bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life history scaling and the division of energy in forests
Authors: Grady John M. , Read Quentin D. , Record Sydne , Rüger Nadja , Zarnetske Phoebe L. , Dell Anthony I. , Hubbell Stephen P. , Michaletz Sean T. , Shenkin Alexander , Enquist Brian J. 
Published: June 2020

AbstractThe competition for light has long been regarded as a key axis of niche partitioning that promotes forest diversity, but available evidence is contradictory. Despite strong tradeoffs between growth and survival with light, field tests suggest neutral forces govern tree composition across forest gaps and resource use across size classes. Here we integrate scaling and niche theory, and use data from >114,000 woody plants in a tropical, old growth forest to test and predict patterns of niche partitioning with size and light. Consistent with predictions, the relative abundance, production, light capture, and richness of species in life histories with fast growth follow a power law relationship, increasing 1–2 orders of magnitude along a solar and size gradient. Competitive neutrality between size classes emerges above the sapling layer, where increasing access to light is counterbalanced by stronger self-shading. Convergent power law patterns of resource partitioning across taxa and spatial scale suggest general life history tradeoffs drive the organization of diverse communities.
A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782) provides insights into its osmoregulation and sex reversal
Authors: Zhu Kecheng , Zhang Nan , Liu Bao-Suo , Guo Liang , Guo Hua-Yang , Jiang Shi-Gui , Zhang Dianchang 
Published: June 2020

AbstractThe yellowfin seabreamAcanthopagrus latusis the economically most important Sparidae fish species in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. To elucidate genetic mechanisms of osmoregulation and sex reversal in this fish, a high-quality reference genome of the yellowfin seabream was generated by a combination of Illumina and PacBio technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. Moreover, among the 19,631 protein-coding genes, we found that theARRDC3andGSTAgene families related to osmoregulation underwent an extensive expansion in two euryhaline Sparidae fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.
The regulatory genome of the malaria vectorAnopheles gambiae: integrating chromatin accessibility and gene expression
Authors: Ruiz José L. , Ranford-Cartwright Lisa C. , Gómez-Díaz Elena 
Published: June 2020

ABSTRACTAnopheles gambiaemosquitoes are primary human malaria vectors, but we know very little about mechanisms of transcriptional regulation. We profiled chromatin accessibility by ATAC-seq in laboratory-rearedAn. gambiaemosquitoes experimentally infected with the human malaria parasitePlasmodium falciparum. By integrating ATAC-seq, RNA-seq and ChIP-seq data we showed a positive correlation between accessibility at promoters and introns, gene expression and active histone marks. By comparing expression and chromatin structure patterns in different tissues, we were able to infer cis-regulatory elements controlling tissue specific gene expression and to predict the in vivo binding sites of relevant transcription factors. The ATAC-seq assay also allowed the precise mapping of active regulatory regions, including novel transcription start sites and enhancers that annotate to mosquito immune-response genes. This study is important not only for advancing our understanding of mechanisms of transcriptional regulation in the mosquito vector of human malaria, but the information is of great potential for developing new mosquito-control and anti-malaria strategies.
Long-range neural coherence encodes stimulus information in primate visual cortex
Authors: Kermani Mojtaba , Zavitz Elizabeth , Oakley Brian , Price Nicholas S.C. , Hagan Maureen A. , Wong Yan T. 
Published: June 2020

AbstractIn the primary visual cortex, neurons with similar receptive field properties are bound together through widespread networks of horizontal connections that span orientation columns. How connectivity across the cortical surface relates to stimulus information is not fully understood. We recorded spiking activity and the local field potential (LFP) from the primary visual cortex of marmoset monkeys and examined how connectivity between distant orientation columns affect the encoding of visual orientation.Regardless of their spatial separation, recording sites with similar orientation preferences have higher coherence between spiking activity and the local field potential than sites with different preferred orientation. Using information theoretic methods, we measured the amount of stimulus information that is shared between pairs of sites. More stimulus information can be decoded from pairs with the same preferred stimulus orientation than the pairs with a different preferred orientation, and the amount of information is significantly correlated with the magnitude of beta-band spike-LFP coherence. These effects remained after controlling for firing rate differences.Our results thus show that spike-LFP synchronization in the beta-band is associated with the encoding of stimulus information within the primary visual cortex of marmoset monkeys.Significance StatementA fundamental step in processing images in the visual cortex is coordinating the neural activity across distributed populations of neurons. Here, we demonstrate that populations of neurons in the primary visual cortex of marmoset monkeys with the same stimulus orientation preference temporally coordinate their activity patterns when presented with a visual stimulus. We find maximum synchronization in the beta range depends on the similarity of orientation preference at each pair of the neural population.
Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins
Authors: Li Xiaobing , Xiao Kangpeng , Chen Xiaoyuan , Liang Xianghui , Zhang Xu , Zhang Zhipeng , Zhai Junqiong , Wang Ruichen , Zhou Niu , Chen Zu-Jin , Su Renwei , Zhou Fuqing , Holmes Edward C. , Irwin David M. , Chen Rui-Ai , He Qian , Wu Ya-Jiang , Wang Chen , Du Xue-Qing , Peng Shi-Ming , Xie Wei-Jun , Shan Fen , Li Wan-Ping , Dai Jun-Wei , Shen Xuejuan , Feng Yaoyu , Xiao Lihua , Chen Wu , Shen Yongyi 
Published: June 2020

AbstractSARS-CoV-2 is having severe impact on public health at a global scale. Malayan pangolin SARS-CoV-2-related coronavirus (SARSr-CoV-2) is closely related to SARS-CoV-2. We show that CT scans of virus-positive pangolins reveal bilateral ground-glass opacities in lungs in similar manner to COVID-19 patients. The virus infected multiple organs in pangolins, with the lungs being the major target. Histological expression showed that ACE2 and TMPRSS2 are co-expressed with viral RNA. Transcriptome analysis revealed an inadequate interferon response, with different dysregulated chemokines and cytokines responses in pregnant and non-pregnant adults and fetuses. Viral RNA and protein were detected in three fetuses providing evidence for vertical virus transmission. In sum, our study identifies the biological framework of SARSr-CoV-2 in pangolins, revealing striking similarities to COVID-19 in humans.
Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals: Streptomyces strains and phages for antibiotic discovery
Authors: Montaño Elizabeth T. , Nideffer Jason F. , Brumage Lauren , Erb Marcella , Derman Alan I. , Davis John Paul , Estrada Elena , Fu Sharon , Le Danielle , Vuppala Aishwarya , Tran Cassidy , Luterstein Elaine , Lakkaraju Shivani , Panchagnula Sriya , Ren Caroline , Doan Jennifer , Tran Sharon , Soriano Jamielyn , Fujita Yuya , Gutala Pranathi , Fujii Quinn , Lee Minda , Bui Anthony , Villarreal Carleen , Shing Samuel R. , Kim Sean , Freeman Danielle , Racha Vipula , Ho Alicia , Kumar Prianka , Falah Kian , Dawson Thomas , Enustun Eray , Prichard Amy , Gomez Ana , Khanna Kanika , Trigg Shelly , Pogliano Kit , Pogliano Joe 
Published: June 2020

AbstractThe threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare’s most potent antibiotics are becoming obsolete. Approximately two-thirds of the world’s antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, in order to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 101 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistantStaphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) againstS. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.
Fecal microbiota transplantation reconstructs the gut microbiota of septic mice and protects the intestinal mucosal barrier
Authors: Gai Xiaowei , Wang Huawei , Li Yaqing , Zhao Haotian , He Cong , Wang Zihui , Zhao Heling 
Published: June 2020

AbstractThe gastrointestinal (GI) tract has long been hypothesized to play an integral role in the pathophysiology of sepsis, and gut microbiota (GM) dysbiosis may be the key factor. Previous studies has confirmed that microbiome is markedly altered in critical illness. We aimed to confirm the existence of gut microbiota imbalance in the early stage of sepsis, observe the effect of fecal microbiota transplantation (FMT) on sepsis, and explore whether FMT can reconstruct the GM of septic mice and restore its protective function on the intestinal mucosal barrier. Through the study of flora, mucus layer, tight junction, immune barrier, and short-chain fatty acid changes in septic mice and fecal microbiota transplanted mice, we found that GM imbalance exists early in sepsis. FMT can improve morbidity and effectively reduce mortality in septic mice. After the fecal bacteria were transplanted, the abundance and diversity of the gut flora were restored, and the microbial characteristics of the donors changed. FMT can effectively reduce epithelial cell apoptosis, improve the composition of the mucus layer, upregulate the expression of tight junction proteins, and reduce intestinal permeability and the inflammatory response, thus protecting the intestinal barrier function. After FMT, Lachnospiraceae contributes the most to intestinal protection through enhancement of the L-lysine fermentation pathway, resulting in the production of acetate and butanoate, and may be the key bacteria for short-chain fatty acid metabolism and FMT success.
Structural details of amyloid beta oligomers in complex with human prion protein as revealed by solid-state MAS NMR spectroscopy
Authors: König Anna S. , Rösener Nadine S. , Gremer Lothar , Flender Daniel , Hoyer Wolfgang , Neudecker Philipp , Willbold Dieter , Heise Henrike 
Published: June 2020

ABSTRACTHuman PrP (huPrP) is a high-affinity receptor for oligomeric Aβ. Synthetic oligomeric Aβ species are known to be heterogeneous, dynamic and transient, rendering their structural investigation particularly challenging. Here, we used huPrP to preserve Aβ oligomers by co-precipitating them into large hetero-assemblies to investigate the conformation of Aβ(1-42) oligomers and huPrP in the complex by solid-state MAS NMR spectroscopy. The disordered N-terminal region of huPrP becomes immobilized in the complex and therefore visible in dipolar spectra without adopting chemical shifts characteristic of a regular secondary structure. Most of the well-defined C-terminal part of huPrP is part of the rigid complex, and solid-state NMR spectra suggest a loss in regular secondary structure in the last two α-helices. For Aβ(1-42) oligomers in complex with huPrP, secondary chemical shifts reveal a substantial β-strand content. Importantly, not all Aβ(1-42) molecules within the complex have identical conformations. Comparison with the chemical shifts of synthetic Aβ fibrils suggests that the Aβ oligomer preparation represents a heterogeneous mixture of β-strand-rich assemblies, of which some have the potential to evolve and elongate into different fibril polymorphs, reflecting a general propensity of Aβ to adopt variable β-structure conformers.
Organization of DNA replication origin firing inXenopusegg extracts : the role of intra-S checkpoint
Authors: Ciardo Diletta , Haccard Olivier , Narassimprakash Hemalatha , Arbona Jean-Michel , Hyrien Olivier , Audit Benjamin , Marheineke Kathrin , Goldar Arach 
Published: June 2020

AbstractDuring cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of the cell cycle. Origins fire as synchronous clusters which is proposed to be regulated by the intra-S checkpoint. By modelling the unchallenged, the checkpoint-inhibited and the checkpoint protein Chk1 over-expressed replication pattern of single DNA molecules fromXenopussperm chromatin replicated in egg extracts, we demonstrate that the quantitative modelling of data requires: 1) a segmentation of the genome into regions of low and high probability of origin firing; 2) that regions with high probability of origin firing escape intra-S checkpoint regulation and 3) the variability of the rate of DNA synthesis close to replication forks is a necessary ingredient that should be taken in to account in order to describe the dynamic of replication origin firing. This model implies that the observed origin clustering emerges from the apparent synchrony of origin firing in regions with high probability of origin firing and challenge the assumption that the intra-S checkpoint is the main regulator of origin clustering.Author summaryDNA replication is one of the fundamental cell functions. The genome of eukaryotic organisms is duplicated from multiple positions named replication origins. Single molecule experiments allow to visualise the dynamics of spatio-temporal patterns created during replication process. The dynamic of replication process is regulated by checkpoints. However, the influence and the role of checkpoint regulation in the dynamics of spatio-temporal patterns of DNA replication is not understood. In this work we build a minimal, process-based and data rooted numerical model that allows to decipher the impact of checkpoint regulation on the dynamics of spatio-temporal pattern of DNA replication.
Dissection-independent production of a protective whole-sporozoite malaria vaccine
Authors: Blight Joshua , Sala Katarzyna A. , Atcheson Erwan , Kramer Holger , El-Turabi Aadil , Real Eliana , Dahalan Farah A. , Bettencourt Paulo , Dickinson Emma , Alves Eduardo , Salman Ahmed M. , Janse Chris J. , Ashcroft Frances , Hill Adrian V. S. , Reyes-Sandoval Arturo , Blagborough Andrew M. , Baum Jake 
Published: June 2020

AbstractComplete protection against human malaria challenge has been achieved using infected mosquitoes as the delivery route for immunization withPlasmodiumparasites. Strategies seeking to replicate this efficacy with either a manufactured whole-parasite or subunit vaccine, however, have shown only limited success. A major roadblock to whole parasite vaccine progress and understanding of the human infective sporozoite form in general, is reliance on manual dissection for parasite isolation from infected mosquitoes. We report here the development of a four-step process based on whole mosquito homogenization, slurry and density-gradient filtration, combined with free-flow electrophoresis that is able to rapidly produce a pure, aseptic sporozoite inoculum from hundreds of mosquitoes. MurineP. bergheior human-infectiveP. falciparumsporozoites produced in this way are 2-3-fold more infective within vitrohepatocytes and can confer sterile protection when immunized intravenously with subsequent challenge using a mouse malaria model. Critically, we can also demonstrate for the first time 60-70% protection when the same parasites are administered via intramuscular (i.m.) route. In developing a process amenable to industrialisation and demonstrating efficacy by i.m. route these data represent a major advancement in capacity to produce a whole parasite malaria vaccine at scale.One-Sentence SummaryA four-step process for isolating pure infective malaria parasite sporozoites at scale from homogenized whole mosquitoes, independent of manual dissection, is able to produce a whole parasite vaccine inoculum that confers sterilizing protection.
BEHAVIOURAL AND MOLECULAR EFFECTS OF CANNABIDIOLIC ACID IN MICE
Authors: Alegre-Zurano Laia , Martín-Sánchez Ana , Valverde Olga 
Published: June 2020

ABSTRACTAimsCannabidiolic acid (CBDA) is one of the most abundant phytocannabinoid acids in theCannabis Sativaplant. It has been shown it is able to exert some therapeutic effects such as antiemetic, anti-inflammatory, anxiolytic or antidepressant, although some of them remain under debate. In the present study we aim to assess the potential effects of CBDA on different behaviours and on the modulation of neuroinflammatory markers in the prefrontal cortex (PFC).Main methodsthe effects of acute and/or chronic CBDA (0.001-1 mg/kg i.p.) treatment were evaluated on cognitive, emotional, motivational and nociceptive behaviours in male CD1 mice. For this, Y-maze and elevated plus maze paradigms, spontaneous locomotor activity, social interaction, hot-plate, formalin and tail suspension tests were used. We also studied the effects of CBDA on the rewarding responses of cocaine in the conditioned place preference (CPP) paradigm. PFC was dissected after acute and chronic CBDA treatments to evaluate inflammatory markers.Key findingsacute CBDA treatment induced antinociceptive responses in the hot-plate test. A 10-day chronic CBDA treatment reduced despair-like behaviour in the tail suspension test. CBDA did not alter the remaining behavioural tests assayed, including cocaine-induced reward in the CPP. Regarding the biochemical analysis, chronic CBDA treatment diminished peroxisome proliferator-activated receptor gamma (PPAR-γ) and increased interleukin-6 (IL-6) protein levels in PFC.Significancethese results show that CBDA has limitedin vivoeffects modulating mice behaviour, highlighting the current disagreement regarding its therapeutic potential.
High-throughput 5’P sequencing enables the study of degradation-associated ribosome stalls
Authors: Zhang Yujie , Pelechano Vicent 
Published: June 2020

ABSTRACTRNA degradation is critical for gene expression and mRNA quality control. mRNA degradation is connected to the translation process up to the degree that 5’-3’ mRNA degradation follows the las translating ribosome. Here we present an improved high-throughput 5’P degradome RNA sequencing method (HT-5Pseq). HT-5Pseq is easy, scalable and uses affordable duplex-specific nuclease based rRNA depletion. We investigatein vivoribosome stalls focusing on translation termination. By comparing ribosome stalls identified by ribosome profiling, disome-seq and HT-5PSeq we identify that degradation-associated ribosome stalls are often enriched in Arg preceding the stop codon. On the contrary, mRNAs depleted for those stalls use more frequently TAA stop codon preceded by hydrophobic amino acids. Finally, we shown that termination stalls identified by HT-5Pseq, and not by other approaches, are associated to decreased mRNA stability. Our work suggests that ribosome stalls associated to mRNA decay can be easily captured by investigating the 5’P degradome.
Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence
Authors: Vattepu Ravi , Klausmeyer Rachel A. , Ayella Allan , Yadav Rahul , Dille Joseph T. , Saiz Stan V. , Beck Moriah R. 
Published: June 2020

ABSTRACTImmunoglobulin (Ig) domains are the most prevalent protein domain structure and share a highly conserved folding pattern; however, this structural family of proteins is also the most diverse in terms of biological roles and tissue expression. Ig domains vary significantly in amino acid sequence but share a highly conserved tryptophan in the hydrophobic core of this beta-stranded protein. Palladin is an actin binding and bundling protein that has five Ig domains and plays an important role in normal cell adhesion and motility. Mutation of the core tryptophan in one Ig domain of palladin has been identified in a pancreatic cancer cell line, suggesting a crucial role for this sole tryptophan in palladin Ig domain structure, stability, and function. We found that actin binding and bundling was not completely abolished with removal of this tryptophan despite a partially unfolded structure and significantly reduced stability of the mutant Ig domain as shown by circular dichroism investigations. In addition, this mutant palladin domain displays a tryptophan-like fluorescence attributed to an anomalous tyrosine emission at 345 nm. Our results indicate that this emission originates from a tyrosinate that may be formed in the excited ground state by proton transfer to a nearby glutamyl residue. Furthermore, this study emphasizes the importance of tryptophan in protein structural stability and illustrates how tyrosinate emission contributions may be overlooked during the interpretation of the fluorescence properties of proteins.SHORT ABSTRACTThis study explores the functional and structural consequences of a point mutation in palladin, an Ig domain protein first identified in a pancreatic tumor cancer cell line. While exploring the consequences of mutating this conserved tryptophan in the hydrophobic core of the most prevalent domain structure found in proteins, an anomalous tyrosine fluorescence phenomenon was exposed.