bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing management strategies for conserving communities of climate-threatened species with a stochastic metacommunity model
Authors: Backus Gregory A. , Huang Yansong , Baskett Marissa L.
Published: June 2022

Many species are shifting their ranges to keep pace with climate change, but habitat fragmentation and limited dispersal could impede these range shifts. In the case of climate-vulnerable foundation species such as tropical reef corals and temperate forest trees, such limitations might put entire communities at risk of extinction. Restoring connectivity through corridors, stepping-stones or enhanced quality of existing patches could prevent the extinction of several species, but dispersal-limited species might not benefit if other species block their dispersal. Alternatively, managers might relocate vulnerable species between habitats through assisted migration, but this is generally a species-by-species approach. To evaluate the relative efficacy of these strategies, we simulated the climate-tracking of species in randomized competitive metacommunities with alternative management interventions. We found that corridors and assisted migration were the most effective strategies at reducing extinction. Assisted migration was especially effective at reducing the extinction likelihood for short-dispersing species, but it often required moving several species repeatedly. Assisted migration was more effective at reducing extinction in environments with higher stochasticity, and corridors were more effective at reducing extinction in environments with lower stochasticity. We discuss the application of these approaches to an array of systems ranging from tropical corals to temperate forests.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands
Authors: Pescador David S. , Delgado-Baquerizo Manuel , Fiore-Donno Anna Maria , Singh Brajesh K. , Bonkowski Michael , Maestre Fernando T.
Published: June 2022

Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
Outpatient clonal propagation propelled rapid regional establishment of an emergent carbapenem-resistant Acinetobacter baumannii lineage ST499Pas
Authors: Calix Juan J. , Stockler de Almeida Maria C. , Potter Robert F. , Wallace Meghan A. , Burnham Carey-Ann D. , Dantas Gautam
Published: June 2022

Combating the evolving health threat posed by carbapenem-resistant Acinetobacter baumannii (CRAb) requires knowing how this non-commensal organism establishes regional pools and propagates among at-risk hosts. We report a 2017-2019 surge of CRAb among patients receiving care in a USA multicenter system. This surge occurred during a period of sustained reduction in hospital-acquired CRAb infections and coincided with marked reduction of CRAb cases associated with distinctly more resistant antibiotypes. Isolate whole genome sequencing revealed surge isolates belonged to an emergent Pasteur scheme sequence type 499 (ST499Pas). Detailed query of health records guided by isolate genome comparative analyses revealed multiple clonal clusters linked to various outpatient healthcare settings (i.e., long term healthcare facilities, surgical and wound clinics, and other unidentified factors) but no evidence of a shared intrahospital source. We show that emergent CRAb lineages can rapidly establish a regional presence even without gains in breadth of antibiotic resistance and negligible contribution from sustained intrahospital transmission. The emergence of ST499Pas despite regional eradication of other CRAb lineages shows how control efforts could be sidestepped via outpatient epidemiological niches. We also establish an approach to investigate the propagation of CRAb lineages that can inform subsequent local surveillance efforts outside of hospital settings.
Migratory behavior is positively associated with genetic diversity in butterflies
Authors: García-Berro Aurora , Talla Venkat , Vila Roger , Wai Hong Kar , Shipilina Daria , Chan Kok Gan , Pierce Naomi E. , Backström Niclas , Talavera Gerard
Published: June 2022

Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost and benefit trade-offs at the species level. Migratory insects often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long-term population size dynamics in migratory insects, as an alternative to classical local and short-term approaches such as regional field monitoring. We analyze whole-genome sequences from 97 Lepidoptera species and show that migratory species have significantly higher levels of genome-wide heterozygosity, a proxy for effective population size, than non-migratory species. Also, we contribute whole-genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distribution range. This species exhibits one of the highest levels of heterozygosity described in Lepidoptera (2.95% ± 0.15). Coalescent modeling (PSMC) shows historical demographic stability inV. cardui, and high effective population size estimates of 2 to 20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a “compensatory” demographic model for migratory r-strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the delimitations of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect’s migratory nature and population dynamics at large spatiotemporal scales.
Reuniens transiently synchronizes memory networks at beta frequencies
Authors: Jayachandran Maanasa , Viena Tatiana D. , Garcia Andy , Veliz Abdiel Vasallo , Leyva Sofia , Roldan Valentina , Vertes Robert P. , Allen Timothy A.
Published: June 2022

Using episodic memories to help guide decisions requires top-down medial prefrontal cortex interactions with the hippocampus. Mechanistically, this integrated prefrontal-hippocampal memory state is thought to be organized by synchronized network oscillations and mediated by connectivity with the nucleus reuniens of the thalamus. Here, we recorded local field potentials from the prefrontal-reuniens-hippocampal network while rats were engaged in a nonspatial sequence memory task which helps isolate memory-related activity from running-related oscillations. We found that synchronous prefrontal-hippocampal beta bursts (15-30 Hz) were dominant during memory trials, whereas synchronous theta (6-12 Hz) was highest during running. Beta rose during a trial and peaked just before a decision, whereas theta was highest during running. Beta bursts first appeared in reuniens and then in prefrontal and hippocampal sites simultaneously, suggesting beta could be directly driven by reuniens. To test this, we used an optogenetic approach (retroAAV-ChR2) to see if reuniens was capable of driving prefrontal-hippocampal beta synchrony. Reuniens activation induced prefrontal-hippocampal beta coherence, and reduced theta coherence, resembling the observed memory-driven network state. These findings demonstrate for the first time that reuniens contributes to memory by driving transient synchronous beta in the prefrontal-hippocampal system facilitating coherent interactions that sub-serve memory-based decision making.
A conserved role of α2δ subunit of calcium channel in nicotine motivated behavior
Authors: Salim Chinnu , Batsaikhan Enkhzul , Kan Ann Ke , Chen Hao , Jee Changhoon
Published: June 2022

Identifying genetic variants associated with nicotine-motivated behavioral traits is an important strategy to understand the fundamental mechanisms underpinning smoking and tobacco abuse. For suitable emulation of behavioral phenotype with the full advantage of this invertebrate model, we newly established a worm model of nicotine seeking by Conditioned Cue Preference (CCP). We demonstrated that C. elegans also exhibited pivotal features of nicotine-motivated behaviors as in mammals. First, we identified the nicotine-elicited cue preference is mediated by nicotinic acetylcholine receptors in worms. Additionally, we exhibited dopamine is also required for the development of CCP. Subsequently, we identified the nAChRs subunits associated with the facilitation of nicotine preference. Accordingly, we validated human GWAS candidates associated with nicotine dependence involved in the role of those nAChR subunits. we addressed the cross-species functional validation to determine the GWAS candidate genes have authentic roles in nicotine seeking associated with tobacco abuse. The loss of function strain of CACNA2D3 orthologue, calcium voltage-gated channel auxiliary subunit alpha2delta 3, was tested for CCP. We also tested the knock-out (KO) strain of the CACNA2D2 orthologue, calcium voltage-gated channel auxiliary subunit alpha2delta 2, which is closely related to CACNA2D3 in the same family and shared the human smoking phenotypes. Our orthogonal test suggests the functional conservation of the α2δ subunit of calcium channel in nicotine motivated behavior.
The disadvantage of derivation: conserved systematic flaws in primary data have repeatedly biased the phylogenetic inference of Temnospondyli (Tetrapoda, Amphibia)
Authors: Gee Bryan M.
Published: June 2022

Phylogenetic analyses and their resultant tree topologies underlie paleobiological studies. Regardless of the type of study, the relationships of focal taxa are foundational, whether implemented in a qualitative or a quantitative framework. This reliance places a premium on the continued refinement of both phylogenetic methods and inference. Temnospondyls are a diverse clade of non-amniote (‘amphibian’) tetrapods whose phylogenetic relationships have been extensively explored due to their speciose nature, widespread occurrence in Paleozoic and Mesozoic paleoenvironments, and putative relationship to extant amphibians. Despite being studied by a diversity of workers, there is only one dataset that is widely employed to test the broad-scale relationships of Temnospondyli, that of Schoch (2013). This dataset has been reused in several high-profile studies testing the question of lissamphibian origins, and the original resultant topology has been widely adopted by taxonomic specialists and non-specialists alike. However, close examination of this matrix reveals discernible patterns of problematic codes related to non-homology, dependency, and unsubstantiated data (e.g., codes for postcranial characters for taxa with no known postcrania). These patterns, in conjunction with their prevalence, warrant a thorough survey of the entire matrix and subsequent reanalysis of its various forms to test whether previously published findings regarding the relationships of temnospondyls and the origins of lissamphibians are substantiated. A thorough reassessment of this matrix and several of its high-profile derivates revealed that the phylogeny of temnospondyls is more poorly known than depicted by the literature and that certain hypotheses of lissamphibian origins within Temnospondyli lack phylogenetic support.
Amino acid availability acts as a metabolic rheostat to determine the magnitude of ILC2 responses
Authors: Hodge Suzanne H. , Krauss Maria Z. , Kaymak Irem , King James , Howden Andrew J.M. , Panic Gordana , Grencis Richard K. , Swann Jonathan R. , Sinclair Linda V. , Hepworth Matthew R.
Published: June 2022

Group 2 innate lymphoid cells (ILC2) are functionally poised, tissue-resident lymphocytes that respond rapidly to damage and infection at mucosal barrier sites. ILC2 reside within complex microenvironments where they are subject to cues from the diet, commensal microbiota and invading pathogens – most notably helminths. Emerging evidence suggests ILC2 are acutely sensitive not only to canonical activating signals, but also perturbations in nutrient and metabolite availability. In the context of helminth infection, we identify amino acid availability as a nutritional cue in regulating ILC2 responses. ILC2 were found to be uniquely pre-primed to import amino acids via the large neutral amino acid transportersSlc7a5andSlc7a8. Cell-intrinsic deletion of these transporters impaired ILC2 expansion, but not cytokine production, in part via tuning of mTOR activation. These findings implicate the import of amino acids as a metabolic requisite for optimal ILC2 responses, and further highlight nutritional cues as critical regulators of innate immune responses within mucosal barrier tissues.
Topology-based fluorescence image analysis for automated cell identification and segmentation
Authors: Panconi L. , Makarova M. , Lambert E. R. , May R.C. , Owen D.M.
Published: June 2022

Cell segmentation refers to the body of techniques used to identify cells in images and extract biologically relevant information from them; however, manual segmentation is laborious and subjective. We present Topological Boundary Line Estimation using Recurrence Of Neighbouring Emissions (TOBLERONE), a topological image analysis tool which identifies persistent homological image features as opposed to the geometric analysis commonly employed. We demonstrate that topological data analysis can provide accurate segmentation of arbitrarily-shaped cells, offering a means for automatic and objective data extraction. One cellular feature of particular interest in biology is the plasma membrane, which has been shown to present varying degrees of lipid packing, or membrane order, depending on the function and morphology of the cell type. With the use of environmentally-sensitive dyes, images derived from confocal microscopy can be used to quantify the degree of membrane order. We demonstrate that TOBLERONE is capable of automating this task.
A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data
Authors: Cheng Yuqi , Fan Xingyu , Zhang Jianing , Li Yu
Published: June 2022

Cell type annotation is critical to understand the cell population heterogeneity in the single-cell RNA sequencing (scRNA-seq) analysis. Due to their fast, precise, and user-friendly advantages, automatic annotation methods are gradually replacing traditional unsupervised clustering approaches in cell type identification practice. However, current supervised annotation tools are easily overfitting, thus favoring large cell populations but failing to learn the information of smaller populations. This drawback will significantly mislead biological analysis, especially when the rare cell types are important. Here, we present scBalance, an integrated sparse neural network framework that leverages the adaptive weight sampling and dropout techniques for the auto-annotation task. Using 20 scRNA-seq datasets with different scales and different imbalance degrees, we systematically validate the strong performance of scBalance for both intra-dataset and inter-dataset annotation tasks. Furthermore, we also demonstrate the scalability of scBalance on identifying rare cell types in million-level datasets by uncovering the immune landscape in bronchoalveolar cells. Up to now, scBalance is the first and only auto-annotation tool that expands scalability to 1.5 million cells dataset. In addition, scBalance also shows a fast and stable speed outperforming commonly used tools across all scales of datasets. We implemented scBalance in a user-friendly manner that can easily interact with Scanpy, which makes scBalance a superior tool in the increasingly important Python-based platform.
COP9 signalosome component CSN-5 stabilizes PUF proteins FBF-1 and FBF-2 inCaenorhabditis elegansgermline stem cells
Authors: Osterli Emily , Ellenbecker Mary , Wang Xiaobo , Terzo Mikaya , Jacobson Ketch , Cuello DeAnna , Voronina Ekaterina
Published: June 2022

RNA-binding proteins FBF-1 and FBF-2 (FBFs) are required for germline stem cell maintenance and the sperm/oocyte switch inCaenorhabditis elegans, though the mechanisms controlling FBF protein levels remain unknown. We identified an interaction between both FBFs and CSN-5, a component of the COP9 (constitutive photomorphogenesis 9) signalosome. Here, we find that the MPN (Mpr1/Pad1 N terminal) metalloprotease domain of CSN-5 interacts with the PUF (Pumilio and FBF) RNA-binding domain of FBFs and the interaction is conserved for human homologs PUM1 and CSN5. The interaction between FBF-2 and CSN-5 can be detectedin vivoby proximity ligation.csn-5mutation results in destabilization of FBF proteins, a decrease in the numbers of germline stem cells, and disruption of the switch from spermatogenesis to oogenesis. The loss ofcsn-5does not decrease the levels of a related PUF protein PUF-3 andcsn-5(lf) phenotype is not enhanced byfbf-1/2depletion, suggesting that the effect is specific to FBFs. The effect ofcsn-5on germline sex determination is largely independent of the COP9 signalosome and is cell autonomous. Surprisingly, regulation of FBF protein levels involves a combination of COP9-dependent and –independent mechanisms differentially affecting FBF-1 and FBF-2. This work supports a previously unappreciated role for CSN-5 in stabilization of germline stem cell regulatory proteins FBF-1 and FBF-2.

Author Summary

Germ cell development and reproductive success in the nematodeC. elegansrely on the function of germline stem cells. Continued maintenance of these cells is supported by the activity of conserved RNA-binding proteins FBF-1 and FBF-2 (FBFs). However, it is unknown how FBF protein levels are regulated. Here, we identify a direct interaction between FBFs and CSN-5, a component of the COP9 signalosome best known for its role in regulating protein degradation. We find that CSN-5 promotes FBF stability and allows for accumulation of steady-state protein levels, thereby promoting FBF function. Incsn-5mutants, we find a significant reduction of FBF proteins, decrease of stem cells, and failure to promote oogenesis consistent with compromised FBF function. Furthermore, CSN-5 contributes to FBF protein stability through two mechanisms. This work demonstrates a previously unappreciated role for CSN-5 in stabilization of FBF proteins. Based on our finding that the FBF/CSN-5 interaction is conserved and detectable between homologous human proteins, we speculate this relationship might be relevant for understanding stem cell maintenance in a range of species, from nematodes to humans.
Thermal Pain and Detection Threshold Modulation in Augmented Reality
Authors: Eckhoff Daniel , Sandor Christian , Cheing Gladys L. Y. , Schnupp Jan , Cassinelli Alvaro
Published: June 2022

Augmented Reality (AR) overlays computer-generated visual, auditory or other sensory information on the real world. Due to recent advancements in AR it can be difficult for the user to differentiate between sensory information coming from real and virtual objects, leading to interesting phenomena. For example, an AR experience in which users can experience their own hands in flames has been shown to elicit heat illusions on the affected hands. In this study, we investigate the potential that AR has for top-down modulation of pain and thermal perception. We assessed thermal pain and detection thresholds on the participant’s right hand when they experienced that hand covered in virtual flames in AR. We compared that experience to a baseline condition with no additional stimuli as well to a control condition that sees the hand covered by unrealistic blue flames to compensate the distraction factor. We found that experiencing a burning hand in AR induced analgesic and hyperalgesic effects as participants began to feel heat related pain on lower temperatures and cold related pain on higher temperatures. That experience also significantly changed the lowest temperature at which participants started perceiving warmth. These results demonstrate that pain and thermal perception can be manipulated by altering the perception of our body in AR.
Sequencing from leftover material of stored rapid Ag Tests (Ag-RDTs): a gamechanger in genomic surveillance?
Authors: Rector Annabel , Bloemen Mandy , Schiettekatte Gilberte , Maes Piet , Van Ranst Marc , Wollants Elke
Published: June 2022

Archived lateral flow antigen-detection rapid diagnostic tests (Ag-RDTs), used in the diagnosis of COVID-19, were successfully used to extract viral nucleic acids for subsequent RT-qPCR and sequencing by Sanger or Nanopore whole genome sequencing (WGS). The method was successfully applied with different brands of SARS-CoV-2 Ag-RDTs, but also with Ag-RDTs for detection of influenza, rotavirus and adenovirus 40/41. The buffer used in the Ag-RDT had an important influence on the RNA yield from the test stripand the efficiency of subsequent sequencing. Our finding that the test strip in rapid Ag tests is suited to preserve viral genomic material, even for months at room temperature, and therefore can serve as source material for genetic characterization, could improve global coverage of genomic surveillance for SARS-CoV-2 as well as for other viruses.
HEART rate variability biofeedback for LOng Covid symptoms (HEARTLOC): protocol for a feasibility study
Authors: Corrado J , Halpin SJ , Preston N , Whiteside D , Tarrant R , Davison J , O’Connor RJ , Casson AJ , Sivan M
Published: June 2022

Introduction

Long covid (LC), also known as Post-COVID-19 syndrome, refers to symptoms persisting 12 weeks after COVID-19 infection. It affects up to 1 in 7 people contracting the illness and causes a wide range of symptoms, including fatigue, breathlessness, palpitations, dizziness, pain and brain fog. Many of these symptoms can be linked to dysautonomia or dysregulation of the autonomic nervous system after SARS-CoV2 infection. This study aims to test the feasibility and estimate the efficacy, of the Heart Rate Variability Biofeedback (HRV-B) technique via a standardised slow diaphragmatic breathing programme in individuals with LC.

Methods and Analysis

30 adult LC patients with symptoms of palpitations or dizziness and an abnormal NASA Lean Test (NLT) will be selected from a specialist Long COVID rehabilitation service. They will undergo a 4-week HRV-B intervention using a Polar chest strap device linked to the Elite HRV phone application while undertaking the breathing exercise technique for two 10-min periods every day for at least 5 days a week. Quantitative data will be gathered during the study period using: HRV data from the chest strap and wrist-worn Fitbit, the modified COVID-19 Yorkshire Rehabilitation Scale (C19-YRSm), composite autonomic symptom score (COMPASS 31), World Health Organisation Disability Assessment Schedule (WHODAS 2.0) and EQ-5D-5L health related quality of life measures. Qualitative feedback on user experience and feasibility of using the technology in a home setting will also be gathered. Standard statistical tests for correlation and significant difference will be used to analyse the quantitate data.

Ethics and Dissemination

The study has received ethical approval from Health Research Authority (HRA) Leicester South Research Ethics Committee (21/EM/0271). Dissemination plans include academic and lay publications.

Study Registration

Clinicaltrials.gov No: NCT05228665

Strengths and limitations of the study

To our knowledge, this is the first study of HRVB in long covid and will provide new information regarding the feasibility of the technology-based intervention in this condition.

The estimation of efficacy will determine the scope and sample size for a larger controlled trial in the condition that currently has no definitive treatments

The study will provide preliminary evidence on the correlation between long covid symptoms and dysautonomia.

The limitation of this study is the small sample size of 30 participants which might not give an accurate estimate of efficacy.

HRV-B is a technology-based intervention, therefore its take-up could be limited in those with a lack of experience in using digital technology in daily life, particularly those from less privileged backgrounds.
AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers
Authors: Koutsovoulos Georgios D. , Noriot Solène Granjeon , Bailly-Bechet Marc , Danchin Etienne G. J. , Rancurel Corinne
Published: June 2022

Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.

Availability and implementation

AvP is written in Python and is available under GNU General Public License v3.0 at (https://github.com/GDKO/AvP).
Postsynaptic GluA3 subunits are required for the appropriate assembly of AMPA receptor GluA2 and GluA4 subunits on mammalian cochlear afferent synapses and for presynaptic ribbon modiolar-pillar morphological distinctions
Authors: Rutherford Mark A. , Bhattacharyya Atri , Xiao Maolei , Cai Hou Ming , Pal Indra , Rubio María E.
Published: June 2022

The encoding of acoustic signals in the cochlea depends on α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs), but relatively little is known about their reliance on specific pore-forming subunits. With 5-week-old male GluA3KO mice, we determined cochlear function, synapse ultrastructure, and AMPAR subunit molecular anatomy at ribbon synapses between inner hair cells (IHCs) and spiral ganglion neurons (SGNs). GluA3KO and wild-type (GluA3WT) mice reared in ambient sound pressure level (SPL) of 55-75 dB had similar ABR thresholds, wave-1 amplitudes, and latencies. Ultrastructurally, the IHC modiolar-pillar differences in presynaptic ribbon size and shape, and synaptic vesicle size seen in GluA3WT were diminished or reversed in GluA3KO. The quantity of paired synapses (presynaptic ribbons juxtaposed with postsynaptic GluA2 and GluA4) was similar, however, GluA2-lacking synapses (ribbons paired with GluA4 but not GluA2) were observed only in GluA3KO. SGNs of GluA3KO mice had AMPAR arrays of smaller overall volume, containing less GluA2 and greater GluA4 immunofluorescence intensity relative to GluA3WT (3-fold difference in mean GluA4:GluA2 ratio). The expected modiolar-pillar gradient in ribbon volume was observed in IHCs of GluA3WT but not GluA3KO. Unexpected modiolar-pillar gradients in GluA2 and GluA4 volume were present in GluA3KO. GluA3 is essential to the morphology and molecular composition of IHC-ribbon synapses. We propose the hearing loss seen in older male GluA3KO mice results from progressive synaptopathy evident in 5-week-old mice as increased abundance of GluA2-lacking, GluA4 monomeric, Ca2+-permeable AMPARs.
CHI3L1 enhances melanoma lung metastasis via regulation of t cell co-stimulators and CTLA-4/B7 axis
Authors: Ma Bing , Kamle Suchitra , Akosman Bedia , Khan Hina , Lee Chang Min , Lee Chun Geun , Elias Jack A.
Published: June 2022

ICOS/ICOSL and CD28/B7-1/B7-2 are T cell co-stimulators and CTLA-4 is an immune checkpoint inhibitor that play critical roles in the pathogenesis of neoplasia. Chitinase 3-like-1 (CHI3L1) is induced in many cancers where it portends a poor prognosis and contributes to tumor metastasis. Here we demonstrate that CHI3L1 inhibits the expression of ICOS, ICOSL and CD28 while stimulating CTLA-4 and the B7 moieties in melanoma lung metastasis. We also demonstrate that RIG-like helicase innate immune activation augments T cell co-stimulation, inhibits CTLA-4 and suppresses pulmonary metastasis. At least additive antitumor responses were seen in melanoma lung metastasis treated with anti-CTLA-4 and anti-CHI3L1 antibodies in combination. Synergistic cytotoxic T cell-induced tumor cell death and the heightened induction of the tumor suppressor PTEN were seen in co-cultures of T and tumor cells treated with bispecific antibodies that target both CHI3L1 and CTLA-4. Thus, CHI3L1 contributes to pulmonary metastasis by inhibiting T cell co-stimulation and stimulating CTLA-4. The simultaneous targeting of CHI3L1 and the CTLA-4 axis with individual and, more powerfully with bispecific antibodies, represent promising therapeutic strategies for pulmonary metastasis.
To share or not to share? iEEG evidence for state-dependent inequity encoding in the human OFC
Authors: Marciano Deborah , Staveland Brooke R. , Lin Jack , Saez Ignacio , Hsu Ming , Knight Robert T.
Published: June 2022

Social decision-making requires the integration of reward valuation and social cognition systems, both dependent on the orbitofrontal cortex (OFC). How these two OFC functions interact is largely unknown. We recorded intracranial activity from the OFC of ten patients making choices in the context of different types of inequity (disadvantageous vs. advantageous). We found that high-frequency activity (70-150 HZ) encoded the amount of self-reward, consistent with previous reports. We also observed novel evidence for encoding in human OFC of the social counterpart’s reward as well as the type of inequity being experienced. Additionally, we find social context modulates reward encoding: depending on inequity type, reward encoding was switched on and off rapidly within electrodes, across trials. These results provide direct evidence for explicit encoding of self- and other- rewards in the human OFC, and for rapid and reversible changes in encoding schemes driven by socially relevant contexts.
Humoral Responses in the Omicron Era following Three-Dose SARS-CoV-2 Vaccine Series in Kidney Transplant Recipients
Authors: McEvoy Caitriona M. , Hu Queenie , Abe Kento T. , Yau Kevin , Oliver Matthew J. , Levin Adeera , Gingras Anne-Claude M. , Hladunewich Michelle , Yuen Darren
Published: June 2022

Background:
Kidney transplant recipients (KTR) have a diminished response to SARS-CoV-2 vaccination in comparison to immunocompetent individuals. Deeper understanding of the antibody response in KTRs following third-dose vaccination would enable identification of those who remain unprotected against Omicron and require additional treatment strategies.
Methods:
We profiled antibody responses in KTRs pre- and at one and three months post-third-dose SARS-CoV2 mRNA-based vaccine. Anti-spike and anti-RBD IgG levels were determined by ELISA. Neutralization against wild-type, Beta, Delta and Omicron (BA.1) variants was determined using a SARS-CoV-2 spike pseudotyped lentivirus assay.
Results:
44 KTRs were analysed at 1 and 3 months (n=26) post-third-dose. At one month, the proportion of participants with a robust antibody response had increased significantly from baseline, but Omicron-specific neutralizing antibodies were detected in just 45% of KTRs. Median binding antibody levels declined at 3 months, but the proportion of KTRs with a robust antibody response was unchanged. 38.5% KTRs maintained Omicron-specific neutralization at 3 months. No clinical variables were significantly associated with detectable Omicron neutralizing antibodies, but anti-RBD titres appeared to identify those with Omicron-specific neutralizing capacity.
Conclusion:
Over 50% of KTRs lack an Omicron-specific neutralization response 1 month following a third mRNA-vaccine dose. Among responders, binding and neutralizing antibody responses were well preserved at 3 months. Anti-RBD antibody titres may be a useful identifier of patients with detectable Omicron neutralizing antibody response.
Trial registration: Clinical Trials Ontario: ID 3604
ScanTecc classifies primary cancers via cell-free extrachromosomal circular DNA in peripheral blood
Authors: Fang Jingwen , Xu Yehong , Wang Jing , Shan Benjie , Ding Kaiyang , Li Shouzhen , Yu Qiaoni , Zhang Wen , Shao Yunying , Yang Jiaxuan , Liu Ke , Xu Guangtao , Yao Xinfeng , Sun Ruoming , Zhang Mengyuan , Zhang Zhihong , Pan Yueyin , Guo Chuang , Qu Kun
Published: June 2022

Extrachromosomal circular DNA (eccDNA) is gaining substantial attention in basic and clinical research for its contribution to tumor heterogeneity, biogenesis, and evolution. However, its presence and molecular features in peripheral blood from cancer patients are poorly understood. Here, we demonstrated the existence of eccDNA molecules in cancer patients’ plasma using atomic-force microscopy and high throughput sequencing technology. We then developed a method named ScanTecc (ScreeningcancerTypes with cell-freeeccDNA) that integrates cell-free circular DNA sequencing and machine learning approaches for cancer patient screening and classification. We applied ScanTecc on a total of 413 patients with multiple types of human primary cancers and 52 healthy individuals and found a significantly greater number and more extended size of eccDNAs in patients’ peripheral blood. ScanTecc accurately distinguished cancer patients (including early stages I and II) from healthy individuals with an overall prediction rate of 0.85 and identified distinct cancer types with an overall prediction rate of 0.84. Our study provides evidence for a non-invasive approach potentially applicable for early detection of cancer patients in clinics.
Factors Associated with Receipt and Parental Intent for COVID-19 Vaccination of Children Ages 5–11 years
Authors: Santibanez Tammy A. , Lendon Jessica Penn , Singleton James A. , Black Carla L. , Zhou Tianyi , Kriss Jennifer L. , Jain Anurag , Elam-Evans Laurie D. , Masters Nina B. , Peacock Georgina
Published: June 2022

Background and Objectives

COVID-19 vaccine was first recommended for children ages 5–11 years on November 2, 2021. This report describes COVID-19 vaccination coverage and parental intent to vaccinate their child ages 5–11 years, overall, by sociodemographic characteristics, and by social and behavioral drivers of vaccination, the fourth month after recommendation.

Methods

We analyzed data from 5,438 interviews conducted in February 2022 from the National Immunization Survey-Child COVID Module (NIS-CCM), a national random-digit-dial cellular telephone survey of households with children.

Results

30.9% of children ages 5–11 were vaccinated with ≥1 dose of COVID-19 vaccine, 35.2% were unvaccinated and the parent reported they probably or definitely would get the child vaccinated or were unsure, and 33.9% were unvaccinated and the parent probably or definitely would not get the child vaccinated. Vaccination coverage and parental intent differed by sociodemographic variables, including income, health insurance status, and rurality. Parental intent to vaccinate children also differed by ethnicity and race. Concern about the child getting COVID-19 and confidence in vaccine importance and safety were positively associated with vaccination receipt and intent to get the child vaccinated.

Conclusions

By the fourth month of the COVID-19 vaccination program for children ages 5–11 years, less than one-third were vaccinated, and coverage was lower for some sociodemographic subgroups. An additional one-third of children had a parent who was open to vaccinating the child. Efforts to address parental concerns regarding vaccine safety and to convey the importance of the vaccine might improve vaccination coverage.
TomoTwin: Generalized 3D Localization of Macromolecules in Cryo-electron Tomograms with Structural Data Mining
Authors: Rice Gavin , Wagner Thorsten , Stabrin Markus , Raunser Stefan
Published: June 2022

Cryoelectron tomography enables the visualization of cellular environments in extreme detail through the lens of a benign observer; what remains lacking however are tools to analyze the full amount of information contained within these densely packed volumes. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: a robust, first in class general picking model for cryo-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space which separates macromolecules according to their 3-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network each time a new protein is to be located. TomoTwin is open source and available at https://github.com/MPI-Dortmund/tomotwin-cryoet.
An Atlas of Cells in the Human Tonsil
Authors: Massoni-Badosa Ramon , Soler-Vila Paula , Aguilar-Fernández Sergio , Nieto Juan C. , Elosua-Bayes Marc , Marchese Domenica , Kulis Marta , Vilas-Zornoza Amaia , Bühler Marco Matteo , Rashmi Sonal , Alsinet Clara , Caratù Ginevra , Moutinho Catia , Ruiz Sara , Lorden Patricia , Lunazzi Giulia , Colomer Dolors , Frigola Gerard , Blevins Will , Palomino Sara , Gomez-Cabrero David , Agirre Xabier , Weniger Marc A. , Marini Federico , Cervera-Paz Francisco Javier , Baptista Peter M. , Vilaseca Isabel , Prosper Felipe , Küppers Ralf , Gut Ivo Glynne , Campo Elias , Martin-Subero José Ignacio , Heyn Holger
Published: June 2022

Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census of cell types forming the human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well as spatial transcriptomics, resulting in an atlas of >357,000 cells. We provide a glossary of 121 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease. Here, we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.
Yeast U6 snRNA made by RNA polymerase II is less stable but functional
Authors: Lipinski Karli A. , Chi Jing , Chen Xin , Hoskins Aaron A. , Brow David A.
Published: June 2022

U6 small nuclear (sn)RNA is the shortest and most conserved snRNA in the spliceosome and forms a substantial portion of its active site. Unlike the other four spliceosomal snRNAs, which are synthesized by RNA polymerase (RNAP) II, U6 is made by RNAP III. To determine if some aspect of U6 function is incompatible with synthesis by RNAP II, we created a U6 snRNA gene with RNAP II promoter and terminator sequences. This “U6-II” gene is functional as the sole source of U6 snRNA in yeast, but its transcript is much less stable than U6 snRNA made by RNAP III. Addition of the U4 snRNA Sm protein binding site to U6-II increased its stability and led to formation of U6-II•Sm complexes. We conclude that synthesis of U6 snRNA by RNAP III is not required for its function and that U6 snRNPs containing the Sm complex can form in vivo. The ability to synthesize U6 snRNA with RNAP II relaxes sequence restraints imposed by intragenic RNAP III promoter and terminator elements and allows facile control of U6 levels via regulators of RNAP II transcription.
The wheat head blight pathogen Fusarium graminearum recruits facultative endohyphal bacteria from the soil, making the fungal-bacterial holobiont nitrogen-fixing and increasing the fungal pathogenicity
Authors: Ali Hina , Pei Mengtian , Li Hongchen , Fang Wenqin , Khan Hamid Ali , Nadeem Tariq , Olsson Stefan
Published: June 2022

In nature, fungal endophytes often have facultative endohyphal bacteria. Can a fungal pathogen such as Fusarium graminearum, pathogenic on wheat, get facultative endohyphal bacteria from soil (FEB) and how does the FEB affect the fungal phenotype? We constructed a growth system/microcosm that allowed a molecularly well-studied F. graminearum isolate, PH-1, to grow through natural soil and then be re-isolated on a gentamicin-containing medium, allowing endohyphal growth of the bacteria while killing eventual bacteria growing on the agar medium. We had labelled the F. graminearum PH-1 with a His1mCherry gene staining the fungal nuclei fluorescent red to confirm re-isolation of the same isolate we sent through the soil. Through qPCR of the 16SrRNA gene in the bacteria using universal primers combined with qPCR of the mCherry gene of DNA from the re-isolated cultures of the Fg-FEB holobionts growing on gentamicin-containing media, it was found that most of the holobiont isolates contained about 10 16SrRNA genes per fungal mCherry gene. The Fg-FEB holobiont isolates were sub-cultured several times, and the FEB content on lab media was stable. Sequencing the 16SrRNA gene from several Fg-FEB holobiont isolates revealed known endophytic bacteria capable of nitrogen fixation. We compared the pathogenicity of one of the Fg-FEB holobionts Fg-S.maltophilia, with the background without FEB and found that it was more pathogenic than without FEB. We could also show that the bacterial 16SrRNA load per fungal His1mCherry gene inside the wheat stayed the same as in culture. Finally, we tested if the Fg-S.maltophilia was capable of nitrogen fixation and could show that it, on a nitrogen-free medium, formed a dense mycelium containing proteins at similar levels as on regular nitrogen-containing media. Our results could indicate that naturally occurring fungal pathogens outside lab conditions might contain facultative endohyphal bacteria, positively affecting their pathogenicity and ecological fitness.
Myeloid reprogramming by JAK inhibition enhances checkpoint blockade therapy
Authors: Zak Jaroslav , Pratumchai Isaraphorn , Marro Brett S. , Marquardt Kristi L. , Zavareh Reza Beheshti , Lairson Luke L. , Oldstone Michael B. A. , Varner Judith A. , Bachanova Veronika , Teijaro John R.
Published: June 2022

Unleashing anti-tumor T cell activity by checkpoint inhibition is effective in many cancer patients but clinical response rates remain limited. Myeloid derived suppressor cells erode antitumor lymphocyte numbers and function, and correlate with resistance to checkpoint inhibitors. By screening small molecule libraries, we identified JAK inhibitors’ ability to rescue T cell function. Despite its documented immune suppressive properties, the prototypical JAK inhibitor ruxolitinib enhanced the efficacy of immune checkpoint blockade in cancer. This effect correlated with loss of suppressive gene expression, and acquisition of immunostimulatory molecular markers and T cell stimulatory activity in myeloid cells. In preclinical models, ruxolitinib significantly improved the function and increased the total numbers of activated tumor-infiltrating NK and CD4 T cells compared to checkpoint blockade alone and the efficacy was conditional on granulocytic cells. In addition to myeloid reprogramming in the tumor, ruxolitinib blunts G-CSF signaling in the bone marrow to prevent expression of suppressive and chemotaxis genes in neutrophils. In a clinical trial of Hodgkin lymphoma patients resistant to checkpoint inhibitors, treatment with ruxolitinib significantly reduced neutrophil-to-lymphocyte ratios and levels of suppressive markers in myeloid cells but increased numbers of cytokine-producing T cells. These results support the therapeutic potential of JAK inhibition in combination with checkpoint inhibitors in cancer and highlight the potential of reshaped myeloid immunity to improve immunotherapy.

One sentence summary: Ruxolitinib reshapes myeloid immunity to synergize with checkpoint inhibitors