bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activation of pancreatic β-cell genes by multiplex epigenetic CRISPR-editing
Authors: Alejandra Gimenez Carla , Lucia Curti , Ho Hyon Sung , Luis Grosembacher , Juan Ross Pablo , Federico Pereyra-Bonnet 
Published: July 2020

ABSTRACTCRISPR-based systems for epigenetic editing are promising molecular tools that could be harnessed for directed differentiation of pluripotent stem cells. We used the CRISPR/dCas9-VP160, CRISPR/dCas9-TET1 and CRISPR/dCas9-P300 systems for multiplex epigenetic editing and activation of human beta pancreatic genes (PDX1, NEUROG3, PAX4andINS). The CRISPR/dCas9-P300 system was the most effective at activating genes with reduced number of sgRNA. Using small number of sgRNA per gene was important to induce multiplex gene activation. Combined activation of transcription factors (TFs) involved in beta cell development resulted inINSgene expression; in which sequential TFs activation was more effective than simultaneous activation. Full CRISPR RNA-based delivery system was able to activate all targeted genes. Overall, this study shows the utility of CRISPR tools for epigenetic editing and directed cellular differentiation.
Top-down engineering of complex communities by directed evolution
Authors: Chang Chang-Yu , Vila Jean C.C. , Bender Madeline , Li Richard , Mankowski Madeleine C. , Bassette Molly , Borden Julia , Golfier Stefan , Sanchez Paul G. , Waymack Rachel , Zhu Xinwen , Diaz-Colunga Juan , Estrela Sylvie , Rebolleda-Gomez Maria , Sanchez Alvaro 
Published: July 2020

AbstractDirected evolution has been used for decades to engineer biological systems from the top-down. Generally, it has been applied at or below the organismal level, by iteratively sampling the mutational landscape in a guided search for genetic variants of higher function. Above the organismal level, a small number of studies have attempted to artificially select microbial communities and ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is still limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. To address this issue, we have developed a flexible modeling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions, in a wide range of ecological conditions. By artificially selecting hundreds ofin-silicomicrobial metacommunities under identical conditions, we examine the fundamental limits of the two main breeding methods used so far, and prescribe modifications that significantly increase their power. We identify a range of directed evolution strategies that, particularly when applied in combination, are better suited for the top-down engineering of large, diverse, and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search for dynamically stable and ecologically and functionally resilient high-functioning communities.
TheParacaedibacter-like endosymbiont ofBodo saltans(Kinetoplastida) uses multiple putative toxin-antitoxin systems to maintain its host association
Authors: Midha Samriti , Rigden Daniel J. , Siozios Stefanos , Hurst Gregory D. D. , Jackson Andrew P. 
Published: July 2020

AbstractBacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protistBodo saltans(Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other α-proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by whichB. saltansbecomes addicted to its endosymbiont. Consistent with this idea, attempts to cureBodoof endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts ofParacaedibacter-likebacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.
Identification, Mapping and Relative Quantitation of SARS-CoV-2 Spike Glycopeptides by Mass-Retention Time Fingerprinting
Authors: Chalk R. , Greenland W. , Moreira T. , Coker J. , Mukhopadhyay S.M.M , Williams E. , Manning C. , Bohstedt T. , McCrorie R. , Fernandez-Cid A. , Burgess-Brown N.A. 
Published: July 2020

AbstractWe describe a novel analytical method for rapid and robust identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using any LC-TOF mass spectrometer, requires no specialised knowledge of glycan analysis and makes use of the differential resolving power of reversed phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. While this has previously been viewed as a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike. This database allows any ESI-TOF equipped lab to reliably identify and quantify spike glycans from a single overnight elastase protein digest in less than 90 minutes.
Development of predictive QSAR models on the phosphopeptide binding affinity against 14-3-3 isoforms
Authors: Fan Ying , Wang Xiaojun , Wang Chao 
Published: July 2020

Abstract14-3-3s present in multiple isoforms in human cells and mediate signal transduction by binding to phosphoserine-containing proteins. Recent findings have demonstrated that 14-3-3s act as a key factor in promoting chemoresistance of cancer. Here, we aimed to develop the predictive models that can determine the binding affinity of phosphopeptide fragments against 14-3-3s. It is found that the hydrophobic property of residues in phosphopeptides has a significant contribution to the binding affinity for most of 14-3-3 isoforms. The conserved patterns of 14-3-3 biding motifs were verified by our predictions. A group of peptide sequences were predicted with high binding affinity and high sequence conservation, which had agreement with 14-3-3s ligands. Overall, our results demonstrate that how the residues are likely to function in 14-3-3s interaction and the computational methods we introduced may contribute to the further research.
DLX5/6GABAergic expression affects social vocalization: implications for human evolution
Authors: Levi Giovanni , de Lombares Camille , Giuliani Cristina , Iannuzzi Vincenzo , Aouci Rym , Garagnani Paolo , Franceschi Claudio , Grimaud-Hervé Dominique , Narboux-Nême Nicolas 
Published: July 2020

ABSTRACTDLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. TheDLX5/6locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation ofDlx5/6in mouse GABAergic neurons (Dlx5/6VgatCremice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%.Here, we show thatDlx5/6VgatCremice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygousDlx5/6VgatCremice emitted more than 700 and up to 1400 calls/10min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals.The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull and brain shape…) overlap those affected in the “domestication syndrome”. We therefore explored the possibility that DLX5/6 played a role in human evolution and “self-domestication” comparingDLX5/6genomic regions from Neanderthal and modern humans. We identify an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that coversDLX5/6coding and regulatory sequences. TheDLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. TheDLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting their involvement in the co-evolution of longevity, sociability and speech.
The Defensive Activation theory: dreaming as a mechanism to prevent takeover of the visual cortex
Authors: Eagleman David M. , Vaughn Don A. 
Published: July 2020

AbstractRegions of the brain maintain their territory with continuous activity: if activity slows or stops (e.g., because of blindness), the territory tends to be taken over by its neighbors. A surprise in recent years has been the speed of takeover, which is measurable within an hour. These findings lead us to a new hypothesis on the origin of dream sleep. We hypothesize that the circuitry underlying dreaming serves to amplify the visual system’s activity periodically throughout the night, allowing it to defend its territory against takeover from other senses. We find that measures of plasticity across 25 species of primates correlate positively with the proportion of rapid eye movement (REM) sleep. We further find that plasticity and REM sleep increase in lockstep with evolutionary recency to humans. Finally, our hypothesis is consistent with the decrease in REM sleep and parallel decrease in neuroplasticity with aging.
PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Authors: Mateos Pablo Acera , Balboa Renzo F. , Easteal Simon , Eyras Eduardo , Patel Hardip R. 
Published: July 2020

AbstractViral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Usingin silicodata, PACIFIC recovers the presence and relative concentrations of viruses with >99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independentin vitrocell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.
nPhase: An accurate and contiguous phasing method for polyploids
Authors: Abou Saada Omar , Tsouris Andreas , Friedrich Anne , Schacherer Joseph 
Published: July 2020

AbstractWhile genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes,i.e.deducing haplotypes from genomic data, remains a challenge. Despite numerous attempts, no existing polyploid phasing method provides accurate and contiguous haplotype predictions. To address this need, we developed nPhase, a ploidy agnostic pipeline and algorithm that leverage the accuracy of short reads and the length of long reads to solve reference alignment-based phasing for samples of unspecified ploidy (https://github.com/nPhasePipeline/nPhase). nPhase was validated on virtually constructed polyploid genomes of the model speciesSaccharomyces cerevisiae, generated by combining sequencing data of homozygous isolates. nPhase obtained on average >95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover >90% of each chromosome (heterozygosity rate ≥0.5%). This new phasing method opens the door to explore polyploid genomes through applications such as population genomics and hybrid studies.
Tissue-specific and interferon-inducible expression of non-functional ACE2 through endogenous retrovirus co-option
Authors: Ng Kevin , Attig Jan , Bolland William , Young George R. , Major Jack , Wack Andreas , Kassiotis George 
Published: July 2020

SummaryAngiotensin-converting enzyme 2 (ACE2) is an entry receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), as well as a regulator of several physiological processes.ACE2has recently been proposed to be interferon-inducible, suggesting that SARS-CoV-2 may exploit this phenomenon to enhance viral spread and questioning the efficacy of interferon treatment in Coronavirus disease 2019 (COVID-19). Using a recentde novotranscript assembly that captured previously unannotated transcripts, we describe a novel isoform ofACE2, generated by co-option of an intronic long terminal repeat (LTR) retroelement promoter. The novel transcript, termedLTR16A1-ACE2, exhibits specific expression patterns across the aerodigestive and gastrointestinal tracts and, importantly, is highly responsive to interferon stimulation. In stark contrast, expression of canonicalACE2is completely unresponsive to interferon stimulation. Moreover, theLTR16A1-ACE2translation product is a truncated, unstable ACE2 form, lacking domains required for SARS-CoV-2 binding and therefore unlikely to contribute to or enhance viral infection.
Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor
Authors: Miozzo Federico , Stickley Luca , Valencia-Alarcón Eva P. , Dorcikova Michaela , Petrelli Francesco , Tas Damla , Loncle Nicolas , Nikonenko Irina , Dib Peter Bou , Nagoshi Emi 
Published: July 2020

ABSTRACTThe degeneration of dopaminergic (DA) neurons in the substantia nigra is a hallmark of Parkinson’s disease (PD). Dysregulation of developmental transcription factors is implicated in dopaminergic neurodegeneration, but the underlying molecular mechanisms remain largely unknown.Drosophila Fer2is a prime example of a developmental transcription factor required for the birth and maintenance of midbrain DA neurons. Using an approach combining ChIP-seq, RNA-seq, and genetic epistasis experiments with PD-linked genes, here we demonstrate thatFer2controls a transcriptional network to maintain mitochondrial structure and function, and thus confers dopaminergic neuroprotection against genetic and oxidative insults. We further show that conditional ablation ofNato3,a mouse homolog ofFer2, in differentiated DA neurons results in locomotor impairments and mitochondrial abnormality in aged mice. Our results reveal the essential and conserved role ofFer2 homologs in the mitochondrial maintenance of midbrain DA neurons, opening new perspectives for modelling and treating PD.
How predictability affects habituation to novelty?
Authors: Ueda Kazutaka , Sekoguchi Takahiro , Yanagisawa Hideyoshi 
Published: July 2020

AbstractOne becomes accustomed to repeated exposures, even for a novel event. In the present study, we investigated how predictability affects habituation to novelty by applying a mathematical model of arousal that we previously developed, and conducted a psychophysiological experiment to test the model prediction. We formalized habituation to novelty as a decrement in Kullback-Leibler divergence from Bayesian prior to posterior (i.e., information gain) representing arousal evoked from a novel event through Bayesian update. The model predicted an interaction effect between initial uncertainty and initial prediction error (i.e., predictability) on habituation to novelty: The greater the initial uncertainty, the faster the information gain decreases (i.e., the sooner one is habituated). Experimental results using subjective reports of surprise and event-related potential (P300) evoked by visual-auditory incongruity supported the model prediction. Our findings suggest that in highly uncertain situations, repeated exposure to stimuli may enhance habituation to novel stimuli.
Can combined compost and biochar application improve the quality of a highly weathered coastal savanna soil?
Authors: Frimpong Kwame Agyei , Abban-Baidoo Emmanuel , Marschner Bernd 
Published: July 2020

AbstractSoil fertility decline represents a major constraint to crop productivity in sub-Saharan Africa. Many studies have shown that addition of biochar or compost can effectively improve soil quality. Biochar produced from crop residues are often N-poor but rich in stable C while poultry manure composts, which is often rich in nutrients including N decomposes rapidly under high rainfall and temperature conditions. Combined biochar and compost application can compensate for the shortcomings of each other such that their interactive effect is likely to improve soil quality. A 30-days incubation experiment was carried out on a Haplic acrisol amended with corn cob biochar, rice husk biochar, coconut husk biochar, poultry manure compost and composted rice husk or corn cob biochar to examine the effect of compost and biochar, applied singly, in combination or as co-compost on basal soil respiration, and soil quality indicators such as soil pH; soil microbial carbon; cation exchange capacity; total organic carbon, total nitrogen and available nitrogen concentration. The results showed that addition of the different amendments increased soil pH compared with the untreated control with the combined corn cob and rice biochar and compost treatments recording the highest pH values. Basal respiration following sole compost, composted biochar and combined biochar and compost application were significantly greater than the sole biochar and the control treatments. TOC increased by 37% in the sole compost treatment to 117.3% in the combined corn cob biochar and compost treatment, respectively. MBC increased by 132.2% in the combined rice husk biochar and compost treatment and by 247% in the sole compost treatment compared to the control. The study has demonstrated the potential of compost, biochar and especially composted biochar to enhance soil quality, C stabilization and reduce soil C loss through basal respiration.
Activating NK- receptors, homing selectins and inhibitory Siglecs recognize EBOLA-GP and HPV-L1NK
Authors: Jarahian Mostafa , Marstaller Katharina , Wurmbäck Heribert , Banna Nadine , Ahani Roshanak , Etemadzadeh Hossein , Boller Lea Katharina , Azadmanesh Kayhan , Cid-Arregui Angel , Berger Martin R , Momburg Frank , Watzl Carsten 
Published: July 2020

AbstractThe Ebola virus glycoprotein (EBOV)-GP is extensively glycosylated. Its expression induces a physical alteration of surface adhesion molecules, which causes cell rounding and detachment of the infected cells. This phenomenon likely plays a crucial role in viral pathogenicity. In this study, we show that such morphological changes are cell line-dependent as well as dependent on the surface proteins that interact with EBOV-GP incisandtrans. We have generated data showing that natural killer (NK) cell receptors (NCRs: NKp44 and NKp46), selectins (CD62E/P/L) and inhibitory Siglecs function as receptors for Ebola-GP and human papilloma virus (HPV-L1). We used HEK293 cells transfected with Ebola-GP and recombinant fusion proteins containing the extracellular domain of each of these receptors linked to the Fc of human IgG1, which showed significant differences in their virus-binding behavior compared to HEK293 cells transfected with empty vector. Further, to demonstrate that EBOV-GP is a ligand for NKp44 and other NK-receptors, and to investigate their role in immune escape, we also used human HEK-293, HeLa- and hamster CHO-GP-transfectants. Our data show that the NK receptors NKp44 and NKp46 play a key role in recognizing EBOV (Ebolavirus) and strongly suggest that other inhibitory (Siglec-7, Siglec-5) and non-inhibitory homing receptors (P-Selectin, L-Selectin, E-Selectin, and DC-SIGNR/DC-SIGN) take part in the interaction with virus particles. In addition, we show that NKp44, and NKp46, Siglec-7, and -5, and P-, L-, E-selectins as well as of and DC-SIGNR/DC-SIGN bind to the artificial viral envelope of a lentiviral vector that contains EBOV-GP. Altogether we prove that NCRs and a range of other inhibitory and activating receptors can interact with viral envelope/capsid proteins and that such interaction could play an important role in the elimination of virus infected cells. Our findings could be used to develop new strategies for prevention and treatment of infections by these viruses.Author summaryThe innate immune system is able to recognize specifically certain virus components. Here we show that activating NK-cell receptors (NKp44, and NKp46) are involved in such interaction by using HEK293 and CHOK1 cells transfected with the Ebola virus glycoprotein (EBOV-GP) and by binding studies with purified EBOV-GP. In detail, we have found moderate to strong affinity of Siglecs (Siglec-7, and -5), selectins (P-, L-, E-Selectin) and DC-SIGNR/DC-SIGN to purified EBOV-GP, and to cells transfected with EBOV-GP as well as to the envelope of a lentiviral vector carrying the EBOV-GP. Our findings show that NKp44, and NKp46, Siglec-7, and -5, as well as P-and L-selectins have a strong affinity to EBOV-G.
The BMP antagonistGremlin1contributes to the development of cortical excitatory neurons, motor balance and fear responses
Authors: Ichinose Mari , Suzuki Nobumi , Wang Tongtong , Kobayashi Hiroki , Vrbanac Laura , Ng Jia Q , Wright Josephine A , Lannagan Tamsin R M , Gieniec Krystyna A , Lewis Martin , Ando Ryota , Enomoto Atsushi , Koblar Simon , Thomas Paul , Worthley Daniel L , Woods Susan L 
Published: July 2020

AbstractBone morphogenetic protein (BMP) signaling is required for early forebrain development and cortical formation. How the endogenous modulators of BMP signaling regulate the structural and functional maturation of the developing brain remains unclear. Here we show that expression of the BMP antagonist,Grem1, marks a neuroprogenitor that gives rise to layer V and VI glutamatergic neurons in the embryonic mouse brain. Lineage tracing ofGrem1-expressing cells in the embryonic brain was examined by administration of tamoxifen to pregnantGrem1creERT Rosa26LSLTdtomatomice at 13.5 days post coitum (dpc), followed by collection of embryos later in gestation. In addition, at 14.5 dpc, bulk mRNA seq analysis of differentially expressed transcripts between FACS sortedGrem1positive and negative cells was performed. We also generatedEmx1-cremediatedGrem1conditional knockout mice (Emx1-Cre;Grem1flox/flox) in which theGrem1gene was deleted specifically in the dorsal telencephalon.Grem1Emx1cKOanimals had reduced cortical thickness, especially layers V and VI and impaired motor balance and fear sensitivity compared to littermate controls. This study has revealed new roles for Grem1 in the structural and functional maturation of the developing cortex.Summary statementThe BMP antagonist,Grem1, marks neuroprogenitors that give rise to deep layer glutamatergic neurons in the embryonic mouse brain.Grem1conditional knockout mice display cortical and behavioural abnormalities.