bluuebunny/crossref_metadata_2025 huggingface dataset:
Type-1 IFN primed monocytes in pathogenesis of idiopathic pulmonary fibrosis
Authors: Fraser Emily , Denney Laura , Blirando Karl , Vuppusetty Chaitanya , Antanaviciute Agne , Zheng Yuejuan , Repapi Emmanouela , Iotchkova Valentina , Taylor Stephen , Ashley Neil , St Noble Victoria , Benamore Rachel , Hoyles Rachel , Clelland Colin , Rastrick Joseph M D , Hardman Clare S , Alham Nasullah K , Rigby Rachel E , Rehwinkel Jan , Ho Ling-Pei
Published: January 2020

Idiopathic pulmonary fibrosis (IPF) is the most severe form of lung fibrosis. It is progressive, and has an extremely poor outcome and limited treatment options. The disease exclusively affects the lungs, and thus less attention has been focused on blood-borne immune cells. which could be a more effective therapeutic target than lung-based cells. Here, we questioned if circulating monocytes, which has been shown to be increased in IPF, bore abnormalities that might contribute to its pathogenesis. We found that levels of circulating monocytes correlated directly with the extent of fibrosis in the lungs, and increased further during acute clinical deterioration. Monocytes in IPF were phenotypically distinct, displaying increased expression of CD64, a type 1 IFN gene expression signature and a greater magnitude of type 1 IFN response when stimulated. These abnormalities were accompanied by markedly raised CSF-1 levels in the serum, prolonged survival of monocytesex vivo, and increased numbers of monocytes in lung tissue. Our study defines the key monocytic abnormalities in IPF, proposing type 1 IFN-primed monocytes as a potential driver of an aberrant repair response and fibrosis. It provides a rationale for targeting monocytes and identifies monocytic CD64 as a potential specific therapeutic target for IPF.
Multiplex genetic engineering exploiting pyrimidine salvage pathway-based self-encoded selectable markers
Authors: Birštonas Lukas , Dallemulle Alex , López-Berges Manuel S. , Jacobsen Ilse D. , Offterdinger Martin , Abt Beate , Straßburger Maria , Bauer Ingo , Schmidt Oliver , Sarg Bettina , Lindner Herbert , Haas Hubertus , Gsaller Fabio
Published: January 2020

Selectable markers are indispensable for genetic engineering, yet their number and variety is limited. Most selection procedures for prototrophic cells rely on the introduction of antibiotic resistance genes. New minimally invasive tools are needed to facilitate sophisticated genetic manipulations. Here, we characterized three endogenous genes in the human fungal pathogenAspergillus fumigatusfor their potential as markers for targeted genomic insertions of DNAs-of-interest (DOIs). Since these genes are involved in uptake and metabolization of pyrimidines, resistance to the toxic effects of prodrugs 5-fluorocytosine and 5-fluorouracil can be used to select successfully integrated DOIs. We show that DOI integration, resulting in the inactivation of these genes, caused no adverse effects with respect to nutrient requirements, growth or virulence. Beside the individual use of markers for site-directed integration of reporter cassettes including the 17-kb penicillin biosynthetic cluster, we demonstrate their sequential use inserting three fluorescent protein encoding genes into a single strain for simultaneous multicolor localization microscopy. In addition toA. fumigatus, we validated the applicability of this novel toolbox inPenicillium chrysogenumandFusarium oxysporum.

Enabling multiple targeted insertions of DOIs without the necessity for exogenous markers, this technology has the potential to significantly advance genetic engineering.
Serum α-Klotho levels correlate with episodic memory changes related to cardiovascular exercise in older adults
Authors: Becke Andreas , Maass Anne , Kreutz Michael R. , Duezel Emrah
Published: January 2020

Aerobic exercise is a potential life-style intervention to delay cognitive decline and neurodegeneration. Elevated serum levels of the anti-aging protein α-Klotho (αKL) are a potential mediating factor of exercise benefits on cognition. Here, we examined in older adults how exercise-related changes of αKL levels in serum relate to changes in cerebral blood flow (CBF), hippocampal volumes and episodic memory. We analyzed data from a previously published intervention study in which forty cognitively healthy subjects were pseudo-randomly assigned to either a cardiovascular exercise group (treadmill training, n=21) or control group (indoor progressive-muscle relaxation/stretching, n=19). 3-Tesla gadolinium perfusion imaging was used to track hippocampal CBF changes and high resolution 7-Tesla-T1-images were used to track hippocampal volume changes. Changes in episodic memory performance were measured using the complex figure test (CFT). Longitudinal changes were compared between groups and analyzed with a multiple linear regression approach. CFT and hippocampal volume changes significantly predicted changes in serum αKL levels. For CFT, this effect was found in the exercise but not the control group. Collectively the data suggest that αKL level increases induced by exercise can be associated with improved hippocampal function in older adults.
Early life stress causes persistent impacts on the microbiome of Atlantic salmon
Authors: Webster Tamsyn M. Uren , Consuegra Sofia , de Leaniz Carlos Garcia
Published: January 2020

Intensively farmed fish are commonly stressed, often leading to immune impairment and increased susceptibility to disease. Microbial communities associated with the gut and skin are vital to host immune function, but little is known about how stress affects the fish microbiome, especially during the sensitive early life stages. We compared the effects of two aquaculture-relevant stressors on the gut and skin microbiome of Atlantic salmon fry: an acute cold stress during late embryogenesis, and a chronic environmental stress during the larval stage. Acute cold stress had a lasting effect on the structure of both the gut and the skin microbiome, likely due to disruption of the egg shell microbial communities which seed the initial colonisation of the teleost microbiome upon hatching. In contrast, chronic post hatch stress altered the structure of the gut microbiome, but not that of the skin. Both types of stressors promoted similar Gammaproteobacteria ASVs, particularly within the generaAcinetobacterandAeromonaswhich include several important fish pathogens and, in the gut, reduced the abundance of Lactobacillales. This suggests that there may be common signatures of stress in the salmon microbiome, which may represent useful stress biomarkers in aquaculture.
Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps
Authors: Kopperud Bjørn Tore , Lidgard Scott , Liow Lee Hsiang
Published: January 2020

We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences [TMO]) in an automated procedure. We compare these results with data from the Ocean Biogeographic Information System (OBIS). Using OBIS and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined OBIS and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for cheilostomes for the first time, with peaks in the temperate zones. 79% of the georeferenced species we retrieved from TMO (N = 1780) and OBIS (N = 2453) are non-overlapping and underestimate known species richness, even in combination. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that latitudinal species richness patterns deviate from the canonical LDG. Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.
Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
Authors: Morales-Hojas Ramiro , Sun Jingxuan , Iraizoz Fernando Alvira , Tan Xiaoling , Chen Julian
Published: January 2020

Genetic diversity of populations has important ecological and evolutionary consequences, which are fundamental to improve the sustainability of agricultural production. Studies of how differences in agricultural management and environment influence the population structure of insect pests are fundamental to predict outbreaks and optimise control programmes. Here, we have studied the population genetic diversity and evolution ofSitobion avenaeandSitobion miscanthi(previously mistaken forS. avenae), which are among the most relevant aphid pests of cereals across Europe and China, respectively. We have used a genomic approach that allows the identification of weak geographic structure and migration patterns at scales that were previously not discernible. In the present study, we show that the population structure in present day populations are different from that described in previous studies, which suggests that they have evolved recently possibly as a response to human-induced changes in agriculture. In the UK,S. avenaeis predominantly anholocyclic and, as a result of the evolution of insecticide resistance, a superclone is now dominant across the geographic distribution in the country and the genetic diversity is low. In China,S. miscanthipopulations are mostly holocyclic, with one sexual stage in autumn to produce overwintering eggs, and there are six genetically differentiated subpopulations and high genetic differentiation between geographic locations, which suggests that further taxonomical research is needed. Unlike in the case ofS. avenaein England, there is no evidence for insecticide resistance and there is no predominance of a single lineage inS. miscanthiin China.
Fear conditioning prompts sparser representations of conditioned threat in primary visual cortex
Authors: Yin Siyang , Bo Ke , Liu Yuelu , Thigpen Nina , Keil Andreas , Ding Mingzhou
Published: January 2020

Repeated exposure to threatening stimuli alters sensory responses. We investigated the underlying neural mechanism by recording simultaneous EEG-fMRI from human participants viewing oriented gratings during Pavlovian fear conditioning. In acquisition, one grating (the CS+) was paired with a noxious noise, the unconditioned stimulus (US). The other grating (CS-) was never paired with US. In habituation, which preceded acquisition, and in final extinction, the same two gratings were presented without the US. Using fMRI-BOLD multivoxel patterns in primary visual cortex during habituation as reference, we found that during acquisition, aversive learning selectively prompted systematic changes in multivoxel patterns evoked by the CS+. Specifically, CS+ evoked voxel patterns in V1 became sparser as aversive learning progressed, and the sparse pattern was preserved in extinction. Concomitant with the voxel pattern changes, occipital alpha oscillations were increasingly more desynchronized during CS+ (but not CS-) trials. Across acquisition trials, the rate of change in CS+-related alpha desynchronization was correlated with the rate of change in multivoxel pattern representations of the CS+. Furthermore, alpha oscillations co-varied with BOLD in the right temporal-parietal junction, but not with BOLD in the amygdala. Thus, fear conditioning prompts persistent sparsification of threat cue representations, likely mediated by attention-related mechanisms.
Quantitative genetics of temperature performance curves ofNeurospora crassa
Authors: Moghadam Neda N. , Sidhu Karendeep , Summanen Pauliina A. M. , Ketola Tarmo , Kronholm Ilkka
Published: January 2020

Earth’s temperature is increasing due to anthropogenic CO2emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organism’s physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation to higher temperatures, therefore we studied the quantitative genetics of growth rates in different temperatures that make up the thermal performance curve of the fungal model systemNeurospora crassa. We studied the amount of genetic variation for thermal performance curves and examined possible genetic constraints by estimating theG-matrix. We observed a substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions, we did not find strong evidence for genetic trade-offs for growth between hotter and colder temperatures. We also simulated short term evolution of thermal performance curves ofN. crassa, and suggest that they can have versatile responses to selection.
Bumblebee worker body size affects new worker production in different resource environments
Authors: Kerr Natalie Z. , Malfi Rosemary L. , Williams Neal M. , Crone Elizabeth E.
Published: January 2020

Behavior and organization of social groups is thought to be vital to the functioning of societies, yet the contributions of various roles within social groups have been difficult to quantify. A common approach to quantifying these role-based contributions is evaluating the performance of individuals at conducting certain roles, these studies ignore how these performances might scale up to effects at the population-level. Manipulative experiments are another common approach to determine population-level effects, but they often ignore potential feedbacks associated with these various roles.

Here, we evaluate the effects of worker size distribution in bumblebee colonies on worker production, using functional linear models. Functional linear models are a recent correlative technique that has been used to assess lag effects of environmental drivers on plant performance. We demonstrate potential applications of this technique to explore contributions of social animals to ecological phenomenon.

We found that the worker size distribution differentially affected new worker production across three resource environments. Specifically, more larger workers had mostly positive effects and more smaller workers had negative effects on worker production. Most of these effects were only detected under low or fluctuating resource environments suggesting that the advantage of colonies with larger-bodied workers becomes more apparent under stressful conditions.

We demonstrate the wider ecological application of functional linear models. We highlight the advantages and limitations when considering these models, and how they are a valuable complement to many of these performance-based and manipulative experiments.
Hierarchical complexity of the macro-scale neonatal brain
Authors: Blesa Manuel , Galdi Paola , Cox Simon R. , Sullivan Gemma , Stoye David Q. , Lamb Gillian J. , Quigley Alan J. , Thrippleton Michael J. , Escudero Javier , Bastin Mark E. , Smith Keith M. , Boardman James P.
Published: January 2020

The human adult structural connectome has a rich nodal hierarchy, with highly diverse connectivity patterns aligned to the diverse range of functional specializations in the brain. The emergence of this hierarchical complexity in human development is unknown. Here, we substantiate the hierarchical tiers and hierarchical complexity of brain networks in the newborn period; assess correspondences with hierarchical complexity in adulthood; and investigate the effect of preterm birth, a leading cause of atypical brain development and later neurocognitive impairment, on hierarchical complexity. We report that neonatal and adult structural connectomes are both composed of distinct hierarchical tiers, and that hierarchical complexity is greater in term born neonates than in preterms. This is due to diversity of connectivity patterns of regions within the intermediate tiers, which consist of regions that underlie sensorimotor processing and its integration with cognitive information. For neonates and adults, the highest tier (hub regions) is ordered, rather than complex, with more homogeneous connectivity patterns in structural hubs. This suggests that the brain develops first a more rigid structure in hub regions allowing for the development of greater and more diverse functional specialization in lower level regions, while connectivity underpinning this diversity is dysmature in infants born preterm.
Isolation and complete genome sequencing of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamilyAutographivirinae
Authors: Pedersen Julie Stenberg , Carstens Alexander Byth , Djurhuus Amaru Miranda , Kot Witold , Hansen Lars Hestbjerg
Published: January 2020

Pectobacterium carotovorumis the causative agent of bacterial soft rot on various plant species. The use of phages for plant disease control have gained increased awareness over the past years. We here describe the isolation and characterization of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamilyAutographivirinae. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames (ORFs). Gene synteny and products seem to be somewhat conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the subfamilyAutographivirinae.We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the subfamilyAutographivirinae.
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus
Authors: Ma Jingwei , Do Myan , Le Gros Mark. A. , Peskin Charles S. , Larabell Carolyn A. , Mori Yoichiro , Isaacson Samuel A.
Published: January 2020

For a chemical signal to propagate across a cell, it must navigate a tortuous environment involving a variety of organelle barriers. In this work we study mathematical models for a basic chemical signal, the arrival times at the nuclear membrane of proteins that are activated at the cell membrane and diffuse throughout the cytosol. Organelle surfaces within human B cells are reconstructed from soft X-ray tomographic images, and modeled as reflecting barriers to the molecules’ diffusion. We show that signal inactivation sharpens signals, reducing variability in the arrival time at the nuclear membrane. Inactivation can also compensate for an observed slowdown in signal propagation induced by the presence of organelle barriers, leading to arrival times at the nuclear membrane that are comparable to models in which the cytosol is treated as an open, empty region. In the limit of strong signal inactivation this is achieved by filtering out molecules that traverse non-geodesic paths.
Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation
Authors: McDaniel Elizabeth A. , Peterson Benjamin , Stevens Sarah L.R. , Tran Patricia Q. , Anantharaman Karthik , McMahon Katherine D.
Published: January 2020

Methylmercury is a potent, bioaccumulating neurotoxin that is produced by specific microorganisms by methylation of inorganic mercury released from anthropogenic sources. ThehgcABgenes were recently discovered to be required for microbial methylmercury production in diverse anaerobic bacteria and archaea. However, the full phylogenetic and metabolic diversity of mercury methylating microorganisms has not been fully explored due to the limited number of cultured, experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury methylating microorganisms identified byhgcAsequence identity from publicly available isolate genomes and metagenome-assembled genomes (MAGs), as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known, and the distribution ofhgcAis most likely due to several independent horizontal gene transfer events. Identified methylating microorganisms possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. Using a metatranscriptomic survey of a thawing permafrost gradient from which we identified 111 putative mercury methylators, we demonstrate that specific methylating populations may contribute tohgcAexpression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify methylators based uponhgcApresence and describe their putative functions in the environment.

IMPORTANCE

Specific anaerobic microorganisms among theDeltaproteobacteria, Firmicutes, andEuryarchaeotahave been shown to produce the bioaccumulating neurotoxin methylmercury. Accurately assessing the sources of microbial methylmercury production in the context of phylogenetic identification, metabolic guilds, and activity in the environment is crucial for understanding the constraints and effects of mercury impacted sites. Advances in next-generation sequencing technologies have enabled large-scale, cultivation-independent surveys of diverse and poorly characterized microorganisms of numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators, and their depth-discrete activities in the environment. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.
Progesterone modulates theta oscillations in the frontal-parietal network
Authors: Riddle Justin , Ahn Sangtae , McPherson Trevor , Girdler Susan , Frohlich Flavio
Published: January 2020

The neuroactive metabolites of the steroid hormones progesterone (P4) and testosterone (T) are GABAergic modulators that influence cognitive control, yet the specific effect of P4 and T on brain network activity remains poorly understood. Here, we investigated if a fundamental oscillatory network activity pattern related to cognitive control, frontal midline theta (FMT) oscillations, are modulated by steroids hormones, P4 and T. We measured the concentration P4 and T using salivary enzyme immunoassay and FMT oscillations using high-density electroencephalography (EEG) during the eyes-open resting state in fifty-five healthy female and male participants. Electrical brain activity was analyzed using Morlet wavelet convolution, beamformer source localization, background noise spectral fitting, and phase amplitude coupling analysis. Steroid hormone concentrations and biological sex were used as predictors for scalp and source-estimated theta oscillations and for top-down theta-gamma phase amplitude coupling. Elevated concentrations of P4 predicted increased FMT oscillatory amplitude across both sexes, and no relationship was found with T. The positive correlation with P4 was specific to the frontal-midline electrodes and survived correction for the background noise of the brain. Using source localization, FMT oscillations were localized to the frontal-parietal network. Additionally, theta amplitude within the frontal-parietal network, but not the default mode network, positively correlated with P4 concentration. Finally, P4 concentration correlated with increased coupling between FMT phase and posterior gamma amplitude. Our results suggest that P4 concentration modulates brain activity via upregulation of theta oscillations in the frontal-parietal network and increased top-down control over posterior cortical sites.

Significance Statement

The neuroactive metabolites of the steroid hormones progesterone (P4) and testosterone (T) are GABAergic modulators that influence cognitive control, yet the specific effect of P4 and T on brain network activity remains poorly understood. Here, we investigated if a fundamental oscillatory network activity pattern related to cognitive control, frontal midline theta (FMT) oscillations, are modulated by steroids hormones, P4 and T. Our results suggest that P4 concentration modulates brain activity via upregulation of theta oscillations in the frontal-parietal network and increased top-down control over posterior cortical sites.
Impact of DNA sequences in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex
Authors: Paul Debamita , Mu Hong , Dai Qing , Tavakoli Amirrasoul , He Chuan , Broyde Suse , Min Jung-Hyun
Published: January 2020

Rad4/XPC is a key DNA damage sensor for nucleotide excision repair (NER) in eukaryotes. Rad4/XPC recognizes diverse bulky lesions by flipping out two lesion-containing nucleotide pairs and inserting a β-hairpin from the BHD3 domain (β-hairpin3) into the DNA duplex. We have previously observed that Rad4 can form the same ‘open’ structure when covalently tethered to a normal DNA sequence containing consecutive C/G’s (CCC/GGG) and that a similar open-like structure can be formed even when the β-hairpin3 is lacking. Here, we report a crystal structure of the Δβ-hairpin3 mutant tethered to a sequence containing alternating C/G’s (CGC/GCG). In contrast to the previous structures, Rad4 bound to CGC/GCG in a 180°-reversed manner, capping the end of the duplex without flipping out the nucleotides. MD simulations showed that CGC/GCG was inherently less ‘openable’ than CCC/GGG and that Rad4 failed to engage with its minor groove, a hallmark of productive binding towards ‘opening’. These results reveal that DNA sequences significantly influence the thermodynamic barrier for DNA opening by Rad4, which may render certain DNA structures/sequences resistant to ‘opening’ despite a long residence time of Rad4. The reverse- mode may indicate unproductive binding for NER whereas the DNA end-binding may hint at Rad4/XPC’s functions beyond NER.
Cyclodextrin polymer coatings resist protein fouling, mammalian cell adhesion, and bacterial attachment
Authors: Learn Greg D. , Lai Emerson J. , von Recum Horst A.
Published: January 2020

Undesired attachment of proteins, cells/bacteria, and organisms on material surfaces is problematic in industrial and health care settings. In this study, polymer coatings are synthesized from subunits of cyclodextrin, an additive/excipient found in food/pharmaceutical formulations. These unique polymers, which have been applied mainly towards sustained drug delivery applications, are evaluated in this study for their ability to mitigate non-specific protein adsorption, mammalian cell (NIH/3T3) adhesion, and bacterial cell (Staphylococcus aureus, Escherichia coli) attachment. Effects of cyclodextrin polymer composition, particularly incorporation of nonpolar crosslinks, on material properties and passive anti-biofouling performance are investigated. Results suggest that lightly-crosslinked cyclodextrin polymers possess excellent passive resistance to protein, cell, and bacterial attachment, likely due to the hydrophilic and electrically neutral surface properties of these coatings. At the same time, anti-biofouling performance decreased with increasing crosslink ratios, possibly a reflection of decreased polymer mobility, increased rigidity, and increased hydrophobic character. Cyclodextrin-based materials may be broadly useful as coatings in industrial or medical applications where biofouling-resistant and/or drug-delivering surfaces are required.
Maturation of human induced pluripotent stem cell-derived cardiomyocytes for modeling hypertrophic cardiomyopathy
Authors: Knight Walter E. , Cao Yingqiong , Lin Ying-Hsi , Sparagna Genevieve C. , Bai Betty , Zhao Yuanbiao , Chi Congwu , Du Yanmei , Londono Pilar , Reisz Julie A. , Brown Benjamin C. , Taylor Matthew R. G. , Ambardekar Amrut V , Cleveland Joseph C. , McKinsey Timothy A. , Jeong Mark Y. , Walker Lori A. , Woulfe Kathleen C. , D’Alessandro Angelo , Chatfield Kathryn C. , Xu Hongyan , Bristow Michael R. , Buttrick Peter M. , Song Kunhua
Published: January 2020

Rationale

Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) are a powerful platform for biomedical research. However, they are immature, which is a barrier to modeling adult-onset cardiovascular disease.

Objective

We sought to develop a simple method which could drive cultured hiPSC-CMs towards maturity across a number of phenotypes.

Methods and results

Cells were cultured in fatty acid-based media and plated on micropatterned surfaces to promote alignment and elongation. These cells display many characteristics of adult human cardiomyocytes, including elongated cell morphology, enhanced maturity of sarcomeric structures, metabolic behavior, and increased myofibril contractile force. Most notably, hiPSC-CMs cultured under optimal maturity-inducing conditions recapitulate the pathological hypertrophy caused by either a pro-hypertrophic agent or genetic mutations.

Conclusions

The more mature hiPSC-CMs produced by the methods described here will serve as a usefulin vitroplatform for characterizing cardiovascular disease.
Biases and Blind-Spots in Genome-Wide CRISPR Knockout Screens
Authors: Dede Merve , Kim Eiru , Hart Traver
Published: January 2020

It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, beyond library-specific false negatives previously described. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared to false negatives. Cumulative analyses across tissues suggest only a small number of lineage-specific essential genes and that these genes are highly enriched for transcription factors that define pathways of tissue differentiation. In addition, we show that half of all constitutively-expressed genes are never hits in any CRISPR screen, and that these never-essentials are highly enriched for paralogs. Together these observations strongly suggest that functional buffering masks single knockout phenotypes for a substantial number of genes, describing a major blind spot in CRISPR-based mammalian functional genomics approaches.
Expected impacts of climate change on tree ferns distribution and diversity patterns in subtropical Atlantic Forest
Authors: de Gasper André Luís , Grittz Guilherme Salgado , Russi Carlos Henrique , Schwartz Carlos Eduardo , Rodrigues Arthur Vinicius
Published: January 2020

Tree ferns are common elements in the Atlantic Forest domain, sometimes reaching more than half of total dominance at forest sites. Just as most groups, climate change might impact the distribution and diversity of tree ferns. To investigate the extent of these impacts in the subtropical Atlantic Rainforest, we measured the changes in species distribution, α- and β-diversity between current climate and future climatic scenarios for 2050. Most tree ferns species tend to lose their distribution area. Hence, species richness tends to decrease in the future, especially in the Rainforest sites. In general, β-diversity tend to not change on the regional scale, but some sites can change its relative singularity in composition. Our results show that climate change can impact distribution and α-diversity of tree ferns, but with no trend to cause homogenization in the tree ferns of the study area. Protected Areas (PAs) in our study region manage to withhold more α-diversity than areas without PAs — the same applies to β-diversity. Our study offers a new light into the effects of climate change in tree ferns by integrating the evaluation of its impacts on distribution, α- and β-diversity in all study areas and inside PAs.
Accumulation of an unprecedented 5′-deoxyadenos-4′-yl radical unmasks the kinetics of the radical-mediated C-C bond formation step in MoaA catalysis
Authors: Pang Haoran , Lilla Edward A. , Zhang Pan , Zhang Du , Shields Thomas P. , Scott Lincoln G. , Yang Weitao , Yokoyama Kenichi
Published: January 2020

RadicalS-adenosyl-L-methionine (SAM) enzymes catalyze various free radical-mediated reactions. In these enzymes, the rate-determining SAM cleavage kinetically masks all the subsequent steps. Due to this kinetic masking, detailed mechanistic characterization of radical transformations catalyzed by these enzymes is very difficult. Here, we report a successful kinetic characterization of the radical C-C bond formation catalyzed by a MoaA radical SAM enzyme. MoaA catalyzes an unprecedented 3′,8-cyclization of GTP into 3′,8-cyclo-7,8-dihydro-GTP (3′,8-cH2GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterization, we found that MoaA accumulates a 5′-deoxyadenos-4′-yl radical (5′-dA-C4′•) under the turnover conditions, and forms (4′S)-5′-deoxyadenosine ((4′S)-5′-dA), which is a C-4′ epimer of the naturally occurring (4′R)-5′-dA. Together with kinetic characterizations, these observations revealed the presence of a shunt pathway in which an on-pathway intermediate, GTP C-3′ radical, abstracts H-4′ atom from 5′-dA to transiently generate 5′-dA-C4′• that is subsequently reduced stereospecifically to yield (4′S)-5′-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics, and determined the rate of the on-pathway 3′,8-cyclization step as 2.7 ± 0.7 s−1. Together with DFT calculations, this observation suggested that the 3′,8-cyclization is accelerated by 6 ∼ 9 orders of magnitude by MoaA. Potential contributions of the active-site amino acid residues, and their potential relationships with human Moco deficiency disease are discussed. This is the first determination of the magnitude of catalytic rate acceleration by a radical SAM enzyme, and provides the foundation for understanding how radical SAM enzymes achieve highly specific radical catalysis.
Dissociation of dorso-lateral and dorso-medial prefrontal cortex contributions to familiarity and recollective processes in primates
Authors: Wu Zhemeng , Kavanova Martina , Hickman Lydia , Lin Fiona , Boschin Erica , Galeazzi Juan M. , Verhagen Lennart , Buckley Mark J.
Published: January 2020

According to dual-process theories, recognition memory draws upon both familiarity and recollection. It remains unclear how primate prefrontal cortex (PFC) contributes to familiarity and recollection processes but frequency-specific neuronal activities are considered to play a key role. Here, non-human primate (NHP) electrophysiological local field potential (LFP) recordings first showed that a specific subregion of macaque PFC (i.e., dorsolateral PFC, dlPFC) was implicated in task performance at a specific frequency (i.e., increased beta power in the 10-15 Hz range observed in correct versus error trials) in a specific phase of a recognition memory task (i.e., during sample presentation). Then, to assess generalization to humans and causality we targeted left human dlPFC (BA 9/46) as well as left dorsomedial prefrontal cortex (BA 8/9) for comparison, and also vertex as a control, with transcranial magnetic stimulation at a frequency in the middle of the low-beta range observed in NHP (i.e. 12.5 Hz) and compared that to non-frequency-specific stimulation, and also to a no-stimulation control, during occasional sample presentations within a similar task. Hence we investigated hypotheses about the causal importance for human memory of a location-specific, frequency-specific, and task-epoch-specific intervention derived directly from the NHP electrophysiological observations. Using a dual-process signal detection (DPSD) model based on analysing receiver operating characteristics (ROC) curves, we showed beta-frequency TMS caused decreased recollection when targeted to human dlPFC, but enhanced familiarity when targeted to dorsomedial prefrontal cortex. Non-frequency-specific patterns of stimulation to all sites, and beta-frequency stimulation to vertex, were all without behavioural effect. This study provides causal evidence that PFC-mediated contributions to object recognition memory are modulated by beta-frequency activity; more broadly it provides translational evidence bridging NHPs and humans by emphasizing functional roles of beta-frequency activity in homologous brain regions in recognition memory.

Highlights

low beta power in NHP dlPFC during stimulus encoding was related to behaviour

human rTMS study used parameters derived from NHP observations to test causality

low beta rTMS to human dlPFC, but not dmPFC, impairs recollection

low beta rTMS to human dmPFC, but not dlPFC, enhances familiarity

provides cross-species validation of prefrontal beta power to primate recognition
A hybrid spectral library combining DIA-MS data and a targeted virtual library substantially deepens the proteome coverage
Authors: Lou Ronghui , Tang Pan , Ding Kang , Li Shanshan , Tian Cuiping , Li Yunxia , Zhao Suwen , Zhang Yaoyang , Shui Wenqing
Published: January 2020

Data-independent acquisition mass spectrometry (DIA-MS) is a rapidly evolving technique that enables relatively deep proteomic profiling with superior quantification reproducibility. DIA data mining predominantly relies on a spectral library of sufficient proteome coverage that, in most cases, is built on data-dependent acquisition-based analysis of the same sample. To expand the proteome coverage for a pre-determined protein family, we report herein on the construction of a hybrid spectral library that supplements a DIA experiment-derived library with a protein family-targeted virtual library predicted by deep learning. Leveraging this DIA hybrid library substantially deepens the coverage of three transmembrane protein families (G protein coupled receptors; ion channels; and transporters) in mouse brain tissues with increases in protein identification of 37-87%, and peptide identification of 58-161%. Moreover, of the 412 novel GPCR peptides exclusively identified with the DIA hybrid library strategy, 53.6% were validated as present in mouse brain tissues based on orthogonal experimental measurement.
Estrogen attenuates the growth of human papillomavirus positive epithelial cells
Authors: Bristol Molly L. , James Claire D. , Wang Xu , Fontan Christian T. , Morgan Iain M.
Published: January 2020

Human papillomaviruses (HPVs) are small, double-stranded DNA viruses that are significant risk factors in the development of cancer, and HPV accounts for approximately 5% of all worldwide cancers. Recent studies using data from The Cancer Genome Atlas (TCGA) have demonstrated that elevated levels of estrogen receptor alpha (ERα) are associated with improved survival in oropharyngeal cancers, and these elevated receptor levels were linked with human papillomavirus positive cancers (HPV+cancers). There has been a dramatic increase in HPV-related head and neck squamous cell carcinomas (HPV+HNSCCs) over the last two decades and therapeutic options for this ongoing health crisis are a priority; currently there are no anti-viral therapeutics available for combating HPV+cancers. During our own TGCA studies on head and neck cancer we had also discovered the overexpression of ERα in HPV+cancers. Here we demonstrate that 17β-estradiol (estrogen) attenuates the growth/cell viability of HPV+cancersin vitro, but not HPV negative cancer cells. In addition, N/Tert-1 cells (foreskin keratinocytes immortalized with hTERT) containing HPV16 have elevated levels of ERα and growth sensitivity following estrogen treatment when compared with parental N/Tert-1. Finally, we demonstrate that there are potentially two mechanisms contributing to the attenuation of HPV+ cell growth following estrogen treatment. First, estrogen represses the viral transcriptional long control region (LCR) downregulating early gene expression, including E6/E7. Second, expression of E6 and E7 by themselves sensitizes cells to estrogen. Overall our results support the recent proposal that estrogen could be exploited therapeutically for the treatment of HPV positive oral cancers.

Importance

Human papillomaviruses cause around 5% of all human cancers, yet there are no specific anti-viral therapeutic approaches available for combating these cancers. These cancers are currently treated with standard chemo-radiation therapy (CRT). Specific anti-viral reagents are desperately required, particularly for HPV+HNSCC whose incidence is increasing and for which there are no diagnostic tools available for combating this disease. Using data from The Cancer Genome Atlas (TCGA) ourselves and others determined that the estrogen receptor α (ERα) is overexpressed in HPV+HNSCC, and that elevated levels are associated with an improved disease outcome. This has led to the proposal that estrogen treatment could be a novel therapeutic approach for combating HPV+cancers. Here we demonstrate that estrogen attenuates the growth of HPV+epithelial cells using multiple mechanisms, supporting the idea that estrogen has potential as a therapeutic agent for the treatment of HPV+HNSCC.
Risk prediction with office and ambulatory blood pressure using artificial intelligence
Authors: Guimarães Pedro , Keller Andreas , Böhm Michael , Lauder Lucas , Ayala José L. , Banegas José R. , de la Sierra Alejandro , Vinyoles Ernest , Gorostidi Manuel , Segura Julián , Ruiz-Hurtado Gema , Ruilope Luis M. , Mahfoud Felix
Published: January 2020

Background

To develop and validate a novel, machine learning-derived model for prediction of cardiovascular (CV) mortality risk using office (OBP) and ambulatory blood pressure (ABP), to compare its performance with existing risk scores, and to assess the possibility of predicting ABP phenotypes (i.e. white-coat, ambulatory and masked hypertension) utilizing clinical variables.

Methods

Using data from 63,910 patients enrolled in the Spanish ABP monitoring registry, machine-learning approaches (logistic regression, support vector machine, gradient boosted decision trees, and deep neural networks) and stepwise forward feature selection were used for the classification of the data.

Results

Over a median follow-up of 4.7 years, 3,808 deaths occurred from which 1,295 were from CV causes. The performance for all tested classifiers increased while adding up to 10 features and converged thereafter. For the prediction of CV mortality, deep neural networks yielded the highest clinical performance. The novel mortality prediction models using OBP (CV-MortalityOBP) and ABP (CV-MortalityABP) outperformed all other risk scores. The area under the curve (AUC) achieved by the novel approach, using OBP variables only, was already significantly higher when compared with the AUC of Framingham score (0.685 vs 0.659, p = 1.97×10−22), the SCORE (0.679 vs 0.613, p = 6.21×10−22), and ASCVD (0.722 vs 0.639, p = 8.03×10−30) risk score. However, prediction of CV mortality with ABP instead of OBP data led to a significant increase in AUC (0.781 vs 0.752, p = 1.73×10−42), accuracy, balanced accuracy and sensitivity. The sensitivity and specificity for detection of ambulatory, masked, and white-coat hypertension ranged between 0.653-0.661 and 0.573-0.651, respectively.

Conclusion

We developed a novel risk calculator for CV death using artificial intelligence based on a large cohort of patients included in the Spanish ABP monitoring registry. The receiver operating characteristic curves for CV-MortalityOBP and CV-MortalityABP with deep neural networks models outperformed all other risk metrics. Prediction of CV mortality using ABP data led to a significant increase in performance metrics. The prediction of ambulatory phenotypes using clinical characteristics, including OBP, was limited.
Retrospective evaluation of a filtering trabeculotomy in comparison to conventional trabeculectomy byexact matching
Authors: Strzalkowska A. , Strzalkowski P. , Al Yousef Y. , Hillenkamp J. , Grehn F. , Loewen N. A.
Published: January 2020

Purpose

To compare 2-year results of a filtering trabeculotomy (FTO) to conventional trabeculectomy (TE) in open-angle glaucoma by exact matching.

Methods

110 patients received an FTO and 86 a TE. FTO avoided the need for an iridectomy due to a preserved trabeculo-Descemet window anterior to the scleral flap. TE employed a trabecular block excision and iridectomy. Mitomycin C was used in both. FTO and TE were exact-matched by baseline intraocular pressure (IOP) and the number of glaucoma medications. Complete and qualified success (IOP ≤18 mmHg and IOP reduction ≥ 30%, with or without medication) were primary endpoints. IOP, visual acuity (BCVA), complications and intervention were secondary endpoints.

Results

44 FTO were exact-matched to 44 TE. The IOP baseline in both groups was 22.5±4.7 mmHg on 3±0.9 medications. At 24 months, complete success was reached by 59% in FTO and 66% in TE and qualified success by 59% in FTO and 71% in TE. In FTO, IOP was reduced to 12.4±4.3 mmHg at 12 months and 13.1±4.1 mmHg at 24 months. In TE, IOP was 11.3±2.2 mmHg at 12 months and 12.0±3.5 mmHg at 24 months. Medications could be reduced at 24 months to 0.6±1.3 in FTO and 0.2±0.5 in TE. There were no significant differences between the two groups in IOP, medications, complications or interventions at any point.

Conclusion

Modifying aqueous flow through a limited trabeculotomy in FTO yielded clinical outcomes similar to traditional TE but allowed to avoid an iridectomy.
The impact and implications of vehicle collisions on the endangered and endemic Zanzibar red colobus (Piliocolobus kirkii)
Authors: Olgun Harry , Mohammed Mzee Khamis , Mzee Abbas Juma , Green M. E. Landry , Davenport Tim R. B. , Georgiev Alexander V.
Published: January 2020

Roads can affect wildlife in a variety of negative ways. Studies of road ecology have mostly concentrated in the northern hemisphere despite the potentially greater impact on biodiversity that roads may have in tropical habitats. Here, we examine a 4-year opportunistic dataset (January 2016 – December 2019) on mammalian roadkill observed along a road intersecting Jozani-Chwaka Bay National Park, Unguja, Zanzibar. In particular, we assess the impact of collisions on the population of an endangered and endemic primate, the Zanzibar red colobus (Piliocolobus kirkii). Primates accounted for the majority of roadkill. Monthly rainfall variation was not associated with roadkill frequency for mammals and specifically for the Zanzibar red colobus. No single age-sex class of colobus was found dead more often than expected given their availability in the local population. The exact effect of roadkill on colobus populations in habitats fragmented by roads is unknown given the lack of accurate, long-term life history data for this species. However, the frequency of kills documented in this study suggests further mitigation measures may be important. Our data show that mortality from collisions with vehicles in some groups of colobus are comparable to rates of mortality experienced by other primate populations from natural predation. Unlike natural predators, however, vehicles are not ‘selective’ in their targeting of ‘prey’. The long-term implications of such a ‘predation regime’ on this species remain to be established.