bluuebunny/crossref_metadata_2025 huggingface dataset:
The tight rope act: A multicenter regional experience of tourniquets in acute trauma resuscitation
Authors: Tatebe Leah Carey , Schlanser Victoria , Hampton David , Chang Grace , Hanson Isaac , Doherty James , Issa Nabil , Ghandour Hani , Kingsley Samuel , Stewart Amy , Anstadt Michael , Dennis Andrew
Published: December 2021

BACKGROUND

As tourniquets have become more prevalent, device use has been questioned. This study sought to characterize the incidence, indication, and efficacy of tourniquet placement in acute trauma resuscitation.

METHODS

Nine regional level 1 trauma centers prospectively enrolled for 12 months adult patients (18 years or older) who had a tourniquet placed. Age, sex, mechanism, tourniquet type, indication, applying personnel, location placed, level of occlusion, and degree of hemostasis were collected. Major vascular injury, imaging and operations performed, and outcomes were assessed. Analyses were performed with significance at p < 0.05.

RESULTS

A total of 216 tourniquet applications were reported on 209 patients. There were significantly more male patients (183 [88%]) and penetrating injuries (186 [89%]) with gunshots being most common (127 [61%]). Commercial tourniquets were most often used (205 [95%]). Ninety-two percent were placed in the prehospital setting (by fire/paramedics, 56%; police, 33%; bystanders, 2%). The most common indications were pooling (47%) and pulsatile (32%) hemorrhage. Only 2% were for amputation. The most frequent location was high proximal extremity (70%). Four percent were placed over the wound, and 0.5% were distal to the wound. Only 61% of applications were arterial occlusive. Median application time was 30 minutes (interquartile range, 20–40 minutes). Imaging was performed in 54% of patients. Overall, 36% had a named arterial injury. Tourniquet application failed to achieve hemostasis in 22% of patients with a named vascular injury. There was no difference in hemostasis between those with and without vascular injury (p = 0.12) or between who placed the tourniquet (p = 0.07). Seventy patients (34%) required vascular operations. Thirty-four percent of patients were discharged home without admission.

CONCLUSION

Discerning which injuries require tourniquets over pressure dressings remains elusive. Trained responders had high rates of superfluous and inadequate deployments. As tourniquets continue to be disseminated, emphasis should be placed on improving education, device development, and quality control.

LEVEL OF EVIDENCE

Prognostic/Epidemiologic, Level III.
Hepatitis C virus core protein inhibits hepatitis B virus replication by downregulating HBx levels via Siah-1-mediated proteasomal degradation during coinfection
Authors: Lee Sujeong , Yoon Hyunyoung , Han Jiwoo , Jang Kyung Lib
Published: December 2021

Most clinical and experimental studies have suggested that hepatitis C virus (HCV) is dominant over hepatitis B virus (HBV) during coinfection, although the mechanism remains unclear. Here, we found that HCV core protein inhibits HBV replication by downregulating HBx levels during coinfection in human hepatoma cells. For this effect, HCV core protein increased reactive oxygen species levels in the mitochondria and activated the ataxia telangiectasia mutated-checkpoint kinase two pathway in the nucleus, resulting in an upregulation of p53 levels. Accordingly, HCV core protein induced p53-dependent activation of seven in absentia homolog one expression, an E3 ligase of HBx, resulting in the ubiquitination and proteasomal degradation of HBx. The effect of the HCV core protein on HBx levels was accurately reproduced in both a 1.2-mer HBV replicon and in vitro HBV infection systems, providing evidence for the inhibition of HBV replication by HCV core protein. The present study may provide insights into the mechanism of HCV dominance in HBV- and HCV-coinfected patients.
Application of fungal copper carbonate nanoparticles as environmental catalysts: organic dye degradation and chromate removal
Authors: Liu Feixue , Shah Dinesh Singh , Csetenyi Laszlo , Gadd Geoffrey Michael
Published: December 2021

Biomineralization is a ubiquitous process in organisms to produce biominerals, and a wide range of metallic nanoscale minerals can be produced as a consequence of the interactions of micro-organisms with metals and minerals. Copper-bearing nanoparticles produced by biomineralization mechanisms have a variety of applications due to their remarkable catalytic efficiency, antibacterial properties and low production cost. In this study, we demonstrate the biotechnological potential of copper carbonate nanoparticles (CuNPs) synthesized using a carbonate-enriched biomass-free ureolytic fungal spent culture supernatant. The efficiency of the CuNPs in pollutant remediation was investigated using a dye (methyl red) and a toxic metal oxyanion, chromate Cr(VI). The biogenic CuNPs exhibited excellent catalytic properties in a Fenton-like reaction to degrade methyl red, and efficiently removed Cr(VI) from solution due to both adsorption and reduction of Cr(VI). X-ray photoelectron spectroscopy (XPS) identified the oxidation of reducing Cu species of the CuNPs during the reaction with Cr(VI). This work shows that urease-positive fungi can play an important role not only in the biorecovery of metals through the production of insoluble nanoscale carbonates, but also provides novel and simple strategies for the preparation of sustainable nanomineral products with catalytic properties applicable to the bioremediation of organic and metallic pollutants, solely and in mixtures.
From fruit growth to ripening in plantain: a careful balance between carbohydrate synthesis and breakdown
Authors: Campos N.A. , Colombie S. , Moing Annick , Cassan C. , Amah D. , Swennen R. , Gibon Y. , Carpentier S.C.
Published: December 2021

We investigated the fruit development in two plantain banana cultivars from two weeks after bunch emergence till twelve weeks through high-throughput proteomics, major metabolite quantification and metabolic flux analyses. We give for the first time an insight at early stages of starch synthesis and breakdown. Starch and sugar synthesis and breakdown are processes that take place simultaneously. During the first eight to ten weeks the balance between synthesis and breakdown is clearly in favour of sugar breakdown and a net starch synthesis occurs. During this period, plantain fruit accumulates up to 48% of starch. The initiation of the ripening process is accompanied with a shift in balance towards net starch breakdown. The key enzymes related to this are phosphoglucan water dikinase (PWD), phosphoglucan phosphatase, α-1,6-glucosidase starch debranching enzyme (DBE), alpha glucan phosphorylase (PHS) and 4-alpha glucanotransferase disproportioning enzyme (DPE). The highest correlations with sucrose have been observed for PHS and DPE. There is also a significant correlation between the enzymes involved in ethylene biosynthesis, starch breakdown, pulp softening and ascorbate biosynthesis. The faster ending of maturation and starting of ripening in the Agbagba cultivar are linked to the key enzymes 1-aminocyclopropane-1-carboxylate oxidase and DPE. This knowledge of the mechanisms that regulate starch and sugar metabolisms during maturation and ripening is fundamental to determine the harvest moment, reduce postharvest losses and improve final product quality of breeding programs.
C/EBPδ-induced epigenetic changes control the dynamic gene transcription of S100A8 and S100A9
Authors: Jauch-Speer Saskia-L. , Wolf Jonas , Herrera-Rivero Marisol , Martens Leonie , Chasan Achmet Imam , Witten Anika , Markus Birgit , Schieffer Bernhard , Vogl Thomas , Stoll Monika , Roth Johannes , Fehler Olesja
Published: December 2021

The proinflammatory alarmins S100A8 and S100A9 are among the most abundant proteins in neutrophils and monocytes but completely silenced after differentiation to macrophages. The molecular mechanisms of the extraordinarily dynamic transcriptional regulation of s100a8 and s100a9 genes, however, are only barely understood. Using an unbiased genome-wide CRISPR/Cas9 knockout based screening approach in immortalized murine monocytes we identified the transcription factor C/EBPδ as a central regulator of S100A8 and S100A9 expression. S100a8 and S100a9 expression was further controlled by the C/EBPδ-antagonists ATF3 and FBXW7. We confirmed the clinical relevance of this regulatory network in subpopulations of human monocytes in a clinical cohort of cardiovascular patients. Moreover, we identified specific C/EBPδ-binding sites within s100a8 and s100a9 promoter regions, and demonstrated that C/EBPδ-dependent JMJD3-mediated demethylation of H3K27me3 is indispensable for their expression. Overall, our work uncovered C/EBPδ as a novel regulator of S100A8 and S100A9 expression. Therefore, C/EBPδ represents a promising target for modulation of inflammatory conditions that are characterised by S100A8 and S100A9 overexpression.
Microdomain protein Nce102 is a local sensor of plasma membrane sphingolipid balance
Authors: Zahumenský Jakub , Fernandes Caroline Mota , Veselá Petra , Poeta Maurizio Del , Konopka James B. , Malínský Jan
Published: December 2021

Sphingolipids are essential building blocks of eukaryotic membranes and important signalling molecules, tightly regulated in response to environmental and physiological inputs. Mechanism of sphingolipid level perception at the plasma membrane remains unclear. In Saccharomyces cerevisiae, Nce102 protein has been proposed to function as sphingolipid sensor as it changes its plasma membrane distribution in response to sphingolipid biosynthesis inhibition. We show that Nce102 redistributes specifically in regions of increased sphingolipid demand, e.g., membranes of nascent buds. Furthermore, we report that production of Nce102 increases following sphingolipid biosynthesis inhibition and Nce102 is internalized when excess sphingolipid precursors are supplied. This suggests that the total amount of Nce102 in the plasma membrane is a measure of the current need for sphingolipids, whereas its local distribution marks sites of high sphingolipid demand. Physiological role of Nce102 in regulation of sphingolipid synthesis is demonstrated by mass spectrometry analysis showing reduced levels of complex sphingolipids and long-chain bases in nce102Δ deletion mutant. Nce102 behaves analogously in human fungal pathogen Candida albicans, suggesting a conserved principle of local sphingolipid control across species.
Game of Theories: An Agent-Based Model of How Variation in Contest Cost-Benefits Determines the Evolution of Contest Resolution Rules
Authors: Pinto Nelson Silva
Published: December 2021

Game-theory based models are used to understand rules that animals use to settle contests over indivisible resources. However, the empirical literature of contests indicates controversial support to models, with some species supporting different models and other species showing no support to any model. Since strategies used to resolve contests may have different associated costs, it is possible that different conditions have determined the evolution of distinct assessment strategies used by animals. We used an agent-based model to explore the importance of the following conditions: resource availability, probability of reproduction with resource, and damage costs on evolution of assessment strategies. We used self- and mutual-assessment models as a heurist framework to build agents with different assessment strategies. In our model, agents competed for resources in scenarios with different combinations of resource availability, probability of reproduction with resource, and damage costs. We found that agents following the self-assessment with damage strategy were prevalent in scenarios with no probability of reproduction without the resource, independently of other variables. We also found that agents following the non-aggressive strategy occurred in all scenarios. However, agents using the non-aggressive strategy were prevalent only in scenarios with probability of reproduction with the resource. Finally, we observed that agents using mutual-assessment occurred only in a scenario with high risk of damage, low availability of resources, and with probability of reproduction without the resource. These results indicate that agents following the self-assessment with damage and non-aggressive strategies may be able to stay at most scenarios.
Metabolic dysregulation induces impaired lymphocyte memory formation during severe SARS-CoV-2 infection
Authors: Gurshaney Sanjeev , Alvarez Anamaria Morales , Ezhakunnel Kevin , Manalo Andrew , Huynh Thien-Huong , Le Nhat-Tu , Lupu Daniel S. , Gardell Stephen J. , Nguyen Hung
Published: December 2021

Cellular metabolic dysregulation is a consequence of COVID-19 infection that is a key determinant of disease severity. To understand the mechanisms underlying these cellular changes, we performed high-dimensional immune cell profiling of PBMCs from COVID-19-infected patients, in combination with single cell transcriptomic analysis of COVID-19 BALFs. Hypoxia, a hallmark of COVID-19 ARDS, was found to elicit a global metabolic reprogramming in effector lymphocytes. In response to oxygen and nutrient-deprived microenvironments, these cells shift from aerobic respiration to increase their dependence on anaerobic processes including glycolysis, mitophagy, and glutaminolysis to fulfill their bioenergetic demands. We also demonstrate metabolic dysregulation of ciliated lung epithelial cells is linked to significant increase of proinflammatory cytokine secretion and upregulation of HLA class 1 machinery. Augmented HLA class-1 antigen stimulation by epithelial cells leads to cellular exhaustion of metabolically dysregulated CD8 and NK cells, impairing their memory cell differentiation. Unsupervised clustering techniques revealed multiple distinct, differentially abundant CD8 and NK memory cell states that are marked by high glycolytic flux, mitochondrial dysfunction, and cellular exhaustion, further highlighting the connection between disrupted metabolism and impaired memory cell function in COVID-19. Our findings provide novel insight on how SARS-CoV-2 infection affects host immunometabolism and anti-viral response during COVID-19.

Graphical Abstract

Highlights

Hypoxia and anaerobic glycolysis drive CD8, NK, NKT dysfunction

Hypoxia and anaerobic glycolysis impair memory differentiation in CD8 and NK cells

Hypoxia and anaerobic glycolysis cause mitochondrial dysfunction in CD8, NK, NKT cells
Characterization of the interaction between SARS-CoV-2 Membrane Protein and Proliferating Cell Nuclear Antigen (PCNA) as a Potential Therapeutic Target
Authors: Zambalde Érika Pereira , Betim Pavan Isadora Carolina , Silva Mancini Mariana Camargo , Severino Matheus Brandemarte , Scudero Orlando Bonito , Morelli Ana Paula , Amorim Mariene Ribeiro , dos Santos Karina Bispo , Góis Mariana Marcela , de Toledo-Teixeira Daniel Augusto , Parise Pierina Lorencini , Mauad Thais , Dolhnikoff Marisa , Saldiva Paulo Hilário Nascimento , Marques-Souza Henrique , Proenca-Modena José Luiz , Ventura Armando Morais , Simabuco Fernando Moreira
Published: December 2021

SARS-CoV-2 is an emerging virus from the Coronaviridae family and is responsible for the ongoing COVID-19 pandemic. In this work, we explored the previously reported SARS-CoV-2 structural membrane protein (M) interaction with human Proliferating Cell Nuclear Antigen (PCNA). The M protein is responsible for maintaining virion shape, and PCNA is a marker of DNA damage which is essential for DNA replication and repair. We validated the M PCNA interaction through immunoprecipitation, immunofluorescence co-localization, and a PLA assay. In cells infected with SARS-CoV-2 or transfected with M protein, using immunofluorescence and cell fractioning, we documented a reallocation of PCNA from the nucleus to the cytoplasm and the increase of PCNA and γH2AX (another DNA damage marker) expression. We also observed an increase of PCNA and γH2AX expression in the lung of a COVID-19 patient by immunohistochemistry. In addition, the inhibition of PCNA translocation by PCNA I1 and Verdinexor led to a reduction of plaque formation in an in vitro assay. We, therefore, propose that the transport of PCNA to the cytoplasm and its association with M could be a virus strategy to manipulate cell functions and may be considered a target for COVID-19 therapy.
Insights on the mutational landscape of the SARS-CoV-2 Omicron variant
Authors: Miller Nathaniel L. , Clark Thomas , Raman Rahul , Sasisekharan Ram
Published: December 2021

The SARS-COV2 Omicron variant has sparked global concern due to the possibility of enhanced transmissibility and escape from vaccines and therapeutics. In this study, we describe the mutational landscape of the Omicron variant using amino acid interaction (AAI) networks. AAI network analysis is particularly well suited for interrogating the impact of constellations of mutations as occur on Omicron that may function in an epistatic manner. Our analyses suggest that as compared to previous variants of concern, the Omicron variant has increased antibody escapebreadthdue to mutations in class 3 and 4 antibody epitopes as well as increased escapedepthdue to accumulated mutations in class 1 antibody epitopes. We note certain RBD mutations that might further enhance Omicron’s escape, and in particular advise careful surveillance of two subclades bearing R346S/K mutations with relevance for certain therapeutic antibodies. Further, AAI network analysis suggests that the function of certain therapeutic monoclonal antibodies may be disrupted by Omicron mutations as a result of the cumulative indirect perturbations to the epitope surface properties, despite point-mutation analyses suggesting these antibodies are tolerant of the set of Omicron mutations in isolation. Finally, for several Omicron mutations that do not appear to contribute meaningfully to antibody escape, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBD-RBD interface.
A Quantitative Systems Pharmacology Model of the Pathophysiology and Treatment of COVID-19 Predicts Optimal Timing of Pharmacological Interventions
Authors: Rao Rohit , Musante Cynthia J. , Allen Richard
Published: December 2021

A quantitative systems pharmacology (QSP) model of the pathogenesis and treatment of SARS-CoV-2 infection can streamline and accelerate the development of novel medicines to treat COVID-19. Simulation of clinical trials allows in silico exploration of the uncertainties of clinical trial design and can rapidly inform their protocols. We previously published a preliminary model of the immune response to SARS-CoV-2 infection. To further our understanding of COVID-19 and treatment we significantly updated the model by matching a curated dataset spanning viral load and immune responses in plasma and lung. We identified a population of parameter sets to generate heterogeneity in pathophysiology and treatment and tested this model against published reports from interventional SARS-CoV-2 targeting Ab and anti-viral trials. Upon generation and selection of a virtual population, we match both the placebo and treated responses in viral load in these trials. We extended the model to predict the rate of hospitalization or death within a population. Via comparison of the in silico predictions with clinical data, we hypothesize that the immune response to virus is log-linear over a wide range of viral load. To validate this approach, we show the model matches a published subgroup analysis, sorted by baseline viral load, of patients treated with neutralizing Abs. By simulating intervention at different timepoints post infection, the model predicts efficacy is not sensitive to interventions within five days of symptom onset, but efficacy is dramatically reduced if more than five days pass post-symptom onset prior to treatment.
Dimensionality and homogeneity of the Colombian version of the Cocaine Craving Questionnaire (CCQ-N-10)
Authors: Cassiani-Miranda Carlos Arturo , Scoppetta Orlando , Quintero-Gómez Tito Cesar , Arraut-Camargo Eduard , Castaño-Pérez Guillermo , Cabanzo-Arenas Diego Fernando , Campo-Arias Adalberto
Published: December 2021

Background and aim

It is essential to have a validated instrument to measure craving for cocaine use. However, in Colombia, there is no instrument to screen cocaine craving. The study aimed to determine the homogeneity and dimensionality of the CCQ-N-10 in patients with cocaine use disorder in Colombia.

Materials and methods

An adaptation and subsequent analysis of the psychometric properties of the CCQ-N-10 scale was carried out with 102 hospitalized or outpatient adults diagnosed with substance use disorders in addiction units in Bucaramanga, Colombia. Internal consistency and construct validity were estimated by confirmatory factor analysis and correlation analysis with scales with similar objectives.

Results

An omega coefficient of 0.93 was obtained, and adjustment indicators of the confirmatory model were acceptable (RMSEA of 0.08, CFI and TLI of 0.99) when two of the original scale items were removed from the original scale analysis.

Conclusions

This study shows that the craving scale reduced to eight items can be helpful to assess the construct in the Colombian population; However, the small sample size makes it challenging to carry out other analyzes to corroborate its psychometric properties.
Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York
Authors: Duerr Ralf , Dimartino Dacia , Marier Christian , Zappile Paul , Levine Samuel , François Fritz , Iturrate Eduardo , Wang Guiqing , Dittmann Meike , Lighter Jennifer , Elbel Brian , Troxel Andrea B. , Goldfeld Keith S. , Heguy Adriana
Published: December 2021

In 2021, Delta has become the predominant SARS-CoV-2 variant worldwide. While vaccines effectively prevent COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occur. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contribute to increased rates of breakthrough infections compared to unvaccinated controls. Here, we show a steep and near complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthroughs increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. Our data indicate a limited impact of vaccine escape in favor of Delta’s increased epidemic growth in times of waning vaccine protection.
Nonlinear dynamics in auditory cortical activity reveal the neural basis of perceptual warping in speech categorization
Authors: Carter Jared A. , Buder Eugene H. , Bidelman Gavin M.
Published: December 2021

Surrounding context influences speech listening, resulting in dynamic shifts to category percepts. To examine its neural basis, event-related potentials (ERPs) were recorded during vowel identification with continua presented in random, forward, and backward orders to induce perceptual nonlinearities. Behaviorally, sequential order shifted listeners’ categorical boundary vs. random delivery revealing perceptual warping (biasing) of the heard phonetic category dependent on recent stimulus history. ERPs revealed later (∼300 ms) activity localized to superior temporal and middle/inferior frontal gyri that predicted listeners’ hysteresis magnitudes. Findings demonstrate that top-down, stimulus history effects on speech categorization are governed by interactions between frontotemporal brain regions.
Trailing-edge zombie forests can increase population persistence in the face of climate change
Authors: Decker Robin R. , Baskett Marissa L. , Hastings Alan
Published: December 2021

Climate-driven habitat shifts pose challenges for dispersal-limited, late-maturing taxa such as trees. Older trees are often the most reproductive individuals in the population, but as habitats shift, these individuals can be left behind in the trailing range edge, generating “zombie forests” that may persist long after the suitable habitat has shifted. Are these zombie forests vestiges of ecosystems past or do they play an ecological role? To understand how zombie forests affect population persistence, we developed a spatially explicit, stage-structured model of tree populations occupying a shifting habitat. Our model shows that seed dispersal from zombie forests to the range core can considerably increase the maximum rate of climate change that a population can withstand. Moreover, the entire core population can ultimately descend from recruitment-limited zombie forests, highlighting their demographic value. Our results suggest that preserving trailing-edge zombie forests can greatly increase population persistence in the face of climate change.
High genetic diversity of bivalve transmissible neoplasia in the blue mussel Mytilus trossulus Gould from the subarctic Sea of Okhotsk
Authors: Skazina M.A. , Odintsova N.A. , Maiorova M.A. , Frolova L.T. , Dolganova I.A. , Regel K.V. , Strelkov P.P.
Published: December 2021

There are increasing findings of the bivalve transmissible neoplasia derived from the Pacific mussel Mytilus trossulus (MtrBTN) in populations of different Mytilus species worldwide. The Subarctic is an area where this disease has not yet been sought despite the fact that Mytilus spp. are widespread there, and M. trossulus itself is a boreal species. We used cytological and histological techniques to diagnose disseminated neoplasia in a sample of M. trossulus from Magadan in the subarctic Sea of Okhotsk. Neoplasia was identified in 11 of 214 mussels studied. Using mtDNA COI sequencing, we revealed genotypes identical or nearly identical to known MtrBTN ones in the hemolymph of most of the diseased mussels. Both MtrBTN evolutionary lineages have been identified, the widespread MtrBTN2, and MtrBTN1, so far only known from M. trossulus in British Columbia on the other side of the Pacific from Magadan. In addition, MtrBTN2 was represented by two common diverged mtDNA haplolineages. These conclusions have been confirmed for selected cancerous mussels by molecular cloning of COI and additional nuclear and mtDNA genes. On the background of high genetic diversity, different cancers were similar in terms of ploidy (range 4.0 - 5.8n) and nuclear to cell ratio. Our study provides the first description of neoplasia and MtrBTN in mussels from the Sea of Okhotsk and from the Subarctic, of both MtrBTN1 and MtrBTN2 in the same mussel population, and the first direct comparison between these transmissible cancers.
Single cell quantification of ribosome occupancy in early mouse development
Authors: Tonn Tori , Ozadam Hakan , Han Crystal , Segura Alia , Tran Duc , Catoe David , Salit Marc , Cenik Can
Published: December 2021

Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key regulatory mechanism of genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high coverage measurements enabled the first analysis of allele-specific ribosome engagement in early development and led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes. Finally, by integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle stage oocytes is the predominant determinant of protein abundance in the zygote. Taken together, these findings resolve the long-standing paradox of low correlation between RNA expression and protein abundance in early embryonic development. The novel Ribo-ITP approach will enable numerous applications by providing high coverage and high resolution ribosome occupancy measurements from ultra-low input samples including single cells.
Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells
Authors: Autio Matias I. , Motakis Efthymios , Perrin Arnaud , Amin Talal Bin , Tiang Zenia , Do Dang Vinh , Wang Jiaxu , Tan Joanna , Tan Wei Xuan , Keong Teo Adrian Kee , Foo Roger S.-Y.
Published: December 2021

Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites in vitro using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easy targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.
Time series scRNAseq analysis in mouse and human informs optimization of rapid astrocyte differentiation protocols
Authors: Frazel PW , Labib D , Fisher T , Brosh R , Pirianian N , Marchildon A , Boeke JD , Fossati V , Liddelow SA
Published: December 2021

Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence in the brain and spinal cord. Here we used single-cell RNA sequencing (scRNAseq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human induced pluripotent stem cells. We computationally identify candidate genes involved in fate specification of glia in both species, and report heterogeneous expression of astrocyte surface markers across differentiating cells. We then used our scRNAseq data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multiomic, dual single nuclei (sn)RNAseq/snATACseq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.
No evidence of fetal defects or anti-syncytin-1 antibody induction following COVID-19 mRNA vaccination
Authors: Lu-Culligan Alice , Tabachnikova Alexandra , Tokuyama Maria , Lee Hannah J. , Lucas Carolina , Monteiro Valter Silva , Muenker M. Catherine , Mohanty Subhasis , Huang Jiefang , Kang Insoo , Cruz Charles Dela , Farhadian Shelli , Campbell Melissa , Yildirim Inci , Shaw Albert C. , Ko Albert I. , Omer Saad B. , Iwasaki Akiko
Published: December 2021

The impact of coronavirus disease 2019 (COVID-19) mRNA vaccination on pregnancy and fertility has become a major topic of public interest. We investigated two of the most widely propagated claims to determine 1) whether COVID-19 mRNA vaccination of mice during early pregnancy is associated with an increased incidence of birth defects or growth abnormalities, and 2) whether COVID-19 mRNA-vaccinated human volunteers exhibit elevated levels of antibodies to the human placental protein syncytin-1. Using a mouse model, we found that intramuscular COVID-19 mRNA vaccination during early pregnancy at gestational age E7.5 did not lead to differences in fetal size by crown-rump length or weight at term, nor did we observe any gross birth defects. In contrast, injection of the TLR3 agonist and double-stranded RNA mimic polyinosinic-polycytidylic acid, or poly(I:C), impacted growth in utero leading to reduced fetal size. No overt maternal illness following either vaccination or poly(I:C) exposure was observed. We also found that term fetuses from vaccinated murine pregnancies exhibit high circulating levels of anti-Spike and anti-RBD antibodies to SARS-CoV-2 consistent with maternal antibody status, indicating transplacental transfer. Finally, we did not detect increased levels of circulating anti-syncytin-1 antibodies in a cohort of COVID-19 vaccinated adults compared to unvaccinated adults by ELISA. Our findings contradict popular claims associating COVID-19 mRNA vaccination with infertility and adverse neonatal outcomes.
Lysophosphatidylcholine induces heat pain hypersensitivity in obese mice fed with a high-fat diet through activation of peripheral Acid-Sensing Ion Channel 3
Authors: Ahmed Negm , Katharina Stobbe , Lucile Fleuriot , Delphine Debayle , Emmanuel Deval , Eric Lingueglia , Carole Rovere , Jacques Noel
Published: December 2021

Diet induced obesity is one of the major causes of obesity, which affects 13% of the world’s adult population. Obesity is correlated to chronic pain regardless of other components of the metabolic syndrome. Our study focuses on investigating the effect of high-fat diet induced obesity on peripheral sensory neurons activity and pain perception, followed by deciphering the underlying cellular and molecular mechanisms that involve Acid-Sensing Ion Channel 3 (ASIC3). We show here that heat sensitive C-fibers from mice made obese by consumption of a high-fat diet exhibited an increased activity during baseline and upon heating. Obese mice showed long-lasting heat pain hypersensitivity once obesity was well established, while mechanical sensitivity was not affected. We found that the serum of obese mice was enriched in lysophosphatidylcholine (LPC) species (LPC16:0, LPC18:0 and LPC18:1), which activate ASIC3 channels and increased peripheral neuron excitability. Genetic deletion and in vivo pharmacological inhibition of ASIC3 protected and rescued mice from obesity-induced thermal hypersensitivity. Our results identify ASIC3 channels in DRG neurons and circulating LPC species that activate them as a mechanism contributing to heat pain hypersensitivity associated with high-fat diet induced obesity.
Intermittent brain network reconfigurations and the resistance to social media influence
Authors: Pinto Italo’Ivo Lima Dias , Rungratsameetaweemana Nuttida , Flaherty Kristen , Periyannan Aditi , Meghdadi Amir , Richard Christian , Berka Chris , Bansal Kanika , Garcia Javier Omar
Published: December 2021

Since their development, social media has grown as a source of information and has a significant impact on opinion formation. Individuals interact with others and content via social media platforms in a variety of ways but it remains unclear how decision making and associated neural processes are impacted by the online sharing of informational content, from factual to fabricated. Here, we use EEG to estimate dynamic reconfigurations of brain networks and probe the neural changes underlying opinion change (or formation) within individuals interacting with a simulated social media platform. Our findings indicate that the individuals who changed their opinions are characterized by less frequent network reconfigurations while those who did not change their opinions tend to have more flexible brain networks with frequent reconfigurations. The nature of these frequent network configurations suggests a fundamentally different thought process between intervals in which individuals are easily influenced by social media and those in which they are not. We also show that these reconfigurations are distinct to the brain dynamics during an in-person discussion with strangers on the same content. Together, these findings suggest that brain network reconfigurations may not only be diagnostic to the informational context but also the underlying opinion formation.

Author Summary

Distinctive neural underpinnings of opinion formation and change during in-person and online social interactions are not well understood. Here, we analyze EEG recordings of the participants interacting with a simulated social media platform and during an in-person discussion using a network-based analysis approach. We show that the structure of network reconfigurations during these interactions is diagnostic of the opinion change and the context in which information was received.
Predicting the Toxicity of Druggable Proteins to Human Tissues
Authors: Hao Yun , Thangaraj Phyllis , Tatonetti Nicholas P.
Published: December 2021

Assessing in vivo tissue toxicity of therapeutic targets remains a major challenge in drug development and drug safety research. We developed TissueTox, an algorithm that learns from multi-omic features of a target protein and predicts toxicity in human body systems and tissues. Predicted TissueTox scores accurately differentiate drugs that failed clinical trials from those that succeeded, and, importantly, can be used to identify the tissues where toxic events occurred.
Molecular mechanism of claudin-15 strand flexibility
Authors: Fuladi Shadi , McGuinness Sarah , Shen Le , Weber Christopher R. , Khalili-Araghi Fatemeh
Published: December 2021

Claudins are one of the major components of tight junctions that play a key role in formation and maintaining epithelial barrier function. Tight junction strands are dynamic and capable of adapting their structure in response to large-scale tissue rearrangement and cellular movement. Here, we present molecular dynamics simulations of claudin-15 strands of up to 225 nm in length in two parallel lipid membranes and characterize their mechanical properties. The persistence length of claudin-15 strands is comparable with experiments leading to a curvature of 0.12 nm−1 at room temperature. Our results indicate that lateral flexibility of claudin strands is due to an interplay of three sets of interfacial interaction networks between four linear claudin strands in the membranes. In this model, claudins are assembled into interlocking tetrameric ion channels along the strand that slide with respect to each other as the strands curve over sub-micrometer length scales. These results suggest a novel molecular mechanism underlying claudin-15 strand flexibility. It also sheds light on the inter-molecular interactions and their role in maintaining epithelial barrier function.
The eukaryotic translation initiation factor eIF4E reprogrammes the splicing machinery and drives alternative splicing
Authors: Ghram Mehdi , Morris Gavin , Culjkovic-Kraljacic Biljana , Mars Jean-Clement , Gendron Patrick , Skrabanek Lucy , Revuelta Maria Victoria , Cerchietti Leandro , Guzman Monica L , Borden Katherine LB
Published: December 2021

Aberrant RNA splicing contributes to the pathogenesis of many malignancies including Acute Myeloid Leukemia (AML). While mutation is the best described mechanism underpinning aberrant splicing, recent studies show that predictions based on mutations alone likely underestimate the extent of this dysregulation. Here, we show that elevation of the eukaryotic translation initiation factor eIF4E reprogrammes splicing of nearly a thousand RNAs in model cell lines. Further, in AML patient specimens which did not harbour known splice factor mutations, ∼4000 transcripts were differentially spliced based on eIF4E levels and this was associated with poor prognosis. Inhibition of eIF4E in cell lines reverted the eIF4E-dependent splice events examined. Splicing targets of eIF4E act in biological processes consistent with its role in malignancy. This altered splicing program likely arose from eIF4E-dependent increases in the production of spliceosome components including SF3B1 and U2AF1 which are frequently mutated in AML. Notably, eIF4E did not drive mutation of these factors, only their production. eIF4E also physically associated with many splice factors including SF3B1, U2AF1, and UsnRNAs. Interestingly, eIF4E interacted with both pre-mRNA splicing substrates as well as the resulting product RNAs suggesting that eIF4E could chaperone RNAs throughout splicing as well as other aspects of post-splicing transcript regulation. Importantly, many eIF4E-dependent splice events differed from those arising from splice factor mutation and were more extensive highlighting that these splicing profiles arise from distinct, but potentially overlapping, mechanisms. In all, our studies provide a paradigm for how dysregulation of a single factor, eIF4E, can reprogramme splicing.
mCherry contains a fluorescent protein isoform that interferes with its reporter function
Authors: Fages-Lartaud Maxime , Tietze Lisa , Elie Florence , Lale Rahmi , Hohmann-Marriott Martin Frank
Published: December 2021

Fluorescent proteins are essential reporters in cell biology and molecular biology. Here, we reveal that red-fluorescent proteins possess an alternative translation initiation site that produces a short functional protein isoform. The short isoform creates significant background fluorescence that biases the outcome of expression studies. Our investigation identifies the short protein isoform, traces its origin, and determines the extent of the issue within the family of red fluorescent protein. Our analysis shows that the short isoform defect of the red fluorescent protein family may affect the interpretation of many published studies. Finally, we provide a re-engineered mCherry variant that lacks background expression as an improved tool for imaging and protein expression studies.
GOLDEN TANGERINE TOMATO ROOTS SHOW INCREASED ACCUMULATION OF ACYCLIC CAROTENOIDS, LESS ABSCISIC ACID, DROUGHT SENSITIVITY, AND IMPAIRED ENDOMYCORRHIZAL COLONIZATION
Authors: Nayak Jwalit J , Anwar Sidra , Krishna Priti , Chen Zhong-Hua , Plett Jonathan M. , Foo Eloise , Cazzonelli Christopher I.
Published: December 2021

Heirloom golden tomato fruit varieties are highly nutritious as they accumulate tetra-cis-lycopene, which has a higher bioavailability and recognised health benefits in treating anti-inflammatory diseases compared to all-trans-lycopene isomers found in red tomatoes. We investigated if photoisomerization of tetra-cis-lycopene occurs in roots of the goldentangerineMicro-Tom variety (tangmic), and how this affects root to shoot biomass, mycorrhizal colonization, abscisic acid accumulation, and responses to drought.tangmicplants grown in soil under glasshouse conditions displayed a reduction in height, number of flowers, fruit yield, and root length compared to wild type (WT). Soil inoculation withRhizophagus irregularisrevealed fewer arbuscules and other fungal structures in the endodermal cells of roots intangmicrelative to WT. The roots oftangmichyperaccumulated acycliccis-carotenes, while only trace levels of xanthophylls and abscisic acid were detected. In response to a water deficit, leaves from thetangmicplants displayed a rapid decline in maximum quantum yield of photosystem II compared to WT, indicating a defective root to shoot signalling response to drought. The lack of xanthophylls biosynthesis intangmicroots reduced abscisic acid levels, thereby likely impairing endomycorrhiza colonisation and drought-induced root to shoot signalling.

Research Highlights

Photoisomerization of prolycopene to lycopene is limited in root plastids.

Roots oftangerinereveal an important tissue sink to store micronutrients such as prolycopene.

Roots oftangerinelack ABA and show impaired mycorrhizal colonization.

Thetangerineplant is drought sensitive and has a smaller biomass as well as reduced yield.
Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and nucleosome assembly
Authors: Li Shuang , Shi Yan , Dang Yanna , Hu Bingjie , Xiao Lieying , Zhao Panpan , Wang Shaohua , Zhang Kun
Published: December 2021

Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during early embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and early embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in early embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in expression genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine early development.
Recut: a Concurrent Framework for Sparse Reconstruction of Neuronal Morphology
Authors: Marrett Karl , Zhu Muye , Chi Yuze , Choi Chris , Chen Zhe , Dong Hong-Wei , Park Chang Sin , Yang X. William , Cong Jason
Published: December 2021

Advancement in modern neuroscience is bottlenecked by neural reconstruction, a process that extracts 3D neuron morphology (typically in tree structures) from image volumes at the scale of hundreds of GBs. We introduce Recut, an automated and accelerated neural reconstruction pipeline, which provides a unified, and domain specific sparse data representation with 79× reduction in the memory footprint. Recut’s reconstruction can process 111 Kneurons/day or 79 TB/day on a 24-core workstation, placing the throughput bottleneck back on microscopic imaging time. Recut allows the full brain of a mouse to be processed in memory on a single server, at 89.5× higher throughput over existing I/O-bounded methods. Recut is also the first fully parallelized end-to-end automated reconstruction pipeline for light microscopy, yielding tree morphologies closer to ground truth than the state-of-the-art while removing involved manual steps and disk I/O overheads. We also optimized pipeline stages to linear algorithmic complexity for scalability in dense settings and allow the most timing-critical stages to optionally run on accelerated hardware.