bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a non-infectious control for viral hemorrhagic fever PCR assays
Authors: Knox Matthew A , Bromhead Collette , Hayman David TS
Published: May 2023

Assay validation is an essential component of disease surveillance but can be problematic in low resource settings where access to positive control material is limited and a safety risk for handlers. Here we describe techniques for validating the PCR based detection ofCrimean-Congo hemorrhagic fever orthonairovirus, Ebola virus, Lassa virus, Marburg virus andRift Valley Fever phlebovirus. We designed non-infectious synthetic DNA oligonucleotide sequences incorporating primer binding sites suitable for multiple assays, and a T7 promotor site which was used to transcribe the sequence. Transcribed RNA was used as template in a dilution series, extracted and amplified with RT-PCR and RT-qPCR to demonstrate successful recovery and determine limits of detection in a range of laboratory settings. Our results are adaptable to any assay requiring validation of nucleic acid extraction and/or amplification, particularly where sourcing reliable, safe material for positive controls is infeasible.

Author Summary

The majority of zoonoses originate in wildlife and tend to emerge from biodiverse regions in low to middle income countries, frequently among deprived populations of at-risk people with a lack of access to diagnostic capacity or surveillance. Diseases such as Crimean-Congo Hemorrhagic Fever, Rift Valley Fever, Ebola Virus Disease, Marburg Virus Disease and Lassa Fever are viral hemorrhagic fevers (VHFs) and among the most neglected and serious threats to global public health. This threat is partly due to the severity of disease caused by these pathogens, but also because their geographical distribution is close to human populations with often limited access to medical or diagnostic laboratory services. In our study we describe and validate techniques for PCR based detection of five VHF viruses using a synthetic, multi-target non-infectious positive control. Our work has applications in assay design and optimization, particularly where access to source material is problematic or requires high level biosafety containment, as is the case with VHF viruses. This approach can help learners train in techniques used in nucleic acid extraction, amplification, and sequencing of VHF viruses, but can be used for any targets, with potential for multiplexing from a single positive control.
The significance of mitochondrial haplogroups in preeclampsia risk
Authors: Olsen Kristina Wendelboe , Hedley Paula L. , Hagen Christian M. , Rode Line , Placing Sophie , Wøjdemann Karen R , Shalmi Anne-Cathrine , Sundberg Karin , Nørremølle Anne , Tabor Ann , Elson Joanna L. , Christiansen Michael
Published: May 2023

Objective

To determine whether mitochondrial haplogroups function as disease-modifiers or as susceptibility factors in preeclampsia using a traditional haplogroup association model.

Methods

This retrospective study haplotyped 235 control and 78 preeclamptic pregnancies from Denmark using either real-time PCR or Sanger sequencing depending on the rarity of the haplogroup.

Results

No significant association between haplogroups and the risk of preeclampsia was found, nor was any role for haplogroups in disease severity uncovered.

Conclusion

Mitochondrial haplogroups are not associated with preeclampsia or the severity of preeclampsia in the Danish population. However, this study cannot exclude a role for less common mtDNA variation. Models that can examine these should be applied in preeclamptic patients.

Graphical Abstract
Epigenomic profiling of the infrapatellar fat pad in osteoarthritis
Authors: Kreitmaier Peter , Park Young-Chan , Swift Diane , Gilly Arthur , Wilkinson J Mark , Zeggini Eleftheria
Published: May 2023

Osteoarthritis is a prevalent, complex disease of the joints, and affects multiple intra-articular tissues. Here, we have examined genome-wide DNA methylation profiles of primary infrapatellar fat pad and matched blood samples from 70 osteoarthritis patients undergoing total knee replacement surgery. Comparing the DNA methylation profiles between these tissues reveal widespread epigenetic differences. We produce the first genome-wide methylation quantitative trait locus (mQTL) map of fat pad, and make the resource available to the wider community. Using two-sample Mendelian randomization and colocalization analyses, we resolve osteoarthritis GWAS signals and provide insights into the molecular mechanisms underpinning disease aetiopathology. Our findings provide the first view of the epigenetic landscape of infrapatellar fat pad primary tissue in osteoarthritis.
Modulation of visually induced self-motion illusions by α transcranial electric stimulation over the superior parietal cortex
Authors: Harquel Sylvain , Cian Corinne , Torlay Laurent , Cousin Emilie , Barraud Pierre-Alain , Bougerol Thierry , Guerraz Michel
Published: May 2023

Growing popularity of virtual reality systems has led to a renewed interest in understanding the neurophysiological correlates of the illusion of self-motion (vection), a phenomenon that can be both intentionally induced or avoided in such systems, depending on the application. Recent research has highlighted the modulation of α power oscillations over the superior parietal cortex during vection, suggesting the occurrence of inhibitory mechanisms in the sensorimotor and vestibular functional networks to resolve the inherent visuo-vestibular conflict. The present study aims to further explore this relationship and investigate whether neuromodulating these waves could causally affect the quality of vection. In a crossover design, 22 healthy volunteers received 13 minutes of high-amplitude, focused α-tACS over the superior parietal cortex while experiencing visually induced vection triggered by optokinetic stimulation. The tACS was tuned to each participant’s individual α peak frequency, with θ-tACS and sham stimulation serving as controls. Overall, participants experienced better quality vection during α-tACS compared to control θ-tACS and sham stimulations, as quantified by the intensity of vection. The observed neuromodulation supports a causal relationship between parietal α oscillations and visually induced self-motion illusions, with their entrainment triggering over-inhibition of the conflict within the sensorimotor and vestibular functional networks. These results confirm the potential of non-invasive brain stimulation for modulating visuo-vestibular conflicts, which could help to enhance the sense of presence in virtual reality environments.
Nighthawk: acoustic monitoring of nocturnal bird migration in the Americas
Authors: Van Doren Benjamin M. , Farnsworth Andrew , Stone Kate , Osterhaus Dylan M. , Drucker Jacob , Van Horn Grant
Published: May 2023

Animal migration is one of nature’s most spectacular phenomena, but migratory animals and their journeys are imperiled across the globe. Migratory birds are among the most well-studied animals on Earth, yet relatively little is known about in-flight behavior during nocturnal migration. Because many migrating bird species vocalize during flight, passive acoustic monitoring shows great promise for facilitating widespread monitoring of bird migration.

Here, we present Nighthawk, a deep learning model designed to detect and identify the vocalizations of nocturnally migrating birds. We trained Nighthawk on the in-flight vocalizations of migratory birds using a diverse dataset of recordings from across the Americas.

Our results demonstrate that Nighthawk performs well as a nocturnal flight call detector and classifier for dozens of avian taxa, both at the species level and for broader taxonomic groups (e.g., orders and families). The model accurately quantified nightly nocturnal migration intensity and species phenology and performed well on data from across North America. Incorporating modest amounts of additional annotated audio (50-120 h) into model training yielded high performance on target datasets from both North and South America.

By monitoring the vocalizations of actively migrating birds, Nighthawk provides a detailed window onto nocturnal bird migration that is not presently attainable by other means (e.g., radar or citizen science). Scientists, managers, and practitioners could use acoustic monitoring with Nighthawk for a number of applications, including: monitoring migration passage at wind farms; studying airspace usage during migratory flights; monitoring the changing migrations of species susceptible to climate change; and revealing previously unknown migration routes and behaviors. Overall, this work will empower diverse stakeholders to efficiently monitor migrating birds across the Western Hemisphere and collect data in aid of science and conservation. Nighthawk is freely available athttps://github.com/bmvandoren/Nighthawk.
Urothelium-specific expression of mutationally activatedPik3cainitiates early lesions of non-invasive bladder cancer
Authors: Shuman Lauren , Pham Jonathan , Wildermuth Thomas , Wu Xue-Ru , Walter Vonn , Warrick Joshua I. , DeGraff David J.
Published: May 2023

Despite the fact that ∼70% of bladder cancers are non-invasive and have high recurrence rates, early stage disease is understudied. The relative lack of models to validate the contribution of molecular drivers of bladder tumorigenesis is a significant issue. While mutations inPIK3CAare frequent in human bladder cancer, anin vivomodel for understanding their contribution to bladder tumorigenesis is unavailable. Therefore, aUpk2-Cre/Pik3caH1047Rmouse model expressing one or twoR26-Pik3caH1047Ralleles in a urothelium-specific manner was created.Pik3caH1047Rfunctionality was confirmed by quantifying Akt phosphorylation and mice were characterized by assessing urothelial thickness, nuclear atypia, and expression of luminal and basal markers at 6 and 12 months of age. At 6 months,Pik3caH1047Rmice developed increased urothelial thickness and nuclear atypia, however, at 12 months,Pik3caH1047Rmice did not exhibit progressive disease. Immunohistochemistry shows urothelium maintained luminal differentiation characterized by high Foxa1 and Pparγ expression. In addition, mice were subjected to low-dose carcinogen exposure (N-Butyl-N-(4-hydroxybutyl)nitrosamine (BBN)). Surprisingly,Pik3caH1047Rmice exhibited no significant differences after exposure relative to mice without exposure. Furthermore, ssGSEA analysis of invasive human tumors showed those with mutantPIK3CAdo not exhibit significantly increased PI3K/AKT pathway activity compared to wildtypePIK3CAtumors. Overall, these data suggest thatPik3caH1047Rcan elicit early tumorigenic changes in the urothelium, but progression to invasion may require additional genetic alterations.
A genome catalog of the early-life human skin microbiome
Authors: Shen Zeyang , Robert Lukian , Stolpman Milan , Che You , Walsh Audrey , Saffery Richard , Allen Katrina J. , Eckert Jana , Young Angela , Deming Clay , Chen Qiong , Conlan Sean , Laky Karen , Li Jenny Min , Chatman Lindsay , Kashaf Sara Saheb ,   NISC Comparative Sequencing Program, Kong Heidi H. , Frischmeyer-Guerrerio Pamela A. , Perrett Kirsten P. , Segre Julia A.
Published: May 2023

Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.
Reintroduction of resistant frogs facilitates landscape-scale recovery in the presence of a lethal fungal disease
Authors: Knapp Roland A. , Wilber Mark Q. , Byrne Allison Q. , Joseph Maxwell B. , Smith Thomas C. , Rothstein Andrew P. , Grasso Robert L. , Rosenblum Erica Bree
Published: May 2023

Vast alteration of the biosphere by humans is causing a sixth mass extinction, driven in part by an increase in emerging infectious diseases. The emergence of the lethal fungal pathogen (Batrachochytrium dendrobatidis; “Bd”) has devastated global amphibian biodiversity, with hundreds of species experiencing declines or extinctions. With no broadly applicable methods available to reverse these impacts in the wild, the future of many amphibians appears grim. The once-common mountain yellow-legged (MYL) frog is emblematic of amphibians threatened by Bd. Although most MYL frog populations are extirpated following disease outbreaks, some persist and eventually recover. Frogs in these recovering populations have increased resistance against Bd infection, consistent with evolution of resistant genotypes and/or acquired immunity. We conducted a 15-year landscape-scale reintroduction study and show that frogs collected from recovering populations and reintroduced to vacant habitats can reestablish populations despite the presence of Bd. In addition, results from viability modeling suggest that many reintroduced populations have a low probability of extinction over 50 years. To better understand the role of evolution in frog resistance, we compared the genomes of MYL frogs from Bd-naive and recovering populations. We found substantial differences between these categories, including changes in immune function loci that may confer increased resistance, consistent with evolutionary changes in response to Bd exposure. These results provide a rare example of how reintroduction of resistant individuals can allow the landscape-scale recovery of disease-impacted species. This example has broad implications for the many taxa worldwide that are threatened with extinction by novel pathogens.

Significance Statement

Understanding how species persist despite accelerating global change is critical for the conservation of biodiversity. Emerging infectious diseases can have particularly devastating impacts, and few options exist to reverse these effects. We used large-scale reintroductions of disease-resistant individuals in an effort to recover a once-common frog species driven to near-extinction by a disease that has decimated amphibian biodiversity. Introduction of resistant frogs allowed reestablishment of viable populations in the presence of disease. In addition, resistance may be at least partially the result of natural selection at specific immune function genes, which show evidence for selection in recovering populations. The evolution of resistance and reintroduction of resistant individuals could play an important role in biodiversity conservation in our rapidly changing world.
Synaptic turnover promotes efficient learning in bio-realistic spiking neural networks
Authors: Malakasis Nikos , Chavlis Spyridon , Poirazi Panayiota
Published: May 2023

While artificial machine learning systems achieve superhuman performance in specific tasks such as language processing, image and video recognition, they do so use extremely large datasets and huge amounts of power. On the other hand, the brain remains superior in several cognitively challenging tasks while operating with the energy of a small lightbulb. We use a biologically constrained spiking neural network model to explore how the neural tissue achieves such high efficiency and assess its learning capacity on discrimination tasks. We found that synaptic turnover, a form of structural plasticity, which is the ability of the brain to form and eliminate synapses continuously, increases both the speed and the performance of our network on all tasks tested. Moreover, it allows accurate learning using a smaller number of examples. Importantly, these improvements are most significant under conditions of resource scarcity, such as when the number of trainable parameters is halved and when the task difficulty is increased. Our findings provide new insights into the mechanisms that underlie efficient learning in the brain and can inspire the development of more efficient and flexible machine learning algorithms.
A CRISPR-induced DNA break can trigger crossover, chromosomal loss and chromothripsis-like rearrangements
Authors: Samach Aviva , Mafessoni Fabrizio , Gross Or , Melamed-Bessudo Cathy , Filler-Hayut Shdema , Dahan-Meir Tal , Amsellem Ziva , Pawlowski Wojciech P. , Levy Avraham A.
Published: May 2023

The fate of DNA double-strand breaks (DSBs) generated by the Cas9 nuclease has been thoroughly studied. Repair via non-homologous end-joining (NHEJ) or homologous recombination (HR) is the common outcome. However, little is known about unrepaired DSBs and the type of damage they can trigger in plants. In this work, we designed a new assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (Betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay we detected a flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole genome sequencing, molecular, and cytological analyses, supports a model in which breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a new tool for precise breeding via targeted crossover detection. It also uncovers CRISPR mediated chromothripsis-lke events that had not been previously identified in plants.
Surrogate markers of metabolic syndrome (MetS) and insulin resistance (IR) in children and young adults with type 1 diabetes: A systematic review & meta-analysis
Authors: Khandagale Sukeshini Baban , Kamble Vinesh S , Oza Chirantap , Bhor Shital , Khadilkar Anuradha Vaman , Khare Satyajeet Pramod
Published: May 2023

Introduction: Metabolic syndrome (MetS), a collection of risk factors for cardiovascular disease, and Insulin resistance (IR) are associated with diabetes. The diagnosis of both these conditions are based on specific clinical parameters. However, the efficacy of these parameters has not been systematically studied in paediatric population with T1DM. Methodology: We performed a systematic review and meta-analysis in paediatric populations of type 1 diabetes. We assessed the strength of association of the parameters of MetS and IR. The meta-analysis was performed using a metaphor package in R. A random effect model was used to study the strength of association by estimating Hedges g. Results: The systematic review resulted in identification of 30 studies on MetS and IR in paediatric patients with T1DM. Insulin dosage and HbA1C, markers for glycaemic condition showed no association with MetS in patients with T1DM. In the lipid profile, increased triglyceride (TG) and low-density lipoprotein (LDL) showed better effect size than reduced high-density lipoprotein (HDL). In case of insulin resistance, heterogeneous nature of studies made it difficult to carry out a meta-analysis. A descriptive review of existing and novel markers is thus provided. Conclusion: Lack of association between markers of glycaemic condition suggested that MetS may develop independently of glycaemic control in children with T1DM. Other than TG and HDL, LDL may be used in the diagnosis of MetS. From the descriptive analysis it could be observed that a standard protocol for the diagnosis of IR is needed.
CLICK- chemoproteomics and molecular dynamics simulation reveals pregnenolone targets and their binding conformations in Th2 cells
Authors: Roy Sougata , Roy Sudeep , Mahata Bidesh , Pramanik Jhuma , Hennrich Marco L. , Gavin Anne-Claude , Teichmann Sarah A.
Published: May 2023

Pregnenolone (P5) is synthesized as the first bioactive steroid in the mitochondria from cholesterol. CD4+ and CD8+ immune cells synthesize P5de novo, P5 in turn play important role in immune homeostasis and regulation. However, P5’s biochemical mode of action in immune cells is still emerging. We envisage that revealing the complete spectrum of P5-target proteins in immune cells would have multifold applications, not only in basic understanding of steroids biochemistry in immune cells but also in developing new therapeutic applications. We employed a CLICK-enabled probe to capture P5-binding proteins in live Th2 cells. Subsequently, using high-throughput quantitative proteomics we identified the P5-interactome in CD4+ Th2 cells. Our study revealed P5’s conserved mode of action in CD4+ and CD8+ immune cells. We identified novel proteins from mitochondrial and endoplasmic reticulum membranes to be the primary mediators of P5’s biochemistry in CD4+ and CD8+ immune cells. Applying advanced computational algorithms, we were able to generate near-native maps of P5-protein key molecular interactions that can lead to successful designing of novel molecular therapeutics strategies.
Proteasomal regulation of ASK family kinases dictates cell fate under hyperosmotic stress
Authors: Zhou Xiangyu , Watanabe Kengo , Morishita Kazuhiro , Hamazaki Jun , Murata Shigeo , Naguro Isao , Ichijo Hidenori
Published: May 2023

The proteasome has an essential role in proteostasis maintenance and is critical for cell survival under proteotoxic conditions including hyperosmotic stress. However, it is unknown how proteasome activity is linked to cell survival/death under hyperosmotic stress. We have previously reported that apoptosis signal-regulating kinase 3 (ASK3) contributes to cell survival through its inactivation under hyperosmotic stress. 19S regulatory particle subunits of the proteasome were enriched in the ASK3 inactivator candidates identified through our genome-wide small interfering RNA (siRNA) screen. In this study, we demonstrate that the proteasome regulates ASK3 inactivation through its proteolytic activity. Intriguingly, the proteasome inactivates ASK3 via degradation of not ASK3 per se but another ASK family member ASK1 which activates ASK3 in a kinase activity-dependent manner. Furthermore, the elevated ASK1 level under proteasome inhibition sensitizes cells to hyperosmotic stress. These findings suggest that ASK family maintenance links proteasome capacity to cell fate bifurcation under hyperosmotic stress.
Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus
Authors: Bartholdy Bjørn Peare , Velsko Irina M. , Gur-Arieh Shira , Fagernäs Zandra , Warinner Christina , Henry Amanda G.
Published: May 2023

Abstract

Dental calculus is increasingly used by researchers to study dietary patterns in past populations. The benefits of using dental calculus for this purpose have been clearly demonstrated in previous studies, with dental calculus harbouring a wealth of microremains and biomarkers for health and diet within its mineral matrix. Previous studies have demonstrated some of the limitations and biases of how methods of processing may overlook, or even remove, some of the important information contained within the mineralised matrix. However, there are many factors that are impossible to account forin vivoand in archaeological material, such as exact dietary intake, and individual factors such as pH and enzyme activity, leaving some limitations that may not be addressed through these types of studies and will require a different approach.

We present a protocol for creating a calcifying oral biofilm model that can be used to explore the biases and limitations of dental calculus as a medium for paleodietary reconstructions. We report the microbial and mineral composition of our model in an effort to validate the model calculus as an appropriate proxy to natural dental calculus. The microbial profile and species diversity of our model was determined using metagenomic classification with the nf-core/eager pipeline and Kraken2, and compared to various reference samples from oral sites, including saliva, plaque, and dental calculus. We then assessed whether our model calculus mineralises in a manner similar to natural dental calculus using Fourier transform infrared (FTIR) spectroscopy. The metagenomic classification showed a microbial profile predominantly made up of (facultative) anaerobes, with a community structure that was somewhat distinct from other oral reference samples. The core genera of the model consisted of oral species, but clustered separately from oral reference samples, with a higher abundance of anaerobes.

Mineral and organic components of our model mimic that of the modern and archaeological reference calculus that was used as a comparison. There was an overall increase in the inorganic component relative to organic over the course of the experiment, with carbonated hydroxyapatite as the principal compound, consistent with natural human-derived calculus.

We conclude that oral biofilm models, such as the one presented in this study, have great potential to validate current methods used in the analysis of archaeological dental calculus, and should be used to complement, rather than replace currentin vivostudies.
Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates
Authors: Du Jingjie , Khemmani Mark , Halverson Thomas , Ene Adriana , Limeira Roberto , Tinawi Lana , Hochstedler-Kramer Baylie R. , Noronha Melline Fontes , Putonti Catherine , Wolfe Alan J.
Published: May 2023

Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladderE. coliisolates and 387 gutE. coliisolates supports the hypothesis that phylogroup distribution and functions ofE. colistrains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
Real TimeIn vivoAnalysis of Pancreatic Beta-cell Autophagic Flux Reveals Impairment Before Onset of Autoimmune Diabetes
Authors: Melnyk Olha , Muralidharan Charanya , Duffett Bryce E. , Novak Alissa N. , Perez-Aviles Glorian , Martinez Michelle M. , Crowder Justin J. , Linnemann Amelia K.
Published: May 2023

The catabolic pathway of autophagy is critical for pancreatic beta-cell function and is defective in established type 1 diabetes (T1D). However, it is unclear when and how this critical cell process becomes defective during diabetes pathogenesis. To study the nature of autophagy dysfunction in the context of autoimmune diabetes, we utilized intravital microscopy to study autophagic fluxin vivoin real time. We generated a custom AAV8- packaged mCherry-eGFP-LC3B biosensor driven by the insulin promoter for beta-cell-selective expression. For real time autophagic flux evaluation, fluorescent signal from eGFP and mCherry fluorophores was correlated in space and time to follow the process of autophagosome-lysosome fusion. We observed autophagic flux defects in the beta-cells of non-obese diabetic (NOD) mouse model of T1D prior to hyperglycemia onset that were less apparent in mice without a functional immune system. We also evaluated autophagic flux in human donor islets that were transplanted under the kidney capsule of immune incompetent mice. Collectively, we provide the first evaluation of autophagic fluxin vivoin 4D and demonstrate that autophagy defects precede hyperglycemia in NOD mice suggesting a potential causative role for these defects in beta-cell demise during T1D pathogenesis.
"Cold" Orthogonal Translation by Psychrophilic Pyrrolysyl-tRNA Synthetase Boosts Genetic Code Expansion
Authors: Koch Nikolaj G. , Goettig Peter , Rappsilber Juri , Budisa Nediljko
Published: May 2023

Using orthogonal translation systems (OTSs) is the most efficient way to produce unnatural proteins by incorporating non-canonical amino acids (ncAAs) into the genetic code. Traditionally, efforts to expand substrate specificity start with a (hyper-)stable enzyme capable of withstanding the structural changes resulting from necessary mutations. However, we adopt a radically different approach by starting with an enzyme that evolved to cope with instability, potentially offering resilience to mutations. By engineering a psychrophilic ("cold") OTS fromMethanococcoides burtonii,we developed an alternative to the commonly used mesophilic and thermophilic systems. This OTS exhibited remarkablein vivoefficiency and promiscuity, even at very low ncAA concentrations. Given the broad range of applicable host organisms, we anticipate that Cold-OTS will significantly advance the transformation of the expanded genetic code from an academic discipline into a high-value chemistry-driven biotechnology.
HIV-1 Vpr-induced DNA damage activates NF-κB through ATM-NEMO independent of cell cycle arrest
Authors: Sandoval Carina , Nisson Karly , Fregoso Oliver I.
Published: May 2023

Lentiviral accessory genes enhance replication through diverse mechanisms. HIV-1 accessory protein Vpr modulates the host DNA damage response (DDR) at multiple steps through DNA damage, cell cycle arrest, the degradation of host proteins, and both the activation and repression of DDR signaling. Vpr also alters host and viral transcription; however, the connection between Vpr-mediated DDR modulation and transcriptional activation remains unclear. Here, we determined the cellular consequences of Vpr-induced DNA damage using Vpr mutants that allow us to separate the ability of Vpr to induce DNA damage from cell cycle arrest and other DDR phenotypes including host protein degradation and repression of DDR. RNA-sequencing of cells expressing Vpr or Vpr mutants identified that Vpr alters cellular transcription through mechanisms both dependent and independent of cell cycle arrest. In tissue-cultured U2OS cells and primary human monocyte-derived macrophages (MDMs), Vpr-induced DNA damage activates the ATM-NEMO pathway and alters cellular transcription via NF-κB/RelA signaling. HIV-1 infection of primary MDMs validated Vpr-dependent NF-κB transcriptional activation during infection. Both virion delivered andde novoexpressed Vpr induced DNA damage and activated ATM-NEMO dependent NF-κB transcription, suggesting that engagement of the DDR and transcriptional reprogramming can occur during early and late stages of viral replication. Together, our data identifies a mechanism by which Vpr activates NF-κB through DNA damage and the ATM-NEMO pathway, which occur independent of cell cycle arrest. We propose this is essential to overcoming restrictive environments, such as in macrophages, to enhance viral transcription and replication.

IMPORTANCE

The HIV accessory protein Vpr is multi-functional and required for viral replicationin vivo, yet how Vpr enhances viral replication is unknown. Emerging literature suggests that a conserved function of Vpr is engagement of the host DNA damage response (DDR). For example, Vpr activates DDR signaling, causes DDR-dependent cell cycle arrest, promotes degradation of various DDR proteins, and alters cellular consequences of DDR activation. However, a central understanding of how these phenotypes connect and how they affect HIV-infected cells remains unknown. Here, we found that Vpr-induced DNA damage alters the host transcriptome by activating an essential transcription pathway, NF-κB. This occurs early during infection of primary human immune cells, suggesting NF-κB activation and transcriptome remodeling are important for establishing productive HIV-1 infection. Together, our study provides novel insights into how Vpr alters the host environment through the DDR, and what roles Vpr and the DDR play to enhance HIV replication.
House price bubble detection in Ukraine
Authors: Shmygel Alona , Hoesli Martin
Published: May 2023

Purpose

The purpose of this paper is to present a framework for the assessment of the fundamental value of house prices in the largest Ukrainian cities, as well as to identify the thresholds, the breach of which would signal a bubble.

Design/methodology/approach

House price bubbles are detected using two approaches: ratios and regression analysis. Two variants of each method are considered. The authors calculate the price-to-rent and price-to-income ratios that can identify a possible overvaluation or undervaluation of house prices. Then, the authors perform regression analyses by considering individual multi-factor models for each city and by using a within regression model with one-way (individual) effects on panel data.

Findings

The only pronounced and prolonged period of a house price bubble is the one that coincides with the Global Financial Crisis. The bubble signals produced by these methods are, on average, simultaneous and in accordance with economic sense.

Research limitations/implications

The framework described in this paper can serve as a model for the implementation of a tool for detecting house price bubbles in other countries with emerging, small and open economies, due to adjustments for high inflation and significant dependence on reserve currencies that it incorporates.

Practical implications

A tool for measuring fundamental house prices and a bubble indicator for housing markets will be used to monitor the systemic risks stemming from the real estate market. Thus, it will help the National Bank of Ukraine maintain financial stability.

Social implications

The framework presented in this research will contribute to the enhancement of the systemic risk analysis toolkit of the National Bank of Ukraine. Therefore, it will help to prevent or mitigate risks that might originate in the real estate market.

Originality/value

The authors show how to implement an instrument for detecting house price bubbles in Ukraine. This will become important in the context of the after-war reconstruction of Ukraine, with mortgages potentially becoming the main tool for the financing of the rebuilding/renovation of the residential real estate stock.
Host, environment, and anthropogenic factors drive landscape dynamics of an environmentally transmitted pathogen: Sarcoptic mange in the bare‐nosed wombat
Authors: Ringwaldt E. M. , Brook B. W. , Buettel J. C. , Cunningham C. X. , Fuller C. , Gardiner R. , Hamer R. , Jones M. , Martin A. M. , Carver S.
Published: May 2023

Understanding the spatial dynamics and drivers of wildlife pathogens is constrained by sampling logistics, with implications for advancing the field of landscape epidemiology and targeted allocation of management resources. However, visually apparent wildlife diseases, when combined with remote‐surveillance and distribution modelling technologies, present an opportunity to overcome this landscape‐scale problem.

Here, we investigated dynamics and drivers of landscape‐scale wildlife disease, using clinical signs of sarcoptic mange (caused by Sarcoptes scabiei) in its bare‐nosed wombat (BNW; Vombatus ursinus) host. We used 53,089 camera‐trap observations from over 3261 locations across the 68,401 km2 area of Tasmania, Australia, combined with landscape data and ensemble species distribution modelling (SDM). We investigated: (1) landscape variables predicted to drive habitat suitability of the host; (2) host and landscape variables associated with clinical signs of disease in the host; and (3) predicted locations and environmental conditions at greatest risk of disease occurrence, including some Bass Strait islands where BNW translocations are proposed.

We showed that the Tasmanian landscape, and ecosystems therein, are nearly ubiquitously suited to BNWs. Only high mean annual precipitation reduced habitat suitability for the host. In contrast, clinical signs of sarcoptic mange disease in BNWs were widespread, but heterogeneously distributed across the landscape.

Mange (which is environmentally transmitted in BNWs) was most likely to be observed in areas of increased host habitat suitability, lower annual precipitation, near sources of freshwater and where topographic roughness was minimal (e.g. human modified landscapes, such as farmland and intensive land‐use areas, shrub and grass lands). Thus, a confluence of host, environmental and anthropogenic variables appear to influence the risk of environmental transmission of S. scabiei. We identified that the Bass Strait Islands are highly suitable for BNWs and predicted a mix of high and low suitability for the pathogen.

This study is the largest spatial assessment of sarcoptic mange in any host species, and advances understanding of the landscape epidemiology of environmentally transmitted S. scabiei. This research illustrates how host‐pathogen co‐suitability can be useful for allocating management resources in the landscape.
Different governments, similar agendas? Analyzing more than seven decades of Norwegian policy agendas presented in executive speeches
Authors: Jungblut Jens , Kavli Tuva Marie , Valgermo Jon Bøe
Published: May 2023

Norwegian politics have undergone significant changes since 1945. This paper analyzes over seven decades of policy agendas outlined in Norwegian executive speeches focusing on the composition and development of the agenda using categories from the Comparative Agendas Project. The analysis focuses on (a) the dynamics of agenda changes over time, (b) the diversity and distribution of attention, and (c) in how far external shocks or partisan factors drive major agenda shifts. Our results show that the Norwegian executive agenda has become more encompassing over time, that it is comparatively diverse, and that diversity increases as Norwegian politics becomes more complex. While there is generally a high degree of stability in the agenda, sudden punctuations also occur. Partisan factors only play a limited role in explaining these attention shifts, while external shocks seem to be more relevant.
Circular non‐coding RNA circ_0072088 serves as a ceRNA, targeting the miR‐1225‐5p/WT1 axis to regulate non‐small cell lung cancer cell malignant behavior
Authors: Zhu Xiaofang , Wan Jing , You Xu , Yang Wanli , Zhao Lei
Published: May 2023

Background

Circular RNA (circRNA) circ_0072088 has been reported to be associated with NSCLC cell growth, migration, and invasion. However, the role and mechanism of circ_0072088 on NSCLC development have not yet been determined.

Methods

Circ_0072088, microRNA‐1225 (miR‐1225‐5p), and Wilms' tumor (WT1) suppressor gene level was detected by reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR). Migration, invasion, and apoptosis were detected using transwell and flow cytometry assays. Matrix metallopeptidase 9 (MMP9), hexokinase 2 (HK2), and WT1 were examined using western blot assay. The biological role of circ_0072088 on NSCLC tumor growth was examined by the xenograft tumor model in vivo. Circular RNA Interactome and TargetScan were used to predict the binding between miR‐1225‐5p and circ_0072088 or WT1, followed by confirmation using a dual‐luciferase reporter.

Results

Circ_0072088 and WT1 were highly expressed in NSCLC tissues and cells, and miR‐1225‐5p was decreased. Knockdown of circ_0072088 might repress migration, invasion, and glycolysis, and facilitate apoptosis of NSCLC cells in vitro. Circ_0072088 silencing also blocked NSCLC tumor growth in vivo. Mechanistically, circ_0072088 acted as a sponge of miR‐1225‐5p to regulate WT1 expression.

Conclusion

Circ_0072088 knockdown could inhibit cell growth, migration, invasion, and glycolysis partially by regulating the miR‐1225‐5p/WT1 axis, thus providing a promising therapeutic target for NSCLC treatment.
Prepubertal castration eliminates sex differences in lifespan and growth trajectories in genetically heterogeneous mice
Authors: Jiang Nisi , Cheng Catherine J. , Gelfond Jonathan , Strong Randy , Diaz Vivian , Nelson James F.
Published: May 2023

Sex differences in aging and longevity have been widely observed, with females consistently outliving males across human populations. However, the mechanisms driving these disparities remain poorly understood. In this study, we explored the influence of post‐pubertal testicular effects on sex differences in aging by prepubertally castrating genetically heterogeneous (UM‐HET3) mice, a unique mouse model that emulates human sex differences in age‐related mortality. Prepubertal castration eliminated the longevity disparity between sexes by reducing the elevated early‐ to mid‐life mortality rate observed in males and extending their median lifespan to match that of females. Additionally, castration extended the duration of body weight growth and attenuated the inverse correlation between early‐age body weight and lifespan in males, aligning their growth trajectories with those of females. Our findings suggest that post‐pubertal testicular actions in genetically diverse mice are primarily responsible for sex differences in longevity as well as growth trajectories. These findings offer a foundation for further investigation into the fundamental mechanisms driving sex‐specific aging patterns and the development of potential pro‐longevity interventions.
Methylation of eNOS in the rat penile corpus cavernosum under different pathological states and its relationship with erectile function
Authors: Wang Na , Jiang Qilan , Xie Libo , Cheng Bo , Liu Qin‐Wen , Jiang Rui
Published: May 2023

Background

It has been shown that methylation in the promoter region of eNOS can downregulate eNOS expression resulting in the endothelial dysfunction. However, it is unclear whether low androgen levels and type 1 diabetes cause ED by methylating the promoter region of eNOS in the penile corpus cavernosum.

Objective

To clarify the effects of type 1 diabetes and hypo‐androgen status on the methylation level of the promoter region of the eNOS gene in penile cavernous tissue and their relationship with the erectile function.

Methods

Fifty‐eight eight‐week‐old male Sprague–Dawley rats were randomly divided into six groups (n = 6): sham operation group, castration group, castration+testosterone (cast+T) group, normoglycemia group, diabetic group, and diabetic+methyltransferase inhibitor (5‐aza‐dc, 1.5 mg/kg) group. The ICPmax/MAP, serum T, the concentration of nitric oxide (NO), the expression of DNMT1, DNMT3a, DNMT3b, and eNOS, and the methylation level of the eNOS promoter region in penile corpus cavernosum of rat were examined 4 weeks after surgery in the sham‐operated group, the castration group, and the castration + testosterone replacement group. Those tests were examined after 6 weeks using of methylation inhibitors in the normoglycemic group, the diabetic group, and the diabetic + methylation inhibitor group.

Results

ICPmax/MAP, DNMT1, DNMT3a, DNMT3b, eNOS, and NO levels were significantly lower in castrated rats than in sham and cast+T rats (P < 0.05). ICPmax/MAP, eNOS, and NO levels were lower, and DNMT1, DNMT3a, and DNMT3b expression levels were significantly increased in the diabetic group compared with the normoglycemic and diabetic+methyltransferase inhibitor groups (P < 0.05). There was no significant difference in the methylation level of the promoter region of eNOS in penile cavernous tissue of castrated rats compared with the sham group or the testosterone replacement group. The methylation level of the promoter region of eNOS in penile cavernous tissue was significantly higher in the diabetic group than in the normoglycemic group and diabetic+methyltransferase inhibitor group (P < 0.05).

Conclusion

Although low androgen status inhibited the level of methyltransferase in rat penile cavernous tissue, did not affect the level of methylation in the promoter region of eNOS. Hyperglycemia inhibits the NO level in the penile cavernous tissue and the erectile function of rats by upregulating the methyltransferase level in the penile cavernous tissue and the methylation level in the promoter region of eNOS. Methylation inhibitors can partly improve the erectile function in type 1 diabetic rats.
Changing patterns of care for pancreas cancer in Victoria: the 2022 Pancreas Tumour Summit
Authors: Pilgrim Charles H. C. , Finn Norah , Stuart Ella , Philip Jennifer , Steel Simone , Croagh Dan , Lee Belinda , Tebbutt Niall C.
Published: May 2023

Background

The Victorian Government convened the second Pancreas Cancer Summit in 2021 to identify unwarranted variation in care 2016–2019, and to assess trends compared with the first Summit 2017 (reporting 2011–2015). State‐wide administrative data were assessed at population level in alignment with optimal care pathways across all stages of the cancer care continuum.

Methods

Data linkage performed by Centre for Victorian Data Linkage combined data from Victorian Cancer Registry with other administrative data sets including Victorian Admitted Episodes Dataset, Victorian Radiotherapy Minimum Data Set, Victorian Emergency Minimum Dataset and Victorian Death Index. A Cancer Service Performance Indicator audit was carried out providing an in‐depth analysis of identified areas of interest.

Results

Of 3138 Victorians diagnosed with pancreas ductal adenocarcinoma 2016–2019, 63% were metastatic at diagnosis. One‐year survival increased between time periods, from 29.7% overall 2011–2015 (59.1% for non‐metastatic, and 15.1% metastatic) to 32.5% overall 2016–2019 (P < 0.001), 61.2% non‐metastatic (P = 0.008), 15.7% metastatic (P = NS). A higher proportion of non‐metastatic patients progressed to surgery (35% vs. 31%, P = 0.020), and more received neoadjuvant therapy (16% vs. 4%, P < 0.001). Postoperative mortality following pancreatectomy at 30 and 90 days remained low at 2%. Utilization of 5FU‐based chemotherapy regimens increased between 2016 and 2020. Multidisciplinary Meeting (MDM) presentation was still below the 85% target (74%) as was supportive care screening (39%, target 80%).

Conclusions

Surgical outcomes remain world‐class and there has been an appropriate shift in chemotherapy administration towards neoadjuvant timing with increasing use of 5FU‐based regimens. MDM presentation rates, supportive care and overall care coordination remain areas of deficiency.