bluuebunny/crossref_metadata_2025 huggingface dataset:
Agrin promotes coordinated therapeutic processes leading to improved cardiac repair in pigs
Authors: Baehr Andrea , Umansky Kfir Baruch , Bassat Elad , Klett Katharina , Jurisch Victoria , Bozoglu Tarik , Hornaschewitz Nadja , Solyanik Olga , Kain David , Ferrero Bartolo , Cohen-Rabi Renee , Krane Markus , Cyran Clemens , Soehnlein Oliver , Laugwitz Karl Ludwig , Hinkel Rabea , Kupatt Christian , Tzahor Eldad
Published: November 2019

Ischemic heart diseases are classified among the leading cause of death and reduced life quality worldwide. Although revascularization strategies significantly reduce mortality after acute myocardial infarction (MI), a significant number of MI patients develop chronic heart failure over time. We have recently reported that a fragment of the extra cellular matrix (ECM) protein Agrin promotes cardiac regeneration following MI in adult mice. Here, we tested the therapeutic potential of Agrin in a preclinical porcine model, comprising either 3 or 28 days (d) reperfusion period. We first demonstrate that local (antegrade) delivery of recombinant human Agrin (rhAgrin) to the infarcted pig heart can target the affected regions in an efficient and clinically-relevant manner. Single dose of rhAgrin resulted in significant improvement in heart function, infarct size, fibrosis and adverse remodeling parameters 28 days post MI. Short-term MI experiment along with complementary murine MI studies revealed myocardial protection, improved angiogenesis, inflammatory suppression and cell cycle re-entry, as Agrin’s mechanisms of action. We conclude that a single dose of Agrin is capable of reducing ischemia reperfusion injury and improving cardiac function, demonstrating that Agrin could serve as a therapy for patients with acute MI and potentially heart failure.
Binding of a tetracationicmeso-porphyrin to polyadenylic acid: a spectroscopic study
Authors: Ryazanova Olga , Voloshin Igor , Zozulya Victor
Published: November 2019

Binding of a tetracationic porphyrin (TMPyP4+) to poly(rA) has been studied in neutral buffered solution of low ionic strength in a wide range of molar phosphate-to-dye ratios (P/D) using absorption spectroscopy, polarized fluorescence and fluorimetric titration. Two competitive binding modes were identified: partial intercalation of porphyrin chromophores between adenine bases prevailing atP/D> 20 and its outside binding to poly(rA) backbone dominating atP/D< 6. Both of them were accompanied by enhancement of the porphyrin emission. Absence of the emission quenching near stoichiometricP/Dratios allowed us to assume that external binding occurs without the self-stacking of the porphyrin chromophores.
Single Cell RNA Sequencing Reveals Heterogeneity of Human MSC Chondrogenesis: Lasso Regularized Logistic Regression to Identify Gene and Regulatory Signatures
Authors: Huynh Nguyen P.T. , Kelly Natalie H. , Katz Dakota B. , Pham Minh , Guilak Farshid
Published: November 2019

Bone marrow-derived mesenchymal stem cells (MSCs) exhibit the potential to undergo chondrogenesis in vitro, forming de novo tissues with a cartilage-like extracellular matrix that is rich in glycosaminoglycan and collagen type II. However, it is now apparent that MSCs comprise an inhomogeneous population of cells, and the fate of individual subpopulations during this differentiation process is not well understood. We analyzed the trajectory of MSC differentiation during chondrogenesis using single cell RNA sequencing (scRNA-seq). Using a machine learning technique – lasso regularized logistic regression – we showed that multiple subpopulations of cells existed at all stages during MSC chondrogenesis and were better-defined by transcription factor activity rather than gene expression. Trajectory analysis indicated that subpopulations of MSCs were not intrinsically specified or restricted, but instead remained multipotent and could differentiate into three main cell types: cartilage, hypertrophic cartilage, and bone. Lasso regularized logistic regression showed several advances in scRNA-seq analysis, namely identification of a small number of highly influential genes or transcription factors for downstream validation, and cell type classification with high accuracy. Additionally, we showed that MSC differentiation trajectory may exhibit donor to donor variation, although key influential pathways were comparable between donors. Our data provide an important resource to study gene expression and to deconstruct gene regulatory networks in MSC differentiation.
Integrating the host plant phylogeny, plant traits, intraspecific competition and repeated measures using a phylogenetic mixed model of field behaviour by polyphagous herbivores, the leaf-cutting ants
Authors: Weerathunga Manasee , Mikheyev Alexander S.
Published: November 2019

Herbivores use a wide range of factors to choose their host, including their own physiological states, physical characteristics of plants, and the degree of competition. Field observations of herbivores in their native habitats provide a means for simultaneously estimating the relative importance of these factors, but statistical analysis of all these factors may be challenging. Here we used a 7-wk dataset of leaf-cutting ant (Atta cephalotes) foraging in a diverse neotropical arboretum containing 193 tree species (822 trees) to examine the relative role of tree phylogeny, territoriality and tree functional characteristics using a phylogenetic generalized least squares (PGLS) model. We observed that 54 tree species (117 trees) were foraged by the ants. This pattern was not random, but reflected known features of leaf-cutting ant foraging behaviour, such as the preference for larger trees and the decreased likelihood of foraging at the periphery of a colony’s territory. However, random effects such as tree phylogeny, the identity of individual trees and colony-specific effects, explained most of the variation in foraging data. A significant phylogenetic effect on foraging likelihood (λ = 0.28), together with repeated measures of foraging on the same tree species, allowed estimation of relative palatability for each plant species. PGLS models can be flexibly scaled to include other covariates for even more complex investigation of foraging behaviour, and the link function can be modified to include the amount of plants foraged. As a result, PGLS can be used as a flexible framework for the study of LCA foraging.
PGR5 is required for efficient Q cycle in the cytochromeb6fcomplex during cyclic electron flow
Authors: Buchert Felix , Mosebach Laura , Gäbelein Philipp , Hippler Michael
Published: November 2019

Proton Gradient Regulation 5 (PGR5) is involved in the control of photosynthetic electron transfer but its mechanistic role is not yet clear. Several models have been proposed to explain phenotypes such as a diminished steady state proton motive force (pmf) and increased photodamage of photosystem I (PSI). Playing a regulatory role in cyclic electron flow (CEF) around PSI, PGR5 contributes indirectly to PSI protection by enhancing photosynthetic control, which is a pH-dependent downregulation of electron transfer at the cytochromeb6fcomplex (b6f). Here, we re-evaluated the role of PGR5 in the green algaChlamydomonas reinhardtiiand conclude thatpgr5possesses a dysfunctionalb6f. Our data indicate that theb6flow-potential chain redox activity likely operated in two distinct modes – via the canonical Q cycle during linear electron flow and via an alternative Q cycle during CEF, attributing a ferredoxin-plastoquinone reductase activity to theb6f. The latter mode allowed efficient oxidation of the low-potential chain in the WTb6f. A switch between the two Q cycle modes was dependent of PGR5 and relied on unknown stromal electron carrier(s), which were a general requirement forb6factivity. In CEF-favouring conditions the electron transfer bottleneck inpgr5was theb6fand insufficient flexibility in the low-potential chain redox tuning might account for the mutantpmfphenotype and the secondary consequences. Models of our findings are discussed.
PRISM: Recovering cell type specific expression profiles from composite RNA-seq data
Authors: Häkkinen Antti , Zhang Kaiyang , Alkodsi Amjad , Andersson Noora , Erkan Erdogan Pekcan , Dai Jun , Kaipio Katja , Lamminen Tarja , Mansuri Naziha , Huhtinen Kaisa , Vähärautio Anna , Carpén Olli , Hynninen Johanna , Hietanen Sakari , Lehtonen Rainer , Hautaniemi Sampsa
Published: November 2019

A major challenge in analyzing cancer patient transcriptomes is that the tumors are inherently heterogeneous and evolving. We analyzed 214 bulk RNA samples of a longitudinal, prospective ovarian cancer cohort and found that the sample composition changes systematically due to chemotherapy and between the anatomical sites, preventing direct comparison of treatment-naive and treated samples. To overcome this, we developed PRISM, a latent statistical framework to simultaneously extract the sample composition and cell type specific whole-transcriptome profiles adapted to each individual sample. Our results indicate that the PRISM-derived composition-free transcriptomic profiles and signatures derived from them predict the patient response better than the composite raw bulk data. We validated our findings in independent ovarian cancer and melanoma cohorts, and verified that PRISM accurately estimates the composition and cell type specific expression through whole-genome sequencing and RNA in situ hybridization experiments. PRISM is freely available with full source code and documentation.
Reorienting Spatial Attention within Visual Working Memory
Authors: Han Sizhu , Ku Yixuan
Published: November 2019

Attention and working memory (WM) are intertwined core cognitive processes. Through four experiments with 133 participants, we dissociated the impact of two types of covert spatial attention, endogenous vs. exogenous, on visual WM. Behavioral results consistently indicated that exogenous attentional cues were more advantageous than endogenous ones in enhancing the precision of visual WM under load-2, while they equalized under load-4. In addition, physiological and neural data explained the mechanisms. Converging evidence from eye-tracking, electroencephalography, and magnetoencephalography suggested that fast attentional processing induced by exogenous cues lead to early top-down information from the dorsal lateral prefrontal cortex (DLPFC) to sensory cortices. The differential frontal activities were further correlated with the behavioral distinctions between exogenous and endogenous cues, and transcranial magnetic stimulation over DLPFC at the same time period abolished the exogenous advantage. Taken together, traditionally considered bottom-up attentional processing induced by exogenous cues rapidly engages top-down signals from the frontal cortex, which leads to stronger behavioral benefits compared with the benefits produced by endogenous cues under the low load condition.
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Authors: Patoori Sruti , Jean-Charles Nathalie , Gopal Ariana , Sulaiman Sacha , Gopal Sneha , Wang Brian , Souferi Benjamin , Emerson Mark M.
Published: November 2019

Background

The vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. These cells do not express Vsx2, but co-express the transcription factors (TFs) Onecut1 and Otx2, which bind to ThrbCRM1. The components of the gene regulatory networks that control the transition from multipotent to fate-restricted gene expression are not known. This work aims to identify and evaluate cis-regulatory elements proximal to Onecut1 to identify the gene regulatory networks involved in RPC fate-restriction.

Method

We identified regulatory elements through ATAC-seq and conservation, followed by reporter assays to screen for activity based on temporal and spatial criteria. The regulatory elements of interest were subject to deletion and mutation analysis to identify functional sequences and evaluated by quantitative flow cytometry assays. Finally, we combined the enhancer::reporter assays with candidate TF overexpression to evaluate the relationship between the TFs, the enhancers, and early vertebrate retinal development. Statistical tests included ANOVA, Kruskal-Wallis, or unpaired t-tests.

Results

Two regulatory elements, ECR9 and ECR65, were identified to be active in ThrbCRM1(+) restricted RPCs. Candidate bHLH binding sites were identified as critical sequences in both elements. Overexpression of candidate bHLH TFs revealed specific enhancer-bHLH interactions. Nhlh1 overexpression expanded ECR65 activity into the Vsx2(+) RPC population, and overexpression of NeuroD1/NeuroG2/NeuroD4 had a similar effect on ECR9. Furthermore, bHLHs that were able to activate ectopic ECR9 reporter were able to induce endogenous Otx2 expression.

Conclusions

This work reports a large-scale screen to identify spatiotemporally specific regulatory elements near the Onecut1 locus. These elements were used to identify distinct populations in the developing retina. In addition, fate-restricted regulatory elements responded differentially to bHLH factors, and suggest a role for retinal bHLHs upstream of the Otx2 and Onecut1 genes during the formation of restricted RPCs from multipotent RPCs.
An animal society based on kin competition, not kin cooperation
Authors: Vickruck Jessica L. , Richards Miriam H.
Published: November 2019

Animals respond to competition among kin for critical breeding resources in two ways: avoidance of direct fitness costs via dispersal of siblings to breed separately, and formation of kin-based societies in which subordinates offset direct fitness costs of breeding competition via altruism and increased indirect fitness. Here we provide the first evidence that kin competition can promote the evolution of societies based on non-kin cooperation. For eastern carpenter bees, nests are a critical breeding resource in perpetually short supply, leading to strong competition among females. Observations of individually marked and genotyped females demonstrate that sisters disperse from their natal nests to join social groups of nonrelatives. By forming social groups of non-kin, females increase their chances of successful reproduction, while avoiding the indirect fitness cost of competition among sisters.

One Sentence Summary

We describe the first known example of an animal society based on avoidance of kin competition rather than on promotion of kin cooperation.
Biophysical mechanism of ultrafast helical twisting contraction in the giant unicellular ciliate Spirostomum ambiguum
Authors: Xu L. X. , Bhamla M. S.
Published: November 2019

The biophysical mechanism of cytoskeletal structures has been fundamental to understanding of cellular dynamics. Here, we present a mechanism for the ultrafast contraction exhibited by the unicellular ciliateSpirostomum ambiguum. Powered by a Ca2+binding myoneme mesh architecture, Spirostomum is able to twist its two ends in the same direction and fully contract to 75% of its body length within five milliseconds, followed by a slow elongation mechanism driven by the uncoiling of the microtubules. To elucidate the principles of this rapid contraction and slow elongation cycle, we used high-speed imaging to examine the same-direction coiling of the two ends of the cell and immunofluorescence techniques to visualize and quantify the structural changes in the myoneme mesh, microtubule arrays, and the cell membrane. Lastly, we provide support for our hypotheses using a simple physical model that captures key features of Spirostomum’s ultrafast twisting contraction.

SIGNIFICANCE

Ultrafast movements are ubiquitous in nature, and some of the most fascinating ultrafast biophysical systems are found on the cellular level. Quantitative studies and models are key to understand the biophysics of these fast movements. In this work, we study Spirostomum’s ultrafast contraction by using high-speed imaging, labeling relevant cytoskeletal structures, and building a physical model to provide a biophysical mechanism especially of the helical same direction twisting of this extremely large single cell organism. Deeper understanding of how single cells can execute extreme shape changes hold potential for advancing basic cell biophysics and also inspire new cellular inspired actuators for engineering applications.
Diurnal variations in the motility of algal populations
Authors: Jin D. , Kotar J , Silvester E. , Leptos K. C. , Croze O. A.
Published: November 2019

The motility of microalgae has been studied extensively, particularly in model microorganisms such asChlamy-domonas reinhardtii. For this and other microalgal species, diurnal cycles are well-known to control the metabolism, growth and cell division. Diurnal variations, however, have been largely neglected in quantitative studies of motility. Here, we demonstrate using tracking microscopy how the motility statistics ofC. reinhardtiiare modulated by diurnal cycles. We discovered that the mean swimming speed is greater during the dark period of a diurnal cycle. From this measurement, using a hydrodynamic power balance, we conjecture that this is a result of the mean flagellar beat frequency being modulated by the flagellar ATP. Our measurements also quantify the diurnal variations of the orientational and gravitactic transport ofC. reinhardtii. We discuss the implications of our frequency results in the context of cellular bioenergetics. Further, we explore the population-level consequences of diurnal variations of motility statistics by evaluating a prediction for how the gravitactic steady state changes with time during a diurnal cycle.

SIGNIFICANCE

We report tracking microscopy measurements which demonstrate that the mean swimming speed ofC. reinhardtiiis significantly greater during the dark period of a diurnal cycle. Using hydrodynamic (low Reynolds number) power balance, we also inferred the mean flagellar beat frequency from the swimming speed, hypothesising that the observed variations in this frequency correlate with the diurnal regulation of flagellar ATP. Diurnal variations of the orientational and gravitactic transport ofC. reinhardtiiwere also quantified and used in a continuum model to predict that, at the population scale, the steady state vertical distribution ofC. reinhardtiiis broader during the dark period. Our findings could have significant implications for microalgal biotechnologies, e.g. microalgal harvesting, and plankton migration in the ocean.
Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA-binding, and long term behavioral consequences
Authors: Kopp Nathan D. , Nygaard Kayla R. , McCullough Katherine B. , Maloney Susan E. , Gabel Harrison W. , Dougherty Joseph D.
Published: November 2019

Gtf2ird1 and Gtf2i may mediate aspects of the cognitive and behavioral phenotypes of Williams Syndrome (WS) – a microdeletion syndrome encompassing these transcription factors (TFs). Knockout mouse models of each TF show behavioral phenotypes. Here we identify their genomic binding sites in the developing brain, and test for additive effects of their mutation on transcription and behavior. Both TFs target constrained chromatin modifier and synaptic protein genes, including a significant number of ASD genes. They bind promoters, strongly overlap CTCF binding and TAD boundaries, and moderately overlap each other, suggesting epistatic effects. We used single and double mutants to test whether mutating both TFs will modify transcriptional and behavioral phenotypes of single Gtf2ird1 mutants. Despite little difference in DNA-binding and transcriptome-wide expression, Gtf2ird1 mutation caused balance, marble burying, and conditioned fear phenotypes. However, mutating Gtf2i in addition to Gtf2ird1 did not further modify transcriptomic or most behavioral phenotypes, suggesting Gtf2ird1 mutation alone is sufficient.
Independent evolution of lateral inhibition mechanisms in different lineages of land plants: MpFEW RHIZOIDS1 miRNA-mediated lateral inhibition controls rhizoid cell patterning in Marchantia polymorpha
Authors: Thamm Anna , Saunders Timothy E , Dolan Liam
Published: November 2019

Lateral inhibition patterns differentiated cells during development in bacteria, metazoans and land plants. Tip-growing rhizoid cells develop among flat epidermal cells in the epidermis of the early diverging land plant Marchantia polymorpha. We show that the majority of rhizoid cells develop individually but some develop in linear, one-dimensional clusters of between two and seven rhizoid cells in wild type plants. The distribution of rhizoid cells can be accounted for within a simple model of lateral inhibition. The model also predicted that, in the absence of lateral inhibition, rhizoid cell clusters would be two-dimensional with larger clusters than those formed with lateral inhibition. Rhizoid differentiation in Marchantia polymorpha is positively regulated by the ROOT HAIR DEFECTIVE SIX-LIKE1 (MpRSL1) basic Helix Loop Helix (bHLH) transcription factor which is directly repressed by the FEW RHIZOIDS1 (MpFRH1) miRNA. To test if MpFRH1 miRNA acts during lateral inhibition we generated loss-of-function mutants that did not produce the MpFRH1 miRNA. Two-dimensional clusters of rhizoids develop in Mpfrh1loss-of-function (lof) mutants as predicted by the model for plants that lack lateral inhibition. Furthermore, clusters of up to nine rhizoid cells developed in the Mpfrh1lof mutants compared to a maximum number of seven observed in wild type. The higher steady state levels of MpRSL1 mRNA in Mpfrh1lof mutants indicate that MpFRH1-mediated lateral inhibition involves the repression of MpRSL1 activity. Together the modelling and genetic data indicate that the pattern of cell differentiation in the M. polymorpha epidermis is consistent with a lateral inhibition process in which MpFRH1 miRNA represses MpRSL1. This discovery suggests that novel mechanisms of lateral inhibition may operate in different lineages of land plants, unlike metazoans where the conserved Delta-Notch signaling system controls lateral inhibition in diverse metazoan lineages.
pepFunk, a tool for peptide-centric functional analysis in metaproteomic human gut microbiome studies
Authors: Simopoulos Caitlin M.A. , Ning Zhibin , Zhang Xu , Li Leyuan , Walker Krystal , Lavallée-Adam Mathieu , Figeys Daniel
Published: November 2019

Enzymatic digestion of proteins before mass spectrometry analysis is a key process in metaproteomic workflows. Canonical metaproteomic data processing pipelines typically involve matching spectra produced by the mass spectrometer to a theoretical spectra database, followed by matching the identified peptides back to parent proteins. However, the nature of enzymatic digestion produces peptides that can be found in multiple proteins due to conservation or chance, presenting difficulties with protein and functional assignment. To combat this challenge, we developed a peptide-centric metaproteomic workflow focused on the analysis of human gut microbiome samples. Our workflow includes a curated peptide database annotated with KEGG terms and a pathway enrichment analysis adapted for peptide level data. Analysis using our peptide-centric workflow is fast and identifies more enriched KEGG pathways than protein-centric analysis. Our workflow is open source and available as a web application or source code to be run locally.
Bax and Bak jointly control survival and dampen the early unfolded protein response in pancreatic β-cells under glucolipotoxic stress
Authors: White Sarah A. , Zhang Lisa , Yang Yu Hsuan Carol , Luciani Dan S.
Published: November 2019

ER stress and apoptosis contribute to the loss of pancreatic β-cells under the pro-diabetic conditions of glucolipotoxicity. Although activation of the canonical pathway of intrinsic apoptosis is known to require Bax and Bak, their individual and combined involvement in glucolipotoxic β-cell death have not been demonstrated. It has also remained an open question if Bax and Bak in β-cells have non-apoptotic roles in mitochondrial function and ER stress signaling, as suggested in other cell types. Using mice with individual or combined β-cell deletion of Bax and Bak, we demonstrated that glucolipotoxic β-cell deathin vitrohappens in sequential stages; first via non-apoptotic mechanisms and later by apoptosis, which Bax and Bak were redundant in triggering. In contrast, they had non-redundant roles in mediating staurosporine-induced β-cell apoptosis. We further established that Bax and Bak do not affect normal glucose-stimulated β-cell Ca2+responses, insulin secretion, orin vivoglucose tolerance. Finally, our experiments revealed that Bax and Bak together dampen the unfolded protein response in β-cells during the early stages of chemical- or glucolipotoxicity-induced ER stress. These findings identify novel roles of the canonical apoptosis machinery in modulating stress signals that are important for the pathobiology of β-cells in diabetes.
High-Resolution 3D Fluorescent Imaging of Intact Tissues
Authors: El-Nachef Danny , Martinson Amy M. , Yang Xiulan , Murry Charles E. , MacLellan W. Robb
Published: November 2019

Histological analysis of fluorescently labeled tissues has been a critical tool to understand molecular organization in situ. However, assessing molecular structures within large cells and in the context of human organ anatomy has been challenging because it requires penetration of staining reagents and light deep into opaque tissues, while also conforming to the spatial constraints of high-resolution objective lenses. This methodology article describes optimized sample preparation for sub-micron resolution 3D imaging in human and rodent tissues, yielding imaging depth (>100 µm) and resolution (<0.012 µm3 voxel size) that has previously been limited to whole-mount in vitro organoid systems, embryos, and small model organisms. Confocal images of adult human and rodent organs, including heart, kidney, and liver, were generated for several chemical and antibody stains in cleared tissue sections >100 µm thick. This method can be readily adopted by any lab performing routine histology and takes 3 days from the start of tissue preparation to 3D images.
The impact of global selection on local adaptation and reproductive isolation
Authors: Bisschop Gertjan , Setter Derek , Rafajlović Marina , Baird Stuart J.E. , Lohse Konrad
Published: November 2019

Despite the homogenising effect of strong gene flow between two populations, adaptation under symmetric divergent selection pressures results in partial reproductive isolation: adaptive substitutions act as local barriers to gene flow, and if divergent selection continues unimpeded, this will result in complete reproductive isolation of the two populations, i.e. speciation. However, a key issue in framing the process of speciation as a tension between local adaptation and the homogenising force of gene flow is that the mutation process is blind to changes in the environment and therefore tends to limit adaptation. Here we investigate how globally beneficial mutations (GBMs) affect divergent local adaptation and reproductive isolation. When phenotypic divergence is finite, we show that the presence of GBMs limits local adaptation, generating a persistent genetic load at the loci which contribute to the trait under divergent selection and reducing genome-wide divergence. Furthermore, we show that while GBMs cannot prohibit the process of continuous differentiation, they induce a substantial delay in the genome-wide shutdown of gene flow.
The breast cancer oncogene IKKε coordinates mitochondrial function and serine metabolism
Authors: Xu Ruoyan , Jones William , Wilcz-Villega Ewa , Costa A. Sofia H. , Rajeeve Vinothini , Bentham Robert B. , Bryson Kevin , Nagano Ai , Yaman Busra , Barasa Sheila Olendo , Wang Yewei , Chelala Claude , Cutillas Pedro , Szabadkai Gyorgy , Frezza Christian , Bianchi Katiuscia
Published: November 2019

The IκB kinase ε (IKKε) is a key molecule at the crossroads of inflammation and cancer. Known for its role as an activator of NFκB and IRF3 signalling leading to cytokine secretion, the kinase is also a breast cancer oncogene, overexpressed in a variety of tumours. However, to what extent IKKε remodels cellular metabolism is currently unknown. Here we used a combination of metabolomics and phosphoproteomics to show that IKKε orchestrates a complex metabolic reprogramming that affects mitochondrial metabolism and serine biosynthesis. Acting independently of its canonical signalling role, IKKε upregulates the serine biosynthesis pathway (SBP) mainly by limiting glucose and pyruvate derived anaplerosis of the TCA cycle. In turn, this elicits activation of the transcription factor ATF4 and upregulation of the SBP genes. Importantly, pharmacological inhibition of the IKKε-induced metabolic phenotype reduces proliferation of breast cancer cells. Finally, we show that in a set of basal ER negative and highly proliferative human breast cancer tumours, IKKε and PSAT1 expression levels are positively correlated corroborating the link between IKKε and the SBP in the clinical context.
VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences
Authors: Kieft Kristopher , Zhou Zhichao , Anantharaman Karthik
Published: November 2019

Background

Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes.

Design

Here we present VIBRANT, the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of virome function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a novel v-score metric that circumvents traditional boundaries to maximize identification of lytic viral genomes and integrated proviruses, including highly diverse viruses. VIBRANT highlights viral auxiliary metabolic genes and metabolic pathways, thereby serving as a user-friendly platform for evaluating virome function. VIBRANT was trained and validated on reference virus datasets as well as microbiome and virome data.

Results

VIBRANT showed superior performance in recovering higher quality viruses and concurrently reduced the false identification of non-viral genome fragments in comparison to other virus identification programs, specifically VirSorter and VirFinder. When applied to 120,834 metagenomically derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94.5% of the viruses, whereas VirFinder and VirSorter achieved less powerful performance, averaging 48.1% and 56.0%, respectively. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER and Prophage Hunter for the ability to extract integrated provirus regions from host scaffolds, VIBRANT performed comparably and even identified proviruses that the other programs did not. To demonstrate applications of VIBRANT, we studied viromes associated with Crohn’s Disease to show that specific viral groups, namely Enterobacteriales-like viruses, as well as putative dysbiosis associated viral proteins are more abundant compared to healthy individuals, providing a possible viral link to maintenance of diseased states.

Conclusions

The ability to accurately recover viruses and explore viral impacts on microbial community metabolism will greatly advance our understanding of microbiomes, host-microbe interactions and ecosystem dynamics.
Inferring parameters of the distribution of fitness effects of new mutations when beneficial mutations are strongly advantageous and rare
Authors: Booker Tom R.
Published: November 2019

Characterising the distribution of fitness effects (DFE) for new mutations is central in evolutionary genetics. Analysis of molecular data under the McDonald-Kreitman test has suggested that adaptive substitutions make a substantial contribution to between-species divergence. Methods have been proposed to estimate the parameters of the distribution of fitness effects for positively selected mutations from the unfolded site frequency spectrum (uSFS). However, when beneficial mutations are strongly selected and rare, they may make little contribution to standing variation and will thus be difficult to detect from the uSFS. In this study, I analyse uSFS data from simulated populations subject to advantageous mutations with effects on fitness ranging from mildly to strongly beneficial. When advantageous mutations are strongly selected and rare, there are very few segregating in populations at any one time. Fitting the uSFS in such cases leads to underestimates of the strength of positive selection and may lead researchers to false conclusions regarding the relative contribution adaptive mutations make to molecular evolution. Fortunately, the parameters for the distribution of fitness effects for harmful mutations are estimated with high accuracy and precision. The results from this study suggest that the parameters of positively selected mutations obtained by analysis of the uSFS should be treated with caution and that variability at linked sites should be used in conjunction with standing variability to estimate parameters of the distribution of fitness effects in the future.
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription
Authors: Li Lingting , Molodtsov Vadim , Lin Wei , Ebright Richard H. , Zhang Yu
Published: November 2019

All organisms--bacteria, archaea, and eukaryotes--have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription-initiation-factor structural module pre-organizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription-initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate, and define details of, stepwise, RNA-extension-driven displacement of the “σ finger” of the bacterial transcription initiation factor σ. The structures reveal that--for both the primary σ factor and extracytoplasmic (ECF) σ factors, and for both 5’-triphosphate RNA and 5’-hydroxy RNA--the “σ finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5’-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.

SIGNIFICANCE STATEMENT

The “σ finger” of the bacterial initiation factor σ binds within the RNA polymerase active-center cleft and blocks the path of nascent RNA. It has been hypothesized that the σ finger must be displaced during initial transcription. By determining crystal structures defining successive steps in initial transcription, we demonstrate that the σ finger is displaced in stepwise fashion, driven by collision with the RNA 5’-end, as nascent RNA is extended from ∼5 nt to ∼10 nt during initial transcription, and we show that this is true for both the primary σ factor and alternate σ factors. Stepwise displacement of the σ finger can be conceptualized as stepwise compression of a “protein spring” that stores energy for subsequent breakage of protein-DNA and protein-protein interactions in promoter escape.
Sub-2 Å Resolution Structure Determination Using Single-Particle Cryo-EM at 200 keV
Authors: Wu Mengyu , Lander Gabriel C. , Herzik Mark A.
Published: November 2019

Although the advent of direct electron detectors (DEDs) and software developments have enabled the routine use of single-particle cryogenic electron microscopy (cryo-EM) for structure determination of well-behaved specimens to high-resolution, there nonetheless remains a discrepancy between the resolutions attained for biological specimens and the information limits of modern transmission electron microscopes (TEMs). Instruments operating at 300 kV equipped with DEDs are the current paradigm for high-resolution single-particle cryo-EM, while 200 kV TEMs remain comparatively underutilized for purposes beyond sample screening. Here, we expand upon our prior work and demonstrate that one such 200 kV microscope, the Talos Arctica, equipped with a K2 DED is capable of determining structures of macromolecules to as high as ∼1.7 Å resolution. At this resolution, ordered water molecules are readily assigned and holes in aromatic residues can be clearly distinguished in the reconstructions. This work emphasizes the utility of 200 keV for high-resolution single-particle cryo-EM and applications such as structure-based drug design.
TESTT Space: groundwork and experiment in a complex arts organisation
Authors: Hudson Martyn , Donkin Hazel
Published: November 2019

Purpose

The purpose of this paper is to document and describe an omni-disciplinary ethnography of a complex arts and cultural regeneration organisation in Durham (TESTT Space). The organization and its art spaces are hybrid combination tools explicitly designed to test and experiment with ideas, social forms, human interactions and arts practice. Its ground or practice is a repurposed meanwhile space in a city centre embedded in a unique cultural landscape of local communities, a University and a World Heritage Site. The research attempted to understand its groundwork, its interactions and its civic mission and aspirations in a time of radical change and rupture.

Design/methodology/approach

The authors assumed an ethnographic approach, working with and within this organisation for a year, thinking of the research as embedded, intimate research and committed to social change. It was a work of co-production – working with studio-holders, curators, artists and facilitators using a range of triangulated qualitative research methods. These include structured interviews, auto-ethnography, ethnography of spaces, arts-led research, art as research and research as art.

Findings

TESTT Space has allowed both the retention of artists in the city and the propulsion of artists into the world. It has offered different ways of engaging in the complex lives of artists and curators, allowing them to test aesthetics and try out new social models. It has thought up its own network as a thinking practice, has developed its own politics, civics and imagined a set of new futures.

Originality/value

The paper documents interactions and aspirations, describing the lived phenomenological experience of being in this experimental space.
Does IPO prospectus in Malaysia disclose relevant risk?
Authors: Ng Sin Huei , Lee Chen Suen
Published: November 2019

Purpose

The study intends to shed lights on whether the risk factors disclosed in the initial public offering (IPO) prospectus in Malaysia are able to reflect the actual risks of stocks once they are traded on the exchange. In other words, the purpose of this paper is to explore whether prospective investors will be able to benefit, in terms of the more accurate risk information, from the risk disclosures in the IPO-prospectus.

Design/methodology/approach

Using data obtained from 118 IPO prospectuses of Malaysian companies that issued shares on Bursa Malaysia in the period from 2009 to 2016, the authors investigated whether the “risk factor” section in the IPO prospectuses provides sufficient risk-relevant information to investors. To determine whether companies disclose risk-relevant information, a detailed content analysis of the risk sections was carried out to obtain an aggregate measure of risk disclosure.

Findings

The findings revealed that the aggregate measures of risk extracted from these texts did not successfully predict the following outcomes: the volatility of companies’ future stock prices, the sensitivity of future stock prices to market-wide fluctuations and the severe declines in future stock prices.

Practical implications

As indicated by the findings, the authors, therefore, deduce that the IPO prospectuses of Malaysian companies do not provide sufficient risk-relevant information in the risk factor section. The findings imply that overall the management of Malaysian companies would neither be able nor willing to disclose the right and relevant information to the public via IPO prospectus.

Originality/value

Many corporate risk disclosure studies focus primarily on the disclosures of annual reports of companies. The study intends to fill the gap by focusing on the risk disclosure in the IPO-prospectus. Risk disclosures in IPO-prospectus are farmore extensive than annual reports and, therefore, provide a richness of information that will not be available in the annual reports.
Unfair milk prices? Lessons from a split-sample choice experiment
Authors: Höhler Julia , Schreiner Julia A.
Published: November 2019

Purpose

In times of “milk price crises”, “fair” milk prices are repeatedly demanded. Various studies indicate an increased willingness to pay (WTP) for the additional attribute of price fairness. Nevertheless, market shares have been low so far. The purpose of this paper is to discuss three possible reasons for this: low reference prices, socially desirable responses in choice experiments and the lack of justification of the claim “fair” by further attributes.

Design/methodology/approach

In a split sample, one group facing alternatives with a higher price range and the other with a lower price range, the consumer’s choices are examined. This study uses a social desirability scale for controlling biases in the stated WTP. In addition, the claim “fair” is complemented with a guaranteed price, grazing, regional production and CO2-reduction. A random parameter logit model specified in WTP space is employed to estimate milk consumers’ (n=480) preferences for “fair” milk. Furthermore, a latent class approach reveals information about the source of preference heterogeneity for fair milk attributes among the two groups of the split sample.

Findings

This study finds statistically significant differences between the two price ranges. In the low price range, additional attributes can trigger an additional WTP. In the high price range, there is no statistically significant additional WTP. WTP’s dependence on price levels could explain why the market share for “fair” milk has so far been low.

Originality/value

This paper contributes to the study of the effect of split samples in choice experiments. In addition, it promotes the understanding of price fairness in milk and its determinants.
The impact of corporate social responsibility on firms’ financial performance, evidence from the food and beverage industry
Authors: Nirino Niccolò , Miglietta Nicola , Salvi Antonio
Published: November 2019

Purpose

The purpose of this paper is to investigate the impact of corporate social responsibility (CSR) on firms’ financial performance (FP) in the food and beverage (F&B) sector.

Design/methodology/approach

The authors developed a conceptual model that hypothesizes a positive effect of CSR governance on CSR outcomes (environmental and social) and these on firm’s FP. Gathering data from 190 F&B companies, the authors empirically tested the validity of the model through an ordinary least squares regression analysis.

Findings

The findings highlight the positive impact of CSR governance on environmental and social outcomes, showing real societal concerns among companies’ stakeholders in the F&B industry. Studies on the effect of CSR outcomes on FP have shown mixed results. On one side, the social outcomes positively impact a firm’s performance; on the other side, environmental outcomes show insignificant or non-positive effects depending on different measurements of FP.

Originality/value

Despite the mixed set of results between CSR and a firm’s performance in the literature, this research provides a new framework in which the impact of CSR on FP is analysed through the effectiveness of CSR governance on CSR outcomes (social and environmental). Moreover, this study contributes to the CSR literature understanding the impact of both environment and social concerns by companies on firm’s FP in F&B context.
Behavior-based pricing between organic and general food enterprises
Authors: Liu Kanying , Lan Yong , Li Wei
Published: November 2019

Purpose

The pursuit of healthy and high-quality organic food has gradually become a trend. However, some researchers do not believe that the quality of organic food is higher than general food. Consumers’ changed preference for different quality food will also affect the sales strategy of food producer. The purpose of this paper is to consider behavior-based pricing (BBP) and decision-making problems between organic and general food enterprises, based on consumers’ heterogeneity.

Design/methodology/approach

In this study, two different types of consumers are considered: consumers without preference difference and consumers with an organic food preference. This paper sets up two two-stage hoteling differential pricing models in the duopoly market, including organic and general food enterprises. Then, the optimal loyal price and poaching price of the two types of enterprises are solved, and the influence of each parameter on the pricing, market and profit of the two enterprises is analyzed.

Findings

This paper finds that, with the increase of the initial market share, the pricing strategies of organic food enterprises change from a loyal price lower than the poaching price to a loyal price higher than the poaching price, whereas the general food producer has the opposite pricing strategy. Furthermore, the difference in consumption utility between the two food types has a positive influence on the price of organic food, and a negative influence on the price of general food. In contrast, the consumer share without preference difference has a negative effect on organic food prices and a positive impact on the price of general food.

Originality/value

The contribution is constructive as no prior research has focused on the BBP and decision-making problems between organic and general food, and it considers the two types of consumers. Besides, the results also provide guidelines for choosing marketing strategies for organic and general food enterprises.