bluuebunny/crossref_metadata_2025_split huggingface dataset:
A minimally morphologically destructive approach for DNA retrieval and whole genome shotgun sequencing of pinned historic Dipteran vector species
Authors: Korlević Petra , McAlister Erica , Mayho Matthew , Makunin Alex , Flicek Paul , Lawniczak Mara K. N. 
Published: June 2021

AbstractMuseum collections contain enormous quantities of insect specimens collected over the past century, covering a period of increased and varied insecticide usage. These historic collections are therefore incredibly valuable as genomic snapshots of organisms before, during, and after exposure to novel selective pressures. However, these samples come with their own challenges compared to present-day collections, as they are fragile and retrievable DNA is low yield and fragmented. In this paper we tested several DNA extraction procedures across pinned historic Diptera specimens from four disease vector genera:Anopheles, Aedes, CulexandGlossina. We identify an approach that minimizes morphological damage while maximizing DNA retrieval for Illumina library preparation and sequencing that can accommodate the fragmented and low yield nature of historic DNA. We identify several key points in retrieving sufficient DNA while keeping morphological damage to a minimum: an initial rehydration step, a short incubation without agitation in a low salt Proteinase K buffer, and critical point drying of samples post-extraction to prevent tissue collapse caused by air drying. The suggested method presented here provides a solid foundation for exploring the genomes and morphology of historic Diptera collections.Significance statementLarge museum collections of pinned insects could provide important snapshots of genomes through time, but unfortunately DNA retrieval from such fragile samples often leads to severe morphological damage, especially in delicate species such as disease transmitting Diptera. In this study we have worked on a combined method that minimizes morphological damage while maximizing the retrieval of DNA from dry pinned Diptera species. We identified the importance of tissue rehydration, gentle DNA lysis buffer incubation, and critical point drying to restore collapsed tissues. We hope this approach will make it possible for more historic insect specimens to become available for genomic research while ensuring they remain intact for morphological studies.
Hippocampal neurons code individual episodic memories in humans
Authors: Kolibius L. D. , Roux F. , Parish G. , Wal M. Ter , Plas M. Van Der , Chelvarajah R. , Sawlani V. , Rollings D. T. , Lang J. , Gollwitzer S. , Walther K. , Hopfengärtner R. , Kreiselmeyer G. , Hamer H. , Staresina B. P. , Wimber M. , Bowman H. , Hanslmayr S. 
Published: June 2021

AbstractThe hippocampus is an essential hub for episodic memory processing. However, how human hippocampal single neurons code multi-element associations remains unknown. Some argue that each hippocampal neuron codes for an invariant element within an episode. Instead, others have proposed that hippocampal neurons bind together all elements present in a discrete episodic memory. Here, we provide evidence for the latter. We show that individual neurons, which we term Episode Specific Neurons (ESNs), code discrete episodic memories using either a rate code or a temporal firing code. We find evidence for these neurons exclusively in the hippocampus. Importantly, these ESNs do not reflect the coding of a particular element in the episode (i.e., concept or time). Instead, they code for the conjunction of the different elements that make up the episode.One-Sentence SummaryIndividual neurons in the hippocampus code for discrete episodic memories.
Single-cell imaging reveals that Staphylococcus aureus is highly competitive against Pseudomonas aeruginosa on surfaces
Authors: Niggli Selina , Wechsler Tobias , Kümmerli Rolf 
Published: June 2021

AbstractPseudomonas aeruginosa and Staphylococcus aureus frequently occur together in polymicrobial infections, and their interactions can complicate disease progression as well as treatment options. While interactions between P. aeruginosa and S. aureus have been extensively described using planktonic batch cultures, little is known about whether and how individual cells interact with each other on solid substrates. This is important, because in infections, both species frequently colonize surfaces to form microcolony aggregates and biofilms. Here, we performed single-cell time-lapse fluorescence microscopy combined with automated image analysis to describe interactions between P. aeruginosa PAO1 with three different S. aureus strains (Cowan I, 6850, JE2) during microcolony growth on agarose surfaces. While P. aeruginosa is usually considered the dominant species, we found that the competitive balance tips in favor of S. aureus on surfaces. We observed that all S. aureus strains accelerated the onset of microcolony growth in competition with P. aeruginosa and significantly compromised P. aeruginosa growth prior to physical contact. These results suggest that S. aureus deploys mechanisms of both resource competition and interference competition via diffusible compounds. JE2 was the most competitive S. aureus strain, simply usurping P. aeruginosa microcolonies when coming into direct contact, while 6850 was the weakest competitor itself suppressed by P. aeruginosa. Moreover, P. aeruginosa reacted to the assault of S. aureus by showing increased directional growth and expedited expression of quorum sensing regulators controlling the synthesis of competitive traits. Altogether, our results reveal that quantitative single-cell live imaging has the potential to uncover microbial behaviors that cannot be predicted from batch culture studies, and thereby contribute to our understanding of interactions between pathogens that co-colonize host-associated surfaces during polymicrobial infections.
Myeloid cell interferon responses correlate with clearance of SARS-CoV-2
Authors: Singh Dhiraj K. , Aladyeva Ekaterina , Das Shibali , Singh Bindu , Esaulova Ekaterina , Swain Amanda , Ahmed Mushtaq , Cole Journey , Moodley Chivonne , Mehra Smriti , Schlesinger Larry S. , Artyomov Maxim N. , Khader Shabaana A. , Kaushal Deepak 
Published: June 2021

AbstractThe emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. While studies have reported immune profiling using single cell RNA sequencing in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. We performed longitudinal single-cell RNA sequencing of bronchoalveolar lavage (BAL) cell suspensions from adult rhesus macaques infected with SARS-CoV-2 (n=6) to delineate the early dynamics of immune cells changes. The bronchoalveolar compartment exhibited dynamic changes in transcriptional landscape 3 days post-SARS-CoV-2-infection (3dpi) (peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline). We observed the accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I IFN response was highly induced in the plasmacytoid dendritic cells. The presence of a distinct HLADR+CD68+CD163+SIGLEC1+macrophage population exhibiting higher angiotensin converting enzyme 2 (ACE2) expression was also observed. These macrophages were significantly recruited to the lungs of macaques at 3dpi and harbored SARS-CoV-2, while expressing a strong interferon-driven innate anti-viral gene signature. The accumulation of these responses correlated with decline in viremia and recovery. The recruitment of a myeloid cell-mediated Type I IFN response is associated with the rapid clearance of SARS-CoV-2 infection in macaques.
Spatiotemporal characterization of glial cell activation in an Alzheimer’s disease model by spatially resolved transcriptome
Authors: Choi Hongyoon , Lee Eun Ji , Shin Jin Seop , Kim Hyun , Bae Sungwoo , Choi Yoori , Lee Dong Soo 
Published: June 2021

ABSTRACTThe pathophysiological changes that occur with the progression of Alzheimer’s disease (AD) are well known, but understanding the spatiotemporal heterogeneity of the brain is needed. Here, we investigated the spatially resolved transcriptome in a 5XFAD AD model of different ages to understand regional changes at the molecular level. We identified early alterations in the white matter (WM) of the AD model before the definite accumulation of amyloid plaques in the gray matter (GM). Changes in the early stage of the disease were involved primarily in glial cell activation in WM, whereas the changes were prominent in the later stage of pathology in GM. We confirmed that disease-associated microglia (DAM) and astrocyte (DAA) signatures also showed initial changes in WM and that activation spreads to GM. Trajectory inference using microglial gene sets revealed the subdivision of DAMs with different spatial patterns. Taken together, these results help to understand the spatiotemporal changes associated with reactive glial cells as a major pathophysiology of AD and provide information for diagnosis and prognosis based on spatiotemporal changes caused by amyloid accumulation in AD.
Double-μPeriscope: a tool for multi-layer optical recordings, optogenetic stimulations or both
Authors: Suzuki Mototaka , Aru Jaan , Larkum Matthew E. 
Published: June 2021

AbstractIntelligent behavior and cognitive functions in mammals depend on cortical microcircuits made up of a variety of excitatory and inhibitory cells that form a forest-like complex across six layers. Mechanistic understanding of cortical microcircuits requires both manipulation and monitoring of multiple layers and interactions between them. However, existing techniques are limited as to simultaneous monitoring and stimulation at different depths without damaging a large volume of cortical tissue. Here, we present a relatively simple and versatile method for delivering light to any two cortical layers simultaneously. The method uses a tiny optical probe consisting of two micro-prisms mounted on a single shaft. We demonstrate the versatility of the probe in three sets of experiments: first, two distinct cortical layers were optogenetically and independently manipulated; second, one layer was stimulated while the activity of another layer was monitored; third, the activity of thalamic axons distributed in two distinct cortical layers were simultaneously monitored in awake mice. Its simple-design, versatility, small-size and low-cost allow the probe to be applied widely to address important biological questions.
Herpes simplex virus 1 inhibits phosphorylation of RNA polymerase II CTD serine-7
Authors: Whisnant Adam W. , Dionisi Oliver Dyck , Grothey Arnhild , Rappold Julia M. , Marante Ana Luiza , Subramanian Sharada S. , Dölken Lars 
Published: June 2021

AbstractTranscriptional activity of RNA polymerase II (Pol II) is orchestrated by post-translational modifications of the C-terminal domain (CTD) of the largest Pol II subunit, RPB1. Herpes Simplex Virus type 1 (HSV-1) usurps the cellular transcriptional machinery during lytic infection to efficiently express viral mRNA and shut down host gene expression. The viral immediate-early protein ICP22 interferes with serine 2 phosphorylation (pS2) of the Pol II CTD by targeting CDK9. The functional implications of this are poorly understood. Here, we report that HSV-1 also induces a global loss of serine 7 phosphorylation (pS7). This effect was dependent on the expression of the two viral immediate-early proteins, ICP22 and ICP27. While lytic HSV-1 infection results in efficient Pol II degradation late in infection, we show that pS2/S7 loss precedes the drop in Pol II level. Interestingly, mutation of the RPB1 polyubiquitination site mutation K1268, which prevents proteasomal RPB1 degradation during transcription-coupled DNA repair, displayed loss of pS2/S7 but retained much higher overall RPB1 protein levels even at late times of infection, indicating that this pathway mediates bulk Pol II protein loss late in infection but is not involved in early CTD dysregulation. Using α-amanitin-resistant CTD mutants, we observed differential requirements for Ser2 and Ser7 for production of viral proteins, with Ser2 facilitating viral immediate-early gene expression and Ser7 appearing dispensable. Despite dysregulation of CTD phosphorylation and different requirements for Ser2/7, all CTD modifications tested could be visualized in viral replication compartments by immunofluorescence. These data expand the known means that HSV-1 employs to create pro-viral transcriptional environments at the expense of host responses.
A bacterial extracellular vesicle-based intranasal vaccine against SARS-CoV-2 protects against disease and elicits neutralizing antibodies to wild-type and Delta variants
Authors: Jiang Linglei , Driedonks Tom A.P. , Jong Wouter S.P. , Dhakal Santosh , Berg van Saparoea H. Bart van den , Sitaras Ioannis , Zhou Ruifeng , Caputo Christopher , Littlefield Kirsten , Lowman Maggie , Chen Mengfei , Lima Gabriela , Gololobova Olesia , Smith Barbara , Mahairaki Vasiliki , Richardson M. Riley , Mulka Kathleen R. , Lane Andrew P. , Klein Sabra L. , Pekosz Andrew , Brayton Cory F. , Mankowski Joseph L. , Luirink Joen , Villano Jason S. , Witwer Kenneth W. 
Published: June 2021

ABSTRACTSeveral vaccines have been introduced to combat the coronavirus infectious disease-2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current SARS-CoV-2 vaccines include mRNA-containing lipid nanoparticles or adenoviral vectors that encode the SARS-CoV-2 Spike (S) protein of SARS-CoV-2, inactivated virus, or protein subunits. Despite growing success in worldwide vaccination efforts, additional capabilities may be needed in the future to address issues such as stability and storage requirements, need for vaccine boosters, desirability of different routes of administration, and emergence of SARS-CoV-2 variants such as the Delta variant. Here, we present a novel, well-characterized SARS-CoV-2 vaccine candidate based on extracellular vesicles (EVs) of Salmonella typhimurium that are decorated with the mammalian cell culture-derived Spike receptor-binding domain (RBD). RBD-conjugated outer membrane vesicles (RBD-OMVs) were used to immunize the golden Syrian hamster (Mesocricetus auratus) model of COVID-19. Intranasal immunization resulted in high titers of blood anti-RBD IgG as well as detectable mucosal responses. Neutralizing antibody activity against wild-type and Delta variants was evident in all vaccinated subjects. Upon challenge with live virus, hamsters immunized with RBD-OMV, but not animals immunized with unconjugated OMVs or a vehicle control, avoided body mass loss, had lower virus titers in bronchoalveolar lavage fluid, and experienced less severe lung pathology. Our results emphasize the value and versatility of OMV-based vaccine approaches.
Distinct timescales for the neuronal encoding of vocal signals in a high-order auditory area
Authors: Cazala Aurore , Del Negro Catherine , Giret Nicolas 
Published: June 2021

AbstractThe ability of the auditory system to selectively recognize natural sound categories with a tolerance to variations within categories is thought to be crucial for vocal communication. Subtle variations, however, may have functional roles. To date, how the coding of the balance between tolerance and sensitivity to variations in acoustic signals is performed at the neuronal level requires further studies. We investigated whether neurons of a high-order auditory area in a songbird species, the zebra finch, are sensitive to natural variations in vocal signals by recording responses to repeated exposure to similar and variant sound sequences. We took advantage of the intensive repetition of the male songs which subtly vary from rendition to rendition. In both anesthetized and awake birds, responses based on firing rate during sequence presentation did not show any clear sensitivity to these variations, unlike the temporal reliability of responses based on a 10 milliseconds resolution that depended on whether variant or similar sequences were broadcasted and the context of presentation. Results therefore suggest that auditory processing operates on distinct timescales, a short one to detect variations in individual’s vocal signals, longer ones that allow tolerance in vocal signal structure and the encoding of the global context.
Single-cell RNA-sequencing of Nicotiana attenuata petal cells reveals the entire biosynthetic pathway of a floral scent
Authors: Kang Moonyoung , Choi Yuri , Kim Hyeonjin , Kim Sang-Gyu 
Published: June 2021

AbstractHigh-throughput single-cell RNA sequencing (scRNA-seq) identifies distinct cell populations based on cell-to-cell heterogeneity in gene expression. By examining the distribution of the density of gene expression profiles, the metabolic features of each cell population can be observed. Here, we employ the scRNA-seq technique to reveal the entire biosynthetic pathway of a flower volatile. The corolla (petals) of the wild tobacco Nicotiana attenuata emits a bouquet of scents that are composed mainly of benzylacetone (BA), a rare floral volatile. Protoplasts from the N. attenuata corolla were isolated at three different time points, and the transcript levels of >16,000 genes were analyzed in 3,756 single cells. We performed unsupervised clustering analysis to determine which cell clusters were involved in BA biosynthesis. The biosynthetic pathway of BA was uncovered by analyzing gene co-expression in scRNA-seq datasets and by silencing candidate genes in the corolla. In conclusion, the high-resolution spatiotemporal atlas of gene expression provided by scRNA-seq reveals the molecular features underlying cell-type-specific metabolism in a plant.
Innate, translation-dependent silencing of an invasive transposon in Arabidopsis
Authors: Oberlin Stefan , Rajeswaran Rajendran , Trasser Marieke , Barragán-Borrero Verónica , Schon Michael A. , Plotnikova Alexandra , Loncsek Lukas , Nodine Michael D. , Marí-Ordóñez Arturo , Voinnet Olivier 
Published: June 2021

AbstractCo-evolution between hosts’ and parasites’ genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence-degeneration and, ultimately, loss-of-autonomy of most transposable elements (TEs). Recognition of newly-invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this response’s activation, we studied the single-copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically-reactivated. In Ty1/Copia-elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly-nuclear flGAG-POL, during which an unusually intense ribosomal stalling event coincides precisely with the starting-point of sRNA production exclusively on shGAG. mRNA breakage occurring at this starting-point yields unconventional 5’OH RNA fragments that evade RNA-quality-control and concomitantly likely stimulate RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) to initiate sRNA production. This hitherto-unrecognized “translation-dependent silencing” (TdS) is independent of codon-usage or GC-content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against de novo invasive TEs that underlies their associated sRNA patterns.
Ureides are similarly accumulated in response to UV-C irradiation and wound but differently remobilized during recovery in Arabidopsis leaves
Authors: Soltabayeva Aigerim , Bekturova Aizat , Kurmanbayeva Assylay , Oshanova Dinara , Nurbekova Zhadyrassyn , Srivastava Sudhakar , Standing Dominic , Sagi Moshe 
Published: June 2021

AbstractTo examine a role of purine degraded metabolites in response to wounding or UV-C stress, the Arabidopsis wild-type and Atxdh1 KO mutants, defective in xanthine dehydrogenase1 (XDH1), were exposed to wounding and UV-C irradiation stress. In Atxdh1 mutant, wounding or UV-C stresses resulted in lower fresh-weight, increased senescence symptoms and higher tissue cell death rate compared to Wild-type. Additionally, Wild-type exhibited lower levels of oxidative stress indicators; reactive oxygen species and malondialdehyde than Atxdh1 mutant leaves. Notably, purine degradation transcripts and proteins were orchestrated to lead to enhanced ureide levels in Wild-type leaves 24 h after applying UV-C or wound stress. Yet, different remobilization of the accumulated ureides was noticed 72 h after stresses application. In plants treated with UV-C the allantoin level was highest in young leaves, whereas in wounded plants it was lowest in the young leaves, accumulated mainly in the middle and wounded leaves. The results indicate that in UV-C treated Wild-type, during the recovery period from stress, ureides are remobilized from the lower older leaves to support young leaf growth. In contrast, after wounding, the ureides are remobilized to the young leaves, yet more to the middle wounded leaves, to function as antioxidants and/or healing agents.HighlightUV-C and wound triggers purine degradation in old and damaged leaves to increase ureides accumulation in stress dependent rate. Impairment in purine degradation results in premature senescence in leaves.
Stress in mothers of children with neurodevelopmental disorders
Authors: Hemati Alamdarloo Ghorban , Majidi Farzad 
Published: June 2021

PurposeMost parents experience stress when their children are diagnosed with some kind of disability. This paper aims to compare the level of stress among mothers of children with neurodevelopmental disorders.Design/methodology/approachResearch sample consisted of 150 mothers of children with neurodevelopmental disorders (50 mothers of children with autism spectrum disorder, 50 mothers of children with intellectual disability and 50 mothers of children with specific learning disorder selected by convenience sampling). The Stress Response Inventory was used for measuring stress. One-way analysis of variance, multivariate analysis of variance and Scheffe post hoc tests were used for data analysis.FindingsThe results showed that the stress of mothers of children with autism spectrum disorder was significantly higher than to the other groups of mothers. It was also observed that the stress of mothers of children with intellectual disability was significantly higher than the mothers of children with the specific learning disorder.Originality/valueTherefore, designing and implementing preventive and interventional programs to decrease the stress of mothers of children with neurodevelopmental disorders, especially mothers of children with autism spectrum disorder is necessary.