cell lines have subpopulations with PD-L1 expression. In addition, we show that interferon-gamma strongly induce PD-L1 expression in the per se PD-L1 negative CT26.WT cells and enhance the PD-L1 expression in MC-38 cells, of which both are murine colon cancer cell lines. In conclusion, our work provides an in vitro proof-of-concept of PCI-enhanced targeting and eradication of PD-L1 positive immunosuppressive cells. This light-controlled combinatorial strategy has a potential to advance cancer immunotherapy and should be explored in preclinical studies.
Contrasting resistance and resilience to light variation of the coupled oxic and anoxic components of an experimental microbial ecosystem
Authors: Suleiman Marcel , Pennekamp Frank , Choffat Yves , Petchey Owen L. 
Published: August 2021

AbstractUnderstanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used phototrophic oxic-anoxic micro-ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities is affected by light deprivation. Continuous measurements were performed to describe oxygen dynamics (mean/min/max/amplitude) and time-series of full-length 16S rRNA sequencing were used to quantify changes in alpha- and beta-diversity. In the top oxic layer, oxygen concentration decreased significantly under light deprivation, but showed resilience in mean, minimum and maximum after light conditions were restored. Only the amplitude of diurnal fluctuations in oxygen concentrations did not recover fully, and instead tended to remain lower in treated ecosystems. Alpha-diversity of the top oxic layer communities showed a delayed increase after light conditions were restored, and was not resilient. In contrast, alpha-diversity of the anoxic bottom layer communities increased due to the stressor, but was resilient. Community composition changed significantly during light deprivation, showed resilience in the oxic layer and lack of resilience in the anoxic layer. Alpha-diversity and the amplitude of oxygen within and among treatments were strongly correlated, suggesting that higher diversity could lead to less variable oxygen concentrations, or vice versa. Our experiment showed that light deprivation induces multifaceted responses of community function and structure, hence focusing on a single stability component could potentially be misleading.
Metabolomics and Transcriptomics unravel the mechanism of browning resistance in Agaricus bisporus
Authors: Cai Zhi-Xin , Chen Mei-Yuan , Lu Yuan-Ping , Guo Zhong-Jie , Zeng Zhi-Heng , Zheng Hui-Qing , Liao Jian-Hua 
Published: August 2021

AbstractAgaricus bisporus is widely used on the world market. The easy browning of mushroom surface is one of the most intuitive factors affecting consumer purchase. A certain cognition on browning mechanism have been made after years of research. At present, people slow down the browning of mushrooms mainly by improving preservation methods. In addition, breeding is also a reliable way. In the production practice, we have identified some browning resistant varieties,and we selected a browning-resistant variety to compare with ordinary variety to reveal the resistance mechanism. Using transcriptomics and metabolomics, the differences in gene expression and metabolite levels were revealed, respectively. The results showed that differentially expressed genes (DEGs) like AbPPO4, AbPPO3 and AbPPO2 were differently expressed and these DEGs involved in many pathways that related to browning. The expression of AbPPO expression play an important role in the browning of A. bisporus and multiple PPO family members are involved in the regulation of browning. However, the resistance to browning cannot be judged only by the expression level of AbPPOs. Formetabolomics, most of the different metabolites were organic acids. These organic acids had a higher level in anti-browning (BT) than easy-browning varieties (BS), although the profile was very heterogeneous. On the contrary, the content of trehalose in BS was significantly higher than that in BT. Higher organic acids decreased pH and further inhibited PPO activity. In addition, the BS had a higher content of trehalose, which might play roles in maintain the activity of PPO. The difference of browning resistance between BS and BT is mainly due to the differential regulation mechanism of PPO.
Judgement Bias During Pregnancy in Domestic Pigs
Authors: Bushby Emily V. , Cotter Sheena C. , Wilkinson Anna , Friel Mary , Collins Lisa M. 
Published: August 2021

AbstractIn humans and rats, changes in mood and affect are known to occur during pregnancy, however it is unknown how gestation may influence mood in other non-human mammals. This study assessed changes in pigs’ judgment bias as a measure of affective state throughout gestation. Pigs were trained to complete a spatial judgement bias task with reference to positive and negative locations. We tested gilts before mating, and during early and late pregnancy, by assessing their responses to ambiguous probe locations. Pigs responded increasingly negatively to ambiguous probes as pregnancy progressed and there were consistent inter-individual differences in baseline optimism. This suggests that the pigs’ affective state may be altered during gestation, although as a non-pregnant control group was not tested, an effect of learning cannot be ruled out. These results suggest that judgement bias is altered during pregnancy in domestic pigs, consequently raising novel welfare considerations for captive multiparous species.
The temporal dynamics of the Stroop effect from childhood to young and older adulthood
Authors: Ménétré E. , Laganaro M. 
Published: August 2021

AbstractIt is well admitted that children and older adults tend to show longer response latencies at the Stroop task than young adults. The present study aims at clarifying the rational of such changes from childhood to adulthood and in ageing by comparing the impacted cognitive processes across age groups. More precisely, the aim was to clarify if all processes take more time to be executed, hence implying that longer latencies rely mainly on processing speed or if an additional process lengthens the resolution of the conflict in children and/or older adults. To this aim we recorded brain electrical activity using EEG in school-age children, young and older adults while they performed a classic verbal Stroop task. To decompose the signal in the underlying brain networks, we used microstates analyses and compared congruent, incongruent and neutral trials across the three age-groups. Behaviorally, children and older adults presented longer latencies and larger Stroop effects relative to young adults. The microstates results showed that children tend to present different brain configurations compared to both adult groups, even though some brain configurations remained identical among the three groups. In particular, additional brain networks were involved in children to perform the Stroop task, which party account for the longer latencies in this group. By contrast, in aging the results favor the general slowing hypothesis rather than a decline in a specific process since all involved brain networks were similar in the two adult groups but slowed down in the older one.
A bacterium-like particle vaccine displaying Zika virus prM-E induces systemic immune responses in mice
Authors: Jin Hongli , Bai Yujie , Wang Jianzhong , Jiao Cuicui , Liu Di , Zhang Mengyao , Li Entao , Huang Pei , Gong Zhiyuan , Song Yumeng , Xu Shengnan , Feng Na , Zhao Yongkun , Wang Tiecheng , Li Nan , Gao Yuwei , Yang Songtao , Xia Xianzhu , Wang Hualei 
Published: August 2021

AbstractThe emergence of Zika virus (ZIKV) infection, which is an unexpectedly associated with congenital defects, has prompted the development of safe and effective vaccines. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has emerged as a versatile and highly effective platform for delivering target proteins for vaccines. In this article, we developed a bacterium-like particle vaccine ZI-Δ-PA-GEM based on the GEM-PA system. The fusion protein ZI-Δ-PA, which contains the prM-E-Δ protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3, was expressed. The fusion protein was successfully displayed on the GEM surface, forming ZI-Δ-PA-GEM. Moreover, when BALB/c mice were immunized intramuscularly with ZI-Δ-PA-GEM combined with 201 VG and poly(I:C) adjuvants, durable ZIKV-specific IgG and protective neutralizing antibody responses were induced. Potent B cell/DC activation was also be stimulated early after immunization. Remarkably, splenocyte proliferation, the secretion of multiple cytokines, T/B cell activation and central memory T cell responses were elicited. These data indicate that ZI-Δ-PA-GEM is a promising bacterium-like particle vaccine candidate for ZIKV.Author summaryBecause Zika virus (ZIKV) infection is considered as an example of “disease X”, the development of a safe and effective ZIKV vaccine is essential. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has been used in many vaccine studies due to its advantages. In this study, prM-E-△ protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3 was fusion expressed, termed ZI-△-PA. Then the fusion protein ZI-△-PA could be displayed on the surface of GEM, forming ZI-△-PA-GEM. The author evaluated the immunogenicity of ZI-△-PA-GEM with the 201 VG and poly(I:C) adjuvants. The study demonstrates that ZI-△-PA-GEM induced mice to produce neutralizing antibody and specific cellular immune responses. The author believe that the bacterium-like particle vaccine ZI-△-PA-GEM has the potential to be used as the ZIKV vaccine.
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions
Authors: Moutinho Thomas J. , Neubert Benjamin C. , Jenior Matthew L. , Papin Jason A. 
Published: August 2021

AbstractGenome-scale metabolic network reconstructions (GENREs) are valuable tools for understanding microbial community metabolism. The process of automatically generating GENREs includes identifying metabolic reactions supported by sufficient genomic evidence to generate a draft metabolic network. The draft GENRE is then gapfilled with additional reactions in order to recapitulate specific growth phenotypes as indicated with associated experimental data. Previous methods have implemented absolute mapping thresholds for the reactions automatically included in draft GENREs; however, there is growing evidence that integrating annotation evidence in a continuous form can improve model accuracy. There is a need for flexibility in the structure of GENREs to better account for uncertainty in biological data, unknown regulatory mechanisms, and context specificity associated with data inputs. To address this issue, we present a novel method that provides a framework for quantifying combined genomic, biochemical, and phenotypic evidence for each biochemical reaction during automated GENRE construction. Our method, Constraint-based Analysis Yielding reaction Usage across metabolic Networks (CANYUNs), generates accurate GENREs with a quantitative metric for the cumulative evidence for each reaction included in the network. The structure of a CANYUN GENRE allows for the simultaneous integration of three data inputs while maintaining all supporting evidence for biochemical reactions that may be active in an organism. CANYUNs is designed to maximize the utility of experimental and annotation datasets and to ultimately assist in the curation of the reference datasets used for the automatic reconstruction of metabolic networks. We validated CANYUNs by generating an E. coli K-12 model and compared it to the manually curated reconstruction iML1515. Finally, we demonstrated the use of CANYUNs to build a model by generating an E. coli Nissle CANYUN GENRE using novel phenotypic data that we collected. This method may address key challenges for the procedural construction of metabolic networks by leveraging uncertainty and redundancy in biological data.
A diabetic milieu increases cellular susceptibility to SARS-CoV-2 infections in engineered human kidney organoids and diabetic patients
Authors: Garreta Elena , Prado Patricia , Stanifer Megan , Monteil Vanessa , del Pozo Carmen Hurtado , Ullate-Agote Asier , Vilas-Zornoza Amaia , Romero Juan Pablo , Jonsson Gustav , Oria Roger , Leopoldi Alexandra , Hagelkruys Astrid , Moya-Rull Daniel , González Federico , Marco Andrés , Tarantino Carolina , Domingo-Pedrol Pere , HasanAli Omar , Ventura-Aguiar Pedro , María Campistol Josep , Prosper Felipe , Mirazimi Ali , Boulant Steeve , Penninger Josef M. , Montserrat Nuria 
Published: August 2021

SummarySARS-CoV-2 infections lead to a high risk of hospitalization and mortality in diabetic patients. Why diabetic individuals are more prone to develop severe COVID-19 remains unclear. Here, we established a novel human kidney organoid model that mimics early hallmarks of diabetic nephropathy. High oscillatory glucose exposure resulted in metabolic changes, expansion of extracellular membrane components, gene expression changes determined by scRNAseq, and marked upregulation of angiotensin-converting enzyme 2 (ACE2). Upon SARS-CoV-2 infection, hyperglycemic conditions lead to markedly higher viral loads in kidney organoids compared to normoglycemia. Genetic deletion of ACE2, but not of the candidate receptor BSG/CD147, in kidney organoids demonstrated the essential role of ACE2 in SARS-CoV-2 infections and completely prevented SARS-CoV-2 infection in the diabetogenic microenvironment. These data introduce a novel organoid model for diabetic kidney disease and show that diabetic-induced ACE2 licenses the diabetic kidney to enhanced SARS-CoV-2 replication.
Across functional boundaries: making non-neutralizing antibodies to neutralize HIV-1 and mediate Fc-mediated effector killing of infected cells
Authors: Richard Jonathan , Nguyen Dung N. , Tolbert William D. , Gasser Romain , Ding Shilei , Vézina Dani , Gong Shang Yu , Prévost Jérémie , Gendron-Lepage Gabrielle , Medjahed Halima , Gottumukkala Suneetha , Finzi Andrés , Pazgier Marzena 
Published: August 2021

AbstractIn HIV-1 infection, many antibodies (Abs) are elicited to Envelope (Env) epitopes that are conformationally masked in the native trimer and are only available for antibody recognition after the trimer binds host cell CD4. Among these are epitopes within the Co-Receptor Binding Site (CoRBS) and the constant region 1 and 2 (C1-C2 or Cluster A region). In particular, C1-C2 epitopes map to the gp120 face interacting with gp41 in the native, ‘closed’ Env trimer present on HIV-1 virions or expressed on HIV-1 infected cells. Antibodies targeting this region are therefore non-neutralizing and their potential as mediators of antibody depended cellular cytoxicity (ADCC) of HIV-1 infected cells diminished by a lack of available binding targets. Here we present the design of Ab-CD4 chimeric proteins that consist of the Ab-IgG1 of a CoRBS or Cluster A specificity to the extracellular domain 1 and 2 of human CD4. Our Ab-CD4 hybrids induce potent ADCC against infected primary CD4+ T cells and neutralize tier 1 and 2 HIV-1 viruses. Furthermore, competition binding experiments reveal that the observed biological activities rely on both the antibody and CD4 moieties confirming their cooperativity in triggering conformational rearrangements of Env. Our data indicate the utility of these Ab-CD4 hybrids as antibody therapeutics effective in eliminating HIV-1 through the combined mechanisms of neutralization and ADCC. This is also the first report of single-chain-Ab-based molecules capable of opening ‘closed’ Env trimers on HIV-1 particles/infected cells to expose the Cluster A region and activate ADCC and neutralization against these non-neutralizing targets.ImportanceHighly conserved epitopes within the co-receptor binding site (CoRBS) and constant region 1 and 2 (C1C2 or Cluster A) are only available for antibody recognition after the HIV-1 Env trimer binds host cell CD4, therefore they are not accessible on virions and infected cells where the expression of CD4 is downregulated. Here we have developed new antibody fusion molecules in which domains 1 and 2 of soluble human CD4 are linked with monoclonal antibodies of either the CoRBS or Cluster A specificity. We optimized the conjugation sites and linker lengths to allow each of these novel bispecific fusion molecules to recognize native “closed” Env trimers and induce the structural rearrangements required for exposure of the epitopes for antibody binding. Our in vitro functional testing shows that our Ab-CD4 molecules can efficiently target and eliminate HIV-1 infected cells through antibody depended cellular cytoxicity (ADCC) and inactivate HIV-1 virus through neutralization.
Two parallel sRNA amplification cycles contribute to RNAi inheritance in C. elegans
Authors: Ouyang John Paul Tsu , Zhang Wenyan , Seydoux Geraldine 
Published: August 2021

AbstractRNA-mediated interference (RNAi) is a conserved mechanism that uses small RNAs (sRNAs) to tune gene expression. In C. elegans, exposure to dsRNA induces the production of gene-specific sRNAs that are propagated to progeny not exposed to the dsRNA trigger. We present evidence that RNAi inheritance is mediated by two parallel sRNA amplification loops. The first loop, dependent on the nuclear Argonaute HRDE-1, targets nascent transcripts, and reduces but does not eliminate productive transcription at the locus. The second loop, dependent on the conserved helicase ZNFX-1, targets mature transcripts and concentrates them in perinuclear condensates (nuage). Each amplification loop generates a distinct class of sRNAs, with the ZNFX-1 loop responsible for the bulk of sRNA production on the region targeted by the trigger. By independently targeting nascent and mature transcripts, the HRDE-1 and ZNFX-1 loops ensure maximum silencing in progeny not exposed to the trigger.