bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods
Authors: Wright Carrie , Rajpurohit Anandita , Burke Emily E. , Williams Courtney , Collado-Torres Leonardo , Kimos Martha , Brandon Nicholas J. , Cross Alan J. , Jaffe Andrew E. , Weinberger Daniel R. , Shin Joo Heon
Published: October 2018

High-throughput sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of the biases associated with small RNA sequencing have focused on adapter ligation bias with limited evaluation of reverse transcription or amplification biases. Furthermore, evaluations of the accuracy of quantifications of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited and no study has yet evaluated differences in the quantification of isomiRs of altered length. In addition, no studies have yet compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases. All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency. Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
Outpatient prescribing of four major antibiotic classes and prevalence of antimicrobial resistance in US adults
Authors: Goldstein Edward , MacFadden Derek R. , Lee Robyn S. , Lipsitch Marc
Published: October 2018

Background

There is limited information on the relation between antibiotic use and antibiotic resistance in the US.

Methods

We used multivariable logistic regression to relate state-specific rates of outpatient prescribing overall for fluoroquinolones, penicillins, macrolides, and cephalosporins between 2011-2014 to state-specific prevalence of resistance for select combinations of antibiotics/bacteria among catheter-associated urinary tract infections (CAUTIs) in the CDC Patient Safety Atlas data between 2011-2014 for adults aged 65+y and 19-64y, adjusting for potential confounders.

Results

Rates of fluoroquinolone prescribing were positively associated with prevalence of fluoroquinolone resistance in Escherichia coli and Pseudomonas aeruginosa (both age groups), resistance to extended-spectrum (ES) cephalosporins in E. coli (aged 19-64y), and resistance to methicillin in Staphylococcus aureus (aged 19-64y). Rates of penicillin prescribing were positively associated with prevalence of resistance to fluoroquinolones in E. coli (aged 65+) and P. aeruginosa (both age groups), and resistance to ES cephalosporins in Klebsiella spp. (both age groups). Rates of cephalosporin prescribing were negatively associated with prevalence of resistance to fluoroquinolones in E. coli and resistance to ES cephalosporins in Klebsiella spp. (both age groups). Average annual temperature was positively associated with prevalence of resistance to ES cephalosporins in E. coli and P. aeruginosa, and resistance to fluoroquinolones in E. coli.

Conclusions

Our results suggest that prescribing of fluoroquinolones and penicillins to US adults is associated with prevalence of antibiotic resistance, including ESBLs and MRSA. Further work is needed to understand the potential benefit of replacing fluoroquinolones and penicillins by other antibiotics for reducing prevalence of antibiotic resistance.
Resolving Tumour Clonal Heterogeneity and Spatial Complexity using Nuclear Tandem Epitope Protein (nTEP) Barcoding
Authors: Gill Michael B. , Koplev Simon , Machel Anne C. , Miller Martin L.
Published: October 2018

Tumours are composed of an array of unique cancer cell clones along with many non-tumour cells such as immune cells, fibroblasts and endothelial cells, which make up the complex tumour microenvironment. To better understand the co-evolution of tumour clones and cells of the tumour microenvironment, we require tools to spatially resolve heterotypic cellular interactions at the single cell level. We present a novel protein-based barcoding technology termed nuclear tandem epitope protein (nTEP) barcoding, which can be designed to combinatorially encode and track dozens to hundreds of tumour clones in their spatial context within complex cellular mixtures using multiplexed antibody-based imaging. Here we provide proof-of-principle of nTEP barcoding and develop the technology, which relies on lentiviral - based stable expression of a nuclear-localised fluorophore that contains unique combinations of protein epitope tags that can be decoded by a limited set of antibodies. By generating a series of cell lines expressing unique nTEP barcodes, we were able to robustly identify and spatially deconvolve specific clones present within highly complex cell mixtures at the single cell level using state-of-the-art iterative indirect immunofluorescence imaging (4i). We define the utility of nTEP-barcoding as a powerful tool for visualising and resolving tumour heterogeneity at the cellular level, and envision its usage in mouse tumour models for understanding how tumour clones modulate and interact with stromal- and immune cells in cancer.
A stochastic model of corneal epithelium maintenance and recovery following perturbation
Authors: Moraki E. , Grima R. , Painter K. J.
Published: October 2018

Various biological studies suggest that the corneal epithelium is maintained by active stem cells located in the limbus, the so-called Limbal Epithelial Stem Cell (LESC) hypothesis. While numerous mathematical models have been developed to describe corneal epithelium wound healing, only a few have explored the process of corneal epithelium homeostasis. In this paper we present a purposefully simple stochastic mathematical model based on a chemical master equation approach, with the aim of clarifying the main factors involved in the maintenance process. Model analysis provides a set of constraints on the numbers of stem cells, division rates, and the number of division cycles required to maintain a healthy corneal epithelium. In addition, our stochastic analysis reveals noise reduction as the epithelium approaches its homeostatic state, indicating robustness to noise. Finally, recovery is analysed in the context of perturbation scenarios.
The Effect of Retro-inverse D-Amino Acid Aβ-peptides on Aβ-Fibril Formation
Authors: Xi Wenhui , Hansmann Ulrich H. E.
Published: October 2018

Peptides build from D-amino acids resist enzymatic degradation. The resulting extended time of biological activity makes them prime candidates for the development of pharmaceuticals. Of special interest are D-retro inverso (DRI)peptides where a reversed sequence of D-amino acids leads to molecules with almost the same structure, stability and bioactivity as the parent L-peptides but increased resistance to proteolytic degradation. Here, we study the effect of DRI-Aβ40 and DRI-Aβ42 peptides on fibril formation. Using molecular dynamics simulations, we compare the stability of typical amyloid fibril models with such where the L-peptides are replaced by DRI-Aβ40 and DRI-Aβ42 peptides. We then explore the likelihood for cross fibrilization of Aβ L-and DRI-peptides by investigating how presence of DRI peptides alters elongation and stability of L-Aβ-fibrils. Our data suggest that full-length DRI-peptides may enhance the fibril formation and decrease the ratio of soluble toxic Aβ oligomers, pointing out a potential for D-amino-acid-based drug design targeting Alzheimer’s disease.
A human impact metric for coastal ecosystems with application to seagrass beds in Atlantic Canada
Authors: Murphy Grace E.P. , Wong Melisa , Lotze Heike K.
Published: October 2018

Coastal biogenic habitats are particularly vulnerable to cumulative human impacts from both terrestrial and marine realms. Yet the broad spatial scale used in current global or regional approaches of quantifying multiple anthropogenic stressors are not relevant to the local or bay-wide scales affecting most coastal biogenic habitats. To fill this gap, we developed a standardized human impact metric to quantify the magnitude of anthropogenic impacts to coastal ecosystems more broadly, and biogenic habitats in particular. We applied this metric to 180 seagrass beds (Zostera marina), an important biogenic habitat prioritized for marine protection, across Atlantic Canada. Our impact metric includes five bay-scale and four local-scale terrestrial and marine-based impacts. Results show that seagrass beds and coastal bays in Atlantic Canada exist across a wide gradient of human impacts. Considerable differences in the range and intensity of impacts within and between regions provide insight into where coastal bays and seagrass ecosystems are expected to be most and least affected by individual or cumulative human threats. We discuss implications for management and conservation planning, and the general application of our impact metric to other coastal regions and habitats in Canada and beyond.
An ER CREC family protein regulates the egress proteolytic cascade in malaria parasites
Authors: Fierro Manuel A. , Asady Beejan , Brooks Carrie F. , Cobb David W. , Villegas Alejandra , Moreno Silvia N.J. , Muralidharan Vasant
Published: October 2018

The endoplasmic reticulum (ER) is thought to play an essential role during egress of malaria parasites because the ER is assumed to be the calcium (Ca2+) signaling hub and required for biogenesis of egress-related organelles. However, no proteins localized to the parasite ER have been shown to play a role in egress of malaria parasites. In this study, we generated conditional mutants of the Plasmodium falciparumEndoplasmic Reticulum-resident Calcium-binding protein (PfERC), a member of the CREC family. Knockdown of PfERC shows that this gene is essential for asexual growth of P. falciparum. Analysis of the intraerythrocytic lifecycle revealed that PfERC is essential for parasite egress but not required for protein trafficking or Ca2+ storage. We found that PfERC knockdown prevents the rupture of the parasitophorous vacuole membrane. This is because PfERC knockdown inhibited the proteolytic maturation of the subtilisin-like serine protease, SUB1. Using double mutant parasites, we show that PfERC is required for the proteolytic maturation of the essential aspartic protease, Plasmepsin X, which cleaves SUB1. Further, we show that processing of substrates downstream of the proteolytic cascade is inhibited by PfERC knockdown. Thus, these data establish the ER-resident CREC family protein, PfERC, as a key early regulator of the egress proteolytic cascade of malaria parasites.
Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
Authors: Zhou Zilu , Xu Bihui , Minn Andy , Zhang Nancy R
Published: October 2018

Detection of genetically distinct subclones and profiling the transcriptomic differences between them is important for studying the evolutionary dynamics of tumors, as well as for accurate prognosis and effective treatment of cancer in the clinic. For the profiling of intra-tumor transcriptional heterogeneity, single cell RNA-sequencing (scRNA-seq) is now ubiquitously adopted in ongoing and planned cancer studies. Detection of somatic DNA mutations and inference of clonal membership from scRNA-seq, however, is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that detects genetically distinct subclones, assigns each single cell to a subclone, and reconstructs the phylogenetic tree describing the tumor’s evolutionary history. DENDRO utilizes information from single nucleotide mutations in transcribed regions and accounts for technical noise and expression stochasticity at the single cell level. The accuracy of DENDRO was benchmarked on spike-in datasets and on scRNA-seq data with known subpopulation structure. We applied DENDRO to delineate subclonal expansion in a mouse melanoma model in response to immunotherapy, highlighting the role of neoantigens in treatment response. We also applied DENDRO to primary and lymph-node metastasis samples in breast cancer, where the new approach allowed us to better understand the relationship between genetic and transcriptomic intratumor variation.
Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide
Authors: Islam Zahra F. , Cordero Paul R.F. , Feng Joanna , Chen Ya-Jou , Bay Sean K. , Jirapanjawat Thanavit , Gleadow Roslyn M. , Carere Carlo R. , Stott Matthew B. , Chiri Eleonora , Greening Chris
Published: October 2018

Bacteria within aerated environments often exist within a variety of dormant forms. In these states, bacteria endure adverse environmental conditions such as organic carbon starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that facilitate the persistence of the environmentally widespread but understudied bacterial phylum Chloroflexi. A transcriptome study revealed thatThermomicrobium roseum(class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to organic carbon limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H2), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments were used to show thatT. roseumaerobically respires H2and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the enzymes mediating atmospheric H2and CO oxidation, namely group 1h [NiFe]-hydrogenases and type I carbon monoxide dehydrogenases, are widely distributed in Chloroflexi genomes and have been acquired on at least two occasions through separate horizontal gene transfer events. Consistently, we confirmed that the sporulating isolateThermogemmatisporasp. T81 (class Ktedonobacteria) also oxidises atmospheric H2and CO during persistence. This study provides the first axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H2oxidation. This adds to the growing body of evidence that atmospheric trace gases serve as dependable energy sources for the survival of dormant microorganisms.
Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability
Authors: Boza Gergely , Worsley Sarah F. , Yu Douglas W. , Scheuring Istvan
Published: October 2018

Understanding the mechanisms promoting the assembly and maintenance of host-beneficial microbiomes is an open problem. An increasing amount of evidence supports the idea that animal and plant hosts can use ‘private resources’ and the ecological phenomenon known as ‘community bistability’ to favour some microbial strains over others. We briefly review empirical evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotic compounds to suppress non-beneficial, competitor strains, and (iii) provide resources (for a limited time) that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. By explicitly modelling localized microbial interactions and diffusion dynamics, we further show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that that there is a wide range of conditions under which hosts can promote the assembly of a self-sustaining defensive microbiome. This, in turn, supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.
Oxygen plasma focused ion beam scanning electron microscopy for biological samples
Authors: Sergey Gorelick , Denis Korneev , Ava Handley , Gediminas Gervinskas , Viola Oorschot , Owen L. Kaluza , Ruby H.P. Law , Moira O’ Bryan , Roger Pocock , James C. Whisstock , Alex de Marco
Published: October 2018

Over the past decade, gallium Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) has been established as a key technology for cellular tomography. The utility of this approach, however, is severely limited both by throughput and the limited selection of compatible sample preparation protocols. Here, we address these limitations and present oxygen plasma FIB (O-PFIB) as a new and versatile tool for cellular FIB-SEM tomography. Oxygen displays superior resin compatibility to other ion beams and produces curtain-free surfaces with minimal polishing. Our novel approach permits more flexible sample preparation and 30% faster data collection when compared to using gallium ion sources. We demonstrate this alternative FIB is applicable to a variety of embedding procedures and biological samples including brain tissue and whole organisms. Finally, we demonstrate the use of O-PFIB to produce targeted FIB-SEM tomograms through fiducial free en-block correlative light and electron microscopy.
Resistance Gene-Directed Genome Mining of 50 Aspergillus species
Authors: Kjærbølling Inge , Vesth Tammi , Andersen Mikael R.
Published: October 2018

Fungal secondary metabolites are a rich source of valuable natural products. Genome sequencing have revealed an enormous potential from predicted biosynthetic gene clusters. It is however currently a time consuming task and an unfeasible task to characterize all biosynthetic gene cluster and to identify possible uses of the compounds. A rational approach is needed to identify promising gene clusters responsible for producing valuable compounds. Several valuable bioactive clusters have been shown to include a resistance gene which is a paralog of the target gene inhibited by the compound. This mechanism can be used to design a rational approach selecting those clusters.

We have developed a pipeline FRIGG (Fungal Resistance Gene-directed Genome mining) identifying putative resistance genes found in biosynthetic gene clusters based on homology patterns of the cluster genes. The FRIGG pipeline has been run using 51 Aspergillus and Penicillium genomes, identifying 72 unique protein families with putative resistance genes using various settings in the pipeline. The pipeline was also able to identify the characterized resistance gene inpE from the Fellutamide B cluster thereby validating the approach.

We have successfully developed an approach identifying putative valuable bio-active clusters based on a specific resistance mechanism. This approach will be highly useful as an ever increasing amount of genomic data becomes available — the art of identifying and selecting clusters producing novel valuable compounds will only become more crucial.

Importance

Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites, some of these compounds are bioactive and used as pharmaceuticals such as penicillin, cyclosporin and statin. With whole genome sequencing it became apparent that the genetic potential for secondary metabolite production is much bigger than expected. As an increasing number of species are whole genome sequenced an immense number of secondary metabolite genes are predicted and the question of how to selectively identify novel bioactive compounds from this information arises. To address this question, we have created a pipeline identifying genes likely involved in the production of bioactive compounds based on a resistance gene hypothesis approach.
Genetics of human plasma lipidome: Understanding lipid metabolism and its link to diseases beyond traditional lipids
Authors: Tabassum Rubina , Rämö Joel T. , Ripatti Pietari , Koskela Jukka T. , Kurki Mitja , Karjalainen Juha , Hassan Shabbeer , Nunez-Fontarnau Javier , Kiiskinen Tuomo T.J. , Söderlund Sanni , Matikainen Niina , Gerl Mathias J. , Surma Michal A. , Klose Christian , Stitziel Nathan O. , Laivuori Hannele , Havulinna Aki S. , Service Susan K. , Salomaa Veikko , Pirinen Matti , Jauhiainen Matti , Daly Mark J. , Freimer Nelson B. , Palotie Aarno , Taskinen Marja-Riitta , Simons Kai , Ripatti Samuli
Published: October 2018

Aim

Genetic investigation of human plasma lipidome to get insights into lipid-related disorders beyond traditional lipid measures.

Methods and Results

We performed a genome-wide association study (GWAS) of 141 lipid species (n=2,181 individuals), followed by phenome-wide scans (PheWAS) with 44 clinical endpoints related to cardiometabolic, psychiatric and gastrointestinal disorders (n=456,941 individuals). SNP-based heritability for lipid species ranged from 0.10-0.54. Lipids with long-chain polyunsaturated fatty acids showed higher heritability and genetic sharing, suggesting considerable genetic regulation at acyl chains levels. We identified 35 genomic regions associated with at least one lipid species (P<5×10−8), revealing 37 new SNP-lipid species pair associations e.g. new association between ABCG5/8 and CE(20:2;0). PheWAS of lipid-species-associated loci suggested new associations of BLK with obesity, FADS2 with thrombophlebitis, and BLK and SPTLC3 with gallbladder disease (false discovery rate <0.05). The association patterns of lipid-species-associated loci supplied clues to their probable roles in lipid metabolism e.g. suggestive role of SYNGR1, MIR100HG, and PTPRN2 in desaturation and/or elongation of fatty acids. At known lipid loci (FADS2, APOA5 and LPL), genetic associations provided detailed insights to their roles in lipid biology and diseases. We also show that traditional lipid measures may fail to capture lipids such as lysophospatidylcholines (LPCs) and phosphatidylcholines (PCs) that are potential disease risk factors, but are not included in routine screens. The full genome-wide association statistics are available on the web-based database (http://35.205.141.92).

Conclusion

Our study reveals genetic regulation of plasma lipidome and highlights the potential of lipidomic profiling in disease gene mapping.
Hereditary Pancreatitis Model by Blastocyst Complementation in Mouse
Authors: Asai Ayumu , Konno Masamitsu , Koseki Jun , Kawamoto Koichi , Arai Takahiro , Satoh Taroh , Eguchi Hidetoshi , Mori Masaki , Doki Yuichiro , Ishii Hideshi
Published: October 2018

Summary Statement

The present study is the first report for reproducing human disease by utilizing blastocyst complementation method and would lead to the development of novel therapy for human disease.

The application of pluripotent stem cell is expected to contribute to the elucidation of the unknown mechanism of human diseases. However, in vitro induction of cells in several organs, such as the pancreas and liver, remains difficult; therefore, reproduction of those diseases in a model has not been feasible. To reproduce human hereditary pancreatitis (HP), which is most frequently caused by the mutations in thePRSS1gene, we performed the blastocyst complementation (BC) method. In the BC method, mouse embryonic stem (ES) cells harboring CRISPR/CAS9-mediated mutations in thePrss1were injected into the blastocysts of deficientPdx1gene mice, which is a critical transcription factor in the pancreas. The results showed that the blastocysts injected into thePrss1-mutant ES cells induced trypsin activation. This implied that the mouse phenotype mimics that of human HP and that the BC method was useful for the reproduction and study of pancreatic disorders. The present study opens the possibility of investigating uncharacterized human diseases by utilizing the BC method.
A comprehensive genetic characterisation of the mitochondrial Ca2+ uniporter in Drosophila
Authors: Tufi Roberta , Gleeson Thomas P. , Stockum Sophia von , Hewitt Victoria L. , Lee Juliette J. , Terriente-Felix Ana , Sanchez-Martinez Alvaro , Ziviani Elena , Whitworth Alexander J.
Published: October 2018

Mitochondrial Ca2+ uptake is an important mediator of metabolism and cell death. Identification of components of the highly conserved mitochondrial Ca2+ uniporter has opened it up to genetic analysis in model organisms. Here we report a comprehensive genetic characterisation of the known uniporter components conserved in Drosophila. While loss of MCU or EMRE abolishes fast mitochondrial Ca2+ uptake, this results in surprisingly mild phenotypes. In contrast, loss of the regulatory gatekeeper component MICU1 has a much more severe phenotype, being developmental lethal, consistent with unregulated Ca2+ uptake. Mutants for MICU3 are viable with mild neurological phenotypes. Genetic interaction studies reveal that MICU1 and MICU3 are not functionally interchangeable. More surprisingly, loss of MCU or EMRE does not suppress MICU1 mutant lethality, suggesting that the lethality results from MCU-independent functions. This study helps shed light on the physiological requirements of the mitochondrial Ca2+ uniporter, and provides a suite of tools to interrogate their interplay in homeostasis and disease conditions.
Antagonistic pathogen-mediated selection favours the maintenance of innate immune gene polymorphism in a widespread wild ungulate
Authors: Quéméré Erwan , Hessenauer Pauline , Galan Maxime , Fernandez Marie , Merlet Joël , Chaval Yannick , Morellet Nicolas , Verheyden Hélène , Gilot-Fromont Emmanuelle , Charbonnel Nathalie
Published: October 2018

Toll-like Receptors (TLR) play a central role in recognition and host frontline defence against a wide range of pathogens. A number of recent studies have shown that TLR genes (Tlrs) often exhibit a large polymorphism in natural populations. Yet, there is little knowledge on how this polymorphism is maintained and how it influences disease susceptibility in the wild. In a previous work, we showed that someTlrsexhibit similarly high levels of genetic diversity thanMhcand contemporary signatures of balancing selection in roe deer (Capreolus capreolus), an abundant and widespread ungulate in Europe.Here, we tested whether Mhc-DrborTlr(Tlr2, Tlr4andTlr5) diversity is driven bypathogen-mediated selection. Weexamined the relationships between their genotype (heterozygosity status and presence of specific alleles) and infections withToxoplasmaandChlamydia, two intracellular pathogens known to cause reproductive failure in ungulates. We showed thatToxoplasmaandChlamydiaexposures vary significantly across year and landscape structure with few co-infection events detected, and that the two pathogens act antagonistically onTlr2polymorphism. By contrast, we found no evidence of association withMhc-Drband a limited support forTlrheterozygosity advantage. Our study confirmed the importance of looking beyondMhcgenes in wildlife immunogenetic studies. It also emphasized the necessity to consider multiple pathogen challenges and their spatiotemporal variation to improve our understanding of vertebrate defence evolution against pathogens.
The Hippo network kinase STK38 contributes to protein homeostasis by inhibiting BAG3-mediated autophagy
Authors: Klimek Christina , Jahnke Ricarda , Wördehoff Judith , Kathage Barbara , Stadel Daniela , Behrends Christian , Hergovich Alexander , Höhfeld Jörg
Published: October 2018

Chaperone-assisted selective autophagy (CASA) initiated by the cochaperone Bcl2-associated athanogene 3 (BAG3) represents an important mechanism for the disposal of misfolded and damaged proteins in mammalian cells. Under mechanical stress, the cochaperone cooperates with the small heat shock protein HSPB8 and the cytoskeleton-associated protein SYNPO2 to degrade force-unfolded forms of the actin-crosslinking protein filamin. This is essential for muscle maintenance in flies, fish, mice and men. Here, we identify the serine/threonine protein kinase 38 (STK38), which is part of the Hippo signaling network, as a novel interactor of BAG3. STK38 was previously shown to facilitate cytoskeleton assembly and to promote mitophagy as well as starvation and detachment induced autophagy. Significantly, our study reveals that STK38 exerts an inhibitory activity on BAG3-mediated autophagy. Inhibition relies on a disruption of the functional interplay of BAG3 with HSPB8 and SYNPO2 upon binding of STK38 to the cochaperone. Of note, STK38 attenuates CASA independently of its kinase activity, whereas previously established regulatory functions of STK38 involve target phosphorylation. The ability to exert different modes of regulation on central protein homeostasis (proteostasis) machineries apparently allows STK38 to coordinate the execution of diverse macroautophagy pathways and to balance cytoskeleton assembly and degradation.

Abbreviations

BAG3, BCL2-associated athanogene; CASA, chaperone-assisted selective autophagy; CHIP, carboxy terminus of HSP70 interacting protein; EPS, electrical pulse stimulation; GST, glutathione-S-transferase; mTOR, mechanistic target of rapamycin; mTORC1, mechanistic target of rapamycin complex 1; STK38, serine/threonine protein kinase 38.
Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis
Authors: Rutowicz Kinga , Lirski Maciej , Mermaz Benoît , Schubert Jasmin , Teano Gianluca , Mestiri Imen , Kroteń Magdalena A. , Fabrice Tohnyui Ndinyanka , Fritz Simon , Grob Stefan , Ringli Christoph , Cherkezyan Lusik , Barneche Fredy , Jerzmanowski Andrzej , Baroux Célia
Published: October 2018

Chromatin in eukaryotes provides a tunable platform to control gene expression and convey an epigenetic memory throughout cell divisions. H1 linker histones are abundant components with an intrinsic potential in influencing chromatin structure and function. We detail the impact of H1 depletion in Arabidopsis on fine-scale chromatin organization, transcription and development. While required for chromocenter assembly, H1s are dispensable for transposable element (TE) silencing and peripheral positioning of heterochromatin. In euchromatin, H1 regulates nucleosome density, mobility, and regular distribution of nanoscale chromatin domains. While necessary to maintain epigenetic patterns, H1 only moderately affects transcription. Its depletion is associated with failures in transitional fate changes such as lateral root initiation, root hair production, stomata patterning but also flowering and dormancy regulation. Therefore, Arabidopsis H1 variants are chromatin architects mediating nano‐ and microscale levels-of-organization operating downstream of epigenetic and transcriptional establishment processes and contribute to epigenetic reorientations in developmental transitions.
Immediate visualization of recombination events and chromosome segregation defects in fission yeast meiosis
Authors: Li Dmitriy , Rocl Marianne , Yuecel Raif , Lorenz Alexander
Published: October 2018

Schizosaccharomyces pombe, also known as fission yeast, is an established model for studying chromosome biological processes. Over the years research employing fission yeast has made important contributions to our knowledge about chromosome segregation during meiosis, as well as meiotic recombination and its regulation. Quantification of meiotic recombination frequency is not a straightforward undertaking, either requiring viable progeny for a genetic plating assay, or relying on laborious Southern blot analysis of recombination intermediates. Neither of these methods lends itself to high-throughput screens to identify novel meiotic factors. Here, we establish visual assays novel toSz. pombefor characterizing chromosome segregation and meiotic recombination phenotypes. Genes expressing red, yellow, and/or cyan fluorophores from spore-autonomous promoters have been integrated into the fission yeast genomes, either close to the centromere of chromosome I to monitor chromosome segregation, or on the arm of chromosome III to form a genetic interval at which recombination frequency can be determined. The visual recombination assay allows straightforward and immediate assessment of the genetic outcome of a single meiosis by epi-fluorescence microscopy without requiring tetrad dissection. We also demonstrate that the recombination frequency analysis can be automatized by utilizing imaging flow cytometry to enable high-throughput screens. These assays have several advantages over traditional methods for analysing meiotic phenotypes.
Local online learning in recurrent networks with random feedback
Authors: Murray James M.
Published: October 2018

A longstanding challenge for computational neuroscience has been the development of biologically plausible learning rules for recurrent neural networks (RNNs) enabling the production and processing of time-dependent signals such as those that might drive movement or facilitate working memory. Classic gradient-based algorithms for training RNNs have been available for decades, but they are inconsistent with known biological features of the brain, such as causality and locality. In this work we derive an approximation to gradient-based learning that comports with these biologically motivated constraints. Specifically, the online learning rule for the synaptic weights involves only local information about the pre- and postsynaptic activities, in addition to a random feedback projection of the RNN output error. In addition to providing mathematical arguments for the effectiveness of the new learning rule, we show through simulations that it can be used to train an RNN to successfully perform a variety of tasks. Finally, to overcome the difficulty of training an RNN over a very large number of timesteps, we propose an augmented circuit architecture that allows the RNN to concatenate short-duration patterns into sequences of longer duration.
Effects of weight and height on hand selection: a low-cost virtual reality paradigm
Authors: James McDermott Eric , Himmelbach Marc
Published: October 2018

The main objective was to evaluate the ability of a virtual reality (VR) system to reliably detect the so-called switch-point of a user; the distinguishing plane between free-choice use of the left and right hand. Independent variables of height and weight were incorporated into the study design and their effects on hand selection were analyzed. The paradigm utilized the Leap Motion Hand Tracker, along with a custom script written in C# and was realized through a Unity3D application. Stimuli appeared in random locations on the computer screen, and required the participant to reach with the hand of their choice to contact them with a virtual hand inside the virtual space. We observed main effects of height and weight on switch-points across the group. We found increased use of the dominant hand as stimuli height increased, as well as a significant increase in overall use of the dominant hand when a 500 gram weighted glove was worn by the non-dominant hand. We validated the average switch-points in VR as compared to real-world setups in previous studies. Our results are in line with previously published real-world data, supporting the use of this paradigm in future VR experiments and applications.
Combined linkage and association mapping of putative QTLs controlling black tea quality and drought tolerance traits
Authors: Koech Robert. K. , Mose Richard , Kamunya Samson M. , Apostolides Zeno
Published: October 2018

The advancements in genotyping have opened new approaches for identification and precise mapping of Quantitative Trait Loci (QTLs) in plants, particularly by combining linkage and association mapping (AM) analysis. In this study, a combination of linkage and the AM approach was used to identify and authenticate putative QTLs associated with black tea quality traits and percent relative water content (%RWC). The population structure analysis clustered two parents and their respective 261 F1 progenies from the two reciprocal crosses into two clusters with 141 tea accessions in cluster one and 122 tea accessions in cluster two. The two clusters were of mixed origin with tea accessions in population TRFK St. 504 clustering together with tea accessions in population TRFK St. 524. A total of 71 putative QTLs linked to black tea quality traits and %RWC were detected in interval mapping (IM) method and were used as cofactors in multiple QTL model (MQM) mapping where 46 putative QTLs were detected. The phenotypic variance for each QTL ranged from 2.8–23.3% in IM and 4.1–23% in MQM mapping. Using Q-model and Q+K-model in AM, a total of 49 DArTseq markers were associated with 16 phenotypic traits. Significant marker-trait association in AM were similar to those obtained in IM, and MQM mapping except for six more putative QTLs detected in AM which are involved in biosynthesis of secondary metabolites, carbon fixation and abiotic stress. The combined linkage and AM approach appears to have great potential to improve the selection of desirable traits in tea breeding.
A short HBV RNA region induces RNR-R2 expression in non-cycling cells and in primary human hepatocytes
Authors: Ricardo-Lax Inna , Broennimann Karin , Adler Julia , Michailidis Eleftherios , de Jong Ype P , Reuven Nina , Shaul Yosef
Published: October 2018

Hepatitis B virus infects non-dividing cells in which dNTPs are scarce. HBV replication requires dNTPs. To cope with this constraint the virus induces the DNA damage response (DDR) pathway culminating in RNR-R2 expression and the generation of an active RNR holoenzyme, the key regulator of dNTP levels. Previously we reported that the HBx open reading frame (ORF) triggers this pathway. Unexpectedly however, we report here that the production of HBx protein is not essential. We found that a small region of 125 bases within the HBx transcript is sufficient to induce RNR-R2 expression in growth arrested HepG2 cells and in primary human hepatocytes (PHH). The observed HBx embedded regulatory element is named ERE. We demonstrate that ERE is functional as a positive strand RNA polymerase-II transcript. Remarkably, ERE is sufficient to induce the Chk1-E2F1-RNR-R2 DDR pathway, previously reported to be activated by HBV. Furthermore, we found that ERE activates ATR but not ATM in eliciting this DDR pathway in upregulating RNR-R2. These findings demonstrate the multitasking role of HBV transcripts in mediating virus-host cell interaction, a mechanism that explains how such a small genome effectively serves such a pervasive virus.

Author summary

The hepatitis B virus (HBV) infects the human liver and over 250 million people worldwide are chronically infected with HBV and at risk for cirrhosis and liver cancer. HBV has a very small DNA genome with only four genes, much fewer than other viruses. For propagation the virus consumes dNTPs, the building blocks of DNA, in much higher amounts than the infected cells provide. To cope with this constraint, the virus manipulates the cells to increase the production of dNTPs. We found that the virus activates the cellular response to DNA damage upon which the cells increase the production of dNTPs, but instead of repairing cellular DNA, the virus uses them for production of its own DNA. Usually viruses manipulate host cells with one or more of their unique proteins, however the small HBV genome cannot afford having such a unique gene and protein. Instead, we found that here the virus relies on RNA to manipulate the host cells. Our findings highlight the unprecedented principle of a multitasking viral RNA that is not only designed to be translated into proteins but also harbors an independent role in activating the cellular DNA damage response.
Joint analysis of gene expression levels and histological images identifies genes associated with tissue morphology
Authors: Ash Jordan T. , Darnell Gregory , Munro Daniel , Engelhardt Barbara E.
Published: October 2018

Histological images are used to identify and to characterize complex phenotypes such as tumor stage. Our goal is to associate histological image phenotypes with high-dimensional genomic markers; the limitations to incorporating histological image phenotypes in genomic studies are that the relevant image features are difficult to identify and extract in an automated way, and confounders are difficult to control in this high-dimensional setting. In this paper, we use convolutional autoencoders and sparse canonical correlation analysis (CCA) on histological images and gene expression levels from paired samples to find subsets of genes whose expression values in a tissue sample correlate with subsets of morphological features from the corresponding sample image. We apply our approach, ImageCCA, to three data sets, two from TCGA and one from GTEx v6, and we find three types of biological associations. In TCGA, we find gene sets associated with the structure of the extracellular matrix and cell wall infrastructure, implicating uncharacterized genes in extracellular processes. Across studies, we find sets of genes associated with specific cell types, including muscle tissue and neuronal cells, and with cell type proportions in heterogeneous tissues. In the GTEx v6 data, we find image features that capture population variation in thyroid and in colon tissues associated with genetic variants, suggesting that genetic variation regulates population variation in tissue morphological traits. The software is publicly available at:https://github.com/daniel-munro/imageCCA.
The emergence of multiple retinal cell types through efficient coding of natural movies
Authors: Ocko Samuel A. , Lindsey Jack , Ganguli Surya , Deny Stephane
Published: October 2018

One of the most striking aspects of early visual processing in the retina is the immediate parcellation of visual information into multiple parallel pathways, formed by different retinal ganglion cell types each tiling the entire visual field. Existing theories of efficient coding have been unable to account for the functional advantages of such cell-type diversity in encoding natural scenes. Here we go beyond previous theories to analyze how a simple linear retinal encoding model with different convolutional cell types efficiently encodes naturalistic spatiotemporal movies given a fixed firing rate budget. We find that optimizing the receptive fields and cell densities of two cell types makes them match the properties of the two main cell types in the primate retina, midget and parasol cells, in terms of spatial and temporal sensitivity, cell spacing, and their relative ratio. Moreover, our theory gives a precise account of how the ratio of midget to parasol cells decreases with retinal eccentricity. Also, we train a nonlinear encoding model with a rectifying nonlinearity to efficiently encode naturalistic movies, and again find emergent receptive fields resembling those of midget and parasol cells that are now further subdivided into ON and OFF types. Thus our work provides a theoretical justification, based on the efficient coding of natural movies, for the existence of the four most dominant cell types in the primate retina that together comprise 70% of all ganglion cells.
Parallel patterns of development between independent cases of hybrid seed inviability in Mimulus
Authors: Coughlan Jenn M. , Willis John H.
Published: October 2018

Rationale

Hybrid seed inviability (HSI) is a common reproductive barrier in angiosperms, yet the evolutionary and developmental drivers of HSI remain largely unknown. We test whether conflict between maternal and paternal interests in resource allocation to developing offspring (i.e. parental conflict) are associated with HSI and determine the degree of developmental parallelism between independent incidences of HSI in Mimulus.

Methods

We quantified HSI between M. guttatus and two clades of M. decorus with oppositely asymmetric incompatibilities and surveyed development of hybrid and parental seeds.

Key Results

Crosses between M. guttatus and both clades of M. decorus show parent-of-origin effects on reciprocal F1 seed development, but in opposing directions. Inviable hybrid seeds exhibit paternal excess phenotypes, wherein endosperm is large and chaotic while viable hybrid seeds produce endosperm cells that are smaller and less prolific (i.e. maternal-excess phenotypes).

Main Conclusions

We find strong parent-of-origin effects on development in reciprocal F1s in multiple incidences of HSI in Mimulus. These patterns suggest that parental conflict may be an important force generating HSI in this group, and mismatches between maternal and paternal contributions to developing seeds result in repeatable developmental defects in hybrids.
Less-skilled pilot decision support
Authors: Rohacs Jozsef , Jankovics Istvan , Rohacs Daniel
Published: October 2018

Purpose

The purpose of this paper is to overview the systems and their elements developing for supporting the less-skilled pi-lots.

Design/methodology/approach

Several European (like EPATS, SAT-Rdmp, Pplane, Esposa, Clean Sky2) and national projects (NASA SATS, Hungarian SafeFly) develop the personal/small aircraft and personal/small aircraft transportation systems. The projects had analysed the safety aspects, too, and they underlined the aircraft will be controlled by so-called less-skilled pilots (owners, renters), having less experiences. The paper defines the cross-connected controls, introduces the methods of subjective analysis in pilot decision processes, improves the pilot workload model, defines the possible workload management and describes the developing pilot decision support system.

Findings

Analysing the personal/small aircraft safety aspects, a unique and important safety problem induced by less-skilled pilots has been identified. The considerable simplification of the air-craft control system, supporting the pilot subjective decisions and introducing the pilot work-load management, may eliminate this problem.

Research limitations/implications

Only the system elements have been used in concept validation tests.

Practical implications

The developing pilot supporting system in its general form has on - board and ground sub-systems, too, except a series of elements integrated into the pilot cockpit environment and control system. Several system elements (sensors, integrated controls, etc.) might be implement now, but the total system need further studies. The subjective decision process needs further development of the methodology and concept validation.

Social implications

The system may catalyse the society acceptance of the personal aircraft and their safer piloting, applicability.

Originality/value

The paper introduces an original supporting system for less-skilled pilots.