bluuebunny/crossref_metadata_2025 huggingface dataset:
Extracellular CIRP as a Novel Endogenous TREM-1 Ligand to Fuel Inflammation
Authors: Denning Naomi-Liza , Aziz Monowar , Murao Atsushi , Gurien Steven D. , Ochani Mahendar , Prince Jose M. , Wang Ping
Published: June 2019

Extracellular cold-inducible RNA-binding protein (eCIRP) is a recently-discovered damage-associated molecular pattern. Understanding the precise mechanism by which it exacerbates inflammation in sepsis is essential. Here we identified that eCIRP is a new biologically active endogenous ligand of triggering receptor expressed on myeloid cells-1 (TREM-1), fueling inflammation in sepsis and ischemia-reperfusion. Surface plasmon resonance revealed a strong binding affinity between eCIRP and TREM-1, and FRET assay confirmed eCIRP’s interaction with TREM-1 in macrophages. TREM-1 inhibition, either by its siRNA or a decoy peptide LP17, dramatically reduced eCIRP-induced inflammation. We developed a novel 7-aa peptide derived from human eCIRP, M3, which blocked the interaction of TREM-1 and eCIRP. M3 suppressed inflammation induced by eCIRP or agonist TREM-1 Ab crosslinking in murine macrophages or human peripheral blood monocytes. M3 also inhibited eCIRP-induced systemic inflammation and tissue injury. Treatment with M3 further protected mice from sepsis and intestinal ischemia-reperfusion, improved acute lung injury, and increased survival. Thus, we have discovered a novel TREM-1 ligand and developed a new peptide M3 to block eCIRP-TREM-1 interaction and improve the outcome of sepsis and sterile inflammation.
Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma
Authors: Ma Man Chun John , Tadros Saber , Bouska Alyssa , Heavican Tayla , Yang Haopeng , Deng Qing , Moore Dalia , Akhter Ariz , Hartert Keenan , Jain Neeraj , Showell Jordan , Ghosh Sreejoyee , Street Lesley , Davidson Marta , Carey Christopher , Tobin Joshua , Perumal Deepak , Vose Julie M. , Lunning Matthew A. , Sohani Aliyah R. , Chen Benjamin J. , Buckley Shannon , Nastoupil Loretta J. , Davis R. Eric , Westin Jason R. , Fowler Nathan H. , Parekh Samir , Gandhi Maher , Neelapu Sattva , Stewart Douglas , Bhalla Kapil , Iqbal Javeed , Greiner Timothy , Rodig Scott J. , Mansoor Adnan , Green Michael R.
Published: June 2019

B-cell non-Hodgkin’s lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level. But rarer subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared using the same methodology to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 685 B-NHL tumors at high depth; including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated in the majority of tumor from each subtype, including the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations and DNA copy number alterations. The cumulative burden of mutations within a single cluster were more discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic cooperation that contribute to disease etiology. We therefore provide the first cross-sectional analysis of mutations and DNA copy number alterations across major B-NHL subtypes and a framework of co-occurring genetic alterations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis.
Towards a gold standard for benchmarking gene set enrichment analysis
Authors: Geistlinger Ludwig , Csaba Gergely , Santarelli Mara , Ramos Marcel , Schiffer Lucas , Law Charity , Turaga Nitesh , Davis Sean , Carey Vincent , Morgan Martin , Zimmer Ralf , Waldron Levi
Published: June 2019

Background

Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected data sets and biological reasoning on the relevance of resulting enriched gene sets. However, this is typically incomplete and biased towards the goals of individual investigations.

Results

We present a general framework for standardized and structured benchmarking of enrichment methods based on defined criteria for applicability, gene set prioritization, and detection of relevant processes. This framework incorporates a curated compendium of 75 expression data sets investigating 42 different human diseases. The compendium features microarray and RNA-seq measurements, and each dataset is associated with a precompiled GO/KEGG relevance ranking for the corresponding disease under investigation. We perform a comprehensive assessment of 10 major enrichment methods on the benchmark compendium, identifying significant differences in (i) runtime and applicability to RNA-seq data, (ii) fraction of enriched gene sets depending on the type of null hypothesis tested, and (iii) recovery of thea prioridefined relevance rankings. Based on these findings, we make practical recommendations on (i) how methods originally developed for microarray data can efficiently be applied to RNA-seq data, (ii) how to interpret results depending on the type of gene set test conducted, and (iii) which methods are best suited to effectively prioritize gene sets with high relevance for the phenotype investigated.

Conclusion

We carried out a systematic assessment of existing enrichment methods, and identified best performing methods, but also general shortcomings in how gene set analysis is currently conducted. We provide a directly executable benchmark system for straightforward assessment of additional enrichment methods.

Availability

http://bioconductor.org/packages/GSEABenchmarkeR
Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae
Authors: de Bernardi Schneider Adriano , Jacob Machado Denis , Janies Daniel
Published: June 2019

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Unfortunately, most cladograms of Flaviviridae focus on specific lineages, ignore outgroups, and rely on midpoint rooting, hampering their ability to test ingroup monophyly and estimate ingroup relationships. This problem is partly due to the lack of fully annotated genomes of Flaviviridae, which has genera with slightly different gene content, hindering genome analysis without partitioning. To tackle these problems, we developed an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology-based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining non curated sequences. We further demonstrate that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by our annotation strategy, enhances the phylogenetic analyses of these viruses for all optimality criteria that we tested (parsimony, maximum likelihood, and posterior probability). The final tree sheds light on the phylogenetic relationship of viruses that are divergent from most Flaviviridae and should be reclassified, especially the soybean cyst nematode virus 5 (SbCNV-5) and the Tamana bat virus. We also corroborate the close phylogenetic relationship of dengue and zika viruses with an unprecedented degree of support.
NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance
Authors: Glover Marissa L. , Burroughs A. Max. , Egelhofer Thea A. , Pule Makena N. , Aravind L. , Arribere Joshua A.
Published: June 2019

Cellular translation surveillance rescues ribosomes that stall on problematic mRNAs. During translation surveillance, endonucleolytic cleavage of the problematic mRNA is a critical step in rescuing stalled ribosomes. However, the nuclease(s) responsible remain unknown. Here we identify NONU-1 as a novel endoribonuclease required for translation surveillance pathways including No-Go and Nonstop mRNA Decay. We show that: (1) NONU-1 reduces Nonstop and No-Go mRNA levels; (2) NONU-1 contains an Smr RNase domain required for mRNA decay and with properties similar to the unknown endonuclease; and (3) the domain architecture and catalytic residues of NONU-1 are conserved throughout metazoans and eukaryotes, respectively. We extend our results inC. elegansto homologous factors inS. cerevisiae, showing conservation of function of the NONU-1 protein across billions of years of evolution. Our work establishes the identity of a previously unknown factor critical to translation surveillance and will inform mechanistic studies at the intersection of translation and mRNA decay.
Infect While the Iron is Scarce: Nutrient Explicit Phage-Bacteria Games
Authors: Muratore Daniel , Weitz Joshua S.
Published: June 2019

Marine microbial primary production is influenced by the availability and uptake of essential nutrients, including iron. Although marine microbes have evolved mechanisms to scavenge sub-nanomolar concentrations of iron, recent observations suggest that viruses may co-opt these very same mechanisms to facilitate infection. The “Ferrojan Horse Hypothesis” proposes that viruses incorporate iron atoms into their tail fiber proteins to adsorb to target host receptors. Here, we propose an evolutionary game theoretic approach to consider the joint strategies of hosts and viruses in environments with limited nutrients (like iron). We analyze the bimatrix game and find that evolutionarily stable strategies depend on the stability and quality of nutrient conditions. For example, in highly stable iron conditions, virus pressure does not change host uptake strategies. However, when iron levels are dynamic, virus pressure can lead to fluctuations in the extent to which hosts invest in metabolic machinery that increases both iron uptake and susceptibility to viral infection. Altogether, this evolutionary game model provides further evidence that viral infection and nutrient dynamics jointly shape the fate of microbial populations.
Manipulation of Seedling Traits with Pulsed Light in Closed Controlled Environments
Authors: Song Shiwei , Kusuma Paul , Carvalho Sofia D. , Li Yan , Folta Kevin M.
Published: June 2019

There is substantial interest in growing crops in closed controlled environments, yet the energy requirements are high. Energy is required to produce light, but also to remove the heat generated when producing light. The goal of the current work examines a possible approach to decrease the energy requirement. The effect of pulsed light treatments was examined by monitoring seedling traits during early photomorphogenic development. Daily light integral remained unchanged between treatments, but the frequency of the pulses was varied. Developmental traits (such as inhibition of hypocotyl elongation rate) were most conspicuous during a normal photoperiod, as in twelve hours light, twelve hours darkness. Consistent with historical reports, when treatments were delivered in shorter durations (e.g. 1 hour on/off) photomorphogenic development was hindered, with the same daily light integral. However, at even shorter light intervals (e.g. seconds) seedlings developed as if they were provided full 12 h treatments. Extension of the dark period following a 5 s pulse was tested to determine the effect on seedling traits. The results showed that the dark period could be extended to at least 10 s without affecting seedling development, and extension to 20 s only had slight effects on seedling traits. The mechanism of the phenomenon was examined in Arabidopsis photosensory mutants, with substantial contributions from the phyA and cry1 pathways. The results suggest that pulsed light with extended dark periods can decrease energy input by at least 30% to >50% without affecting visible seedling traits. These pilot experiments in seedlings demonstrate that implementation of short-interval, pulsed-light strategies may lower energy requirements for growing crops in artificially illuminated environments.
Attraction of Triatoma infestans (Klug) to adhesive yeast-baited trap under laboratory conditions
Authors: Cardozo Miriam , Fiad Federico G. , Crocco Liliana B. , Gorla David E.
Published: June 2019

Existing methods to detect domestic triatomines have low sensitivity. As early house infestation detection is epidemiologically important, the exploration of better methods is required. Hence, we measured the attractiveness of a yeast-baited trap to adults and nymphs of Triatoma infestans, under laboratory conditions.

The assays were conducted in an experimental arena, with an experimental and a control traps placed at opposite sides and one refuge in the center area. Insects where released and the number of triatomines in the yeast and control traps were counted, after 3, 6 and 24 hours of the beginning of the experiment. We use generalized linear models within a multimodel inference approach to model the number of insects in the trap, using insect age classes, time after assay initiation and date of the experiment as predictors.

Our results show that the attraction to CO2 depends upon the life stage of the insects. During the 24 hours of experiment a constant number of adults were attracted to the yeast trap, while nymphs show attraction only up to the first three hours after the initiation of CO2 liberation. Undoubtedly, the orientation response to chemical cues deserves further studies to be fully understood.
Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants
Authors: Ferrari Camilla , Mutwil Marek
Published: June 2019

The glaucophyte Cyanophora paradoxa represents the most basal member of the Archaeplastida kingdom, however the function and expression of most of its genes are unknown. This information is needed to uncover how functional gene modules, i.e. groups of genes performing a given function, evolved in the plant kingdom.

We have generated a gene expression atlas capturing responses of Cyanophora to various abiotic stresses. This data was included in the CoNekT-Plants database, enabling comparative transcriptomic analyses across two algae and six land plants.

We demonstrate how the database can be used to study gene expression, co-expression networks and gene function in Cyanophora, and how conserved transcriptional programs can be identified. We identified gene modules involved in phycobilisome biosynthesis, response to high light and cell division. While we observed no correlation between the number of differentially expressed genes and the impact on growth of Cyanophora, we found that the response to stress involves a conserved, kingdom-wide transcriptional reprogramming, which is activated upon most stresses in algae and land plants.

The Cyanophora stress gene expression atlas and the tools found in https://conekt.plant.tools/ database provide a useful resource to reveal functionally related genes and stress responses in the plant kingdom.
Aneuploidy Spectrum Analysis as a Primer for Copy Number Profiling of Cancer Cells
Authors: Samir Khalil Ahmed Ibrahim , Chattopadhyay Anupam , Sanyal Amartya
Published: June 2019

Motivation

Hyperploidy and segmental aneuploidy are hallmarks of cancer cells due to chromosome segregation errors and genomic instability. In such situations, accurate aneuploidy profiling of cancer data is critical for calibration of copy number (CN)-detection tools. Additionally, cancer cell populations suffer from different levels of clonal heterogeneity and aneuploidy alterations over time. The degree of heterogeneity adversely affects the segregation of the depth of coverage (DOC) signal into integral CN states. This, in turn, strongly influences the reliability of this data for ploidy profiling and copy number variation (CNV) analysis.

Results

We developed AStra framework for aneuploidy profiling of cancer data and assessing their suitability for copy number analysis without any prior knowledge of the input sequencing data. AStra estimates the best-fit aneuploidy profile as the spectrum with most genomic segments around integral CN states. We employ this spectrum to extract the CN-associated features such as the homogeneity score (HS), whole-genome ploidy level, and CN correction factor. The HS measures the percentage of genomic regions around CN states. It is used as a reliability assessment of sequencing data for downstream aneuploidy profiling and CNV analysis. We evaluated the accuracy of AStra using 31 low-coverage datasets from 20 cancer cell lines. AStra successfully identified the aneuploidy spectrum of complex cell lines with HS greater than 75%. Benchmarking against nQuire tool showed that AStra is superior in detecting the ploidy level using both low- and high-coverage data. Furthermore, AStra accurately estimated the ploidy of 26/27 strains of MCF7 (hyperploid) cell line which exhibit varied levels of aneuploidy spectrum and heterogeneity. Remarkably, we found that HS is strongly correlated with the doubling time of these strains.

Availability and implementation

AStra is an open source software implemented in Python and is available at https://github.com/AISKhalil/AStra
Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution
Authors: Braga Mariana P , Landis Michael , Nylin Sören , Janz Niklas , Ronquist Fredrik
Published: June 2019

Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such associations make the simplifying assumption that parasites have a single host. Many methods also focus on congruence between host and parasite phylogenies, using cospeciation as the null model. However, there is an increasing body of evidence suggesting that the host ranges of parasites are more complex: that host ranges often include more than one host and evolve via gains and losses of hosts rather than through cospeciation alone. Here, we develop a Bayesian approach for inferring coevolutionary history based on a model accommodating these complexities. Specifically, a parasite is assumed to have a host repertoire, which includes both potential hosts and one or more actual hosts. Over time, potential hosts can be added or lost, and potential hosts can develop into actual hosts or vice versa. Thus, host colonization is modeled as a two-step process, which may potentially be influenced by host relatedness or host traits. We first explore the statistical behavior of our model by simulating evolution of host-parasite interactions under a range of parameters. We then use our approach, implemented in the program RevBayes, to infer the coevolutionary history between 34 Nymphalini butterfly species and 25 angiosperm families.
Terasaki Spiral Ramps and Intracellular Diffusion
Authors: Huber Greg , Wilkinson Michael
Published: June 2019

The sheet-like endoplasmic reticulum (ER) of eukaryotic cells has been found to be riddled with spiral dislocations, known as ‘Terasaki ramps’, in the vicinity of which the doubled bilayer membranes which make up ER sheets can be approximately modeled by helicoids. Here we analyze diffusion on a surface with locally helicoidal topological dislocations, and use the results to argue that the Terasaki ramps facilitate a highly efficient transport of water-soluble molecules within the lumen of the endoplasmic reticulum.
Metaecosystem dynamics drive community composition in experimental multilayered spatial networks
Authors: Harvey Eric , Gounand Isabelle , Fronhofer Emanuel A. , Altermatt Florian
Published: June 2019

Cross-ecosystem subsidies are studied with a focus on resource exchange at local ecosystem boundaries. This perspective ignores regional dynamics that can emerge via constraints imposed by the landscape, potentially leading to spatially-dependent effects of subsidies and spatial feedbacks. Using miniaturized landscape analogues of river dendritic and terrestrial lattice spatial networks, we manipulated and studied resource exchange between the two whole networks. We found that community composition in dendritic networks depended on the resource pulse from the lattice network, with the strength of this effect declining in larger downstream patches. In turn, this spatially-dependent effect imposed constraints on the lattice network with populations in that network reaching higher densities when connected to more central patches in the dendritic network. Consequently, localized cross-ecosystem fluxes, and their respective effects on recipient ecosystems, must be studied in a perspective taking into account the explicit spatial configuration of the landscape.

Statement of authorship

EH, IG, EAF and FA designed the research; EH conducted the lab experiment with support from IG, EAF and FA, processed the experimental data with methodological developments from IG, and carried out the analysis of experimental data; all authors participated in results interpretation; EH wrote the first draft of the manuscript; All authors significantly contributed to further manuscript revisions.
Prolonged ovarian storage of matureDrosophilaoocytes dramatically increases meiotic spindle instability
Authors: Greenblatt Ethan J. , Obniski Rebecca , Mical Claire , Spradling Allan C.
Published: June 2019

More than 95% of fertilizedDrosophilaoocytes from outbred stocks develop fully regardless of maternal age, in contrast to human oocytes, which frequently generate non-viable aneuploid embryos. SinceDrosophilaoocytes are normally stored only briefly prior to ovulation, unlike their human counterparts, we investigated the effects of storage on oocyte quality. Using a novel system to acquire oocytes held for known periods, we analyzed by ribosome profiling how translation and cellular function change over time. Oocyte developmental capacity decays in a precise temperature-dependent manner over 1-4 weeks, due to a progressive inability to complete meiosis. Meiotic metaphase genes, theFmr1translational regulator, and the small heat shock protein chaperonesHsp26andHsp27are preferentially translated during storage, and oocytes lackingHsp26andHsp27age prematurely. However translation falls generally 2.3-fold with age despite constant mRNA levels, and this inability to maintain translational equilibrium correlates with oocyte functional decline. These findings show that meiotic chromosome segregation inDrosophilaoocytes is uniquely sensitive to prolonged quiescence, and suggest that the extended storage of mature human oocytes contributes to their chromosome instability. If so, then these problems may be more amenable to intervention than previously supposed.
Concurrent Genome and Epigenome Editing by CRISPR-Mediated Sequence Replacement
Authors: Alexander Jes , Findlay Gregory M. , Kircher Martin , Shendure Jay
Published: June 2019

Recent advances in genome editing have facilitated the direct manipulation of not only the genome, but also the epigenome. Genome editing is typically performed by introducing a single CRISPR/Cas9-mediated double stranded break (DSB), followed by NHEJ or HDR mediated repair. Epigenome editing, and in particular methylation of CpG dinucleotides, can be performed using catalytically inactive Cas9 (dCas) fused to a methyltransferase domain. However, for investigations of the role of methylation in gene silencing, studies based on dCas9-methyltransferase have limited resolution and are potentially confounded by the effects of binding of the fusion protein. As an alternative strategy for epigenome editing, we tested CRISPR/Cas9 dual cutting of the genome in the presence of in vitro methylated exogenous DNA, i.e. to drive replacement of the DNA sequence intervening the dual cuts via NHEJ. In a proof-of-concept at the HPRT1 promoter, successful replacement events with heavily methylated alleles of a CpG island resulted in functional silencing of the HPRT1 gene. Although still limited in efficiency, our study demonstrates concurrent epigenome and genome editing in a single event, and opens the door to investigations of the functional consequences of methylation patterns at single CpG dinucleotide resolution. Our results furthermore support the conclusion that promoter methylation is sufficient to functionally silence gene expression.
Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated By Cis Noncoding Mutations
Authors: Przytycki Pawel F , Singh Mona
Published: June 2019

Identifying cancer-relevant mutations in noncoding regions is extremely challenging due to the large numbers of such mutations, their low levels of recurrence, and the general difficulty in interpreting their impact. To uncover genes that are dysregulated due to somatic mutations in cis, we build upon the concept of differential allele-specific expression (ASE) and introduce methods to identify genes within an individual’s cancer whose ASE differs from what is found in matched normal tissue. When applied to breast cancer tumor samples, our methods readily detect the known allele-specific effects of copy number variation and nonsense-mediated decay. Further, genes that are found to recurrently exhibit differential ASE across samples are cancer relevant. Genes with cis mutations are enriched for differential ASE, and we find 147 potentially functional noncoding mutations cis to genes that exhibit significant differential ASE. Overall, our results suggest that differential ASE is a promising means for discovering gene dysregulation within an individual due to cis noncoding mutations.
Interactions in milk suggest a physiological role for β-lactoglobulin
Authors: Crowther J.M. , Broadhurst M. , Laue T. , Jameson G.B. , Hodgkinson A.J. , Dobson R.C.J.
Published: June 2019

β-Lactoglobulin is the most abundant protein in the whey fraction of ruminant milks, yet is absent in human milk. It has been studied intensively due to its impact on the processing and allergenic properties of ruminant milk products. However, the physiological function of β-lactoglobulin remains unclear. Sedimentation velocity experiments have identified new interactions between fluorescently-labelled β-lactoglobulin and other components in milk. Co-elution experiments support that these β-lactoglobulin interactions occur naturally in milk and provide evidence that the interacting partners are immunoglobulins, while further sedimentation velocity experiments confirm that an interaction occurs between these molecules. Ruminants (e.g. cows and goats) are born without circulating immunoglobulins, which they must obtain from their mothers’ milk, whilst humans obtain immunoglobulins both through milk and during gestation via the placenta. We propose that β-lactoglobulin serves to protect immunoglobulins within ruminant milk during digestion, ensuring their efficient transfer from mother to offspring.

Statement of Significance

β-Lactoglobulin is an abundant protein in the whey fraction of ruminant milks (e.g. cow and goat milk), yet it is completely absent in human milk. While this protein has been extensively studied, due to its impact on the processing and allergenic properties of milk, its physiological function remains unclear. We fluorescently labelled β-lactoglobulin to monitor its interactions with other milk components within its physiological environment, milk. Under these near physiological conditions β-lactoglobulin is capable of interacting with several classes of immunoglobulins. Immunoglobulins are susceptible to digestion, but are required to confer immunity from the mother to the offspring. We propose that β-lactoglobulin serves to protect immunoglobulins within ruminant milk during digestion, ensuring their efficient transfer from mother to offspring.
Passenger Hotspot Mutations in Cancer
Authors: Hess Julian M. , Bernards Andre , Kim Jaegil , Miller Mendy , Taylor-Weiner Amaro , Haradhvala Nicholas J. , Lawrence Michael S. , Getz Gad
Published: June 2019

Hotspots, or mutations that recur at the same genomic site across multiple tumors, have been conventionally interpreted as strong universal evidence of somatic positive selection, unequivocally pinpointing genes driving tumorigenesis. Here, we demonstrate that this convention is falsely premised on an inaccurate statistical model of background mutagenesis. Many hotspots are in fact passenger events, recurring at sites that are simply inherently more mutable rather than under positive selection, which current background models do not account for. We thus detail a log-normal-Poisson (LNP) background model that accounts for variation in site-specific mutability in a manner consistent with models of mutagenesis, use this model to show that the tendency to generate passenger hotspots pervades all common mutational processes, and apply it to a ~10, 000 patient cohort from The Cancer Genome Atlas to nominate driver hotspots with far fewer false positives compared to conventional methods. As the biomedical community faces critical decisions in prioritizing putative driver mutations for deep experimental characterization to assess therapeutic potential, we offer our findings as a guide to avoid wasting valuable scientific resources on passenger hotspots.
Genomic profiling of 553 uncharacterized neurodevelopment patients reveals a high proportion of recessive pathogenic variant carriers in an outbred population
Authors: Lee Youngha , Park Soojin , Lee Jin Sook , Kim Soo Yeon , Cho Jaeso , Yoo Yongjin , Lee Sangmoon , Yoo Taekyeong , Lee Moses , Seo Jieun , Lee Jeongeun , Kneissl Jana , Lee Jean , Jeon Hyoungseok , Jeon Eun Young , Hong Sung Eun , Kim Eunha , Kim Hyuna , Kim Woo Joong , Kim Jon Soo , Ko Jung Min , Cho Anna , Lim Byeong Chan , Kim Won Seop , Choi Murim , Chae Jong-Hee
Published: June 2019

Background

A substantial portion of Mendelian disease patients suffers from genetic variants that are inherited in a recessive manner. A precise understanding of pathogenic recessive variants in a population would assist in pre-screening births of such patients. However, a systematic understanding of the contribution of recessive variants to Mendelian diseases is still lacking.

Methods

Genetic diagnosis and variant discovery of 553 undiagnosed Korean patients with complex neurodevelopmental problems (KND for Korean NeuroDevelopmental cohort) were performed using whole exome sequencing of patients and their parents. Pathogenic variants were selected and evaluated based on a comparison to patient symptoms and genetic properties of the variants were analyzed.

Results

Disease-causing variants, including newly discovered variants, were identified in in 57.5% of the probands of the KND cohort. Of the 553 patients, 47.4% harbored variants that were previously reported as being pathogenic, and 35.1% of the previous reported pathogenic variants were inherited in a recessive manner. Genes that cause recessive disorders tend to be less constrained by loss-of-function variants and enriched in metabolic and mitochondrial pathways. This observation was applied to an estimation that approximately 1 in 17 healthy Korean individuals carry at least one of these pathogenic variants that develop severe neurodevelopmental problems in a recessive manner. Furthermore, the feasibility of these genes for carrier screening was evaluated.

Conclusions

We suggest that the odds are high for healthy individuals carrying a potentially pathogenic variant, and its genetic properties. Our results will serve as a foundation for recessive variant screening to reduce occurrences of rare Mendelian disease patients. Additionally, our results highlight the utility and necessity of whole exome sequencing-based diagnostics for improving patient care in a country with a centralized medical system.
Engineered illumination devices for optogenetic control of cellular signaling dynamics
Authors: Repina Nicole A. , McClave Thomas , Bao Xiaoping , Kane Ravi S. , Schaffer David V.
Published: June 2019

Spatially and temporally varying patterns of morphogen signals during development drive cell fate specification at the proper location and time. However, currentin vitromethods typically do not allow for precise, dynamic, spatiotemporal control of morphogen signaling and are thus insufficient to readily study how morphogen dynamics impact cell behavior. Here we show that optogenetic Wnt/β-catenin pathway activation can be controlled at user-defined intensities, temporal sequences, and spatial patterns using novel engineered illumination devices for optogenetic photostimulation and light activation at variable amplitudes (LAVA). The optical design of LAVA devices was optimized for uniform illumination of multi-well cell culture plates to enable high-throughput, spatiotemporal optogenetic activation of signaling pathways and protein-protein interactions. Using the LAVA devices, variation in light intensity induced a dose-dependent response in optoWnt activation and downstream Brachyury expression in human embryonic stem cells (hESCs). Furthermore, time-varying and spatially localized patterns of light revealed tissue patterning that models embryonic presentation of Wnt signalsin vitro. The engineered LAVA devices thus provide a low-cost, user-friendly method for high-throughput and spatiotemporal optogenetic control of cell signaling for applications in developmental and cell biology.
Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples
Authors: Lewandowski Kuiama , Xu Yifei , Pullan Steven T. , Lumley Sheila F. , Foster Dona , Sanderson Nicholas , Vaughan Alison , Morgan Marcus , Bright Nicole , Kavanagh James , Vipond Richard , Carroll Miles , Marriott Anthony C. , Gooch Karen E , Andersson Monique , Jeffery Katie , Peto Timothy EA , Crook Derrick W. , Walker A Sarah , Matthews Philippa C.
Published: June 2019

Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential of a diagnostic test for influenza which also provides insights on transmission, evolution and drug resistance, and simultaneously detects other viruses. We therefore set out to apply Oxford Nanopore Technology to metagenomic sequencing of respiratory samples. We generated influenza reads down to a limit of detection of 102-103 genome copies/ml in pooled samples, observing a strong relationship between the viral titre and the proportion of influenza reads (p = 4.7×10-5). Applying our methods to clinical throat swabs, we generated influenza reads for 27/27 samples with high-to-mid viral titres (Cycle threshold (Ct) values <30) and 6/13 samples with low viral titres (Ct values 30-40). No false positive reads were generated from 10 influenza-negative samples. Thus Nanopore sequencing operated with 83% sensitivity (95% CI 67-93%) and 100% specificity (95% CI 69-100%) compared to the current diagnostic standard. Coverage of full length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza titres, we were able to reconstruct >99% complete sequence for all eight gene segments. We also detected Human Coronavirus and generated a near complete Human Metapneumovirus genome from clinical samples. While further optimisation is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza and other respiratory viruses.
Three quantitative trait loci explain more than 60% of phenotypic variation for chill coma recovery time inDrosophila ananassae
Authors: Königer Annabella , Arif Saad , Grath Sonja
Published: June 2019

Ectothermic species such as insects are particularly vulnerable to climatic fluctuations. Nevertheless, many insects that evolved and diversified in the tropics have successfully colonized temperate regions all over the globe. To shed light on the genetic basis of cold tolerance in such species, we conducted a quantitative trait locus (QTL) mapping experiment for chill coma recovery time (CCRT) inDrosophila ananassae, a cosmopolitan species that has expanded its range from tropical to temperate regions.

We created a mapping population of recombinant inbred advanced intercross lines (RIAILs) from two founder strains with diverging CCRT phenotypes. The RIAILs were phenotyped for their CCRT and, together with the founder strains, genotyped for polymorphic markers with double-digest restriction site-associated DNA (ddRAD) sequencing. Using a hierarchical mapping approach that combined standard interval mapping and a multiple-QTL model, we mapped three QTL which altogether explained 64% of the phenotypic variance. For two of the identified QTL, we found evidence of epistasis. To narrow down the list of cold tolerance candidate genes, we cross-referenced the QTL intervals with genes that we previously identified as differentially expressed in response to cold inD. ananassae, and with thermotolerance candidate genes ofD. melanogaster. Among the 58 differentially expressed genes that were contained within the QTL,GF15058showed a significant interaction of the CCRT phenotype and gene expression. Further, we identified the orthologs of fourD. melanogasterthermotolerance candidate genes,MtnA,klarsicht,CG5246(D.ana/GF17132) andCG10383(D.ana/GF14829) as candidates for cold tolerance inD. ananassae.
Peroxiredoxin promotes longevity and H2O2-resistance in yeast through redox-modulation of protein kinase A
Authors: Roger Friederike , Picazo Cecilia , Reiter Wolfgang , Libiad Marouane , Asami Chikako , Hanzén Sarah , Gao Chunxia , Lagniel Gilles , Welkenhuysen Niek , Labarre Jean , Nyström Thomas , Grøtli Morten , Hartl Markus , Toledano Michel B. , Molin Mikael
Published: June 2019

Peroxiredoxins are H2O2scavenging enzymes that also carry H2O2signaling and chaperone functions. In yeast, the major cytosolic peroxiredoxin, Tsa1 is required for both promoting resistance to H2O2and extending lifespan upon caloric restriction. We show here that Tsa1 effects both these functions not by scavenging H2O2, but by repressing the nutrient signaling Ras-cAMP-PKA pathway at the level of the protein kinase A (PKA) enzyme. Tsa1 stimulates sulfenylation of cysteines in the PKA catalytic subunit by H2O2and a significant proportion of the catalytic subunits are glutathionylated on two cysteine residues. Redox modification of the conserved Cys243 inhibits the phosphorylation of a conserved Thr241 in the kinase activation loop and enzyme activity, and preventing Thr241 phosphorylation can overcome the H2O2sensitivity of Tsa1-deficient cells. Results support a model of aging where nutrient signaling pathways constitute hubs integrating information from multiple aging-related conduits, including a peroxiredoxin-dependent response to H2O2.
Accessing the rich carbon nitride materials chemistry by heat treatments of ammonium thiocyanate, NH4SCN
Authors: Larsen Finn Krebs , Hasen Mamakhel Aref , Overgaard Jacob , Jørgensen Jens-Erik , Kato Kenichi , Brummerstedt Iversen Bo
Published: June 2019

Carbon nitride materials include functional materials, and their chemical diversity and complexity are becoming increasingly appreciated. Heating of NH4SCN leads to a range of new carbon nitride compounds, which have been structurally characterized by single-crystal X-ray diffraction. Heating at ambient pressure to 175°C leads to guanidinium thiocyanate, H6CN3SCN (1), and when maintaining that temperature for about 12 h a water-insoluble carbon nitride product is formed, which is a co-crystal between melamine and melamium thiocyanate, [H6C3N6]·[H10C6N11]+·[SCN]− (2). In situ powder X-ray diffraction measurements of this material reveal a gradual transformation from (2), via two intermediate products, to a final melon-like end product. The first of these forms between 350 and 400°C, and is an adduct of melam and melamium thiocyanate, [H9C6N11]·2[H10C6N11]+·2[SCN]− (3). The second forms between 400 and 480°C, and is identified as melem, 2,5,8-triamino-tri-s-triazine, H6C6N10 (4). On heating of (2) in a sealed ampoule to 600°C, various crystals were obtained and six crystal structures were determined from the batch: 1,3,5-triazine-2,4,6-triamino, H6C3N6 (5), 1,3,5-triazine-2,4-diamino, H5C3N5 (6), 1,1′,3,3′,5,5′-triazine-2,2′,4,4′-tetraamino, H8C6N10 (7), 2[H6C3N6]·[H10C6N11]+·[SCN]− (8) and 2[H6C3N6]·[H7C3N6]+·[SCN]− (9). Finally, a recrystallized decomposition product was found to be [H6C3N6]·[H7C3N6]+·[SCN]−·[H2O] (10).
Reaction of 2-[(2-aminoethyl)amino]ethanol with pyridine-2-carbaldehyde and complexation of the products with CuII and CdII along with docking studies
Authors: Mardani Zahra , Hakimi Mohammad , Moeini Keyvan , Mohr Fabian
Published: June 2019

The reaction between 2-[2-(aminoethyl)amino]ethanol and pyridine-2-carbaldehyde in a 1:2 molar ratio affords a mixture containing 2-({2-[(pyridin-2-ylmethylidene)amino]ethyl}amino)ethanol (PMAE) and 2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine (POPME). Treatment of this mixture with copper(II) chloride or cadmium(II) chloride gave trichlorido[(2-hydroxyethyl)({2-[(pyridin-2-ylmethylidene)amino]ethyl})azanium]copper(II) monohydrate, [Cu(C10H16N3O)Cl3]·H2O or [Cu(HPMAE)Cl3]·H2O, 1, and dichlorido{2-[2-(pyridin-2-yl)oxazolidin-3-yl]-N-(pyridin-2-ylmethylidene)ethanamine}cadmium(II), [CdCl2(C16H18N4O)] or [CdCl2(POPME)], 2, which were characterized by elemental analysis, FT–IR, Raman and 1H NMR spectroscopy and single-crystal X-ray diffraction. PMAE is potentially a tetradentate N3O-donor ligand but coordinates to copper here as an N2 donor. In the structure of 1, the geometry around the Cu atom is distorted square pyramidal. In 2, the Cd atom has a distorted octahedral geometry. In addition to the hydrogen bonds, there are π–π stacking interactions between the pyridine rings in the crystal packing of 1 and 2. The ability of PMAE, POPME and 1 to interact with ten selected biomolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B-DNA) was investigated by docking studies and compared with doxorubicin.
Price analysis of extra virgin olive oil
Authors: D’Adamo Idiano , Falcone Pasquale Marcello , Gastaldi Massimo
Published: June 2019

Purpose

The price of extra virgin olive oil (EVOO) is highly subjected to variability. In this way, the consumer is not able to perceive a price of reference. The purpose of this paper is to investigate this topic, trying to define a range suitable for the selling of EVOO.

Design/methodology/approach

A mathematical model is applied to the three price levels (i.e. production, intermediate and selling). It studies the relationship among main variables: purchase cost of olives, the production cost of olive oil, the yield of olives obtained by the technological process and the profit margin. To define the input data, 25 producers of olives and 25 owners of olive oil mills are involved.

Findings

The production of EVOO depends strictly on the production of olives, which typically is subdivided in a year of “high production” and in a year of “low production.” The price of EVOO is subjected to a great variability; however, it is possible to propose a range that varies from €7.0 per liter to €8.7 per liter.

Research limitations/implications

The level of acidity influences significantly the quality of olive oil, and this model has the limit to not analyze the variation of the price in function of this parameter.

Originality/value

This study is the first to propose a pricing model to evaluate EVOO. The literature section supports this assumption.
A comparative analysis of the attitudes of rural and urban consumers towards cultured meat
Authors: Shaw Elaine , Mac Con Iomaire Máirtín
Published: June 2019

Purpose

The purpose of this paper is to perform a comparative analysis on the attitudes of rural and urban Irish consumers towards cultured meat.

Design/methodology/approach

A mixed methods exploratory sequential design was used. This involved collecting qualitative data first, through group interviews, and using the results of these to design the questionnaires for the quantitative data collection, which was analysed using SPSS 24.0 ®.

Findings

Urban consumers were more receptive towards cultured meat and more concerned about the environmental impact of current meat production practices. Rural consumers were more concerned about the possible damaging effect cultured meat production could have on agri-business and the livelihood of Irish farmers. The safety of the technology emerged as the biggest concern for both sets of consumers.

Research limitations/implications

The sample size used for the qualitative research resulted in a 95% confidence level and a confidence interval of 5.55. A larger sample number would give a tighter confidence interval and a more accurate representation of consumers’ attitudes.

Practical implications

This research could give guidance to food companies of how to market cultured meat products towards Irish consumers based on their concerns and their perceived benefits of the technology.

Social implications

This research added to previous research performed in Ireland showing that urban consumers are more receptive towards new food technologies than their rural counterparts.

Originality/value

This is the first paper comparing the attitudes of rural and urban Irish consumers towards cultured meat and adds to the literature on this emerging subject area.
How and when environmental regulation induces middle managers’ proactive behavior
Authors: Bao Haixu , Wang Haizhen (Jane) , Sun Chenglin
Published: June 2019

Purpose

The purpose of this paper is to explore how middle managers respond to the career challenges caused by environmental regulation. In particular, this paper examines whether environmental regulation strength is positively related to middle managers’ openness toward change, and whether middle managers’ openness toward change is positively related to proactive behavior. Furthermore, the moderating role of top managers’ bottom-line mentality in these two relationships is examined.

Design/methodology/approach

Cross-sectional survey research (n=155) was conducted. During a training program, data were collected from 155 middle managers from a listed company that manufactures primary products. With these data the authors examined the main relationship and also explored the moderating effect of top managers’ bottom-line mentality.

Findings

Analysis of the findings indicates that perceived environmental regulation strength influences middle managers’ openness toward change and consequently their proactive behavior. In addition, top managers’ bottom-line mentality moderates both the link between environmental regulation strength and openness toward change and the link between openness toward change and proactive behavior.

Originality/value

The findings of this study reveal how environmental regulation induces middle managers’ proactive behavior, and the influence of top managers’ mentality on how middle managers respond to environmental regulation both cognitively and behaviorally.