bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Angiotensin‐(1‐12) [Ang‐(1‐12)] is a Hypertension and Cardiac Disease Biomarker
Authors: Ferrario Carlos Maria , Groban Leanne , Iyer Seethalakshmi R. , Ahmad Sarfaraz , Wright Kendra N. , Burnett John C.
Published: April 2020

Background

Ang‐(1‐12) is a primary non‐renin dependent substrate for direct tissue angiotensin II (Ang II) formation by chymase. This discovery challenges conventional thinking and explains the large residual risk of cardiovascular events in patients medicated with blockers of the renin angiotensin system (RAS). Here we report the first demonstration of circulating Ang‐(1‐12) as a biomarker of essential hypertension (EH) and cardio‐renal remodeling.

Methods

The cohort of patients from Olmsted County MN included 52 healthy adult volunteers (21 females), age 54 ± 8 years, and 23 essential hypertensive (EH) patients (14 females) age 61 ± 8 years with systolic blood pressure (SBP) ≥140 mm Hg prior to recruitment. Clinical examination, standardized BP measurements, and venous blood were obtained for measurements of plasma concentrations of angiotensinogen (AGT), Ang‐(1‐12), Ang II, aldosterone, renin activity, N‐terminal pro–B‐type natriuretic peptide (NT‐proBNP) and atrial and brain natriuretic peptides (ANP and BNP, respectively). All values are Means ± SD. Data were analyzed by 2‐way ANOVA for sex and hypertension.

Results

Plasma Ang‐(1‐12) levels in EHs [SBP: 134 ± 14 mm Hg; Ang‐(1‐12): 1,463 ± 446] were higher than normotensives [SBP: 117 ± 13 mm Hg; Ang‐(1‐12): 1,353 ± 379 fmol/mL, hypertension effect: P<0.05], irrespective of sex. Hypertension associated with increases in pulse pressure, PRA, and plasma AGT and NT‐proBNP concentrations (see Figure
). The elevation in circulating NT‐proBNP levels with hypertension was accounted for by a 4.6‐fold increase in hypertensive males (165 ± 134 pg/mL) while the 1.5‐fold rise in plasm NT‐proBNP did reach significance (134 ± 127 pg/mL, p> 0.05).

Conclusions

We show for the first time that Ang‐(1‐12) circulates in humans and its concentrations are elevated by chronic hypertension. We further demonstrate a sexual dimorphic pattern in hypertensives with respect to NT‐proBNP, the latter a biomarker for cardiac remodeling. Whether this represents a natriuretic system‐related compensatory mechanism, or worsening pathology, due to an elevated noncanonical RAS specific to male hypertensives remains to be studied. Further investigation to fully define the role of Ang‐(1‐12) as a cardiac disease biomarker in a larger, gender and ethnic diverse population and its relationship to hypertension and myocardial structure is warranted.

Support or Funding Information

Supported by grant HL‐051952 from the NHLBI of the NIH

Lines are means ± SD

Figure 1
Exercise promotes satellite cell contribution to myofibers in a load‐dependent manner
Authors: D’Hulst Gommaar , Masschelein Evi , Palmer Andrew , Bar-Nur Ori , De Bock Katrien
Published: April 2020

Satellite cells (SCs) are required for muscle repair following injury and are involved in muscle remodeling during exercise. Increased muscular activity stimulates SC accumulation and function, but to what extend alternations in mechanical load control SC fusion remains to be elucidated. To investigate SC contribution to myofibers during exercise training, we labeled SCs by excising tdTomato (mT) in Pax7CreERT2/+; Rosa26mTmG/+ mice, resulting in an mEGFP (mG) labeling of all PAX7+ cells and derived myofibers (Figure
1A). Using this genetic lineage tracing model, we here show that SCs extensively contribute to myofibers during exercise and that this occurs exclusively in hindlimb plantar flexors. Upon 8‐weeks of voluntary free running (VRun), 60% of all m. soleus myofibers had at least one SC fused (mG+). Moreover, adding load to the wheel (VResRun) increased the number of mG+ myofibers to 80%, indicating that SC fusion during exercise is load dependent (Figure
1B). Since only the VResRun showed substantial muscle hypertrophy in both m. soleus and m. plantaris, this data suggests that next to hypertrophy, also endurance‐training adaptions are mirrored by extensive SC fusion. Finally, exercise training induced a shift towards an oxidative fiber type, but SC fusion was similar in oxidative and glycolytic fibers. Collectively, we show that voluntary running strongly induces SC fusion in both free and resistance running conditions, but the latter only induced muscle hypertrophy. Thus, our findings suggest that SC fusion cannot only serve hypertrophy, since we also observed significant contribution under ‘endurance’ settings.

Support or Funding Information

Internal funding ETH Zurich

Exercise induces satellite cell fusion in a load‐dependent manner. (A) mouse model and experimental protocol. (B) mG expression in mouse hindlimb muscle under sedentary (control) and running (VRun and VResRun) conditions. *** p<0.001, ** p<0.01.

Figure 1
Codon Optimization of Gene Editing CRISPR‐SaCas9 Plasmid Increases Protein Expression in Human Liver Cells to Boost in vivo Therapeutic Knockout Application Efficiency
Authors: Madejski Irene R. , Sundaresan Avirath , Groshong Tyler L. , Holmes Grace D. , Gupta Ishir G. , De Luke
Published: April 2020

The CRISPR‐Cas9 gene editing technology shows great promise in revolutionizing the treatment of genetic disease; however, the current focus on treatment by ex vivo delivery is limited to blood diseases. In vivo treatment can substantially extend the clinical reach of the technology, but is limited by a challenging delivery process: the large size of the Cas9 gene (~4500bp) inhibits delivery by the small viral vectors and lipid nanoparticles used. We propose that a codon‐optimized saCas9 plasmid will lead to significantly higher protein expression than the presently used genes; this can compensate for the low delivery efficiency and has great potential to improve the viability of in vivo CRISPR‐Cas9 therapies. Here we present Western Blot fluorescence data showing that optimization leads to increased Cas9 production and subsequently increased CRISPR‐Cas9 editing efficiency.

A commonly used parent saCas9 sequence was selected from Addgene’s public plasmid database. A novel, codon‐optimized gene sequence was engineered from the parent using GenScript’s OptimumGene™ algorithm. Both the optimized gene and parent gene were transfected into human HepG2 liver cells, and Western Blot/ELISA protein quantification of the optimized plasmid compared with three sample plasmids demonstrated that the codon‐optimized gene expressed the saCas9 protein at ~3.5× the rate of the commercial sequence. The same set of optimized and commercial plasmids were then transfected into GFP‐stable HepG2 cells in parallel with GFP‐specific sgRNA; the cells transfected with optimized saCas9 demonstrated a significantly higher GFP knockout rate than cells transfected with commercially available control plasmids, as measured through GFP detection stay and Western Blot on GFP proteins. The augmented Cas9 protein expression supported by the novel saCas9 sequence can better enable in vivo CRISPR‐Cas9 treatments.

Support or Funding Information

This research was supported by The Nueva School.

ELISA protein quantification assay indicated that codon‐optimized SaCas9 displayed a 3.17‐fold and a 3.5‐fold increase in expression over its parent gene in Sample Group 1 and Sample Group 2, respectively.

Figure 1
Use of Specific Inhibitory Antibodies for P450 Reaction Phenotyping of Investigational Drugs
Authors: Lasker Jerome Michael
Published: April 2020

Identifying the CYP450 enzymes underlying metabolism of investigational drugs (i.e., P450 reaction phenotyping; PRP) is critical to the development of effective therapeutics. Information gained from such studies can: a) provide insight into structural modifications of test drugs in order to improve metabolic stability and; b) specify an estimate of drug‐drug interaction potential as well as that of interindividual and species differences in oxidative metabolism. CYP450 chemical inhibitors (e.g., a‐naphthoflavone and sulfaphenazole) are often used in reaction phenotyping studies but the outcome is sometimes equivocal due to the non‐specific effects of these chemical agents plus their capacity to undergo P450‐dependent catabolism. In contrast, inhibitory P450 antibodies offer high specificity and irreversibility, and may thus represent a superior approach for characterizing individual P450 enzyme involvement in drug metabolism. We recently developed a compilation of highly‐specific polyclonal and monoclonal antibodies to the CYP450s comprising the major oxidative drug‐metabolizing enzymes in human liver, including CYP1A2, CYP2C8, CYP2C9, CYP2C19, CYP2D6 and CYP3A4 (aka CYP ImmunoInhibit antibodies). As shown here, each of these antibodies proved capable of eliciting > 80% inhibition of probe drug metabolism by the cognate P450 antigens in human liver microsomes (HLMx), while giving insignificant effects on different CYP450s (Figure
1). The inhibition observed with each of the six CYP450 antibodies was not only highly‐specific but was also dose‐dependent, with maximal inhibition (80–90%) achieved at IgG:microsomal protein ratios ranging from 0.1 mg/mg to 3 mg/mg (Figure
2). Control (pre‐immune) antibodies had no effect on substrate metabolism. Such results show that inhibitory antibodies coupled with HLMx represent an alternative and powerful approach to chemical inhibitors for evaluating involvement of specific P450 enzymes in the hepatic metabolism of investigational drugs. Interestingly, studies ongoing with CYP ImmunoInhibit antibodies and MetMax™ cryopreserved human hepatocytes, which are liver cells that have been permeabilized and cryopreserved, have given analogous results to those achieved with HLMx. The utilization of inhibitory antibodies with HLMx represents an accurate model for PRP of new therapeutics due to the specificity of these immunoreagents, and the irreversible nature of the inhibition achieved, an important benefit when working with metabolically‐stable test agents.

Specific Inhibition of Microsomal Drug Metabolism by CYP ImmunoInhibit Antibodies

Figure 1

Dose‐Response Inhibition of Microsomal Drug Metabolism by CYP ImmunoInhibit Antibodies

Figure 2
White angico gum reduces the mast cell count in the duodenum and jejunum of mice subjected to intestinal mucositis
Authors: Pimenta Helder Bindá , Menslin Kimberlly , Cunha João Luiz , Nunes João Victor , Oliveira Ana Carolina , da Silva Stephany Caroline , Biason Giovanna , ALVES Ronny Helson , Vidinha Alice Cristina , Lopes Matheus , Santos Victor Rodrigo , Queiroz Herdeson Araújo , de Farias Sérgio Augusto , Nicolau Júlia Fernanda Alencar , de Carvalho Vale Larice , Barbosa Maria Lucianny Lima , Cerqueira Gilberto Santos
Published: April 2020

Intestinal mucositis was induced by the administration of 5‐FU in a single dose of 450mg/kg on the first day of the protocol in Swiss mice, and groups of animals that received dosages of angico branco were treated between the second and the fifth day, culminating in euthanasia and removal of intestinal segments for further analysis. Initially, through histopathological and morphometric findings, the severity of mucositis was demonstrated in this study, through aspects related to tissue architecture, focusing on the reduction and vacuolization of intestinal villi, crypt necrosis, infiltration of inflammatory cells, loss of inflammation cell architecture, decreased villus/crypt ratio, caused in the group of animals that received the 5‐FU dose. However, the group of animals that were treated with angico branco gum at a dose of 400mg/kg, after induction of intestinal mucositis, attenuation of these deleterious effects promoted by 5‐FU was observed, among which we can mention: less inflammatory infiltrate, maintenance of cellular architecture, attenuation of villus shortening and crypt depth, decrease of crypt necrosis, also evidenced by the better villus/crypt ratio. These effects, however, were not seen in the ileum. Treatment with white angelic gum at doses of 100 mg/kg; 200 mg/kg and 400 mg/kg promoted a statistically significant reduction (p <0.05) in the number of mast cells when confronted with the 5‐FU group in the duodenum and jejunum. In contrast, treatment with white angico gum reversed the mastocytosis observed by the increase in mast cell count in the intestinal segments of animals submitted to mucositis. In addition, the saline group did not show an increase in mast cells when compared to the group with 5‐FU. Studies that evaluated the role of mast cells in mucositis also revealed the participation of these substances in the course of intestinal mucositis (PEREIRA JUNIOR, 2017; MIRANDA, 2018). The study by Nogueira et al. (2017) also demonstrated a significant increase in the number of total and degranulated mast cells in the intestinal segments of animals subjected to irinotecan‐induced intestinal mucositis, with a release of pro‐inflammatory mediators in the inflammatory condition. Through the results found in this study it can be concluded that the gum of angico reduced the mast cell count and preserved the number of goblet cells after induction of intestinal mucositis induced by 5‐FU in mice.

White angico gum reduces the mast cell count in the duodenum, jejunum of mice subjected to intestinal mucositis induced by 5‐FU.

Figure 1
Exercise‐induced Extracellular Vesicles’ Effect on Stress.
Authors: Yoon Kyeong Jin , Cho Hae-Sung , Lee WonSang , Moon HyoYoul
Published: April 2020

Modern society changes faster and more complicated. It causes stress on mentally and physically. Especially stress can increase anxiety. The evidence that anxiety is associated with mental disorder such as depression and suicide is increasing. This phenomenon elevates social burden in public health.

Exercise induces releasing extracellular vesicles (EVs) into circulation system that can be signaling molecules between organs. EVs have micro RNAs (miRNA) that regulate genes through inhibiting translation or degrading messenger RNA. Also, previous studies found that EVs can cross the blood‐brain barrier and it may be the role of neurotransmitters. However, the underlying mechanism of EVs on stress is not fully elucidated.

To investigate the direct role of exercise‐derived EVs on brain function, we isolated the EVs from serum of sedentary or voluntary exercised mice. Then we analyzed the behavioral changes with chronic unpredictable mild stress (CUMS) induced anxiety mice after administration of total 0.3 ug of exercise or sedentary derived EVs into the left cerebral ventricle. We found that exercise derived EVs reduced the symptom of anxiety in a nest building test compared to control groups while there were no differences in the rotarod test or oft between groups. Furthermore, we observed that exercise‐derived EVs enhanced the neurogenic markers such as NOR1 and PAX6.

We further characterized the changes of miRNA profile packaged in serum EVs after 4 weeks of voluntary exercise. miRNA sequencing results showed that 82 miRNAs (46 genes up and 36 genes down) changed by exercise. Using bioinformatics tools, we found that 17 miRNAs were commonly related with response to oxygen level. Among 8353 predicted targeting genes regulated by these 17 miRNAs, we selected 190 genes which were overlapped above 4 miRNAs. 13.04% of 190 genes were related with central nervous system neuron differentiation and TOR signaling, respectively and 8.7% of genes connected with sarcoplasmic reticulum.

These results suggest that exercise‐derived EVs may be involved in anti‐anxiety like effect of exercise partially via neurogenesis. We believe our findings can propose the possibility of therapeutic strategy through exercise‐derived EVs in anxiety disorder.

Support or Funding Information

This work was supported by the National Research Foundation (NRF, 700‐20190019), Korea Mouse Phenotype Center (NRF, 2019M3A9D5A01102794) and Research Resettlement Fund for the new faculty of Seoul National University.

Characters of Extracellular vehicles.

Figure 1

Injection of EVs in stress treated mice.

Figure 2
A framework for parsing heritable information
Authors: Jose Antony M.
Published: April 2020

Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here, I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.) and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This entity–sensor–property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.
Science and War at the Limit of Empire: William Griffith with the Army of the Indus
Authors: Fleetwood Lachlan
Published: April 2020

In 1839, at the outset of the First Anglo-Afghan War, East India Company surgeon and naturalist William Griffith (1810–1845) set out for Afghanistan with the so-called ‘Army of the Indus’. That science, empire, and war were inextricably linked in the nineteenth century is widely acknowledged by scholars, as is the way that natural history collecting was dependent on military (and especially naval) infrastructure. However, the everyday practices and negotiations that underpinned collecting in the context of colonial warfare remain less well understood. Here, Griffith's scientific activities—especially the collection of plant and fish specimens—provide an instructive case, constantly circumscribed by his operating within an invading and then occupying army. Tensions frequently emerged between military and scientific objectives, as well as between Griffith and the numerous collectors and assistants he relied on within the army column and occupied territory (including a broker named Abdul Rozak, a series of fishermen, and a mullah at Kandahar). By making a close study of the relationship between military and scientific practice during the First Anglo-Afghan War (later remembered as one of the most notorious ‘disasters’ in the history of the British Empire), this article demonstrates the intimate linkages between imperial violence and knowledge production in this period. More broadly, an examination of Griffith's collecting practices reveals the way in which imperial geographical and environmental perceptions of Afghanistan were shaped and reified at a crucial moment in its history.
A damage model for collagen fibres with an application to collagenous soft tissues
Authors: Holzapfel Gerhard A. , Ogden Ray W.
Published: April 2020

We propose a mechanical model to account for progressive damage in collagen fibres within fibrous soft tissues. The model has a similar basis to the pseudoelastic model that describes the Mullins effect in rubber but it also accounts for the effect of cross-links between collagen fibres. We show that the model is able to capture experimental data obtained from rat tail tendon fibres, and the combined effect of damage and collagen cross-links is illustrated for a simple shear test. The proposed three-dimensional framework allows a straightforward implementation in finite-element codes, which are needed to analyse more complex boundary-value problems for soft tissues under supra-physiological loading or tissues weakened by disease.
The generalized viscoelastic spring
Authors: Soldatos Kostas P.
Published: April 2020

A spring/rod model is presented that describes one-dimensional behaviour of solids susceptible to large or small viscoelastic deformation. Derivation of its constitutive equation is underpinned by the fact that the internal energy, which the elastic part of deformation stores in the spring, changes in time with the observed strain as well as with some, unknown part of the strain-rate. The latter emerges through the action of a viscous flow potential and is the source of inelastic deformation. Thus, unlike its conventional viscoelasticity counterparts, the model does not postulate
a priori
a rule that relates strain with viscous flow formation. Instead, it considers that such a rule, as well as other important features of combined elastic and inelastic material response, should become known
a posteriori
through the solution of a relevant, well-posed boundary value problem. This paper begins with considerations compatible with large viscoelastic deformations and gradually progresses through simpler modelling situations. The latter also include the case of small viscoelastic strain that underpins formulation of classical, spring-dashpot viscoelastic models. In an example application, a relevant closed-form solution is obtained for a spring undergoing small viscoelastic deformation under the influence of a viscous flow potential which is quadratic in the stress.
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region
Authors: Maurano Matthew T. , Ramaswami Sitharam , Zappile Paul , Dimartino Dacia , Boytard Ludovic , Ribeiro-dos-Santos André M. , Vulpescu Nicholas A. , Westby Gael , Shen Guomiao , Feng Xiaojun , Hogan Megan S. , Ragonnet-Cronin Manon , Geidelberg Lily , Marier Christian , Meyn Peter , Zhang Yutong , Cadley John , Ordoñez Raquel , Luther Raven , Huang Emily , Guzman Emily , Arguelles-Grande Carolina , Argyropoulos Kimon V. , Black Margaret , Serrano Antonio , Call Melissa E. , Kim Min Jae , Belovarac Brendan , Gindin Tatyana , Lytle Andrew , Pinnell Jared , Vougiouklakis Theodore , Chen John , Lin Lawrence H. , Rapkiewicz Amy , Raabe Vanessa , Samanovic Marie I. , Jour George , Osman Iman , Aguero-Rosenfeld Maria , Mulligan Mark J. , Volz Erik M. , Cotzia Paolo , Snuderl Matija , Heguy Adriana
Published: April 2020

Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in Spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.
Dynamic Detection of Delayed Cerebral Ischemia Using Machine Learning
Authors: Megjhani Murad , Terilli Kalijah , Alkhachroum Ayham , Roh David J. , Agarwal Sachin , Connolly E. Sander , Velazquez Angela , Boehme Amelia , Claassen Jan , Park Soojin
Published: April 2020

Objective

To develop a machine learning based tool, using routine vital signs, to assess delayed cerebral ischemia (DCI) risk over time.

Methods

In this retrospective analysis, physiologic data for 540 consecutive acute subarachnoid hemorrhage patients were collected and annotated as part of a prospective observational cohort study between May 2006 and December 2014. Patients were excluded if (i) no physiologic data was available, (ii) they expired prior to the DCI onset window (< post bleed day 3) or (iii) early angiographic vasospasm was detected on admitting angiogram. DCI was prospectively labeled by consensus of treating physicians. Occurrence of DCI was classified using various machine learning approaches including logistic regression, random forest, support vector machine (linear and kernel), and an ensemble classifier, trained on vitals and subject characteristic features. Hourly risk scores were generated as the posterior probability at timet. We performed five-fold nested cross validation to tune the model parameters and to report the accuracy. All classifiers were evaluated for good discrimination using the area under the receiver operating characteristic curve (AU-ROC) and confusion matrices.

Results

Of 310 patients included in our final analysis, 101 (32.6%) patients developed DCI. We achieved maximal classification of 0.81 [0.75-0.82] AU-ROC. We also predicted 74.7 % of all DCI events 12 hours before typical clinical detection with a ratio of 3 true alerts for every 2 false alerts.

Conclusion

A data-driven machine learning based detection tool offered hourly assessments of DCI risk and incorporated new physiologic information over time.
Early forecasts of the evolution of the COVID-19 outbreaks and quantitative assessment of the effectiveness of countering measures
Authors: Daddi Emanuele , Giavalisco Mauro
Published: April 2020

We discovered that the time evolution of the inverse fractional daily growth of new infections,N/ΔN, in the current outbreak of COVID-19 is accurately described by a universal function, namely the two-parameter Gumbel cumulative function, in all countries that we have investigated. While the two Gumbel parameters, as determined bit fits to the data, vary from country to country (and even within different regions of the same country), reflecting the diversity and efficacy of the adopted containment measures, the functional form of the evolution of ΔN/Nappears to be universal. The result of the fit in a given region or country appears to be stable against variations of the selected time interval. This makes it possible to robustly estimate the two parameters from the data data even over relatively small time periods. In turn, this allows one to predict with large advance and well-controlled confidence levels, the time of the peak in the daily new infections, its magnitude and duration (hence the total infections), as well as the time when the daily new infections decrease to a pre-set value (e.g. less than about 2 new infections per day per million people), which can be very useful for planning the reopening of economic and social activities. We use this formalism to predict and compare these key features of the evolution of the COVID-19 disease in a number of countries and provide a quantitative assessment of the degree of success in in their efforts to countain the outbreak.
COVID-19-Associated Acute Disseminated Encephalomyelitis – A Case Report
Authors: Zhang Tianshu , Rodricks Michael B. , Hirsh Ellen
Published: April 2020

We present the first described case of acute disseminated encephalomyelitis (ADEM) in a COVID-19 patient. The clinical features with head CT and brain MRI changes were described. Our described case is an atypical presentation of the novel coronavirus in a young patient and is illustrative of the possible approaches to explore the treatable differential etiologies.
Smoking does not alter treatment effect of intravenous thrombolysis in mild to moderate acute ischemic stroke – a Dutch String-of-Pearls Institute (PSI) Stoke Study
Authors: Kufner Anna , Ebinger Martin , Luijckx Gert Jan , Endres Matthias , Siegerink Bob ,   Dutch String-of-Pearls Stroke Study Group
Published: April 2020

Background

The smoking-thrombolysis paradox refers to a better outcome in smokers who suffer from acute ischemic stroke (AIS) following treatment with thrombolysis. However, studies on this subject have yielded contradictory results and an interaction analysis of exposure to smoking and thrombolysis in a large, multicenter database is lacking.

Methods

Consecutive AIS patients admitted within 12 hours of symptom onset between 2009 and 2014 from the prospective, multicenter stroke registry (Dutch String-of-Pearls Stroke Study) were included for this analysis. We performed a generalized linear model for functional outcome three months post-stroke depending on risk of the exposure variables (smoking yes/no, thrombolysis yes/no). The following confounders were adjusted for: smoking, hypertension, atrial fibrillation, stroke severity, and stroke etiology.

Results

Out of 468 patients, 30.6% were smokers and median baseline NIHSS was 3 (interquartile range 1-6). Smoking alone had a crude and adjusted relative risk (RR) of 0.99 (95% CI 0.89-1.10) and 0.97 (95%CI 0.87-1.01) for good outcome (modified Rankin Score ≤2), respectively. A combination of exposure variables (smoking and thrombolysis) did not change the results significantly (crude RR 0.87 [95% CI 0.74-1.03], adjusted RR 1.1 [95%CI 0.93-1.33]). Smoking alone had an adjusted RR of 1.2 (95% CI 0.6-2.7) for recanalization following thrombolysis (N=88).

Conclusions

In patients with mild to moderate AIS admitted within 12 hours of symptom onset, smoking did not modify treatment effect of thrombolysis.
A scientometric overview of CORD-19
Authors: Colavizza Giovanni , Costas Rodrigo , Traag Vincent A. , van Eck Nees Jan , van Leeuwen Thed , Waltman Ludo
Published: April 2020

As the COVID-19 pandemic unfolds, researchers from all disciplines are coming together and contributing their expertise. CORD-19, a dataset of COVID-19 and coronavirus publications, has been made available along-side calls to help mine the information it contains and to create tools to search it more effectively. We analyse the delineation of the publications included in CORD-19 from a scientometric perspective. Based on a comparison to the Web of Science database, we find that CORD-19 provides an almost complete coverage of research on COVID-19 and coronaviruses. CORD-19 contains not only research that deals directly with COVID-19 and coronaviruses, but also research on viruses in general. Publications from CORD-19 focus mostly on a few well-defined research areas, in particular: coronaviruses (primarily SARS-CoV, MERS-CoV and SARS-CoV-2); public health and viral epidemics; molecular biology of viruses; influenza and other families of viruses; immunology and antivirals; clinical medicine. CORD-19 publications that appeared in 2020, especially editorials and letters, are disproportionately popular on social media. While we fully endorse the CORD-19 initiative, it is important to be aware that CORD-19 extends beyond research on COVID-19 and coronaviruses.
Harmful DNA:RNA hybrids are formedin cisand in a Rad51-independent manner
Authors: Lafuente-Barquero Juan , Martin-Alonso Marta San , Gómez-González Belén , Aguilera Andrés
Published: April 2020

DNA:RNA hybrids constitute a well-known source of recombinogenic DNA damage. The current literature is in agreement with DNA:RNA hybrids being produced co-transcriptionally by the invasion of the nascent RNA molecule producedin ciswith its DNA template. However, it has also been suggested that recombinogenic DNA:RNA hybrids could be facilitated by the invasion of RNA molecules producedin transin a Rad51-mediated reaction. Here, we tested the possibility that such DNA:RNA hybrids producedin transconstitute a source of recombinogenic DNA damage taking advantage of Rad51-independent single-strand annealing recombination assays and new constructs designed to induce expression of mRNA transcriptsin transin the yeastSaccharomyces cerevisiae.We show that unscheduled and recombinogenic DNA:RNA hybrids are formed incisduring transcription and in a Rad51-independent manner.
Surface electrostatics govern the emulsion stability of biomolecular condensates
Authors: Welsh Timothy J. , Krainer Georg , Espinosa Jorge R. , Joseph Jerelle A. , Sridhar Akshay , Jahnel Marcus , Arter William E. , Saar Kadi L. , Alberti Simon , Collepardo-Guevara Rosana , Knowles Tuomas P.J.
Published: April 2020

Liquid–liquid phase separation underlies the formation of biological condensates. Physically, such systems are microemulsions which have a general propensity to fuse and coalesce; however, many condensates persist as independent droplets inside cells. This stability is crucial for their functioning, but the physicochemical mechanisms that control the emulsion stability of condensates remain poorly understood. Here, by combining single-condensate zeta potential measurements, optical microscopy, tweezer experiments, and multiscale molecular modelling, we investigate how the forces that sustain condensates impact their stability against fusion. By comparing PR25:PolyU and FUS condensates, we show that a higher condensate surface charge correlates with a lower fusion propensity, and that this behavior can be inferred from their zeta potentials. We reveal that overall stabilization against fusion stems from a combination of repulsive forces between condensates and the effects that surface electrostatics have on lowering surface tension, thus shedding light on the molecular determinants of condensate coalescence.
A method for validating the accuracy of NMR protein structures
Authors: Fowler Nicholas J. , Sljoka Adnan , Williamson Mike P.
Published: April 2020

We present a method, Accuracy of NMR Structures using Random Coil Index and Rigidity (ANSURR), that measures the accuracy of NMR protein structures. It provides a residue-by-residue comparison of two measures of local rigidity: the Random Coil Index [RCI] (a measure of the extent to which backbone chemical shifts adopt random coil values); and local rigidity predicted by mathematical rigidity theory using the computational method Floppy Inclusion and Rigid Substructure Topology [FIRST], calculated from an NMR structural model. We compare RCI and FIRST using acorrelation score(which assesses the location of secondary structure), and anRMSD score(which measures overall rigidity, and mainly assesses hydrogen bond correctness). We test the performance of ANSURR using: (a) structures refined in explicit solvent, which have much better RMSD score than unrefined structures, though similar correlation; (b) decoy structures generated for 89 NMR structures. The experimental NMR structures are usually better, though helical and sheet structures behave differently; (c) conventional predictors of structural accuracy such as number of restraints per residue, restraint violations, energy of structure, RMSD of the ensemble (precision of the calculation), Ramachandran distribution, and clashscore. Comparisons of NMR to crystal structures show that secondary structure is equally accurate in both, but crystal structures tend to be too rigid in loops, whereas NMR structures tend to be too floppy overall.
SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology
Authors: Ogando Natacha S. , Dalebout Tim J. , Zevenhoven-Dobbe Jessika C. , Limpens Ronald W. , van der Meer Yvonne , Caly Leon , Druce Julian , de Vries Jutte J. C. , Kikkert Marjolein , Bárcena Montserrat , Sidorov Igor , Snijder Eric J.
Published: April 2020

The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of nonstructural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (Remdesivir, Alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that - upon passaging in Vero E6 cells - SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative ‘furin-like cleavage site’ in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays.
Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index
Authors: Laforest-Lapointe Isabelle , Becker Allan B. , Mandhane Piushkumar J. , Turvey Stuart E. , Moraes Theo J. , Sears Malcolm R. , Subbarao Padmaja , Sycuro Laura K. , Azad Meghan B. , Arrieta Marie-Claire
Published: April 2020

Artificial sweetener consumption by pregnant women has been associated with an increased risk of infant obesity, but the underlying mechanisms are unknown. We aimed to determine if maternal consumption of artificially sweetened beverages (ASB) during pregnancy is associated with modifications of infant gut bacterial community composition during the first year of life, and whether these alterations are linked with infant body mass index (BMI) at one year of age. This research included 100 infants from the prospective Canadian CHILD Cohort Study, selected based on maternal ASB consumption during pregnancy (50 non-consumers and 50 daily consumers). We identified four microbiome clusters, of which two recapitulated the maturation trajectory of the infant gut bacterial communities from immature to mature and two deviated from this trajectory. Maternal ASB consumption was associated with the depletion of several Bacteroides sp. and higher infant BMI. As we face an unprecedented rise in childhood obesity, future studies should evaluate the causal role of gut microbiota in the association between maternal ASB consumption, infant development and metabolism, and body composition.
Simulating Multiple Substrate Binding Events by γ-Glutamyltransferase using Accelerated Molecular Dynamics
Authors: Oliva Francesco , Flores-Canales Jose C. , Pieraccini Stefano , Morelli Carlo F. , Sironi Maurizio , Schiøtt Birgit
Published: April 2020

γ-glutamyltransferase (GGT) is an enzyme that uses γ-glutamyl compounds as substrate and catalyzes their transfer into a water molecule or an acceptor substrate with varied physiological-function in bacteria, plants and animals. Crystal structures of GGT are known for different species and in different states of the chemical reaction; however, structural dynamics of the substrate binding to the catalytic site of GGT is unknown. Here, we modeledEscherichia ColiGGT’s glutamine binding by using a swarm of accelerated molecular dynamics (aMD) simulations. Characterization of multiple binding events identified three structural binding motifs composed of polar residues in the binding pocket that govern glutamine binding into the active site. Simulated open and closed conformations of a lid-loop protecting the binding cavity suggests its role as a gating element by allowing or blocking substrates entry into the binding pocket. Partially open states of the lid-loop are accessible within thermal fluctuations, while the estimated free energy cost of a complete open state is 2.4 kcal/mol. Our results suggest that both specific electrostatic interactions and GGT conformational dynamics dictate the molecular recognition of substrate-GGT complexes.
Time-resolved cryoEM using Spotiton
Authors: Dandey Venkata P. , Budell William C. , Wei Hui , Bobe Daija , Maruthi Kashyap , Kopylov Mykhailo , Eng Edward , Kahn Peter A. , Hinshaw Jenny E. , Kundu Nidhi , Nimigean Crina M. , Fan Chen , Sukomon Nattakan , Darst Seth , Saecker Ruth , Chen James , Malone Brandon , Potter Clinton S. , Carragher Bridget
Published: April 2020

We present an approach for preparing cryoEM grids to study short-lived molecular states. Using piezo electric dispensing, two independent streams of ~50 pL sample drops are deposited within 10 ms of each other onto a nanowire EM grid surface, and the mixing reaction stops when the grid is vitrified in liquid ethane, on the order of ~100 ms later. We demonstrate the utility of this approach for four biological systems where short-lived states are of high interest.
Functional Interrogation ofHOXA9Regulome in MLLr Leukemia via Reporter-based CRISPR/Cas9 screen
Authors: Zhang Hao , Zhang Yang , Wright Shaela , Hyle Judith , Zhao Lianzhong , An Jie , Zhou Xinyue , Zhao Xujie , Shao Ying , Lee Hyeong-Min , Chen Taosheng , Zhou Yang , Lu Rui , Li Chunliang
Published: April 2020

AberrantHOXA9expression is a hallmark of most aggressive acute leukemias, including human acute myeloid leukemia (AML) and subtypes of acute lymphoblastic leukemia (ALL).HOXA9overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding ofHOXA9regulation in leukemia is limited, hindering development of therapeutic strategies to treatHOXA9-driven leukemia. To mitigate these challenges, we generated the firstHOXA9-mCherryknock-in reporter in an MLL-rearranged (MLLr) B-ALL cell line to dissectHOXA9regulation. By utilizing the reporter and CRISPR/Cas9 mediated screens, we identified transcription factors controllingHOXA9expression, including a novel regulator, USF2 and its homolog USF1. USF1/USF2 depletion significantly down-regulatedHOXA9expression and impaired MLLr leukemia cell proliferation. Ectopic expression of HOXA9-MEIS1 fusion protein rescued the impaired leukemia cell proliferation upon USF2 loss. Cut&Run analysis revealed the direct occupancy of USF2 ontoHOXA9promoter in MLLr leukemia cells. Collectively, theHOXA9reporter facilitated the functional interrogation of theHOXA9regulome and has advanced our understanding of the molecular regulation network inHOXA9-driven leukemia.
A CRISPR-Cas9–engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions
Authors: de los Santos Miguel Rodríguez , Rivalan Marion , David Friederike S. , Stumpf Alexander , Pitsch Julika , Tsortouktzidis Despina , Velasquez Laura Moreno , Voigt Anne , Schilling Karl , Mattei Daniele , Long Melissa , Vogt Guido , Knaus Alexej , Fischer-Zirnsak Björn , Wittler Lars , Timmermann Bernd , Robinson Peter N. , Horn Denise , Mundlos Stefan , Kornak Uwe , Becker Albert J. , Schmitz Dietmar , Winter York , Krawitz Peter M.
Published: April 2020

Pathogenic germline mutations inPIGVlead to glycosylphosphatidylinositol biosynthesis deficiency (GPIBD). Individuals with pathogenic biallelic mutations in genes of the glycosylphosphatidylinositol (GPI) anchor pathway exhibit cognitive impairments, motor delay, and often epilepsy. Thus far, the pathophysiology underlying the disease remains unclear, and suitable rodent models that mirror all symptoms observed in human patients have not been available. Therefore, we used CRISPR-Cas9 to introduce the most prevalent hypomorphic missense mutation in European patients,Pigv:c.1022C>A (p.A341E), at a site that is conserved in mice. Mirroring the human pathology, mutantPigv341Emice exhibited deficits in motor coordination, cognitive impairments, and alterations in sociability and sleep patterns, as well as increased seizure susceptibility. Furthermore, immunohistochemistry revealed reduced synaptophysin immunoreactivity inPigv341Emice, and electrophysiology recordings showed decreased hippocampal synaptic transmission that could underlie impaired memory formation. In single-cell RNA sequencing,Pigv341E-hippocampal cells exhibited changes in gene expression, most prominently in a subtype of microglia and subicular neurons. A significant reduction inAbl1transcript levels in several cell clusters suggested a link to the signaling pathway of GPI-anchored ephrins. We also observed elevated levels ofHdctranscripts, which might affect histamine metabolism with consequences for circadian rhythm. This new mouse model will not only open the doors to further investigation into the pathophysiology of GPIBD, but will also deepen our understanding of the role of GPI-anchor–related pathways in brain development.

Significance statement

Inherited GPI-anchor biosynthesis deficiencies (IGDs) explain many cases of syndromic intellectual disability. Although diagnostic methods are improving, the pathophysiology underlying the disease remains unclear. Furthermore, we lack rodent models suitable for characterizing cognitive and social disabilities. To address this issue, we generated the first viable mouse model for an IGD that mirrors the condition in human patients with a behavioral phenotype and susceptibility to epilepsy. Using the new model, we obtained neurological insights such as deficits in synaptic transmission that will facilitate understanding of the pathophysiology of IGDs.
Digestive parameters during gestation of Holstein heifers
Authors: Vieira Pereira Jéssica Marcela , Marcondes Marcos Inácio , de Campos Valadares Filho Sebastião , Caton Joel , Lacerda Sguizzato Anna Luiza , Silva Alex Lopes , da Silva Julia Travassos , Lima Moraes Valber Carlos , Gomes Lucas Faria , Rotta Polyana Pizzi
Published: April 2020

Our objective was to estimate nutrient intake, ruminal flow, total apparent and ruminal digestibility, rates of passage and digestion, ruminal and omasal pH, blood metabolite concentrations, and body measurements during gestation of Holstein heifers. Eleven pregnant Holstein heifers, 8 of which fitted with a rumen cannula (450 ± 27.6 kg of body weight and 20 ± 3.5 months of initial age) were used. All heifers received the same diet composed of corn silage, soybean meal, corn meal, minerals and vitamins, with a corn silage:concentrate ratio of 50:50 (on a dry matter basis), aiming an average daily gain of approximately 1.0 kg. The sampling periods were established according to the days of gestation: 145, 200, and 255 with a duration of 10 days per period. Total fecal samples were collected to estimate dry matter, organic matter, crude protein, and neutral detergent fiber digestibility. Blood samples were collected to analyze metabolites (non-esterified fatty acids, β-hydroxybutyrate, urea, and glucose). Data were analyzed as a repeated measurements scheme, using MIXED procedure, with differences declared whenP< 0.05. Dry matter intake expressed in kg/day increased from d-145 to d-200, and remaining stable until d-255 of gestation. The same results were observed for organic matter and crude protein intake, increasing 15.0 and 35.8% respectively. In contrast, when dry matter intake was evaluated as % body weight, we observed a decrease of 16.7% from d-200 to d-255. Days of gestation did not influence ruminal flow of dry matter, organic matter, crude protein, and neutral detergent fiber. We observed an increase in the ruminal digestibility of neutral detergent fiber by 20.5%. The apparent total-tract digestibility of dry matter, organic matter, and crude protein changed over days of gestation, with an increase of 11.9, 8.5, and 9.8%, respectively, when comparing d-145 with d-200. The rate of digestion of neutral detergent fiber increased from 2.0 to 3.5% h-1. Glucose levels decreased, while β-hydroxybutirate and non-esterified fatty acids increased from d-145 to d-255. In conclusion, our results demonstrate a reduction in dry matter intake in % body weight due to pregnancy. It also shows an increase in total apparent digestibility through gestation, which imply a greater efficiency of use of nutrients by pregnant animals. Thus, further research is still needed to consolidate such results and to elucidate the mechanism about nutrient usage during the final third of gestation in heifers.