bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPRi inDeinococcus radiodurans
Authors: Misra Chitra S. , Pandey Neha , Appukuttan Deepti , Rath Devashish 
Published: November 2022

AbstractThe extremely radiation resistant bacterium,Deinococcus radiodurans, is a microbe of importance, both, for studying stress tolerance mechanisms and as a chassis for industrial biotechnology. However, the molecular tools available for use in this organism continue to be limiting. In view of this, the CRISPR-Cas tools provide a large repertoire of applications for gene manipulation. We show the utility of the type I-E Cascade system for knocking down gene expression in this organism. A single-vector system was designed for expression of the Cascade components as well as the crRNA. The type I-E Cascade system was better tolerated than the type II-A Cas9 system inD. radiodurans. An assayable acid phosphatase gene,phoNintegrated into the genome of this organism could be knocked down to 10% of its activity using the Cascade system. Cascade-based knockdown ofssb, a gene important for radiation resistance resulted in poor recovery post irradiation. Targeting the Radiation and Desiccation Resistance Motif (RDRM), upstream of thessb, prevented de-repression of its expression upon radiation exposure. In addition to this, multi-locus targeting was demonstrated on the deinococcal genome, by knocking down bothphoNandssbexpression simultaneously. The programmable CRISPRi tool developed in this study will facilitate study of essential genes, hypothetical genes, cis-elements involved in radiation response as well as enable metabolic engineering in this organism. Further the tool is amenable for implementing high-throughput approaches for such studies.
Enzymatic assembly of small synthetic genes with repetitive elements
Authors: Nguyen Michael T. A. , Gobry Martin Vincent , Vallina Néstor Sampedro , Pothoulakis Georgios , Andersen Ebbe Sloth 
Published: November 2022

AbstractGene synthesis efficiency has greatly improved in recent years but is limited when it comes to repetitive sequences and results in synthesis failure or delays by DNA synthesis vendors. This is representing a major obstacle for the development of synthetic biology, since repetitive elements are increasingly being used in design of genetic circuits and design of biomolecular nanostructures. Here, we describe a method for the assembly of small synthetic genes with repetitive elements: First, a gene of interest is splitin silicointo small synthons of up to 80 base pairs flanked by Golden Gate-compatible overhangs. Then, synthons are made by oligo extension and finally assembled into a synthetic gene by Golden Gate Assembly. We demonstrate the method by constructing eight challenging genes with repetitive elements e.g., multiple repeats of RNA aptamers and RNA origami scaffolds with multiple identical aptamers. The genes range in size from 133 to 456 base pairs and are assembled with fidelities of up to 87.5 %. The method was developed to facilitate our own specific research but may be of general use for constructing challenging and repetitive genes and thus a valuable addition to the molecular cloning toolbox.
MERISTEM-DEFECTIVE / DEFECTIVELY ORGANIZED TRIBUTARIES2 regulates the balance between stemness and differentiation in the root meristem through RNA splicing control
Authors: Thompson Helen L. , Shen Weiran , Matus Rodrigo , Kakkar Medhavi , Jones Carl , Dolan David , Grellscheid Sushma , Yang Xiyan , Zhang Na , Mozaffari-Jovin Sina , Chen Chunli , Zhang Xianlong , Topping Jennifer F. , Lindsey Keith 
Published: November 2022

ABSTRACTPlants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. TheMERISTEM-DEFECTIVE(MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES(DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identifiedRSZ33andACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem.MDFexpression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing targetSR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response and cell differentiation pathways.Summary statementThe protein MERISTEM-DEFECTIVE regulates Arabidopsis meristem function through its role as a splicing factor, mediated through splicing targets RSZ33, ACC1 and SR34.
Promoting translational readthrough to augment fibrillin-1 (FBN1) deposition in Marfan syndrome fibroblasts: A proof-of-concept study
Authors: Balic Zerina , Hubmacher Dirk 
Published: November 2022

AbstractMarfan syndrome (MFS) is a connective tissue disorder characterized by long bone overgrowth, enlargement of the aorta, ocular anomalies and other symptoms. Current treatment focuses on managing aortic aneurysms to avoid dissection or rupture. However, no cures are available. MFS is caused by one of >1,800 dominant pathogenic variants inFBN1, which encodes the extracellular matrix (ECM) protein fibrillin-1. A significant number ofFBN1variants result in premature termination codons (PTCs). Recently, small molecules were identified that can promote translational readthrough of PTCs and were evaluated in preclinical and clinical trials for several genetic disorders. Here, we show that the translational readthrough drugs ataluren and gentamicin ameliorated FBN1 deposition in some MFS patient-derived skin fibroblast lines harboring PTC variants inFBN1. In contrast, inhibitors of NMD were cytotoxic to the skin fibroblast lines that we analyzed. We conclude that promoting translational readthrough of PTC variants inFBN1could result in a therapeutic benefit for MFS patients with specific PTCs inFBN1and that its efficacy will likely depend on the PTC sequence context, the amino acids that are incorporated in FBN1 after PTC suppression and the overall increase of FBN1 deposition in the ECM.
Apicomplexans predict thermal stress mortality in the Mediterranean coralParamuricea clavata
Authors: Bonacolta Anthony M , Miravall Jordi , Gómez-Gras Daniel , Ledoux Jean-Baptiste , López-Sendino Paula , Garrabou Joaquim , Massana Ramon , del Campo Javier 
Published: November 2022

AbstractThe octocoralParamuricea clavatais an ecosystem architect of the Mediterranean temperate reefs that is currently threatened by episodic mass mortality events related to global warming. Local average thermal regimes nor recent thermal history have been shown to play a significant role in population thermotolerance in this species. The microbiome, however, may play an active role in the thermal stress susceptibility of corals, potentially holding the answer as to why corals show differential sensitivity to heat-stress. To investigate this, the prokaryotic and eukaryotic microbiome ofP. clavatacollected from around the Mediterranean was characterized before experimental heat-stress to determine if its microbial composition influences the thermal response of the holobiont. We found that the prokaryotic community was not informative in predicting the thermal susceptibility ofP. clavata. On the other hand, members ofP. clavata’smicroeukaryotic community were significantly correlated with thermal stress sensitivity. Syndiniales from theDino-Group I Clade 1were significantly enriched in thermally resistant corals, while the apicomplexan corallicolids were significantly enriched in thermally susceptible corals. Corallicolids are associated with 70% of coral genera around the world, yet the ecological role of this general anthozoan symbiont has yet to be determined. We hypothesize thatP. clavatamortality following heat-stress may be caused by a shift from apparent commensalism to parasitism in the corallicolid-coral host relationship driven by the added stress. Our results show the potential importance of corallicolids and the rest of the microeukaryotic community of corals to understanding thermal stress response in corals and provides a useful tool to guide conservation efforts and future research into coral-associated microeukaryotes.
Active smelling in the American cockroach
Authors: Hoffmann Antoine , Couzin-Fuchs Einat 
Published: November 2022

2AbstractMotion plays an essential role in sensory acquisition. From changing the position in which information can be acquired to fine scale probing and active sensing, animals actively control the way they interact with the environment. In olfaction, movement impacts the time and location of odour sampling as well as the flow of odour molecules around the olfactory organs. Employing a high-resolution analysis, we investigate how the insect antennae interact with the olfactory environment in a species with a well studied olfactory system – the American cockroach. Cockroaches were tested in a wind-tunnel setup during the presentation of odours with different attractivity levels: colony extract, butanol and linalool. Our analysis revealed significant changes in antennal kinematics when odours are presented, including a shift towards the stream position, an increase in vertical movement and high-frequency local oscillations. Nevertheless, the antennal shifting occurred predominantly in a single antenna while the overall range covered by both antennae was maintained throughout. These findings hold true for both static and moving stimuli and are more pronounced for attractive odours. Furthermore, we find that upon odour encounter, there is an increased occurrence of high-frequency antennal sweeps and vertical strokes, which are shown to impact the olfactory environment’s statistics directly. Our study lays out a tractable system for exploring the tight coupling between sensing and movement, in which antennal sweeps, in parallel to mammalian sniffing, are actively involved in facilitating odour capture and transport, generating odour intermittency in environments with low air movement where cockroaches dwell.
Accuracy and completeness of long read metagenomic assemblies
Authors: Buttler Jeremy , Drown Devin 
Published: November 2022

AbstractMicrobes, we can learn how microbes influence the surrounding environment, contribute to human health, and understand which pathogen interactions result in differences in disease severity. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library on the VolTRAX V2 sequence using a MinION mk1b. We basecalled using the latest version of Guppy with the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10x read depth. Polishing assemblies using Medaka had a predictable improvement in quality. Some assemblers struggled with particular members of the bacterial community, but we found Flye to be the most robust across taxa. We found Flye was the most effective assembler for recovering plasmids. Based on Flye’s consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies.
Molecular and cellular similarities in the brain of SARS-CoV-2 and Alzheimer’s disease individuals
Authors: Griggs Elizabeth , Trageser Kyle , Naughton Sean , Yang Eun-Jeong , Mathew Brian , Van Hyfte Grace , Hellmers Linh , Jette Nathalie , Estill Molly , Shen Li , Fischer Tracy , Pasinetti Giulio Maria 
Published: November 2022

AbstractInfection with the etiological agent of COVID-19, SARS-CoV-2, appears capable of impacting cognition, which some patients with Post-acute Sequelae of SARS-CoV-2 (PASC). To evaluate neuro-pathophysiological consequences of SARS-CoV-2 infection, we examine transcriptional and cellular signatures in the Broadman area 9 (BA9) of the frontal cortex and the hippocampal formation (HF) in SARS-CoV-2, Alzheimer’s disease (AD) and SARS-CoV-2 infected AD individuals, compared to age- and gender-matched neurological cases. Here we show similar alterations of neuroinflammation and blood-brain barrier integrity in SARS-CoV-2, AD, and SARS-CoV-2 infected AD individuals. Distribution of microglial changes reflected by the increase of Iba-1 reveal nodular morphological alterations in SARS-CoV-2 infected AD individuals. Similarly, HIF-1α is significantly upregulated in the context of SARS-CoV-2 infection in the same brain regions regardless of AD status. The finding may help to inform decision-making regarding therapeutic treatments in patients with neuro-PASC, especially those at increased risk of developing AD.TeaserSARS-CoV-2 and Alzheimer’s disease share similar neuroinflammatory processes, which may help explain neuro-PASC.
Alternative paths to immune activation: the role of costimulatory risk genes for polygenic inflammatory disease in T helper cells
Authors: Voda Alexandru-Ioan , Correa Kristina , Hamp Jonathan , Moscrop Chloe , Dustin Michael , Jostins-Dean Luke 
Published: November 2022

AbstractT cell activation pathways have been repeatedly implicated by genetic studies as being enriched for risk genes for immune and inflammatory diseases. Many of these risk genes code for costimulatory receptors or ligands. Costimulatory receptors are cell surface proteins on T cells, which are engaged by costimulatory ligands on antigen-presenting cells. Both costimulation and antigen binding are required to trigger T cell activation. In order to study the different pathways activated by these costimulatory risk molecules, and the role they may play in inflammatory disease genetics, we carried out gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) profiling of naive and memory CD4+ T cells (N=5 donors) activated via four different costimulatory receptors: CD28 (the standard molecule used forin vitroactivation studies), along with alternative costimulatory molecules ICOS, CD6, and CD27.Most, but not all, activation genes and regions are shared by different costimulation conditions. Alternative costimulation induced lower proliferation and cytokine production, but higher lysosome production, altered metabolic processing, and indications of “signal seeking” behaviour (homing and expression of costimulatory and cytokine receptors). We validated a number of these functions at the surface protein level using orthogonal experimental techniques. We found the strongest enrichment of heritability for inflammatory bowel disease in shared regions upregulated by all costimulatory molecules. However, some risk variants and genes were only induced by alternative costimulation, and the impact of these variants on expression were less often successfully mapped in studies of T cells activated by traditional CD28 costimulation. This suggests that future genetics studies of gene expression in activated T cells may benefit from including alternative costimulation conditions.
Theta oscillations and minor hallucinations in Parkinson’s disease reveal decrease in frontal lobe functions and later cognitive decline
Authors: Bernasconi Fosco , Pagonabarraga Javier , Bejr-Kasem Helena , Martinez-Horta Saul , Kulisevsky Jaime , Blanke Olaf 
Published: November 2022

AbstractCognitive decline and hallucinations are common and debilitating non-motor symptoms, occurring during later phases of Parkinson’s disease (PD). Minor hallucinations (MH), appear at early phases and have been suggested to predict cognitive impairment in PD, however, this has not been well-established by clinical research. Here, we investigated whether non-demented PD patients with MH show altered brain oscillations and whether such MH-related electrophysiological changes are associated with cognitive impairments that increase over time. Combining model-driven EEG analysis with neuropsychiatric and neuropsychological examinations in 75 PD patients, we reveal enhanced frontal theta oscillations in PD patients suffering from MH and link these oscillatory changes with lower cognitive frontal-subcortical functions. Neuropsychological follow-up examinations five years later confirmed MH-specific theta oscillations and revealed a stronger decline in frontal-subcortical functions in MH-patients with stronger frontal theta alterations, defining an MH and theta oscillation-based early marker of a cognitive decline in PD.
Mouse HP1γ regulates TRF1 expression and telomere stability
Authors: Stylianakis Emmanouil , Festenstein Richard , Vannier Jean-Baptiste 
Published: November 2022

AbstractAimsTElomeric Repeat-containing RNA are long non-coding RNAs generated from the telomeres. TERRAs are essential for the establishment of heterochromatin marks at telomeres, which serve for the binding of Heterochromatin Protein 1 (HP1), a protein family of epigenetic modifiers involved with chromatin compaction and gene silencing. While HP1γ is enriched on gene bodies of actively transcribed human and mouse genes, it is unclear if its transcriptional role is important for HP1γ function in telomere cohesion and telomere maintenance. We aimed to study the effect of mouse HP1γ on the transcription of telomere factors and molecules that can affect telomere maintenance.Main methodsWe investigated the telomere function of HP1γ by using deficient mouse embryonic fibroblasts (MEFs) deriving from 13.5 embryonic day embryos compared to their litter mate controls. We used gene expression analysis of HP1γ deficient MEFs and validated the molecular and mechanistic consequences of HP1γ loss by telomere FISH, immunofluorescence, RT-qPCR and DNA-RNA Immunoprecipitation (DRIP).Key findingsLoss of HP1γ in primary MEFs leads to a downregulation of various telomere and telomere-accessory transcripts, including shelterin protein TRF1. Its downregulation is associated with increased telomere replication stress and DNA damage (γH2AX), effects more profound in females. We suggest that the source for the impaired telomere maintenance is a consequence of increased telomeric DNA-RNA hybrids and TERRAs arising at and from mouse chromosomes 18 and X.SignificanceOur results suggest an important transcriptional control by mouse HP1γ of various telomere factors including TRF1 protein and TERRAs that has profound consequences on telomere stability, with a potential sexually dimorphic nature.
Multiple genes evolved for fungal septal pore plugging identified via large-scale localization and functional screenings
Authors: Mamun Md. Abdulla Al , Cao Wei , Nakamura Shugo , Maruyama Jun-ichi 
Published: November 2022

ABSTRACTMulticellular organisms exhibit cytoplasmic exchange using porous structures for cooperation among cells. Fungal multicellular lineages have evolved septal pores for this function. Interconnected hyphal cells possess the risk of wound-related cytoplasmic loss unless the septal pores are plugged. However, the gene evolution of regulatory mechanisms underlying fungal septal pore plugging remains poorly understood. To identify novel septal components, 776 uncharacterized proteins were identified using genomic comparisons between septal pore-bearing and -lacking ascomycete species. We then determined their subcellular localizations, and in total 62 proteins localized to the septum or septal pore. We analyzed the effects of deleting the encoding genes on septal pore plugging upon hyphal wounding. Of the 62 proteins, 23 were involved in regulating septal pore plugging. Here, using orthologous group and phylogenetic analyses, this study suggests that septal pore regulation has evolved either by co-option of preexisting genes or by Pezizomycotina-specific gene acquisition.
Legal issues of the broadcast and simultaneous Internet transmission of open university courses
Authors: Haruo Kodama 
Published: November 2022

PurposeThe purpose of this paper is to investigate the legal issues of simultaneous Internet transmission of broadcasting programs of the Open University of Japan (OUJ) and to take legal measures to promote the mutual utilization of open university courses in Japan, the UK, China and Korea.Design/methodology/approachThe author examines the legal relationship regarding Internet simultaneous distribution of broadcast courses at the OUJ. The author then considers the legal relationship between the UK, China and South Korea regarding the simultaneous transmission of broadcast courses over the internet. Based on that consideration, this paper clarifies legal measures to promote its utilization.FindingsInternet transmission of broadcasting courses will be webcasting. Arguably, it can be assumed to be streaming and on-demand, albeit controversial. Webcasting will be publicly transmitted, but there is only an on-demand provision for Internet transmission. As webcasting is streaming and on-demand, it involves reproduction of broadcasting courses. Therefore, webcasting needs to provide streaming provision for public transmission rights and associate them with reproduction right.Originality/valueThe originality of this paper lies in clarifying the legal response of the object, subject and rights of webcasting from the perspective of the OUJ, in order to dispel legal problems that may arise in the future against this unexplored phenomenon. Additionally, this paper is valuable in that it presents legal consistency from the point of view of the comparative laws of Japan, the UK, China and South Korea, based on an examination of the legal response in Japan.