bluuebunny/crossref_metadata_2025_split huggingface dataset:
The benefits of herbivory outweigh the costs of bioerosion in a eutrophic coral community
Authors: Dytnerski James K. , Marshall Katie E. , Baker David M. , Russell Bayden D. 
Published: June 2021

AbstractHerbivores play an integral part in maintaining the health of coral reefs by suppressing the growth of algae and accumulation of sediment and facilitating coral growth. However, in predator-depleted systems where densities of herbivores are unnaturally high, grazing can have detrimental effects on corals through excessive bioerosion. Yet, these benefits and costs are rarely investigated concurrently, especially in eutrophic systems where grazers may play a disproportionate role. We used a year-long exclusion experiment to elucidate the effect of natural densities of the dominant herbivore (the sea urchinDiadema setosum) on coral communities in a heavily fished and eutrophic system (Hong Kong, China). To assess benthic community response to grazing, we monitored the survival and growth of three locally abundant coral species (Pavona decussata, Platygyra carnosusandPoritessp.), algal and sediment accumulation, and bioerosion of coral skeletons across seasons. We found that urchins maintained our experimental coral assemblages, and when excluded, there was a 25 to 75-fold increase in algal-sediment matrix accumulation. Contrary to predictions, there was no general response of corals to urchin presence;Porites sp.survivorship increased whileP. decussatawas unaffected, and growth rates of both species was unchanged. Surprisingly,P. carnosusexperienced higher mortality and bioerosion of up to 33% of their buoyant weight when urchins were present. Therefore, under natural densities, sea urchins clear substrate of algae and sediment, increase survival, maintain growth rates and health of coral assemblages, yet can accelerate the bioerosion of species with porous skeletons following mortality.
Identification and differentiation of Pseudomonas species in field samples using an rpoD amplicon sequencing methodology
Authors: Lauritsen Jonas Greve , Hansen Morten Lindqvist , Bech Pernille Kjersgaard , Jelsbak Lars , Gram Lone , Strube Mikael Lenz 
Published: June 2021

ABSTRACTSpecies of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural or industrial settings, the organisms must be profiled at species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760 nt region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a sixteen membered Pseudomonas species mock community. All 16 species were correctly and semi-quantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3V4 amplicon sequencing only correctly identified one species. We analysed the Pseudomonas profile in thirteen soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the microbial community, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and ten from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD-amplicon approach identified more species than found by cultivation, including hard-to-culture non-fluorescent pseudomonads, as well as more than found by 16S rRNA V3V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method.ImportanceA high throughput sequence-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant-growth promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.
Enhanced virus translation enables miR-122-independent Hepatitis C Virus propagation
Authors: Panigrahi Mamata , Palmer Michael A , Wilson Joyce A 
Published: June 2021

ABSTRACTThe 5’UTR of the Hepatitis C Virus genome forms RNA structures that regulate virus replication and translation. The region contains a viral internal ribosomal entry site and a 5’ terminal region. Binding of the liver specific miRNA, miR-122, to two conserved binding sites in the 5’ terminal region regulates viral replication, translation, and genome stability, and is essential for efficient virus replication, but its precise mechanism of its action is still under debate. A current hypothesis is that miR-122 binding stimulates viral translation by facilitating the viral 5’ UTR to form the translationally active HCV IRES RNA structure. While miR-122 is essential for detectable virus replication in cell culture, several viral variants with 5’ UTR mutations exhibit low level replication in the absence of miR-122. We show that HCV mutants capable of replicating independently of miR-122 also replicate independently of other microRNAs generated by the canonical miRNA synthesis pathway. Further, we also show that the mutant genomes display an enhanced translation phenotype that correlates with their ability to replicate independently of miR-122. Finally, we provide evidence that translation regulation is the major role for miR-122, and show that miR-122-independent HCV replication can be rescued to miR-122-dependent levels by the combined impacts of 5’ UTR mutations that stimulate translation, and by stabilizing the viral genome by knockdown of host exonucleases and phosphatases that degrade the genome. Thus, we provide a model suggesting that translation stimulation and genome stabilization are the primary roles for miR-122 in the virus life cycle.IMPORTANCEThe unusual role of miR-122 in promoting HCV propagation is incompletely understood but is essential for an HCV infection. To better understand its role, we have analyzed HCV mutants capable of replicating independently of miR-122. Our data show that the ability of viruses to replicate independently of miR-122 correlates with enhanced virus translation, but that genome stabilization is required to restore efficient HCV replication. This suggests that viruses must gain both abilities to escape the need for miR-122 and impacts the possibility that HCV can evolve to replicate outside of the liver.
Synthetic Cooling Agents in US-marketed E-cigarette Refill Liquids and Popular Disposable E-cigarettes: Chemical Analysis and Risk Assessment
Authors: Jabba Sairam V. , Erythropel Hanno C. , Torres Deyri Garcia , Delgado Lauren A. , Woodrow Jackson G. , Anastas Paul T. , Zimmerman Julie B. , Jordt Sven-Eric 
Published: June 2021

AbstractBackgroundMenthol, through its cooling and pleasant sensory effects, facilitates smoking and tobacco product initiation, resulting in the high popularity of mint/menthol-flavored E-cigarettes. More recently, E-cigarette vendors started marketing synthetic cooling agents as additives that impart a cooling effect but lack a characteristic minty odor. Knowledge about content of synthetic coolants in US-marketed E-cigarette products and associated health risks is limited.MethodsE-liquid vendor sites were searched with the terms “koolada”, “kool/cool”, “ice”, or WS-3/WS-23, denoting individual cooling agents, and relevant refill E-liquids were purchased. “Ice” flavor varieties of Puffbar, the most popular disposable E-cigarette brand, were compared with non-”Ice” varieties. E-liquids were characterized, and synthetic coolants quantified using GC/MS. Margin of exposure (MOE), a risk assessment parameter, was calculated to assess the risk associated with synthetic coolant exposure from E-cigarette use.ResultsWS-3 was detected in 24/25 refill E-liquids analyzed. All Puffbar flavor varieties contained either WS-23 (13/14) or WS-3 (5/14), in both “Ice”- and non-”Ice” flavors. Modeling consumption of WS-3 from vaped E-liquids, resulted in MOEs below the safe margin of 100 for most daily use scenarios. MOEs for WS-23 were <100 for 10/13 Puffbar flavors in all use scenarios. Puffbar power specifications are identical to Juul devices.ConclusionsSynthetic cooling agents (WS-3/WS-23) were present in US-marketed E-cigarettes, at levels that may result in consumer exposures exceeding safety thresholds set by regulatory agencies. Synthetic coolants are not only found in mint-or menthol-flavored products, but also in fruit- and candy-flavored products, including popular disposable E-cigarette products such as Puffbar.ImplicationsSynthetic cooling agents are widely used in “kool/cool”- and “ice”-flavored E-liquids and in E-liquids without these labels, both as a potential replacement for menthol or to add cooling ‘notes’ to non-menthol flavors. These agents may be used to bypass current and future regulatory limits on menthol content in tobacco products, and not just E-cigarettes. Since synthetic cooling agents are odorless, they may not fall under the category of “characterizing flavor”, potentially circumventing regulatory measures based on this concept. Regulators need to consider the additional health risks associated with exposure to synthetic cooling agents.
Habitat Protection Indexes - new monitoring measures for the conservation of coastal and marine habitats
Authors: Kumagai Joy A. , Favoretto Fabio , Pruckner Sara , Rogers Alex D. , Weatherdon Lauren V. , Aburto-Oropeza Octavio , Niamir Aidin 
Published: June 2021

AbstractA worldwide call to implement habitat protection aims to halt biodiversity loss. To monitor the extent of coastal and marine habitats within protected areas (PAs) in a standardized, open source, and reproducible way, we constructed the Local and the Global Habitat Protection Indexes (LHPI and GHPI, respectively). The LHPI pinpoints the jurisdictions with the greatest opportunity to expand their own PAs, while the GHPI showcases which jurisdictions contribute the most in area to the protection of these habitats globally. Jurisdictions were evaluated to understand which have the highest opportunity to contribute globally to the protection of habitats by meeting a target of 30% coverage of PAs with Areas Beyond National Jurisdiction (ABNJ) having the greatest opportunity to do so. While we focus on marine and coastal habitats, our workflow can be extended to terrestrial and freshwater habitats. These indexes are useful to monitor aspects of Sustainable Development Goal 14 and the emerging post-2020 Global Biodiversity Framework, to understand the current status of international cooperation on coastal and marine habitats conservation.
Molecular insights into differentiated ligand recognition of the human parathyroid hormone receptor 2
Authors: Wang Xi , Cheng Xi , Zhao Lihua , Wang Yuzhe , Ye Chenyu , Zou Xinyu , Dai Antao , Cong Zhaotong , Chen Jian , Zhou Qingtong , Xia Tian , Jiang Hualiang , Xu Eric H. , Yang Dehua , Wang Ming-Wei 
Published: June 2021

AbstractThe parathyroid hormone receptor 2 (PTH2R) is a class B1 G protein-coupled receptor (GPCR) involved in regulation of calcium transport, nociception mediation, and wound healing. Naturally occurring mutations in PTH2R were reported to cause hereditary diseases, including syndromic short stature. Here we report the cryo-electron microscopy structure of PTH2R bound to its endogenous ligand, tuberoinfundibular peptide (TIP39), and a heterotrimeric Gs protein at a global resolution of 2.8 Å. The structure reveals that TIP39 adopts a unique loop conformation at N terminus and deeply inserts into the orthosteric ligand-binding pocket in the transmembrane (TM) domain. Molecular dynamics (MD) simulation and site-directed mutagenesis studies uncover the basis of ligand specificity relative to three PTH2R agonists, TIP39, PTH, and PTH-related peptide (PTHrP). We also compare the action of TIP39 with an antagonist lacking six residues from the peptide N terminus, TIP(7–39), which underscores the indispensable role of the N terminus of TIP39 in PTH2R activation. Additionally, we unveil that a disease-associated mutation G258D significantly diminished cAMP accumulation induced by TIP39. Together, these results not only provide structural insights into ligand specificity and receptor activation of class B1 GPCRs, but also offer a foundation to systematically rationalize the available pharmacological data to develop novel therapies for various disorders associated with PTH2R.
High-quality complete genome resource of tomato rhizosphere strain Pseudomonas donghuensis P482, a representative of a species with biocontrol activity against plant pathogens
Authors: Krzyżanowska Dorota M. , Iwanicki Adam , Czajkowski Robert , Jafra Sylwia 
Published: June 2021

AbstractStrain P482 was isolated from a tomato rhizosphere and classified as Pseudomonas donghuensis. The P. donghuensis species was first established in 2015 and currently comprises only four strains: P482, HYST, SVBP6, and 22G5. P. donghuensis strains antagonize plant pathogens, including bacteria, fungi and oomycetes, and therefore are of high interest regarding their biological control potential to combat plant diseases. The antimicrobial activity of P. donghuensis P482 is based on the production of iron scavenging compound 7-hydroxytropolone, antifungal volatile organic compounds, and yet unidentified secondary metabolite(s). Here, we report a complete genome resource for P. donghuensis strain P482. The genome consists of a single chromosome (5 656 185 bp) with 5258 ORFs (5158 protein-coding genes, 74 tRNAs, 22 rRNAs, 3 ncRNAs and 1 tmRNA) and no plasmid. We believe that the information of the first high-quality, complete genome of P. donghuensis will provide resources for analyses targeting the biological control potential of this species and understanding the traits essential for plant-microbe interaction.
The extracellular matrix supports cancer cell growth under amino acid starvation by promoting tyrosine catabolism
Authors: Nazemi Mona , Yanes Bian , Martinez Montserrat Llanses , Walker Heather , Bard Frederic , Rainero Elena 
Published: June 2021

ABSTRACTBreast and pancreatic tumours are embedded in a collagen I-rich extracellular matrix (ECM) network, where nutrients are scarce due to limited blood flow and elevated tumour growth. Metabolic adaptation is required for cancer cells to endure these conditions. Here, we demonstrated that the presence of ECM supported the growth of invasive breast cancer cells, but not non-transformed mammary epithelial cells, and pancreatic cancer cells under amino acid starvation, through a mechanism that required macropinocytosis-dependent ECM uptake. Importantly, we showed that this behaviour was acquired during carcinoma progression. ECM internalisation, followed by lysosomal degradation, contributed to the upregulation of the intracellular levels of several amino acids, most notably tyrosine and phenylalanine. This resulted in elevated tyrosine catabolism on ECM under starvation, leading to increased fumarate levels, potentially feeding into the tricarboxylic acid cycle. Interestingly, this pathway was required for ECM-dependent cell growth under amino acid starvation, as the knockdown of p-hydroxyphenylpyruvate hydroxylase-like protein (HPDL), the third enzyme of the pathway, opposed cell growth on ECM in both 2D and 3D systems, without affecting cell proliferation on plastic. Finally, high HPDL expression correlated with poor prognosis in breast and pancreatic cancer patients. Collectively, our results highlight that the ECM in the tumour microenvironment represents an alternative source of nutrients to support cancer cell growth, by regulating phenylalanine and tyrosine metabolism.
Second-Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern
Authors: Kovacech Branislav , Fialova Lubica , Filipcik Peter , Skrabana Rostislav , Zilkova Monika , Paulenka-Ivanovova Natalia , Kovac Andrej , Palova Denisa , Paulíkova Rolkova Gabriela , Tomkova Katarina , Csokova Natalia Turic , Markova Karina , Skrabanova Michaela , Sinska Kristina , Basheer Neha , Majerova Petra , Hanes Jozef , Parrak Vojtech , Prcina Michal , Cehlar Ondrej , Cente Martin , Piestansky Juraj , Fresser Michal , Novak Michal , Slavikova Monika , Borsova Kristina , Cabanova Viktoria , Brejova Bronislava , Vinař Tomas , Nosek Jozef , Klempa Boris , Zilka Norbert , Kontsekova Eva 
Published: June 2021

AbstractRecently emerged SARS-CoV-2 variants show resistance to some antibodies that were authorized for emergency use. We employed hybridoma technology combined with authentic virus assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize new variants of SARS-CoV-2. AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 and B.1.351. Finally, the combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. The neutralizing properties were fully reproduced in chimeric mouse-human versions, which may represent a promising tool for COVID-19 therapy.
Cas12a is a dynamic and precise RNA-guided nuclease without off-target activity on λ-DNA
Authors: Paul Bijoya , Chaubet Loïc , Verver Emma , Montoya Guillermo 
Published: June 2021

AbstractCas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here we combined optical tweezers with fluorescence to monitor Cas12a binding onto λ-DNA, providing insight into its DNA binding and cleavage mechanisms. At low forces Cas12a binds DNA specifically with two off-target sites, while at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. Despite the multiple binding events, cleavage is only observed on the target site at low forces, when the DNA is flexible. Activity assays show that the preferential off-target sites are not cleaved, and the λ-DNA is severed at the target site. This precision is also observed in Cas12a variants where the specific dsDNA and the unspecific ssDNA cleavage are dissociated or nick the target DNA. We propose that Cas12a and its variants are precise endonucleases that efficiently scan the DNA for its target but only cleave the selected site in the λ-DNA.
Discovering fragment length signatures of circulating tumor DNA using Non-negative Matrix Factorization
Authors: Renaud Gabriel , Nørgaard Maibritt , Lindberg Johan , Grönberg Henrik , De Laere Bram , Jensen Jørgen Bjerggaard , Borre Michael , Andersen Claus Lindbjerg , Sørensen Karina Dalsgaard , Maretty Lasse , Besenbacher Søren 
Published: June 2021

ABSTRACTSequencing of cell-free DNA (cfDNA) is currently being used to detect cancer by searching both for mutational and non-mutational alterations. Recent work has shown that the length distribution of cfDNA fragments from a cancer patient can inform tumor load and type. Here, we propose non-negative matrix factorization (NMF) of fragment length distributions as a novel method to study fragment lengths in cfDNA samples.Using shallow whole-genome sequencing (sWGS) of cfDNA from a cohort of patients with metastatic castration-resistant prostate cancer (mCRPC), we demonstrate how NMF accurately infers the true tumor fragment length distribution as an NMF component - and that the sample weights of this component correlate with ctDNA levels (r=0.75). We further demonstrate how using several NMF components enables accurate cancer detection on data from various early stage cancers (AUC=0.96). Finally, we show that NMF, when applied across genomic regions, can be used to discover fragment length signatures associated with open chromatin.
In vivo profiling of site-specific human cancer cell states in zebrafish
Authors: Segal Dagan , Mazloom-Farsibaf Hanieh , Chang Bo-Jui , Roudot Philippe , Rajendran Divya , Fiolka Reto , Warren Mikako , Amatruda James F. , Danuser Gaudenz 
Published: June 2021

AbstractTissue microenvironments affect the functional states of cancer cells, but determining these influences in vivo has remained a significant challenge. We present a quantitative high-resolution imaging assay of cancer cell morphology in zebrafish xenografts to probe functional adaptation to variable cell extrinsic cues and molecular interventions. We focus on Ewing Sarcoma, a pediatric cancer driven by a single oncogenic fusion protein EWSR1-FLI1, and with little to no additional somatic mutations, making it a prototypical form of cancer whose adaptation to microenvironments is likely driven by acute, non-genomic mechanisms. Using computer vision analysis of 3D cell shapes, we find systematic shifts in the distribution of cell morphotypes between distinct sites in the fish embryo. We also find site-specific morphological responses to differential expression of EWSR1-FLI1. Combining these data we propose a model where Ewing Sarcoma cancer cell plasticity is sensitive both to expression fluctuation of EWSR1-FLI1 and signals from the surrounding tissue microenvironment, with either or both factors possibly contributing to the oncogenic potential of these cells.
Geometry of inter-areal interactions in mouse visual cortex
Authors: Iyer Ramakrishnan , Siegle Joshua H. , Mahalingam Gayathri , Olsen Shawn , Mihalas Stefan 
Published: June 2021

AbstractThe response of a set of neurons in an area is the result of the sensory input, the interaction of the neurons within the area as well as the long range interactions between areas. We aimed to study the relation between interactions among multiple areas, and if they are fixed or dynamic. The structural connectivity provides a substrate for these interactions, but anatomical connectivity is not known in sufficient detail and it only gives us a static picture. Using the Allen Brain Observatory Visual Coding Neuropixels dataset, which includes simultaneous recordings of spiking activity from up to 6 hierarchically organized mouse cortical visual areas, we estimate the functional connectivity between neurons using a linear model of responses to flashed static grating stimuli. We characterize functional connectivity between populations via interaction subspaces. We find that distinct subspaces of a source area mediate interactions with distinct target areas, supporting the notion that cortical areas use distinct channels to communicate. Most importantly, using a piecewise linear model for activity within each trial, we find that these interactions evolve dynamically over tens of milliseconds following a stimulus presentation. Inter-areal subspaces become more aligned with the intra-areal subspaces during epochs in which a feedforward wave of activity propagates through visual cortical areas. When the short-term dynamics are averaged over, we find that the interaction subspaces are stable over multiple stimulus blocks. These findings have important implications for understanding how information flows through biological neural networks composed of interconnected modules, each of which may have a distinct functional specialization.