bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive hearing aid benefit in children with mild/moderate hearing loss: A registered, double-blind, randomized clinical trial
Authors: Stewart Hannah J. , Cash Erin K. , Pinkl Joseph , von Mentzer Cecilia Nakeva ,   CCHMC Division of Audiology, Hunter Lisa L. , Moore David R.
Published: July 2021

Objectives

We completed a registered double-blind randomized control trial to compare acclimatization to two hearing aid algorithms by experienced pediatric hearing aid users with mild to moderate hearing loss. We hypothesized that extended use (up to 13 months) of the adaptive algorithm with integrated directionality and noise reduction, OpenSound Navigator (OSN), would result in improved performance compared to the control algorithm, omnidirectional (Omni), on auditory, cognitive and academic tasks.

Design

We recruited 42 children, aged 6 - 13 years old, through Cincinnati Children’s Hospital Medical Center’s Division of Audiology. Two children withdrew from the study due to noncompliance or discomfort. The remaining 40 children were paired by age (within one year) and hearing loss (level and configuration). The individuals from each pair were randomly assigned to a group: OSN (experimental) and Omni (control). Each child completed an audiology evaluation, hearing aid fitting, a follow up audiological appointment and two research visits up to 13 months apart. Research visit outcome measures covered speech perception (in quiet and in noise), novel grammar and word learning, cognition, academic ability and caregiver report of listening behaviours.

Results

The children with the experimental algorithm did not show improved performance on the outcome measures compared to the control algorithm. There was a significant relationship between age at first hearing aid use and Reading and Mathematical ability across all participants. Data from six children were not included in the analysis due to daily hearing aid usage of less than 6 hours.

Conclusions

Use of the experimental algorithm (OSN) neither enhanced nor reduced performance on auditory, cognitive and academic tasks compared to the control algorithm (Omni).
Paradoxical Sex-Specific Patterns of Autoantibodies Response to SARS-CoV-2 Infection
Authors: Liu Yunxian , Ebinger Joseph E. , Mostafa Rowann , Budde Petra , Gajewski Jana , Walker Brian , Joung Sandy , Wu Min , Bräutigam Manuel , Hesping Franziska , Schäfer Elena , Schubert Ann-Sophie , Zucht Hans-Dieter , Braun Jonathan , Melmed Gil Y. , Sobhani Kimia , Arditi Moshe , Van Eyk Jennifer E. , Cheng Susan , Fert-Bober Justyna
Published: July 2021

Background

Amidst the millions of individuals affected directly by the pandemic, pronounced sex differences in the susceptibility and response to SARS-CoV-2 infection remain poorly understood. Emerging evidence has highlighted the potential importance of autoimmune activation in modulating not only the acute response but also recovery trajectories following SARS-CoV-2 exposure. Given that immune-inflammatory activity can be sex-biased in the setting of severe COVID-19 illness, we deliberately examined sex-specific autoimmune reactivity to SARS-CoV-2 in the absence of extreme clinical disease.

Methods

We used a bead-based array containing over 90 autoantigens previously linked to a range of classic autoimmune diseases to assess autoantibody (AAB) titers in 177 participants. All participants had confirmed evidence of prior SARS-CoV-2 infection based on presence of positive anti-nucleocapsid IgG serology results (Abbott Diagnostics, Abbott Park, Illinois). We used multivariate analysis to determine whether sex-bias was associated with increased rates of AABs reactivity and symptom burden after SARS-CoV2 infection.

Results

82.4% of AABs reactivity was associated with being male compared to 17.6% with female. We found a diversity of AABs responses that exhibited sex-specific patterns of frequency distribution as well as associations with symptomatology and symptom burden.

Conclusion

Our results reveal a remarkable sex-specific prevalence and selectivity of AAB responses to SARS-CoV-2. Further understanding of the nature of triggered and persistent AAB activation among men and women exposed to SARS-CoV-2 will be essential for developing effective interventions against immune-mediated sequelae of COVID-19.
SARS-CoV-2 Spike Pseudoviruses: A Useful tool to study virus entry and address emerging neutralization escape phenotypes
Authors: Kalkeri Raj , Cai Zhaohui , Lin Shuling , Farmer John , Kuzmichev Yury V. , Koide Fusataka
Published: July 2021

SARS-CoV-2 genetic variants are emerging around the globe. Unfortunately, several SARS-CoV-2 variants, especially, variants of concern (VOC) are less susceptible to neutralization by the convalescent and post-vaccination sera, raising concerns of increased disease transmissibility and severity. Recent data suggests the SARS-CoV-2 neutralizing anti-body levels as a good correlate of vaccine mediated protection. However, currently used BSL3 based virus micro-neutralization (MN) assays are more laborious, time consuming and expensive, underscoring the need for BSL2 based, cost effective neutralization assays against SARS-CoV-2 variants. In light of this unmet need, we have developed a BSL2 pseudovirus based neutralization assay (PBNA) in cells expressing Angiotensin Converting Enzyme-2 (ACE2) receptor for SARS-CoV-2. The assay is reproducible (R2=0.96), demonstrates a good dynamic range and high sensitivity. Our data suggests that the biological Anti-SARS-CoV-2 research reagents such as NIBSC 20/130 show lower neutralization against B.1.351 RSA and B1.1.7 UK VOC, whereas a commercially available monoclonal antibody MM43 retains activity against both these variants. SARS-CoV-2 Spike Pseudovirus based neutralization assays for VOC would be useful tools to measure the neutralization ability of candidate vaccines in both preclinical models and clinical trials and further help develop effective prophylactic countermeasures against emerging neutralization escape phenotypes.
Post-COVID Syndrome. A Case Series and Comprehensive Review
Authors: Anaya Juan-Manuel , Rojas Manuel , Salinas Martha L. , Rodríguez Yhojan , Roa Geraldine , Lozano Marcela , Rodríguez-Jiménez Mónica , Montoya Norma , Zapata Elizabeth ,   Post-COVID study group, Monsalve Diana M , Acosta-Ampudia Yeny , Ramírez-Santana Carolina
Published: July 2021

The existence of a variety of symptoms with a duration beyond the acute phase of COVID-19, is referred to as post-COVID syndrome (PCS). We aimed to report a series of patients with PCS attending a Post-COVID Unit and offer a comprehensive review on the topic. Adult patients with previously confirmed SARS-CoV-2 infection were systematically assessed through a semi-structured and validated survey. Total IgG, IgA and IgM serum antibodies to SARS-CoV-2 were evaluated by an electrochemiluminescence immunoassay. A systematic review of the literature and meta-analysis were conducted, following PRISMA guidelines. Univariate and multivariate methods were used to analyze data. Out of a total of 100 consecutive patients, 53 were women, the median of age was 49 years (IQR: 37.8 to 55.3), the median of post-COVID time after the first symptoms was 219 days (IQR: 143 to 258), and 65 patients were hospitalized during acute COVID-19. Musculoskeletal, digestive (i.e., diarrhea) and neurological symptoms including depression (by Zung scale) were the most frequent observed in PCS patients. A previous hospitalization was not associated with PCS manifestation. Arthralgia and diarrhea persisted in more than 40% of PCS patients. The median of anti-SARS-CoV-2 antibodies was 866.2 U/mL (IQR: 238.2 to 1681). Despite this variability, 98 patients were seropositive. Based on autonomic symptoms (by COMPASS 31) two clusters were obtained with different clinical characteristics. Levels of anti-SARS-CoV-2 antibodies were not different between clusters. A total of 40 articles (11,196 patients) were included in the meta-analysis. Fatigue/muscle weakness, dyspnea, pain and discomfort, anxiety/depression and impaired concentration were presented in more than 20% of patients reported. In conclusion, PCS is mainly characterized by musculoskeletal, pulmonary, digestive and neurological involvement including depression. PCS is independent of severity of acute illness and humoral response. Long-term antibody responses to SARS-CoV-2 infection and a high inter-individual variability were confirmed. Future studies should evaluate the mechanisms by which SARS-CoV-2 may cause PCS and the best therapeutic options.

Highlights

PCS is mainly characterized by musculoskeletal, pulmonary, digestive and neurological involvement including depression.

PCS is independent of severity of acute illness and humoral immune response.

Autonomic symptoms may help to classify patients with PCS.

Long-term antibody responses to SARS-CoV-2 infection and a high inter-individual variability were confirmed.
Unnecessary antibiotic treatment of children hospitalized with RSV-bronchiolitis: risk factors and prescription patterns
Authors: Obolski Uri , Kassem Eias , Na’amnih Wasef , Tannous Shebly , Kagan Viktoria , Muhsen Khitam
Published: July 2021

Background

Respiratory syncytial virus (RSV) is a main cause of respiratory tract infections, especially affecting young children. Antibiotics are often unnecessarily prescribed for the treatment of RSV. Such treatments can have effects on antibiotic resistance in future bacterial infections of treated patients and the general population.

Objectives

We sought to understand the risk factors for and patterns of unnecessary antibiotic prescription in children with RSV.

Methods

In a single center retrospective study in Israel, we obtained data of children aged <2 years (n=1015) hospitalized for RSV-bronchiolitis during 2008-2018, and ascertained not to have bacterial coinfections. Antibiotic misuse was defined as prescription of antibiotics during hospitalization of the study population. Patient and clinical variables were assessed as predictors of unnecessary antibiotic treatment in a multivariable logistic regression model.

Results

Unnecessary antibiotic treatment rate of children infected with RSV and ascertained not to have a bacterial coinfection was estimated at 33.4% (95% CI 30.5%-36.4%). Increased likelihood of antibiotic misuse was associated with drawing bacterial cultures, and with variables indicative of a severe patient status: lower oxygen saturation, higher body temperature, tachypnea and prior recent emergency room visit. Older age and female sex were also associated with increased likelihood of unnecessary antibiotic treatment.

Conclusions

Unnecessary antibiotic treatment in RSV patients was highly common and may be largely attributed to the physicians’ perception of patients’ severity. Improving prescription guidelines, implementing antibiotic stewardship programs and utilizing decision support systems may help achieve a better balance between prescribing and withholding antibiotic treatment.
Artificial Intelligence-rationalized balanced PPARα/γ dual agonism resets the dysregulated macrophage processes in inflammatory bowel disease
Authors: Katkar Gajanan D. , Sayed Ibrahim M. , Anandachar Mahitha Shree , Castillo Vanessa , Vidales Eleadah , Toobian Daniel , Usmani Fatima , Sawires Joseph R. , Leriche Geoffray , Yang Jerry , Sandborn William J. , Das Soumita , Sahoo Debashis , Ghosh Pradipta
Published: July 2021

A computational platform, the Boolean network explorer (BoNE), has recently been developed to infuse AI-enhanced precision into drug discovery; it enables querying and navigating invariant Boolean Implication Networks of disease maps for prioritizing high-value targets. Here we usedBoNEto query an Inflammatory Bowel Disease (IBD)-map and prioritize a therapeutic strategy that involves dual agonism of two nuclear receptors, PPARα/γ. Balanced agonism of PPARα/γ was predicted to modulate macrophage processes, ameliorate colitis in network-prioritized animal models, ‘reset’ the gene expression network from disease to health, and achieve a favorable therapeutic index that tracked other FDA-approved targets. Predictions were validated using a balanced and potent PPARα/γ-dual agonist (PAR5359) in two pre-clinical murine models, i.e.,Citrobacter rodentium-induced infectious colitis and DSS-induced colitis. Using a combination of selective inhibitors and agonists, we show that balanced dual agonism promotes bacterial clearance more efficiently than individual agonists, bothin vivoandin vitro. PPARa is required and its agonism is sufficient to induce the pro-inflammatory cytokines and cellular ROS, which are essential for bacterial clearance and immunity, whereas PPARg-agonism blunts these responses, delays microbial clearance and induces the anti-inflammatory cytokine, IL10; balanced dual agonism achieved controlled inflammation while protecting the gut barrier and ‘reversal’ of the transcriptomic network. Furthermore, dual agonism reversed the defective bacterial clearance observed in PBMCs derived from IBD patients. These findings not only deliver a macrophage modulator for use as barrier-protective therapy in IBD, but also highlight the potential ofBoNEto rationalize combination therapy.
A Novel Proposal for an Index for Regional Cerebral Perfusion Pressure – A Theoretical Approach Using Fluid Dynamics
Authors: Kameyama Masashi , Momose Toshimitsu
Published: July 2021

Cerebral blood flow (CBF) / cerebral blood volume (CBV) ratio derived by [15O] H2O/ CO2 and CO positron emission tomography (PET) examination has been used empirically as an index for cerebral perfusion pressure (CPP). However, this equation lacks a theoretical basis and furthermore, has not been confirmed to be proportionate to CPP, as direct measurement of local CPP is not practical.

We have developed a new index for CPP using the Poiseuille equation based on a simple model. Our model suggests that CBF/CBV2 is proportionate to CPP and that it is mathematically a more accurate index than CBF/CBV.
The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities
Authors: Gundersen Madeleine Stenshorne , Morelan Ian , Andersen Tom , Bakke Ingrid , Vadstein Olav
Published: July 2021

Understanding how periodical disturbances affect the community assembly processes is vital for predicting temporal dynamics in microbial communities. The effect of dilutions as disturbances are poorly understood. We used a marine bacterial community to investigate the effect of disturbance (+/-) and carrying capacity (high/low) over 50 days in a dispersal-limited 2x2 factorial crossover study in triplicates. The community's disturbance regime was crossed halfway. We modelled the rate of change in community composition between replicates and used this rate to quantify selection and ecological drift. The disturbed communities increased in Bray-Curtis similarity with 0.011+/-0.0045 (Period 1) and 0.0092+/-0.0080 day-1 (Period 2), indicating that selection dominated community assembly. The undisturbed communities decreased in similarity at a rate of -0.015+/-0.0038 day-1 in Period 1 and were stable in Period 2 at 0.00050+/-0.0040 day-1, suggesting drift structured community assembly. Interestingly, carrying capacity had minor effects on community dynamics. This study is the first to show that stochastic effects are suppressed by periodical disturbances resulting in exponential growth periods due to density-independent biomass loss and resource input. The increased contribution of selection as a response to disturbances implies that ecosystem prediction is achievable.
Ecotoxicological effects of silver nanoparticles in marine mussels
Authors: Calisi A. , Lorusso C. , Gallego-Urrea J.A. , Hassellöv M. , Dondero F.
Published: July 2021

In the marine bioindicator species M. galloprovincialis Lam we predicted toxicity and bioaccumulation of 5 nm alkane-coated and 50 nm uncoated silver nanoparticles (AgNPs) along with Ag+, as a function of the actual dose level. We generated a time persistence model of silver concentration in seawater and used the Area Under the Curve (AUC) as independent variable in hazard assessment. This approach allowed us to evaluate unbiased ecotoxicological endpoints for acute (survival) and chronic toxicity (byssal adhesion). Logistic regression analysis rendered LC5096h values of 0.68 ± 0.08; 1.00 ± 0.20; 1.00 ± 0.42 mg h L−1 respectively for Ag+, 5 nm and 50 nm AgNP posing no evidence the silver form is a necessary variable to predict the survival outcome. By contrast, for byssal adhesion regression analysis revealed a much higher toxicological potential of Ag+ vs AgNPs, 0.0021 ± 0.0009; 0.053 ± 0.016; 0.021 (no computable error for 50 nm AgNP) mg h L−1, and undoubtedly confirmed a role of the silver form.

Bioaccumulation was higher for Ag+ > 5 nm AgNP > 50 nm AgNP reflecting a parallel with the preferential uptake route / target organ.

We, eventually, provided a full range of toxicological endpoints to derive risk quotients.
Singlet oxygen leads to structural changes to chloroplasts during degradation in the Arabidopsis thaliana plastid ferrochelatase two mutant
Authors: Fisher Karen E. , Krishnamoorthy Praveen , Joens Matthew S. , Chory Joanne , Fitzpatrick James A. J. , Woodson Jesse D.
Published: July 2021

During photosynthesis, chloroplasts can produce large amounts of reactive oxygen species (ROS), particularly under stressful conditions. Along with other nutrients, chloroplasts also contain 80% of a leaf’s nitrogen supply. For these reasons, chloroplasts are prime targets for cellular degradation to protect cells from photo-oxidative damage and to redistribute nutrients to sink tissues. Multiple chloroplast degradation pathways have been described and are induced by photo-oxidative stress and nutrient starvation. However, the mechanisms by which damaged or senescing chloroplasts are identified, transported to the central vacuole, and ultimately degraded are not well characterized. Here, we investigated the subcellular structures involved with degrading chloroplasts induced by the ROS singlet oxygen (1O2) in the Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant. Using a three-dimensional serial-block face electron microscopy analysis, we show up to 35% of degrading chloroplasts in fc2 mutants protrude into the central vacuole. While the location of a chloroplast within a cell had no effect on the likelihood of its degradation, chloroplasts in spongy mesophyll cells were degraded at a higher rate than those in palisade mesophyll cells. To determine if degrading chloroplasts have unique structural characteristics allowing them to be distinguished from healthy chloroplasts, we analyzed fc2 seedlings grown under different levels of photo-oxidative stress. A clear correlation was observed between chloroplast swelling, 1O2-signaling, and the state of degradation. Finally, plastoglobule enzymes involved in chloroplast disassembly were shown to be upregulated while plastoglobules increased their association with the thylakoid grana, implicating an interaction between 1O2-induced chloroplast degradation and senescence pathways.
Absolute copy number fitting from shallow whole genome sequencing data
Authors: Sauer Carolin M , Eldridge Matthew D , Vias Maria , Hall James A , Boyle Samantha , Macintyre Geoff , Bradley Thomas , Markowetz Florian , Brenton James D
Published: July 2021

Low-coverage or shallow whole genome sequencing (sWGS) approaches can efficiently detect somatic copy number aberrations (SCNAs) at low cost. This is clinically important for many cancers, in particular cancers with severe chromosomal instability (CIN) that frequently lack actionable point mutations and are characterised by poor disease outcome. Absolute copy number (ACN), measured in DNA copies per cancer cell, is required for meaningful comparisons between copy number states, but is challenging to estimate and in practice often requires manual curation. Using a total of 60 cancer cell lines, 148 patient-derived xenograft (PDX) and 142 clinical tissue samples, we evaluate the performance of available tools for obtaining ACN from sWGS. We provide a validated and refined tool called Rascal (relative to absolute copy number scaling) that provides improved fitting algorithms and enables interactive visualisation of copy number profiles. These approaches are highly applicable to both pre-clinical and translational research studies on SCNA-driven cancers and provide more robust ACN fits from sWGS data than currently available tools.
Distinct but cooperating brain networks supporting semantic cognition
Authors: Jung JeYoung , Lambon Ralph Matthew A.
Published: July 2021

Semantic cognition is a complex brain function involving multiple processes from sensory systems, semantic systems, to domain-general cognitive systems, reflecting its multifaceted nature. However, it remain unclear how these systems cooperate with each other to achieve effective semantic cognition. Here, we investigated the neural networks involved in semantic cognition using independent component analysis (ICA). We used a semantic judgement task and a pattern matching task as a control task with two levels of difficulty to disentangle task-specific networks from domain-general networks and to delineate task-specific involvement of these networks. ICA revealed that semantic processing recruited two task-specific networks (semantic network [SN] and extended semantic network [ESN]) as well as domain general networks including the frontoparietal network (FPN) and default mode network (DMN). Specifically, two distinct semantic networks were differently modulated by task difficulty. The SN was coupled with the extended semantic network and FPN but decoupled with the DMN, whereas the ESN was synchronised with the FPN and DMN. Furthermore, the degree of decoupling between the SN and DMN was associated with semantic performance. Our findings suggest that human higher cognition is achieved by the neural dynamics of brain networks, serving distinct and shared cognitive functions depending on task demands.
Paninvasion severity assessment of a U.S. grape pest to disrupt the global wine market
Authors: Huron Nicholas A. , Behm Jocelyn E. , Helmus Matthew R.
Published: July 2021

Economic impacts from plant pests are often felt at the regional scale, yet some impacts expand to the global scale through the alignment of a pest’s invasion potentials. Such globally invasive species (i.e., paninvasives) are like the human pathogens that cause pandemics. Like pandemics, assessing paninvasion risk for an emerging regional pest is key for stakeholders to take early actions that avoid market disruption. Here, we develop the paninvasion severity assessment framework and use it to assess a rapidly spreading regional U.S. grape pest, the spotted lanternfly planthopper(Lycorma delicatula;SLF), to spread and disrupt the global wine market. We found that SLF invasion potentials are aligned globally because important viticultural regions with suitable environments for SLF establishment also heavily trade with invaded U.S. states. If the U.S. acts as an invasive bridgehead, Italy, France, Spain, and other important wine exporters are likely to experience the next SLF introductions. Risk to the global wine market is high unless stakeholders work to reduce SLF invasion potentials in the U.S. and globally.
Comparison of Neutralizing Antibody Titers Elicited by mRNA and Adenoviral Vector Vaccine against SARS-CoV-2 Variants
Authors: Tada Takuya , Zhou Hao , Samanovic Marie I. , Dcosta Belinda M. , Cornelius Amber , Mulligan Mark J. , Landau Nathaniel R.
Published: July 2021

The increasing prevalence of SARS-CoV-2 variants has raised concerns regarding possible decreases in vaccine efficacy. Here, neutralizing antibody titers elicited by mRNA-based and an adenoviral vector-based vaccine against variant pseudotyped viruses were compared. BNT162b2 and mRNA-1273-elicited antibodies showed modest neutralization resistance against Beta, Delta, Delta plus and Lambda variants whereas Ad26.COV2.S-elicited antibodies from a significant fraction of vaccinated individuals were of low neutralizing titer (IC50 <50). The data underscore the importance of surveillance for breakthrough infections that result in severe COVID-19 and suggest the benefit of a second immunization following Ad26.COV2.S to increase protection against the variants.
Emergence and fragmentation of the alpha-band driven by neuronal network dynamics
Authors: Zonca Lou , Holcman David
Published: July 2021

Rhythmic neuronal network activity underlies brain oscillations. To investigate how connected neuronal networks contribute to the emergence of the α-band and the regulation of Up and Down states, we study a model based on synaptic short-term depression-facilitation with afterhyperpolarization (AHP). We found that the α-band is generated by the network behavior near the attractor of the Up-state. Coupling inhibitory and excitatory networks by reciprocal connections leads to the emergence of a stable α-band during the Up states, as reflected in the spectrogram. To better characterize the emergence and stability of thalamocortical oscillations containing α and δ rhythms during anesthesia, we model the interaction of two excitatory with one inhibitory networks, showing that this minimal network topology leads to a persistent α-band in the neuronal voltage characterized by dominant Up over Down states. Finally, we show that the emergence of the α-band appears when external inputs are suppressed, while the fragmentation occurs at small synaptic noise or with increasing inhibitory inputs. To conclude, interaction between excitatory neuronal networks with and without AHP seems to be a general principle underlying changes in network oscillations that could apply to other rhythms.

Author summary

Brain oscillations recorded from electroencephalograms characterize behaviors such as sleep, wakefulness, brain evoked responses, coma or anesthesia. The underlying rhythms for these oscillations are associated at a neuronal population level to fluctuations of the membrane potential between Up (depolarized) and Down (hyperpolarized) states. During anesthesia with propofol, a dominant alpha-band (8-12Hz) can emerge or disappear, but the underlying mechanisms remain unclear. Using modeling, we report that the alpha-band appears during Up states in neuronal populations driven by short-term synaptic plasticity and noise. Moreover, we show that three connected networks representing the thalamocortical loop reproduce the dynamics of the alpha-band, which emerges following the arrest of excitatory stimulations, but can disappear by increasing inhibitory inputs. To conclude, short-term plasticity in well connected neuronal networks can explain the emergence and fragmentation of the alpha-band.
Small-molecule cocktails induce the differentiation of human adipose-derived mesenchymal stem cells into hepatocyte-like cells
Authors: Yin Kan , Xu Yang , Wu Di , Yang Weiyan , Dong Naijun , Li Ning , Zhao Robert Chunhua
Published: July 2021

At present, liver transplantation and hepatocyte therapy are common methods for the treatment of end-stage liver diseases, but they are restricted due to the shortage of liver donors and the safety and effectiveness of hepatocyte sources. Human adipose-derived mesenchymal stem cells (HAD-MSCs) have been applied to efficiently and stably induce phenotypic and functional liver cells or tissues in vitro due to their advantages such as wide sources and easy access to materials. In this study, the HAD-MSCs liver differentiation induction system was established and optimized based on the “cocktail method” of chemical small molecule compounds. We used HAD-MSCs as seed cells and gradually obtained mature hepatoid cells with normal phenotype and function after induction with small molecule compounds and growth factor system in vitro. The hepatoid cells induced by the two groups showed high similarity in phenotype and functional characteristics of mature hepatocytes. The differentiation system of human adipose mesenchymal stem cells into hepatocytes induced by small-molecule compounds in vitro was successfully constructed. This study will lay a foundation for the optimization of liver differentiation strategies and provide a reliable source of functional liver cells for clinical studies of liver diseases.
Structural model of PORCN illuminates disease-associated variants and drug binding sites
Authors: Yu Jia , Liao Pei Ju , Xu Weijun , Jones Julie R. , Everman David B. , Flanagan-Steet Heather , Keller Thomas H. , Virshup David M.
Published: July 2021

Wnt signaling is essential for normal development and is a therapeutic target in cancer. The enzyme PORCN, or porcupine, is a membrane-bound O-acyltransferase (MBOAT) that is required for the post-translational modification of all Wnts, adding an essential mono-unsaturated palmitoleic acid to a serine on the tip of Wnt hairpin 2. Inherited mutations in PORCN cause focal dermal hypoplasia, and therapeutic inhibition of PORCN slows the growth of Wnt-dependent cancers. Here, based on homology to mammalian MBOAT proteins we develop and validate a molecular structural model of PORCN. The model accommodates palmitoleoyl-CoA and Wnt hairpin 2 in two tunnels in the conserved catalytic core, shedding light on the catalytic mechanism. The model predicts how previously uncharacterized human variants of uncertain significance can alter PORCN function. Drugs including ETC-159, IWP-L6 and LGK-974 dock in the PORCN catalytic site, providing insights into PORCN pharmacologic inhibition. This structural model provides mechanistic insights into PORCN substrate recognition and catalysis as well as the inhibition of its enzymatic activity and can facilitate the development of improved inhibitors and the understanding of disease relevant PORCN mutants.
A novel nanoluciferase transgenic reporter to measure proteinuria in zebrafish
Authors: Naylor Richard W. , Lemarie Emmanuel , Jackson-Crawford Anthony , Bernard Davenport J. , Mironov Aleksandr , Lowe Martin , Lennon Rachel
Published: July 2021

The zebrafish is an important animal system for modelling human diseases. This includes kidney dysfunction as the embryonic kidney (pronephros) shares considerable molecular and morphological homology with the human nephron. Zebrafish also have a high fecundity, with females capable of laying 200-300 eggs per week, thereby facilitating chemical and mutation screening. A key clinical indicator of kidney disease is proteinuria, but a high-throughput readout of proteinuria in the zebrafish is lacking. Coupling the advantages of the zebrafish system with a tool to measure proteinuria will advance the scope for testing the efficacy of drugs to treat kidney diseases. Here, we generated a stable transgenic zebrafish line using the l-fabp10 liver-specific promoter to over-express a nanoluciferase molecule fused with the D3 domain of Receptor-Associated-Protein (RAP) to create NL-D3. In the healthy state, NL-D3 is excreted, but when embryos were treated with chemicals that affected either proximal tubular reabsorption (cisplatin, gentamicin) or glomerular filtration (angiotensin II, Hanks Balanced Salt Solution, Bovine Serum Albumin), NL-D3 presence in the urine increased. Similarly, depletion of several gene products associated with kidney disease (nphs1, nphs2, lrp2a, ocrl, col4a3, col4a4, and col4a5) also induced NL-D3 proteinuria. Furthermore, we found that treating col4a4 depleted zebrafish larvae (a model of Alport syndrome) with captopril reduced proteinuria. Our findings confirm the use of the NL-D3 transgenic zebrafish as a robust and quantifiable proteinuria reporter. Given the feasibility of high-throughput assays in zebrafish, this novel reporter will permit screening for drugs that ameliorate proteinuria and thereby prioritise candidates for further translational studies.

Significance Statement

The zebrafish has become an important system for modelling kidney disease. However, proteinuria, an important clinical indicator of kidney dysfunction, is not easily detected in zebrafish. Here, we describe a transgenic line that uses a nanoluciferase reporter to enable detection of proteinuria in multiple models of glomerular and proximal tubular kidney disease in the zebrafish. In this system proteinuria can be accurately measured in a high-throughput manner and will enable the screening of drugs that affect glomerular filtration or protein re-uptake in the proximal tubule.
Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells
Authors: Rothenburger Tamara , Thomas Dominique , Schreiber Yannick , Wratil Paul R. , Pflantz Tamara , Knecht Kirsten , Digianantonio Katie , Temple Joshua , Schneider Constanze , Baldauf Hanna-Mari , McLaughlin Katie-May , Rothweiler Florian , Bilen Berna , Farmand Samira , Bojkova Denisa , Costa Rui , Ferreirós Nerea , Geisslinger Gerd , Oellerich Thomas , Xiong Yong , Keppler Oliver T. , Wass Mark N. , Michaelis Martin , Cinatl Jindrich
Published: July 2021

Background

SAMHD1 mediates resistance to anti-cancer nucleoside analogues, including cytarabine, decitabine, and nelarabine that are commonly used for the treatment of leukaemia, through cleavage of their triphosphorylated forms. Hence, SAMHD1 inhibitors are promising candidates for the sensitisation of leukaemia cells to nucleoside analogue-based therapy. Here, we investigated the effects of the cytosine analogue CNDAC, which has been proposed to be a SAMHD1 substrate, in the context of SAMHD1.

Methods

CNDAC was tested in 13 acute myeloid leukaemia (AML cell lines), in 26 acute lymphoblastic leukaemia cell lines, ten AML sublines adapted to various antileukaemic drugs, 24 single cell-derived clonal AML sublines, and primary leukaemic blasts from 24 AML patients. Moreover, 24 CNDAC-resistant sublines of the AML cell lines HL-60 and PL-21 were established. The SAMHD1 gene was disrupted using CRISPR/Cas9 and SAMHD1 depleted using RNAi, and the viral Vpx protein. Forced DCK expression was achieved by lentiviral transduction. SAMHD1 promoter methylation was determined by PCR after treatment of genomic DNA with the methylation-sensitive HpaII endonuclease. Nucleoside (analogue) triphosphate levels were determined by LC-MS/MS. CNDAC interaction with SAMHD1 was analysed by an enzymatic assay and by crystallisation.

Results

Although the cytosine analogue CNDAC was anticipated to inhibit SAMHD1, SAMHD1 mediated intrinsic CNDAC resistance in leukaemia cells. Accordingly, SAMHD1 depletion increased CNDAC triphosphate (CNDAC-TP) levels and CNDAC toxicity. Enzymatic assays and crystallisation studies confirmed CNDAC-TP to be a SAMHD1 substrate. In 24 CNDAC-adapted acute myeloid leukaemia (AML) sublines, resistance was driven by DCK (catalyses initial nucleoside phosphorylation) loss. CNDAC-adapted sublines displayed cross-resistance only to other DCK substrates (e.g. cytarabine, decitabine). Cell lines adapted to drugs not affected by DCK or SAMHD1 remained CNDAC sensitive. In cytarabine-adapted AML cells, increased SAMHD1 and reduced DCK levels contributed to cytarabine and CNDAC resistance.

Conclusion

Intrinsic and acquired resistance to CNDAC and related nucleoside analogues are driven by different mechanisms. The lack of cross-resistance between SAMHD1/ DCK substrates and non-substrates provides scope for next-line therapies after treatment failure.
Ultra-lightweight living structural material for enhanced stiffness and environmental sensing
Authors: Park Heechul , Schwartzman Alan F. , Tang Tzu-Chieh , Wang Lei , Lu Timothy K.
Published: July 2021

Natural materials such as bone, wood, and bamboo can inspire the fabrication of stiff, lightweight structural materials. Biofilms are one of the most dominant forms of life in nature. However, little is known about their physical properties as a structural material. Here we report an Escherichia coli biofilm having a Young’s modulus close to 10 GPa with ultra-low density, indicating a high-performance structural material. The mechanical and structural characterization of the biofilm and its components illuminates its adaptable bottom-up design, consisting of lightweight microscale cells covered by a dense network of amyloid nanofibrils on the surface. We engineered E. coli such that 1) carbon nanotubes assembled on the biofilm, enhancing its stiffness to over 30 GPa, or that 2) the biofilm sensitively detected heavy metal as an example of an environmental toxin. These demonstrations offer new opportunities for developing responsive living structural materials to serve many real-world applications.
Profiling of human neural crest chemoattractant activity as replacement of fetal bovine serum for in vitro chemotaxis assays
Authors: Dolde Xenia , Karreman Christiaan , Wiechers Marianne , Schildknecht Stefan , Leist Marcel
Published: July 2021

Fetal bovine serum (FBS) is the only known stimulus for migration of human neural crest cells (NCCs). Non-animal chemoattractants are desirable for the optimization of chemotaxis assays to be incorporated in a test battery for reproductive and developmental toxicity. We confirmed here in an optimized transwell assay that FBS triggers directed migration along a concentration gradient. The responsible factor was found to be a protein in the 30-100 kDa size range. In a targeted approach, we tested a large panel of serum constituents known to be chemotactic for NCCs in animal models (e.g. VEGF, PDGF, FGF, SDF-1/CXCL12, ephrins, endothelin, Wnt, BMPs). None of the corresponding human proteins showed any effect in our chemotaxis assays based on human NCCs. We then examined, whether human cells would produce any factor able to trigger NCC migration in a broad screening approach. We found that HepG2 hepatoma cells produced chemotaxis-triggering activity (CTA). Using chromatographic methods and by employing the NCC chemotaxis test as bioassay, the responsible protein was enriched by up to 5000-fold. We also explored human serum and platelets as direct source, independent of any cell culture manipulations. A CTA was enriched from platelet lysates several thousand-fold. Its temperature and protease- sensitivity suggested also a protein component. The capacity of this factor to trigger chemotaxis was confirmed by single-cell video-tracking analysis of migrating NCCs. The human CTA characterized here may be employed in the future for the setup of assays testing for the disturbance of directed NCC migration by toxicants.
Megasatellite formation and evolution in vertebrates
Authors: Descorps-Declère Stéphane , Richard Guy-Franck
Published: July 2021

Since the formation of the first proto-eukaryotes, more than 1.5 billion years ago, eukaryotic gene repertoire as well as genome complexity has significantly increased. Among genetic elements that are responsible for this increase in genome coding capacity and plasticity are tandem repeats such as microsatellites, minisatellites and their bigger brothers, megasatellites. Although microsatellites have been thoroughly studied in many organisms for the last 20 years, little is known about the distribution and evolution of mini- and megasatellites. Here, we describe the first genome-wide analysis of megasatellites in 58 vertebrate genomes, belonging to 12 monophyletic groups. We show that two bursts of megasatellite formation occurred, one after the radiation between agnatha et gnathostomata fishes and the second one later, in therian mammals. Megasatellites are frequently encoded in genes involved in transcription regulation (zinc-finger proteins) and intracellular trafficking, but also in cell membrane metabolism, reminiscent of what was observed in fungi genomes. The presence of many introns within young megasatellites suggests a model in which an exon-intron DNA segment is first duplicated and amplified before the accumulation of mutations in intronic parts partially erase the tandem repeat in such a way that it becomes detectable only in exonic regions. In addition, evidence for the genetic transfer of megasatellites between unrelated genes suggests that megasatellite formation and evolution is a very dynamic and still ongoing process in vertebrate genomes.
Integrative multi-omics landscape of non-structural protein 3 of severe acute respiratory syndrome coronaviruses
Authors: Shi Ruona , Feng Zhenhuan , Zhang Xiaofei
Published: July 2021

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is currently a global pandemic. Extensive investigations have been performed to study the clinical and cellular effects of SARS-CoV-2 infection. Mass spectrometry-based proteomics studies have revealed the cellular changes due to the infection and identified a plethora of interactors for all SARS-CoV-2 components, except for the longest non-structural protein 3 (NSP3). Here, we expressed the full-length NSP3 proteins of SARS-CoV and SARS-CoV-2 to investigate their unique and shared functions using multi-omics methods. We conducted interactome, phosphoproteome, ubiquitylome, transcriptome, and proteome analyses of NSP3-expressing cells. We found that NSP3 plays essential roles in cellular functions such as RNA metabolism and immune response such as NF-kB signal transduction. Interestingly, we showed that SARS-CoV-2 NSP3 has both endoplasmic reticulum and mitochondrial localizations. In addition, SARS-CoV-2 NSP3 is more closely related to mitochondrial ribosomal proteins, whereas SARS-CoV NSP3 is related to the cytosolic ribosomal proteins. In summary, our multi-omics studies of NSP3 enhance our understanding of the functions of NSP3 and offer valuable insights for the development of anti-SARS strategies.
Plasticity of the dopaminergic phenotype and of locomotion in larval zebrafish induced by changes in brain excitability during the embryonic period
Authors: Bataille Sandrine , Jalaber Hadrien , Colin Ingrid , Remy Damien , Affaticati Pierre , Froc Cynthia , Vernier Philippe , Demarque Michaël
Published: July 2021

During the embryonic period, neuronal communication starts before the establishment of the synapses with alternative forms of neuronal excitability, called here Embryonic Neuronal Excitability (ENE). ENE has been shown to modulate the unfolding of development transcriptional programs but the global consequences for the developing organisms are not all understood. Here we monitored calcium transients in zebrafish embryos as a proxy for ENE to assess the efficacy of transient pharmacological treatments to either increase or decrease ENE. Increasing or decreasing ENE for 24 hours at 2 days post fertilization (dpf), at the end of the embryonic period, promoted respectively an increase or a decrease in the numbers of dopamine (DA) neurons in the telencephalon and in the olfactory bulb of zebrafish larvæ at 6 dpf. This plasticity of dopaminergic specification occurs within a stable population of vMAT2-positive cells, hence identifying an unanticipated biological marker for this reserve pool of of DA neurons that can be recruited by increasing ENE.

Modulating ENE also affected larval locomotion several days after the end of the treatments. In particular, the increase of ENE from 2 to 3 dpf promoted hyperlocomotion of larvæ at 6 dpf, reminiscent of endophenotypes reported for Attention Deficit with Hyperactivity Disorders and schizophrenia in zebrafish. These results provide a convenient framework to identify environmental factors that could disturb ENE as well as to study the molecular mechanisms linking ENE to neurotransmitter specification, with relevance to the pathogenesis of neurodevelopmental disorders.

Significance Statement

- Spontaneous calcium transients, used as a proxy for Embryonic Neuronal Excitability (ENE), are detected in the forebrain of embryonic zebrafish.

- Short-term pharmacological treatments by bath application could increase or decrease ENE.

- The post-mitotic differentiation of the dopaminergic phenotype is modulated by ENE in the zebrafish forebrain.

- The plasticity of the dopaminergic specification occurs within a reserve pool of vMAT2-positive cells.

- Transient increase of ENE at the end of the embryonic period induces hyperlocomotion, a phenotype associated with ADHD and schizophrenia in this model.

- Our results open clinically relevant perspectives to study the pathogenesis of neurodevelopmental disorders in zebrafish.
Rosin Soap Exhibits Virucidal Activity
Authors: Bell Stephen H , Fairley Derek J , Kettunen Hannele , Vuorenmaa Juhani , Orte Juha , Bamford Connor G G , McGrath John W
Published: July 2021

Chemical methods of virus inactivation are used routinely to prevent viral transmission in both a personal hygiene capacity but also in at-risk environments like hospitals. Several ‘virucidal’ products exist, including hand soaps, gels and surface disinfectants. Resin acids, which can be derived from Tall oil produced from trees, have been shown to exhibit anti-bacterial activity. However, whether these products or their derivatives have virucidal activity is unknown. Here, we assessed the capacity of Rosin soap to inactivate a panel of pathogenic mammalian viruses in vitro. We show that Rosin soap can inactivate the human enveloped viruses: influenza A virus (IAV), respiratory syncytial virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For IAV, rosin soap could provide a 100,000-fold reduction in infectivity. However, Rosin soap failed to affect the non-enveloped encephalomyocarditis virus (EMCV). The inhibitory effect of Rosin soap against IAV infectivity was dependent on its concentration but not dependent on incubation time nor temperature. Together, we demonstrate a novel chemical inactivation method against enveloped viruses, which could be of use in preventing virus infections in certain settings.

Importance

Viruses remain a significant cause of human disease and death, most notably illustrated through the current Covid-19 pandemic. Control of virus infection continues to pose a significant global health challenge to the human population. Viruses can spread through multiple routes, including via environmental and surface contamination where viruses can remain infectious for days. Methods to inactivate viruses on such surfaces may help mitigate infection. Here we present evidence identifying a novel ‘virucidal’ product in Rosin soap, which is produced from Tall oil from coniferous trees. Rosin soap was able to rapidly and potently inactivate influenza virus and other enveloped viruses.