bluuebunny/crossref_metadata_2025 huggingface dataset:
More severe pneumonitis in children predicts the need for admission and elevation of some but not all markers of severe Covid-19
Authors: Walsh Paul , Hankins Andrea , Bang Heejung
Published: March 2022

Unlike most other viral pneumonitis, SARS-CoV-2 often causes hyperferritinemia, elevations in D-dimer, lactate dehydrogenase (LDH), transaminases, troponin, CRP, and other inflammatory markers. We questioned (1) if the severity of pneumonitis observed on lung ultrasound was associated with hospitalization and (2) could lung ultrasound be used to stratify which children needed blood tests?

Methods

We did a retrospective cross-sectional review of children aged between 14 days and 21 years of age being evaluated for Covid-19 in our pediatric emergency department from 30/November/2019 to 14/August/2021 who had had a point-of-care lung ultrasound. Lung ultrasounds were categorized using a 6-point ordinal scale. We used logistic regression to estimate the adjusted effect of lung ultrasound on hospital admission. We performed ordinary least square regression for the association between lung ultrasound severity and laboratory abnormalities. We adjusted these using propensity score derived inverse probability weighting to account for the non-random decision to obtain laboratory investigations.

Results

We identified 500 point-of-care lung ultrasounds of which 427 could be assigned a severity category. Increasing lung ultrasound severity was associated with increased hospital admission OR 1.36(95% CI 1.08, 1.72.) Ferritin, LDH, transaminases, and D-dimer, but not CRP or troponin were significantly associated with more than moderately severe lung ultrasounds. D-Dimer, CRP, and troponin were sometimes elevated even when lung ultrasound was normal.

Conclusion

Severity of pneumonitis was associated with hospital admission. Ferritin, LDH, transaminases, and D-dimer were increased in more than moderately severe pneumonitis but lung ultrasound did not predict elevation of other markers.
Electrocardiography-Based Prediction of Sudden Cardiac Death in Heart Failure Patients: Application of Artificial Intelligence
Authors: Shiraishi Yasuyuki , Goto Shinichi , Niimi Nozomi , Katsumata Yoshinori , Goda Ayumi , Takei Makoto , Saji Mike , Nishihata Yosuke , Sano Motoaki , Fukuda Keiichi , Kohno Takashi , Yoshikawa Tsutomu , Kohsaka Shun
Published: March 2022

Background

Although predicting sudden cardiac death (SCD) in patients with heart failure (HF) is critical, the current predictive model is suboptimal. Electrocardiography-based artificial intelligence (ECG-AI) algorithms may better stratify risk. We assessed whether the ECG-AI index established here could better predict SCD in HF and whether the ECG-AI index and conventional predictors of SCD can improve SCD stratification.

Methods

In a prospective observational study, four tertiary care hospitals in metropolitan Tokyo that enrolled 2,559 patients hospitalized with HF who were successfully discharged after acute decompensation. ECG data collected during the index hospitalization were extracted from the hospitals’ electronic medical record systems. The ECG-AI index is the output from an AI model that was trained to predict the risk of SCD based on ECG input. The association between ECG-AI index and SCD was evaluated with adjustment for left ventricular ejection fraction (LVEF), New York Heart Association (NYHA) class, and competing risk of non-SCD. The outcome measure was a composite of SCD and implantable cardioverter-defibrillator activation. The ECG-AI index was established using a derivation (hospital A) and validation cohort (hospital B), and its ability was evaluated in a test cohort (hospitals C and D).

Results

The ECG-AI index plus classical predictive guidelines (i.e., LVEF ≤ 35%, NYHA class II–III) significantly improved the discriminative value of SCD (area under the receiver operating characteristic curve, 0.66 vs. 0.59; p=0.017; Delong’s test) with good calibration (p=0.11; Hosmer–Lemeshow test) and improved net reclassification (36%; 95% confidence interval, 9%–64%; p=0.009). The Fine-Gray model considering the competing risk of non-SCD demonstrated that the ECG-AI index was independently associated with SCD (adjusted sub-distributional hazard ratio, 1.25; 95% confidence interval, 1.04–1.49; p=0.015). An increased proportional risk of SCD vs. non-SCD with increasing ECG-AI index was also observed (low, 16.7%; intermediate, 18.5%; high, 28.7% risk; p for trend = 0.023). Similar findings were observed in patients aged ≤75 years with a non-ischemic etiology and an LVEF >35%.

Conclusions

Among patients with HF, ECG-based AI significantly improved the SCD risk stratification compared to the conventional indication for implantable cardioverter-defibrillators inclusive of LVEF and NYHA class.
An umbrella review and meta-analysis of the use of renin-angiotensin system drugs and COVID-19 outcomes: what do we know so far?
Authors: Kurdi Amanj , Weir Natalie , Mueller Tanja
Published: March 2022

Backgrounds

Evidence from several meta-analyses are still controversial about the effects of angiotensin-converting enzyme inhibitors (ACEIs)/angiotensin-receptor blockers (ARBs) on COVID-19 outcomes.

Purpose

Umbrella review of systematic reviews/meta-analysis to provide comprehensive assessment of the effect of ACEIs/ARBs on COVID-19 related outcomes by summarising the currently available evidence.

Data Source

Medline (OVID), Embase, Scopus, Cochrane library and medRxiv from inception to 1stFebruary 2021.

Study Selection

Systematic reviews with meta-analysis that evaluated the effect of ACEIs/ARBs on COVID-19 related clinical outcomes

Data Extraction

Two reviewers independently extracted the data and assessed studies’ risk of bias using AMSTAR 2 Critical Appraisal Tool.

Data Synthesis

Pooled estimates were combined using the random-effects meta-analyses model including several sub-group analyses. Overall, 47 reviews were eligible for inclusion. Out of the nine COVID-19 outcomes evaluated, there was significant associations between ACEIs/ARBs use and each of death (OR=0.80, 95%CI=0.75-0.86; I2=51.9%), death/ICU admission as composite outcome (OR=0.86, 95%CI=0.80-0.92; I2=43.9%), severe COVID-19 (OR=0.86, 95%CI=0.78-0.95; I2=68%), and hospitalisation (OR=1.23, 95%CI=1.04-1.46; I2= 76.4%). The significant reduction in death/ICU admission, however, was higher among studies which presented adjusted measure of effects (OR=0.63, 95%CI=0.47-0.84) and were of moderate quality (OR=0.74, 95%CI=0.63-0.85).

Limitations

The effect of unmeasured confounding could not be ruled out. Only 21.3% (n=10) of the studies were of ‘moderate’ quality.

Conclusion

Collective evidence from observational studies indicate a good quality evidence on the significant association between ACEIs/ARBs use and reduction in death and death/ICU admission, but poor-quality evidence on both reducing severe COVID-19 and increasing hospitalisation. Our findings further support the current recommendations of not discontinuing ACEIs/ARBs therapy in patients with COVID-19.

Registration

The study protocol was registered in PROSPERO (CRD42021233398).

Funding Source

None
DNAmFitAge: Biological Age Indicator Incorporating Physical Fitness
Authors: McGreevy Kristen M. , Radak Zsolt , Torma Ferenc , Lu Ake T. , Belsky Daniel W. , Binder Alexandra , Ferrucci Luigi , Marioni Riccardo E. , Cox Simon , Kober Michael , Corcoran David L. , Horvath Steve
Published: March 2022

Physical fitness is a well-known correlate of health and the aging process. DNA methylation (DNAm) data lend themselves for estimating chronological and biological age through epigenetic clocks. However, current epigenetic clocks did not yet use measures of mobility, strength, lung, or endurance physical fitness parameters in their construction. Here, we develop blood DNAm biomarkers for fitness parameters gait speed (walking speed), hand grip strength, forced expiratory volume in one second (FEV1), and maximal oxygen uptake (VO2max). We then use these DNAm biomarkers to construct DNAmFitAge, a new biological age indicator that incorporates physical fitness with epigenetic mortality risk estimators. Adjusting DNAmFitAge for chronological age generates a novel measure of epigenetic age acceleration, FitAgeAcceleration, which is informative for physical activity level (p=1.2E-12), mortality risk (p=5.9E-13), coronary heart disease risk (p=0.0051), comorbidities (p=9.0E-9), and disease-free status (p=1.1E-6) across several large validation datasets. These newly constructed DNAm biomarkers and DNAmFitAge provide researchers and physicians a new method to incorporate physical fitness into epigenetic clocks and emphasizes the effect of lifestyle on the aging process.
A Sliding Window Approach to Optimize the Time-varying Parameters of a Spatially-explicit and Stochastic Model of COVID-19
Authors: Ratnavale Saikanth , Hepp Crystal , Doerry Eck , Mihaljevic Joseph R
Published: March 2022

The implementation of non-pharmaceutical public health interventions can have simultaneous impacts on pathogen transmission rates as well as host mobility rates. For instance, with SARS-CoV-2, masking can influence host-to-host transmission, while stay-at-home orders can influence mobility. Importantly, variations in transmission rates and mobility patterns can influence pathogen-induced hospitalization rates. This poses a significant challenge for the use of mathematical models of disease dynamics in forecasting the spread of a pathogen; to create accurate forecasts in spatial models of disease spread, we must simultaneously account for time-varying rates of transmission and host movement. In this study, we develop a statistical model-fitting algorithm to estimate dynamic rates of SARS-CoV-2 transmission and host movement from geo-referenced hospitalization data. Using simulated data sets, we then test whether our method can accurately estimate these time-varying rates simultaneously, and how this accuracy is influenced by the spatial population structure. Our model-fitting method relies on a highly parallelized process of grid search and a sliding window technique that allows us to estimate time-varying transmission rates with high accuracy and precision, as well as movement rates with somewhat lower precision. Estimated parameters also had lower precision in more rural data sets, due to lower hospitalization rates (i.e., these areas are less data-rich). This model-fitting routine could easily be generalized to any stochastic, spatially-explicit modeling framework, offering a flexible and efficient method to estimate time-varying parameters from geo-referenced data sets.
Developing and piloting a preterm birth registry prioritizing social determinants of health and patient-reported data
Authors: Joudeh Layla , Stookey Jodi , Burch Johanna , Kaplan Rachel L. , Guendelman Sylvia , Armstrong Aline , Jackson Rebecca
Published: March 2022

Biomedical factors and social determinants of health (SDH) affect preterm birth (PTB). Given the complexity of PTB and the increasing rates in the United States, public datasets involving multicomponent variables—from biomedical to structural—can motivate novel interventions to address PTB in the US. The primary aim of this study was to develop a PTB registry based on multi-modal data collection tools that prioritize biomedical and SDH data and identify PTB phenotype (i.e. spontaneous labor, preterm premature rupture of membrane, or medically indicated). The secondary aim of this study was to execute a pilot study to assess feasibility. This study aimed to describe recruitment practices, assess data accessibility and concordance, and to provide an example of how the registry can be used to generate hypothesis and analyze data. We designed the registry through a conceptual model provided by the Dahlgren and Whitehead model of SDH using validated questionnaires and literature on PTB. The registry included a survey, interview, and medical and birth certificate abstraction. To pilot the registry, we recruited 92 participants who delivered preterm, were admitted for risk of preterm delivery, or delivered at term at an urban public hospital. Enrollment was most effective in-person and in the postpartum period. Consent to different parts of the registry was similar regardless of when participants were recruited. There was also a range of data concordance depending on the data source and chosen variable. The registry’s PTB phenotype algorithm identified the correct PTB phenotype 100% of the time. The example analysis demonstrated six unique SDH domains. Participants who delivered preterm reported an average of 11 total stressors and 19.7 protective items and 66% had a significant medical or obstetric comorbidity. Results of this study demonstrate that a PTB registry is feasible and could help advance research to prevent PTB.
Should the governance of individual treatment attempts (″Individuelle Heilversuche ″) include praxis evaluation? Results from qualitative stakeholder interviews.
Authors: Faust Alice , Woydack Lena , Strech Daniel
Published: March 2022

Introduction: Individual treatment attempts (ITAs) are a German concept for the treatment of individual patients by physicians with nonstandard therapeutic approaches. ITAs span from nonstandard off-label drug uses to first–in–human uses of newly developed drugs/ interventions. Due to the lack of evidence, ITAs come with a high amount of uncertainty regarding the risk-benefit ratio. At present, no prospective review and no systematic retrospective evaluation of ITAs are required in Germany; therefore, no opportunity exists for the basic evaluation of the frequency, type, or outcomes of ITAs. Our objective was to explore stakeholders′ attitudes toward the retrospective evaluation (monitoring) or prospective evaluation (review) of ITAs.

Methods: We conducted a qualitative interview study among relevant stakeholder groups. We used the SWOT framework to represent the stakeholders′ attitudes. We applied content analysis to the recorded and transcribed interviews in MAXQDA.

Results: Twenty interviewees participated in the study. The interviewees pointed to several arguments in favor of the retrospective evaluation of ITAs, such as the knowledge gain about and setting and circumstances of ITAs. At the same time, the interviewees expressed concerns regarding the validity and practical relevance of the evaluation results. The viewpoints on review addressed several contextual factors (e.g., different medical disciplines) that should be acknowledged when judging the necessity of a review.

Conclusion: One main conclusion is that the current situation with a complete lack of evaluation insufficiently reflects safety concerns. German health policy decision makers should be more explicit about where and why some sort of evaluation is needed or not needed. Another conclusion is that there is no one-size-fits-all model for evaluating ITAs. Both prospective and retrospective evaluations should be piloted in areas of ITAs with particularly high risks and conflicts of interest, such as in the application of very experimental therapies (e.g., bench-to-bedside applications) outside clinical trials.
Rett syndrome severity estimation with the BioStamp nPoint using interactions between heart rate variability and body movement
Authors: Suresha Pradyumna Byappanahalli , O'Leary Heather , Tarquinio Daniel C. , Von Hehn Jana , Clifford Gari D.
Published: March 2022

Rett syndrome, a rare genetic neurodevelopmental disorder in humans, does not have an effective cure. However, multiple therapies and medications exist to treat symptoms and improve patients’ quality of life. As research continues to discover and evaluate new medications for Rett syndrome patients, there remains a lack of objective physiological and motor activity-based (physio-motor) biomarkers that enable the measurement of the effect of these medications on the change in patients’ Rett syndrome severity. In our work, using a commercially available wearable chest patch, we recorded simultaneous electrocardiogram and three-axis acceleration from 20 patients suffering from Rett syndrome along with the corresponding Clinical Global Impression - Severity score, which measures the overall disease severity on a 7-point Likert scale. We derived physio-motor features from these recordings that captured heart rate variability, activity metrics, and the interactions between heart rate and activity. Further, we developed machine learning (ML) models to classify high-severity Rett patients from low-severity Rett patients using the derived physio-motor features. For the best-trained model, we obtained a pooled area under the receiver operating curve equal to 0.92 via a leave-one-out-patient cross-validation approach. Finally, we computed the feature popularity scores for all the trained ML models and identified physio-motor biomarkers for Rett syndrome.
Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity
Authors: Victor Matheus B. , Leary Noelle , Luna Xochitl , Meharena Hiruy S. , Bozzelli P. Lorenzo , Samaan George , Murdock Mitchell H. , von Maydell Djuna , Effenberger Audrey H. , Cerit Oyku , Wen Hsin-Lan , Liu Liwang , Welch Gwyneth , Bonner Maeve , Tsai Li-Huei
Published: March 2022

Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing late- onset Alzheimer’s disease and its expression in microglia is associated with pro- inflammatory states. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral allele APOE3 is currently unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a distinct metabolic program in microglia that is marked by the accumulation of intracellular neutral lipid stores through impaired lipid catabolism. Importantly, this altered lipid-accumulated state shifts microglia away from homeostatic surveillance and renders APOE4 microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia before and after exposure to neuronal conditioned media, we further established that neuronal soluble cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro- inflammatory signals. Pharmacological blockade of lipogenesis in APOE4 microglia is sufficient to diminish intracellular lipid accumulation and restore microglial homeostasis. Remarkably, unlike APOE3 microglia that support neuronal network activity, co-culture of APOE4 microglia with neurons disrupts the coordinated activity of neuronal ensembles. We identified that through decreased uptake of extracellular fatty acids and lipoproteins, APOE4 microglia disrupts the net flux of lipids which results in decreased neuronal activity via the potentiation of the lipid-gated K+ channel, GIRK3. These findings suggest that neurological diseases that exhibit abnormal neuronal network-level disturbances may in part be triggered by impairment in lipid homeostasis in non-neuronal cells, underscoring a novel therapeutic route to restore circuit function in the diseased brain.

Abstract Figure
Fe3O4nanoparticles to optimize the co-digestion of vinasse, filter cake, and deacetylation liquor: operational aspects and microbiological routes
Authors: Volpi Maria Paula. C. , Mockaitis Gustavo , Moraes Bruna S.
Published: March 2022

The co-digestion of residues from the sugarcane industry has already proven to be a highly attractive process for biogas production through anaerobic digestion (AD). The use of residues such as vinasse (1G) filter cake (1G) and deacetylation liquor (2G) in CSTR operation showed the potential for integrating 1G and 2G ethanol biorefineries through AD in previous work by our research group. The use of nanoparticles (NP) is a favorable way to optimize AD processes, as these additives allow the introduction of nutrients to the process more assertively concerning the distribution and interaction with microorganisms. The present work proposed the optimization of the co-digestion of vinasse, filter cake, and deacetylation liquor in a continuous reactor by adding Fe3O4NP, comparing the results with a previous reactor operation without NP. Initially, tests were carried out in batches with different NP concentrations, resulting in 5 mg L-1as the best concentration to be added in the continuous reactor along the increments of the applied organic rate load (ORL). CH4production reached a maximum value of 2.8 ± 0.1 NLCH4gVS-1and the organic matter removal reached 71 ± 0.9%, in phase VI (ORL of 5.5 gVS L-1day-1). This production was 90% higher than the reactor co-digestion operation without NP. The pH and alkalinity results indicated the methanogenesis stabilization within 60 days of operation: 30 days before when there was no NP added. The AD development was stable, presenting low variations in the oxidation-reduction potential (ORP) and stable organic acid (OA) concentrations, which indicated the propionic acid route to produce CH4was predominant. The main methanogenicArcheaeidentified wasMethanoculleus, indicating that the predominant metabolic route was that of acetate (SAO) coupled with hydrogenotrophic methanogenesis. The use of Fe3O4NP managed to improve the AD from the 1G2G ethanol production residues and stimulated the microbial community growth, not modifying the preferable metabolic pathways.
Interacting active surfaces: a model for three-dimensional cell aggregates
Authors: Torres-Sánchez Alejandro , Winter Max Kerr , Salbreux Guillaume
Published: March 2022

We introduce a modelling and simulation framework for cell aggregates in three dimensions based on interacting active surfaces. Cell mechanics is captured by a physical description of the acto-myosin cortex that includes cortical flows, viscous forces, active tensions, and bending moments. Cells interact with each other via short-range forces capturing the effect of adhesion molecules. We discretise the model constitutive equations using a finite element method, and provide a parallel implementation in C++.
We discuss examples of application of this new framework to simulations involving small and medium-sized aggregates: we consider the shape and dynamics of a cell doublet, a planar cell sheet, and a growing cell aggregate. This framework opens the door to the systematic exploration of the cell to tissue-scale mechanics of cell aggregates, which plays a key role in the morphogenesis of embryos and organoids.
Exon7 Targeted CRISPR-Prime Editing Approaches for SMN2 Gene Editing in Spinal Muscular Atrophy (SMA) Disease Can Increase In Vitro SMN Expression
Authors: Odabas Sibel Pinar , Bal Enes , Yelgen Gamze , Metin Ayse Simay , Karakaya Ebrar , Gulden Gamze , Sert Berranur , Teymur Tarik , Ay Yasin , Tiryaki Nulifer Neslihan , Araz Hasret , Cavrar Ilayda , Tastan Cihan
Published: March 2022

Spinal Muscular Atrophy (SMA) is a fatal neuromuscular disease characterized by motor neuron loss and advanced muscle weakness, which occurs in functional SMN (Survival Motor Neuron) protein deficiency with SMN1 gene-induced deletions and mutations. The incidence of SMA, which is an autosomal recessive disease, is 1/10,000 in the world. The SMN protein acts as a molecular chaperone in the formation of the spliceosome complex, which catalyzes the splicing of pre-mRNA, enabling mRNAs and non-coding RNAs to mature. Since the current SMN1-encoding Adeno-associated virus (AAV) or SMN2 gene targeting antisense oligonucleotide-based strategies cannot provide long-term stable SMN expression in neuron cells, more effective methods need to be developed. CRISPR technology, which adds a new dimension to genetic engineering and gene therapies, makes it possible to treat many genetic diseases. In terms of SMA, some previous studies in the literature prove that it is possible to treat SMA with the CRISPR strategy. Homology Directed Repair (HDR)-based CRISPR technology, which results in a high rate of in-del (insertion-deletion) mutations rather than editing, was shown unsuitable for therapeutic applications. CRISPR-Prime editing (PE) technology is a new generation of gene editing approach that precisely provides various genomic modifications without the need for double-strand breakage or donor DNA sequences. CRISPR-Prime Editing method has also been used in rare diseases such as sickle cell anemia and Tay-Sachs, and their efficiency in editing various pathogenic mutations has been demonstrated. However, CRISPR Prime Editing-mediated gene editing for Spinal Muscular Atrophy (SMA) have not yet been investigated. The c.840 T-C transition and c.859 G-C transformations in the SMN2 gene and the correction of these point mutations with a single pegRNA at the same time were investigated for the first time in this study. Here, we showed that CRISPR-PE systems could increase SMN2 gene activity and SMN protein expression by ensuring exon 7 participation by editing c.840 T-C transition and c.859 G-C transformations. The fact that Prime Editing method showed the efficacy and stability of modifications in SMN2 genes that were investigated in SMN-low Jurkat cells as a proof-of-concept. This study enabled the next step with the CRISPR-Prime Editing approach to be tested ex vivo in primary cell lines from SMA patients and SMN-low neuronal cells.
Three-dimensional structure of the single domain cupredoxin AcoP
Authors: Roger Magali , Leone Philippe , Blackburn Ninan , Horrell Sam , Chicano Tadeo Moreno , Giudici-Orticoni Marie-Thérèse , Abriata Luciano A. , Hura Greg L. , Hough Michael A. , Sciara Giulano , Ilbert Marianne
Published: March 2022

Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper center coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in term of copper-binding ligands, copper center geometry, redox potential, as well as biological function. AcoP is a periplasmic protein belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features: highly resistant to acidic pH, it possesses a constrained green-type copper center of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structure of AcoP at 1.65 Å resolution unveils a typical cupredoxin fold with extended loops, never observed in previously characterized cupredoxins, that might be involved in the interaction of AcoP with its physiological partners. Moreover, the structure shows that the green color of AcoP cannot be attributed to nonclassical copper ligands, its green-colored copper center raising from a long Cu-S (Cys) bond, determined by both X-ray diffraction and EXAFS. The crystal structures of two AcoP mutants confirm that the active center of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active center rigidity due to the presence of an extensive hydrogen bond network.
Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli
Authors: Steinhilper Ralf , Höff Gabriele , Heider Johann , Murphy Bonnie J.
Published: March 2022

The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogen lyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown.

Here we report cryo-EM structures of FHL in its aerobically- and anaerobically-isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in preventing reverse activity in vivo, and evaluate possible structural determinants of the bias toward hydrogen production over its oxidation.
Single-cell analyses of axolotl forebrain organization, neurogenesis, and regeneration
Authors: Lust Katharina , Maynard Ashley , Gomes Tomás , Fleck Jonas Simon , Camp J. Gray , Tanaka Elly M. , Treutlein Barbara
Published: March 2022

Salamanders are important tetrapod models to study brain organization and regeneration, however the identity and evolutionary conservation of brain cell types is largely unknown. Here, we delineate cell populations in the axolotl telencephalon during homeostasis and regeneration, representing the first single-cell genomic and spatial profiling of an anamniote tetrapod brain. We identify glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved GABAergic neuron classes. We infer transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific direct and indirect neurogenesis, and unravel conserved signatures. Following brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield key insights into the organization, evolution, and regeneration of a tetrapod nervous system.
Cfdp1 is Essential for Cardiac Development and Function
Authors: Panagiota Giardoglou , Panos Deloukas , George Dedoussis , Dimitris Beis
Published: March 2022

Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide and account for the most common noncommunicable disease. CVDs describe a wide spectrum of disorders affecting the proper function, physiology and morphogenesis of the heart and blood vessels. The risk of developing cardiovascular diseases is modulated by a combination of environmental and genetic effectors. Thus, it’s highly important to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in coronary artery disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family and up to date, its function and mechanism of action in Cardiovascular Development is still unclear. In this study, we utilize zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology and the ease of experimentally manipulation. We showed that cfdp1 is expressed during development and at 120 hours post fertilization its expression is restricted to the region of the heart and the head. We then generated a cfdp1-null zebrafish line using CRISPR-Cas9 system which led to a lethal phenotype since knockout embryos do not reach adulthood. cfdp1−/− embryos develop arrhythmic hearts and defective cardiac performance exhibiting statistically significant differences in heart features including End Diastolic Volume, Cardiac Output, Ejection Fraction and Stroke Volume. Myocardial trabeculation is also impaired in cfdp1−/− embryonic hearts, implying its regulatory role also in this developmental process. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process.
Deletion of CEP164 in mouse photoreceptors post-ciliogenesis interrupts ciliary intraflagellar transport (IFT)
Authors: Baehr Wolfgang , Reed Michelle , Takemaru Ken-Ichi , Ying Guoxin , Frederick Jeanne M.
Published: March 2022

Centrosomal protein 164 (CEP164) is located at the edge of distal appendages in primary cilia and is necessary for basal body (BB) docking to the apical membrane. To investigate the function of CEP164 before and after BB docking in photoreceptors, we deleted CEP164 during retina embryonic development (Six3Cre), in postnatal rod photoreceptors (iCre75) and in mature retina using tamoxifen induction. BBs dock to the cell cortex during postnatal day 6 (P6) and extend a connecting cilium (CC) and an axoneme. P6 retina-specific knockouts (ret Cep164 -/-) are unable to dock BBs, thereby preventing formation of a CC or outer segments (OS). In rodspecific knockouts (rod Cep164 -/-), Cre expression starts after P9 and CC/OS form. P16 rod Cep164 -/- rods have nearly normal OS lengths, and maintain OS attachment through P21 despite loss of CEP164. Intraflagellar transport components (IFT88, IFT57 and IFT140) were reduced at P16 rod Cep164 -/- BBs and CC tips and nearly absent at P21, indicating impaired intraflagellar transport. Nascent OS discs, labeled with a fluorescent dye on P14 and P18 and harvested on P19, showed continued rod Cep164 -/- disc morphogenesis but absence of P14 discs mid-distally, indicating OS instability. Tamoxifen induction with PROM1 ETCre; Cep164 F/F (tam Cep164 -/-) adult mice affected maintenance of both rod and cone OS. The results suggest that CEP164 is key towards recruitment and stabilization of IFT-B particles at BB/CC. Impairment of IFT may be the main driver of ciliary malfunction observed with hypomorphic CEP164 mutations.
HSV Tegument Protein pUL51 Interacts with Host Dynactin for Viral Spread
Authors: White Shaowen , Tran My , Roller Richard J.
Published: March 2022

Dynein motors are microtubule associated protein complexes that mediate multiple essential cellular processes, such as long-distance cargo trafficking and stabilization of the microtubule organization center. Most of these functions and their regulations depend on the dynein motor subunit dynactin. By using an infection-inducible system, we disrupted dynein motor function after HSV entry by overexpressing a dominant-negative inhibitor of dynein, resulting in a 5-fold growth defect in Vero cells and 1000-fold growth defect in CAD neuronal cells. Also, we found that in infected CAD cells, the dynein complex was recruited to viral assembly sites regardless of microtubule polymerization. Based on these observations, we then identified a novel interaction between conserved HSV-1 tegument protein pUL51 and p150Glued. pUL51 is a palmitoylated Golgi membrane-associated protein that is required for efficient virus assembly and spread. Overexpression of pUL51 alone was sufficient to recruit p150Glued to Golgi membranes. Sequences that are important and sufficient for pUL51-p150Glued interaction were mapped to residues 90 to 124 in pUL51 and residues 548 to 911 in p150Glued. Deletion of a.a 90-124 in pUL51 resulted in a moderate viral growth defect, a profound spread defect, and failure to accumulate both dynactin and the viral spread factor glycoprotein E (gE) at cell-cell junctions. A synthetic peptide that contains pUL51 a.a 90-125 could also inhibit viral growth and spread in pUL51-dependent manner. Taken together, our results suggest that the proper function of pUL51 in efficient viral assembly and spread depends on its interaction with p150Glued.

Author Summary

During their life-long infections, herpesviruses can spread within the human body in spite of a powerful immune response that includes antibodies that inactivate the virus. The virus accomplishes this by targeting its newly made infectious particles to junctions where infected cells meet their uninfected neighbors. Junctional targeting of virus particles requires that the virus hijack normal cellular machinery used for moving large cargoes within the cell, a process that is only partially understood. In this study, we have discovered a critical interaction between a virus protein that is present in all herpesviruses and a host cell cargo-moving protein that is required for virus spread between cells and shown that this interaction is common to several medically important human herpesviruses. We have also identified a short piece of this virus protein that is responsible for the interaction and shown that this short piece can be used to interrupt the interaction and prevent spread of herpes simplex virus (HSV) in cultured cells. Our study provides prove-of-concept evidence that the spread pathway of HSV, and possibly other herpesviruses, can be targeted for therapeutic purposes.
Toxoplasma gondii ROP1 subverts murine and human innate immune restriction
Authors: Butterworth Simon , Torelli Francesca , Lockyer Eloise J. , Wagener Jeanette , Song Ok-Ryul , Broncel Malgorzata , Russell Matt R. G. , Young Joanna C. , Treeck Moritz
Published: March 2022

Toxoplasma gondii is an intracellular parasite that can infect many different host species and is a cause of significant human morbidity worldwide. T. gondii secretes a diverse array of effector proteins into the host cell which are critical for infection; however, the vast majority of these secreted proteins are uncharacterised. Here, we carried out a pooled CRISPR knockout screen in the T. gondii Prugniaud strain in vivo to identify secreted proteins that contribute to parasite immune evasion in the host. We identify 22 putative virulence factors and demonstrate that ROP1, the first-identified rhoptry protein of T. gondii, has a previously unrecognised role in parasite resistance to interferon gamma-mediated innate immune restriction. This function is conserved in the highly virulent RH strain of T. gondii and contributes to parasite growth in both murine and human macrophages. While ROP1 affects the morphology of rhoptries, from where the protein is secreted, it does not affect rhoptry secretion. ROP1 interacts with the host cell protein C1QBP, which appears to facilitate parasite immune evasion. In summary, we identify 22 secreted proteins which contribute to parasite growth in vivo and show that ROP1 is an important and previously overlooked effector in counteracting both murine and human innate immunity.
Phase separation of hnRNP A1 upon specific RNA-binding observed by magnetic resonance
Authors: Ritsch Irina , Lehmann Elisabeth , Emmanouilidis Leonidas , Yulikov Maxim , Allain Frédéric , Jeschke Gunnar
Published: March 2022

Interaction of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) with specific single-stranded RNA and its relation to liquid-liquid phase separation were investigated in vitro by magnetic resonance based on site-directed spin labelling. An ensemble model of free hnRNP A1 in the absence of RNA was derived from distance distributions between spin labelled sites and small angle X-ray scattering. This model revealed a compact state of the low-complexity domain and interaction of this domain with the RNA recognition motifs. Paramagnetic relaxation enhancement NMR spectroscopy confirmed this interaction. The addition of RNA to dispersed solutions of hnRNP A1 induced phase separation, observed by formation of liquid droplets. The phase separation depended on the RNA concentration and sequence, with continuous wave EPR spectroscopy showing that local protein dynamics is affected by point mutations in the RNA sequence. We propose that an interplay of sequence-specific RNA binding and phase transition serves as a regulatory mechanism for RNA segregation in the stress response of cells.
Floating Sphere Assay: A rapid qualitative method for microvolume analysis of gelation
Authors: Tay Uma Jingxin , Goh Megan , Hui Jeralyn Ching Wen , Arumugam Prakash
Published: March 2022

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A huge, unprecedented demand for gelatin coupled with its implications on global sustainability has resulted in the need to discover novel proteins with gelling attributes for applications in the food industry. Currently used gelation assays require large sample volumes and thus the screening for novel gelling proteins is a formidable technical challenge. In this paper, we report the ‘Floating Sphere Assay’ which is a simple, economical, and miniaturized assay to detect minimum gelling concentration with volumes as low as 50 μl. Results from the Floating Sphere Assay are consistent with currently used methods for gelation tests and accurately estimate the Minimum Gelling Concentrations (MGCs) of gelatin, κ-carrageenan and gellan gum. The assay was also able to differentiate the strengths of strong and weak gellan gum gels prepared at pH 3.5 and pH 7.0 respectively. The Floating Sphere Assay can be utilized in high-throughput screens for gelling proteins and can accelerate the discovery of gelatin substitutes.

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Highlights

We report the Floating Sphere Assay that can be used to assesses minimum gelling concentration of solutions with volumes as low as 50 μl.

Observing whether a glass sphere placed on the surface of a test solution floats or sinks is diagnostic of gel formation

Floating Sphere Assay can distinguish a strong gel from a weak gel

Floating Sphere Assay is a rapid and cost-effective approach to screen for novel plant-based gelatin alternatives.
HDAC6 inhibitor ACY-1083 shows lung epithelial protective features in COPD
Authors: Horndahl Jenny , Svärd Rebecka , Berntsson Pia , Wingren Cecilia , Li Jingjing , Abdillahi Suado M , Ghosh Baishakhi , Capodanno Erin , Chan Justin , Ripa Lena , Åstrand Annika , Sidhaye Venkataramana K. , Collins Mia
Published: March 2022

Airway epithelial damage is a common feature in respiratory diseases such as COPD and has been suggested to drive inflammation and progression of disease. These features manifest as remodeling and destruction of lung epithelial characteristics including loss of small airways which contributes to chronic airway inflammation. Histone deacetylase 6 (HDAC6) has been shown to play a role in epithelial function and dysregulation, such as in cilia disassembly, epithelial to mesenchymal transition (EMT) and oxidative stress responses, and has been implicated in several diseases. We thus used ACY-1083, an inhibitor with high selectivity for HDAC6, and characterized its effects on epithelial function including epithelial disruption, cytokine production, remodeling, mucociliary clearance and cell characteristics.

Primary lung epithelial air-liquid interface cultures from COPD patients were used and the impacts of TNF, TGF-β, cigarette smoke and bacterial challenges on epithelial function in the presence and absence of ACY-1083 were tested. Each challenge increased the permeability of the epithelial barrier whilst ACY-1083 blocked this effect and even decreased permeability in the absence of challenge. TNF was also shown to increase production of cytokines and mucins, with ACY-1083 reducing the effect. We observed that COPD-relevant stimulations created damage to the epithelium as seen on immunohistochemistry sections and that treatment with ACY-1083 maintained an intact cell layer and preserved mucociliary function. Interestingly, there was no direct effect on ciliary beat frequency or tight junction proteins indicating other mechanisms for the protected epithelium.

In summary, ACY-1083 shows protection of the respiratory epithelium during COPD-relevant challenges which indicates a future potential to restore epithelial structure and function to halt disease progression in clinical practice.
Dual-Resolving of Lipid Positional and Geometric Isomers of C=C Bonds via Bifunctional Photocycloaddition-Photoisomerization Reaction System and Mass Spectrometry
Authors: Feng Guifang , Gao Ming , Wang Liwei , Chen Jiayi , Hou Menglu , Wan Qiongqiong , Lin Yun , Xu Guoyong , Qi Xiaotian , Chen Suming
Published: March 2022

The biological functions of lipids largely depend on their chemical structures. The position and configuration of C=C bonds are two of the essential attributes that determine the structures of unsaturated lipids. However, simultaneous identification of both attributes remains challenging. Here, we developed a bifunctional visible-light-activated photocycloaddition-photoisomerization reaction system, which enabled the dual-resolving of the positional and geometric isomerism of C=C bonds in lipids when combined with liquid chromatographic mass spectrometry. The dual-pathway reaction mechanism was demonstrated by experiments and density functional theory calculations. Based on this bifunctional reaction system, a workflow of deep structural lipidomics was established, and allowed the revealing of unique patterns of cis-trans-isomers in bacteria, as well as the tracking of C=C positional isomers changes in mouse brain ischemia. This study not only offers a powerful tool for deep lipid structural biology, but also provides a new paradigm for developing the multifunctional visible-light-induced reaction.
A neutrophil - B-cell axis governs disease tolerance during sepsis via Cxcr4
Authors: Gawish Riem , Maier Barbara B. , Obermayer Georg , Watzenböck Martin L. , Gorki Anna-Dorothea , Quattrone Federica , Farhat Asma , Lakovits Karin , Hladik Anastasiya , Korosec Ana , Alimohammadi Arman , Mesteri Ildiko , Oberndorfer Felicitas , Oakley Fiona , Brain John , Boon Louis , Lang Irene , Binder Christoph J. , Knapp Sylvia
Published: March 2022

Sepsis is a life-threatening condition characterized by uncontrolled systemic inflammation and coagulation, leading to multi-organ failure. Therapeutic options to prevent sepsis-associated immunopathology remain scarce.

Here, we established a model of long-lasting disease tolerance during severe sepsis, manifested by diminished immunothrombosis and organ damage in spite of a high pathogen burden. We found that, both neutrophils and B cells emerged as key regulators of tissue integrity. Enduring changes in the transcriptional profile of neutrophils, included upregulated Cxcr4 expression in protected, tolerant hosts. Neutrophil Cxcr4 upregulation required the presence of B cells, suggesting that B cells promoted tissue tolerance by suppressing tissue damaging properties of neutrophils. Finally, therapeutic administration of a Cxcr4 agonist successfully promoted tissue tolerance and prevented liver damage during sepsis. Our findings highlight the importance of a critical B-cell/neutrophil interaction during sepsis and establish neutrophil Cxcr4 activation as a potential means to promote disease tolerance during sepsis.

We show that a B cell/neutrophil interaction in the bone marrow facilitates tissue tolerance during severe sepsis. By affecting neutrophil Cxcr4 expression, B cells can impact neutrophil effector functions. Finally, therapeutic activation of Cxcr4 successfully promoted tissue tolerance and prevented liver damage during sepsis.
Deep learning models for RNA secondary structure prediction (probably) do not generalise across families
Authors: Szikszai Marcell , Wise Michael , Datta Amitava , Ward Max , Mathews David H.
Published: March 2022

Abstract

Motivation

The secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary structure prediction. Many of these papers report impressive results for intra-family predictions, but seldom address the much more difficult (and practical) inter-family problem.

Results

We demonstrate it is nearly trivial with convolutional neural networks to generate pseudo-free energy changes, modeled after structure mapping data, that improve the accuracy of structure prediction for intra-family cases. We propose a more rigorous method for inter-family cross-validation that can be used to assess the performance of learning-based models. Using this method, we further demonstrate that intra-family performance is insufficient proof of generalisation despite the widespread assumption in the literature, and provide strong evidence that many existing learning-based models have not generalised inter-family.

Availability

Source code and data is available at https://github.com/marcellszi/dl-rna.