bluuebunny/crossref_metadata_2025 huggingface dataset:
Endosymbiotic bacteria are prevalent and diverse in agricultural spiders
Authors: White Jennifer A. , Styer Alexander , Rosenwald Laura C. , Curry Meghan M. , Welch Kelton D. , Athey Kacie J. , Chapman Eric G.
Published: March 2019

Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence is poorly characterized in many host taxa. For example, spiders (Araneae) have received little attention, but initial surveys suggest that vertically transmitted symbionts may be common. Here, we characterized endosymbiont infection in a community of agricultural spiders. Using a combination of diagnostic PCR and high-throughput sequencing of the bacterial microbiome, we evaluated symbiont infection in 267 individual spiders representing 14 species in 3 families. We found 27 Operational Taxonomic Units (OTUs) that are likely endosymbiotic, including several strains of Wolbachia, Rickettsia and Cardinium, all of which are vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.
Affordable Remote Monitoring of Plant Growth and Facilities using Raspberry Pi Computers
Authors: Grindstaff Brandin , Mabry Makenzie E. , Blischak Paul D. , Quinn Micheal , Pires J. Chris
Published: March 2019

Premise of the study: Environmentally controlled facilities, such as growth chambers, are essential tools for experimental research. Automated remote monitoring of such facilities with low-cost hardware can greatly improve both the reproducibility and the accurate maintenance of their conditions.

Methods and Results: Using a Raspberry Pi computer, open-source software, environmental sensors, and a camera, we developed a cost-effective system for monitoring growth chamber conditions, which we have called ‘GMpi.’ Coupled with our software, GMpi_Pack, our setup automates sensor readings, photography, alerts when conditions fall out of range, and data transfer to cloud storage services.

Conclusions: The GMpi offers low-cost access to environmental data logging, improving reproducibility of experiments, as well as reinforcing the stability of controlled environmental facilities. The device is also flexible and scalable, allowing customization and expansion to include other features such as machine vision.
Single-cell interactomes of the human brain reveal cell-type specific convergence of brain disorders
Authors: Mohammadi Shahin , Davila-Velderrain Jose , Kellis Manolis
Published: March 2019

The reference human interactome has been instrumental in the systems-level study of the molecular inner workings of the cell, providing a framework to analyze the network context of disease associated gene perturbations. However, reference organismal interactomes do not capture the tissue- and cell type-specific context in which proteins and modules preferentially act. Emerging single-cell profiling technologies, which survey the transcriptional cell-state distribution of complex tissues, could be used to infer the single-cell context of gene interactions. Here we introduce SCINET (Single-Cell Imputation and NETwork construction), a computational framework that reconstructs an ensemble of cell type-specific interactomes by integrating a global, context-independent reference interactome with a single-cell gene expression profile. SCINET addresses technical challenges of single-cell data by robustly imputing, transforming, and normalizing the initially noisy and sparse expression data. Subsequently, cell-level gene interaction probabilities and group-level gene interaction strengths are computed, resulting in cell type specific interactomes. We use SCINET to analyze the human cortex, reconstructing interactomes for the major cell types of the adult human brain. We identify network neighborhoods composed of topologically-specific genes that are central for cell-type influence but not for global interactome connectivity. We use the reconstructed interactomes to analyze the specificity and modularity of perturbations associated with neurodegenerative, neuropsychiatric, and neoplastic brain disorders; finding high variability across diseases, yet overall consistency in patterns of cell-type convergence for diseases of the same group. We infer for each disorder group disease gene networks with preferential cell-type specific activity that can aid the design and interpretation of cell-type resolution experiments. Finally, focusing on the pleiotropy of schizophrenia and bipolar disorder, we show how cell type specific interactomes enable the identification of disease genes with preferential influence on neuronal, glial, or glial-neuronal cells. The SCINET framework is applicable to any organism, cell-type/tissue, and reference network; it is freely available athttps://github.com/shmohammadi86/SCINET.
Transcriptome-based prediction of complex traits in maize
Authors: Azodi Christina B. , Pardo Jeremy , VanBuren Robert , de los Campos Gustavo , Shiu Shin-Han
Published: March 2019

The ability to predict traits from genome-wide sequence information (Genomic Prediction, GP), has improved our understanding of the genetic basis of complex traits and transformed breeding practices. Transcriptome data may also be useful for GP. However, it remains unclear how well transcript levels can predict traits, particularly when traits are scored at different development stages. Using maize genetic markers and transcript levels from seedlings to predict mature plant traits, we found transcript and genetic marker models have similar performance. Surprisingly, genetic markers important for predictions were not close to or identified as regulatory variants for important transcripts. Thus, transcript levels are predictive not simply due to genetic variation. Furthermore, genetic marker models identified only one of 14 benchmark flowering time genes, while transcript models identified five. Our findings highlight that transcriptome data is useful for GP and can provide a link between traits and variation that cannot be readily captured at the sequence level.
Cerebral Blood Flow Increases Across Early Childhood
Authors: Paniukov Dmitrii , Lebel R. Marc , Giesbrecht Gerald , Lebel Catherine
Published: March 2019

Adequate cerebral blood flow (CBF) is essential to proper brain development and function. Detailed characterization of CBF developmental trajectories will lead to better understanding of the development of cognitive, motor, and sensory functions, as well as behaviour in children. Previous studies have shown CBF increases during infancy and decreases during adolescence; however, the trajectories during childhood, and in particular the timing of peak CBF, remain unclear. Here, we used arterial spin labeling to map age-related changes of CBF across a large longitudinal sample that included 279 scans on 96 participants (46 girls and 50 boys) aged 2-7 years. CBF maps were analyzed using hierarchical linear regression for every voxel inside the grey matter mask, controlling for multiple comparisons. The results revealed a significant positive linear association between CBF and age in distributed brain regions including prefrontal, temporal, parietal, and occipital cortex, and in the cerebellum. There were no differences in developmental trajectories between males and females. Our findings suggest that CBF continues to increase at least until the age of 7 years, likely supporting the ongoing improvements in behaviour, cognition, motor, and sensory functions of the children in early childhood.

Highlights

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We mapped cerebral blood flow development longitudinally in 96 typically developing children aged 2-7 years

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Cerebral blood flow increased over the full age range

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No significant differences between males and females were found

Conflicting of Interest

R.M.L. is an employee of GE.
Generic and context-dependent gene modulations duringHydrawhole body regeneration
Authors: Wenger Yvan , Buzgariu Wanda , Perruchoud Chrystelle , Loichot Gregory , Galliot Brigitte
Published: March 2019

The cnidarianHydrais a classical model of whole-body regeneration. Historically,Hydraapical regeneration has received more attention than its basal counterpart, most studies considering these two regenerative processes independently. We present here a transcriptome-wide comparative analysis of apical and basal regeneration after decapitation and mid-gastric bisection, augmented with a characterization of positional and cell-type expression patterns in non-regenerating animals. The profiles of 25’637Hydratranscripts are available on HydrATLAS (https://hydratlas.unige.ch), a web interface allowing a convenient access to each transcript profile. These data indicate that generic impulse-type modulations occur during the first four hours post-amputation, consistent with a similar integration of injury-related cues on both sides of the amputation plane. Initial divergences in gene regulations are observed in regenerating tips between four and eight hours post-amputation, followed by a dramatic transcriptomic reprogramming between eight and 16 hours when regulations become sustained. As expected, central components of apical patterning,Wnt3andHyBra1, are among the earliest genes up-regulated during apical regeneration. During early basal regeneration, a BMP signaling ligand (BMP5-8c) and a potential BMP inhibitor (NBL1)are up-regulated, suggesting that BMP signaling is involved in the basal organizer, as supported by higher levels of phosphorylated Smad in the basal region and by the LiCl-induced extension ofNBL1expression. By contrast, upon ectopic activation of Wnt/β-catenin signaling,NBL1is no longer expressed, basal differentiation is not maintained and basal regeneration is abolished. A tight cross-talk between Wnt/β-catenin apically and BMP signaling basally appears necessary for maintaining and regeneratingHydraanatomy.
Causal Network Inference from Gene Transcriptional Time Series Response to Glucocorticoids
Authors: Lu Jonathan , Dumitrascu Bianca , McDowell Ian C. , Jo Brian , Barrera Alejandro , Hong Linda K. , Leichter Sarah M. , Reddy Timothy E. , Engelhardt Barbara E.
Published: March 2019

Gene regulatory network inference is essential to uncover complex relationships among gene pathways and inform downstream experiments, ultimately paving the way for regulatory network re-engineering. Network inference from transcriptional time series data requires accurate, interpretable, and efficient determination of causal relationships among thousands of genes. Here, we develop Bootstrap Elastic net regression from Time Series (BETS), a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets. We show competitive accuracy on a community benchmark, the DREAM4 100-gene network inference challenge, where BETS is one of the fastest among methods of similar performance but additionally infers whether the causal effects are activating or inhibitory. We apply BETS to transcriptional time series data of 2, 768 differentially-expressed genes from A549 cells exposed to glucocorticoids over a period of 12 hours. We identify a network of 2, 768 genes and 31, 945 directed edges (FDR ≤ 0.2). We validate inferred causal network edges using two external data sources: overexpression experiments on the same glucocorticoid system, and genetic variants associated with inferred edges in primary lung tissue in the Genotype-Tissue Expression (GTEx) v6 project. BETS is freely available as an open source software package athttps://github.com/lujonathanh/BETS.
NOD1 mediates non-canonical inflammasome processing of interleukin-18 in epithelial cells toHelicobacter pyloriinfection
Authors: Tran L. S. , Ying L. , D’Costa K. , Wray-McCann G. , Kerr G. , Le L. , Allison C. C. , Ferrand J. , Chaudhry H. , Emery J. , De Paoli A. , Creed S. , Kaparakis-Liaskos M. , Como J. , Dowling J. , Johanesen P. A. , Kufer T. A. , Pedersen J. S. , Mansell A. , Philpott D. J. , Elgass K. , Abud H. E. , Nachbur U. , Croker B. A. , Masters S. L. , Ferrero R. L.
Published: March 2019

The interleukin-1 family members, IL-1β and IL-18, are processed into their biologically active forms by multi-protein complexes, known as inflammasomes. Although the inflammasome pathways that mediate IL-1β processing in myeloid cells have been extensively studied, those involved in IL-18 processing, particularly in non-myeloid cells, are still poorly understood. Here, we have identified the cytosolic sensor NOD1 as a key regulator of IL-18 processing in epithelial cells responding toHelicobacter pyloriinfection. Importantly, NOD1 processing of IL-18 occurs independently of the canonical inflammasome proteins, NLRP3 and ASC. Instead, NOD1 interacts directly with caspase-1 via homotypic binding of caspase-activation recruitment domains. We show that IL-18 is important in maintaining tissue homeostasis and protecting against pre-neoplastic changes due to gastricH. pyloriinfection. These findings reveal an unanticipated role for NOD1 in a new type of inflammasome that regulates epithelial cell production of bioactive IL-18 with tissue protective functions.
A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring
Authors: Altman Matthew C , Baldwin Nicole , Whalen Elizabeth , Al-Shaikhly Taha , Presnell Scott , Khaenam Prasong , Gersuk Vivian H , Chiche Laurent , Jourde-Chiche Noemie , Phillips J Theodore , Klintmalm Goran , O’Garra Anne , Berry Matthew , Bloom Chloe , Wilkinson Robert J , Graham Christine M , Lipman Marc , Lertmemongkolchai Ganjana , Kheradmand Farrah , Mejias Asuncion , Ramilo Octavio , Palucka Karolina , Pascual Virginia , Banchereau Jacques , Chaussabel Damien
Published: March 2019

Background

While our understanding of the role that the immune system plays in health and disease is growing at a rapid pace, available clinical tools to capture this complexity are lagging. We previously described the construction of a third-generation modular transcriptional repertoire derived from genome-wide transcriptional profiling of blood of 985 subjects across 16 diverse immunologic conditions, which comprises 382 distinct modules.

Results

Here we describe the use of this modular repertoire framework for the development of a targeted transcriptome fingerprinting assay (TFA). The first step consisted in down-selection of the number of modules to 32, on the basis of similarities in changes in transcript abundance and functional interpretation. Next down-selection took place at the level of each of the 32 modules, with each one of them being represented by four transcripts in the final 128 gene panel. The assay was implemented on both the Fluidigm high throughput microfluidics PCR platform and the Nanostring platform, with the list of assays target probes being provided for both. Finally, we provide evidence of the versatility of this assay to assess numerous immune functionsin vivoby demonstrating applications in the context of disease activity assessment in systemic lupus erythematosus and longitudinal immune monitoring during pregnancy.

Conclusions

This work demonstrates the utility of data-driven network analysis applied to large-scale transcriptional profiling to identify key markers of immune responses, which can be downscaled to a rapid, inexpensive, and highly versatile assay of global immune function applicable to diverse investigations of immunopathogenesis and biomarker discovery.
The planktonic protist interactome: where do we stand after a century of research?
Authors: Markussen Bjorbækmo Marit F. , Evenstad Andreas , Røsæg Line Lieblein , Krabberød Anders K. , Logares Ramiro
Published: March 2019

Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts, parasites, predators and/or prey. Symbiosis was the most common interaction (43% of all records), followed by predation (39%) and parasitism (18%). Using bipartite networks, we found that protistan predators seem to be “multivorous”, while parasite-host and symbiont-host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e. Stramenopiles, Alveolata and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the compiled interactions. All in all, despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.
Revealing virulence potential of clinical and environmental Aspergillus fumigatus isolates using Whole-genome sequencing
Authors: Puértolas-Balint F. , Rossen J.W.A. , Oliveira dos Santos C. , Chlebowicz M.A. , Raangs E. , van Putten M.L. , Sola-Campoy P.J. , Han L. , Schmidt M. , García-Cobos S.
Published: March 2019

Aspergillus fumigatus is an opportunistic airborne pathogen and one of the most common causative agents of human fungal infections. A restricted number of virulence factors have been described but none of them lead to a differentiation of the virulence level among different strains. In this study, we analyzed the whole-genome sequence of a set of A. fumigatus isolates from clinical and environmental origin to compare their genomes and to determine their virulence profiles. For this purpose, a database containing 244 genes known to be associated with virulence was built. The genes were classified according to their biological function into factors involved in thermotolerance, resistance to immune responses, cell wall structure, toxins and secondary metabolites, allergens, nutrient uptake and signaling and regulation. No difference in virulence profiles was found between clinical isolates causing an infection and a colonizing clinical isolate, nor between isolates from clinical and environmental origin. We observed the presence of genetic repetitive elements located next to virulence related gene groups, which could potentially influence their regulation. In conclusion, our genomic analysis reveals that A. fumigatus, independently of their source of isolation, are potentially pathogenic at the genomic level, which may lead to fatal infections in vulnerable patients. However, other determinants such as genetic variations in virulence related genes and host-pathogen interactions most likely influence A. fumigatus pathogenicity and further studies should be performed.

Importance

Aspergillus spp. infections are among the most clinically relevant fungal infections also presenting treatment difficulties due to increasing antifungal resistance. The lack of key virulence factors and a broad genomic diversity complicates the development of targeted diagnosis and novel treatment strategies. A widely spread variability in virulence has been reported for experimental, clinical and environmental isolates. Here we provide supporting evidence that members of this species are fully capable of establishing an infection in immunosuppressed hosts according to their virulence content at the genomic level. Due to the possible clinical complications, studies are urgently required linking strain’s virulent phenotype with the genotype to better understand the virulence activation of this important fungal pathogen.
Yellow Fever Vaccine Protects Resistant and Susceptible Mice Against Zika Virus Infection
Authors: Santos Ana C. Vicente , Guedes-da-Silva Francisca H. , Dumard Carlos H. , Ferreira Vivian N. S. , Costa Igor P. S. da , Machado Ruana A. , Barros-Aragão Fernanda G. Q. , Neris Rômulo L. S. , dos-Santos Júlio S. , Assunção-Miranda Iranaia , Figueiredo Claudia P. , Dias André A. , Gomes Andre M. O. , Matos Guedes Herbert L. de , Oliveira Andrea C. , Silva Jerson L.
Published: March 2019

Zika virus (ZIKV) emerged as an important infectious disease agent in Brazil in 2016. Infection usually leads to mild symptoms but severe congenital neurological disorders and Guillain-Barré syndrome have been reported following ZIKV exposure. The development of an effective vaccine against Zika virus is a public health priority, encouraging the preclinical and clinical studies of different vaccine strategies. Here, we describe the protective effect of an already licensed attenuated yellow fever vaccine (17DD) on type-I interferon receptor knockout mice (A129) and immunocompetent (BALB/c) mice infected with ZIKV. Yellow fever virus vaccination results in robust protection against ZIKV, with decreased mortality in the A129 mice, a reduction in the cerebral viral load in all mice, and weight loss prevention in the BALB/c mice. Despite the limitation of yellow fever (17DD) vaccine to elicit antibody production and neutralizing activity against ZIKV, we found that YF immunization prevented the development of neurological impairment induced by intracerebral virus inoculation in adult. Although we used two vaccine doses in our protocol, a single dose was protective, reducing the cerebral viral load. Different Zika virus vaccine models have been tested; however, our work shows that an efficient and certified vaccine, available for use for several decades, effectively protects mice against Zika virus infection. These findings open the possibility for using an available and inexpensive vaccine to a large-scale immunization in the event of a Zika virus outbreak.
Comparative genomics guides elucidation of vitamin B12 biosynthesis in novel human associatedAkkermansia
Authors: Kirmiz Nina , Galindo Kadir , Cross Karissa L. , Luna Estefani , Rhoades Nicholas , Podar Mircea , Flores Gilberto E.
Published: March 2019

Background

Akkermansia muciniphilais a mucin-degrading bacterium found in the gut of most healthy humans and is considered a ‘next-generation probiotic.’ However, knowledge of the genomic and physiological diversity of human associatedAkkermansiais limited, as only one species has been formally described.

Results

To begin to fill this knowledge gap, we reconstructed 35 high-quality metagenome assembled genomes from children and combined them with 40 other publicly available genomes from adults and mice for comparative genomic analysis. We identified at least four species-level phylogroups (AmI-AmIV) with distinct functional potentials. Most notably, we identified the presence of putative cobalamin (vitamin B12) biosynthesis genes within the AmII (n=26/28) and AmIII (n=2/2) phylogroups. To test these predictions, 10 novel strains ofAkkermansiawere isolated from adults and screened for essential vitamin B12 biosynthesis genes via PCR. Two strains of the AmII phylogroup were positive for the presence of vitamin B12 biosynthesis genes, while all AmI strains, including the type strainA. muciniphilaMucT, were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups since cobalamin is a cofactor in propionate metabolism. Results show that theAkkermansiaAmII strain produced acetate and propionate in the absence of supplementation, which is indicative ofde novovitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium.

Conclusions

We identifiedAkkermansiastrains as potentially important vitamin B12 biosynthetic bacteria in the human gut. This novel physiological trait of human associatedAkkermansiamay impact how these bacteria interact with the human host and other members of the human gut microbiome.
Single-step genome-wide association study for resistance toPiscirickettsia salmonisin rainbow trout (Oncorhynchus mykiss)
Authors: Marín-Nahuelpi Rodrigo , Barría Agustín , Cáceres Pablo , López María E. , Bassini Liane N. , Lhorente Jean P. , Yáñez José M.
Published: March 2019

One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteriaPiscirickettsia salmonis. Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selection for resistance is proposed as a viable alternative for control. Genomic information can be used to identify the genomic regions associated with resistance and enhance the genetic evaluation methods to speed up the genetic improvement for the trait. The objectives of this study were to i) identify the genomic regions associated with resistance toP. salmonis; and ii) identify candidate genes associated with the trait. We experimentally challenged 2,130 rainbow trout withP. salmonisand genotyped them with a 57 K SNP array. Resistance toP. salmoniswas defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we identified four genomic regions explaining over 1% of the genetic variance for TD and three for BS. Interestingly, the same genomic region located onOmy27was found to explain the highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, respectively). The identified SNP in this region is located within an exon of a gene related with actin cytoskeletal organization, a protein exploited byP. salmonisduring infection. Other important candidate genes identified are related with innate immune response and oxidative stress. The moderate heritability values estimated in the present study show it is possible to improve resistance toP. salmonisthrough artificial selection in the current rainbow trout population. Furthermore, our results suggest a polygenic genetic architecture and provide novel insights into the candidate genes underpinning resistance toP. salmonisinO. mykiss.
Machine Learning-Assisted Digital PCR and Melt Enables Broad Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Test
Authors: Athamanolap Pornpat , Hsieh Kuangwen , O'Keefe Christine M. , Zhang Ye , Yang Samuel , Wang Jeff (Tza-Huei)
Published: March 2019

Toward combating infectious diseases caused by pathogenic bacteria, there remains an unmet need for diagnostic tools that can broadly identify the causative bacteria and determine their antimicrobial susceptibilities from complex and even polymicrobial samples in a timely manner. To address this need, a microfluidic- and machine learning-based platform that performs broad bacteria identification (ID) and rapid yet reliable antimicrobial susceptibility testing (AST) is developed. Specifically, this new platform builds on "pheno-molecular AST", a strategy that transforms nucleic acid amplification tests (NAATs) into phenotypic AST through quantitative detection of bacterial genomic replication, and utilizes digital PCR and digital high-resolution melt (HRM) to quantify and identify bacterial DNA molecules. Bacterial species are identified using integrated experiment-machine learning algorithm via HRM profiles. Digital DNA quantification allows for rapid growth measurement that reflects susceptibility profiles of each bacterial species within only 30 min of antibiotic exposure. As a demonstration, multiple bacterial species and their susceptibility profiles in polymicrobial urine specimen were correctly identified with a total turnaround time of ~4 hours. With further development and clinical validation, this new platform holds the potential for improving clinical diagnostics and enabling targeted antibiotic treatments.
Quantitative Principles ofcis-translational control by general mRNA sequence features in eukaryotes
Authors: Li Jingyi Jessica , Chew Guo-Liang , Biggin Mark D.
Published: March 2019

BACKGROUND

General translationalcis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements are: mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate together to control translation rates are not well understood.

RESULTS

Here we show that these sequence features specify 42%–81% of the variance in translation rates inS.cerevisiae, S.pombe, Arabidopsis thaliana, M.musculus, andH.Sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25–60 nucleotide segments within mRNA 5’ regions; that changes in tri-nucleotide frequencies between highly and poorly translated 5’ regions are correlated between all species; and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.

CONCLUSIONS

Our work shows that the general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that direct translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and withincis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell.
Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma
Authors: Starrett Gabriel J. , Thakuria Manisha , Chen Tianqi , Marcelus Christina , Cheng Jingwei , Nomburg Jason , Thorner Aaron R. , Slevin Michael K. , Powers Winslow , Burns Robert T. , Perry Caitlin , Piris Adriano , Kuo Frank C. , Rabinowits Guilherme , Giobbie-Hurder Anita , MacConaill Laura E. , DeCaprio James A.
Published: March 2019

Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin mediated by the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep sequencing studies of MCC have identified significant differences between the number and types of point mutations, copy number alterations, and structural variants between virus-positive and virus-negative tumors. In this study, we assembled a cohort of 71 MCC patients and performed deep sequencing with OncoPanel, a next-generation sequencing assay targeting over 400 cancer-associated genes. To improve the accuracy and sensitivity for virus detection compared to traditional PCR and IHC methods, we developed a hybrid capture baitset against the entire MCPyV genome. The viral baitset identified integration junctions in the tumor genome and generated assemblies that strongly support a model of a hybrid, virus-host, circular DNA intermediate during integration that promotes focal amplification of host DNA. Using the clear delineation between virus-positive and virus-negative tumors from this method, we identified recurrent somatic alterations common across MCC and alterations specific to each class of tumor, associated with differences in overall survival. Comparing the molecular and clinical data from these patients revealed a surprising association of immunosuppression with virus-negative MCC and significantly shortened overall survival. These results demonstrate the value of high-confidence virus detection for identifying clinically important features in MCC that impact patient outcome.
5-HT2Bserotonin receptor agonist BW723C86 shapes the macrophage gene profile via AhR and impairs monocyte-to-osteoclast differentiation
Authors: Nieto Concha , Rayo Ignacio , de las Casas-Engel Mateo , Izquierdo Elena , Alonso Bárbara , Vega Miguel A. , Corbí Ángel L.
Published: March 2019

Peripheral serotonin (5-HT) exacerbates or limits inflammatory pathologies through interaction with seven types of 5-HT receptors (5-HT1-7). As central regulators of inflammation, macrophages are critical targets of 5-HT, which promotes their anti-inflammatory and pro-fibrotic polarization primarily via the 5-HT7-Protein Kinase A (PKA) axis. However, anti-inflammatory human macrophages are also characterized by the expression of 5-HT2B, an off-target of anesthetics, anti-parkinsonian drugs and Selective Serotonin Reuptake Inhibitors (SSRI) that contributes to 5-HT-mediated pathologies. Since 5-HT2Bprevents mononuclear phagocyte degeneration in amyotrophic lateral sclerosis and modulates motility of murine microglial processes, we sought to determine the functional and transcriptional consequences of 5-HT2Bactivation in human macrophages. Ligation of 5-HT2Bby the 5-HT2B-specific agonist BW723C86, which exhibits antidepressant- and anxiolytic-like effects in animal models, significantly modified the cytokine profile and the transcriptional signature in macrophages. Importantly, 5-HT2Bagonist-induced transcriptional changes were partly mediated through activation of the Aryl hydrocarbon Receptor (AhR), a ligand-dependent transcription factor that regulates immune responses and the biological responses to xenobiotics. Besides, BW723C86 triggered transcriptional effects that could not be abrogated by 5-HT2Bantagonists and impaired monocyte-to-osteoclast differentiation by affecting the expression of negative (IRF8) and positive (PRDM1) regulators of osteoclastogenesis. Therefore, our results demonstrate the existence of a functional 5-HT2B-AhR axis in human macrophages and indicate that the commonly used 5-HT2Bagonist BW723C86 exhibits 5-HT2B-independent effects. The 5-HT2B-AhR link extends the range of signaling pathways initiated upon 5-HT receptor engagement and identifies a point of convergence for endogenous and exogenous agents with ability to modulate inflammatory responses.

KEY POINTS

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The serotonin receptor 5-HT2Bmodifies the human macrophage transcriptome through activation of the Aryl Hydrocarbon Receptor.

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BW723C86, an agonist used for 5-HT2Bactivationin vivo, exerts 5-HT2B-independent effects and limits monocyte osteoclastogenic potential.
Adult Drosophila Muscle Morphometry through MicroCT reveals dynamics during aging
Authors: Chaturvedi Dhananjay , Prabhakar Sunil , Aggarwal Aman , VijayRaghavan K
Published: March 2019

Indirect Flight Muscles (IFMs) in adult Drosophila have served as a valuable model for studying muscle development. In terms of function, they provide the key power stroke in adult insect flight. Variability in their architecture including of fiber numbers, shape and arrangement may provide insightful clues into adult muscle function. Conventional histological preparations in imaging techniques severely limit exact morphometric analysis of flight muscles, thereby impeding causal or correlative studies between muscle morphology and function. In this study we employ MicroCT scanning on a tissue preparation that retains muscle morphology under homeostatic conditions. We use this method to deliver precise measurements of a subset of IFMs, the Direct Longitudinal Muscles’ (DLMs) size and shape, in male and female Drosophila and changes therein, with age. Our findings reveal several unexpected characteristics of muscle fibers. We also demonstrate application to other insect species making it a valuable tool for histological analysis of insect biodiversity.

Significance Statement

Adult Drosophila muscles serve as models of homeostatic muscles. Accurate analysis of their form and function is key to understanding affects of genetic and physiological states on them. Recording adult muscle shape and volume has so far depended on protocols that inevitably distort tissue. Here, we use a MicroCT scanning based method that delivers changes in shape, size and organization between males and females, with time. This method is a significant step forward in recording muscle structure in situ with applications across species.
Population divergence time estimation using individual lineage label switching
Authors: Beerli Peter , Ashki Haleh , Mashayekhi Somayeh , Palczewski Michal
Published: March 2019

Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayes inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The waiting time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as MIGRATE. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a dataset of the Zika virus; the geographic analyses of the expansion of the pathogen follows a trajectory from Africa to Asia to America, corroborating analyses based only on the dates of incidences. Evaluations of simple divergence models show high accuracy, whereas the accuracy of the results of isolation with migration (IM) models depend on the magnitude of the immigration rate and potentially on the number of samples. High immigration rates lead to a time of the most recent common ancestor of the sample that predates the divergence time, thus loses any potential signal of the divergence event in the sample data. This reduced accuracy with high immigration rates is problematic for all IM methods, including ours.
Interleukin-1 receptor antagonist treatment in acute ischaemic stroke does not alter systemic markers of anti-microbial defence
Authors: McCulloch Laura , Allan Stuart M. , Smith Craig J. , McColl Barry W.
Published: March 2019

Aim

Blockade of the cytokine interleukin-1 (IL-1) with IL-1 receptor antagonist (IL-1Ra) is a candidate treatment for stroke entering phase II/III trials, which acts by inhibiting harmful inflammatory responses. Infection is a common complication after stroke that significantly worsens outcome and is related to stroke-induced deficits in systemic immune function thought to be mediated by the sympathetic nervous system. Therefore, immunomodulatory treatments for stroke, such as IL-1Ra, carry a risk of aggravating stroke-associated infection. Our primary objective was to determine if factors associated with antibody-mediated antibacterial defences were further compromised in patients treated with IL-1Ra after stroke.

Methods

We assessed plasma concentrations of immunoglobulin isotypes and complement components in stroke patients treated with IL-1Ra or placebo and untreated non-stroke controls using multiplex protein assays. Activation of the SNS was determined by measuring noradrenaline, a major SNS mediator.

Results

There were significantly lower plasma concentrations of IgM, IgA, IgG1 and IgG4 in stroke-patients compared to non-stroke controls, however there were no differences between stroke patients treated with placebo or IL-1Ra. Concentrations of complement components associated with the classical pathway were increased and those associated with the alternative pathways decreased in stroke patients, neither being affected by treatment with IL-1Ra. Noradrenaline concentrations were increased after stroke in both placebo and IL-1Ra-treated stroke patients compared to non-stroke controls.

Conclusion

These data show treatment with IL-1Ra after stroke does not alter circulating immunoglobulin and complement concentrations, and is therefore unlikely to further aggravate stroke-associated infection susceptibility through reduced availability of these key anti-microbial mediators.
Ubiquinone biosynthesis over the entire O2range: characterization of a conserved, O2-independent pathway
Authors: Pelosi Ludovic , Vo Chau-Duy-Tam , Abby Sophie Saphia , Loiseau Laurent , Rascalou Bérengère , Chehade Mahmoud Hajj , Faivre Bruno , Goussé Mathieu , Chenal Clothilde , Touati Nadia , Binet Laurent , Cornu David , Fyfe Cameron David , Fontecave Marc , Barras Frédéric , Lombard Murielle , Pierrel Fabien
Published: March 2019

Most bacteria can generate ATP by respiratory metabolism, in which electrons are shuttled from reduced substrates to terminal electron acceptors, via quinone molecules likeubiquinone. Dioxygen (O2) is the terminal electron acceptor of aerobic respiration and serves as a co-substrate in the biosynthesis ofubiquinone. Here, we characterize a novel, O2-independent pathway for the biosynthesis ofubiquinone. This pathway relies on three proteins UbiT (YhbT), UbiU (YhbU) and UbiV (YhbV). UbiT contains an SCP2 lipid-binding domain and is likely an accessory factor of the biosynthetic pathway, while UbiU-UbiV are involved in hydroxylation reactions and represent a novel class of O2-independent hydroxylases. We demonstrate that UbiU-UbiV form a heterodimer, wherein each protein binds a 4Fe-4S cluster via conserved cysteines that are essential for activity. The UbiT, -U, -V proteins are found in α-, β-, γ-proteobacterial clades including several human pathogens, supporting the widespread distribution of a previously-unrecognized capacity to synthesizeubiquinone in the absence of O2. Together, the O2-dependent and O2-independentubiquinone biosynthesis pathways contribute to optimize bacterial metabolism over the entire O2range.

IMPORTANCE

In order to colonize environments with large O2gradients or fluctuating O2levels, bacteria have developed metabolic responses that remain incompletely understood. Such adaptations have been recently linked to antibiotic resistance, virulence and the capacity to develop in complex ecosystems like the microbiota. Here, we identify a novel pathway for the biosynthesis ofubiquinone, a molecule with a key role in cellular bioenergetics. We link three uncharacterized genes ofEscherichia colito this pathway and show that the pathway functions independently from O2. In contrast, the long-described pathway forubiquinone biosynthesis requires O2as substrate. In fact, we find that many proteobacteria are equipped with the O2-dependent and O2-independent pathways, supporting that they are able to synthesizeubiquinone over the entire O2range. Overall, we propose that the novel O2-independent pathway is part of the metabolic plasticity developed by proteobacteria to face varying environmental O2levels.
The effects of cerebellar transcranial direct current stimulation on the cognitive stage of sequence learning
Authors: Ballard Hannah K. , Goen James R. M. , Maldonado Ted , Bernard Jessica A.
Published: March 2019

Though the cerebellum has been previously implicated in explicit sequence learning, the exact role of this structure in the acquisition of motor skills is not completely clear. The cerebellum contributes to both motor and non-motor behavior. Thus, this structure may contribute not only to the motoric aspects of sequence learning, but may also play a role in the cognitive components of these learning paradigms. Therefore, we investigated the consequence of both disrupting and facilitating cerebellar function using high definition transcranial direct current stimulation (HD-tDCS) prior to the completion of an explicit motor sequence learning paradigm. Using a mixed within- and between-subjects design, we employed cathodal (n=21) and anodal (n=23) tDCS (relative to sham), targeting the lateral posterior cerebellum, to temporarily modulate function and investigate the resulting effects on the acquisition of a sequential pattern of finger movements. Results indicate that cathodal stimulation has a positive influence on learning while anodal stimulation has the opposite effect, relative to sham. Though the cerebellum is presumed to be primarily involved in motor function and movement coordination, our results support a cognitive contribution that may come into play during the initial stages of learning. Using tDCS targeting the right posterior cerebellum, which communicates with the prefrontal cortex via closed-loop circuits, we found polarity-specific effects of cathodal and anodal stimulation on sequence learning. Thus, our results substantiate the role of the cerebellum in the cognitive aspect of motor learning and provide important new insights into the polarity-specific effects of tDCS in this area.

New & Noteworthy

The cerebellum contributes to motor and cognitive processes. Investigating the cognitive contributions of the cerebellum in explicit sequence learning stands to provide new insights into this learning domain, and cerebellar function more generally. Using HD-tDCS, we demonstrated polarity-specific effects of stimulation on explicit sequence learning. We speculate that this is due to facilitation of working memory processes. This provides new evidence supporting a role for the cerebellum in the cognitive aspects of sequence learning.
Analyzing dynamic decision-making models using Chapman-Kolmogorov equations
Authors: Barendregt Nicholas W. , Josić Krešimir , Kilpatrick Zachary P.
Published: March 2019

Decision-making in dynamic environments typically requires adaptive evidence accumulation that weights new evidence more heavily than old observations. Recent experimental studies of dynamic decision tasks require subjects to make decisions for which the correct choice switches stochastically throughout a single trial. In such cases, an ideal observer’s belief is described by an evolution equation that is doubly stochastic, reflecting stochasticity in the both observations and environmental changes. In these contexts, we show that the probability density of the belief can be represented using differential Chapman-Kolmogorov equations, allowing efficient computation of ensemble statistics. This allows us to reliably compare normative models to near-normative approximations using, as model performance metrics, decision response accuracy and Kullback-Leibler divergence of the belief distributions. Such belief distributions could be obtained empirically from subjects by asking them to report their decision confidence. We also study how response accuracy is affected by additional internal noise, showing optimality requires longer integration timescales as more noise is added. Lastly, we demonstrate that our method can be applied to tasks in which evidence arrives in a discrete, pulsatile fashion, rather than continuously.