bluuebunny/crossref_metadata_2025 huggingface dataset:
Pain management after dental extractions – non-opioid combination analgesics minimize opioid use for acute dental pain
Authors: Huang Qirong , Rasubala Linda , Gracely Richard , Khan Junad , Eliav Eli , Ren Yanfang
Published: May 2022

Objective

To evaluate long-term changes in pain management strategies and assess the outcomes of opioids and non-opioid combination analgesics after dental extractions.

Methods

This is a cross-sectional study of patients who received dental extractions and analgesic prescriptions in a large dental urgent care center in two 12-month periods: January 2012 to December 2012 (Year-2012) and March 2021 to February 2022 (Year-2022). Data extracted from electronic records include type of dental extractions, analgesics prescribed, and follow-up visits. The primary outcome was failure rate measured by the proportions of patients who returned to the clinic for management of pain after receiving dental extractions and analgesic prescriptions.

Results

A total of 3,357 patients in Year-2012 and 3,785 patients in Year-2022 received analgesic prescriptions in conjunction with dental extractions. Combination analgesics were significantly higher in Year-2022 (62.5%) than in Year-2012 (34.9%) (RR=1.79, 95% CI 1.70-1.89. p<0.0001). Combinations analgesics were almost exclusively opioids and 1,166 patients, or 34.7%, received opioids in Year-2012, compared to none received opioids, 49.4% received ibuprofen/ acetaminophen and 13.1% received gabapentin combinations in Year-2022. After surgical extractions, a majority were prescribed opioids (52.4%), followed by ibuprofen (46.2%) in Year-2012. In contrast, a majority received ibuprofen/acetaminophen (56.2%) or gabapentin combinations (17.3%) in Year-2022. Ibuprofen/acetaminophen had a failure rate (2.2%) lower than gabapentin combinations (4.4%) (RR=0.50, 95%CI 0.31-0.83. p=0.01), or opioid combinations (21.4%) (RR=0.10, 95%CI 0.08-0.14. p<0.0001). Failure rate for gabapentin combinations was lower than opioids (RR=0.21, 95%CI 0.14-0.31. p<0.0001).

Conclusions and Relevance

This study showed a paradigm shift from opioids and single medication analgesics to non-opioids and combination analgesics with ibuprofen, acetaminophen and gabapentin as components in prescribing for pain after dental extractions, which presents an opportunity to minimize or eliminate our reliance on opioids for dental pain.
Academic dependency: the influence of the prevailing international biomedical research agenda on Argentina’s CONICET
Authors: García Carrillo M. , Testoni F. , Gagnon M. A. , Rikap C. , Blaustein M.
Published: May 2022

Background

Previous research within the field of health and biomedical sciences (HBMS) reported that its prevailing research agenda is determined by leading academic institutions and big pharma companies, prioritizing the exploration of novel pharmacological interventions over research on the socio-environmental determinants of disease. Unlike previous studies, which have relied primarily on qualitative analyses, the aim of this investigation is to quantitatively explore if that prevailing international research agenda influences research in semi-peripheral countries and to which extent.

Methods

We used the Web of Science database and the CorText platform to proxy the HBMS research agenda of a prestigious research institution from Latin America: Argentina’s National Research Council (CONICET). We conducted a bibliometric and lexical analysis of 16,309 HBMS scientific articles whereby CONICET was among the authors’ affiliations. The content of CONICET’s agenda was depicted through co-occurrence network maps of the most prevalent multi-terms found in titles, keywords, and abstracts. We compared our findings with previous reports on the international HBMS research agenda.

Results

In line with the results previously reported for the prevailing international agenda, we found that multi-terms linked to molecular biology and cancer research hegemonize CONICET’s HBMS research agenda, whereas multi-terms connecting HBMS research with socio-environmental cues are marginal. However, we also found differences with the international agenda: CONICET’s HBMS agenda shows a marginal presence of multi-terms linked to translational medicine, while multi-terms associated with categories such as pathogens, plant research, agrobiotechnology, and food industry are more represented than in the prevailing agenda.

Conclusions

In line with the academic dependency theory, CONICET’s HBMS research agenda shares topics, priorities, and methodologies with the prevailing HBMS international research agenda. However, CONICET’s HBMS research agenda is internally heterogeneous, appearing to be mostly driven by a combination of elements that not only reflect academic dependency but also economic dependency.
Systematic functional annotation workflow for insects
Authors: Bono Hidemasa , Sakamoto Takuma , Kasukawa Takeya , Tabunoki Hiroko
Published: May 2022

Next generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining nucleotide sequences of target or related genes, with many of the acquired sequences remaining unused because other available sequences are not sufficiently annotated. To address this issue, we have developed a functional annotation workflow for transcriptome-sequenced insects to determine transcript descriptions, which represents a significant improvement over the previous method (functional annotation pipeline for insects). The developed workflow attempts to annotate not only the protein sequences obtained from transcriptome analysis but also the ncRNA sequences obtained simultaneously. In addition, the workflow integrates the expression level information obtained from transcriptome sequencing for application as functional annotation information. Using the workflow, functional annotation was performed on the sequences obtained from transcriptome sequencing of stick insect (Entoria okinawaensis) and silkworm (Bombyx mori), yielding richer functional annotation information than that obtained in our previous study. The improved workflow allows more comprehensive exploitation of transcriptome data and is applicable to other insects because the workflow has been openly developed on GitHub.

Simple Summary

The function of all genes encoded in the genome should be studied for genome editing. The genome editing technology can speeds up insect research for functional analysis of genes. Our knowledge about the functional information of genes is still incomplete currently while genome sequencing of an organism can be completed. The functional information has been annotated based solely on the information that has been obtained from the result of previous biological research. However, this information will be important in determining the target genes for genome editing. In particular, it is very important that this information is in machine-readable form because computer programs mainly parse this information for the understanding of biological systems. In this paper, we describe a workflow-based method for annotating gene functions in insects that make use of transcribed sequence information as well as reference genome and protein sequence databases. Using the developed workflow, we annotated functional information of Japanese stick insect and silkworm, including gene expression as well as sequence analysis. The functional annotation information obtained by the workflow will greatly expand the possibilities of entomological research using genome editing.
Accounting for within-species variation in continuous trait evolution on a phylogenetic network
Authors: Teo Benjamin , Rose Jeffrey P. , Bastide Paul , Ané Cécile
Published: May 2022

Within-species trait variation may be the result of genetic variation, environmental variation or measurement error for example. In phylogenetic comparative studies, failing to account for within-species variation has many adverse effects, such as increased error in testing hypotheses about evolutionary correlations, biased estimates of evolutionary rates, and inaccurate inference of the mode of evolution. These adverse effects were demonstrated in studies that considered a tree-like underlying phylogeny. Comparative methods on phylogenetic networks are still in their infancy. The impact of within-species variation on network-based methods has not been studied. Here, we introduce a phylogenetic linear model in which the phylogeny can be a network, to account for within-species variation in the continuous response trait assuming equal within-species variances across species. We show how inference based on the individual values can be reduced to a problem using species-level summaries, even when the within-species variance is estimated. Our method performs well under various simulation settings, and is robust when within-species variances are unequal across species. When phenotypic (within-species) correlations differ from evolutionary (between-species) correlations, estimates of evolutionary coefficients are pulled towards the phenotypic coefficients, for all methods we tested. Also, evolutionary rates are either underestimated or overestimated, depending on the mismatch between phenotypic and evolutionary relationships. We applied our method to morphological and geographical data fromPolemonium. We find a strong negative correlation of leaflet size with elevation, despite a positive correlation within species. Our method can explore the role of gene flow in trait evolution, by comparing the fit of a network to that of a tree. We find marginal evidence for leaflet size being affected by gene flow, and support for previous observations on the challenges of using individual continuous traits to infer inheritance weights at reticulations. Our method is freely available in theJuliapackagePhyloNetworks.
Cell-free Tumor Methylome Analysis of Small Cell Lung Cancer Patients Identifies Subgroups with Prognostic Associations
Authors: Haq Sami Ul , Schmid Sabine , Aparnathi Mansi K. , Hueniken Katrina , Zhan Luna Jia , Sacdalan Danielle , Li Janice J.N. , Meti Nicholas , Patel Devalben , Cheng Dangxiao , Philip Vivek , Tsao Ming S. , Cabanero Michael , de Carvalho Daniel , Liu Geoffrey , Bratman Scott V. , Lok Benjamin H.
Published: May 2022

Introduction

Small cell lung cancer (SCLC) is a highly aggressive type of cancer with a high risk of recurrence. The SCLC methylome may yield biologic insight but is understudied due to difficulty in acquiring primary patient tissue. Here, we comprehensively profile the SCLC methylome using cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq).

Methods

cfDNA was extracted from plasma samples collected from 74 SCLC patients prior to initiation of first-line treatment and from 20 non-cancer smoker participants. Genomic DNA (gDNA) was also extracted from paired peripheral blood leukocytes from the 74 SCLC patients and 7 accompanying circulating-tumour-cell patient-derived xenografts (CDX). cfDNA and gDNA were used as input for cfMeDIP-seq. We developed PeRIpheral blood leukocyte MEthylation (PRIME) subtraction as an algorithm to improve tumour specificity of cell-free methylome.

Results

SCLC total plasma cfDNA methylation profiles obtained using cfMeDIP-seq are representative of CDX tumour methylation. SCLC cfDNA methylation is distinct from non-cancer plasma. Using PRIME and k-means consensus clustering, we identified two SCLC methylome clusters with prognostic associations. These clusters had methylated biological pathways related to axon guidance, neuroactive ligand−receptor interaction, pluripotency of stem cells, and were differentially methylated at long noncoding RNA, LINEs, SINEs, retrotransposons, and other repeats features.

Conclusions

We have comprehensively profiled the SCLC methylome using cfMeDIP-seq in a large patient cohort and identified methylome clusters with prognostic associations. Our work demonstrates the potential of liquid biopsies in examining SCLC biology encoded in the methylome.
Differential effect of Fas activation on spinal muscular atrophy motoneuron death and induction of axonal growth
Authors: Benlefki Salim , Younes Richard , Challuau Désiré , Bernard-Marissal Nathalie , Hilaire Cécile , Scamps Frédérique , Bowerman Melissa , Kothary Rashmi , Schneider Bernard L , Raoul Cédric
Published: May 2022

Amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) are the most common motoneuron diseases affecting adults and infants, respectively. ALS and SMA are both characterized by the selective degeneration of motoneurons. Although different in their genetic etiology, growing evidence indicate that they share molecular and cellular pathogenic signatures that constitute potential common therapeutic targets. We previously described a motoneuron-specific death pathway elicited by the Fas death receptor, whereby vulnerable ALS motoneurons show an exacerbated sensitivity to Fas activation. However, the mechanisms that drive the loss of SMA motoneurons remains poorly understood. Here, we describe an in vitro model of SMA-associated degeneration using primary motoneurons derived from Smn2B/- SMA mice and show that Fas activation selectively triggers death of the proximal motoneurons. Fas-induced death of SMA motoneurons has the molecular signature of the motoneuron-selective Fas death pathway that requires activation of p38 kinase, caspase-8, -9 and -3 as well as upregulation of collapsin response mediator protein 4 (CRMP4). In addition, Rho Kinase (ROCK) is required for Fas recruitment. Remarkably, we found that exogenous activation of Fas also promotes axonal elongation in both wildtype and SMA motoneurons. Axon outgrowth of motoneurons promoted by Fas requires the activity of ERK, ROCK and caspases. This work defines a dual role of Fas signaling in motoneurons that can elicit distinct responses from cell death to axonal growth.
A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material
Authors: Poretti Manuel , Praz Coraline R. , Sotiropoulos Alexandros G. , Wicker Thomas
Published: May 2022

Plant genomes typically contain ∼35,000 genes, almost all belonging to highly-conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs, however they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley and rye. Applying a set of stringent criteria, we identified 5,942 candidate Triticeae-specific genes (TSGs), of which 2,337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold adaptation. Additionally, we show that 1,079 TSGs have sequence homology to transposable elements (TEs), ∼68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess ∼779 lineage-specific genes per haploid genome. TSGs which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.
Development and Evaluation of a Colloidal Gold Immunofiltration Assay for Penside Diagnosis of Visceral Schistosomosis in Cattle
Authors: Mamane Shivani , Jeyathilakan N. , Latha Bhaskaran. Ravi. , Senthilkumar T. M. A.
Published: May 2022

Background

Visceral schistosomosis caused by Schistosoma spindale is an economically important chronic wasting snail-borne trematode infection which often goes undiagnosed in field condition due to lack of efficient diagnostic assays. ELISA and Colloidal gold immunofiltration assay were used to evaluate the state of active visceral schistosomosis in cattle through detection of antibodies against S. spindale ES antigen.

Methodology/Principle Findings

The present study included development and evaluation of enzyme linked immunosorbent assay (ELISA) and colloidal gold immunofiltration assay (CGIFA) with conventionally prepared S. spindale excretory-secretory (ES) antigen using postmortem mesenteric examination as a reference standard. Statistical analysis was performed using Cochran Q test, Chi-square test and kappa statistics which showed no significant difference between the developed tests and strong agreement with the postmortem examination which was considered as gold standard test. CGIFA showed sensitivity, specificity and accuracy of 92.98 %, 96.74 % and 95.55 % respectively whereas that of ELISA was 94.73 %, 95.12 % and 95% respectively.

Conclusion/Significance

CGIFA was found to be simpler, rapid, effective, less expensive and required least expertise for interpretation of results. It can be used as portable diagnostic device for rapid diagnosis of S. spindale infection at field condition making it an ideal pen side diagnostic kit.
The H3K27me3 epigenetic mark is crucial for callus cell identity and for the acquisition of new fate during root and shoot regeneration
Authors: Mandel Tali , Landau Udi , Kaplan Tommy , Williams Leor Eshed
Published: May 2022

We combined molecular, genomic and genetic approaches to study the molecular mechanisms underlying cell totipotency and competency to regenerate in Arabidopsis.

By performing comparative analysis of mRNA-seq and chromatin landscapes between leaf differentiated cells and callus totipotent cells and between WT callus and calli derived from theemf2mutant, exhibiting impaired regenerative capacity we revealed the following:

1. That callus cells express numerous genes of many developmental pathways such as root, leaf, embryo, shoot, meristem and seed. This suggests a mechanism to allow rapid response to a signal by maintaining genes of all potential developmental pathways active, without the needs to release transcriptional silencing and to go through the intricate multistep process of transcription.2. That key transcription factors that are sufficient to derive differentiation or organogenesis are silenced and marked by the H3K27me3.3. That callus derived from theemf2mutant which is impaired in setting the H3K27methylation, lost the capacity to regenerate and that 78 transcription factors from which 18 regulate flower development, where up-regulated compared with WT callus.

Altogether our results suggest that competency to regenerate is achieved by keeping the chromatin of developmental genes active, and that upon a signal for cell fate switch, a mechanism to repress those genes is required to allow the one desired developmental pathway to dominate. When this mechanism is impaired the capacity to regenerate is decline.
Locus cœruleus noradrenergic neurons phase-lock to prefrontal and hippocampal infra-slow rhythms that synchronize to behavioral events
Authors: Xiang Liyang , Harel Antoine , Todorova Ralitsa , Gao HongYing , Sara Susan J. , Wiener Sidney I.
Published: May 2022

The locus cœruleus (LC) is the primary source of noradrenergic projections to the forebrain, and, in prefrontal cortex, is implicated in decision-making and executive function. LC neurons phase-lock to cortical infra-slow wave oscillations during sleep. Such infra-slow rhythms are rarely reported in awake states, despite their interest, since they correspond to the time scale of behavior. Thus, we investigated LC neuronal synchrony with infra-slow rhythms in awake rats performing an attentional set-shifting task. Local field potential (LFP) oscillation cycles in prefrontal cortex and hippocampus on the order of 0.4 Hz phase-locked to task events at crucial maze locations. Indeed, successive cycles of the infra-slow rhythms showed different wavelengths, as if they are periodic oscillations that can reset phase relative to salient events.

Simultaneously recorded infra-slow rhythms in prefrontal cortex and hippocampus could show different cycle durations as well suggesting independent control. Most LC neurons (including optogenetically identified noradrenergic neurons) recorded here were phase-locked to these infra-slow rhythms, as were hippocampal and prefrontal units recorded on the LFP probes. The infra-slow oscillations also phase-modulated gamma amplitude, linking these rhythms at the time scale of behavior to those coordinating neuronal synchrony. This would provide a potential mechanism where noradrenaline, released by LC neurons in concert with the infra-slow rhythm, would facilitate synchronization or reset of these brain networks, underlying behavioral adaptation.
Hypoxic memory of tumor intrinsic type I interferon suppression promotes breast cancer metastasis
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Amzaleg Yonatan , Moriarty Aidan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher , Torres Evanthia T. Roussos , Klotz Remi , Yu Min
Published: May 2022

Hypoxia is a common feature of many solid tumors due to aberrant proliferation and angiogenesis and has been associated with tumor progression and metastasis. Most of the well-known hypoxia effects are mediated through hypoxia-inducible factors (HIFs), but the long-lasting effect of hypoxia beyond the immediate HIF regulation remains less understood. Here we show that hypoxia exerts a prolonged effect to promote metastasis. Using breast cancer patient-derived circulating tumor cell (CTC) lines and common breast cancer cell lines, we found that hypoxia downregulates tumor intrinsic type I interferon (IFN) signaling and its downstream antigen presentation (AP) machinery in luminal breast cancer cells, via both HIF-dependent and HIF-independent mechanisms. Hypoxia induced IFN/AP suppression can last longer than the hypoxic exposure, presenting a “hypoxic memory” phenotype. Hypoxic memory of IFN/AP downregulation is established by specific hypoxic priming, and cells with hypoxic memory have an enhanced ability for tumorigenesis and metastasis. The histone deacetylase inhibitor (HDACi) Entinostat can erase the hypoxic memory and improve the immune clearance of tumor cells when combined with checkpoint immunotherapies in a syngeneic breast cancer mouse model. These results point to a novel mechanism for hypoxia facilitated tumor progression, through a long-lasting memory that provides advantages for CTCs during the metastatic cascade.

Significance:We revealed a novel hypoxic memory of prolonged suppression of tumor intrinsic type I IFN and AP signals that promote tumorigenesis and metastasis, suggesting novel mechanistic understanding of the immune evasive properties of CTCs.
Foxd1 dependent induction of temporal retinal character is required for visual function
Authors: Hernández-Bejarano María , Gestri Gaia , Monfries Clinton , Tucker Lisa , Dragomir Elena I. , Bianco Isaac H. , Bovolenta Paola , Wilson Stephen W. , Cavodeassi Florencia
Published: May 2022

Appropriate patterning of the retina during embryonic development is assumed to underlie the establishment of spatially localised specialisations that mediate the perception of specific visual features. For instance, in zebrafish, an area involved in high acuity vision (HAA) is thought to be present in the ventro-temporal retina. Here we show that the interplay of the transcription factor Rx3 with Fibroblast Growth Factor and Hedgehog signals, initiates and restricts foxd1 expression to the prospective temporal retina, initiating naso-temporal regionalisation of the retina. Abrogation of FoxD1 results in the loss of temporal and expansion of nasal retinal character, and consequent absence of the HAA. These structural defects correlate with severe visual defects as assessed in optokinetic and optomotor response assays. In contrast, optokinetic responses are unaffected in the opposite condition in which nasal retinal character is lost at the expense of expanded temporal character. Our study indicates that the establishment of temporal retinal character during early retinal development is required for the specification of the HAA, and suggests a prominent role of the temporal retina in controlling specific visual functions.

Summary statement

This study provides a mechanistic link between eye patterning and the establishment of functionally distinct retinal regions and reveals the temporal retina preferentially controls specific aspects of visual function.
DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for next-generation sequencing data
Authors: Marriott Heather , Kabiljo Renata , Khleifat Ahmad Al , Dobson Richard J , Al-Chalabi Ammar , Iacoangeli Alfredo
Published: May 2022

The current widespread adoption of next-generation sequencing (NGS) in all branches of basic and clinical genetics fields means that users with highly variable informatics skills, computing facilities and application purposes need to process, analyse, and interpret NGS data. In this landscape, versatility, scalability, and user-friendliness are key characteristics for an NGS analysis tool. We developed DNAscan2, a highly flexible, end-to-end pipeline for the analysis of NGS data, which (i) can be used for the detection of multiple variant types, including SNVs, small indels, transposable elements, short tandem repeats and other large structural variants; (ii) covers all steps of the analysis, from quality control of raw data to the generation of html reports for the interpretation and prioritisation of results; (iii) is highly adaptable and scalable as it can be deployed and run via either a graphic user interface for non-bioinformaticians, a command line tool for personal computer usage, or as a Snakemake workflow that facilitates parallel multi-sample execution for high-performance computing environments; (iv) is computationally efficient by minimising RAM and CPU time requirements.

Availability and Implementation

DNAscan2 is implemented in Python3 and is available to download as a command-line tool and graphical-user interface at https://github.com/KHP-Informatics/DNAscanv2 or a Snakemake workflow at https://github.com/KHP-Informatics/DNAscanv2_snakemake.
The wild life of ticks: using passive surveillance to determine the distribution and wildlife host range of ticks and the exoticHaemaphysalis longicornis, 2010-2021
Authors: Thompson Alec T. , White Seth A. , Doub Emily E. , Sharma Prisha , Frierson Kenna , Dominguez Kristen , Shaw David , Weaver Dustin , Vigil Stacey L. , Ruder Mark G. , Yabsley Michael J.
Published: May 2022

Background

We conducted a large-scale, passive regional survey of ticks associated with wildlife of the eastern U.S. Our primary goals were to better assess the current geographic distribution of exoticH. longicornisand to identify potential wild mammalian and avian host species. However, this large-scale survey also provided valuable information regarding the distribution and host associations for many other important tick species that utilize wildlife as hosts.

Methods

Ticks were opportunistically collected by cooperating state and federal wildlife agencies. All ticks were placed in the supplied vials and host information was recorded, including host species, age, sex, examination date, location (at least county and state), and estimated tick burden were recorded. All ticks were identified to species using morphology, suspectH. longicorniswere confirmed through molecular techniques.

Results

In total, 1,940 hosts were examined from across 369 counties from 23 states in the eastern U.S. From these submissions, 20,626 ticks were collected and identified belonging to 11 different species. Our passive surveillance efforts detected exoticH. longicornisfrom nine host species from eight states. Notably, some of the earliest detections ofH. longicornisin the U.S. were collected from wildlife through this passive surveillance network. In addition, numerous new county reports were generated forAmblyomma americanum, A. maculatum, Dermacentor albipictus, D. variabilis, andIxodes scapularis.

Conclusions

This study provided data on ticks collected from animals from 23 different states in the eastern U.S. between 2010 – 2021 with the primary goal of better characterizing the distribution and host-associations of the exotic tickH. longicornis; however new distribution data on tick species of veterinary or medical importance was also obtained. Collectively, our passive surveillance has detected numerous new county reports forH. longicornisas well asI. scapularis. Our study utilizing passive wildlife surveillance for ticks across the eastern U.S. is an effective method for surveying a diversity of wildlife host species allowing us to better collect widespread data on current tick distributions relevant to human and animal health.
Cell-autonomous immune dysfunction driven by disrupted autophagy in C9orf72-ALS iPSC-derived microglia contributes to neurodegeneration
Authors: Banerjee Poulomi , Mehta Arpan R , Nirujogi Raja S , Cooper James , James Owen G , Nanda Jyoti , Longden James , Burr Karen , Salzinger Andrea , Paza Evdokia , Newton Judith , Story David , Pal Suvankar , Smith Colin , Alessi Dario R , Selvaraj Bhuvaneish T , Priller Josef , Chandran Siddharthan
Published: May 2022

The most common genetic mutation found in familial and sporadic amyotrophic lateral sclerosis (ALS), as well as fronto-temporal dementia (FTD), is a repeat expansion in the C9orf72 gene. C9orf72 is highly expressed in human myeloid cells, and although neuroinflammation and microglial pathology are widely found in ALS/FTD, the underlying mechanisms are poorly understood. Here, using human induced pluripotent stem cell-derived microglia-like cells (hiPSC-MG) harbouring C9orf72 mutation (mC9-MG) together with gene-corrected isogenic controls (isoC9-MG) and C9ORF72 knock-out hiPSC-MG (C9KO-MG), we show that reduced C9ORF72 protein is associated with impaired phagocytosis and an exaggerated inflammatory response upon stimulation with lipopolysaccharide, driven by sustained activation of NLRP3 inflammasome and NF-κB signalling. Analysis of the hiPSC-MG C9ORF72 interactome revealed an association of C9ORF72 with key regulators of autophagy, a process involved in the homeostatic regulation of the innate immune response. We found impaired initiation of autophagy in C9KO-MG and mC9-MG. Furthermore, through motor neuron-microglial (MN-MG) co-culture studies, we identified that autophagy deficit in mC9-MG led to increased vulnerability of C9 MNs to excitotoxic stimulus. Pharmacological activation of autophagy ameliorated the sustained activation of NLRP3 inflammasome and NF-κB signalling, reversed the phagocytic deficit found in mC9-MG and also reduced MN death in MN-MG co-cultures. We validated these findings in blood-derived macrophages from people with C9orf72 mutation. Our results reveal an important role for C9ORF72 in regulating microglial immune homeostasis and identify dysregulation in human myeloid cells as a contributor to neurodegeneration in ALS/FTD.

Teaser

Disrupted autophagy led immune activation in microglia results in enhanced motor neuronal death in C9orf72-ALS.
Systemic pesticides in a solitary bee pollen food store affect larval development and increase pupal mortality
Authors: Phan Ngoc T. , Joshi Neelendra K. , Rajotte Edwin G. , Zhu Fang , Peter Kari A. , López-Uribe Margarita M. , Biddinger David J.
Published: May 2022

Solitary bees are often exposed to various pesticides applied for pest control on farmland while providing pollination services to food crops1. Increasing evidence suggests that sublethal toxicity of agricultural pesticides affects solitary bees differently than the social bees used to determine regulatory thresholds like honey bees and bumblebees2–4. Studies on solitary bees are challenging because of the difficulties in obtaining large numbers of eggs or young larvae for bioassays. Here we show the toxic and sublethal developmental effects of four widely used plant systemic pesticides on the Japanese orchard bee (Osmia cornifrons). Pollen food stores of this solitary bee were treated with different concentrations of three insecticides (acetamiprid, flonicamid, and sulfoxaflor) and a fungicide (dodine). Eggs were transplanted to the treated pollen and larvae were allowed to feed on the pollen stores after egg hatch. The effects of chronic ingestion of contaminated pollen were measured until adult eclosion. This year-long study revealed that chronic exposure to all tested pesticides delayed larval development and lowered larval and adult body weights. Additionally, exposure to the systemic fungicide resulted in abnormal larval defecation and increased mortality at the pupal stage, indicating potential risk to bees from fungicide exposure. These findings demonstrate potential threats to solitary bees from systemic insecticides and fungicides and will help making policy decisions for mitigating these effects.
Mesenchymal Stromal Cells Donate Mitochondria to Articular Chondrocytes Exposed to Mitochondrial, Environmental, and Mechanical Stress
Authors: Fahey Megan J. , Bennett Maureen P. , Thomas Matthew , Vivancos-Koopman Irene , Browning Lindsay , Bonassar Lawrence J. , Delco Michelle L.
Published: May 2022

Avascular soft tissues of the skeletal system, including articular cartilage, have limited healing capacity, in part due to their low metabolic activity. No drugs are available that can prevent or slow the development of osteoarthritis (OA) after joint injury. Therefore, mesenchymal stromal cell (MSC)-based regenerative therapies are increasingly common in the treatment of OA, but questions regarding their clinical efficacy and mechanisms of action remain unanswered. Our group recently reported that mitochondrial dysfunction is one of the earliest responses of cartilage to injury, resulting in chondrocyte death, extracellular matrix degeneration, and ultimately OA. MSCs have been found to rescue injured cells and improve healing by donating healthy mitochondria in highly metabolic tissues, but mitochondrial transfer has not been investigated in cartilage. Here, we demonstrate that MSCs transfer mitochondria to stressed chondrocytes in cell culture and in injured cartilage tissue. Conditions known induce chondrocyte mitochondrial dysfunction, including stimulation with rotenone/antimycin and hyperoxia, increased transfer. Stressed chondrocytes increased expression of genes related to inflammation and senescence, further supporting the link between mitochondrial dysfunction and transfer. MSC-chondrocyte mitochondrial transfer was blocked by non-specific and specific (connexin-43) gap-junction inhibition. When MSCs were exposed to mechanically injured cartilage they localized to areas of matrix damage and extended cellular processes deep into microcracks, delivering mitochondria to chondrocytes. This work provides insights into the chemical, environmental, and mechanical conditions that can elicit MSC-chondrocyte mitochondrial transfer in vitro and in situ, and our findings suggest a new potential role for MSC-based therapeutics after cartilage injury.

Significance Statement

Recent evidence suggests that although articular cartilage is avascular and relatively metabolically quiescent, acute injury induces chondrocyte mitochondrial dysfunction, driving cartilage degradation and OA. We present the first evidence that MSCs donate mitochondria to articular chondrocytes undergoing mitochondrial dysfunction in vitro and in situ. These findings support a new role for MSCs in the context of cartilage injury and OA, and intercellular mitochondrial transfer may represent a new biological approach to augment mitochondrial capacity in injured chondrocytes. This work establishes multiple experimental models to study MSC mitochondrial donation for the treatment of OA and related degenerative diseases of avascular orthopedic tissues.
petiteFinder: An automated computer vision tool to compute Petite colony frequencies in baker’s yeast
Authors: Nunn Christopher J. , Klyshko Eugene
Published: May 2022

Mitochondrial respiration is central to cellular and organismal health in eukaryotes. In baker’s yeast, however, respiration is dispensable under fermentation conditions. Because yeast are tolerant of this mitochondrial dysfunction, yeast are widely used by biologists as a model organism to ask a variety of questions about the integrity of mitochondrial respiration. Fortunately, baker’s yeast also display a visually identifiable Petite colony phenotype that indicates when cells are incapable of respiration. Petite colonies are smaller than their Grande (wild-type) counterparts, and their frequency can be used to infer the integrity of mitochondrial respiration in populations of cells. In this study, we introduce a deep learning enabled tool,petiteFinder, to leverage the Petite colony phenotype and increase the throughput of the Petite frequency assay. This automated computer vision tool detects Grande and Petite colonies and computes Petite colony frequencies from scanned images of Petri dishes. It addresses issues in scalability and reproducibility of the Petite colony assay which currently relies on laborious manual colony counting methods. Combined with the detailed experimental protocols we provide, we believe this study can serve as a foundation to standardize this assay. Finally, we comment on how Petite colony detection as a computer vision problem highlights ongoing difficulties with small object detection in existing object detection architectures.
Differential integration of activation and repression signals in a multi-enhancer system
Authors: Whitney Peter H. , Shrestha Bikhyat , Xiong Jiahan , Zhang Tom , Rushlow Christine A.
Published: May 2022

Transcription in the early Drosophila blastoderm is coordinated by the collective action of hundreds of enhancers. Many genes are controlled by so-called “shadow enhancers,” which provide resilience to environment or genetic insult, allowing the embryo to robustly generate a precise transcriptional pattern. Emerging evidence suggests that many shadow enhancer pairs do not drive identical expression patterns, however the biological significance of this remains unclear. In this study we characterize the shadow enhancer pair controlling the gene short gastrulation (sog). We removed either the intronic proximal enhancer or the upstream distal enhancer, and monitored sog transcriptional kinetics. Notably, each enhancer differs in sog spatial expression, timing of activation, and RNA Polymerase II loading rates. Additionally, modeling of individual enhancer activities demonstrates that these enhancers integrate activation and repression signals differently. While activation is due to the sum of the two enhancer activities, repression appears to depend on synergistic effects between enhancers. Finally, we examined the downstream signaling consequences resulting from the loss of either enhancer, and found changes in tissue patterning that are well explained by the differences in transcriptional kinetics measured.

SUMMARY STATEMENT

Non-intuitive shadow enhancer synergies are revealed by measuring transcriptional kinetics at the endogenous short gastrulation locus, giving rise to distinct patterning consequences in the dorsal ectoderm of Drosophila embryos.
Development and utility of a PAK1-selective degrader
Authors: Chow Hoi-Yee , Karchugina Sofiia , Groendyke Brian J. , Toenjes Sean , Hatcher John , Donovan Katherine A. , Fischer Eric S. , Abalakov Gleb , Faezov Bulat , Dunbrack Roland , Gray Nathanael S. , Chernoff Jonathan
Published: May 2022

Amplification and/or overexpression of the PAK1 gene is common in several malignancies, and inhibition of PAK1 by small molecules has been shown to impede the growth and survival of such cells. Potent inhibitors of PAK1 and its close relatives, PAK2, and PAK3, have been described, but clinical development has been hindered by recent findings that PAK2 function is required for normal cardiovascular function in adult mice. A unique allosteric PAK1-selective inhibitor, NVS-PAK1-1, provides a potential path forward, but has relatively modest potency in cells. Here, we report the development of BJG-05-039, a PAK1-seletive degrader consisting of the allosteric PAK1 inhibitor NVS-PAK1-1 conjugated to lenalidomide, a recruiter of the E3 ubiquitin ligase substrate adaptor Cereblon (CRBN). BJG-05-039 induced degradation of PAK1, but not PAK2, and displayed enhanced anti-proliferative effects relative to its parent compound in PAK1-dependent, but not PAK2-dependent, cell lines. Notably, BJG-05-039 promoted sustained PAK1 degradation and inhibition of downstream signaling effects at ten-fold lower dosage than NVS-PAK1-1. Our findings suggest that selective PAK1 degradation may confer more potent pharmacological effects compared with catalytic inhibition and highlight the potential advantages of PAK1-targeted degradation.
No circadian clock-gene circuit in the generation of cellular bioluminescence rhythm of CaMV35S::PtRLUC in duckweed
Authors: Watanabe Emiri , Muranaka Tomoaki , Nakamura Shunji , Isoda Minako , Ito Shogo , Oyama Tokitaka
Published: May 2022

Physiological circadian rhythms are coordinated in the plant body in an orderly manner. The coordination of time information has been studied from the aspects of cell–cell local coupling and long-distance communication between tissues. These studies were based on the idea that the behavior of the clock gene circuit represents the physiological rhythms. Here we report the cellular circadian rhythm of a bioluminescence reporter which is not governed by the clock gene circuit in the expressing cells. Using a dual-color bioluminescence monitoring system in Lemna minor transfected with the AtCCA1::LUC+ and CaMV35S::PtRLUC reporters, cellular bioluminescence rhythms with different free-running periods (FRPs) were detected in the same cells. Co-transfection experiments with the two reporters and a clock gene overexpressing effector revealed that the circadian properties of the AtCCA1::LUC+ rhythm, but not those of the CaMV35S::PtRLUC rhythm, were altered in the cells with a dysfunctional clock gene circuit. This indicates that the AtCCA1::LUC+ rhythm is a direct output of the cellular circadian clock while the CaMV35S::PtRLUC rhythm is not. After plasmolysis, the CaMV35S::PtRLUC rhythm disappeared while the AtCCA1::LUC+ rhythm persisted. The plant circadian system consists of both cell-autonomous rhythms and non-cell-autonomous rhythms that are unaffected by the cellular clock.
SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances
Authors: Hui Sandra , Nielsen Rasmus
Published: May 2022

Single cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations. Existing single cell copy number calling methods do not explicitly model the shared evolutionary process of multiple cells, and generally analyze cells independently. Additionally, existing methods for estimating tumor cell phylogenies using copy number profiles are sensitive to profile estimation errors. We present SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data. Using simulations, we show that SCONCE2 has higher accuracy in copy number calling and phylogeny estimation than competing methods. We apply SCONCE2 to previously published single cell sequencing data to illustrate the utility of the method.
Signal Peptide Efficiency: from High-throughput Data to Prediction and Explanation
Authors: Grasso Stefano , Dabene Valentina , Hendriks Margriet M.W.B. , Zwartjens Priscilla , Pellaux René , Held Martin , Panke Sven , van Dijl Jan Maarten , Meyer Andreas , van Rij Tjeerd
Published: May 2022

The passage of proteins across biological membranes via the general secretory (Sec) pathway is a universally conserved process with critical functions in cell physiology and important industrial applications. Proteins are directed into the Sec pathway by a signal peptide at their N-terminus. Estimating the impact of physicochemical signal peptide features on protein secretion levels has not been achieved so far, partially due to the extreme sequence variability of signal peptides. To elucidate relevant features of the signal peptide sequence that influence secretion efficiency, an evaluation of ~12,000 different designed signal peptides was performed using a novel miniaturized high-throughput assay. The results were used to train a machine learning model, and a post-hoc explanation of the model is provided. By describing each signal peptide with a selection of 156 physicochemical features, it is now possible to both quantify feature importance and predict the protein secretion levels directed by each signal peptide. Our analyses allow the detection and explanation of the relevant signal peptide features influencing the efficiency of protein secretion, generating a versatile tool for the in silico evaluation of signal peptides.
Area of Habitat maps for the world’s terrestrial birds and mammals
Authors: Lumbierres Maria , Dahal Prabhat Raj , Soria Carmen D. , Di Marco Moreno , Butchart Stuart H. M. , Donald Paul F. , Rondinini Carlo
Published: May 2022

Area of Habitat (AOH) is ‘the habitat available to a species, that is, habitat within its range’. It complements a geographic range map for a species by showing potential occupancy and reducing commission errors. AOH maps are produced by subtracting areas considered unsuitable for the species from their range map, using information on each species’ associations with habitat and elevation. We present AOH maps for 5,481 terrestrial mammal and 10,651 terrestrial bird species (including 1,816 migratory bird species for which we present separate maps for the resident, breeding and non-breeding areas). Our maps have a resolution of 100 m. On average, AOH covered 66±28% of the range maps for mammals and 64±27% for birds. The AOH maps were validated independently, following a novel two-step methodology: a modelling approach to identify outliers and a species-level approach based on point localities. We used AOH maps to produce global maps of the species richness of mammals, birds, globally threatened mammals and globally threatened birds.
Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation
Authors: Kalliara Eirini , Kardyńska Malgorzata , Bagnall James , Spiller David G. , Muller Werner , Ruckerl Dominik , Biswas Subhra K , Śmieja Jarosław , Paszek Pawel
Published: May 2022

Immune cells fine tune their responses to infection and inflammatory cues. Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon induced JAK-STAT signalling in innate immune macrophages. We demonstrate that transient exposure to IFN-γ stimulation induces a long-term desensitisation of STAT1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls JAK-STAT responses upon re-exposure to stimulus. We show that IFN-α/β1 elicit different level of desensitisation from IFN-γ, where cells refractory to IFN-α/β1 are sensitive to IFN-γ, but notvice versa. We experimentally demonstrate that the underlying feedback mechanism involves regulation of STAT1 phosphorylation but is independent of new mRNA synthesis and cognate receptor expression. A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates JAK-STAT network’s ability to decode relative changes of dose, timing, and type of temporal interferon stimulation. These findings reveal that STAT desensitisation renders cells with signalling memory of type I and II interferon stimulation, which in the future may improve administration of interferon therapy.