bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment
Authors: Gelabert Pere , Sawyer Susanna , Bergström Anders , Collin Thomas C. , Meshveliani Tengiz , Belfer-Cohen Anna , Lordkipanidze David , Jakeli Nino , Matskevich Zinovi , Bar-Oz Guy , Fernandes Daniel M. , Cheronet Olivia , Özdoğan Kadir T. , Oberreiter Victoria , Feeney Robin N. M. , Stahlschmidt Mareike C. , Skoglund Pontus , Pinhasi Ron
Published: January 2021

Archaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history.

Highlights

We demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remains

A single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomes

We show that sediment ancient DNA can reveal important aspects of the human and faunal past

Evidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum

∼0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species
Loss of PIKfyve drives the spongiform degeneration in prion diseases
Authors: Lakkaraju Asvin KK , Frontzek Karl , Lemes Emina , Herrmann Uli , Losa Marco , Marpakwar Rajlakshmi , Aguzzi Adriano
Published: January 2021

Brain-matter vacuolation is a defining trait of all prion diseases, yet its cause is unknown. Here we report that prion infection and prion-mimetic antibodies deplete the phosphatidylinositol kinase PIKfyve in mouse brains, cultured cells, organotypic brain slices, and in brains of Creutzfeldt-Jakob Disease victims. We found that PIKfyve, an inositol kinase involved endolysosomal maturation, is acylated by zDHHC9 and zDHHC21, whose juxtavesicular topology is disturbed by prion infection, resulting in PIKfyve deacylation and destabilization. A protracted unfolded protein response (UPR), typical of prion diseases, also induced PIKfyve deacylation and degradation. Conversely, UPR antagonists restored PIKfyve levels in prion-infected cells. Overexpression of zDHHC9 and zDHHC21, administration of the antiprion polythiophene LIN5044, or supplementation with the PIKfyve reaction product PI(3,5)P2, suppressed prion-induced vacuolation. Thus, PIKfyve emerges as a central mediator of vacuolation and neurotoxicity in prion diseases.
APOBEC1 mediated C-to-U RNA editing: target sequence and trans-acting factor contribution to 177 RNA editing events in 119 murine transcripts in-vivo
Authors: Soleymanjahi Saeed , Blanc Valerie , Davidson Nicholas O.
Published: January 2021

Mammalian C-to-U RNA editing was described more than 30 years ago as a single nucleotide modification in APOB RNA in small intestine, later shown to be mediated by the RNA-specific cytidine deaminase APOBEC1. Reports of other examples of C-to-U RNA editing, coupled with the advent of genome-wide transcriptome sequencing, identified an expanded range of APOBEC1 targets. Here we analyze the cis-acting regulatory components of verified murine C-to-U RNA editing targets, including nearest neighbor as well as flanking sequence requirements and folding predictions. We summarize findings demonstrating the relative importance of trans-acting factors (A1CF, RBM47) acting in concert with APOBEC1. Using this information, we developed a multivariable linear regression model to predict APOBEC1 dependent C-to-U RNA editing efficiency, incorporating factors independently associated with editing frequencies based on 103 Sanger-confirmed editing sites, which accounted for 84% of the observed variance. Co-factor dominance was associated with editing frequency, with RNAs targeted by both RBM47 and A1CF observed to be edited at a lower frequency than RBM47 dominant targets. The model also predicted a composite score for available human C-to-U RNA targets, which again correlated with editing frequency.
Test-retest reliability of tone- and 40 Hz train-evoked gamma oscillations in female rats and their sensitivity to low-dose NMDA channel blockade
Authors: Raza Muhammad Ummear , Sivarao Digavalli V.
Published: January 2021

Rationale

Schizophrenia patients consistently show deficits in sensory-evoked broadband gamma oscillations and click-evoked entrainment at 40 Hz, called the 40 Hz auditory steady-state response (ASSR). Since such evoked oscillations depend on cortical N-methyl D-aspartic acid (NMDA)-mediated network activity, they can serve as pharmacodynamic biomarkers in the preclinical development of drug candidates engaging these circuits. However, there is little test-retest reliability data in preclinical species, a prerequisite for within-subject testing paradigms.

Objectives

We investigated the long-term stability of these measures in a rodent model.

Methods

Female rats with chronic epidural implants were used to record tone- and 40 Hz click-evoked responses at multiple time points and across six sessions, spread over 3 weeks. We assessed reliability using intraclass correlation coefficients (ICC). Separately, we used mixed-effects ANOVA to examine time and session effects. Individual subject variability was determined using the coefficient of variation (CV). Lastly, to illustrate the importance of long-term measure stability for within-subject testing design, we used low to moderate doses of an NMDA antagonist MK801 (0.025-0.15 mg/kg) to disrupt the evoked responses.

Results

We found that 40 Hz ASSR showed good reliability (ICC=0.60-0.75) while the reliability of tone-evoked gamma ranged from fair to good (0.33-0.67). We noted time but no session effects. Subjects showed a lower variance for ASSR over tone-evoked gamma. Both measures were dose-dependently attenuated by NMDA antagonism.

Conclusion

Overall, while both measures use NMDA transmission, 40 Hz ASSR showed superior psychometric properties of higher ICC and lower CV, relative to tone-evoked gamma.
Heparin-modified alginate microspheres enhance neovessel formation in hiPSC-derived endothelial cells and heterocellularin vitromodels by controlled release of VEGF
Authors: Munarin Fabiola , Kabelac Carly , Coulombe Kareen L.K.
Published: January 2021

A formidable challenge in regenerative medicine is the development of stable microvascular networks to restore adequate blood flow or to sustain graft viability and long-term function in implanted or ischemic tissues. In this work, we develop a biomimetic approach to increase the binding affinity of the extracellular matrix for the class of heparin-binding growth factors to localize and control the release of proangiogenic cues while maintaining their bioactivity. Sulfate and heparin moieties are covalently coupled to alginate, and alginate microspheres are produced and used as local delivery depots for vascular endothelial growth factor (VEGF). Release of VEGF from sulfate-alginate and heparin-alginate bulk hydrogels and microspheres was sustained over 14 days.In vitroevaluation with human induced pluripotent stem cell (hiPSC)-derived endothelial cells and aortic ring assay in a chemically-defined hydrogel demonstrates development of primitive three-dimensional vessel-like networks in the presence of VEGF released from the chemically modified alginate microspheres. Furthermore, our results suggest that the sulfate groups available on the chemically modified alginate microspheres promote some new vessel formation even in VEGF-free samples. Based on this evidence, we conclude that sulfate- and heparin-alginate hydrogels are adaptive and bioactive delivery systems for revascularization therapy and translational vascular tissue engineering.
A Network-level Test of the Role of the Co-activated Default Mode Network in Episodic Recall and Social Cognition
Authors: Jackson Rebecca L. , Humphreys Gina F. , Rice Grace E. , Binney Richard J. , Lambon Ralph Matthew A.
Published: January 2021

Resting-state network research is extremely influential, yet the functions of many networks remain unknown. In part, this is due to typical (e.g., univariate) analyses testing the function of individual regions and not the full set of co-activated regions that form a network. Connectivity is dynamic and the function of a region may change based on its current connections. Therefore, determining the function of a network requires assessment at the network-level. Yet popular theories implicating the default mode network (DMN) in episodic memory and social cognition, rest principally upon analyses performed at the level of individual brain regions. Here we use independent component analysis to formally test the role of the DMN in episodic and social processing at the network level. As well as an episodic retrieval task, two independent datasets were employed to assess DMN function across the breadth of social cognition; a person knowledge judgement and a theory of mind task. Each task dataset was separated into networks of co-activated regions. In each, the co-activated DMN, was identified through comparison to ana prioritemplate and its relation to the task model assessed. This co-activated DMN did not show greater activity in episodic or social tasks than high-level baseline conditions. Thus, no evidence was found to support hypotheses that the co-activated DMN is involved in explicit episodic or social processing tasks at a network-level. The networks associated with these processes are described. Implications for prior univariate findings and the functional significance of the co-activated DMN are considered.
Distinct spermiogenic phenotypes underlie sperm elimination in theSegregation Distortermeiotic drive system
Authors: Herbette Marion , Wei Xiaolu , Chang Ching-Ho , Larracuente Amanda M. , Loppin Benjamin , Dubruille Raphaëlle
Published: January 2021

Segregation Distorter(SD) is a male meiotic drive system inDrosophila melanogaster.Males heterozygous for a selfishSDchromosome rarely transmit the homologousSD+chromosome. It is well established that distortion results from an interaction betweenSd, the primary distorting locus on theSDchromosome and its target, a satellite DNA calledRsp,on theSD+chromosome. However, the molecular and cellular mechanisms leading to post-meioticSD+sperm elimination remain unclear. Here we show thatSD/SD+males of different genotypes but with similarly strong degrees of distortion have distinct spermiogenic phenotypes. In some genotypes,SD+spermatids fail to fully incorporate protamines after the removal of histones, and degenerate during the individualization stage of spermiogenesis. In contrast, in otherSD/SD+genotypes, protamine incorporation appears less disturbed, yet spermatid nuclei are abnormally compacted, and mature sperm nuclei are eventually released in the seminal vesicle. Our analyses of differentSD+chromosomes suggest that the severity of the spermiogenic defects associates with the copy number of theRspsatellite. We propose that whenRspcopy number is very high (> 2000), spermatid nuclear compaction defects reach a threshold that triggers a checkpoint controlling sperm chromatin quality to eliminate abnormal spermatids during individualization.
Skin-resident immune cells actively coordinate their distribution with epidermal cells during homeostasis
Authors: Park Sangbum , Matte-Martone Catherine , Gonzalez David G. , Lathrop Elizabeth A. , May Dennis P. , Pineda Cristiana M. , Moore Jessica L. , Boucher Jonathan D. , Marsh Edward D. , Schmitter Axel , Cockburn Katie , Bellaïche Yohanns , Greco Valentina
Published: January 2021

Our organs consist of multiple cell types that ensure proper architecture and function. How different cell types coexist and interact to maintain their homeostasisin vivoremain elusive. The skin epidermis comprises mostly epithelial cells, but also harbors Langerhans cells (LCs) and Dendritic Epidermal T cells (DETCs). In response to injury or infection, LCs and DETCs become activated and play critical immunological roles. During homeostasis, they coexist with epithelial cells in the basal layer of the epidermis. Whether, and how, distributions of LCs and DETCs are regulated during homeostasis is unclear. Here, we addressed this question by tracking LCs, DETCs and epithelial basal cells over time within the skin of live adult mice. We show that LCs and DETCs maintain their overall position despite continuous turnover of neighboring basal epithelial stem cells. Moreover, LCs and DETCs rapidly and maximally explore basal epithelial cell junctions through their dendritic extensions. Altering the epithelial cell density triggers corresponding changes in the immune cell density, but not vice versa, suggesting that epithelial cells determine immune tissue composition in the epidermis. Moreover, LCs and DETCs are organized in a tiling pattern that is actively maintained. When LCs or DETCs are ectopically removed, neighboring epidermal LCs or DETCs, respectively, move into the emptied spaces and re-establish the tiling pattern. Finally, LCs require the GTPase Rac1 to maintain their positional stability, density and tiling pattern. Overall, we discovered that epidermal cells regulate the density of immune cells during homeostasis, and that immune cells actively maintain a non-random spatial distribution, reminiscent of neuronal self-avoidance. We propose that these cellular mechanisms provide the epidermis with an optimal response to environmental insults.
rdrugtrajectory: An R Package for the Analysis of Drug Prescriptions in Electronic Health Care Records
Authors: Nash Anthony , Chang Tingyee E. , Wan Benjamin , Cader M. Zameel
Published: January 2021

Primary care electronic health care records are rich with patient and clinical information. Studying electronic health care records has resulted in marked improvements to national health care processes and patient-care decision making, and is a powerful supplementary source of data for drug discovery effort. We present the R packagerdrugtrajectory, designed to yield demographic and patient-level characteristics of drug prescriptions in the UK Clinical Practice Research Datalink dataset. The package operates over Clinical Practice Research Datalink Gold clinical, referral and therapy datasets and includes features such as first drug prescriptions analysis, cohort-wide prescription information, cumulative drug prescription events, the longitudinal trajectory of drug prescriptions, and a survival analysis timeline builder to identify risks related to drug prescription switching. Therdrugtrajectorypackage has been made freely available via the GitHub repository.
REPEATED INJURY PROMOTES TRACHEOBRONCHIAL TISSUE STEM CELL ATTRITION
Authors: Ghosh Moumita , Hill Cynthia L. , Alsudayri Alfahdah , Lallier Scott W. , Hayes Don , Wijeratne Saranga , Mahoney John E. , Reynolds Susan D.
Published: January 2021

Chronic lung disease has been attributed to stem cell aging and/or exhaustion. To address this issue, we investigated the lifespan of tracheobronchial tissue stem cells (TSC) over time and in response to repeated injury. Chromatin and nucleotide labeling studies in mice indicated that: 1) injury activated a subset of the TSC pool and that this process conserved TSC over time; and 2) activated TSC were predisposed to further proliferation and this activated state lead to terminal differentiation. Analysis of human TSC and clonal isolates indicated that repeated TSC proliferation led to telomere shortening and analysis of TSC from Dyskeratosis Congenita donors indicated that mutations in telomere biology genes accelerated TSC depletion. RNAseq and functional studies indicated that human TSC terminated as a secretory committed cell. These data support a model in which a repeated epithelial injury depletes the TSC pool and initiates the abnormal repair associated with chronic lung disease.
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy
Authors: Chang Chunmei , Shi Xiaoshan , Jensen Liv E. , Yokom Adam L. , Fracchiolla Dorotea , Martens Sascha , Hurley James H.
Published: January 2021

Selective autophagy of damaged mitochondria, intracellular pathogens, protein aggregates, endoplasmic reticulum, and other large cargoes is essential for health. The presence of cargo initiates phagophore biogenesis, which entails the conjugation of ATG8/LC3 family proteins to membrane phosphatidylethanolamine. Current models suggest that the presence of clustered ubiquitin chains on a cargo triggers a cascade of interactions from autophagic cargo receptors through the autophagy core complexes ULK1 and class III PI 3-kinase complex I (PI3KC3-C1), WIPI2, and the ATG7, ATG3, and ATG12-ATG5-ATG16L1 machinery of LC3 lipidation. This model was tested using giant unilamellar vesicles (GUVs), GST-Ub4as a model cargo, the cargo receptors NDP52, TAX1BP1, and OPTN, and the autophagy core complexes. All three cargo receptors potently stimulated LC3 lipidation on GUVs. NDP52- and TAX1BP1-induced LC3 lipidation required the ULK1 complex together with all other components, however, ULK1 kinase activity was dispensable. In contrast, OPTN bypassed the ULK1 requirement completely. These data show that the cargo-dependent stimulation of LC3 lipidation is a common property of multiple autophagic cargo receptors, yet the details of core complex engagement vary considerably and unexpectedly between the different receptors.
Effects of Ihand TASK-like shunting current on dendritic impedance in layer 5 pyramidal-tract neurons
Authors: Kelley Craig , Dura-Bernal Salvador , Neymotin Samuel A. , Antic Srdjan D. , Carnevale Nicholas T. , Migliore Michele , Lytton William W
Published: January 2021

Pyramidal neurons in neocortex have complex input-output relationships that depend on their morphologies, ion channel distributions, and the nature of their inputs, but which cannot be replicated by simple integrate-and-fire models. The impedance properties of their dendritic arbors, such as resonance and phase shift, shape neuronal responses to synaptic inputs and provide intraneuronal functional maps reflecting their intrinsic dynamics and excitability. Experimental studies of dendritic impedance have shown that neocortical pyramidal tract neurons exhibit distance-dependent changes in resonance and impedance phase with respect to the soma. We therefore investigated how well several biophysically-detailed multi-compartment models of neocortical layer 5 pyramidal tract neurons reproduce the location-dependent impedance profiles observed experimentally. Each model tested here exhibited location-dependent impedance profiles, but most captured either the observed impedance amplitude or phase, not both. The only model that captured features from both incorporates HCN channels and a shunting current, like that produced by Twik-related acid-sensitive K+(TASK) channels. TASK-like channel activity in this model was dependent on local peak HCN channel conductance (Ih). We found that while this shunting current alone is insufficient to produce resonance or realistic phase response, it modulates all features of dendritic impedance, including resonance frequencies, resonance strength, synchronous frequencies, and total inductive phase. We also explored how the interaction ofIhand a TASK-like shunting current shape synaptic potentials and produce degeneracy in dendritic impedance profiles, wherein different combinations ofIhand shunting current can produce the same impedance profile.

New & Noteworthy

We simulated chirp current stimulation in the apical dendrites of 5 biophysically-detailed multi-compartment models of neocortical pyramidal tract neurons and found that a combination of HCN channels and TASK-like channels produced the best fit to experimental measurements of dendritic impedance. We then explored how HCN and TASK-like channels can shape the dendritic impedance as well as the voltage response to synaptic currents.
A Bacterial Bile Acid Metabolite Modulates TregActivity through the Nuclear Hormone Receptor NR4A1
Authors: Li Wei , Hang Saiyu , Fang Yuan , Bae Sena , Zhang Yancong , Wang Gang , McCurry Megan D. , Bae Munhyung , Franzosa Eric A. , Huttenhower Curtis , Yao Lina , Devlin A. Sloan , Huh Jun R.
Published: January 2021

Bile acids act as signaling molecules that regulate immune homeostasis, including the differentiation of CD4+T cells into distinct T cell subsets. The bile acid metabolite isoallolithocholic acid (isoalloLCA) enhances the differentiation of anti-inflammatory regulatory T cells (Treg cells) by facilitating the formation of a permissive chromatin structure in the promoter region of the transcription factor forkhead box P3 (Foxp3). Here, we identify gut bacteria that synthesize isoalloLCA from 3-oxolithocholic acid and uncover a gene cluster responsible for the conversion in members of the abundant human gut bacterial phylum Bacteroidetes. We also show that the nuclear hormone receptor NR4A1 is required for the effect of isoalloLCA on Treg cells. Moreover, the levels of isoalloLCA and its biosynthetic genes are significantly reduced in patients with inflammatory bowel diseases, suggesting that isoalloLCA and its bacterial producers may play a critical role in maintaining immune homeostasis in humans.
Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses
Authors: Alli-Balogun Ganiyu O. , Levine Tim P.
Published: January 2021

Ice2p is an integral endoplasmic reticulum (ER) membrane protein in budding yeastS. cerevisiaenamed ICE because it is required for Inheritance of Cortical ER. Ice2p has also been reported to be involved in an ER metabolic branch-point that regulates the flux of lipid either to be stored in lipid droplets or to be used as membrane components. Alternately, Ice2p has been proposed to act as a tether that physically bridges the ER at contact sites with both lipid droplets and the plasma membrane via a long loop on the protein’s cytoplasmic face that contains multiple predicted amphipathic helices. Here we carried out a bioinformatic analysis to increase understanding of Ice2p. Firstly, regarding topology, we found that diverse members of the fungal Ice2 family have ten transmembrane helices, which places the long loop on the exofacial face of Ice2p, where it cannot form inter-organelle bridges. Secondly, we identified Ice2 as a full-length homologue of SERINC (serine incorporator), a family of proteins with ten transmembrane helices found universally in eukaryotes. Since SERINCs are potent restriction factors for HIV and other viruses, study of Ice2p may reveal functions or mechanisms that shed light on viral restriction by SERINCs.
Trans-channel fluorescence learning improves high-content screening for Alzheimer’s disease therapeutics
Authors: Wong Daniel R. , Conrad Jay , Johnson Noah , Ayers Jacob , Laeremans Annelies , Lee Joanne C. , Lee Jisoo , Prusiner Stanley B. , Bandyopadhyay Sourav , Butte Atul J. , Paras Nick , Keiser Michael J.
Published: January 2021

In microscopy-based drug screens, fluorescent markers carry critical information on how compounds affect different biological processes. However, practical considerations may hinder the use of certain fluorescent markers. Here, we present a deep learning method for overcoming this limitation. We accurately generated predicted fluorescent signals from other related markers and validated this new machine learning (ML) method on two biologically distinct datasets. We used the ML method to improve the selection of biologically active compounds for Alzheimer’s disease (AD) from high-content high-throughput screening (HCS). The ML method identified novel compounds that effectively blocked tau aggregation, which would have been missed by traditional screening approaches unguided by ML. The method improved triaging efficiency of compound rankings over conventional rankings by raw image channels. We reproduced this ML pipeline on a biologically independent cancer-based dataset, demonstrating its generalizability. The approach is disease-agnostic and applicable across diverse fluorescence microscopy datasets.
GSDMD Deficiency Protects Against Aortic Rupture
Authors: Ye Dien , Howatt Deborah A. , Li Zhenyu , Daugherty Alan , Lu Hong S. , Wu Congqing
Published: January 2021

Objective

Aortic ruptures are fatal consequences of aortic aneurysms with macrophage accumulation being a hallmark at the site of ruptures. Pyroptosis is critical in macrophage-mediated inflammation. This study determined effects of pyroptosis on aortic dilation and rupture using GSDMD deficient mice.

Approach and Results

In an initial study, maleGsdmd+/+andGsdmd-/-mice in C57BL/6J background (8 – 10 weeks old) were infected with adeno-associated viral vectors encoding mouse PCSK9D377Y gain-of-function mutation and fed a Western diet to induce hypercholesterolemia. After two weeks of AAV infection, angiotensin II (AngII, 1 µg/kg/min) was infused. During the 4 weeks of AngII infusion, 5 of 13Gsdmd+/+mice died of aortic rupture, whereas no aortic rupture occurred inGsdmd-/-mice. In surviving mice, no differences in either ascending or abdominal aortic dilation were observed betweenGsdmd+/+andGsdmd-/-mice. To determine whether protection of GSDMD deficiency against aortic rupture is specific to AngII infusion, we subsequently examined aortic pathologies in mice administered beta-aminopropionitrile (BAPN). BAPN (0.5% wt/vol) was administered in drinking water to maleGsdmd+/+andGsdmd-/-mice (4 weeks old) for 4 weeks. Six of 13Gsdmd+/+mice died of aortic rupture, whereas no aortic rupture occurred inGsdmd-/-mice. In mice survived, no differences of diameters in the ascending, arch, or abdominal aortic regions were observed betweenGsdmd+/+andGsdmd-/-mice.

Conclusions

GSDMD deficiency protects against AngII or BAPN-induced aortic ruptures in mice.

Highlights

GSDMD deficiency protects against angiotensin II-induced aortic rupture in hypercholesterolemic mice.

GSDMD deficiency protects against beta-aminopropionitrile (BAPN)-induced aortic dissection and rupture in C57BL/6J mice.
CRY2missense mutations suppress P53 and enhance cell growth
Authors: Chan Alanna B. , Parico Gian Carlo G. , Fribourgh Jennifer L. , Ibrahim Lara H. , Bollong Michael J. , Partch Carrie L. , Lamia Katja A.
Published: January 2021

Disruption of circadian rhythms increases the risk of several types of cancer. Mammalian cryptochromes (CRY1 and CRY2) are circadian transcriptional repressors that are related to DNA repair enzymes. While CRYs lack DNA repair activity, they modulate the transcriptional response to DNA damage, and CRY2 can promote SCFFBXL3-mediated ubiquitination of c-MYC and other targets. Here, we characterize five mutations in CRY2 observed in human cancers in The Cancer Genome Atlas. We demonstrate that two orthologous mutations of mouse CRY2 (D325H and S510L) accelerate the growth of primary mouse fibroblasts expressing high levels of c-MYC. Neither mutant affects steady state levels of overexpressed c-MYC, and they have divergent impacts on circadian rhythms and on the ability of CRY2 to interact with SCFFBXL3. Unexpectedly, stable expression of either CRY2 D325H or of CRY2 S510L robustly suppresses P53 target gene expression, suggesting that this is the primary mechanism by which they influence cell growth.
iRGD-liposomes enhance tumor delivery and therapeutic efficacy of antisense oligonucleotide drugs against primary prostate cancer and bone metastasis
Authors: Guan Jibin , Guo Hong , Tang Tang , Wang Yihan , Wei Yushuang , Seth Punit , Li Yingming , Dehm Scott M , Ruoslahti Erkki , Pang Hong-Bo
Published: January 2021

Nucleotide-based drugs, such as antisense oligonucleotides (ASOs), have unique advantages in treating human diseases as they provide virtually unlimited ability to target any gene. However, their clinical translation faces many challenges, one of which is poor delivery to the target tissuein vivo. This problem is particularly evident in solid tumors. Here, we functionalized liposomes with a tumor-homing and -penetrating peptide, iRGD, as a carrier of an ASO against androgen receptor (AR) for prostate cancer treatment. The iRGD-liposomes exhibited a high loading efficiency of AR-ASO, and an efficient knockdown of AR gene products was achievedin vitro, including AR splice variants.In vivo, iRGD-liposomes significantly increased AR-ASO accumulation in the tumor tissue and decreased AR expression relative to free ASOs in prostate tumors established as subcutaneous xenografts. Similar results were obtained with intra-tibial xenografts modeling metastasis to bones, the predominant site of metastasis for prostate cancer. In treatment studies, iRGD-liposomes markedly improved the AR-ASO efficacy in suppressing the growth of both subcutaneous xenografts and intra-tibial xenografts. The inhibitory effect on tumor growth was also significantly prolonged by the delivery of the AR-ASO in the iRGD-liposomes. Meanwhile, iRGD-liposomes did not increase ASO accumulation or toxicity in healthy organs. Overall, we provide here a delivery system that can significantly increase ASO accumulation and efficacy in solid tumors. These benefits are achieved without significant side effects, providing a way to increase the antitumor efficacy of ASOs.
Fitness cost associated with enhancedEPSPSgene copy number and glyphosate resistance in anAmaranthus tuberculatuspopulation
Authors: Cockerton Helen M. , Kaundun Shiv S. , Nguyen Lieselot , Hutchings Sarah Jane , Dale Richard P. , Howell Anushka , Neve Paul
Published: January 2021

The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population ofAmaranthus tuberculatus(common waterhemp), which has evolved resistance to glyphosate. Following the production of seed families with contrasting levels of glyphosate resistance, we assessed the growth and fitness of seed families in the absence of glyphosate and determined their ability to compete for resources under intra- and interspecific competition. Further investigation revealed a positive correlation between the level of resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus indicating gene amplification as the mechanism of resistance within the population. Resistant common waterhemp plants were found to have a lower competitive response when compared to the susceptible phenotypes. A substitution rate of 2.76 glyphosate resistant plants was required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.
Double stranded RNA drives innate immune responses, sickness behavior and cognitive impairment dependent on dsRNA length, IFNAR1 expression and age
Authors: McGarry Niamh , Murray Carol L. , Garvey Sean , Wilkinson Abigail , Tortorelli Lucas , Ryan Lucy , Hayden Lorna , Healy Daire , Griffin Eadaoin. W. , Hennessy Edel , Arumugam Malathy , Skelly Donal T. , Mitchell Kevin J. , Cunningham Colm
Published: January 2021

Double stranded RNA is generated during viral replication. The synthetic analogue poly I:C is frequently used to mimic anti-viral innate immune responses in models of psychiatric and neurodegenerative disorders including schizophrenia, autism, Parkinson’s disease and Alzheimer’s disease. Many studies perform limited analysis of innate immunity despite these responses potentially differing as a function of dsRNA molecular weight and age. Therefore fundamental questions relevant to impacts of systemic viral infection on brain function and integrity remain. Here, we studied innate immune-inducing properties of poly I:C preparations of different lengths and responses in adult and aged mice. High molecular weight (HMW) poly I:C (1-6kb, 12 mg/kg) produced more robust sickness behavior and more robust IL-6, IFN-I and TNFα responses than poly I:C of <500 bases (low MW) preparations. This was partly overcome with higher doses of LMW (up to 80 mg/kg), but neither circulating IFNβ nor brain transcription ofIrf7were significantly induced by LMW poly I:C, despite brainIfnbtranscription, suggesting that brain IFN-dependent gene expression is predominantly triggered by circulating IFNβ binding of IFNAR1. In aged animals, poly I:C induced exaggerated IL-6, IL-1β and IFN-I in the plasma and similar exaggerated brain cytokine responses. This was associated with acute working memory deficits selectively in aged mice. Thus, we demonstrate dsRNA length-, IFNAR1- and age-dependent effects on anti-viral inflammation and cognitive function. The data have implications for CNS symptoms of acute systemic viral infection such as those with SARS-CoV-2 and for models of maternal immune activation.
ATAC-seq reveals megabase-scale domains of a bacterial nucleoid
Authors: Melfi Michael D. , Lasker Keren , Zhou Xiaofeng , Shapiro Lucy
Published: January 2021

Here we adapted ATAC-seq to probe chromosome accessibility of bacterial cells. We found that the chromosome of Caulobacter crescentus is composed of eight differentially compacted regions we name Chromosomal Accessibility Domains (CADs). This domain structure is depended on the cell cycle stage, DNA gyrase activity, and the nucleoid-associated protein (NAP) GapR, but not on the function of SMC. We show the chromosome is punctuated by fourhighly transposase-inaccessible transcribed regions (HINTs). The HINTs include Caulobacter’s ribosomal RNA clusters and its largest ribosomal protein gene cluster. Further, we show that HINTs are also formed by rDNA in E. coli and provide evidence that their high levels of transcription do not strictly govern their formation. Overall, this work argues that physical forces, including those created by the activities of DNA gyrase and specific NAPs, significantly contribute to bacterial nucleoid structure at the megabase scale.

Abstract Figure

Significance

In bacteria, chromosomal DNA is highly compacted and organized. Many forces contribute to bacterial DNA compaction, including the transcription, DNA replication, and the activities of topoisomerases and nucleoid-associated proteins. At the megabase scale, the resulting chromosome structure is important for coordinating cell cycle events; for example, inE. colithe improper structuring of a Mb-scale nucleoid domain leads to errors in the fidelity of chromosome segregation. It was previously unknown whether Mb-scale regions of a bacterial chromosome could be differentially compacted, and which factors might contribute to this spatial variation in compaction. Our work provides a novel method for measuring global chromosome compaction in bacteria. By applying this method in the bacteriumCaulobacter crescentus, we show that theCaulobacternucleoid’s compaction varies between megabase-scale domains. We also show that DNA gyrase and the nucleoid-associated protein GapR are key players in shaping the uneven compaction of the chromosome.
Epidermal TRPV4 ion channels regulate UVB induced sunburn by triggering inflammmasome activation and ERK signaling
Authors: Moore Carlene , Choi Shinbe , Moon Gene , Zhang Jennifer , Chen Yong , Liedtke Wolfgang
Published: January 2021

Skin inflammation is an evolutionary-honed protective mechanism that serves to clear noxious cues and irritants and initiate regeneration. Calcium-permeable transient-receptor-potential (TRP) ion channels have critical functions in sensory transduction which is sensitized in skin inflammation. Skin sensory transduction relies on skin-innervating sensory neurons in the dorsal root ganglion (DRG), but also on innervated keratinocytes (KC). The multimodally-activated TRPV4 is robustly expressed in KC, where it can readily be activated by Ultraviolet-B (UVB). Our goal was to deconstruct keratinocyte TRPV4-mediated signaling, specifically how TRPV4 can facilitate inflammatory injury, thus lowering pain thresholds and rendering KC into pain-generator cells. We wanted to uncover the effect of TRPV4-mediated signaling on UVB-induced inflammasome activation in KC given the powerful impact of the activated inflammasome on pro-inflammatory/pro-algesic secretory signaling, using mouse models and cultured human KC. In mice, our evidence suggests that TRPV4 functions as calcium-permeable channel upstream of the KC inflammasome. Furthermore, we found that UVB induced activation of TRPV4 caused rapid - within minutes -Extracellular SignalRegulatedKinase (ERK) phosphorylation, caspase-1 activation and Interleukin-1ß (IL-1ß) secretion. In human primary KC we demonstrated that UVB induced secretion of IL-1ß was dependent on the NLR family pyrin domain containing 1 (NLRP1) inflammasome. Direct chemical TRPV4 activation could also activate NLRP1 and to lesser extent NLPR3. Building on our previous work, we now define at increased resolution TPRV4-dependent forefront signaling mechanisms in KC in response to UVB, showing TRPV4 upstream of the NLRP1 inflammasome, subsequent rapid ERK activation and pro-inflammatory/pro-algesic secretory function.
MCPdb: The Bacterial Microcompartment Database
Authors: Ochoa Jessica M. , Bair Kaylie , Holton Thomas , Bobik Thomas A. , Yeates Todd O.
Published: January 2021

Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, current resources present challenges for understanding the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphazise the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 134 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.
Laminar Mechanisms of Saccadic Suppression in Primate Visual Cortex
Authors: Denagamage Sachira , Morton Mitchell P. , Reynolds John H. , Jadi Monika P. , Nandy Anirvan S.
Published: January 2021

Saccades are a ubiquitous and crucial component of our visual system, allowing for the efficient deployment of the fovea and its accompanying neural resources. Initiation of a saccade is known to cause saccadic suppression, a temporary reduction in visual sensitivity1, 2and visual cortical firing rates3–6. While saccadic suppression has been well characterized at the level of perception and single neurons, relatively little is known about the visual cortical networks governing this phenomenon. Here we examine the effects of saccadic suppression on distinct neural subpopulations within visual area V4. We find cortical layer- and cell type-specific differences in the magnitude and timing of peri-saccadic modulation. Neurons in the input layer show changes in firing rate and inter-neuronal correlations prior to saccade onset, indicating that this layer receives information about impending saccades. Putative inhibitory interneurons in the input layer elevate their firing rate during saccades, suggesting they play a role in suppressing the activity of other cortical subpopulations. A computational model of this circuit recapitulates our empirical observations and demonstrates that an input layer-targeting pathway can initiate saccadic suppression by enhancing local inhibitory activity. Collectively, our results provide a mechanistic understanding of how eye movement signaling interacts with cortical circuitry to enforce visual stability.
A phase 3, multicenter, randomized, double‐blind, vehicle‐controlled, parallel‐group study of 5% sofpironium bromide (BBI‐4000) gel in Japanese patients with primary axillary hyperhidrosis
Authors: Yokozeki Hiroo , Fujimoto Tomoko , Abe Yoichiro , Igarashi Masaru , Ishikoh Akiko , Omi Tokuya , Kanda Hiroki , Kitahara Hiroto , Kinoshita Miwako , Nakasu Ichiro , Hattori Naoko , Horiuchi Yuki , Maruyama Ryuji , Mizutani Haruko , Murakami Yoshiyuki , Watanabe Chiharu , Kume Akihiro , Hanafusa Takaaki , Hamaguchi Masamitsu , Yoshioka Akira , Egami Yuriko , Matsuo Keizo , Matsuda Tomoko , Akamatsu Motoki , Yorozuya Toshiyuki , Takayama Shinichi
Published: January 2021

A phase 3 study was conducted to verify the efficacy and safety of 5% sofpironium bromide (BBI‐4000) gel (hereinafter referred to as sofpironium) administrated for 6 weeks in Japanese patients with primary axillary hyperhidrosis. The primary efficacy end‐point was the proportion of patients who satisfied both criteria of a Hyperhidrosis Disease Severity Score (HDSS) of 1 or 2 at the end of 6‐week treatment and a 50% or more reduction in total gravimetric weight of sweat at the end of treatment relative to baseline. A total of 281 patients were randomized to receive 5% sofpironium (141 patients) or vehicle (140 patients), and all patients were included in the full analysis set (FAS). In the FAS, 70.1% of patients were female, and the median age was 35.0 years. The proportion of patients who achieved the primary efficacy end‐point was 53.9% in the sofpironium group and 36.4% in the vehicle group, with a statistically significant difference of 17.5% (95% confidence interval, 6.02–28.93) between these two groups (P = 0.003). The incidence of adverse events was 44.0% in the sofpironium group and 30.7% in the vehicle group, and the incidence of adverse drug reactions was 16.3% in the sofpironium group and 5.0% in the vehicle group. Reported adverse events were generally mild or moderate in severity. In the sofpironium group, common events (incidence, ≥5%) were nasopharyngitis (14.2%) and dermatitis/erythema at the application site (8.5%/5.7%), with no serious adverse events reported. This study demonstrated the efficacy and safety of 5% sofpironium.
Differing thermal sensitivities in a host–parasitoid interaction: High, fluctuating developmental temperatures produce dead wasps and giant caterpillars
Authors: Moore M. Elizabeth , Hill Christina A. , Kingsolver Joel G.
Published: January 2021

Insect parasitoids, and the arthropod hosts they consume during development, are important ecological players in almost all environments across the globe. As ectothermic organisms, both parasitoid and host are strongly impacted by environmental temperature. If thermal tolerances differ between host insect and parasitoid, then the outcome of their interaction will be determined by the ambient temperature. As mean temperatures continue to rise and extreme temperatures become more frequent, we must determine the effect of high temperature stress on host–parasitoid systems to predict how they will fare in the face of climate change.

The majority of studies conducted on host–parasitoid systems focus on either performance under constant temperature or a fixed metric of thermal tolerance (CTmax) for individual organisms. However, performance at constant temperatures is not predictive of performance under ecologically relevant, fluctuating temperatures and measurements of thermal thresholds provide little information regarding the effects of temperature throughout development. We address this by testing the effects of increasing mean temperature in both constant and fluctuating (±10°C) environments throughout development on the performance of the parasitoid wasp Cotesia congregata and its lepidopteran larval host, Manduca sexta.

The growth of M. sexta was influenced by mean temperature, diurnal fluctuations and parasitization status. Caterpillar growth rate increased with increasing mean temperature, but decreased in response to diurnal fluctuations and parasitization by C. congregata wasps.

Wasp survival decreased with increasing mean temperature and with diurnal fluctuations. The effect of diurnal fluctuations was stronger at higher mean temperatures. Diurnal fluctuations at our highest mean temperature treatment (30 ± 10°C) resulted in complete wasp mortality, and parasitized hosts displayed abnormal physiology, wherein they failed to exhibit wasp emergence, did not enter the prepupal stage, continued to feed and grew up to twofold larger than a normal, unparasitized caterpillar.

Our results indicate hosts and parasitoids in this system have different thermal tolerances during development; the parasitoid wasp suffered complete mortality at a temperature regime that is mildly stressful for the unparasitized caterpillar host species. Our findings suggest C. congregata will suffer more severely under increasing temperatures than M. sexta, with cascading trophic and ecological effects.

A free Plain Language Summary can be found within the Supporting Information of this article.
What impact are subsidies and trade barriers abroad having on Australasian and Brazilian agriculture?*
Authors: Anderson Kym , Valenzuela Ernesto
Published: January 2021

This paper provides new estimates of the extent and economic effects of agricultural policies that provide domestic support or import protection to farmers in countries that compete in the global marketplace with unsubsidised farmers. Analyses earlier this century found that import market access barriers accounted for more than 90 per cent of the global welfare cost of all assistance to farmers, with domestic support measures providing as little as 5 per cent. Since then the share contributed by domestic support has grown greatly in some high‐income and emerging economies, thanks to policy re‐instrumentation. Using the latest version of the GTAP model and database of the global economy, this paper estimates the economic effects of direct farmer subsidies, and of the producer subsidy and consumer tax equivalents of farm trade policies, on farmers in three lightly assisting countries. The estimates adjusted for country size suggest the effects on agricultural exports, net farm income and national economic welfare of such policies are far more adverse for Australia, Brazil and especially New Zealand than for the rest of the world, and that domestic supports abroad are much more important contributors to those losses now than they were at the start of this century.