bluuebunny/crossref_metadata_2025 huggingface dataset:
Cocaine Use and Levamisole-Induced Vasculitis
Authors: Engels Dawn
Published: March 2020

BACKGROUND:

Levamisole is an immunomodulatory medication previously used to treat rheumatoid arthritis and some types of cancers; it was banned for use in humans in 2000 owing to its harmful side effects. Use of levamisole-laced cocaine is associated with a life-threatening syndrome characterized by a necrotizing purpuric rash leading to tissue destruction and necrotic wounds. This Clinical Challenges article summarizes our experience with the care of 2 adult women diagnosed with levamisole-related vasculitis.

CASE:

Case 1 is a 46-year-old woman who presented with joint pain in her hands and legs, along with bilateral ear pain, swelling, and bleeding. She was initially diagnosed with vasculitis and possible systemic lupus erythematosus. She experienced multiple recurrences and exacerbation of her condition over a period of months. She was ultimately diagnosed with levamisole-related vasculitis from recurrent cocaine use resulting in bilateral above the knee amputations. The second case is a 50-year-old woman who presented to our emergency department with redness and swelling of her bilateral lower extremities. She developed blisters and pustules that rapidly evolved into abscesses and red lesions over the course of several months. Her wounds also deteriorated despite topical therapy that occurred in a context of recurring use of cocaine.

CONCLUSIONS:

Our experience with these cases suggests that WOC nurses should consider levamisole-induced vasculitis in all patients presenting with unexplained vasculitis-type lesions, and particularly when these lesions occur in the context of known or suspected use of illicit substances such as cocaine. Given the absence of clinical guidelines for this increasingly prevalent condition, we recommend wound care based on principles of moist wound healing, combined with judicious use of therapies with antimicrobial activity and nonadherent dressings to reduce pain. Finally, we strongly recommend that care of these patients occurs as one part of a multidisciplinary care approach that focuses on cessation of the use of cocaine and all other illicit substances.
Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes
Authors: Freitas Ana R. , Tedim Ana P. , Novais Carla , Lanza Val F. , Peixe Luísa
Published: March 2020

Linezolid-resistant

Enterococcus faecalis

(LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive

E. faecalis

genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from

Firmicutes

. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of

E. faecalis

genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.
Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China
Authors: Wang Chaolong , Liu Li , Hao Xingjie , Guo Huan , Wang Qi , Huang Jiao , He Na , Yu Hongjie , Lin Xihong , Pan An , Wei Sheng , Wu Tangchun
Published: March 2020

BACKGROUND

We described the epidemiological features of the coronavirus disease 2019 (Covid-19) outbreak, and evaluated the impact of non-pharmaceutical interventions on the epidemic in Wuhan, China.

METHODS

Individual-level data on 25,961 laboratory-confirmed Covid-19 cases reported through February 18, 2020 were extracted from the municipal Notifiable Disease Report System. Based on key events and interventions, we divided the epidemic into four periods: before January 11, January 11-22, January 23 - February 1, and February 2-18. We compared epidemiological characteristics across periods and different demographic groups. We developed a susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions.

RESULTS

The median age of the cases was 57 years and 50.3% were women. The attack rate peaked in the third period and substantially declined afterwards across geographic regions, sex and age groups, except for children (age <20) whose attack rate continued to increase. Healthcare workers and elderly people had higher attack rates and severity risk increased with age. The effective reproductive number dropped from 3.86 (95% credible interval 3.74 to 3.97) before interventions to 0.32 (0.28 to 0.37) post interventions. The interventions were estimated to prevent 94.5% (93.7 to 95.2%) infections till February 18. We found that at least 59% of infected cases were unascertained in Wuhan, potentially including asymptomatic and mild-symptomatic cases.

CONCLUSIONS

Considerable countermeasures have effectively controlled the Covid-19 outbreak in Wuhan. Special efforts are needed to protect vulnerable populations, including healthcare workers, elderly and children. Estimation of unascertained cases has important implications on continuing surveillance and interventions.
Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host
Authors: Rosenwald Laura C. , Sitvarin Michael I. , White Jennifer A.
Published: March 2020

Many arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally-inherited symbiont from the genera Wolbachia, Rickettsia, and Rickettsiella. The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella. We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella-infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella, or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally-inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia.
Genome-wide patterns ofde novotandem repeat mutations and their contribution to autism spectrum disorders
Authors: Mitra Ileena , Huang Bonnie , Mousavi Nima , Ma Nichole , Lamkin Michael , Yanicky Richard , Shleizer-Burko Sharona , Lohmueller Kirk E. , Gymrek Melissa
Published: March 2020

Autism Spectrum Disorder (ASD) is an early onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviors1,2. Family studies demonstrate that ASD has a significant genetic basis3with contributions both from inherited andde novovariants. While the majority of variance in liability to ASD is estimated to arise from common genetic variation4, it has been estimated thatde novomutations may contribute to 30% of all simplex cases, in which only a single child is affected per family5. Tandem repeats (TRs), consisting of approximately 1-20bp motifs repeated in tandem, comprise one of the largest sources ofde novomutations in humans6. Yet, largely due to technical challenges they present,de novoTR mutations have not yet been characterized on a genome-wide scale, and their contribution to ASD remains unexplored. Here, we develop novel bioinformatics tools for identifying and prioritizingde novoTR mutations from whole genome sequencing (WGS) data and use these to perform a genome-wide characterization ofde novoTR mutations in ASD-affected probands and unaffected siblings. Compared to recent work on TRs in ASD7, we explicitly infer mutation events and their precise changes in repeat copy number, and primarily focus on more prevalent stepwise copy number changes rather than large or complex expansions. Our results demonstrate a significant genome-wide excess of TR mutations in ASD probands. TR mutations in probands tend to be larger, enriched in fetal brain regulatory regions, and predicted to be more evolutionarily deleterious compared to mutations observed in unaffected siblings. Overall, our results highlight the importance of considering repeat variants in future studies ofde novomutations.
Assessing the Heterogeneity of Cardiac Non-myocytes and the Effect of Cell Culture with Integrative Single Cell Analysis
Authors: Iskra Brian S. , Davis Logan , Miller Henry E. , Chiu Yu-Chiao , Bishop Alexander R. , Chen Yidong , Aune Gregory J.
Published: March 2020

Cardiac non-myocytes comprise a diverse and crucial cell population in the heart that plays dynamic roles in cardiac wound healing and growth. Non-myocytes broadly fall into four cell types: endothelium, fibroblasts, leukocytes, and pericytes. Here we characterize the diversity of the non-myocytesin vivoandin vitrousing mass cytometry. By leveraging single-cell RNA sequencing we inform the design of a mass cytometry panel. To aid in annotation of the mass cytometry datasets, we utilize data integration with a neural network. We introduce approximately 460,000∼ single cell proteomes of non-myocytes as well as 5,000∼ CD31 negative single cell transcriptomes. Using our data, as well as previously reported datasets, we characterize cardiac non-myocytes with high depth in six mice, characterizing novel surface markers (CD9, CD200, Notch3, and FolR2). Further, we find that extended cell culture promotes the proliferation of CD45+CD11b+FolR2+IAIE- myeloid cells in addition to fibroblasts.
Bacteroides uniformis enhances endurance exercise performance through gluconeogenesis
Authors: Morita Hiroto , Kano Chie , Ishii Chiharu , Kagata Noriko , Ishikawa Takamasa , Uchiyama Yoshihide , Hara Susumu , Nakamura Teppei , Fukuda Shinji
Published: March 2020

Athletes require high levels of energy to exercise under extreme conditions. Gut microbiota supplies energy to the host; however, the mechanism how gut microbiota contribute in the athlete is unclear. In this study, we determined that gut microbiota of Japanese long-distance runners differed from that of non-athletes, and the Bacteroides uniformis cell number in the feces correlated with 3,000-m race time. Mice administrated with B. unformis extended the swimming time to exhaustion. Furthermore, acetate and propionate concentrations in the cecum increased in B. uniformis-administered mice subjected to weekly exercise. Expression levels of carnitine palmitoyl transferase la and phosphoenolpyruvate carboxykinase genes were elevated in the liver, suggesting that acetate and propionate produced by B. uniformis improve endurance exercise performance, at least in part, through enhancing gluconeogenesis. In addition, α-cyclodextrin administration increased B. uniformis and improved the performance in humans and mice, thus it is a candidate substance enhancing exercise performance through modification of gut microbiota.
Anti-inflammatory role of GM1 and modulatory effects of gangliosides on microglia functions
Authors: Galleguillos Danny , Wang Qian , Steinberg Noam , Shrivastava Gaurav , Dhami Kamaldeep , Rubinstein Karin , Giuliani Fabrizio , Churchward Matthew , Power Christopher , Todd Kathryn , Sipione Simonetta
Published: March 2020

Gangliosides are sialic acid-containing glycosphingolipids highly enriched in the brain. Located mainly at the plasma membrane, gangliosides play important roles in signaling and cell-to-cell communication. Lack of gangliosides causes severe early onset neurodegenerative disorders, while more subtle deficits have been reported in Parkinson’s disease and in Huntington’s disease, two misfolded protein diseases with a neuroinflammatory component. On the other hand, administration of ganglioside GM1 provides neuroprotection in both diseases and in several other models of neuronal insult. While most studies have focused on the role of endogenous gangliosides and the effects of exogenously administered GM1 in neurons, their contribution to microglia functions that are affected in neurodegenerative conditions is largely unexplored. Microglia are the immune cells of the brain and play important homeostatic functions in health and disease. In this study, we show that administration of exogenous GM1 exerts a potent anti-inflammatory effect on microglia activated with LPS, IL-1β or upon phagocytosis of latex beads. These effects are partially reproduced by L-t-PDMP, a compound that stimulates the activity of the ganglioside biosynthetic pathway, while inhibition of ganglioside synthesis with GENZ-123346 increases microglial transcriptional response to LPS. We further show that administration of GM1 increases the uptake of apoptotic bodies and latex beads by microglia, as well as microglia migration and chemotaxis in response to ATP. On the contrary, decreasing microglial ganglioside levels results in a partial impairment in both microglial activities. Finally, increasing cellular ganglioside levels results in decreased expression and secretion of microglial brain derived neurotrophic factor (BDNF). Altogether, our data suggest that gangliosides are important modulators of microglia functions that are crucial to healthy brain homeostasis, and reveal that administration of ganglioside GM1 exerts an important anti-inflammatory activity that could be exploited therapeutically.
Systematic genome-wide querying of coding and non-coding functional elements inE. coliusing CRISPRi
Authors: Rishi Harneet S. , Toro Esteban , Liu Honglei , Wang Xiaowo , Qi Lei S. , Arkin Adam P.
Published: March 2020

Genome-wide repression screens using CRISPR interference (CRISPRi) have enabled the high-throughput identification of essential genes in bacteria. However, there is a lack of functional studies leveraging CRISPRi to systematically explore targeting of both the coding and non-coding genome in bacteria. Here we perform CRISPRi screens inEscherichia coliMG1655 K-12 targeting ~13,000 genomic features, including nearly all protein-coding genes, non-coding RNAs, promoters, and transcription factor binding sites (TFBSs) using a ~33,000-member sgRNA library, which represents the most compact and comprehensive genome-wide CRISPRi library inE. colito date. Our data reveal insights into the conditional essentiality of the genome with key refinements to screen design and profiling. First, we demonstrate that strong fitness defects associated with essential cellular processes can be resolved using inducible time-series measurements. We show that knockdowns of different classes of genes exhibit distinct, transient responses that are correlated to gene function with genes involved in translation exhibiting the strongest responses. We also query feature essentiality across several biochemical conditions and show that several genes, sRNAs, and operons exhibit conditional phenotypes not reported by previous high-throughput efforts. Second, we evaluate systematically targeting non-genic features (promoters and TFBSs) in theE. coligenome. We show that promoter-targeting guides can be used to add phenotypic confidence to promoter annotations and verify computationally predicted promoters. In contrast to prior studies, we find that promoter knockdowns exhibit a strong targeting orientation dependency where targeting the non-template strand of the promoter closest to the target gene is more effective in knocking down gene expression than other promoter targeting orientations. Unlike eukaryotic genomes, we note that interpreting the effects of TFBS targeting is particularly challenging due to the small size of such features and their proximity to and overlap with other genomic features. Together, this work reveals novel conditionally essential gene phenotypes, provides a characterized set of sgRNAs for futureE. coliCRISPRi screens, and highlights considerations for CRISPRi library design and screening for microbial genome characterization.
Type I toxin-antitoxin systems contribute to mobile genetic elements maintenance inClostridioides difficileand can be used as a counter-selectable marker for chromosomal manipulation
Authors: Peltier Johann , Hamiot Audrey , Garneau Julian R. , Boudry Pierre , Maikova Anna , Fortier Louis-Charles , Dupuy Bruno , Soutourina Olga
Published: March 2020

Toxin-antitoxin (TA) systems are widespread on mobile genetic elements as well as in bacterial chromosomes. According to the nature of the antitoxin and its mode of action for toxin inhibition, TA systems are subdivided into different types. The first type I TA modules were recently identified in the human enteropathogenClostridioides(formerlyClostridium)difficile. In type I TA, synthesis of the toxin protein is prevented by the transcription of an antitoxin RNA during normal growth. Here, we report the characterization of five additional type I TA systems present within phiCD630-1 and phiCD630-2 prophage regions ofC. difficile630. Toxin genes encode 34 to 47 amino acid peptides and their ectopic expression inC. difficileinduces growth arrest. Growth is restored when the antitoxin RNAs, transcribed from the opposite strand, are co-expressed together with the toxin genes. In addition, we show that type I TA modules located within the phiCD630-1 prophage contribute to its stability and mediate phiCD630-1 heritability. Type I TA systems were found to be widespread in genomes ofC. difficilephages, further suggesting their functional importance. We have made use of a toxin gene from one of type I TA modules ofC. difficileas a counter-selectable marker to generate an efficient mutagenesis tool for this bacterium. This tool enabled us to delete all identified toxin genes within the phiCD630-1 prophage, thus allowing investigation of the role of TA in prophage maintenance. Furthermore, we were able to delete the large 49 kb phiCD630-2 prophage region using this improved procedure.
Repression by theArabidopsisTOPLESS corepressor requires association with the core Mediator complex
Authors: Leydon Alexander R. , Wang Wei , Gala Hardik P. , Gilmour Sabrina , Juarez-Solis Samuel , Zahler Mollye L. , Zemke Joseph E. , Zheng Ning , Nemhauser Jennifer L.
Published: March 2020

The plant corepressor TOPLESS (TPL) is recruited to a large number of loci that are selectively induced in response to developmental or environmental cues, yet the mechanisms by which it inhibits expression in the absence of these stimuli is poorly understood. Previously, we had used the N-terminus ofArabidopsis thalianaTPL to enable repression of a synthetic auxin response circuit inSaccharomyces cerevisiae(yeast). Here, we leveraged the yeast system to interrogate the relationship between TPL structure and function, specifically scanning for repression domains. We identified a potent repression domain in Helix 8 located within the CRA domain, which directly interacted with the Mediator middle domain subunits Med21 and Med10. Interactions between TPL and Mediator were required to fully repress transcription in both yeast and plants. In contrast, we found that multimer formation, a conserved feature of many corepressors, had minimal influence on the repression strength of TPL.
A transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell types
Authors: Kozareva Velina , Martin Caroline , Osorno Tomas , Rudolph Stephanie , Guo Chong , Vanderburg Charles , Nadaf Naeem , Regev Aviv , Regehr Wade , Macosko Evan
Published: March 2020

The cerebellum is a well-studied brain structure with diverse roles in motor learning, coordination, cognition, and autonomic regulation. Nonetheless, a complete inventory of cerebellar cell types is presently lacking. We used high-throughput transcriptional profiling to molecularly define cell types across individual lobules of the adult mouse cerebellum. Purkinje and granule neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules. For multiple types of cerebellar interneurons, the molecular variation within each type was more continuous, rather than discrete. For the unipolar brush cells (UBCs)—an interneuron population previously subdivided into two discrete populations—the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties. Most surprisingly, we found that molecular layer interneurons (MLIs) were composed of two molecularly and functionally distinct types. Both show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability, and electrical coupling. Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.
Risk of preeclampsia in patients with genetic predisposition to common medical conditions: a case-control study
Authors: Gray Kathryn J. , Kovacheva Vesela P. , Mirzakhani Hooman , Bjonnes Andrew C. , Almoguera Berta , Wilson Melissa L. , Ingles Sue Ann , Lockwood Charles J. , Hakonarson Hakon , McElrath Thomas F. , Murray Jeffrey C. , Norwitz Errol R. , Karumanchi S. Ananth , Bateman Brian T. , Keating Brendan J. , Saxena Richa
Published: March 2020

Objective

To assess whether women with a genetic predisposition to medical conditions known to increase preeclampsia risk have an increased risk of preeclampsia in pregnancy.

Design

Case-control study.

Setting and population

Preeclampsia cases (n=498) and controls (n=1864) of European ancestry from 5 US sites genotyped on a cardiovascular gene-centric array.

Methods

Significant single nucleotide polymorphisms (SNPs) from 21 traits in 7 disease categories (cardiovascular, inflammatory/autoimmune, insulin resistance, liver, obesity, renal, thrombophilia) with published genome-wide association studies (GWAS) were used to create a genetic instrument for each trait. Multivariable logistic regression was used to test the association of each continuous, scaled genetic instrument with preeclampsia. Odds of preeclampsia were compared across quartiles of the genetic instrument and evaluated for significance using a test for trend.

Main Outcome Measures

preeclampsia.

Results

An increasing burden of risk alleles for elevated diastolic blood pressure (DBP) and increased body mass index (BMI) were associated with an increased risk of preeclampsia (DBP: overall OR 1.11 (1.01-1.21), p=0.025; BMI: OR 1.10 (1.00-1.20), p=0.042), while risk alleles associated with elevated alkaline phosphatase (ALP) were protective (OR 0.89 (0.82-0.97), p=0.008), driven primarily by pleiotropic effects of variants in theFADSgene region. The effect of DBP genetic loci was even greater in early-onset (<34 weeks) preeclampsia cases (OR 1.30 (1.08-1.56), p=0.005). For all other traits, the genetic instrument was not robustly associated with preeclampsia risk.

Conclusions

These results suggest that the underlying genetic architecture of preeclampsia is shared with other disorders, specifically hypertension and obesity.

TWEETABLE ABSTRACT

Genetic predisposition to increased diastolic blood pressure and obesity increases the risk of preeclampsia.
Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity
Authors: Fan Pengxiang , Wang Peipei , Lou Yann-Ru , Leong Bryan J. , Moore Bethany M. , Schenck Craig A. , Combs Rachel , Cao Pengfei , Brandizzi Federica , Shiu Shin-Han , Last Robert L.
Published: March 2020

Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity, recruitment of primary metabolic enzymes and genomic clustering of pathway genes. Solanaceae plant glandular trichomes produce defensive acylsugars, with aliphatic sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster forming a ‘supercluster’, and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to emergence of this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals dynamics behind emergence of novel enzymes from primary metabolism, gene cluster evolution and cell-type specific metabolite diversity.
Satellite cell-derived extracellular vesicles reverse peroxide-induced mitochondrial dysfunction in myotubes
Authors: Shuler Kyle T. , Wilson Brittany E. , Muñoz Eric R. , Mitchell Andrew D. , Selsby Joshua T. , Hudson Matthew B.
Published: March 2020

Satellite cells (SCs) are muscle-specific stem cells that have a central role in muscle remodeling. Despite their therapeutic potential, SC-based therapies have been met with numerous logistical challenges, limiting their ability to effectively treat systemic muscle diseases, such as Duchenne muscular dystrophy (DMD). Delivery of SC-derived extracellular vesicles (SC-EVs) may unlock the potential offered by SCs and overcome their numerous limitations.

Purpose

The purpose of this investigation was to determine the extent to which SC-EVs could restore mitochondrial function in cultured myotubes following oxidative injury.

Methods

SC-EVs were isolated from cultured SCs from C57 mice and quantified using nanoparticle tracking analysis (NTA). C2C12 myotubes were cultured and divided into four treatment groups: untreated control, treated for 24 h with SC-EV, 24 h exposure to 50 μM H2O2followed by a 24 h recovery period with no treatment, or 24 h exposure to 50 μM H2O2followed by a 24 h treatment with SC-EV. Inter-group differences in mitochondrial function were assessed via one-way ANOVA with Tukey post hoc analysis (p<0.05).

Results

Given the seeding density used, we calculated that each SC releases approximately 2.35 × 105± 3.10 × 104EVs per 24 h. Further, using fluorescent microscopy, we verified SC-EVs deliver cargo into myotubes, some of which was localized to the mitochondria. H2O2exposure resulted in a 42% decline in peak mitochondrial respiration (p=0.0243) as well as a 46% reduction in spare respiratory capacity (p=0.0185) relative to the untreated control group. Subsequent treatment with SC-EVs (3.12×108SC-EV; 24 h) following H2O2exposure restored 76% of peak mitochondrial respiration (p=0.0187) and 84% of spare respiratory capacity in the damaged myotubes (p=0.0198). SC-EVs did not affect mitochondrial function in the undamaged myotubes.

Conclusion

Collectively, these data demonstrate SC-EVs may represent a novel therapeutic approach for treatment of myopathies associated with mitochondrial dysfunction.
Engineering an RNA-based tissue-specific platform for genetic editing through use of a miRNA-enabled Cas12a
Authors: Møller Rasmus , Oishi Kohei , tenOever Benjamin R.
Published: March 2020

The capacity to edit genomes using CRISPR-Cas systems holds immense potential for countless genetic-based diseases. However, one significant impediment preventing broad therapeutic utilization isin vivodelivery. While genetic editing at a single cell levelin vitrocan be achieved with high efficiency, the capacity to utilize these same biologic tools in a desired tissuein vivoremains challenging. Non-integrating RNA virus-based vectors constitute efficient platforms for transgene expression and surpass several barriers toin vivodelivery. However, the broad tissue tropism of viral vectors raises the concern for off-target effects. Moreover, prolonged expression of the Cas proteins, regardless of delivery method, can accumulate aberrant RNAs leading to unwanted immunological responses. In an effort to circumvent these shortcomings, here we describe a versatile RNA virus-based technology that can achieve cell-specific activity and self-inactivation by combining host microRNA (miRNA) biology with the CRISPR-Cas12a RNA-guided nuclease. Exploiting the RNase activity of Cas12a, we generated a vector that self-inactivates upon delivery of Cas12a and an accompanying CRISPR RNA (crRNA). Furthermore, we show that maturation of the crRNA can be made dependent on cell-specific miRNAs, which confers cell-specificity. We demonstrate that this genetic editing circuit delivers diminished yet sufficient levels of Cas12a to achieve effective genome editing whilst inducing a minimal immunological response. It can also function in a cell-specific manner thereby facilitatingin vivoediting and mitigating the risk of unwanted, off-target effects.
TURNOVER OR INTRASPECIFIC TRAIT VARIATION: EXPLAINING FUNCTIONAL VARIABILITY IN A NEOTROPICAL ANURAN METACOMMUNITY
Authors: Dalmolin Diego Anderson , Tozetti Alexandro Marques , Ramos Pereira Maria João
Published: March 2020

Trait variation across environmental gradients results from two processes: intraspecific variation (ITV) and turnover. Tadpoles are known to exhibit phenotypic plasticity in several traits in response to the environment, resulting from intra or interspecific variation. Here we evaluate patterns of intraspecific variation in functional traits of adult anurans (head shape, eye size and position, limb length and body mass) and their relationship with environmental variables in an anuran metacommunity in southern Brazil. From anurans sampled from 33 ponds, we decomposed trait variation into ITV and turnover and modelled trait-environment relationships. We predict that the contribution of ITV and turnover to trait variation and trait-environment relationships should vary according to the preferred habitat of the species and the analysed traits. Intraspecific variation accumulated the highest rate of trait variation for arboreal species, while interspecific variation was greater for aquatic-terrestrial species and for the whole set of species. The contributions of turnover and ITV to shifts in community mean trait values were similar between traits, but differed between species sets. Depth, distance between ponds, area ofPinussurrounding the ponds, and types of pond vegetation and substrate strongly influenced trait variation, but their relative contribution depended on the analysed traits and species sets. The great contribution of ITV for head shape and eye size and position suggests the existence of intraspecific adaptations to microhabitats, while turnover dominance in the variation of body mass and limb length suggests differences in dispersal and trophic segregation between species.
Clinical characterization and chest CT findings in laboratory-confirmed COVID-19: a systematic review and meta-analysis
Authors: Vaseghi Golnaz , Mansourian Marjan , Karimi Raheleh , Heshmat-Ghahdarijani Kiyan , Mahdavi Sadegh Baradaran , Pezeshki Amirhossein , Ataei Behrooz , Zandifar Alireza , Shafaat Omid , Javanmard Shaghayegh Haghjoo
Published: March 2020

Background

Imagery techniques have been used as essential parts of diagnostic workup for patients suspected for 2019-nCoV infection, Multiple studies have reported the features of chest computed tomography (CT) scans among a number of 2019-nCoV patients.

Method

Study Identification was carried out in databases (PubMed, Embase and Cochrane Library) to identify published studies examining the diagnosis, the 2019 novel coronavirus (2019-nCoV). Heterogeneity among reported prevalence was assessed by computing p-values of Cochrane Q-test and I2-statics. The pooled prevalence of treatment failure was carried out with a fixed effects meta-analysis model, generating the pooled 95% confidence interval. A random-effect model was used to pool the results since this model could incorporate the heterogeneity of the studies and therefore proved a more generalized result.

Results

According to the combined results of meta-analysis, the total 55% of corona patients were males. The mean age of the patients was 41.31 (34.14, 48.47). Two prevalent clinical symptoms between patients were fever, cough with prevalence of 85%, and 62%, respectively. Either Ground Glass Opacity GGO or consolidation was seen in 86% but 14% hadNO GGO or consolidation.

The other rare CT symptoms were pericardial effusion, and pleural effusion with 4, 5, 7% prevalence, respectively. The most prevalent event was Either GGO or consolidation in 85% of patients.

Conclusion

The most CT-scan abnormality is Either Ground Glass Opacity GGO or consolidation however in few patients none of them might be observed, so trusting in just CT findings will lead to miss some patients.
Virtual-SMLM, a virtual environment for real-time interactive SMLM acquisition
Authors: Griffié J. , Pham T.A. , Sieben C. , Lang R. , Cevher V. , Holden S. , Unser M. , Manley S. , Sage D.
Published: March 2020

Although single molecule localisation microscopy enables for the visualisation of cells nanoscale organisation, its dissemination remains limited mainly due to the complexity of the associated imaging acquisition, impacting on outputs’ reliability and reproducibility. We propose here the first all-in-one fully virtual environment for SMLM acquisition:Virtual-SMLM, including on-the-fly interactivity and real time display. It relies on a novel realistic approach to simulate fluorophores photo-physics based on independent pseudo-continuous emission traces. It also facilitates for user-specific experimental and optical environment design. As such, it constitutes a unique tool for the training of both users and machine learning approaches to automated SMLM, as well as for experimental validation, whilst providing realistic data sets for the development of image reconstruction algorithms and data analysis software.
Processive and stochastic CHH methylation by plant DRM2 and CMT2 revealed by single-read methylome analysis
Authors: Harris Keith D. , Zemach Assaf
Published: March 2020

Cytosine methylome data is commonly generated through next-generation sequencing (NGS). Analyses of this data average methylation states of individual reads. We propose an alternate method of analysing single-read methylome data. Using this method, we identified patterns that relate to the mechanism of two plant non-CG methylating enzymes, DRM2 and CMT2: DRM2 has higher processivity than CMT2, and DRM2-methylated regions have higher variation among cells. Based on these patterns, we developed a classifier that predicts enzyme activity in different species and tissues. To facilitate further single-read analyses, we developed a genome browser optimised for visualising and analysing NGS data at single-read resolution.
Restoration of motor-evoked cortical activity is a distinguishing feature of the most effective rehabilitation therapy after stroke
Authors: Conti Emilia , Mascaro Anna Letizia Allegra , Scaglione Alessandro , de Vito Giuseppe , Calugi Francesco , Pasquini Maria , Pizzorusso Tommaso , Micera Silvestro , Pavone Francesco Saverio
Published: March 2020

Background

An ischemic stroke is followed by the remapping of motor representation and extensive changes in cortical excitability involving both hemispheres. Although stimulation of the ipsilesional motor cortex, especially when paired with motor training, facilitates plasticity and functional restoration, the mechanisms underneath the reshaping of cortical functionality are widely unknown.

Objective

We investigated the spatio-temporal features of motor-evoked cortical activity associated with generalized recovery after stroke, and its dependence on the type of rehabilitative treatment.

Methods

We designed a novel rehabilitative treatment that combines neuro-plasticizing intervention with motor training. Specifically, optogenetic stimulation of peri-infarct excitatory neurons expressing Channelrhodopsin-2 was associated with daily motor training on a robotic device. The effectiveness of the combined therapy was compared with spontaneous recovery and with the single treatments (i.e. individually administered optogenetic stimulation or motor training).

Results

We found that only the combined therapy promotes generalized recovery of forelimb function and the rescue of spatio-temporal features of motor-evoked activity. Generalized recovery results from a new excitatory/inhibitory balance between hemispheres as revealed by the augmented motor response flanked by the increased expression of parvalbumin positive neurons in the peri-infarct area.

Conclusions

Our findings demonstrate that though behavioral recovery is not necessarily associated with the restoration of pre-stroke motor-evoked activity, the reestablishment of pre-stroke activation transients was a distinguishing feature of the most efficient therapeutic approach, the combined therapy.
In vivoimaging of the kinetics of microglial self-renewal and maturation in the adult visual cortex
Authors: Mendes Monique S. , Atlas Jason , Brehm Zachary , Ladron-de-Guevara Antonio , McCall Matthew N. , Majewska Ania K.
Published: March 2020

Microglia are the resident immune cells in the brain with the capacity to autonomously self-renew. Under basal conditions, microglial self-renewal appears to be slow and stochastic, although microglia have the ability to proliferate very rapidly following depletion or in response to injury. Because microglial self-renewal has largely been studied using static tools, the mechanisms and kinetics by which microglia renew and acquire mature characteristics in the adult brain are not well understood. Using chronicin vivotwo-photon imaging in awake mice and PLX5622 (Colony stimulating factor 1 receptor (CSF1R) inhibitor) to deplete microglia, we set out to understand the dynamic self-organization and maturation of microglia following depletion in the visual cortex. We confirm that under basal conditions, cortical microglia show limited turnover and migration. Following depletion, however, microglial repopulation is remarkably rapid and is sustained by the dynamic division of the remaining microglia in a manner that is largely independent of signaling through the P2Y12 receptor. Mathematical modeling of microglial division demonstrates that the observed division rates can account for the rapid repopulation observedin vivo. Additionally, newly-born microglia resemble mature microglia, in terms of their morphology, dynamics and ability to respond to injury, within days of repopulation. Our work suggests that microglia rapidly self-renew locally, without the involvement of a special progenitor cell, and that newly born microglia do not recapitulate a slow developmental maturation but instead quickly take on mature roles in the nervous system.

Graphical Abstract

(a) Microglial dynamics during control condition. Cartoon depiction of the heterogenous microglia in the visual cortex equally spaced. (b) During the early stages of repopulation, microglia are irregularly spaced and sparse. (c) During the later stages of repopulation, the number of microglia and the spatial distribution return to baseline. (d-f) We then created and ran a mathematical model that sampled the number of microglia, (d) the persistent doublets, (e) the rapid divisions of microglia and (f) the secondary divisions of microglia during the peak of repopulation day 2-day 3. The mathematical model suggested that residual microglia can account for the rapid repopulation we observedin vivo.
Human DND1-RRM2 forms a non-canonical domain swapped dimer
Authors: Kumari Pooja , Bhavesh Neel Sarovar
Published: March 2020

Human DND1 (Dead end protein homolog1) is an RNA binding protein. DND1 plays pivotal role in animal development and has been implicated in cancer. DND1 consists of two RNA recognition motifs (RRMs) in tandem and a double stranded RNA binding domain at the C terminal separated by 40 residues flexible linker. The conserved RNP site in the RRM1 domain helps in specific RNA recognition while the RNP sites in RRM2 are not well conserved. DND1 has been reported to be involved in inhibition of microRNA access to target mRNA and it also associate with CCR4-NOT complex that targets mRNA. In order to understand this intriguing contrasting molecular function, we have determined the 2.3 Å resolution crystal structure of the human DND1 RRM2 domain. The structure revealed an interesting non-canonical RRM fold that is maintained by the formation of a domain swapped dimer between β1and β4strands across two chains. The domain swapping is attributed by a hinge loop between α2and β4that helps in mediating a domain swap forming anti-parallel β sheets. We have delineated the structural basis of stable dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies demonstrate the molecular basis for the dimerization of the RRM2 domain and shed light on the possibility for this motif for interaction with other proteins which helps in transcription regulation.

Graphical Abstract

Highlights

First report of a domain swapped dimer formation by an RRM identified through crystal structure determination of the human DND1 RRM2 domain.

RRM2 exhibit domain swapped dimerization attributed by hinge loop and disulfide bond formation.

Dimer formation is under redox regulation.

Major determinants of swapping were identified.

DND1 RRM2 is not involved in RNA recognition.
ppGpp influences protein protection, growth and photosynthesis inPhaeodactylum tricornutum
Authors: Avilan Luisana , Lebrun Regine , Puppo Carine , Citerne Sylvie , Cuiné Stephane , Li-Beisson Yonghua , Menand Benoit , Field Ben , Gontero Brigitte
Published: March 2020

Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta- and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes.

Here, we studied the function of ppGpp in the diatomP. tricornutumusing transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression.

We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments.

Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.
External mechanical cues reveal core molecular pathway behind tissue bending in plants
Authors: Baral Anirban , Morris Emily , Aryal Bibek , Jonsson Kristoffer , Verger Stéphane , Xu Tongda , Bennett Malcolm , Hamant Olivier , Bhalerao Rishikesh P.
Published: March 2020

Tissue folding is a central building block of plant and animal morphogenesis. In dicotyledonous plants, hypocotyl folds to form hook after seedling germination that protects their aerial stem cell niche during emergence from soil. Auxin response factors and auxin transport are classically thought to play a key role in this process. Here we show that the microtubule-severing enzyme katanin contributes to hook formation. However, by exposing hypocotyls to external mechanical cues mimicking the natural soil environment, we reveal that auxin response factors ARF7/ARF19, auxin influx carriers, and katanin are dispensable for apical hook formation, indicating that these factors primarily play the role of catalyzers of tissue bending in the absence of external mechanical cues. Instead, our results reveal the key roles of the non-canonical TMK-mediated auxin pathway, PIN efflux carriers and cellulose microfibrils as components of the core pathway behind hook formation in presence or absence of external mechanical cues.
The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors
Authors: Rouanet Marie , Lulka Hubert , Garcin Pierre , Sramek Martin , Pagan Delphine , Valle Carine , Sarot Emeline , Pancaldi Vera , Lopez Frédéric , Buscail Louis , Cordelier Pierre
Published: March 2020

Toll like receptors are key players in the innate immune system. Recent studies have suggested that they may impact the growth of pancreatic cancer, a disease with no cure. Among them, Toll like receptor-7 shows promise for therapy but may also promote tumor growth. Thus, we aimed to better understand the mechanism of action of Toll like receptor-7 ligands in pancreatic cancer, to open the door for clinical applications.In vitro, Toll like receptor-7 ligands strongly inhibit the proliferation and induce cell death by apoptosis of pancreatic cancer cells.In vivo, while Toll like receptor-7 agonists significantly delay the growth of aggressive tumors engrafted in immunodeficient mice, they instead surprisingly promote tumor growth and accelerate animal death in immunocompetent models. Molecular investigations revealed that Toll like receptor-7 agonists strongly increase the number of tumor-promoting macrophages to drive pancreatic tumorigenesis in immunocompetent mice. This is in stark contrast with Toll like receptor-7 ligands’ great potential to inhibit pancreatic cancer cell proliferationin vitroand tumor growthin vivoin immunosuppressed models. Collectively, our findings shine a light on the duality of action of Toll like receptor-7 agonists in experimental cancer models, and calls into question their use for pancreatic cancer therapy.