bluuebunny/crossref_metadata_2025 huggingface dataset:
18F-FDG PET/CT Imaging of G-CSF–Producing Dedifferentiated Liposarcoma
Authors: Eizuru Yukari , Nakajo Masatoyo , Nakajo Masanori , Shinohara Naohiro , Yoshiura Takashi
Published: June 2021

Granulocyte colony-stimulating factor (G-CSF)–producing tumors are malignant tumors associated with a poor prognosis, and G-CSF–producing liposarcoma is particularly rare. We report a case of G-CSF–producing dedifferentiated liposarcoma. 18F-FDG PET/CT showed abnormal 18F-FDG uptake throughout the bone marrow and in the primary site. When a diffuse bone marrow 18F-FDG uptake was observed on 18F-FDG PET/CT, G-CSF–producing dedifferentiated liposarcoma should be included in the differential diagnosis.
Aberrant Morphologic Patterning of Combined Sagittal and Metopic Craniosynostosis
Authors: Dinis Jacob , Junn Alexandra , Lu Xiaona , Lopez Joseph , Persing John
Published: June 2021

Combined sagittal and metopic craniosynostosis is an uncommon condition that may result in a wide spectrum of cranial morphologies. This occurs as a result of the compound effects of both prematurely fused sutures. The authors present an incidence of sagittal craniosynostosis with a specific altered head morphology, and delayed diagnosis that the authors believe occurred due to structural changes associated with concurrent metopic suture synostosis This patient underscores the limitations of relying on classic diagnostic patterns and highlights the critical role of noninvasive imaging in the diagnosis of craniosynostosis.
Peripheral Dentinogenic Ghost Cell Tumor of the Maxilla
Authors: Altindis Sezen , Tokuc Berkay , Hosgor Hatice , Coskunses Fatih Mehmet
Published: June 2021

Dentinogenic ghost cell tumor (DGCT) is an uncommon locally invasive odontogenic tumor, representing 1.9% to 2.1% of all odontogenic tumors. The main microscopic features of DGCT are an ameloblastoma-like odontogenic epithelial proliferation with sheets of ghost cells and dentinoid material formation. The peripheral variant of this clinical rarity, which represents a less aggressive behavior than central lesions, mostly affects the anterior region of both jaws. In this case report, the authors present a DGCT that was observed in the maxillary posterior region in a 59-year-old female patient. The patient presented with pain and nodular swelling in the right maxillary molar region, which extended from the buccal vestibule to the edentulous area. Additionally, there was a destruction of the underlying bone, as seen radiographically. This case report includes the clinical, radiological, and histopathological features of the lesion, which was diagnosed as a peripheral DGCT without any evidence of recurrence in the 2 years after excision.
Medium-depth Trichloroacetic Acid and Deep Phenol–Croton Oil Chemical Peeling for Facial Rejuvenation: An Update
Authors: Atiyeh Bishara , Oneisi Ahmad , Ghieh Fadi
Published: June 2021

Face-lift is an established rejuvenation modality; however, when performed alone, it lacks the ability to improve the appearance of fine wrinkles and dyschromias that are an important component of facial rejuvenation. Although it is only natural to be attracted by the latest technologically advanced innovative skin resurfacing techniques, chemical peeling has been proven to be a simple and effective method with a relatively good safety profile. Unfortunately, the practice of chemical peeling has relied for a long time on dogmas perpetuated by early reports without any real scientific basis. Moreover, application of peels has been hindered by difficult estimation of penetrance and control of depth. Three decades ago, a shift has occurred from early dogmatic empirical application to better understanding of the peeling formulations and mechanism of action together with appreciation of the interaction between the various components of the peeling formulations in addition to better estimation of clinical end points and peel depth. Given the increasing demand for none or minimally invasive cosmetic procedures, the current review is aimed at highlighting the recent applications of available medium-depth and deep chemical peels for optimal facial rejuvenation and for the treatment of photo-related aging skin changes.
Three-Dimensional Analysis of the Skull Base of Individuals With Cleft Lip and Palate
Authors: Mendes Bruno Coelho , Silva Kaline de Moura , da Silva Carolina Silvano Vilarinho , Santaella Natália Garcia , de Lima Ana Paula da Cunha Barbosa , Borba Alexandre Meireles , Naclério-Homem Maria da Graça
Published: June 2021

Aims:

Identify variations of skull base measurements in individuals with dentofacial deformities associated or not with cleft lip and palate and compare the results with individuals without dentofacial deformities.

Methods and Results:

The individuals were categorized into three different groups: dentofacial deformity without cleft malformation, dentofacial deformity associated with cleft lip and palate, and without facial deformity. The inclusion criteria were individuals over 18 years of age, without any intervention involving facial bones or structures of interest for the study and field of view encompassing from the glabella to the hyoid bone. Poor quality CT scans or lack of adequate medical records were considered exclusion criteria. In the analysis by computerized tomography using the Dolphin Imaging Software, the length determined by the Ba-S and S-N lines was evaluated, as well as the Ba-S-N angle formed by landmarks.

Results:

The length of S-N was not statistically different between the groups, the Ba-S length and the Ba-S-N angle demonstrated statistical difference.

Conclusion:

There was statistically significant difference in the morphometry of the (Ba-S) between groups (FS) and (C). This suggests that the standard values for cephalometric analyzes involving these structures, especially to determine the treatment planning, should be used with caution.
Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance
Authors: Maidana-Kulesza María Noel , Poma Hugo Ramiro , Sanguino-Jorquera Diego Gastón , Reyes Sarita Isabel , Said-Adamo María del Milagro , Remis Martín Mainardi , Gutiérrez-Cacciabue Dolores , Cristóbal Héctor Antonio , Cruz Mercedes Cecilia , González Mónica Aparicio , Rajal Verónica Beatriz
Published: June 2021

The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance to support health authorities. Five sampling points from three rivers (AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River) from the Province of Salta (Argentina), two of them receiving the discharges of the wastewater plants (WWTP) of the city of Salta, were monitored from July to December 2020 during the first wave of COVID-19. Fifteen water samples from each point (75 samples in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantitatively detected by RT-qPCR. In addition, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize the SARS-CoV-2 concentration, which was ultimately compared to the active reported COVID-19 cases. Statistical analyses allowed us to verify the correlation between SARS-CoV-2 and the concentration of fecal indicator bacteria (FIB), as well as to find similarities and differences between sampling points. La Caldera River showed the best water quality, and FIB were within acceptable limits for recreational activities. Although Mojotoro River receives the discharge of the northern WWTP of the city, it did not affect the water quality. Instead, the Arenales River presented the poorest water quality and the river at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to the significant increase of fecal contamination. SARS-CoV-2 was only found in about half of the samples and in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in the Arenales River. None of the two human tracers was detected in CR, only HPyV was found in MR-1, MR-2 and AR-1, and both were quantified in AR-2. The experimental and the normalized (using the two tracers) viral concentrations strongly correlated with the curve of active reported COVID-19 cases; thus, the Arenales River at AR-2 reflected the epidemiological situation of the city. This is, to the best of our knowledge, the first study that showed the dynamic of SARS-CoV-2 concentration in an urban river highly impacted by wastewater and proved that can be used for SARS-CoV-2 surveillance to support health authorities.
Characterizing Long COVID: Deep Phenotype of a Complex Condition
Authors: Deer Rachel R , Rock Madeline A , Vasilevsky Nicole , Carmody Leigh , Rando Halie , Anzalone Alfred J , Callahan Tiffany J , Bramante Carolyn T , Chute Christopher G , Greene Casey S , Gagnier Joel , Chu Haitao , Koraishy Farrukh M , Liang Chen , Liu Feifan , Madlock-Brown Charisse R , Mazzotti Diego R , McNair Douglas S , Parker Ann M , Coleman Ben D , Davis Hannah E , Perry Mallory A , Reese Justin T , Saltz Joel , Solomonides Anthony E , Sule Anupam A , Stein Gary S , Köhler Sebastian , Monteith Teshamae S , Madhira Vithal , Kimble Wesley D , Kavuluru Ramakanth , Hillegass William B , Chan Lauren E , Byrd James Brian , Boudreau Eilis A , Liu Hongfang , McMurry Julie A , Pfaff Emily , Matentzoglu Nicolas , Relevo Rose , Moffitt Richard A , Schuff Robert A , Solway Julian , Spratt Heidi , Bergquist Timothy , Bennett Tellen D , Basson Marc D , Topaloglu Umit , Wang Liwei , Haendel Melissa A , Robinson Peter N
Published: June 2021

Importance

Since late 2019, the novel coronavirus SARS-CoV-2 has given rise to a global pandemic and introduced many health challenges with economic, social, and political consequences. In addition to a complex acute presentation that can affect multiple organ systems, there is mounting evidence of various persistent long-term sequelae. The worldwide scientific community is characterizing a diverse range of seemingly common long-term outcomes associated with SARS-CoV-2 infection, but the underlying assumptions in these studies vary widely making comparisons difficult. Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 infection (PASC or “long COVID”), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations of long COVID.

Observations

We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts of individuals three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to Human Phenotype Ontology (HPO) terms.

Conclusions and Relevance

Patients and clinicians often use different terms to describe the same symptom or condition. Addressing the heterogeneous and inconsistent language used to describe the clinical manifestations of long COVID combined with the lack of standardized terminologies for long COVID will provide a necessary foundation for comparison and meta-analysis of different studies. Translating long COVID manifestations into computable HPO terms will improve the analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared or pooled more effectively. Furthermore, mapping lay terminology to HPO for long COVID manifestations will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, which may improve the stratification and thereby diagnosis and treatment of long COVID.
An Oxford Nanopore-based Characterisation of Sputum Microbiota Dysbiosis in Patients with Tuberculosis: from baseline to 7 days after Antibiotic Treatment
Authors: Sekyere John Osei , Maningi Nontuthuko E. , Matukane Siphiwe Ruthy , Mbelle Nontombi M. , Fourie Petrus Bernard
Published: June 2021

Background

Diagnostics for tuberculosis (TB) and treatment monitoring remains a challenge, particularly in less-resourced laboratories. Further, the comprehensive sputum microbiota of TB patients during treatment are less described, particularly using long-read sequencers.

Methods

DNA from sputum samples collected from newly-diagnosed TB patients were sequenced with Oxford Nanopore’s MinION. MG-RAST and R packages (Phyloseq, α/β diversities, functional components, OTUs networks and ordination plots. Statistical significance of the generated data was determined using GraphPad.

Results & conclusion

Antibiotics reduced the abundance and functional subsystems of each samples’ microbiota from baseline until day 7, when persistent, tolerant, and resistant microbiota, including fungi, grew back again. Variations in microbiota abundance and diversity were patient-specific. Closer microbiome network relationships observed in baseline samples reduced until day 7, when it became closer again. Bacterial microbiota networks and spatial ordination relationships were closer than that of other kingdoms. Actinobacteria phylum and Mycobacterium were more affected by antibiotics than other phyla and genera. Parasites, viruses, and fungi were less affected by antibiotics than bacteria in a descending order. Resistance genes/mechanisms to important antibiotics, plasmids, transposons, insertion sequences, integrative conjugative elements were identified in few samples.

MinION can be adopted clinically to monitor treatment and consequent dysbiosis, and identify both known and unknown pathogens and resistance genes to inform tailored treatment choices, specifically in TB.

Author summary

Tuberculosis (TB), one of the major killers of mankind, continually remains elusive as challenges with early diagnosis and treatment monitoring remain. Herein, we use a single portable sequencer from Oxford Nanopore, the minION, to diagnose TB and monitor its treatment with antibiotics using routine sputum samples. In addition, the presence of other pathogens, important commensals, antibiotic resistance genes, mobile genetic elements, and the effect of the antibiotic treatment on the sputum microbiota were determined from the same data. This makes the minION an important tool that can be used in clinical laboratories to obtain data that can inform live-saving decisions.
An Experimental Test of the Effects of Redacting Grant Applicant Identifiers on Peer Review Outcomes
Authors: Nakamura Richard , Mann Lee S. , Lindner Mark D. , Braithwaite Jeremy , Chen Mei-Ching , Vancea Adrian , Byrnes Noni , Durrant Valerie , Reed Bruce
Published: June 2021

Blinding reviewers to applicant identity has been proposed to reduce bias in peer review. This experimental test used 1200 NIH grant applications, 400 from Black investigators, 400 matched applications from White investigators, and 400 randomly selected applications from White investigators. Applications were reviewed by mail in standard and redacted formats. Redaction reduced, but did not eliminate, reviewers’ ability to correctly guess features of identity. The primary, pre-registered analysis hypothesized a differential effect of redaction according to investigator race in the matched applications. A set of secondary analyses (not pre-registered) used the randomly selected applications from White scientists and tested the same interaction. Both analyses revealed similar effects: Standard format applications from White investigators scored better than those from Black investigators; redaction reduced the size of the difference by about half (e.g. from a Cohen’sdof 0.20 to 0.10 in matched applications); redaction caused applications from White scientists to score worse but had no effect on scores for Black applications. The primary statistical test of the study hypothesis was not significant; the secondary analysis was significant. The findings support further evaluation of peer review models that diminish the influence of applicant identity.
Exon skipping via chimeric antisense U1 snRNAs to correct Retinitis Pigmentosa GTPase-Regulator (RPGR) splice defect
Authors: Covello Giuseppina , Ibrahim Gehan H. , Bacchi Niccolò , Casarosa Simona , Denti Michela Alessandra
Published: June 2021

Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient co-transfection with RPGR minigene reporter systems in HEK-293T and PC-12 cell lines. We thus identified three chimeric U1_asRNAs that efficiently mediate E9a skipping, correcting the genetic defect. Unexpectedly, the U1-5’antisense construct, which exhibited the highest exon-skipping efficiency in PC-12 cells, induced E9a inclusion in HEK-293T cells, indicating caution in the choice of preclinical model systems when testing RNA splicing-correcting therapies. Our data provide a proof of principle for the application of U1_snRNA exon skipping-based approach to correct splicing defects in RPGR.
Haemosporidian Blood Parasites in nestling birds of prey in Mongolia
Authors: Attaran Hamidreza , Luo Jing , Bo Wang , Nabavi Reza , He Hong-xuan
Published: June 2021

Haemosporidians are vector-transmitted intracellular parasites that happen in numerous bird species worldwide and may possibly have important effects for wild bird populations. Studies of haemosporidians most dedicated on Europe and North America, and only newly some study in the Neotropics has been done, where the occurrence and influences of the disease have been less considered and are not understood well. In this study we designed a study in the nestling birds of prey in Mongolia. We sampled blood from 72 raptors at 2 different species and evaluated avian haemosporidian infection by two nested PCR protocol and one Real time PCR protocol. Sequencing a portion of the cytochrome b (cyt b) gene of the parasite. From the sampled birds, 10 % were infected by Plasmodium. Inclusive, our findings advocate a high haemosporidian species richness in the bird community of Mongolia. In view of the frequency of local habitat loss that in this area is living, recognize how avian haemosporidians affect bird populations it is very important; in addition, more exhaustive sampling is required to fully understand the range of avian haemosporidian infection in this area.
Neural dynamics of stroboscopic stimulation at different stimulation frequencies
Authors: Pari Ram Kumar
Published: June 2021

Stroboscopic stimulation has been previously shown to induce visual hallucinations and altered states of consciousness, state by entraining the brain to the driving frequency, similar to those reported during the psychedelics although little systematic research exists on the effect of specific stimulation frequency on experience. The present study investigated the effects of different stroboscopic stimulation frequencies on neural dynamics, such as signal diversity (Lempel-Ziv complexity) and spectral power and attempted to relate these changes to self-reported changes in experiential content. The results indicated that the stimulation frequencies near the alpha band (8 – 12 Hz) caused the greatest increase across all neural measures, with 8 Hz consistently displaying the most pronounced results, relative to baseline. All tested frequencies led to an increase in all experiential dimensions, relative to baseline.
POGZ modulates the DNA damage response in a HP1-dependent manner
Authors: Heath John , Cheyou Estelle Simo , Findlay Steven , Luo Vincent M , Carpio Edgar Pinedo , Lee Jeesan , Djerir Billel , Chen Xiaoru , Morin Théo , Lebeau Benjamin , Karam Martin , Bagci Halil , Grapton Damien , Ursini-Siegel Josie , Côté Jean-Francois , Witcher Michael , Richard Stéphane , Maréchal Alexandre , Orthwein Alexandre
Published: June 2021

The heterochromatin protein HP1 plays a central role in the maintenance of genome stability, in particular by promoting homologous recombination (HR)-mediated DNA repair. However, little is still known about how HP1 is controlled during this process. Here, we describe a novel function of the POGO transposable element derived with ZNF domain protein (POGZ) in the regulation of HP1 during the DNA damage responsein vitro. POGZ depletion delays the resolution of DNA double-strand breaks (DSBs) and correlates with an increased sensitivity to different DNA damaging agents, including the clinically-relevant Cisplatin and Talazoparib. Mechanistically, POGZ promotes homology-directed DNA repair pathways by retaining the BRCA1/BARD1 complex at DSBs, in a HP1-dependent manner.In vivoCRISPR inactivation ofPogzis embryonically lethal andPogzhaplo-insufficiency (Pogz+/Δ) results in a developmental delay, impaired intellectual abilities, a hyperactive behaviour as well as a compromised humoral immune response in mice, recapitulating the main clinical features of the White Sutton syndrome (WHSUS). Importantly,Pogz+/Δmice are radiosensitive and accumulate DSBs in diverse tissues, including the spleen and the brain. Altogether, our findings identify POGZ as an important player in homology-directed DNA repair bothin vitroandin vivo,with clinical implications for the WHSUS.
Trait mindfulness predicts inter-brain coupling during naturalistic face-to-face interactions
Authors: Chen Phoebe , Kirk Ulrich , Dikker Suzanne
Published: June 2021

In recent years, the benefits of practicing mindfulness have raised much public and academic interest. Mindfulness emphasizes cultivating awareness of our immediate experience, and has been associated with compassion, empathy and various other prosocial traits. However, experimental evidence pertaining to its prosocial benefits in social settings is lacking. In this study, we investigate neural correlates of trait mindfulness during naturalistic dyadic interactions, using both individual brain and inter-brain coupling measures. We used the Muse headset, a portable electroencephalogram (EEG) device, to record participants’ brain activity during a ∼10 minutes’ naturalistic dyadic interaction (N = 62) in an interactive art setting. They further completed the Mindful Attention Awareness Scale (MAAS) and the Interpersonal Reactivity Index (IRI). This allowed us to ask whether inter-brain coupling during naturalistic interactions can be predicted by dyads’ affective traits and trait mindfulness, respectively. First, we failed replicating prior laboratory-based findings with respect to individual brain responses as they relate to mindfulness. Trait mindfulnessdid, however, predict inter-brain coupling within dyads, in theta (∼5-8 Hz, p < 0.001) and beta frequencies (∼26-27Hz, p < 0.001). Finally, we found a negative correlation between personal distress and trait mindfulness (t(475) = -5.493, p < 0.001). These findings underscore the importance of conducting social neuroscience research in ecological settings and enrich our understanding of multi-brain neural correlates of mindfulness during social interaction, while raising critical practical considerations regarding the viability of commercially available EEG systems.
ZFP462 targets heterochromatin to transposon-derived enhancers restricting transcription factor binding and expression of lineage-specifying genes
Authors: Yelagandula Ramesh , Stecher Karin , Novatchkova Maria , Michetti Luca , Michlits Georg , Wang Jingkui , Hofbauer Pablo , Pribitzer Carina , Vainorius Gintautas , Isbel Luke , Mendjan Sasha , Schübeler Dirk , Elling Ulrich , Brennecke Julius , Bell Oliver
Published: June 2021

ZNF462haploinsufficiency is linked to Weiss-Kruszka Syndrome, a genetic disorder characterized by a range of neurodevelopmental defects including Autism. Though it is highly conserved in vertebrates and essential for embryonic development the molecular functions ofZNF462are unclear. We identified its murine homolog ZFP462 in a screen for epigenetic gene silencing in mouse embryonic stem cells (mESCs). Here, we show ZFP462 safeguards neural lineage specification by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to mediate epigenetic silencing of endodermal genes. ZFP462 binds to thousands of transposable elements (TEs) that harbor ESC- and endoderm-specific transcription factor (TF) binding sites and act as enhancers. Through physical interaction with G9A/GLP, ZFP462 seeds heterochromatin at TE-derived enhancers restricting the binding of core pluripotency TFs OCT4 and SOX2. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of endodermal genes. Taken together, ZFP462 restricts TF binding and subsequent endodermspecific gene activation by conferring lineage and locus-specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of endodermal genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.
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

Museum 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 statement

Large 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

The 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 Summary

Individual 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

Pseudomonas 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

The 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

The 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

Intelligent 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

Transcriptional 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

Several 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

The 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

High-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.
Rad52 mediates class-switch DNA recombination to IgD
Authors: Xu Yijang , Zhou Hang , Post Ginell , Zan Hong , Casali Paolo
Published: June 2021

While the biology of IgD begins to be better understood, the mechanism of expression of this phylogenetically old and highly conserved Ig remains unknown. In B cells, IgD is expressed together with IgM as transmembrane receptor for antigen through alternative splicing of long primaryVHDJH-Cμ-s-m-Cδ-s-mRNAs, which also underpin secreted (s)IgD. IgD is also expressed through class switch DNA recombination (CSR), as initiated by AID-mediated double-strand DNA breaks (DSBs) in Sμ and σδ, and resolution of such DSBs by a still unknown mechanism. This synapses Sμ with σδ region DSB resected ends leading to insertion of extensive S-S junction microhomologies, unlike Ku70/Ku86-dependent NHEJ which resolves DSB blunt ends in CSR to IgG, IgA and IgE with little or no microhomologies. Our previous demonstration of a novel role of Rad52 in a Ku70/Ku86-independent “short-range” microhomology-mediated synapsis of intra-Sμ region DSBs led us to hypothesize that this homologous recombination DNA annealing factor is also involved in short-range microhomology-mediated alternative endjoining (A-EJ) recombination of Sμ with σδ. We found that induction of IgD CSR by selected stimuli downregulated Zfp318 (the suppressor ofCμ-s-mtranscription termination), promoted Rad52 phosphorylation and Rad52 recruitment to Sμ and σδ, leading to Sμ-σδ recombination with extensive microhomologies,VHDJH-Cδstranscription and sustained IgD secretion. Rad52 ablation in mouseRad52−/−B cells aborted IgD CSRin vitroandin vivoand dampened the specific IgD antibody response to OVA. Further, Rad52 knockdown in human B cells virtually abrogated IgD CSR. Finally, Rad52 phosphorylation was associated with high levels of IgD CSR and anti-nuclear IgD autoantibodies in lupus-prone mice and lupus patients. Thus, Rad52 effects CSR to IgD through microhomology-mediated A-EJ and in concert with Zfp318 modulation. This is a previously unrecognized, critical and dedicated role of Rad52 in mammalian DNA repair that provides a mechanistic underpinning to CSR A-EJ.
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

Co-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.