bluuebunny/crossref_metadata_2025 huggingface dataset:
A mouse-adapted SARS-CoV-2 model for the evaluation of COVID-19 medical countermeasures
Authors: Dinnon Kenneth H. , Leist Sarah R. , Schäfer Alexandra , Edwards Caitlin E. , Martinez David R. , Montgomery Stephanie A. , West Ande , Yount Boyd L. , Hou Yixuan J. , Adams Lily E. , Gully Kendra L. , Brown Ariane J. , Huang Emily , Bryant Matthew D. , Choong Ingrid C. , Glenn Jeffrey S. , Gralinski Lisa E. , Sheahan Timothy P. , Baric Ralph S.
Published: May 2020

Coronaviruses are prone to emergence into new host species most recently evidenced by SARS-CoV-2, the causative agent of the COVID-19 pandemic. Small animal models that recapitulate SARS-CoV-2 disease are desperately needed to rapidly evaluate medical countermeasures (MCMs). SARS-CoV-2 cannot infect wildtype laboratory mice due to inefficient interactions between the viral spike (S) protein and the murine ortholog of the human receptor, ACE2. We used reverse genetics to remodel the S and mACE2 binding interface resulting in a recombinant virus (SARS-CoV-2 MA) that could utilize mACE2 for entry. SARS-CoV-2 MA replicated in both the upper and lower airways of both young adult and aged BALB/c mice. Importantly, disease was more severe in aged mice, and showed more clinically relevant phenotypes than those seen in hACE2 transgenic mice. We then demonstrated the utility of this model through vaccine challenge studies in immune competent mice with native expression of mACE2. Lastly, we show that clinical candidate interferon (IFN) lambda-1a can potently inhibit SARS-CoV-2 replication in primary human airway epithelial cellsin vitro, and both prophylactic and therapeutic administration diminished replication in mice. Our mouse-adapted SARS-CoV-2 model demonstrates age-related disease pathogenesis and supports the clinical use of IFN lambda-1a treatment in human COVID-19 infections.
Virome composition in marine fish revealed by meta-transcriptomics
Authors: Geoghegan Jemma L. , Di Giallonardo Francesca , Wille Michelle , Ortiz-Baez Ayda Susana , Costa Vincenzo A. , Ghaly Timothy , Mifsud Jonathon C. O. , Turnbull Olivia M. H. , Bellwood David R. , Williamson Jane E. , Holmes Edward C.
Published: May 2020

Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterised the viromes of 19 wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterisation. From this, we identified 25 new vertebrate-associated viruses and a further 22 viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in theMatonaviridae(single-strand, negative-sense RNA virus). Other viruses fell within theAstroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, FiloviridaeandFlaviviridaeand were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition – viral richness, abundance and diversity – can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish sampled here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community diversity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.
CheckV: assessing the quality of metagenome-assembled viral genomes
Authors: Nayfach Stephen , Camargo Antonio Pedro , Eloe-Fadrosh Emiley , Roux Simon , Kyrpides Nikos
Published: May 2020

Over the last several years, metagenomics has enabled the assembly of millions of new viral sequences that have vastly expanded our knowledge of Earth’s viral diversity. However, these sequences range from small fragments to complete genomes and no tools currently exist for estimating their quality. To address this problem, we developed CheckV, which is an automated pipeline for estimating the completeness of viral genomes as well as the identification and removal of non-viral regions found on integrated proviruses. After validating the approach on mock datasets, CheckV was applied to large and diverse viral genome collections, including IMG/VR and the Global Ocean Virome, revealing that the majority of viral sequences were small fragments, with just 3.6% classified as high-quality (i.e. > 90% completeness) or complete genomes. Additionally, we found that removal of host contamination significantly improved identification of auxiliary metabolic genes and interpretation of viral-encoded functions. We expect CheckV will be broadly useful for all researchers studying and reporting viral genomes assembled from metagenomes. CheckV is freely available at:http://bitbucket.org/berkeleylab/CheckV.
Systematic review and meta-analysis of the prevalence of Strep Aemmclusters in Africa to inform vaccine development
Authors: Salie Taariq , Engel Kelin , Moloi Annesinah , Muhamed Babu , Dale James B , Engel Mark E
Published: May 2020

Background

Anemm-cluster based system was proposed as a standard typing scheme to facilitate and enhance future studies of Group A Streptococcus (Strep A) epidemiological surveillance, M protein function and vaccine development strategies. We provide an evidence-based distribution of Strep Aemmclusters in Africa and assess the potential coverage of the new 30-valent vaccine in terms of an emm cluster-based approach.

Method

Two reviewers independently assessed studies retrieved from a comprehensive search and extracted relevant data. Meta-analyses were performed (random effects model) to aggregateemmcluster prevalence estimates.

Results

Eight studies (n=1,595 isolates) revealed the predominantemmclusters as E6 (18%, 95% confidence interval (CI), 12.6; 24.0%), followed by E3 (14%, 95%CI, 11.2; 17.4%) and E4 (13%, 95%CI, 9.5; 16.0%). There is negligible variation inemmclusters as regards regions, age and socio-economic status across the continent. Considering anemmcluster-based vaccine strategy, which assumes cross-protection within clusters, the 30-valent vaccine currently in clinical development, would provide hypothetical coverage to 80.3% of isolates in Africa.

Conclusion

This systematic review indicates the most predominant Strep Aemmcluster in Africa is E6 followed by E3, E4 and D4. The current 30-valent vaccine would provide considerable coverage across the diversity ofemmcluster types in Africa. Future efforts could be directed toward estimating the overall potential coverage of the new 30-valent vaccine based on cross-opsonization studies with representative panels of Strep A isolates from populations at highest risk for Strep A diseases.

Importance

Low vaccine coverage is of grave public health concern, particularly in developing countries where epidemiological data are often absent. To inform vaccine development for group A streptococcus (Strep A), we report on the epidemiology of the M Protein emm clusters from Strep A infections in Africa, where Strep A-related illnesses and their sequalae including rheumatic fever and rheumatic heart disease, are of a high burden. This first report of emm clusters across the continent indicate a high probably of coverage by the M Protein-based vaccine currently undergoing testing, were an emm-cluster based approach to be used.
The SARS-CoV-2-like virus found in captive pangolins from Guangdong should be better sequenced
Authors: Hassanin Alexandre
Published: May 2020

Viruses closely related to SARS-CoV-2, which is the virus responsible of the Covid-19 pandemic, were sequenced in several Sunda pangolins (Manis javanica) seized in the Guangdong and Guangxi provinces of China between 2017 and 20191-3. These viruses belong to two lineages: one from Guangdong (GD/P) and the other from Guangxi (GX/P). TheGD/Pviruses are particularly intriguing as the amino-acid sequence of the receptor binding domain of the spike protein is very similar to that of the human SARS-CoV-2 virus (97.4%)2. This characteristic suggests thatGD/Pviruses are capable of binding human ACE2 receptor and may therefore be able to mediate infection of human cells. Whereas all sixGX/Pgenomes were deposited as annotated sequences in GenBank, none of the twoGD/Pgenomes assembled in previous studies2,3are currently available. To overcome this absence, I assembled these genomes from the Sequence Read Archive (SRA) data available for SARS-CoV-2-like viruses detected in five captive pangolins from Guangdong. I found the genome assemblies ofGD/Pvirus of poor quality, having high levels of missing data. Additionally, unexpected reads in the Illumina sequencing data were identified. TheGD/P2Sdataset2contains reads that are identical to SARS-CoV-2, suggesting either the coexistence of two SARS-CoV-2-like viruses in the same pangolin or contamination by the human virus. In the four otherGD/Pdatasets1many mitochondrial reads from pangolin were identified, as well as from three other species, namely, human, mouse and tiger. Importantly, I only identified three polymorphic nucleotide sites between the fiveGD/Psequences. Such low levels of polymorphism may reasonably be accounted for by sequencing errors alone, thus raising the possibility that the five pangolins seized in Guangdong in March 2019 were infected by the same virus strain, most probably during their captivity.
ATAC-seq identifies chromatin landscapes linked to the regulation of oxidative stress in the human fungal pathogenCandida albicans
Authors: Jenull Sabrina , Tscherner Michael , Mair Theresia , Kuchler Karl
Published: May 2020

Human fungal pathogens often encounter fungicidal stress conditions upon host invasion, but they can swiftly adapt by transcriptional reprogramming that enables pathogen survival. Fungal immune evasion is tightly connected to chromatin regulation. Hence, fungal chromatin modifiers pose alternative treatment options to combat fungal infections. Here, we present an ATAC-seq protocol adapted for the opportunistic pathogenCandida albicansto gain further insight into the interplay of chromatin accessibility and gene expression mounted during fungal adaptation to oxidative stress. The ATAC-seq workflow facilitates the robust detection of genomic regions with accessible chromatin, but also allows for the precise modeling of nucleosome positions inC. albcians. Importantly, the data reveal genes with altered chromatin accessibility in upstream regulatory regions, which correlate with transcriptional regulation during the oxidative stress response. Interestingly, many genes show increased chromatin accessibility yet no change in gene expression upon stress exposure. Such chromatin signatures could predict yet unknown regulatory factors under highly dynamic transcriptional control. In addition,de novomotif analysis in genomic regions with increased chromatin accessibility upon hydrogen peroxide treatment shows significant enrichment for Cap1 binding sites, a major factor of oxidative stress responses inC. albicans. Taken together, the ATAC-seq workflow enables the identification of chromatin signatures and uncovers the dynamics of regulatory mechanisms mediating environmental adaptation ofC. albicansto host immune surveillance.

Importance

The opportunistic fungal pathogenCandida albicanscolonizes and infects various tissues and organs of the human host. This is due to its rapid environmental adaptation facilitated by changes in gene expression coupled to chromatin alterations. Recent advances in chromatin profiling approaches, such as the development of ATAC-seq, shed light on the dynamic interplay of chromatin accessibility and transcriptional control. The here presented expansion of the ATAC-seq method toC. albicansdemonstrates the robustness of ATAC-seq to detect dynamic modulations of chromatin accessibility in response to oxidative stress. This work serves as a basis to further exploit this application to characterize regulatory mechanisms that drive fungal environmental adaptation, such as during host invasion, and thus, will open novel antifungal treatment strategies targeting fungal chromatin regulation.
A temperature-dependent translational switch controls biofilm development inVibrio cholerae
Authors: Peso Santos Teresa del , Blake Jonathon , Sit Brandon , Warr Alyson R. , Benes Vladimir , Waldor Matthew K. , Cava Felipe
Published: May 2020

The gastrointestinal pathogenVibrio choleraefrequently forms biofilms during its life cycle. Biofilm formation is vital for protection against environmental stresses and is thought to facilitate intestinal colonization. Adaptation to temperature is crucial forV. choleraesurvival, as the pathogen is exposed to seasonal temperature variations in the aquatic environment, and temperature fluctuations during host-environment transitions. Here, we show thatV. choleraestrains naturally lacking the master biofilm transcriptional regulator HapR are unable to develop colony rugosity at low temperatures. We find that BipA, a ribosome-associated GTPase, accounts for this temperature-dependent control of biofilm formation by repressing translation of the primary biofilm transcriptional activators VpsR and VpsT at low temperatures.In vitrostudies demonstrate that low temperatures influence BipA structural conformation and decrease its sensitivity to proteolysis. Proteomic analyses reveal that BipA exerts temperature-dependent control over >200 proteins inV. choleraeinvolved in a multitude of cell processes, including biofilm assembly. Our study reveals a remarkable new facet of the complexV. choleraebiofilm regulatory cascade and suggests that combined transcriptional-translational control could be a common mechanism by which bacteria adapt to environmental flux.
Light affects behavioral despair involving the clock genePeriod 1
Authors: Olejniczak Iwona , Ripperger Jürgen A. , Sandrelli Federica , Schnell Anna , Mansencal-Strittmatter Laureen , Hui Ka Yi , Brenna Andrea , Fredj Naila Ben , Albrecht Urs
Published: May 2020

Light at night has strong effects on physiology and behavior of mammals. It affects mood in humans, which is exploited as light therapy, and has been shown to reset the circadian clock in the suprachiasmatic nuclei (SCN). This resetting is paramount to align physiological and biochemical timing to the environmental light-dark cycle. Here we provide evidence that light affects mood-related behaviors also in mice by activating the clock genePeriod1 (Per1)in the lateral habenula (LHb), a brain region known to modulate mood-related behaviors. A light pulse given at ZT22 to wild type mice caused profound changes of gene expression in the mesolimbic dopaminergic system including the nucleus accumbens (NAc). Sensory perception of smell and G-protein coupled receptor signaling was affected the most in this brain region. Interestingly, most of these genes were not affected inPer1knock-out animals, indicating that induction ofPer1by light serves as a filter for light-mediated gene induction in the brain. Taken together we show that light affects mood-related behavior in mice at least in part via induction ofPer1in the LHb with consequences on signaling mechanisms in the mesolimbic dopaminergic system.
Using optimal control to understand complex metabolic pathways
Authors: Tsiantis Nikolaos , Banga Julio R.
Published: May 2020

Background

We revisit the idea of explaining and predicting dynamics in biochemical pathways from first-principles. A promising approach is to exploit optimality principles that can be justified from an evolutionary perspective. In the context of the cell, several previous studies have explained the dynamics of simple metabolic pathways exploiting optimality principles in combination with dynamic models, i.e. using an optimal control framework. For example, dynamics of gene expression in small metabolic models can be explained assuming that cells have developed optimal adaptation strategies. Most of these works have considered rather simplified representations, such as small linear pathways, or reduced networks with a single branching point.

Results

Here we consider the extension of this approach to more realistic scenarios, i.e. biochemical pathways of arbitrary size and structure. We first show that exploiting optimality principles for these networks poses great challenges due to the complexity of the associated optimal control problems. Second, in order to surmount such challenges, we present a computational framework based on multicriteria optimal control which has been designed with scalability and efficiency in mind, extending several recent methods. This framework includes mechanisms to avoid common pitfalls, such as local optima, unstable solutions or excessive computation time. We illustrate its performance with several case studies considering the central carbon metabolism ofS. cerevisiaeandB. subtilis. In particular, we consider metabolic dynamics during nutrient shift experiments.

Conclusions

We show how multi-objective optimal control can be used to predict temporal profiles of enzyme activation and metabolite concentrations in complex metabolic pathways. Further, we show how the multicriteria approach allows us to consider general cost/benefit trade-offs that have been likely favored by evolution. In this study we have considered metabolic pathways, but this computational framework can also be applied to analyze the dynamics of other complex pathways, such as signal transduction networks.
The use of two-sample methods for Mendelian randomization analyses on single large datasets
Authors: Minelli Cosetta , Fabiola Del Greco M. , van der Plaat Diana A. , Bowden Jack , Sheehan Nuala A. , Thompson John
Published: May 2020

Background

With genome-wide association data for many exposures and outcomes now available from large biobanks, one-sample Mendelian randomization (MR) is increasingly used to investigate causal relationships. Many robust MR methods are available to address pleiotropy, but these assume independence between the gene-exposure and gene-outcome association estimates. Unlike in two-sample MR, in one-sample MR the two estimates are obtained from the same individuals, and the assumption of independence does not hold in the presence of confounding.

Methods

With simulations mimicking a typical study in UK Biobank we assessed the performance, in terms of bias and precision of the MR estimate, of the fixed-effect and (multiplicative) random-effects meta-analysis method, weighted median estimator, weighted mode estimator and MR-Egger regression, used in both one-sample and two-sample data. We considered scenarios differing for: presence/absence of a true causal effect; amount of confounding; presence and type of pleiotropy (none, balanced or directional).

Results

Even in the presence of substantial correlation due to confounding, all methods performed well when used in one-sample MR except for MR-Egger, which resulted in bias reflecting direction and magnitude of the confounding. Such bias was much reduced in the presence of very high variability in instrumental strength across variants (I2GXof 97%).

Conclusions

Two-sample MR methods can be safely used for one-sample MR performed within large biobanks, expect for MR-Egger. MR-Egger is not recommended for one-sample MR unless the correlation between the gene-exposure and gene-outcome estimates due to confounding can be kept low, or the variability in instrumental strength is very high.

Key Messages

Current availability of phenotypic and genetic data from large biobanks, such as UK Biobank, has led to increasing use of one-sample Mendelian randomization (MR) to investigate causal relationships in epidemiological research

Robust MR methods have been developed to address pleiotropy, but they assume independence between the gene-exposure and gene-outcome association estimates; this holds in two-sample MR but not in one-sample MR

We illustrate the practical implications, in terms of bias and precision of the MR causal effect estimate, of using robust two-sample methods in one-sample MR studies performed within large biobanks

Two-sample MR methods can be safely used for one-sample MR performed within large biobanks, expect for MR-Egger regression

MR-Egger is not recommended for one-sample MR unless the correlation between the gene-exposure and gene-outcome estimates due to confounding can be kept low, or the variability in instrumental strength is very high
VolcaNoseR – a web app for creating, exploring, labeling and sharing volcano plots
Authors: Goedhart Joachim , Luijsterburg Martijn S.
Published: May 2020

Comparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots (https://huygens.science.uva.nl/VolcaNoseR). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome- and proteome-wide datasets.
Mutational processes impact the evolution of anti-EGFR antibody resistance in colorectal cancer
Authors: Woolston Andrew , Barber Louise J , Griffiths Beatrice , Matthews Nik , Rao Sheela , Watkins David , Chau Ian , Starling Naureen , Cunningham David , Gerlinger Marco
Published: May 2020

Anti-EGFR antibodies such as cetuximab are active againstKRAS/NRASwild-type colorectal cancers (CRC) but acquired resistance invariably evolves. Which mutational mechanisms enable resistance evolution and whether adaptive mutagenesis, a transient cetuximab-induced increase in mutagenesis, contributes in patients is unknown. We investigated this in exome sequencing data of 42 baseline and progression biopsies from cetuximab treated CRCs. Mutation loads did not increase from baseline to progression. Evidence for a contribution of cetuximab-induced mutagenesis was limited. However, the mutational Signature 17 was a key contributer of specificKRAS/NRASandEGFRdriver mutations that are common at acquired resistance. Signature 17 activity before treatment predicted shorter progression free survival. This demonstrates the utility of mutational signatures to predict cancer drug resistance evolution.

SIGNIFICANCE

Drug resistance evolution occurs ubiquitously in solid tumours during treatment with targeted drugs. Biomarkers that can be assessed prior to treatment to predict the time to resistance evolution and the genetic resistance mechanisms that will evolve have not been described. We identified the mutational Signature 17 as the first candidate biomarker that predicts shorter time to progression and several specificKRAS/NRASandEGFRmutations that will likely evolve in CRCs during cetuximab treatment. Understanding the mutational mechanism underlying Signature 17 may open opportunities to delay resistance acquisition. The potential of mutational signatures to predict resistance to a broader range of drugs in other tumor types should be assessed.
Eyes are essential for magnetoreception in a mammal
Authors: Caspar Kai R. , Moldenhauer Katrin , Moritz Regina E. , Malkemper E. Pascal , Begall Sabine
Published: May 2020

Several groups of mammals use the Earth’s magnetic field for orientation, but their magnetosensory organ remains unknown. The Ansell’s mole-rat (Fukomys anselli) is a subterranean rodent with innate magnetic orientation behavior. Previous studies proposed that its magnetoreceptors are located in the eye. To test this hypothesis, we assessed magnetic orientation in enucleated mole-rats.

Initially, we demonstrate that enucleation of mole-rats does not lead to changes in routine behaviors. We then studied magnetic compass orientation by employing a well-established nest building assay. To ensure that directional responses were based on magnetic parameters, we tested animals under four magnetic field alignments. In line with previous studies, control animals exhibited a significant preference to build nests in magnetic south-east. In contrast, enucleated mole-rats built nests in random magnetic orientations, suggesting an impairment of their magnetic sense. The results provide robust support for the hypothesis that mole-rats perceive magnetic fields with their minute eyes.
Unlocking the Reversal Potential of Solid Supported Membrane Electrophysiology to Determine Transport Stoichiometry
Authors: Thomas Nathan E. , Henzler-Wildman Katherine A.
Published: May 2020

Transport stoichiometry provides insight into the mechanism and function of ion-coupled transporters, but measuring transport stoichiometry is time-consuming and technically difficult. With the increasing evidence that many ion-coupled transporters employ multiple transport stoichiometries under different conditions, improved methods to determine transport stoichiometry are required to accurately characterize transporter activity. Reversal potential was previously shown to be a reliable, general method for determining the transport stoichiometry of ion-coupled transporters (Fitzgerald & Mindell, 2017). Here, we develop a new technique for measuring transport stoichiometry with greatly improved throughput using solid supported membrane electrophysiology (SSME). Using this technique, we are able to verify the recent report of a fixed 2:1 stoichiometry for the proton:guanidinium antiporter Gdx. Our SSME method requires only small amounts of transporter and provides a fast, easy, general method for measuring transport stoichiometry, which will facilitate future mechanistic and functional studies of ion-coupled transporters.
PyHIST: A Histological Image Segmentation Tool
Authors: Muñoz-Aguirre Manuel , Ntasis Vasilis F. , Guigó Roderic
Published: May 2020

The development of increasingly sophisticated methods to acquire high resolution images has led to the generation of large collections of biomedical imaging data, including images of tissues and organs. Many of the current machine learning methods that aim to extract biological knowledge from histopathological images require several data preprocessing stages, creating an overhead before the proper analysis. Here we present PyHIST (https://github.com/manuel-munoz-aguirre/PyHIST), an easy-to-use, open source whole slide histological image tissue segmentation and preprocessing tool aimed at data preparation for machine learning applications.
From sea surface to seafloor: a benthic allochthonous eDNA survey for the abyssal ocean
Authors: Laroche Olivier , Kersten Oliver , Smith Craig R. , Goetze Erica
Published: May 2020

Diverse and remote deep-sea communities are critically under-sampled and increasingly threatened by anthropogenic impacts. Environmental DNA (eDNA) metabarcoding could facilitate rapid and comprehensive biotic surveys in the deep ocean, yet many aspects of the sources and distribution of eDNA in the deep sea are still poorly understood. In order to examine the influence of the water column on benthic eDNA surveys in regions targeted for deep-sea polymetallic nodule mining, we investigated the occurrence of pelagic eDNA across: (1) two different deep-sea habitat types, abyssal plains and seamounts, (2) benthic sample types, including nodules, sediment, and seawater within the benthic boundary layer (BBL), and (3) sediment depth horizons (0-2 cm, 3-5 cm). Little difference was observed between seamounts and the adjacent abyssal plains in the proportion of legacy pelagic eDNA sampled in the benthos, despite an > 1000 m depth difference for these habitats. In terms of both reads and amplicon sequence variants (ASVs), pelagic eDNA was minimal within sediment and nodule samples (< 2%), and is unlikely to affect benthic surveys that monitor resident organisms at the deep seafloor. However, pelagic eDNA was substantial within the BBL (up to 13 % ASVs, 86% reads), deriving both from the high biomass upper ocean as well as deep pelagic residents. While most pelagic eDNA found in sediments and on nodules could be sourced from the epipelagic for metazoans, protist legacy eDNA sampled on these substrates appeared to originate across a range of depths in the water column. Some evidence of eDNA degradation across a vertical sediment profile was observed for protists, with higher diversity in the 0-2 cm layer and a significantly lower proportion of legacy pelagic eDNA in deeper sediments (3-5 cm). Study-wide, our estimated metazoan sampling coverage ranged from 40% to 74%, despite relatively large sample size. Future deep-sea eDNA surveys should examine oceanographic influences on eDNA transport and residence times, consider habitat heterogeneity at a range of spatial scales in the abyss, and aim to process large amounts of material per sample (with replication) in order to increase the sampling coverage in these diverse deep ocean communities.
Recurrent evolution of vertebrate transcription factors by transposase capture
Authors: Cosby Rachel L. , Judd Julius , Zhang Ruiling , Zhong Alan , Garry Nathaniel , Pritham Ellen J. , Feschotte Cedric
Published: May 2020

How genes with novel cellular functions evolve is a central biological question. Exon shuffling is one mechanism to assemble new protein architectures. Here we show that DNA transposons, which are mobile and pervasive in genomes, have provided a recurrent supply of exons and splice sites to assemble protein-coding genes in vertebrates via exon-shuffling. We find that transposase domains have been captured, primarily via alternative splicing, to form new fusion proteins at least 94 times independently over ∼350 million years of tetrapod evolution. Evolution favors fusion of transposase DNA-binding domains to host regulatory domains, especially the Krüppel-associated Box (KRAB), suggesting transposase capture frequently yields new transcriptional repressors. We show that four independently evolved KRAB-transposase fusion proteins repress gene expression in a sequence-specific fashion. Genetic knockout and rescue of the bat-specificKRABINERfusion gene in cells demonstrates that it binds its cognate transposons genome-wide and controls a vast network of genes andcis-regulatory elements. These results illustrate a powerful mechanism by which a transcription factor and its dispersed binding sites emerge at once from a transposon family.

One Sentence Summary

Host-transposase fusion generates novel cellular genes, including deeply conserved and lineage specific transcription factors.
A gas-and-brake mechanism of bHLH proteins modulates shade avoidance inArabidopsis thaliana
Authors: Buti Sara , Pantazopoulou Chrysoula K. , Hoogers Valérie , van Gelderen Kasper , Reinen Emilie , Pierik Ronald
Published: May 2020

Plants detect proximity of competitors through reduction in the ratio between red and far red light triggering the shade avoidance syndrome, which includes accelerated shoot elongation and early flowering. Shade avoidance is regulated through PHYTOCHROME INTERACTING FACTORs (PIFs), a group of bHLH transcription factors. Another (b)HLH protein, KIDARI (KDR), which is non-DNA-binding, was identified in de-etiolation studies and proposed to interact with LONG HYPOCOTYL IN FAR-RED 1 (HFR1), a (b)HLH protein that inhibits shade avoidance. Here we establish novel roles of KDR in regulating shade avoidance and investigate how KDR regulates the shade avoidance network. We show that KDR is a positive regulator of shade avoidance and interacts with several negative growth regulators. We identify novel interactors using a combination of yeast two-hybrid screening and dedicated confirmations with bimolecular fluorescence complementation. We demonstrate that KDR is translocated primarily to the nucleus when coexpressed with these newly discovered interactors. A genetic approach confirmed that several of these novel interactions are indeed functional to shade avoidance inArabidopsis thaliana, whereas we propose that KDR does not interact with HFR1 to regulate shade avoidance. Based on this, we propose that shade avoidance is regulated by a three-layered gas-and-brake mechanism of bHLH protein interactions, adding an additional layer of complexity to what was previously known.

One-sentence summary

KIDARI is a positive regulator of shade avoidance and part of a three-layer network of bHLH transcription factor interactions.
Host and environmental determinants of microbial community structure in the marine phyllosphere
Authors: Vogel Margaret A. , Mason Olivia U. , Miller Thomas E.
Published: May 2020

Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed thatThalassia testudinum(turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Additionally, results suggested that environmental conditions, including water depth, salinity, and temperature, were the major driver of community structure as blade surface microbial communities varied among sites and over sampling dates. Host condition may be a secondary driver of community structure as compositional changes were also correlated with host characteristics, including leaf growth rates and blade nutrient composition, Additionally, 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples and may represent a core community forT. testudinum. Members of this core community may have ecological importance for determining community structure or in performing key community functions. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.
Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies
Authors: Taerum Stephen J. , Steven Blaire , Gage Daniel J. , Triplett Lindsay R.
Published: May 2020

Protists and microscopic animals are important but poorly understood determinants of plant health. Plant-associated eukaryotes could be surveyed by high-throughput sequencing of 18S ribosomal RNA (rRNA) genes, but the abundance of plant DNA in rhizosphere samples makes 18S rRNA gene amplification with universal primers unfeasible. Here we applied a pipeline to generate peptide nucleic acid (PNA) clamps to suppress the amplification of plant host DNA during 18S rRNA gene library preparation. We designed a PNA clamp, PoacV9_01, specific to the V9 region of the 18S rRNA gene for plants in the family Poaceae. PoacV9_01 suppressed the amplification of five species of grain crops in quantitative PCR reactions. In an 18S rRNA gene sequencing survey of the rhizosphere of maize, PoacV9_01 reduced the relative abundance of plant reads from 65% to 0.6%, while drastically increasing the number and diversity of animal, fungal, and protist reads detected. Thus, PoacV9_01 can be used to facilitate the study of eukaryotes present in grass phytobiomes. In addition, the pipeline developed here can be used to develop PNA clamps that target other plant species.
Nucleoid openness profiling links bacterial genome structure to phenotype
Authors: Al-Bassam Mahmoud M , Moyne Oriane , Chapin Nate , Zengler Karsten
Published: May 2020

Gene expression requires specific structural alternations in the nucleoid structure to enable the access of the transcription machinery into the genomic DNA. In prokaryotes, DNA binding proteins, including nucleoid-associated proteins (NAPs) and transcription factors (TFs), drive the change in structure and gene expression. Currently, studies of global NAP and TF binding are often hindered by the lack of appropriate epigenomic tools. Here, we present POP-seq, a method that providesin vivogenome-wide openness profiles of the bacterial nucleoid. We demonstrate that POP-seq can be used to map the globalin vivoprotein-DNA binding events. Our results highlight a negative correlation between genome openness, compaction and transcription, suggesting that regions that are not accessible to Tn5 transposase are either too compacted or occupied by RNA polymerase. Importantly, we also show that the least open regions are enriched in housekeeping genes, while the most open regions are significantly enriched in genes important for fast adaptation to changing environment. Finally, we demonstrated that the genome openness profile is growth condition specific. Together, those results suggest a model where one can distinguish two types of epigenetic control: one stable, long-term silencing of highly compacted regions, and a second, highly responsive regulation through the dynamic competition between NAPs and RNA polymerase binding. Overall, POP-seq captures structural changes in the prokaryotic chromatin and provides condition-specific maps of global protein-DNA binding events, thus linking overall transcriptional and epigenetic regulation directly to phenotype.
Conjugated activation of myocardial-specific transcription ofGja5by a pair of Nkx2-5-Shox2 co-responsive elements
Authors: Yang Tianfang , Huang Zhen , Li Hua , Wang Linyan , Chen YiPing
Published: May 2020

The sinoatrial node (SAN) is the primary pacemaker in the heart. During cardiogenesis,Shox2andNkx2-5are co-expressed in the junction domain of the SAN and regulate pacemaker cell fate through a Shox2-Nkx2-5 antagonism. Cx40 is a marker of working myocardium and an Nkx2-5 transcriptional output antagonized by Shox2, but the underlying regulatory mechanisms remain elusive. Here we characterized a bona fide myocardial-specificGja5(coding gene of Cx40) distal enhancer consisting of a pair of Nkx2-5 and Shox2 co-bound elements in the regulatory region ofGja5. Transgenic reporter assays revealed that neither element alone, but the conjugation of both elements together, drives myocardial-specific transcription. Genetic analyses confirmed that the activation of this enhancer depends on Nkx2-5 but is inhibited by Shox2in vivo, and its presence is essential forGja5expression in the myocardium but not the endothelial cells of the heart. Furthermore, chromatin conformation analysis showed an Nkx2-5-dependent loop formation between these two elements and theGja5promoterin vivo, indicating that Nkx2-5 bridges the conjugated activation of this enhancer by pairing the two elements to theGja5promoter.
A 5-min RNA preparation method for COVID-19 detection with RT-qPCR
Authors: Ladha Alim , Joung Julia , Abudayyeh Omar O. , Gootenberg Jonathan S. , Zhang Feng
Published: May 2020

RNA extraction has become a bottleneck for detection of COVID-19, in part because of reagent shortages. We present here a rapid protocol that circumvents the need for RNA extraction that is compatible with RT-qPCR-based detection methods.
Genome-wide association studies of cognitive and motor progression in Parkinson's disease
Authors: Tan Manuela MX , Lawton Michael A , Jabbari Edwin , Reynolds Regina H , Iwaki Hirotaka , Blauwendraat Cornelis , Kanavou Sofia , Pollard Miriam I , Hubbard Leon , Malek Naveed , Grosset Katherine A , Marrinan Sarah L , Bajaj Nin , Barker Roger A , Burn David J , Bresner Catherine , Foltynie Thomas , Wood Nicholas W , Williams-Gray Caroline H , Hardy John , Nalls Michael A , Singleton Andrew B , Williams Nigel M , Ben-Shlomo Yoav , Hu Michele TM , Grosset Donald G , Shoai Maryam , Morris Huw R
Published: May 2020

Background: There are currently no treatments that stop or slow the progression of Parkinson's disease (PD). Case-control genome-wide association studies (GWASs) have identified variants associated with disease risk, but not progression.
Objective: To identify genetic variants associated with PD progression in GWASs.
Methods: We analysed three large, longitudinal cohorts: Tracking Parkinson's, Oxford Discovery, and the Parkinson's Progression Markers Initiative. We included clinical data for 3,364 patients with 12,144 observations (mean follow-up 4.2 years). We used a new method in PD, following a similar approach in Huntington's disease, where we combined multiple assessments using a principal components analysis to derive scores for composite, motor, and cognitive progression. These scores were analysed in linear regressions in GWASs. We also performed a targeted analysis of the 90 PD risk loci from the latest case-control meta-analysis.
Results: There was no overlap between variants associated with PD risk, from case-control studies, and PD age at onset versus PD progression. The APOE ϵ4 tagging variant, rs429358, was significantly associated with the rate of composite and cognitive progression in PD. No single variants were associated with motor progression. However in gene-based analysis, variation across ATP8B2, a phospholipid transporter related to vesicle formation, was nominally associated with motor progression (p=5.3 x 10^-6).
Conclusions: This new method in PD improves measurement of symptom progression. We provide strong evidence that the APOE ϵ4 allele drives progressive cognitive impairment in PD. We have also reported loci of interest which need to be tested in further studies.
The actin-modulating protein Synaptopodin mediates long-term survival of dendritic spines
Authors: Yap Kenrick , Drakew Alexander , Smilovic Dinko , Rietsche Michael , Vuksic Mario , Turco Domenico Del , Deller Thomas
Published: May 2020

Large spines are stable and important for memory trace formation. The majority of large spines also contains Synaptopodin (SP), an actin-modulating and plasticity-related protein. Since SP stabilizes F-actin, we speculated that the presence of SP within large spines could explain their long lifetime. Indeed, using time-lapse 2-photon-imaging of SP-transgenic granule cells in mouse organotypic tissue cultures we found that spines containing SP survived considerably longer than spines of equal size without SP. Of note, SP-positive spines that underwent pruning first lost SP before disappearing. Whereas the survival time courses of SP-positive (SP+) spines followed conditional two-phase decay functions, SP-negative (SP-) spines and all spines of SP-deficient animals showed single exponential decays. These results implicate SP as a major regulator of long-term spine stability: SP clusters stabilize spines and the presence of SP indicates spines of high stability.
SGT1 is not required for bacterial PAMP-triggered immunity
Authors: Yu Gang , Xian Liu , Zhuang Haiyan , Macho Alberto P.
Published: May 2020

Plant immune signaling activated by the perception of pathogen-associated molecular patterns (PAMPs) or effector proteins is mediated by PRRs and NLRs, respectively, and often share cellular components and downstream responses. The suppressor of the G2 allele of skp1 (SGT1) is a core immune regulator required for the activation of NLR-mediated immunity. In this work, we examined the requirement of SGT1 for PRR-mediated immune responses in bothNicotiana benthamianaand Arabidopsis. Using complementary genetic approaches, we found that SGT1 is not limiting for early PRR-dependent responses or anti-bacterial immunity. Therefore, we conclude that SGT1 does not play a significant role in bacterial PAMP-triggered immunity.
Efficacy and safety of a combination regimen of phenothrin and ivermectin lotion in patients with head lice in Okinawa, Japan
Authors: Komoda Masayo , Yamaguchi Sayaka , Takahashi Kenzo , Yanase Kazuko , Umezawa Masakazu , Miyajima Atsushi , Yoshimasu Takashi , Sato Eiji , Ozeki Rie , Ishii Norihisa
Published: May 2020

In Japan, pyrethroid‐resistant head lice have been increasing; however, only 0.4% phenothrin, a pyrethroid drug, is available as an over the counter formulation. In recent years, Sumithrin® Lotion containing 5% phenothrin (PHT) was approved for scabies. In the USA, Sklice® Lotion containing 0.5% ivermectin (IVM) is used for the treatment of pyrethroid‐resistant head lice. Therefore, to enhance the treatment of head lice in Japan, we conducted a clinical study to confirm the efficacy and safety of a combination regimen of PHT and IVM (PI regimen). Twelve cases were enrolled and PHT was applied to all patients on day 1. On day 8, five patients (41.7%) were lice free, and PHT was applied again. Notably, seven patients were not lice free and were switched to IVM. The rate of patients who were lice free on the PI regimen, which was the primary end‐point, was 75.0% on day 15 and 91.7% on day 22. No adverse events were reported. A genetic analysis of the head lice collected at each visit revealed a kdr mutation in all patients. These results suggest that the PI regimen is safe and effective for the treatment of pyrethroid‐resistant head lice in Japan.