bluuebunny/crossref_metadata_2025 huggingface dataset:
New Persistent Opioid Use After Inguinal Hernia Repair
Authors: Howard Ryan , Gunaseelan Vidhya , Brummett Chad , Waljee Jennifer , Englesbe Michael , Telem Dana
Published: October 2020

Objective:

To describe the incidence of new persistent opioid use after inguinal hernia repair as well as its associated risk factors.

Summary of Background Data:

The development of new persistent opioid use after surgery is a common complication; however, its incidence following inguinal hernia repair has not been described. Given that roughly 800,000 inguinal hernia repairs are performed annually in the USA, any incidence could have profound implications for patients.

Methods:

A retrospective cross-sectional study of the incidence of new persistent opioid use after inguinal hernia repair using a national database of de-identified administrative health claims of opioid-naïve patients undergoing surgery from 2008 to 2016.

Results:

During the study period, 59,795 opioid-naïve patients underwent inguinal hernia repair and met inclusion criteria. Mean (SD) age was 57.8 (16.1) years and 55,014 (92%) patients were male. Nine hundred twenty-two (1.5%) patients continued filling opioids prescriptions for at least 3 months after surgery. The most significant risk factor for developing new persistent opioid use after surgery was filling an opioid prescription in the 30 days before surgery (odds ratio 4.34, 95% confidence interval 3.75–5.01). These prescriptions were provided by surgeons in 52% of cases and primary care physicians in 16% of cases. Other risk factors for new persistent opioid use included receiving a larger opioid prescription, having more comorbidities, having a major postoperative complication, and certain mental health disorders and pain disorders.

Conclusions:

After undergoing inguinal hernia repair, 1.5% of patients developed new persistent opioid use. Filling an opioid prescription in the 30 days before surgery had the strongest association with this complication.
Evidence-Based and Clinically Relevant Outcomes for Hemorrhage Control Trauma Trials
Authors: Holcomb John B. , Moore Ernest E. , Sperry Jason L. , Jansen Jan O. , Schreiber Martin A. , del Junco Deborah J. , Spinella Philip C. , Sauaia Angela , Brohi Karim , Bulger Eileen M. , Cap Andrew P. , Hess John R. , Jenkins Donald , Lewis Roger J. , Neal Matthew D. , Newgard Craig , Pati Shibani , Pusateri Anthony E. , Rizoli Sandro , Russell Robert T. , Shackelford Stacy A. , Stein Deborah M. , Steiner Marie E. , Wang Henry , Ward Kevin R. , Young Pampee
Published: October 2020

Objective:

To address the clinical and regulatory challenges of optimal primary endpoints for bleeding patients by developing consensus-based recommendations for primary clinical outcomes for pivotal trials in patients within 6 categories of significant bleeding, (1) traumatic injury, (2) intracranial hemorrhage, (3) cardiac surgery, (4) gastrointestinal hemorrhage, (5) inherited bleeding disorders, and (6) hypoproliferative thrombocytopenia.

Background:

A standardized primary outcome in clinical trials evaluating hemostatic products and strategies for the treatment of clinically significant bleeding will facilitate the conduct, interpretation, and translation into clinical practice of hemostasis research and support alignment among funders, investigators, clinicians, and regulators.

Methods:

An international panel of experts was convened by the National Heart Lung and Blood Institute and the United States Department of Defense on September 23 and 24, 2019. For patients suffering hemorrhagic shock, the 26 trauma working-group members met for almost a year, utilizing biweekly phone conferences and then an in-person meeting, evaluating the strengths and weaknesses of previous high quality studies. The selection of the recommended primary outcome was guided by goals of patient-centeredness, expected or demonstrated sensitivity to beneficial treatment effects, biologic plausibility, clinical and logistical feasibility, and broad applicability.

Conclusions:

For patients suffering hemorrhagic shock, and especially from truncal hemorrhage, the recommended primary outcome was 3 to 6-hour all-cause mortality, chosen to coincide with the physiology of hemorrhagic death and to avoid bias from competing risks. Particular attention was recommended to injury and treatment time, as well as robust assessments of multiple safety related outcomes.
Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov
Authors: dos Santos Ferreira Natalia , Hayashi Sant’ Anna Fernando , Massena Reis Veronica , Ambrosini Adriana , Gazolla Volpiano Camila , Rothballer Michael , Schwab Stefan , Baura Valter Antonio , Balsanelli Eduardo , Pedrosa Fabio de Oliveira , Pereira Passaglia Luciane Maria , Maltempi de Souza Emanuel , Hartmann Anton , Cassan Fabricio , Zilli Jerri Edson
Published: October 2020

Azospirillum

sp. strain Sp245T, originally identified as belonging to

Azospirillum brasilense

, is recognized as a plant-growth-promoting rhizobacterium due to its ability to fix atmospheric nitrogen and to produce plant-beneficial compounds.

Azospirillum

sp. Sp245T and other related strains were isolated from the root surfaces of different plants in Brazil. Cells are Gram-negative, curved or slightly curved rods, and motile with polar and lateral flagella. Their growth temperature varies between 20 to 38 °C and their carbon source utilization is similar to other

Azospirillum

species. A preliminary 16S rRNA sequence analysis showed that the new species is closely related to

A. brasilense

Sp7T and

A. formosense

CC-Nfb-7T. Housekeeping genes revealed that

Azospirillum

sp. Sp245T, BR 12001 and Vi22 form a separate cluster from strain

A. formosense

CC-Nfb-7T, and a group of strains closely related to

A. brasilense

Sp7T. Overall genome relatedness index (OGRI) analyses estimated based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between

Azospirillum

sp. Sp245T and its close relatives to other

Azospirillum

species type strains, such as

A. brasilense

Sp7T and

A. formosense

CC-Nfb-7T
, revealed values lower than the limit of species circumscription. Moreover, core-proteome phylogeny including 1079 common shared proteins showed the independent clusterization of

A. brasilense

Sp7T,

A. formosense

CC-Nfb-7T and

Azospirillum

sp. Sp245T, a finding that was corroborated by the genome clustering of OGRI values and housekeeping phylogenies. The DNA G+C content of the cluster of Sp245T was 68.4–68.6 %. Based on the phylogenetic, genomic, phenotypical and physiological analysis, we propose that strain Sp245T together with the strains Vi22 and BR12001 represent a novel species of the genus

Azospirillum

, for which the name Azospirillum baldaniorum sp. nov. is proposed. The type strain is Sp245T (=BR 11005T=IBPPM 219T) (GCF_007827915.1, GCF_000237365.1, and GCF_003119195.2).
Microbacterium excoecariae sp. nov., a novel endophytic actinobacterium isolated from bark of Excoecaria agallocha Linn
Authors: Chen Ming-Sheng , Li Fei , Yan Xiao-Rui , Tuo Li
Published: October 2020

A Gram-stain-positive, aerobic actinobacterium, designated strain CBS5P-1T, was isolated from bark of Excoecaria agallocha Linn collected from Guangxi Zhuang Autonomous Region, PR China. Cells were short rods. Colonies were light yellow, circular and had entire margins. Strain CBS5P-1T grew at 10–37 °C (optimum, 30 °C) and pH 6.0–12.0 (optimum, pH 7.0–8.0). Its nearest phylogenetic neighbour was

Microbacterium amylolyticum

DSM 24221T with 97.1 % 16S rRNA gene sequence similarity. The genomic DNA G+C content of strain CBS5P-1T was 71.8 mol%. Anteiso-C15  : 0, anteiso-C17 : 0, iso-C16 : 0 and C16:0 were predominant cellular fatty acids. Major menaquinones were MK-11 and MK-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The combination of chemotaxonomic, phylogenetic and phenotypic data clearly distinguished strain CBS5P-1T from its phylogenetic neighbour. Accordingly, the name Microbacterium excoecariae sp. nov. is proposed to accommodate this new member of the genus

Microbacterium

. The type strain is CBS5P-1T (=KCTC 49239T=CGMCC 1.13862T).
LuftiBus in the school (LUIS): a population-based study on respiratory health in schoolchildren
Authors: Mozun Rebeca , Kuehni Claudia E. , Pedersen Eva S. L. , Goutaki Myrofora , Kurz Johanna M. , de Hoogh Kees , Usemann Jakob , Singer Florian , Latzin Philipp , Moeller Alexander
Published: October 2020

Respiratory disease is common in children and strongly associated with lifestyle and environmental exposures. Thus, it is important to study the epidemiology locally. LuftiBus in the school (LUIS) was set up to assess the respiratory health of schoolchildren in the canton of Zurich, Switzerland.

LUIS is a cross-sectional population-based study that was carried out 2013 to 2016. Children aged 6-17 years living in the canton of Zurich were eligible to participate. All schools in the canton were approached and the school head decided whether the school would participate and with which classes. Consenting parents answered a standardized questionnaire at home and assenting children completed a shorter questionnaire by interview at school. Trained technicians measured children’s lung function including spirometry, double tracer gas single-breath washout (DTG-SBW) and fractional exhaled nitric oxide (FeNO). Address histories of participants were geocoded to be linked with area-based socioeconomic measures and environmental exposures like spatiotemporal air pollution estimates for specific time periods and locations. A subgroup was seen again 12 months later using the same procedures to collect longitudinal data.

The study included 3870 children at baseline and 655 at the one-year follow-up. Median age was 12.7 years; 281 (8%) had wheezed in the past year. At baseline we collected 3457 (89%) parental and 3546 (92%) children’s questionnaires, and 3393 (88%) FeNO, 3446 (89%) spirometry, and 1795 (46%) DTG-SBW measurements.

LUIS is a rich resource of health-related data, with information on lung function, environmental exposures and respiratory health on Swiss schoolchildren.

Take home message

LuftiBus in the school (LUIS) is a population-based study with detailed lung function data and rich information on respiratory health in Swiss schoolchildren.
Estimating incidence of infection from diverse data sources: Zika virus in Puerto Rico, 2016
Authors: Quandelacy Talia M. , Healy Jessica M. , Greening Bradford , Rodriguez Dania M. , Chung Koo-Whang , Kuehnert Matthew J. , Biggerstaff Brad J. , Dirlikov Emilio , Mier-y-Teran-Romero Luis , Sharp Tyler M. , Waterman Stephen , Johansson Michael A.
Published: October 2020

Emerging epidemics are challenging to track. Only a subset of cases is recognized and reported, as seen with the Zika virus (ZIKV) epidemic where large proportions of infection were asymptomatic. However, multiple imperfect indicators of infection provide an opportunity to estimate the underlying incidence of infection. We developed a modeling approach that integrates a generic Time-series Susceptible-Infected-Recovered epidemic model with assumptions about reporting biases in a Bayesian framework and applied it to the 2016 Zika epidemic in Puerto Rico using three indicators: suspected arboviral cases, suspected Zika-associated Guillain-Barré Syndrome cases, and blood bank data. Using this combination of surveillance data, we estimated the peak of the epidemic occurred during the week of August 15, 2016 (the 33rdweek of year), and 120 to 140 (50% credible interval [CrI], 95% CrI: 97 to 170) weekly infections per 10,000 population occurred at the peak. By the end of 2016, we estimated that approximately 890,000 (95% CrI: 660,000 to 1,100,000) individuals were infected in 2016 (26%, 95% CrI: 19% to 33%, of the population infected). Utilizing multiple indicators offers the opportunity for real-time and retrospective situational awareness to support epidemic preparedness and response.
On Modeling of COVID-19 for the Indian Subcontinent using Polynomial and Supervised Learning Regression
Authors: Neve Dishita , Patel Honey , Dhiman Harsh S.
Published: October 2020

COVID-19, a recently declared pandemic by WHO has taken the world by storm causing catastrophic damage to human life. The novel cornonavirus disease was first incepted in the Wuhan city of China on 31st December 2019. The symptoms include fever, cough, fatigue, shortness of breath or breathing difficulties, and loss of smell and taste. Since the devastating phenomenon is essentially a time-series representation, accurate modeling may benefit in identifying the root cause and accelerate the diagnosis. In the current analysis, COVID-19 modeling is done for the Indian subcontinent based on the data collected for the total cases confirmed, daily recovered, daily deaths, total recovered and total deaths. The data is treated with total confirmed cases as the target variable and rest as feature variables. It is observed that Support vector regressions yields accurate results followed by Polynomial regression. Random forest regression results in overfitting followed by poor Bayesian regression due to highly correlated feature variables. Further, in order to examine the effect of neighbouring countries, Pearson correlation matrix is computed to identify geographic cause and effect.
SM-Omics: An automated platform for high-throughput spatial multi-omics
Authors: Vickovic Sanja , Lötstedt Britta , Klughammer Johanna , Segerstolpe Åsa , Rozenblatt-Rosen Orit , Regev Aviv
Published: October 2020

The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial Transcriptomics (ST) has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of ST at scale, by presenting Spatial Multiomics (SM-Omics) as a fully automated high-throughput platform for combined and spatially resolved transcriptomics and antibody-based proteomics.
C9orf72- derived proline:arginine poly-dipeptides disturb cytoskeletal architecture
Authors: Shiota Tomo , Nagata Riko , Kikuchi Sotaro , Nanaura Hitoki , Matsubayashi Masaya , Nakanishi Mari , Kobashigawa Shinko , Nagayama Kazuaki , Sugie Kazuma , Yamashiro Yoshito , Mori Eiichiro
Published: October 2020

Amyotrophic lateral sclerosis (ALS) is an irreversible neurodegenerative disease caused by the degeneration of motor neurons, and cytoskeletal instability is considered to be involved in neurodegeneration. A hexanucleotide repeat expansion of theC9orf72, one of the most common causes of familial ALS, produces toxic proline:arginine (PR) poly-dipeptides. PR poly-dipeptides binds polymeric forms of low complexity sequences and intracellular puncta, thereby altering intermediate filaments (IFs). However, how PR poly-dipeptides affect the cytoskeleton, including IFs, microtubules and actin filaments, remains unknown. Here we performed a synthetic PR poly-dipeptide treatment on mammalian cells and investigated how it affects morphology of cytoskeleton and cell behaviors. We observed that PR poly-dipeptide treatment induce the degradation of vimentin bundles at perinucleus and dissociation of β-tubulin network. PR poly-dipeptides also lead to alteration of actin filaments toward to cell contours and strength cortical actin filaments via activation of ERM (ezrin/radixin/moesin) proteins. In addition, we found that PR poly-dipeptides promote phosphorylation of paxillin and recruitment of vinculin on focal adhesions, which lead to maturation of focal adhesions. Finally, we evaluated the effects of PR poly-dipeptides on mechanical property and stress response. Interestingly, treatment of PR poly-dipeptides increased the elasticity of the cell surface, leading to maladaptive response to cyclic stretch. These results suggest that PR poly-dipeptides cause mechanically sensitive structural reorganization and disrupt the cytoskeleton architecture.
Evidence of antigenic imprinting in sequential Sarbecovirus immunization
Authors: Lv Huibin , So Ray T. Y. , Yuan Meng , Liu Hejun , Lee Chang-Chun D. , Yip Garrick K. , Ng Wilson W. , Wilson Ian A. , Peiris Malik , Wu Nicholas C. , Mok Chris K. P.
Published: October 2020

Antigenic imprinting, which describes the bias of antibody response due to previous immune history, can influence vaccine effectiveness and has been reported in different viruses. Give that COVID-19 vaccine development is currently a major focus of the world, there is a lack of understanding of how background immunity influence antibody response to SARS-CoV-2. This study provides evidence for antigenic imprinting inSarbecovirus, which is the subgenus that SARS-CoV-2 belongs to. Specifically, we sequentially immunized mice with two antigenically distinctSarbecovirusstrains, namely SARS-CoV and SARS-CoV-2. We found that the neutralizing antibodies triggered by the sequentially immunization are dominantly against the one that is used for priming. Given that the impact of the background immunity on COVID-19 is still unclear, our results will provide important insights into the pathogenesis of this disease as well as COVID-19 vaccination strategy.
Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung
Authors: Kalocsay Marian , Maliga Zoltan , Nirmal Ajit J. , Eisert Robyn J. , Bradshaw Gary A. , Solomon Isaac H , Chen Yu-An , Pelletier Roxanne J. , Jacobson Connor A. , Mintseris Julian , Padera Robert F. , Martinot Amanda J. , Barouch Dan H. , Santagata Sandro , Sorger Peter K.
Published: October 2020

Normal tissue physiology and repair depends on communication with the immune system. Understanding this communication at the molecular level in intact tissue requires new methods. The consequences of SARS-CoV-2 infection, which can result in acute respiratory distress, thrombosis and death, has been studied primarily in accessible liquid specimens such as blood, sputum and bronchoalveolar lavage, all of which are peripheral to the primary site of infection in the lung. Here, we describe the combined use of multiplexed deep proteomics with multiplexed imaging to profile infection and its sequelae directly in fixed lung tissue specimens obtained from necropsy of infected animals and autopsy of human decedents. We characterize multiple steps in disease response from cytokine accumulation and protein phosphorylation to activation of receptors, changes in signaling pathways, and crosslinking of fibrin to form clots. Our data reveal significant differences between naturally resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans. The approach we describe is broadly applicable to other tissues and diseases.

Proteomics of infected tissue reveals differences in inflammatory and thrombotic responses between resolving and lethal COVID-19.
A Common Methodological Phylogenomics Framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
Authors: Utro Filippo , Levovitz Chaya , Rhrissorrakrai Kahn , Parida Laxmi
Published: October 2020

We present a common methodological framework to infer the phylogenomics from genomic data, be it reads of SARS-CoV-2 of multiple COVID-19 patients or bulk DNAseq of the tumor of a cancer patient. The commonality is in the phylogenetic retrodiction based on the genomic reads in both scenarios. While there is evidence of heteroplasmy, i.e., multiple lineages of SARS-CoV-2 in the same COVID-19 patient; to date, there is no evidence of sublineages recombining within the same patient. The heterogeneity in a patient’s tumor is analogous to intra-patient heteroplasmy and the absence of recombination in the cells of tumor is a widely accepted assumption. Just as the different frequencies of the genomic variants in a tumor presupposes the existence of multiple tumor clones and provides a handle to computationally infer them, we postulate that so do the different variant frequencies in the viral reads, offering the means to infer the multiple co-infecting sublineages. We describe the Concerti computational framework for inferring phylogenies in each of the two scenarios. To demonstrate the accuracy of the method, we reproduce some known results in both scenarios. We also make some additional discoveries. We uncovered new potential parallel mutation in the evolution of the SARS-CoV-2 virus. In the context of cancer, we uncovered new clones harboring resistant mutations to therapy from clinically plausible phylogenetic tree in a patient.
From amazing work to I beg to differ - analysis of bioRxiv preprints that received one public comment till September 2019
Authors: Malički Mario , Costello Joseph , Alperin Juan Pablo , Maggio Lauren A.
Published: October 2020

While early commenting on studies is seen as one of the advantages of preprints, the nature of such comments, and the people who post them, have not been systematically explored. We analysed comments posted between 21 May 2015 and 9 September 2019 for 1,983 bioRxiv preprints that received only one comment. Sixty-nine percent of comments were posted by non-authors (n=1,366), and 31% by preprint authors (n=617). Twelve percent of non-author comments (n=168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (n=577, 42%), suggestions (n=399, 29%), or criticisms (n=226, 17%). Authors’ comments most commonly contained publication status updates (n=354, 57%), additional study information (n=158, 26%), or solicited feedback for the preprints (n=65, 11%). Our study points to the value of preprint commenting, but further studies are needed to determine the role that comments play in shaping preprint versions and eventual journal publications.
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
Authors: Zhang Junpeng , Liu Lin , Xu Taosheng , Zhang Wu , Zhao Chunwen , Li Sijing , Li Jiuyong , Rao Nini , Le Thuc Duy
Published: October 2020

Background

Existing computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells, rather than the miRNA regulation unique to individual cells. Recent advance in single-cell miRNA-mRNA co-sequencing technology has opened a way for investigating miRNA regulation at single-cell level. However, as currently single-cell miRNA-mRNA co-sequencing data is just emerging and only available at small-scale, there is a strong need of novel methods to exploit existing single-cell data for the study of cell-specific miRNA regulation.

Results

In this work, we propose a new method,CSmiR(Cell-SpecificmiRNA regulation) to use single-cell miRNA-mRNA co-sequencing data to identify miRNA regulatory networks at the resolution of individual cells. We applyCSmiRto the miRNA-mRNA co-sequencing data in 19 K562 single-cells to identify cell-specific miRNA-mRNA regulatory networks for understanding miRNA regulation in each K562 single-cell. By analyzing the obtained cell-specific miRNA-mRNA regulatory networks, we observe that the miRNA regulation in each K562 single-cell is unique. Moreover, we conduct detailed analysis on the cell-specific miRNA regulation associated with the miR-17/92 family as a case study. Finally, through exploring cell-cell similarity matrix characterized by cell-specific miRNA regulation,CSmiRprovides a novel strategy for clustering single-cells to help understand cell-cell crosstalk.

Conclusions

To the best of our knowledge,CSmiRis the first method to explore miRNA regulation at a single-cell resolution level, and we believe that it can be a useful method to enhance the understanding of cell-specific miRNA regulation.
Mechanical competition alters the cellular interpretation of an endogenous genetic programme
Authors: Bhide Sourabh , Gombalova Denisa , Mönke Gregor , Stegmaier Johannes , Zinchenko Valentyna , Kreshuk Anna , Belmonte Julio M , Leptin Maria
Published: October 2020

The intrinsic genetic programme of a cell is not sufficient to explain all of the cell’s activities. External mechanical stimuli are increasingly recognized as determinants of cell behaviour. In the epithelial folding event that constitutes the beginning of gastrulation inDrosophila, the genetic programme of the future mesoderm leads to the establishment of a contractile actomyosin network that triggers apical constriction of cells, and thereby, tissue folding. However, some cells do not constrict but instead stretch, even though they share the same genetic programme as their constricting neighbours. We show here that tissue-wide interactions force these cells to expand even when an otherwise sufficient amount of apical, active actomyosin is present. Models based on contractile forces and linear stress-strain responses do not reproduce experimental observations, but simulations in which cells behave as ductile materials with non-linear mechanical properties do. Our models show that this behaviour is a general emergent property of actomyosin networks [in a supracellular context, in accordance with our experimental observations of actin reorganisation within stretching cells.
A Structured Professional Development Curriculum for Postdoctoral Fellows Leads to Recognized Knowledge Growth
Authors: Steen Kaylee , Vornhagen Jay , Weinberg Zara Y. , Boulanger-Bertolus Julie , Rao Arvind , Gardner Margery Evans , Subramanian Shoba
Published: October 2020

Postdoctoral training enables research independence and professional readiness. National reports have emphasized professional development as a critical component of this training period. In response, many institutions are establishing transferable skills training workshops for postdocs; however, the lack of structured programs and an absence of methods to assess outcomes beyond participant satisfaction surveys are critical gaps in postdoctoral training. To address these shortcomings, we took the approach of structured programming and developed a method for controlled assessment of outcomes. Our program You3(You, Your Team, Your Project), co-designed by postdoctoral fellows, focused on a structured array of management and leadership skills agnostic of ultimate career path(s). We then measured outcomes in a controlled manner, by systematically comparing perceived knowledge and growth of participants with non-participants as the control group. You3participants discern greater growth, independent of number of years in training, in competencies overall compared to the control group. This growth was shown by multiple criteria including self-reporting and associative analysis. Correspondingly, You3participants reported greater knowledge in 75% of the modules when compared to controls. These data indicate that structured learning, where postdocs commit to a curriculum via a cohort-structure, leads to positive outcomes and provides a framework for programs to assess outcomes in a rigorous manner.
Arachidonic acid metabolism controls macrophage alternative activation through regulating oxidative phosphorylation in PPARG dependent manner
Authors: Xu Miao , Wang Xiaohong , Jia Xudong , Li Yongning , Geng Xue , Zhang Lishi , Yang Hui
Published: October 2020

Macrophages polarization is mainly controlled by metabolic reprogramming in microenvironment, thus leading to distinct outcomes of various diseases. However, the role of lipid metabolism in the regulation of macrophage alternative activation is incompletely understood. Using human THP-1 and mouse bone marrow derived macrophages polarization models, we revealed a pivotal role for arachidonic acid metabolism in controlling the polarization of M1 and M2 macrophages. We demonstrated that M2 macrophage polarization was inhibited by arachidonic acid, but inversely facilitated by its derived metabolite prostaglandin E2 (PGE2). Furthermore, PPARG bridges these two unconnected processes via modulating oxidative phosphorylation. These results highlight the critical role of arachidonic acid metabolism as an immune regulator in modulating metabolic homeostasis and pathological process.
Transcriptome profiling of the Olig2-expressing astrocyte subtype reveals their unique molecular signature
Authors: Ohayon David , Aguirrebengoa Marion , Escalas Nathalie , Soula Cathy
Published: October 2020

Astrocytes are recognized to be a heterogeneous population of cells that differ morphologically, functionally and molecularly. Whether this heterogeneity results from generation of distinct astrocyte cell lineages, each functionally specialized to perform specific tasks, remains an open question. In this study, we used RNA-seq analysis to determine the global transcriptome profile of the Olig2-expressing astrocyte subtype (Olig2-AS), a specific spinal astrocyte subtype which segregates early during development from Olig2 progenitors and differs from other spinal astrocytes by the expression of Olig2. We identified 245 differentially expressed genes. Among them, 135 exhibit higher levels of expression when compared to other populations of spinal astrocytes, indicating that these genes can serve as a ‘unique’functional signature of Olig2-AS. Further analysis highlighted, in particular, enrichment in Olig2-AS of a set of genes specialized in regulating synaptic activity. Our work thus reveals that Olig2 progenitors produce a unique astrocyte subtype specialized to perform certain specific functions.
Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments
Authors: Chen Yu , van Pelt-KleinJan Eunice , van Olst Berdien , Douwenga Sieze , Boeren Sjef , Bachmann Herwig , Molenaar Douwe , Nielsen Jens , Teusink Bas
Published: October 2020

Cells adapt to different conditions via gene expression that tunes metabolism and stress resistance for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade-offs1; Resource allocation under proteome constraints has emerged as a powerful paradigm to explain regulatory strategies in bacteria2. It is unclear, however, to what extent these constraints can predict evolutionary changes, especially for microorganisms that evolved under nutrient-rich conditions, i.e., multiple available nitrogen sources, such as the lactic acid bacteriumLactococcus lactis. Here we present an approach to identify preferred nutrients from integration of experimental data with a proteome-constrained genome-scale metabolic model ofL. lactis(pcLactis), which explicitly accounts for gene expression processes and associated constraints. Using glucose-limited chemostat data3, we identified the uptake of glucose and arginine as dominant constraints, whose pathway proteins were indeed upregulated in evolved mutants. However, above a growth rate of 0.5 h-1, pcLactis suggests that available enzymes function at their maximum capacity, which allows an increase in growth rate only by altering gene expression to change metabolic fluxes, as was mainly observed for arginine metabolism. Thus, our integrative analysis of flux and proteomics data with a proteome-constrained model is able to identify and explain the constraints that form targets of regulation and fitness improvement in nutrient-rich growth environments.
Behavioral phenotyping of mice lacking the deubiquitinase USP2
Authors: Srikanta Shashank Bangalore , Stojkovic Katarina , Cermakian Nicolas
Published: October 2020

Ubiquitin specific peptidase 2 (USP2) is a deubiquitinating enzyme expressed almost ubiquitously in the body, including in multiple brain regions. We previously showed that mice lacking USP2 present altered locomotor activity rhythms and response of the clock to light. However, the possible implication of USP2 in regulating other behaviors has yet to be tested. To address this, we ran a battery of behavioral tests onUsp2KO mice. Firstly, we confirmed our prior findings of increased daily activity and reduced activity fragmentation inUsp2KO mice. Further, mice lacking USP2 showed impaired motor coordination and equilibrium, a decrease in anxiety-like behavior, a deficit in short-term recognition memory and in sensorimotor gating. On the other hand, no effects ofUsp2gene deletion were found on spatial memory. Hence, our data uncover the implication of USP2 in different behaviors and expands the range of the known functions of this deubiquitinase.
Chitosan nanoparticle vaccine loaded with crude extracellular proteins ofC. perfringensandSalmonellaflagella is partially protective against necrotic enteritis in broiler chickens
Authors: Akerele Gabriel , Ramadan Nour , Mortada Muhammed , Shanmugasundaram Revathi , Renu Sankar , Renukaradhya Gourapura J. , Selvaraj Ramesh K
Published: October 2020

Necrotic enteritis (NE) causes significant economic losses and food shortages world-wide. There are currently no licensed commercial vaccines against NE in broilers. Chitosan nanoparticles were formulated with extracellular proteins ofC. perfringenssurface-tagged withSalmonellaflagellar proteins. One-day-old male broiler chicks were completely randomized to 3 treatments: Non-vaccinated non-challenged as negative control, Vaccinated-challenged, and non-vaccinated challenge as positive control. On day of hatch, d7, and d14 post-hatch, vaccinated-challenged birds were orally gavage with 50μg vaccine in 0.5ml PBS while positive control birds were gavage with 0.5ml PBS only. Birds in the vaccinated-challenged and positive control groups were orally infected on d14 post-hatch, with 5,000 oocysts/bird ofE. maxima, followed by log 8 CFU of a virulent strain of C. perfringens on d19, d20, and d21 post-hatch. From d14 to 21 and d14 to 28 post-hatches, mortality in the vaccinated-challenged group was higher than that in the positive control group, approaching statistical significance (p=0.07). On d21 post-hatch, the mean lesion score of 3 birds/cage in the vaccinated-challenged group was higher than the positive control group, approaching statistical significance (p = 0.05). From d 14 to 28 post-hatch, the feed intake was higher and feed conversion ratio lower in the vaccinated-challenged group compared to the positive control group (p<0.05). On d21 post-hatch, antigen specific recall proliferation in the vaccinated-challenged group was higher than that in the negative and positive control groups (p<0.05). On d21 post-hatch, cecal tonsils CD8+ T lymphocytes expression in the vaccinated-challenged group was similar to the negative control group (p>0.05) but higher than that in the positive control group (p<0.05). Finally, vaccination resulted in an increase in ileal mRNA levels of zonula occluding on d21 post-hatch. In conclusion, there were numerical but not statistically significant decrease in NE lesions and mortality in vaccinated and challenged broilers. Further studies are needed to improve the efficacy of the vaccine and understand the mechanism underlying protection in vaccinated birds.
Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent
Authors: Patwardhan Sushmita , Smedile Francesco , Giovannelli Donato , Vetriani Costantino
Published: October 2020

Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO2, H2S. At Tor Caldara, filamentous microbial biofilms, mainly composed ofEpsilon- andGammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential andin situexpression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO2the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of theEpsilonproteobacteriadominated the young microbial biofilms, whileGammaproteobacteriabecome prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.
Mechanisms of allosteric and mixed mode aromatase inhibitors
Authors: Souza Samson A. , Held Abby , Lu Wenjie , Drouhard Brendan , Avila Bryant , Leyva-Montes Raul , Hu Michelle , Miller Bill R. , Ng Ho Leung
Published: October 2020

Aromatase (Cyp19) catalyzes the last biosynthetic step of estrogens in mammals and is a primary drug target for hormone-related breast cancer. However, treatment with aromatase inhibitors is often associated with adverse effects and drug resistance. In this study, we used virtual screening targeting a predicted cytochrome P450 reductase binding site on aromatase to discover four novel non-steroidal aromatase inhibitors. The inhibitors have potencies comparable to the noncompetitive tamoxifen metabolite, endoxifen. Our two most potent inhibitors, AR11 and AR13, exhibit both mixed-type and competitive-type inhibition. The cytochrome P450 reductase-Cyp19 coupling interface likely acts as a transient binding site. Our modeling shows that our inhibitors bind better at different sites near the catalytic site. Our results predict the location of multiple ligand binding sites on aromatase. The combination of modeling and experimental results supports the important role of the reductase binding interface as a low affinity, promiscuous ligand binding site. Our new inhibitors may be useful as alternative chemical scaffolds that may show different adverse effects profiles than current clinically used aromatase inhibitors.
Exploring the pH-dependent structure-dynamics-function relationship of human renin
Authors: Ma Shuhua , Henderson Jack A. , Shen Jana
Published: October 2020

Renin is a pepsin-like aspartyl protease and an important drug target for the treatment of hypertension; despite three decades’ research, its pH-dependent structure-function relationship remains poorly understood. Here we employed the continuous constant pH molecular dynamics (CpHMD) simulations to decipher the acid/base roles of renin’s catalytic dyad and the conformational dynamics of the flap, which is a common structural feature among aspartyl proteases. The calculated pKa’s suggest that the catalytic Asp38 and Asp226 serve as the general base and acid, respectively, in agreement with experiment and supporting the hypothesis that renin’s neutral optimum pH is due to the substrate-induced pKashifts of the aspartic dyad. The CpHMD data confirmed our previous hypothesis that hydrogen bond formation is the major determinant of the dyad pKaorder. Additionally, our simulations showed that renin’s flap remains open regardless of pH, although a Tyr-inhibited state is occasionally formed above pH 5. These findings are discussed in comparison to the related aspartyl proteases, includingβ-secretases 1 and 2, capthepsin D, and plasmepsin II. Our work represents a first step towards a systematic understanding of the pH-dependent structure-dynamics-function relationships of pepsin-like aspartyl proteases that play important roles in biology and human disease states.
Sequential Measurements of Catalytic Activities of Multi-Drug-Resistance Transporters and Cytochrome P450 Enzymes by Cytometry of Reaction Rate Constant
Authors: Koshkin Vasilij , Oliveira Mariana Bleker de , Kochmann Sven , Peng Chun , Krylov Sergey N.
Published: October 2020

Cytometry of reaction rate constant (CRRC) is an accurate and robust approach to characterize cell-population heterogeneity using rate constants of cellular processes for which kinetic mechanisms are known. We work on a CRRC-based method to develop predictors of tumor chemoresistance driven by two processes: drug extrusion by multi-drug-resistance (MDR) transporters and drug inactivation by cytochrome-P450 enzymes (CYP). Each of the two possess is studied with its specific substrate and the process activity is characterized by a corresponding unimolecular rate constant. Due to the incompatibility of MDR and CYP assays, MDR and CYP activities may be difficult to measure simultaneously suggesting that they may need to be measured sequentially. The sequential measurements may also impose a problem: the results of the second assay may be affected by artifacts exerted by the first assay. The goal of this work was to understand whether the cells have a memory of the first assay that significantly affects the results of the second assay. To achieve this goal, we compared CRRC results for two orders of sequential measurements: the MDR→CYP order in which MDR activity is measured before CYP activity and the CYP→MDR order in which CYP activity is measured before MDR activity. It was found that the results of the CYP assay were similar in both orders; on the contrary, the results of the MDR assay were significantly different. Our findings suggest that MDR and CYP activity can be studied sequentially provided that MDR activity is measured first and CYP activity second.
Predicting Cell-Penetrating Peptides: Building and Interpreting Random Forest based prediction Models
Authors: Yadahalli Shilpa , Verma Chandra S.
Published: October 2020

Targeting intracellular pathways with peptide drugs is becoming increasingly desirable but often limited in application due to their poor cell permeability. Understanding cellular permeability of peptides remains a major challenge with very little structure-activity relationship known. Fortunately, there exist a class of peptides called Cell-Penetrating Peptides (CPPs), which have the ability to cross cell membranes and are also capable of delivering biologically active cargo into cells. Discovering patterns that make peptides cell-permeable have a variety of applications in drug delivery. In the current study, we build prediction models for CPPs exploring features covering a range of properties based on amino acid sequences, using Random forest classifiers which are often more interpretable than other ensemble machine learning algorithms. While obtaining prediction accuracies of ~96%, we also interpret our prediction models using TreeInterpreter, LIME and SHAP to decipher the contributions of important features and optimal feature space for CPP class. We propose that our work might offer an intuitive guide for incorporating features that impart cell-penetrability into the design of novel CPPs.
Double-layer flexible neuronal probe with closely spaced electrodes for high-densityin-vivobrain recordings
Authors: Pimenta Sara , Rodrigues José A. , Machado Francisca , Ribeiro João F. , Maciel Marino J. , Bondarchuk Oleksandr , Monteiro Patrícia , Gaspar João , Correia José H. , Jacinto Luis
Published: October 2020

Flexible probes for brain activity recordings are an attractive emerging approach that reduces mechanical mismatch between probe and neuronal tissue, thus minimizing the risk of brain damage or glial scaring. Although promising, flexible probes still present some technical challenges namely: i) how to overcome probe buckling during brain insertion given its intrinsically low mechanical rigidity; ii) how to fabricate closely spaced electrode configurations for high density recordings by standard lithography techniques in the flexible substrate. Here, we present a new flexible probe based solely on standard and low-cost lithography processes, which has closely spaced 10 μm diameter gold electrode sites on a polyimide substrate with inter-site distances of only 5 μm. By using a double-layer design and fabrication approach we were able to accommodate closely spaced electrode sites at two different depths from probe surface while also providing additional stiffening, just sufficient to prevent probe buckling during brain insertion. Detailed probe characterization through metrology of structural and electrical properties and chemical composition analysis, as well as functional assessment throughin vivohigh-density recordings of neuronal activity in the mouse cortex, confirmed the viability of this new fabrication approach and that this probe can be used for obtaining high quality brain recordings with excellent signal-to-noise ratio (SNR).
Temporal changes in metabolism late in seed development affect biomass composition in soybean
Authors: Kambhampati Shrikaar , Aznar-Moreno Jose A. , Bailey Sally R. , Arp Jennifer J. , Chu Kevin L. , Bilyeu Kristin D. , Durrett Timothy P. , Allen Doug K
Published: October 2020

The inverse correlation between protein and oil production in soybeans is well-documented; however, it has been based primarily on the composition of mature seeds. Though this is the cumulative result of events over the course of soybean seed development, it does not convey information specific to metabolic fluctuations during developmental growth regimes. Maternal nutrient supply via seed coat exudate measurements and metabolite levels within the cotyledon were assessed across development to identify trends in the accumulation of central carbon and nitrogen metabolic intermediates. Active metabolic operation during late seed development was probed through transient labeling with13C substrates. The results indicated: i) a drop in lipid during seed maturation with a concomitant increase in carbohydrates, ii) a transition from seed filling to maturation phase characterized by quantitatively balanced changes in the carbon use and CO2release, iii) changes in measured carbon and nitrogen resources supplied maternally over development, iv)13C metabolites processed through gluconeogenesis towards sustained carbohydrate accumulation as the maternal nutrient supply diminishes, and v) oligosaccharide biosynthetic metabolism during seed coat senescence at maturation. These results highlight temporal engineering targets for altering final biomass composition to increase the value of soybeans and a path to breaking the inverse seed protein and oil correlation.

One-sentence summary

Assessment of temporal changes in metabolism during soybean seed development indicated that lipid turnover during maturation contributes carbon for gluconeogenic production of carbohydrates.