bluuebunny/crossref_metadata_2025 huggingface dataset:
Using wastewater-based epidemiology with local indicators of opioid and illicit drug use to overcome data gaps in Montana
Authors: Margetts Miranda , Keshaviah Aparna , Hu Xindi C. , Troeger Victoria , Sykes Jordan , Bishop Nicholas , Jones-Lepp Tammy , Henry Marisa , Keil Deborah E.
Published: April 2020

Opioid misuse takes an enormous toll on the health and economy of the U.S., costing 130 lives per day, and an estimated 157 billion dollars per year. Mitigating the epidemic requires better information on the mix of drugs being used in a community and when and where drug use concentrates. Many widely used data sources, such as national population surveys, have a two-year lag before the data are available, and underestimate the prevalence of drug use because they rely on self-reported information about a stigmatized behavior. For rural populations, the data gap is compounded by privacy policies that suppress key information (for example, opioid-related death rates) in small populations. Municipal wastewater testing is an innovative approach to assessing community-level drug use that can provide near real-time, cost-effective, and unbiased measures of drug use. Importantly, wastewater-based data cannot reveal who is using a particular drug, mitigating privacy concerns. The methodology is routinely used across Europe and Australia as part of a holistic multi-indicator monitoring and alert system. When combined with geospatial mapping and advanced analytics, wastewater-based data can help locate geographic hotspots of use and provide an early warning for new substances entering into a community. We conducted a pilot study to compare temporal trends in estimates of per-capita drug use between wastewater-based data and other local data sources in two municipalities (one urban, one rural) in Montana. In the first phase of our study (Bishop et al, 2020, manuscript is in submission to Sci Total Environ), we optimized testing to estimate per-capita drug use in wastewater in an urban and rural municipality. Here, we report the value of these data for public health officials to predict rather than react to changes in drug use patterns. We also illustrate how rural populations can use the methodology to assess the impacts of local law enforcement efforts and evaluate the effectiveness of programs, such as the prescription take-back program, to improve public health and safety.
Plasma lipidomics identifies a signature of NAFLD in children that couples with cardiometabolic outcomes in adults
Authors: Mann Jake P. , Jenkins Benjamin , Furse Samuel , Snowden Stuart G. , Alisi Anna , Draijer Laura G. ,   EU-PNAFLD investigators, Karnebeek Kylie , Kelly Deirdre A. , Koot Bart G. , Mosca Antonella , Salvestrini Camilla , van Mourik Indra , Vreugdenhil Anita , Zilbauer Matthias , Koulman Albert
Published: April 2020

Non-alcoholic fatty liver disease (NAFLD) is an increasingly common condition in children and adults characterized by insulin resistance and altered lipid metabolism. Affected patients are at increased risk of cardiovascular disease (CVD) and children with NAFLD are likely to be at risk of premature cardiac events. Evaluation of the plasma lipid profile of children with NAFLD offers the opportunity to investigate these perturbations and understand how closely they mimic the changes seen in adults with cardiometabolic disease. We hypothesized that change in the concentration of lipid species in pediatric NAFLD would mimic the alterations known to be associated with CVD in adults (and be largely reflective of insulin resistance). Here, we performed untargeted liquid chromatography mass spectrometry (LC-MS) plasma lipidomics on 287 children: 19 lean controls, 146 from an obese cohort, and 122 NAFLD cases who had undergone liver biopsy. Associations between lipid species and liver histology were assessed using regression adjusted for age and sex. Results were then replicated using data from 9,500 adults with metabolic phenotyping. Phosphatidylcholine (PC) and triglyceride (TG) desaturation and chain length were inversely associated with histological severity of paediatric NAFLD. Nine lipids species (lyso-PC, PC, and TG classes) were also associated with hepatic steatosis and insulin resistance in an independent cohort of adults. Five of the 9 lipids replicated in the adults cohort (including PC(36:4)) have been directly linked to death and cardiometabolic disease in adults, as well as indirectly via genetic variants that influence the concentration of these species. Together, these findings suggest that lipid metabolism is altered in paediatric NAFLD in a similar way as in cardiometabolic disease in adults and it is therefore critical to alleviate insulin resistance in these children to mitigate their long-term morbidity.
PreTA: A network meta-analysis ranking metric measuring the probability of being preferable than the average treatment
Authors: Nikolakopoulou Adriani , Mavridis Dimitris , Chiocchia Virginia , Papakonstantinou Theodoros , Furukawa Toshi A , Salanti Georgia
Published: April 2020

Background

Network meta-analysis (NMA) produces complex outputs as many comparisons between interventions are of interest and a treatment ranking is often included in the aims of the evidence synthesis. The estimated relative treatment effects are usually displayed in a forest plot or in a league table and several ranking metrics are calculated and presented, such as the median and mean treatment ranks.

Methods

We estimate relative treatment effects of each competing treatment against a fictional ‘average’ treatment using the ‘deviation from the means’ coding that has been used to parametrize categorical covariates in regression models. Based on this alternative parametrization of the NMA model, we present a new ranking metric (PreTA: Preferable Than Average) interpreted as the probability that a treatment is better than a fictional treatment of average performance.

Results

We compare PreTA with existing probabilistic ranking metrics in 232 networks of interventions. We use two networks of interventions, a network of 18 antidepressants for acute depression and a network of four interventions for heavy menstrual bleeding, to illustrate the methodology. The agreement between PreTA and existing ranking metrics depends on the precision with which relative effects are estimated.

Conclusions

PreTA is a viable alternative to existing ranking metrics which can be interpreted as the probability of being better than the ‘average’ treatment. It enriches the decision-making arsenal with a ranking metric which is interpreted as a probability and considers the entire ranking distributions of the involved treatments.
Augmented Curation of Clinical Notes from a Massive EHR System Reveals Symptoms of Impending COVID-19 Diagnosis
Authors: Wagner Tyler , Shweta FNU , Murugadoss Karthik , Awasthi Samir , Venkatakrishnan AJ , Bade Sairam , Puranik Arjun , Kang Martin , Pickering Brian W. , O’Horo John C. , Bauer Philippe R. , Razonable Raymund R. , Vergidis Paschalis , Temesgen Zelalem , Rizza Stacey , Mahmood Maryam , Wilson Walter R. , Challener Douglas , Anand Praveen , Liebers Matt , Doctor Zainab , Silvert Eli , Solomon Hugo , Anand Akash , Barve Rakesh , Gores Gregory J. , Williams Amy W. , Morice William G. , Halamka John , Badley Andrew D. , Soundararajan Venky
Published: April 2020

Understanding temporal dynamics of COVID-19 patient symptoms could provide fine-grained resolution to guide clinical decision-making. Here, we use deep neural networks over an institution-wide platform for the augmented curation of clinical notes from 77,167 patients subjected to COVID-19 PCR testing. By contrasting Electronic Health Record (EHR)-derived symptoms of COVID-19-positive (COVIDpos; n=2,317) versus COVID-19-negative (COVIDneg; n=74,850) patients for the week preceding the PCR testing date, we identify anosmia/dysgeusia (27.1-fold), fever/chills (2.6-fold), respiratory difficulty (2.2-fold), cough (2.2-fold), myalgia/arthralgia (2-fold), and diarrhea (1.4-fold) as significantly amplified in COVIDpos over COVIDneg patients. The combination of cough and fever/chills has 4.2-fold amplification in COVIDpos patients during the week prior to PCR testing, and along with anosmia/dysgeusia, constitutes the earliest EHR-derived signature of COVID-19. This study introduces an Augmented Intelligence platform for the real-time synthesis of institutional biomedical knowledge. The platform holds tremendous potential for scaling up curation throughput, thus enabling EHR-powered early disease diagnosis.
COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling
Authors: Raimúndez Elba , Dudkin Erika , Vanhoefer Jakob , Alamoudi Emad , Merkt Simon , Fuhrmann Lara , Bai Fan , Hasenauer Jan
Published: April 2020

Epidemiological models are widely used to analyse the spread of diseases such as the global COVID-19 pandemic caused by SARS-CoV-2. However, all models are based on simplifying assumptions and on sparse data. This limits the reliability of parameter estimates and predictions.

In this manuscript, we demonstrate the relevance of these limitations by performing a study of the COVID-19 outbreak in Wuhan, China. We perform parameter estimation, uncertainty analysis and model selection for a range of established epidemiological models. Amongst others, we employ Markov chain Monte Carlo sampling, parameter and prediction profile calculation algorithms.

Our results show that parameter estimates and predictions obtained for several established models on the basis of reported case numbers can be subject to substantial uncertainty. More importantly, estimates were often unrealistic and the confidence / credibility intervals did not cover plausible values of critical parameters obtained using different approaches. These findings suggest, amongst others, that several models are oversimplistic and that the reported case numbers provide often insufficient information.
More prevalent, less deadly? Bayesian inference of the COVID19 Infection Fatality Ratio from mortality data
Authors: Delius G. W. , Powell B. J. , Bees M. A. , Constable G. W. A. , MacKay N. J. , Pitchford J. W.
Published: April 2020

We use an established semi-mechanistic Bayesian hierarchical model of the COVID-19 pandemic [1], driven by European mortality data, to estimate the prevalence of immunity. We allow the infection-fatality ratio (IFR) to vary, adapt the model’s priors to better reflect emerging information, and re-evaluate the model fitting in the light of current mortality data. The results indicate that the IFR of COVID-19 may be an order of magnitude smaller than the current consensus, with the corollary that the virus is more prevalent than currently believed. These results emerge from a simple model and ought to be treated with caution. They emphasise the value of rapid community-scale antibody testing when this becomes available.
High frequency neuronal bursting is essential for circadian and sleep behaviors inDrosophila
Authors: Fernandez-Chiappe Florencia , Frenkel Lia , Colque Carina Celeste , Ricciuti Ana , Hahm Bryan , Cerredo Karina , Muraro Nara Inés , Ceriani María Fernanda
Published: April 2020

Circadian rhythms have been extensively studied inDrosophila, however, still little is known about how the electrical properties of clock neurons are specified. We have performed a behavioral genetic screen through the downregulation of candidate ion channels in the lateral ventral neurons (LNvs) and show that the hyperpolarization-activated cation current Ihis important for the behaviors that the LNvs command: temporal organization of locomotor activity and sleep. Using whole-cell patch clamp electrophysiology we demonstrate that small LNvs are bursting neurons, and that Ihis necessary to achieve the high frequency bursting firing pattern characteristic of both types of LNvs. Since firing in bursts has been associated to neuropeptide release, we hypothesized that Ihwould be important for LNvs communication. Indeed, herein we demonstrate that Ihis fundamental for the recruitment of PDF filled dense core vesicles to the terminals at the dorsal protocerebrum and for their timed release, and hence for the temporal coordination of circadian behaviors.
Identifying female phenotypes that promote behavioral isolation in a sexually dimorphic species of fish (Etheostoma zonale)
Authors: Roberts Natalie S. , Mendelson Tamra C.
Published: April 2020

In sexually dimorphic species characterized by exaggerated male ornamentation, behavioral isolation is often attributed to female preferences for conspecific male signals. Yet, in a number of sexually dimorphic species, male mate choice also results in behavioral isolation. In many of these cases, the female traits that mediate species boundaries are unclear. Females in sexually dimorphic species typically lack many of the elaborate traits that are present in males and that are often diagnostic of species. In a diverse and largely sexually dimorphic group of fishes called darters (Percidae:Etheostoma), male mate choice contributes to behavioral isolation between a number of species; however, it is not clear which female traits males prefer. In the current study, we identified the dominant female pattern for two sympatric species,Etheostoma zonaleandE. barrenense, using pattern energy analysis, and we used discriminate function analysis to identify which aspects of female patterning can reliably classify species. We then tested the role of female features in male mate choice forE. zonale, by measuring male preference for computer animations displaying the identified (species-specific) conspecific features as well as the dominant male pattern that is preferred by females. We found that the region above the lateral line is important in mediating male mate preferences, with males spending significantly more time with animations exhibiting conspecific female patterning in this region than with animations exhibiting heterospecific female patterning. Our results suggest that the aspects of female phenotypes that are the target of male mate choice are different from the male phenotypes that characterize species. This research highlights the importance of using objective measures in the study of behavioral isolation via male mate choice.
PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection
Authors: Li Po-E , Russell Joseph A. , Yarmosh David , Shteyman Alan G. , Parker Kyle , Wood Hillary , Aspinwall J.R. , Winegar Richard , Davenport Karen , Lo Chien-chi , Bagnoli John , Davis Phillip , Jacobs Jonathan L. , Chain Patrick S.G.
Published: April 2020

Metagenomics is emerging as an important tool in biosurveillance, public health, and clinical applications. However, ease-of-use for execution and data analysis remains a barrier-of-entry to the adoption of metagenomics in applied health and forensics settings. In addition, these venues often have more stringent requirements for reporting, accuracy, and precision than the traditional ecological research role of the technology. Here, we present PanGIA (Pan-Genomics forInfectiousAgents), a novel bioinformatics analysis platform for hosting, processing, analyzing, and reporting shotgun metagenomics data of complex samples suspected of containing one or more pathogens. PanGIA was developed to address gaps that often preclude clinicians, medical technicians, forensics personnel, or other non-expert end-users from the routine application of metagenomics for pathogen identification. Though primarily designed to detect pathogenic microorganisms within clinical and environmental metagenomics data, PanGIA also serves as an analytical framework for microbial community profiling and comparative metagenomics. To provide statistical confidence in PanGIA’s taxonomic assignments, the system provides two independent estimations of probability for species and strain level detection. First, PanGIA integrates coverage data with ‘uniqueness’ information mapped across each reference genome for a stand-alone determination of confidence for each query sequence at each taxonomy level. Second, if a negative-control sample is provided, PanGIA compares this sample with a corresponding experimental unknown sample and determines a measure of confidence associated with ‘detection above background’. An integrated graphical user interface allows interactive interrogation and enables users to summarize multiple sample results by confidence score, normalized read abundance, reference genome linear coverage, depth-of-coverage, RPKM, and other metrics to detect specific organisms-of-interest. Comparison testing of the PanGIA algorithm against a number of recent k-mer, read-mapping, and marker-gene based taxonomy classifiers across various real-world datasets with spiked targets shows superior mean positive predictive value, sensitivity, and specificity. PanGIA can process a five million paired-end read dataset in under 1 hour on commodity computational hardware. The source code and documentation are publicly available athttps://github.com/LANL-Bioinformatics/PanGIAorhttps://github.com/mriglobal/PanGIA. The database for PanGIA can be downloaded fromftp://bioinformatics.mriglobal.org/. The full GUI-based PanGIA analysis environment is available in a Docker container and can be installed fromhttps://hub.docker.com/r/poeli/pangia/.
Greater local diversity under older species pools may arise from enhanced competitive equivalence
Authors: Leopold Devin R. , Fukami Tadashi
Published: April 2020

Local ecological communities tend to contain more species when they are located within a geologically older region, a pattern that has traditionally been attributed to the accumulation of species in the regional species pool. In this explanation, local species interactions are assumed to play a minor role in the formation of the regional species pool, which is instead thought to be driven by speciation and dispersal occurring across larger areas. Here, we provide evidence suggesting a more important role of local species interactions than generally assumed. In an experiment in which we assembled 320 local communities of root-associated fungi under 80 species pools, we varied the species richness of the experimental species pools and the mean age of the sites from which we collected the fungal species across a 4-myr soil chronosequence in Hawaii. We found that realized local species diversity in the assembled communities increased more extensively with increasing species-pool richness when species were from older sites. We also found that older species pools had lower functional and phylogenetic diversity, indicating that the evolution of greater competitive equivalence among potential colonists enabled higher local diversity under older species pools. Our results suggest that the tendency of older regions to have higher local richness arises not simply because older species pools are more speciose, but also because the constituent species have evolved traits that allow them to co-occur more readily in local communities.
Candida aurisphenotypic heterogeneity determines pathogenicityin vitro
Authors: Brown Jason L , Delaney Chris , Short Bryn , Butcher Mark C , McKloud Emily , Williams Craig , Kean Ryan , Ramage Gordon
Published: April 2020

Candida aurisis an enigmatic yeast that provides substantial global risk in healthcare facilities and intensive care units. A unique phenotype exhibited by certain isolates ofC. aurisis their ability to form small clusters of cells known as aggregates, which have been to a limited extent described in the context of pathogenic traits. In this study, we screened several non-aggregative and aggregativeC. aurisisolates for biofilm formation, where we observed a level of heterogeneity amongst the different phenotypes. Next, we utilised an RNA-sequencing approach to investigate the transcriptional responses during biofilm formation of a non-aggregative and aggregative isolate of the initial pool. Observations from these analyses indicate unique transcriptional profiles in the two isolates, with several genes identified relating to proteins involved in adhesion and invasion of the host in other fungal species. From these findings we investigated for the first time the fungal recognition and inflammatory responses of a three-dimensional skin epithelial model to these isolates. In these models, a wound was induced to mimic a portal of entry forC. auris. We show both phenotypes elicited minimal response in the model minus induction of the wound, yet in the wounded tissue both phenotypes induced a greater response, with the aggregative isolate more pro-inflammatory. This capacity of aggregativeC. aurisbiofilms to generate such responses in the wounded skin highlights how this opportunistic yeast is a high risk within the intensive care environment where susceptible patients have multiple indwelling lines.

Importance

Candida aurishas recently emerged as an important cause of concern within healthcare environments due to its ability to persist and tolerate commonly used antiseptics and disinfectants, particularly when surface attached (biofilms). This yeast is able to colonise and subsequently infect patients, particularly those that are critically ill or immunosuppressed, which may result in death. We have undertaken analysis on two different types of this yeast, using molecular and immunological tools to determine whether either of these has a greater ability to cause serious infections. We describe that both isolates exhibit largely different transcriptional profiles during biofilm development. Finally, we show that the inability to form small aggregates (or clusters) of cells has an adverse effect on the organisms immuno-stimulatory properties, suggestive the non-aggregative phenotype may exhibit a certain level of immune evasion.
Astrocytes and neurons share brain region-specific transcriptional signatures
Authors: Herrero-Navarro Álvaro , Puche-Aroca Lorenzo , Moreno-Juan Verónica , Sempere-Ferràndez Alejandro , Espinosa Ana , Susín Rafael , Torres-Masjoan Laia , Leyva-Díaz Eduardo , Karow Marisa , Figueres-Oñate María , López-Mascaraque Laura , López-Atalaya José P. , Berninger Benedikt , López-Bendito Guillermina
Published: April 2020

Neuronal cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterised by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and glia. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis revealed the existence of common nucleus-specific progenitors for neurons and glia. Consistent with their shared molecular signature, regional specificity was maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.
Determining the Depth Limit of Bioluminescent Sources in Scattering Media
Authors: Raghuram Ankit , Ye Fan , Adams Jesse K. , Shaner Nathan , Robinson Jacob T. , Veeraraghavan Ashok
Published: April 2020

Bioluminescence has several potential advantages compared to fluorescence microscopy forin vivobiological imaging. Because bioluminescence does not require excitation light, imaging can be performed for extended periods of time without phototoxicity or photobleaching, and optical systems can be smaller, simpler, and lighter. Eliminating the need for excitation light may also affect how deeply one can image in scattering biological tissue, but the imaging depth limits for bioluminescence have yet to be reported. Here, we perform a theoretical study of the depth limits of bioluminescence microscopy and find that cellular resolution imaging should be possible at a depth of 5-10 mean free paths (MFPs). This limit is deeper than the depth limit for confocal microscopy and slightly lower than the imaging limit expected for two-photon microscopy under similar conditions. We also validate our predictions experimentally using tissue phantoms. Overall we show that with advancements in the brightness of bioluminescent indicators, it should be possible to achieve deep, long-term imaging in biological tissue with cellular resolution.
The environment-sensing aryl-hydrocarbon receptor inhibits the chondrogenic fate of modulated smooth muscle cells in atherosclerotic lesions
Authors: Kim Juyong Brian , Zhao Quanyi , Nguyen Trieu , Pjanic Milos , Cheng Paul , Wirka Robert , Nagao Manabu , Kundu Ramendra , Quertermous Thomas
Published: April 2020

Introduction

Smooth muscle cells (SMC) play a critical role in atherosclerosis. The Aryl hydrocarbon receptor (AHR) is an environment-sensing transcription factor that contributes to vascular development, and has been implicated in coronary artery disease (CAD) risk. We hypothesized that AHR can affect atherosclerosis by regulating phenotypic modulation of SMC.

Methods

We combined RNA-Seq, ChIP-Seq, ATAC-Seq and in-vitro assays in human coronary artery SMC (HCASMC), with single-cell RNA-Seq (scRNA-Seq), histology, and RNAscope in an SMC-specific lineage-tracingAhrknockout mouse model of atherosclerosis to better understand the role ofAHRin vascular disease.

Results

Genomic studies coupled with functional assays in cultured HCASMC revealed thatAHRmodulates HCASMC phenotype and suppresses ossification in these cells. Lineage tracing and activity tracing studies in the mouse aortic sinus showed that theAhrpathway is active in modulated SMC in the atherosclerotic lesion cap. Furthermore, scRNA-Seq studies of the SMC-specific Ahr knockout mice showed a significant increase in the proportion of modulated SMC expressing chondrocyte markers such asCol2a1andAlpl, which localized to the lesion neointima. These cells, which we term “chondromyocytes” (CMC), were also identified in the neointima of human coronary arteries. In histological analyses, these changes manifested as larger lesion size, increased lineage-traced SMC participation in the lesion, decreased lineage-traced SMC in the lesion cap, and increased alkaline phosphatase activity in lesions in theAhrknockout compared to wild-type mice. We propose thatAHRis likely protective based on these data and inference from human genetic analyses.

Conclusion

Overall, we conclude thatAHRpromotes maintenance of lesion cap integrity and diminishes the disease related SMC-to-CMC transition in atherosclerotic tissues.
Modeling robust and efficient coding in the mouse primary visual cortex using computational perturbations
Authors: Cai Binghuang , Billeh Yazan N. , Chettih Selmaan N. , Harvey Christopher D. , Koch Christof , Arkhipov Anton , Mihalas Stefan
Published: April 2020

Investigating how visual inputs are encoded in visual cortex is important for elucidating the roles of cell populations in circuit computations. We here use a recently developed, large-scale model of mouse primary visual cortex (V1) and perturb both single neurons as well as functional- and cell-type defined population of neurons to mimic equivalent optogenetic perturbations. First, perturbations were performed to study the functional roles of layer 2/3 excitatory neurons in inter-laminar interactions. We observed activity changes consistent with the canonical cortical model (Douglas and Martin 1991). Second, single neuron perturbations in layer 2/3 revealed a center-surround inhibition-dominated effect, consistent with recent experiments. Finally, perturbations of multiple excitatory layer 2/3 neurons during visual stimuli of varying contrasts indicated that the V1 model has both efficient and robust coding features. The circuit transitions from predominantly broad like-to-like inhibition at high contrasts to predominantly specific like-to-like excitation at low contrasts. Thesein silicoresults demonstrate how the circuit can shift from redundancy reduction to robust codes as a function of stimulus contrast.
Engineering T cells to enhance 3D migration through structurally and mechanically complex tumor microenvironments
Authors: Tabdanov Erdem D. , Rodríguez-Merced Nelson J. , Cartagena-Rivera Alexander X. , Puram Vikram V. , Callaway Mackenzie K. , Ensminger Ethan A. , Pomeroy Emily J. , Yamamoto Kenta , Lahr Walker S. , Webber Beau R. , Moriarity Branden S. , Zhovmer Alexander S. , Provenzano Paolo P.
Published: April 2020

Defining the principles of T cell migration in structurally and mechanically complex tumor microenvironments is critical to understanding sanctuaries from antitumor immunity and optimizing T cell-related therapeutic strategies. To enhance T cell migration through complex microenvironments, we engineered nanotextured platforms that allowed us to define how the balance between T cell phenotypes influences migration in response to tumor-mimetic structural and mechanical cues and characterize a mechanical optimum for migration that can be perturbed by manipulating an axis between microtubule stability and force generation. In 3D environments and live tumors, we demonstrate that microtubules instability, leading to increased Rho pathway-dependent cell contractility, promotes migration while clinically used microtubule-targeting chemotherapies profoundly decrease effective migration. Indeed, we show that rational manipulation of the microtubule-contractility axis, either pharmacologically or through genome engineering, results in engineered T cells that more effectively move through and interrogate 3D matrix and tumor volumes. This suggests that engineering cells to better navigate through 3D microenvironments could be part of an effective strategy to enhance efficacy of immune therapeutics.
Two novel 7-epi-zingiberene derivatives with biological activity fromSolanum habrochaitesare produced by a single cytochrome P450 monooxygenase
Authors: Zabel Sebastian , Brandt Wolfgang , Porzel Andrea , Athmer Benedikt , Kortbeek Ruy , Bleeker Petra , Tissier Alain
Published: April 2020

Secretions from glandular trichomes potentially protect the plant against a variety of aggressors. In the tomato genus, wild species constitute a rich source of chemical diversity produced at the leaf surface by glandular trichomes. Previously, 7-epi-zingiberene produced in several accessions ofSolanum habrochaiteswas found to confer resistance to whiteflies (Bemisia tabaci) and other insect pests. Here, we identify two derivatives of 7-epi-zingiberene fromS. habrochaitesthat had not been reported as yet. We identified them as 9-hydroxy-zingiberene and 9-hydroxy-10,11-epoxyzingiberene. Using a combination of genetics and transcriptomics we identified a single cytochrome P450 oxygenase, ShCYP71D184 that carries out two successive oxidations to generate the two sesquiterpenoids. Bioactivity assays showed that only 9-hydroxy-10,11-epoxyzingiberene exhibits substantial toxicity againstB. tabaci. In addition, both 9-hydroxy-zingiberene and 9-hydroxy-10,11-epoxyzingiberene display substantial growth inhibitory activities against a range of microorganisms, includingBacillus subtilis,Phytophtora infestansandBotrytis cinerea. Our work shows that trichome secretions from wild tomato species can provide protection against a wide variety of organisms. In addition, the availability of the genes encoding the enzymes for the pathway of 7-epi-zingiberene derivatives makes it possible to introduce this trait in cultivated tomato by precision breeding.
Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma
Authors: Hayden Annette , Manousopoulou Antigoni , Cowie Andrew , Walker Robert , Sharpe Benjamin P. , Harrington Jack , Izadi Fereshteh , Kyle Ewan , Saunders John H. , Parsons Simon L. , Ritchie Alison A. , Clarke Philip A. , Collier Pamela , Garbis Spiros D. , Rose-Zerilli Matthew , Grabowska Anna M. , Underwood Timothy J.
Published: April 2020

Background and aims

Esophageal adenocarcinoma (EAC) is chemoresistant in the majority of cases. The tumor-promoting biology of cancer associated fibroblasts (CAF) make them a target for novel therapies. Phosphodiesterase type 5 inhibitors (PDE5i) have been shown to regulate the activated fibroblast phenotype in benign disease. We investigated the potential for CAF modulation in EAC using PDE5i to enhance the efficacy of chemotherapy.

Methods

EAC fibroblasts were treated with PDE5i and phenotypic effects examined using immunoblotting, immunohistochemistry, gel contraction, transwell invasion, organotypics, single cell RNAseq and shotgun proteomics. The combination of PDE5i with standard-of-care chemotherapy (Epirubicin, 5-Fluorouracil and Cisplatin) was tested for safety and efficacy in validated near-patient model systems (3D tumor growth assays (3D-TGAs) and patient derived xenograft (PDX) mouse models).

Results

PDE5i treatment reduced α–SMA expression in CAFs by 50% (p<0.05), associated with a significant reduction in the ability of CAFs to contract collagen-1 gels and induce cancer cell invasion, (p<0.05). RNAseq and proteomic analysis of CAF and EAC cell lines revealed PDE5i specific regulation of pathways related to fibroblast activation and tumor promotion. 3D-TGA assays confirmed the importance of stromal cells to chemoresistance in EAC, which could be attenuated by PDE5i. Chemotherapy+PDE5i in PDX-bearing mice was safe and significantly reduced PDX tumor volume (p<0.05).

Conclusion

PDE5 is a candidate for clinical trials to alter the fibroblast phenotype in esophageal cancer. We demonstrate the specificity of PDE5i for fibroblasts to prevent transdifferentiation and revert the CAF phenotype. Finally, we confirm the efficacy of PDE5i in combination with chemotherapy in close-to-patientin vitroandin vivoPDX-based model systems.
Unveiling cells’ local environment during cryopreservation by correlativein situspatial and thermal analyses
Authors: Qin Kankan , Eschenbrenner Corentin , Ginot Felix , Dedovets Dmytro , Coradin Thibaud , Deville Sylvain , Fernandes Francisco M.
Published: April 2020

Cryopreservation is the only fully established procedure to extend the lifespan of living cells and tissues, a key to activities spanning from fundamental biology to clinical practice. Despite its prevalence and impact, central aspects of cryopreservation, such as the cell’s physico-chemical environment during freezing, remain elusive. Here we address that question by couplingin situmicroscopic directional freezing to visualize cells and their surroundings during freezing with the freezing medium phase diagram. We extract the freezing medium spatial distribution in cryopreservation, providing a tool to describe the cell vicinity at any point during freezing. We show that two major events define the cells’ local environment over time: the interaction with the moving ice front and with the vitreous moving front – a term we introduce here. Our correlative strategy may be applied to cells relevant in clinical research and practice, and help designing new cryoprotective media based on local physico-chemical cues.
K-means Based Unsupervised Feature Selection to Prioritize Biomarkers of Different Disease Clinical Phases
Authors: Jiang Xue , Wang Weidi , Xu Jing , Wang Zhen , Lin Guan Ning
Published: April 2020

Huntington’s disease is caused by a single gene mutation, which is potentially a good model for development of biomarkers corresponding to different disease phase and clinical phenotypes. Hypothesis-driven and omics discovery approaches have not yet identified effective candidate biomarkers in HD. So, it is urgent to develop engagement and disease-phase specific biomarkers. The advanced sequencing technology makes it possible to develop data-driven methods for biomarkers discovery. Therefore, in this study, we designed k-means based unsupervised feature selection (KFS) method to prioritize biomarkers of different disease clinical phases. KFS first conducts k-means clustering on the samples with gene expression data, then it conducts feature selection based on the feature selection matrix to prioritize biomarkers of different samples. By conducting alternative iteration of clustering and feature selection to screen key genes which corresponding to the complex clinical phenotypes of different disease phases. Further gene ontology and enrichment analysis highlight potential molecular mechanisms of HD. Our experimental analyses have uncovered new disease-related genes and disease-associated pathways, which in turn have provided insight into the molecular mechanisms during the disease progression.
Open database searching enables the identification and comparison of bacterial glycoproteomes without defining glycan compositions prior to searching
Authors: Izaham Ameera Raudah Ahmad , Scott Nichollas E.
Published: April 2020

Mass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. While glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach usingN-linked glycopeptides ofCampylobacter fetus subsp. fetusas well asO-linked glycopeptides ofAcinetobacter baumanniiandBurkholderia cenocepaciarevealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses prior to database searching. Utilising this approach, we demonstrate how wide tolerance searching can be used to compare glycan utilisation across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.
Nicotinamide promotes differentiation of pancreatic endocrine progenitors from human pluripotent stem cells through poly (ADP-ribose) polymerase inhibition
Authors: Woodford Curtis , Yin Ting , Chang Huntley H , Regeenes Romario , Vellanki Ravi N , Mohan Haneesha , Wouters Bradly G , Rocheleau Jonathan V , Wheeler Michael B , Zandstra Peter W
Published: April 2020

The generation of pancreatic endocrine progenitor cells is an important step in the differentiation of beta cells from human pluripotent stem cells (hPSC). This stage is marked by the expression of Nkx6.1, a transcription factor with well understood downstream targets but with unclear upstream regulators. In hPSC differentiation, Nkx6.1 is strongly induced by nicotinamide, a derivative of vitamin B3, which has three known functions within a cell. Nicotinamide inhibits two classes of enzymes known as poly-ADP-ribose polymerases (PARPs) and sirtuins. It also contributes to the cellular pool of nicotinamide adenosine deoxynucleotide (NAD+) after conversion in the nicotinamide salvage pathway. Induction of Nkx6.1 expression in pancreatic endocrine progenitors by nicotinamide was mimicked by 3 PARP inhibitors (PJ34, olaparib, NU1025). Small molecule inhibition of the nicotinamide salvage pathway reduced Nkx6.1 expression but not Pdx1 expression and caused alteration in NAD+/NADH ratio. Nkx6.1 expression was not affected by sirtuin inhibition. Metabolic profiling of differentiating pancreatic and endocrine progenitors showed that oxygen consumption increases as differentiation progresses, and that nicotinamide reduces oxygen consumption rate. Expression of Nkx6.1 and other beta cell related genes, including Ins2 and Pdx1 increased in mouse islets after exposure to nicotinamide. In summary, nicotinamide induced Nkx6.1 expression in differentiating human pancreatic endocrine progenitors through inhibition of the PARP family of enzymes. Nicotinamide administration was also associated with increased NAD+/NADH ratio, without affecting Nkx6.1 expression. Similarly, the association between nicotinamide and Nkx6.1 expression was also seen in isolated mouse islets. These observations show a link between the regulation of beta cell identity and the effectors of NAD+metabolism, suggesting possible therapeutic targets in the field of diabetes.
A general 3D model for growth dynamics of sensory-growth systems: from plants to robotics
Authors: Porat Amir , Tedone Fabio , Palladino Michele , Marcati Pierangelo , Meroz Yasmine
Published: April 2020

In recent years there has been a rise in interest in the development of self-growing robotics inspired by the moving-by-growing paradigm of plants. In particular, climbing plants capitalize on their slender structures to successfully negotiate unstructured environments, while employing a combination of two classes of growth-driven movements: tropic responses, which direct growth in the direction of an external stimulus, and inherent nastic movements, such as periodic circumnutations, which promote exploration. In order to emulate these complex growth dynamics in a 3D environment, a general and rigorous mathematical framework is required. Here we develop a general 3D model for rod-like organs adopting the Frenet-Serret frame, providing a useful framework from the standpoint of robotics control. Differential growth drives the dynamics of the organ, governed by both internal and external cues. We describe the numerical method required to implement this model, and perform numerical simulations of a number of key scenarios, showcasing the applicability of our model. In the case of responses to external stimuli, we consider a distant stimulus (such as sunlight and gravity), a point stimulus (a point light source), and a line stimulus which emulates twining of a climbing plant around a support. We also simulate circumnutations, the response to an internal oscillatory cue, associated with search processes. Lastly we also demonstrate the superposition of both the response to an external stimulus together with circumnutations. Lastly we consider a simple example illustrating the possible use of an optimal control approach in order to recover tropic dynamics, in a way which may be relevant for robotics use. In all, the model presented here is general and robust, paving the way for a deeper understanding of plant response dynamics, as well as novel control systems for newly developed self-growing robots.
Neural Signatures of α2 Adrenergic Agonist-Induced Unconsciousness and Awakening by Antagonist
Authors: Ballesteros Jesus J. , Briscoe Jessica , Ishizawa Yumiko
Published: April 2020

How the brain dynamics transition during anesthetic-induced altered states of consciousness is not completely understood. Theα2 adrenergic agonist is a unique anesthetic that generates unconsciousness selectively throughα2 adrenergic receptors and related circuits. We studied intracortical neuronal dynamics during transitions of loss of consciousness (LOC) with theα2 adrenergic agonist dexmedetomidine and return of consciousness (ROC) in a functionally interconnecting somatosensory and ventral premotor network in non-human primates. LOC, ROC and full task performance recovery were all associated with distinct neural changes. The early recovery demonstrated characteristic intermediate dynamics distinguished by sustained high spindle activities. Awakening by theα2 adrenergic antagonist completely eliminated this intermediate state and instantaneously restored awake dynamics and the top task performance while the anesthetic was still being infused. The results suggest that instantaneous functional recovery is possible following anesthetic-induced unconsciousness and the intermediate recovery state is not a necessary path for the brain recovery.
Enteroendocrine cells couple nutrient sensing to nutrient absorption by regulating ion transport
Authors: McCauley Heather A. , Matthis Andrea L. , Enriquez Jacob R. , Nichol Jonah , Sanchez J. Guillermo , Stone William J. , Sundaram Nambirajan , Helmrath Michael A. , Montrose Marshall H. , Aihara Eitaro , Wells James M.
Published: April 2020

The ability to absorb ingested nutrients is an essential function of all metazoans and utilizes a wide array of nutrient transporters found on the absorptive enterocytes of the small intestine. A unique population of patients has previously been identified with severe congenital malabsorptive diarrhea upon ingestion of any enteral nutrition. The intestines of these patients are macroscopically normal, but lack enteroendocrine cells (EECs), suggesting an essential role for this rare population of nutrient-sensing cells in regulating macronutrient absorption. We used human and mouse models of EEC deficiency to identify a new role for the EEC hormone peptide YY in regulating ion-coupled absorption of glucose and dipeptides the small intestine. We found that peptide YY is required in to maintain normal electrophysiology in the presence of vasoactive intestinal polypeptide, a potent stimulator of ion secretion produced by enteric neurons. Administration of peptide YY to EEC-deficient mice restored normal electrophysiology, improved glucose and peptide absorption, diminished diarrhea and rescued postnatal survival. These data suggest that peptide YY is a key regulator of macronutrient absorption in the small intestine and may be a viable therapeutic option to treat patients with malabsorption.
Ligand-directed covalent labelling of a GPCR with a fluorescent tag
Authors: Stoddart Leigh A , Kindon Nicholas D , Otun Omolade , Harwood Clare R. , Patera Foteini , Veprintsev Dmitry B , Woolard Jeanette , Briddon Stephen J , Franks Hester A , Hill Stephen J , Kellam Barrie
Published: April 2020

Here, we describe rational design of a compound that covalently and selectively labels a G protein-coupled receptor (GPCR) in living cells with a fluorescent moiety. Using wild-type adenosine A2Areceptor as a model system, we show fluorescent labelling without impeding access to the orthosteric binding site and demonstrate its use in endogenously expressing systems. This offers a non-invasive and selective approach to study function and localisation of native GPCRs.
The relationship of mRNA with protein expression in CD8+T cells associates with gene class and gene characteristics
Authors: Nicolet Benoît P. , Wolkers Monika C.
Published: April 2020

T cells are key players in our defence against infections and malignancies. When T cells differentiate or become activated, they undergo substantial alterations in gene expression. Even though RNA expression levels are now well documented throughout different stages of T cells, it is not well understood how mRNA expression translates into the protein landscape. By combining paired RNA sequencing and massspectrometry data of primary human CD8+T cells, we report that mRNA expression is a poor proxy for the overall protein output, irrespective of the differentiation or activation status. Yet, gene class stratification revealed a function-specific correlation of mRNA with protein expression. This gene class-specific expression pattern associated with differences in gene characteristics such as sequence conservation and untranslated region (UTR) lengths. In addition, the presence of AU-rich elements in the 3’UTR associated with alterations in mRNA and protein abundance T cell activation dependent, gene class-specific manner. In conclusion, our study highlights the role of gene characteristics as a determinant for gene expression in T cells.