bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diurnal variations in the motility of algal populations
Authors: Jin D. , Kotar J , Silvester E. , Leptos K. C. , Croze O. A. 
Published: November 2019

ABSTRACTThe 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.SIGNIFICANCEWe 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

AbstractGtf2ird1 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

ABSTRACTLateral 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

AbstractEnzymatic 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

ABSTRACTER 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

AbstractHistological 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

AbstractDespite 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

ABSTRACTThe 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

AbstractBackgroundViruses 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.DesignHere 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.ResultsVIBRANT 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.ConclusionsThe 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

AbstractCharacterising 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

ABSTRACTAll 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 STATEMENTThe “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

AbstractAlthough 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.