bluuebunny/crossref_metadata_2025 huggingface dataset:
The DNA damage inducible lncRNA SCAT7 regulates genomic integrity and topoisomerase 1 turnover in lung adenocarcinoma
Authors: Statello Luisa , Ali Mohamad M , Reischl Silke , Mahale Sagar , Kosalai Subazini Thankaswamy , Huarte Maite , Kanduri Chandrasekhar
Published: February 2021

Despite the rapid improvements in unveiling the importance of lncRNAs in all aspects of cancer biology, there is still a void in mechanistic understanding of their role in the DNA damage response. Here we explored the potential role of the oncogenic lncRNA SCAT7 (ELF3-AS1) in the maintenance of genome integrity. We show that SCAT7 is upregulated in response to DNA-damaging drugs like cisplatin and camptothecin, where SCAT7 expression is required to promote cell survival. SCAT7 silencing leads to decreased proliferation of cisplatin-resistant cells in vitro and in vivo through interfering with cell cycle checkpoints and DNA repair molecular pathways. SCAT7 regulates ATR signaling, promoting homologous recombination. Importantly, SCAT7 also takes part in proteasome-mediated topoisomerase I (TOP1) degradation, and its depletion causes an accumulation of TOP1–cc structures responsible for the high levels of intrinsic DNA damage. Thus, our data demonstrate that SCAT7 is an important constituent of the DNA damage response pathway and serves as a potential therapeutic target for hard-to-treat drug resistant cancers.
Identity: rapid alignment-free prediction of sequence alignment identity scores using self-supervised general linear models
Authors: Girgis Hani Z , James Benjamin T , Luczak Brian B
Published: February 2021

Pairwise global alignment is a fundamental step in sequence analysis. Optimal alignment algorithms are quadratic—slow especially on long sequences. In many applications that involve large sequence datasets, all what is needed is calculating the identity scores (percentage of identical nucleotides in an optimal alignment—including gaps—of two sequences); there is no need for visualizing how every two sequences are aligned. For these applications, we propose Identity, which produces global identity scores for a large number of pairs of DNA sequences using alignment-free methods and self-supervised general linear models. For the first time, the new tool can predict pairwise identity scores in linear time and space. On two large-scale sequence databases, Identity provided the best compromise between sensitivity and precision while being faster than BLAST, Mash, MUMmer4 and USEARCH by 2–80 times. Identity was the best performing tool when searching for low-identity matches. While constructing phylogenetic trees from about 6000 transcripts, the tree due to the scores reported by Identity was the closest to the reference tree (in contrast to andi, FSWM and Mash). Identity is capable of producing pairwise identity scores of millions-of-nucleotides-long bacterial genomes; this task cannot be accomplished by any global-alignment-based tool. Availability: https://github.com/BioinformaticsToolsmith/Identity.
Les directives pour le traitement par surfactant exogène chez le nouveau-né
Authors: Ng Eugene H , Shah Vibhuti
Published: February 2021

Le traitement par surfactant exogène joue un rôle essentiel dans la prise en charge des nouveau-nés atteints du syndrome de détresse respiratoire (maladie des membranes hyalines) parce qu’il améliore la survie et limite les troubles respiratoires. Puisque la ventilation non invasive est de plus en plus utilisée comme principal mode d’assistance respiratoire chez le nouveau-né prématuré à la naissance, l’administration prophylactique de surfactant n’est plus bénéfique. L’administration précoce de surfactant sous forme de traitement de rattrapage est préconisée chez les nouveau-nés dont le syndrome de détresse respiratoire s’aggrave. La stratégie qui consiste à intuber, administrer du surfactant, puis extuber (INSURE) est largement acceptée en pratique clinique, mais des méthodes non invasives plus récentes à l’aide d’un cathéter fin, d’un masque laryngé ou d’un nébuliseur sont en cours d’adoption ou d’exploration. Selon des données limitées, un traitement d’appoint par surfactant exogène pourrait être efficace pour traiter d’autres affections que le syndrome de détresse respiratoire, telles que le syndrome d’aspiration méconiale.
The Use of Biochar for Plant Pathogen Control
Authors: Poveda Jorge , Martínez-Gómez Ángela , Fenoll Carmen , Escobar Carolina
Published: February 2021

To support the search for alternative, nonchemical plant disease control strategies, we present a review of the pathogen-suppressive effects of biochar, a product derived from agricultural and other organic wastes, used as a soil amendment. A wide range of biochar effects contribute to the control of root or foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms. The induction of systemic plant defenses by biochar in the roots to reduce foliar pathogenic fungi, the activation of stress-hormone responses, as well as changes in active oxygen species are indicative of a coordinated hormonal signaling within the plant. Although scarce data are available for oomycetes and bacterial pathogens, reports indicate that biochar promotes changes in the soil microbiota influencing pathogen motility and colonization, and the induction of plant systemic defenses, both contributing to disease suppression. Biochar also suppresses nematode and insect pests. For plant-parasitic nematodes, the primary modes of action are changes in soil microbial community diversity, the release of nematicidal compounds, and the induction of plant defenses. Use of biochar-based soil amendments is a promising strategy compatible with a circular economy, based on zero waste, as part of integrated pathogen and pest management. Since biochars exert complex and distinct modes of action for the control of plant pathogens, its nature and application regimes should be designed for particular pathogens and its effects studied locally.
Using time use diaries to track changing behavior across successive stages of COVID-19 social restrictions
Authors: Sullivan Oriel , Gershuny Jonathan , Sevilla Almudena , Foliano Francesca , Vega-Rapun Margarita , de Grignon Juana Lamote , Harms Teresa , Walthery Pierre
Published: February 2021

How did people change their behavior over the different phases of the UK COVID-19 restrictions, and how did these changes affect their risk of being exposed to infection? Time use diary surveys are unique in providing a complete chronicle of daily behavior; 24-hour continuous records of the populations’ activities, their social context and their location. We present results from four such surveys, collected in real time from representative UK samples, both before, and at three points over the course of the current pandemic. Comparing across the four waves, we find evidence of substantial changes in the UK population’s behavior relating to activities, locations and social context. We assign different levels of risk to combinations of activities, locations and copresence, to compare risk-related behavior across successive ‘lockdowns’. We find evidence that during the second lockdown (November 2020) there was an increase in high-risk behaviors relative to the first (starting March 2020). This increase is shown to be associated with more paid work time in the workplace. At a time when capacity is still limited both in respect of immunization and track-trace technology, governments must continue to rely on changes in people’s daily behaviors to contain the spread of COVID-19 and similar viruses. Time use diary information of this type, collected in real time across the course of the COVID-19 pandemic, can provide policy-makers with information to assess and quantify changes in daily behaviors, and the impact they are likely to have on overall behavioral-associated risks.
Novel EGFRvIII-CAR transgenic mice for rigorous preclinical studies in syngeneic mice
Authors: Chuntova Pavlina , Hou Yafei , Naka Ryosuke , Goretsky Yitzhar , Nejo Takahide , Kohanbash Gary , Chen Tiffany , Mende Abigail L. , Montoya Megan , Yamamichi Akane , Downey Kira M. , Diebold David , Skinner Jayne , Liang Hong-Erh , Schwer Bjoern , Okada Hideho
Published: February 2021

Background

Rigorous preclinical studies of chimeric antigen receptor (CAR) immunotherapy will require large quantities of consistent and high-quality CAR-transduced T (CART)-cells that can be used in syngeneic mouse glioblastoma (GBM) models. To this end, we developed a novel transgenic (Tg) mouse strain with a fully murinized CAR targeting epidermal growth factor receptor variant III (EGFRvIII).

Methods

We first established the murinized version of EGFRvIII-CAR and validated its function using a retroviral vector (RV) in C57BL/6J mice bearing syngeneic SB28 GBM expressing EGFRvIII. Next, we created C57BL/6J-background Tg mice carrying the anti-EGFRvIII-CAR downstream of a Lox-Stop-Lox cassette in theRosa26locus. We bred these mice with CD4-Cre Tg mice to allow CAR expression on T-cells and evaluated the function of the CART-cells bothin vitroandin vivo. In order to inhibit immunosuppressive myeloid cells within SB28 GBM, we also evaluated a combination approach of CART and an anti-EP4 compound (ONO-AE3-208).

Results

Both RV- and Tg-CART-cells demonstrated specific cytotoxic activities against SB28-EGFRvIII cells. A single intravenous infusion of EGFRvIII-CART-cells prolonged the survival of glioma-bearing mice when preceded by a lymphodepletion regimen with recurrent tumors displaying profound EGFRvIII loss. The addition of ONO-AE3-208 resulted in long-term survival in a fraction of CART-treated mice and those survivors demonstrated delayed growth of subcutaneously re-challenged both EGFRvIII+and parental EGFRvIII−SB28.

Conclusion

Our new syngeneic CAR Tg mouse model can serve as a useful tool to address clinically relevant questions and develop future immunotherapeutic strategies.

Importance of study

The majority of preclinical studies evaluating CART therapy for GBM have utilized xenografts implanted into immunocompromised mice. Because the successful development of these strategies will depend on the understanding of critical interactions between therapeutic cells and the endogenous immune environment, it is essential to develop a novel immunocompetent system which allows us to study these interactions in a robust and reproducible manner. To this end, we created a Tg mouse strain in which all T-cells express a murinized EGFRvIII-CAR. T-cells derived from these mice demonstrated consistent CAR expression and EGFRvIII-specific cytotoxicity while traditional transduction with a CAR vector showed batch-to-batch variability. The syngeneic system also gave us the opportunity to evaluate a combination regimen with blockade of myeloid-derived suppressor cells. The Tg-CART mice represent a novel system for robust, and reproducible preclinical investigations.
Mitochondrial energy dysfunction induces remodeling of the cardiac mitochondrial protein acylome
Authors: Peoples Jessica N. , Ghazal Nasab , Duong Duc M. , Hardin Katherine R. , Seyfried Nicholas T. , Faundez Victor , Kwong Jennifer Q.
Published: February 2021

Mitochondria are increasingly recognized as signaling organelles because, under conditions of stress, mitochondria can trigger various signaling pathways to coordinate the cell’s response. The specific pathway(s) engaged by mitochondria in response to defects in mitochondrial energy production in vivo and in high-energy tissues like the heart are not fully understood. Here, we investigated cardiac pathways activated in response to mitochondrial energy dysfunction by studying mice with cardiomyocyte-specific loss of the mitochondrial phosphate carrier (SLC25A3), an established model that develops cardiomyopathy as a result of defective mitochondrial ATP synthesis. In heart tissue from these mice, mitochondrial energy dysfunction induced a striking pattern of acylome remodeling, with significantly increased post-translational acetylation and malonylation. Mass spectrometry-based proteomics further revealed that energy dysfunction-induced remodeling of the acetylome and malonylome preferentially impacts mitochondrial proteins. Acetylation and malonylation modified a highly interconnected interactome of mitochondrial proteins, and both modifications were present on the enzyme isocitrate dehydrogenase 2 (IDH2). Intriguingly, IDH2 activity was enhanced in SLC25A3-deleted mitochondria, and further study of IDH2 sites targeted by both acetylation and malonylation revealed that these modifications can have site-specific and distinct functional effects. Finally, we uncovered a novel crosstalk between the two modifications, whereby mitochondrial energy dysfunction-induced acetylation of sirtuin 5 (SIRT5), inhibited its function. Because SIRT5 is a mitochondrial deacylase with demalonylase activity, this finding suggests that acetylation can modulate the malonylome. Together, our results position acylations as an arm of the mitochondrial response to energy dysfunction and suggest a mechanism by which focal disruption to the mitochondrial energy production machinery can have an expanded impact on global mitochondrial function.
Kinesin-3 and kinesin-1 motors direct basement membrane protein secretion to a basal sub-region of the basolateral plasma membrane in epithelial cells
Authors: Zajac Allison L. , Horne-Badovinac Sally
Published: February 2021

Basement membranes (BMs) are sheet-like extracellular matrices that line the basal surfaces of all epithelia. Since BM proteins form networks, they likely need to be secreted near the basal surface. However, the location of their secretion site and how it is selected are unknown. Working in theDrosophilafollicular epithelium, we identified two kinesins essential for normal BM formation. Our data suggest the two kinesins work together to transport Rab10+ BM protein-filled secretory vesicles towards the basal surface along the polarized microtubule array common to epithelia. This kinesin transport biases BM protein secretion basally. When kinesins are depleted, BM proteins are mis-secreted to more apical regions of the lateral membrane, creating ectopic BM protein networks between cells that disrupt cell movements and tissue architecture. These results introduce a new transport step in the BM protein secretion pathway and highlight the importance of controlling the sub-cellular exocytic site of network-forming proteins.

Highlights

A kinesin-3 and a kinesin-1 are required for normal basement membrane (BM) assembly

Kinesins move Rab10+ BM secretory vesicles basally on polarized microtubule arrays

Transport biases BM exocytosis to basal subregions of the basolateral membrane

Loss of kinesins creates ectopic BM networks that disrupt tissue architecture
Meta-Analysis of Oxidative Transcriptomes in Insects
Authors: Bono Hidemasa
Published: February 2021

Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data ofDrosophila melanogasterwere found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data ofCaenorhabditis eleganswere curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.
Arylsulfonamide mediated RBM39 degradation causes aberrant splicing of mitotic kinesins
Authors: Coomar Seemon , Penson Alexander , Schwaller Jürg , Abdel-Wahab Omar , Gillingham Dennis
Published: February 2021

Certain arylsulfonamides (ArSulfs) induce an interaction between the E3 ligase substrate adaptor DCAF15 and the critical splicing factor RBM39, ultimately causing its degradation. Although molecules like the ArSulfs, which interfere with splicing decisions, are exciting potential medicines, the molecular glue mechanism of RBM39 degradation introduces complex pleiotropic effects that are difficult to untangle. For example, DCAF15 inhibition, RBM39 degradation, and the downstream proteome effects of splicing changes will all cause different yet overlaid effects. As such the precise cell-killing mechanism by RBM39 loss is largely unknown. By overlaying transcriptome and proteome datasets, we distinguish transcriptional from post-transcriptional effects, pinpointing those proteins most impacted by splicing changes. Our proteomic profiling of several ArSulfs suggests a selective DCAF15/ArylSulf/RBM39RRM2 interaction with a narrow degradation profile. We identify two mitotic kinesin motor proteins that are aberrantly spliced upon RBM39 degradation, and we demonstrate that these are likely contributors to the antiproliferative activity of ArSulfs.
Increasing age is independently associated with higher free water in non-active MS brain - A multi-compartment analysis using FAST-T2
Authors: Zhou Liangdong , Li Yi , Wang Xiuyuan , Sweeney Elizabeth , Zhang Hang , Tanzi Emily B. , Prince Jennette , Su-Ortiz Victor Antonio , Gauthier Susan A. , Nguyen Thanh D.
Published: February 2021

Purpose

To explore the relationship between the cerebral cortical perivascular space (PVS) and aging in non-active MS subjects by using the multi-echo T2 relaxometry based cerebrospinal fluid fraction (CSFF) map.

Methods

Multi-echo spiral T2 data from 111 subjects with non-active multiple sclerosis (MS) were retrospectively investigated by fitting the T2 data into a three-compartment model, the three water compartments including myelin water, intra-extracellular water, and cerebrospinal fluid. Segmentation of T1w image was performed to get the region of interest (ROI) in cerebral cortical regions. The white matter lesion segmentation was conducted using a convolutional neural network (CNN) based segmentation tool. The CSFF in the ROIs were correlated with age by controlling the gender, white matter hyperintensity lesion burden, and MS disease duration. Multiple linear models were created for the analysis of aging effect on the CSFF.

Results

The ROI analysis shows that the CSFF in the cerebral cortical regions (temporal, occipital, parietal, front, hippo, and mtl) are significantly linear increasing with age (p<0.01). The intra-extracellular water fraction (IEWF) in the ROIs are significantly linear decreasing (p<0.01).

Conclusion

The multi-echo T2 based three-compartment model can be used to quantify the CSFF. The linear increase of CSF water contents in the cerebral cortical regions indicates increased perivascular space load in cortex with aging. The quantification of CSFF may provide a way to understand the glymphatic clearance function in aging and neurodegenerations.

Highlights

MR T2 relaxometry is a valid method to quantify the cerebrospinal fluid fraction (CSFF) in cerebral cortical regions

The CSFF in the cerebral cortical regions are positively correlated with age by controlling the white matter lesion load in non-active MS subjects.

Quantification of cerebral CSFF may reflect the perivascular space load in cortex and better interpret the disease progression in neurodegenerative disease, such as MS.
An unusual aspartic acid cluster in the reovirus attachment fiber σ1 mediates stability at low pH
Authors: Glorani Giulia , Ruwolt Max , Holton Nicole , Neu Ursula
Published: February 2021

The reovirus attachment protein σ1 mediates cell attachment and receptor binding and is thought to undergo conformational changes during viral disassembly. σ1 is a trimeric filamentous protein with an α-helical coil-coiled Tail, a triple β-spiral Body, and a globular Head. The Head domain features an unusual and conserved aspartic acid cluster at the trimer interface, which forms the only significant intra-trimer interactions in the Head, and must be protonated to allow trimer formation.

Here we show that all domains of σ1 are remarkably thermostable across a wide range of pH, even at the low pH of the stomach. Interestingly, we determine the optimal pH for stability to be between pH 5-6, a value close to the pH of the endosome and of the jejunum. The σ1 Head is stable at acidic and neutral pH, but detrimerizes at basic pH. When Asp345in the aspartic acid cluster is mutated to asparagine, the σ1 Head loses stability at low pH and is more prone to detrimerize. Overall, the presence of the Body stabilizes the σ1 Head.

Our results confirm a role of the aspartic acid cluster as a pH-dependent molecular switch, and highlight its role in enhancing σ1 stability at low pH.
A functional bacterial-derived restriction modification system in the mitochondrion of a heterotrophic protist
Authors: Milner David S. , Wideman Jeremy G. , Stairs Courtney W. , Dunn Cory D. , Richards Thomas A.
Published: February 2021

The overarching trend in mitochondrial evolution is functional streamlining coupled with gene loss; therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in organellar genomes, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification system originating from a horizontal gene transfer event involving bacteria related to flavobacteria. This restriction modification system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase. We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that toxin-antitoxin selfish elements, such as restriction modification systems, could be co-opted by eukaryotic genomes to drive uniparental organellar inheritance.
Identification ofPectobacteriumspecies isolated from the soft rot of tetecho (Neobuxbaumia tetetzo), a columnar cactus, and associated metagenomics
Authors: Vargas-Peralta David , Narváez-Barragán Delia A. , de Sandozequi Andrés , Romero-Gutiérrez Miguel F. , Segovia Lorenzo , Martínez-Anaya Claudia , Alcaraz Luis David , de la Torre Almaraz Rodolfo
Published: February 2021

Neobuxbaumia tetetzo, commonly known as tetecho, is a columnar cactus endemic to Mexico. In the last 15 years, damage has been observed in young and adult plants ofN. tetetzo, ranging from chlorotic spots with a wet appearance in early stages to tissue necrosis in advanced stages and finally the death of the plant;Pectobacterium brasilienseis the causal agent of the damages. Disease progression may be delayed or accelerated by the involvement of other bacteria, either pathogenic or endophytic, at the site of infection. Our goal was to confirm the presence ofPectobacterium brasiliense, in the soft rot ofN. tetetzoand to determine the presence of other bacteria associated with the rot. We isolated three bacterial strains (A1, A3 and A8) from diseased tissue from three separateN. tetetzoplants, and compare them using biochemical and molecular techniques, such as whole-genome sequencing of strains A1 and A3. Phylogenetic analyzes confirmed that A1 corresponded toP. brasiliense, whereas A3 was more misimlar toP. polaris. Additionally, sequencing of 16S rRNA gene from metagenomic DNA isolated from healthy and diseased tissue ofN. tetetzoindicated the presence of four operational taxonomic units (OTUs) at the order level, unique to the diseased tissue: Actinomycetales, Burkholderiales, Caulobacterales, and Sphingomonadales, with probable participation in the soft rot process.
Heliorhodopsin evolution is driven by photosensory promiscuity in monoderms
Authors: Bulzu Paul-Adrian , Kavagutti Vinicius Silva , Chiriac Maria-Cecilia , Vavourakis Charlotte D. , Inoue Keiichi , Kandori Hideki , Andrei Adrian-Stefan , Ghai Rohit
Published: February 2021

The ability to harness Sun’s electromagnetic radiation by channeling it into high-energy phosphate bonds empowered microorganisms to tap into a cheap and inexhaustible source of energy. Life’s billion-years history of metabolic innovations led to the emergence of only two biological complexes capable of harvesting light: one based on rhodopsins and the other on (bacterio)chlorophyll. Rhodopsins encompass the most diverse and abundant photoactive proteins on Earth and were until recently canonically split between type-1 (microbial rhodopsins) and type-2 (animal rhodopsins) families. Unexpectedly, the long-lived type-1/type-2 dichotomy was recently amended through the discovery of heliorhodopsins (HeRs) (Pushkarev et al. 2018), a novel and exotic family of rhodopsins (i.e. type-3) that evaded recognition in our current homology-driven scrutiny of life’s genomic milieu. Here, we bring to resolution the debated monoderm/diderm occurrence patterns by conclusively showing that HeR distribution is restricted to monoderms. Furthermore, through investigating protein domain fusions, contextual genomic information, and gene co-expression data we show that HeRs likely function as generalised light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. We reason that HeR’s ability to function as sensory rhodopsins is corroborated by their photocycle dynamics (Pushkarev et al. 2018) and that their presence and function in monoderms is likely connected to the increased sensitivity to light-induced damage of these organisms (Maclean et al. 2009).
Video-based quantification of human movement frequency using pose estimation
Authors: Cornman Hannah L. , Stenum Jan , Roemmich Ryan T.
Published: February 2021

Assessment of repetitive movements (e.g., finger tapping) is a hallmark of motor examinations in several neurologic populations. These assessments are traditionally performed by a human rater via visual inspection; however, advances in computer vision offer potential for remote, quantitative assessment using simple video recordings. Here, we evaluated a pose estimation approach for measurement of human movement frequency from smartphone videos. Ten healthy young participants provided videos of themselves performing five repetitive movement tasks (finger tapping, hand open/close, hand pronation/supination, toe tapping, leg agility) at four target frequencies (1-4 Hz). We assessed the ability of a workflow that incorporated OpenPose (a freely available whole-body pose estimation algorithm) to estimate movement frequencies by comparing against manual frame-by-frame (i.e., ground-truth) measurements for all tasks and target frequencies using repeated measures ANOVA, Pearson’s correlations, and intraclass correlations. Our workflow produced largely accurate estimates of movement frequencies; only the hand open/close task showed a significant difference in the frequencies estimated by pose estimation and manual measurement (while statistically significant, these differences were small in magnitude). All other tasks and frequencies showed no significant differences between pose estimation and manual measurement. Pose estimation-based detections of individual events (e.g., finger taps, hand closures) showed strong correlations with manual detections for all tasks and frequencies. In summary, our pose estimation-based workflow accurately tracked repetitive movements in healthy adults across a range of tasks and movement frequencies. Future work will test this approach as a fast, low-cost, accessible approach to quantitative assessment of repetitive movements in clinical populations.
Differential activation of parathyroid and renal Ca2+-sensing receptors underlies the renal phenotype in autosomal dominant hypocalcemia 1
Authors: van Megen Wouter H. , Tan Rebecca , Alexander R. Todd , Dimke Henrik
Published: February 2021

Background

Parathyroid Ca2+-sensing receptor (CaSR) activation inhibits parathyroid hormone (PTH) release, while activation of CaSRs in kidneys and intestine attenuates local transepithelial Ca2+transport. In patients with autosomal dominant hypocalcemia 1 (ADH1) due to activatingCASRmutations, treatment of symptomatic hypocalcemia can be complicated by treatment-induced hypercalciuria, resulting in nephrocalcinosis and renal insufficiency. Although CaSRs throughout the body are activated by increased extracellular Ca2+concentrations, it is not understood why some ADH1 patients have reduced PTH, but not hypercalciuria at presentation, despite CaSR expression in both kidney and parathyroid.

Methods

Activation of the CaSR was studied in mouse models and a ADH1 patient.In vitroCaSR activation was studied in HEK293 cells.

Results

Mice with a gain-of-function mutation inCasrare hypocalcemic with reduced plasma PTH levels. However, renal CaSRs are not activated as indicated by normal urinary calcium handling and unaltered renalCldn14expression. Activation of renal CaSRs only occurred after increasing plasma Ca2+levels. Similarly, calcimimetic administration to wildtype mice induced hypocalcemia without activating renal CaSRs. Moreover, significant hypercalciuria was not observed in an ADH1 patient until blood Ca2+was normalized.In vitroexperiments suggest that increased CaSR levels in the parathyroid relative to the kidney contribute tissue-specific CaSR activation thresholds.

Conclusion

Here we delineate tissue-specific CaSR activation thresholds, where parathyroid CaSR overactivity can reduce plasma Ca2+to levels insufficient to activate renal CaSRs, even with overactivating mutations. These findings may aid in the management of ADH1 patients.
Hybridization dynamics and extensive introgression in theDaphnia longispinaspecies complex: new insights from a high-qualityDaphnia galeatareference genome
Authors: Nickel Jana , Schell Tilman , Holtzem Tania , Thielsch Anne , Dennis Stuart R. , Schlick-Steiner Birgit C. , Steiner Florian M. , Möst Markus , Pfenninger Markus , Schwenk Klaus , Cordellier Mathilde
Published: February 2021

Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genusDaphnia,a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of theDaphnia longispinaspecies complex,Daphnia galeata. We further re-sequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in theDaphnia longispinaspecies complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
Properties of multi-vesicular release from rod photoreceptors support transmission of single photon responses
Authors: Hays CL , Sladek AL , Field GD , Thoreson WB
Published: February 2021

Vision under starlight requires rod photoreceptors to transduce and transmit single photon responses to the visual system. This remarkable sensitivity depends on a small voltage change reliably reducing glutamate release such that post-synaptic rod bipolar cells can robustly detect the signal. To transmit this small signal, we have found that rod vesicle release deviates strongly from a Poisson process under conditions that mimic darkness. Specifically, at their resting membrane potential in darkness, rods exhibit coordinated and regularly timed multivesicular release events. Each release event consisted of ∼17 vesicles and occurred 2-3 times more regularly than expected from a Poisson process. Hyperpolarizing rods to mimic the voltage change produced by a single photon response abruptly reduced the probability of multivesicular release nearly to zero with a rebound increase in release probability at stimulus offset. Simulations of these release dynamics indicate that this regularly timed, multivesicular release promotes transmission of single photon responses to post-synaptic neurons. Furthermore, the mechanism is efficient, requiring fewer vesicles to be released per second than uniquantal release governed by Poisson statistics.
Sleuthing biochemical evidence to elucidate unassigned electron density in a CBL–SLAP2 crystal complex
Authors: Wybenga-Groot Leanne E. , McGlade C. Jane
Published: February 2021

The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL E3 ubiquitin ligase to downregulate antigen, cytokine and tyrosine kinase receptor signalling. In contrast to the phosphotyrosine-dependent binding of CBL substrates through its tyrosine kinase-binding domain (TKBD), CBL TKBD associates with the C-terminal tail of SLAP2 in a phospho-independent manner. To understand the distinct nature of this interaction, a purification protocol for SLAP2 in complex with CBL TKBD was established and the complex was crystallized. However, determination of the complex crystal structure was hindered by the apparent degradation of SLAP2 during the crystallization process, such that only the CBL TKBD residues could initially be modelled. Close examination of the CBL TKBD structure revealed a unique dimer interface that included two short segments of electron density of unknown origin. To elucidate which residues of SLAP2 to model into this unassigned density, a co-expression system was generated to test SLAP2 deletion mutants and define the minimal SLAP2 binding region. SLAP2 degradation products were also analysed by mass spectrometry. The model-building and map-generation features of the Phenix software package were employed, leading to successful modelling of the C-terminal tail of SLAP2 into the unassigned electron-density segments.
A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins
Authors: Tronrud Dale E. , Karplus P. Andrew
Published: February 2021

While broadening the applicability of (φ/ψ)-dependent target values for the bond angles in the peptide backbone, sequence/conformation categories with too few residues to analyze via previous methods were encountered. Here, a method of describing a conformation-dependent library (CDL) using two-dimensional Fourier coefficients is reported where the number of coefficients for individual categories is determined via complete cross-validation. Sample sizes are increased further by selective blending of categories with similar patterns of conformational dependence. An additional advantage of the Fourier-synthesis-based CDL is that it uses continuous functions and has no artifactual steps near the edges of populated regions of φ/ψ space. A set of libraries for the seven main-chain bond angles, along with the ω and ζ angles, was created based on a set of Fourier analyses of 48 368 residues selected from high-resolution models in the wwPDB. This new library encompasses both trans- and cis-peptide bonds and outperforms currently used discrete CDLs.
Valuing ecosystem services of urban forests and open spaces: application of the SEEA framework in Australia*
Authors: Tapsuwan Sorada , Marcos‐Martinez Raymundo , Schandl Heinz , Yu Zefan
Published: February 2021

Around two‐thirds of the global population will live in cities by 2050 requiring large urban infrastructure development. Decision‐makers and planners usually rely on standard economic accounting methods for urban planning and investments on infrastructure assets. However, standard methods fail to account for the ecosystem services benefits that living infrastructure (e.g. urban forests, open spaces) provides to city dwellers. This could generate socially inefficient configurations of urban spaces and compromise the achievement of long‐term urban sustainability targets. In this analysis, we applied a stochastic whole‐of‐life benefit–cost analysis following the System of Environmental‐Economic Accounting (SEEA) framework to compare alternative long‐term management strategies for living infrastructure in Canberra, Australia. Spatially explicit data, i‐Tree Eco and benefit transfer methods were used to estimate the stocks and flows ecosystem services benefits of urban forests and irrigated open spaces from 2018 to 2070. Our analysis suggests that a ’30 per cent canopy cover expansion’ scenario has the highest benefit–cost ratio, while the business as usual scenario, where a net loss of 400 trees is expected per year, offers the lowest benefit–cost ratio. Scenarios of expanding versus not expanding irrigated open spaces in the future both result in a benefit–cost ratio of approximately two.
Effect of the COVID‐19 pandemic first wave and public policy on elective and emergency surgery provision in Southern Queensland
Authors: Fowler Samuel , Zahir Syeda F. , Manning Warrick , Kearney Allison , Sturgess David
Published: February 2021

Background

Several public health initiatives in Australia were implemented in March 2020 to contain the spread of COVID‐19. The effect of these initiatives on surgical provision is unknown. The primary objective was to determine the effect of public health policies and surgical society guidelines implemented during the pandemic on elective and emergency caseload of surgical specialities operating within South East Queensland.

Methods

This observational study utilized non re‐identifiable electronic data to quantify the caseload of surgical specialities across five secondary and tertiary referral hospitals in South East Queensland prior to and during the implementation of such initiatives. All patients undergoing a surgical procedure between 1 March and 24 April 2019 and the same period in 2020 were included. Participants' demographic and clinical information, such as age, the American Society of Anesthesiologists score, surgical date and location, surgical subspecialty and procedure name, was included.

Results

During the 2020 time period, there were 2991 elective cases compared to 4422 surgeries occurring in the same period in 2019 (32.4% reduction). Meanwhile, 2082 emergency surgeries were performed in the 2020 period compared to 2362 in 2019 (12.0% decrease). Ophthalmology and dental/ear, nose and throat/maxillofacial surgery experienced the largest reduction in elective surgeries, whereas emergency caseload increased for vascular and cardiothoracic services, and only slightly decreased for plastics and urology.

Conclusion

The public health initiatives and guidance implemented during the COVID‐19 pandemic reduced surgical specialties' elective caseload. However, emergency caseload was not affected to the same extent. This insight helps to guide resource allocation in future waves of the pandemic.
Intentional suspected suicide exposures by poisoning among adolescents from 2009 to 2018 reported to the Georgia Poison Center and compared nationally
Authors: Overall Britni , Hon Stephanie L. , Jones Alison , Moran Tim P. , Hunt Kevin
Published: February 2021

This retrospective chart review aimed to report the incidence and characteristics of intentional suspected suicide among 13‐ to 19‐year‐olds reported to the Georgia Poison Center (GPC) and compared nationally from 2009 to 2018. Of the 19 733 cases reported to the GPC, 74.9% were females. The total number of cases more than doubled from 2009 to 2018, increasing annually by 10%. Majority (90.1%) of the cases occurred in the home, and 60.4% of the cases resulted in either no effect or minor effect. More than half (66.5%) of the cases involved only one substance. Pharmaceuticals made up 94.5% of the substances used, with analgesics accounting for 42.10% and antidepressants at 20.77%. A significant difference was found in substances used between males and females (P < .001). Females were more likely to use analgesics (45.17% vs 32.90%), and males were more likely to use sedatives/hypnotics/antipsychotics (20.45% vs 13.58%). While the majority of the GPC patients were females, the GPC was more likely to have fewer female patients (74.7% vs 75.7%) and more male patients (25.3% vs 24.3%) than other poison centers. Intentional suspected suicide exposures by poisoning are on the rise and higher among females, demonstrating a need for strengthened intervention and prevention strategies.
CRKL promotes hepatocarcinoma through enhancing glucose metabolism of cancer cells via activating PI3K/Akt
Authors: Guo Chunmei , Gao Chao , Lv Xinxin , Zhao Dongting , Greenaway Frederick T. , Hao Lihong , Tian Yuxiang , Liu Shuqing , Sun Ming‐Zhong
Published: February 2021

Abnormal glucose metabolism may contribute to cancer progression. As a member of the CRK (v‐crk sarcoma virus CT10 oncogene homologue) adapter protein family, CRKL (CRK‐like) associated with the development and progression of various tumours. However, the exact role and underlying mechanism of CRKL on energy metabolism remain unknown. In this study, we investigated the effect of CRKL on glucose metabolism of hepatocarcinoma cells. CRKL and PI3K were found to be overexpressed in both hepatocarcinoma cells and tissues; meanwhile, CRKL up‐regulation was positively correlated with PI3K up‐regulation. Functional investigations revealed that CRKL overexpression promoted glucose uptake, lactate production and glycogen synthesis of hepatocarcinoma cells by up‐regulating glucose transporters 1 (GLUT1), hexokinase II (HKII) expression and down‐regulating glycogen synthase kinase 3β (GSK3β) expression. Mechanistically, CRKL promoted glucose metabolism of hepatocarcinoma cells via enhancing the CRKL‐PI3K/Akt‐GLUT1/HKII‐glucose uptake, CRKL‐PI3K/Akt‐HKII‐glucose‐lactate production and CRKL‐PI3K/Akt‐Gsk3β‐glycogen synthesis. We demonstrate CRKL facilitates HCC malignancy via enhancing glucose uptake, lactate production and glycogen synthesis through PI3K/Akt pathway. It provides interesting fundamental clues to CRKL‐related carcinogenesis through glucose metabolism and offers novel therapeutic strategies for hepatocarcinoma.
Mangiferin prevents myocardial infarction‐induced apoptosis and heart failure in mice by activating the Sirt1/FoxO3a pathway
Authors: Chen Lingli , Li Santie , Zhu Jianyu , You Anfu , Huang Xingzhou , Yi Xinchu , Xue Mei
Published: February 2021

Myocardial infarction (MI) commonly leads to cardiomyocyte apoptosis and heart failure. Mangiferin is a natural glucosylxanthone extracted from mango fruits and leaves, which has anti‐apoptotic and anti‐inflammatory properties in experimental cardiovascular diseases. In the present study, we investigated the role and detailed mechanism of mangiferin in MI. We used ligation of the left anterior descending coronary artery to establish an MI model in vivo, and cardiomyocyte‐specific Sirt1 knockout mice were used to identify the mechanism of mangiferin. For in vitro studies, oxygen and glucose deprivation (OGD) was used to mimic ischaemia in H9c2 cardiomyocytes. In mice, mangiferin treatment increased Sirt1 expression after MI, significantly reduced the infarct area, and prevented MI‐induced apoptosis and heart failure. Mangiferin reduced OGD‐induced cellular apoptosis in H9c2 cells. Meanwhile, Sirt1 knockout/silencing abolished the protective effects of mangiferin. Further studies revealed that mangiferin increased FoxO3a deacetylation by up‐regulating Sirt1, thus preventing apoptosis, and adenovirus‐mediated constitutive acetylation of FoxO3a restricted the anti‐apoptotic effects of mangiferin in vivo and in vitro. Our results indicate that mangiferin prevents cardiomyocyte apoptosis and the subsequent heart failure by activating the Sirt1/FoxO3a pathway in MI, and suggest that mangiferin may have an interesting potential in following studies towards clinical evaluation.
Roles of Krüppel‐like factor 5 in kidney disease
Authors: Li Jia , Liu Liang , Zhou Wen‐Qian , Cai Lu , Xu Zhong‐Gao , Rane Madhavi J.
Published: February 2021

Transcription factor Krüppel‐like factor 5 (KLF5) is a member of the Krüppel‐like factors’ (KLFs) family. KLF5 regulates a number of cellular functions, such as apoptosis, proliferation and differentiation. Therefore, KLF5 can play a role in many diseases, including, cancer, cardiovascular disease and gastrointestinal disorders. An important role for KLF5 in the kidney was recently reported, such that KLF5 regulated podocyte apoptosis, renal cell proliferation, tubulointerstitial inflammation and renal fibrosis. In this review, we have summarized the available information in the literature with a brief description on how transcriptional, post‐transcriptional and post‐translational modifications of KLF5 modulate its function in a variety of organs including the kidney with a focus of its importance on the pathogenesis of various kidney diseases. Furthermore, we also have outlined the current and possible mechanisms of KLF5 activation in kidney diseases. These studies suggest a need for more systemic investigations, particularly for generation of animal models with renal cell‐specific deletion or overexpression of KLF5 gene to examine direct contributions of KLF5 to various kidney diseases. This will promote further experimentation in the development of therapies to prevent or treat various kidney diseases.
A Hyaluronic Acid Hydrogel Loaded with Gentamicin and Vancomycin Successfully Eradicates Chronic Methicillin-Resistant Staphylococcus aureus Orthopedic Infection in a Sheep Model
Authors: Boot Willemijn , Schmid Tanja , D’Este Matteo , Guillaume Olivier , Foster Andrew , Decosterd Laurent , Richards Robert G. , Eglin David , Zeiter Stephan , Moriarty Thomas F.
Published: February 2021

Implantable orthopedic devices have had an enormously positive impact on human health; however, despite best practice, patients are prone to developing orthopedic device-related infections (ODRI) that have high treatment failure rates. One barrier to the development of improved treatment options is the lack of an animal model that may serve as a robust preclinical assessment of efficacy.
Neutrophil-Derived Oncostatin M Triggers Diverse Signaling Pathways during Pneumonia
Authors: Traber Katrina E. , Dimbo Ernest L. , Shenoy Anukul T. , Symer Elise M. , Allen Eri , Mizgerd Joseph P. , Quinton Lee J.
Published: February 2021

Pneumonia is a major public health concern, causing significant morbidity and mortality annually despite the broad use of antimicrobial agents. Underlying many of the severe sequelae of acute lung infections is dysfunction of the immune response, which remains incompletely understood yet is an attractive target of adjunct therapy in pneumonia.
Investigation of Heterochromatin Protein 1 Function in the Malaria Parasite Plasmodium falciparum Using a Conditional Domain Deletion and Swapping Approach
Authors: Bui Hai T. N. , Passecker Armin , Brancucci Nicolas M. B. , Voss Till S.
Published: February 2021

Malaria is caused by unicellularPlasmodiumspecies parasites that repeatedly invade and replicate inside red blood cells. Some blood-stage parasites exit the cell cycle and differentiate into gametocytes that are essential for malaria transmission via the mosquito vector.