bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic variation during culture-adaptation of genetically complexPlasmodium falciparumclinical isolates
Authors: Claessens Antoine , Stewart Lindsay B. , Drury Eleanor , Ahouidi Ambroise D. , Amambua-Ngwa Alfred , Diakite Mahamadou , Kwiatkowski Dominic P. , Awandare Gordon A. , Conway David J. 
Published: September 2022

AbstractExperimental studies on the biology of malaria parasites have been mostly based on laboratory-adapted lines, but there is limited understanding of how these may differ from parasites in natural infections. Loss-of-function mutants have previously been shown to emerge during culture of somePlasmodium falciparumclinical isolates, in analyses that focused on single-genotype infections. The present study included a broader array of isolates, mostly representing multiple-genotype infections which are more typical in areas where malaria is highly endemic. Genome sequence data from multiple time points during several months of culture adaptation of 28 West African isolates were analysed, including previously available sequences along with new genome sequences from additional isolates and timepoints. Some genetically complex isolates eventually became fixed over time to single surviving genotypes in culture, whereas others retained diversity although proportions of genotypes varied over time. Drug-resistance allele frequencies did not show overall directional changes, suggesting that resistance-associated costs are not the main causes of fitness differences among parasites in culture. Loss-of-function mutants emerged during culture in several of the multiple-genotype isolates, affecting genes (includingAP2-HS, EPACandSRPK1) for which loss-of-function mutants were previously seen to emerge in single-genotype isolates. Parasite clones were derived by limiting dilution from six of the isolates, and sequencing identifiedde novovariants not detected in the bulk isolate sequences. Interestingly, most of these were nonsense mutants and frameshifts disrupting the coding sequence ofEPAC, the gene with the largest number of independent nonsense mutants previously identified in laboratory-adapted lines. Analysis of Identity-By-Descent to explore relatedness among clones revealed co-occurring non-identical sibling parasites, illustrative of the natural genetic structure within parasite populations.
Arabidopsis DXO1 affects the processing of precursors of cytoplasmic and chloroplast ribosomal RNA
Authors: Zakrzewska-Placzek Monika , Kwasnik Aleksandra , Krzyszton Michal , Golisz-Mocydlarz Anna , Kufel Joanna 
Published: September 2022

ABSTRACTDecapping 5’-3’ exoribonucleases from the DXO/Rai1 family, are highly conserved among eukaryotes and exhibit diverse enzymatic activities depending on the organism. The biochemical and structural properties of the plant DXO1 differ from the yeast and animal counterparts, which is reflected in the in vivo functions of this enzyme. Here we show that Arabidopsis DXO1 contributes to the efficient processing of rRNA precursors in both nucleolar/cytosol and chloroplast maturation pathways. However, processing defects in DXO1-deficient plants do not depend on the catalytic activity of the enzyme but rely on its plant-specific N-terminal extension. Our RNA sequencing analyses show that the dxo1 mutation deregulates the expression of many ribosomal protein genes, most likely leading to inefficient or delayed pre-rRNA maturation. Strikingly, some of the observed molecular and morphological phenotypes of dxo1 plants are suppressed by the knock-down of XRN3, providing evidence for functional interaction between DXO1 and XRN proteins.HIGHLIGHTArabidopsis DXO1 protein regulates the expression of genes encoding ribosomal proteins and contributes to the correct processing of ribosomal RNA precursors.
The mushroom body output encodes behavioral decision during sensory-motor transformation
Authors: Arican Cansu , Johannes Schmitt Felix , Rössler Wolfgang , Strube-Bloss Martin Fritz , Nawrot Martin Paul 
Published: September 2022

AbstractAnimal behavioral decisions are dynamically formed by evaluating momentary sensory evidence on the background of individual experience and the acute motivational state. In insects, the mushroom body (MB) has been implicated in forming associative memories and in assessing the appetitive or aversive valence of sensory stimuli to bias approach versus avoidance behavior. To study the MB involvement in innate feeding behavior we performed extracellular single-unit recordings from MB output neurons (MBONs) while simultaneously monitoring a defined feeding behavior in response to timed odor stimulation in naïve cockroaches. All animals expressed the feeding behavior almost exclusively in response to food odors. Likewise, MBON responses were invariably and strongly tuned to the same odors. Importantly, MBON responses were restricted to behaviorally responded trials, which allowed the accurate prediction of the occurrence versus non-occurrence of the feeding behavior in individual trials from the neuronal population activity. During responded trials the neuronal activity generally preceded the onset of the feeding behavior, indicating a causal relation. Our results contest the predominant view that MBONs encode stimulus valence. Rather, we conclude that the MB output dynamically encodes the behavioral decision to inform downstream motor networks.
Ultraviolet radiation and dehydration stress induce overlapping transcriptional and metabolic responses in Syntrichia mosses
Authors: Ekwealor Jenna T. B. , Kosina Suzanne , Bowen Benjamin P. , Silva Anderson T. , Northen Trent , Oliver Melvin J. , Mishler Brent D. 
Published: September 2022

SummaryProtection from excess solar radiation and access to sufficient water are important problems for terrestrial plants to solve. Desiccation tolerance (DT), defined as the ability to equilibrate to dry air and resume normal metabolic activity after rehydration, allows organisms to survive dry periods by limiting metabolic activity to periods of moisture availability. We compared separate and combined effects of chronic ultraviolet radiation (UVR) treatments (UV-A and UV-A/B) and a dehydration treatment (as a surrogate for desiccation) in the mosses Syntrichia ruralis and S. caninervis to uncover the nature of correlation between DT and UVR tolerance (UVRT).Using a fully factorial experiment with combined transcriptomics and metabolomics, we tested for cross-talk (overlap in signaling pathways in response to different stressors but separate mechanisms of protection) in the genetic underpinnings of DT and UVRT and cross-tolerance (overlap in the mechanism of protection) these two stressors.Shared transcriptomic response to the two stressors with no significant interaction between them suggested cross-talk between UVRT and DT for S. caninervis. Phenolic metabolites and transcripts were involved in the response to UVR and dehydration in both species.Some candidate UVRT genes and metabolites were induced by UVR in S. ruralis, but not S. caninervis, supporting the hypothesis that S. ruralis has a more plastic, acclimatable UVR response than S. caninervis, and that these differences are predictable by their unique interaction with these stressors as poikilohydric organisms.
Cryogenic electron tomography reveals novel structures in the apical complex of Plasmodium falciparum
Authors: Sun Stella Y. , Segev-Zarko Li-av , Pintilie Grigore D. , Kim Chi Yong , Staggers Sophia R. , Schmid Michael F. , Egan Elizabeth S. , Chiu Wah , Boothroyd John C. 
Published: September 2022

AbstractIntracellular infectious agents, like the malaria parasite, Plasmodium falciparum, face the daunting challenge of how to invade a host cell. This problem may be even harder when the host cell in question is the enucleated red blood cell. Evolution has provided P. falciparum and related single-celled parasites within the phylum Apicomplexa with a collection of organelles at their apical end that mediate invasion. This apical complex includes at least two sets of secretory organelles, micronemes and rhoptries, and several structural features like apical rings and a putative pore through which proteins may be introduced into the host cell during invasion. In this paper, we perform cryogenic electron tomography (cryo-ET) on isolated merozoites to visualize the apical machinery. Through tomography reconstruction of cellular compartments, we see new details of known structures like the rhoptry tip interacting directly with a rosette resembling the recently described rhoptry-secretory-apparatus (RSA), or with an apical vesicle docked beneath the RSA. Subtomogram averaging reveals that the apical rings have a fixed number of repeating units, each of which is similar in overall size and shape to the units in the apical rings of tachyzoites of Toxoplasma gondii. Comparison of these polar rings in Plasmodium and Toxoplasma parasites also reveals them to have a structurally conserved assembly patterning. These results provide new insight into the essential features of this remarkable machinery used by apicomplexan parasites to invade their respective host cells.
BRG1 generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers
Authors: Nocente Marina C. , Karamitsos Anida Mesihovic , Drouineau Emilie , Albawardi Waad , Dulary Cécile , Ribierre Florence , Picaud Hélène , Alibert Olivier , Acker Joël , Aude Jean-Christophe , Gilbert Nick , Ochsenbein Françoise , Chantalat Sophie , Gérard Matthieu 
Published: September 2022

AbstractBRG1, the catalytic subunit of the mammalian SWI/SNF complexes, is essential for chromatin opening at enhancers. However, the nature of the open chromatin remains unclear. Here we show that in addition to producing histone-free DNA, BRG1 generates hemisome-like subnucleosomal particles containing the four core histones associated with 50-80 base pairs of DNA. Our genome-wide analysis indicates that BRG1 makes these particles by targeting and splitting fragile nucleosomes. In mouse embryonic stem cells, these subnucleosomes become anin vivobinding substrate for the master transcription factor OCT4 independently of the presence of OCT4 DNA motifs. At enhancers, the OCT4-subnucleosome interaction increases OCT4 occupancy and amplifies the genomic interval bound by OCT4 by up to one order of magnitude, compared to the region occupied on histone-free DNA. We suggest that BRG1-dependent subnucleosomes orchestrate an epigenetic mechanism that projects OCT4 function in chromatin opening beyond its DNA motifs.
Polar Crystal Habit and 3D Electron Diffraction Reveal the Malaria Pigment Hemozoin as a Selective Mixture of Centrosymmetric and Chiral Stereoisomers
Authors: Klar Paul Benjamin , Waterman David , Gruene Tim , Mullick Debakshi , Song Yun , Gilchrist James B. , Owen C. David , Wen Wen , Biran Idan , Houben Lothar , Regev-Rudzki Neta , Dzikowski Ron , Marom Noa , Palatinus Lukas , Zhang Peijun , Leiserowitz Leslie , Elbaum Michael 
Published: September 2022

AbstractDetoxification of heme in Plasmodium depends on its crystallization into hemozoin. This pathway is a major target of antimalarial drugs. X-ray powder diffraction has established that the unit cell contains a cyclic hematin dimer, yet the pro-chiral nature of heme supports formation of four distinct stereoisomers, two centrosymmetric and two chiral enantiomers. Here we apply emerging methods of in situ cryo-electron tomography and diffraction to obtain a definitive structure of biogenic hemozoin. Individual crystals take a striking polar morphology. Diffraction analysis, supported by density functional theory, indicates a compositional mixture of one centrosymmetric and one chiral dimer, whose absolute configuration has been determined on the basis of crystal morphology and interaction with the aqueous medium. Structural modeling of the heme detoxification protein suggests a mechanism for dimer selection. The refined structure of hemozoin should serve as a guide to new drug development.
A new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Authors: Reinhard John , Starke Leonhard , Klose Christian , Haberkant Per , Hammarén Henrik , Stein Frank , Klein Ofir , Berhorst Charlotte , Stumpf Heike , Sáenz James P. , Hub Jochen , Schuldiner Maya , Ernst Robert 
Published: September 2022

AbstractBiological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work provided insights into the subcellular distribution of lipids, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remained insufficiently characterized. Here we describe a method for purifying organellar membranes from yeast, MemPrep. We demonstrate the purity of our ER preparations by quantitative proteomics and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings have important implications for understanding the role of lipids in membrane protein insertion, folding, and their sorting along the secretory pathway. Application of the combined preparative and analytical platform to acutely stressed cells reveals dynamic ER membrane remodeling and establishes molecular fingerprints of lipid bilayer stress.
A network of Notch-dependent and -independent her genes controls neural stem and progenitor cells in the zebrafish thalamic proliferation zone
Authors: Sigloch Christian E. , Spitz Dominik , Driever Wolfgang 
Published: September 2022

AbstractNeural proliferation zones mediate brain growth, and employ Delta/Notch signaling and HES/HER transcription factors to balance neural stem cell (NSC) maintenance and generation of progenitors and neurons. We investigated Notch-dependency and function of her genes in the thalamic proliferation zone of developing zebrafish larvae. Nine Notch-dependent genes, her2, her4.1-5, her12, her15.1-2, and two Notch-independent genes, her6, her9, are differentially expressed, and define distinct NSC and progenitor populations. her6 prominently executes patterning information to maintain NSCs and the zona limitans intrathalamica Shh signaling activity. her6, her9 double mutants reveal that Notch-independent her genes predominantly regulate NSC maintenance and transition into the progenitor pool. Surprisingly, combined deletion of all Notch-dependent her genes does not affect NSCs or progenitor formation. Combined genetic manipulation of up to eleven Notch-dependent and -independent her genes revealed that Notch-dependent her genes may regulate progenitor progression into neurogenesis, but not progenitor generation itself. The her gene network is partially redundant, with Notch-independent her genes better substituting for loss of Notch-dependent genes than vice versa. Together, her gene regulatory feedback loops and crossregulation contribute to the observed robustness of NSC maintenance.
The genome sequence of the Lumpy Skin Disease virus from the outbreak in India suggests a distinct lineage of the virus
Authors: Bhatt Lenin , Bhoyar Rahul C. , Jolly Bani , Israni Ravi , Vignesh Harie , Scaria Vinod , Sivasubbu Sridhar 
Published: September 2022

ABSTRACTAlthough previously confined to regions within Africa, Lumpy Skin Disease Virus (LSDV) infections have caused significantly large outbreaks in several regions of the world in very recent years. In 2019, an outbreak of the disease was reported from India with low rates of morbidity and no reported mortality. However, in 2022, an ongoing outbreak of LSDV spanning over 7 states in India resulted in a reported mortality of over 80,000 cattle over a short period of three months. Here, we report complete genome sequences of 6 viral isolates of LSDV collected from affected cattle during an ongoing outbreak of the disease in Rajasthan, India. Analysis of the viral sequences suggests the genomes from the 2022 outbreak harbour a large number of genetic variations compared to the reference genome and form a distinct lineage. This report also highlights the importance of genome sequencing and surveillance of transboundary infectious agents and genomic characterisation of outbreaks.
Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates
Authors: Ranganathan Srivastav , Dasmeh Pouria , Furniss Seth , Shakhnovich Eugene 
Published: September 2022

AbstractAssemblies of multivalent RNA-binding protein FUS can exist in the functional liquid-like state as well as less dynamic and potentially toxic amyloid- and hydrogel-like states. How could then cells form liquid-like condensates while avoiding their transformation to amyloids? Here we show how post-translational phosphorylation can provide a “handle” that prevents liquid-solid transition of intracellular condensates containing FUS. Using residue-specific coarse-grained simulations, for 85 different mammalian FUS sequences, we show how the number of phosphorylation sites and their spatial arrangement affect intracluster dynamics preventing conversion to amyloids. All atom simulations further confirm that phosphorylation can effectively reduce the β-sheet propensity in amyloid-prone fragments of FUS. A detailed evolutionary analysis shows that mammalian FUS PLDs are enriched in amyloid-prone stretches compared to control neutrally evolved sequences suggesting that mammalian FUS proteins evolved to self-assemble. However, in stark contrast to proteins that do not phase-separate for their function, mammalian sequences have phosphosites in close proximity to these amyloid-prone regions. These results suggest that evolution uses amyloid-prone sequences in prion-like domains to enhance phase-separation of condensate proteins while enriching phosphorylation sites in close proximity to safe-guard against liquid-solid transitions.Significance StatementIntrinsically disordered regions and prion-like domains are widely observed in proteins that get enriched in membrane-less organelles (MLOs). Mammalian Fused in Sarcoma (FUS) sequences are significantly enriched in amyloid-prone sequences suggesting that they have evolved to self-assemble. While the amyloid-prone stretches promote self-assembly of these proteins at lower threshold concentrations, these assemblies are vulnerable to aberrant liquid-solid phase transitions. Molecular simulations and bioinformatics analyses show that evolution overcomes this challenge by placing phosphosites specifically close to amyloid-prone stretches. Introduction of negatively charged residues at phosphosite locations results in fewer amyloid-prone contacts and thereby lower beta-sheet propensity. Phosphorylation can thus allow cells to utilize amyloid-prone stretches to promote biogenesis of MLOs while protecting against liquid-solid transitions.
Comprehensive re-analysis of hairpin RNAs in fungi reveals ancestral links
Authors: Johnson Nathan R. , Larrondo Luis F. , Álvarez José M. , Vidal Elena A. 
Published: September 2022

AbstractRNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA-like features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/miRNA-like characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 40 fungal species. We extracted and normalized the annotation data for 1,677 reported mi/milRNA-like loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 18 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying around 200 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms.
Emergence of plasmid-mediated RND-type efflux pump gene cluster tmexCD-toprJ in Shewanella xiamenensis in a water environment
Authors: Dao Trung Duc , Takemura Taichiro , Kasuga Ikuro , Hirabayashi Aki , Nga Nguyen Thi , Anh Pham Hong Quynh , Tu Nguyen Dong , Trang Le Thi , Tran Hoang Huy , Shibayama Keigo , Hasebe Futoshi , Suzuki Masato 
Published: September 2022

AbstractThe emergence of the mobile resistance-nodulation-division (RND)-type efflux pump tmexCD-toprJ gene cluster that confers multidrug resistance (MDR), including tigecycline resistance, in gram-negative bacteria poses a global public health threat. However, the spread of such clinically important antimicrobial resistance genes (ARGs) in the natural environment has not yet been well investigated. In this study, we investigated MDR aquatic bacteria in Vietnam. A carbapenem- and tigecycline-resistant Shewanella xiamenensis isolate NUITM-VS2 was obtained from urban drainage in Hanoi, Vietnam, in October 2021. S. xiamenensis NUITM-VS2 showed resistance to most antimicrobials tested, including tigecycline, tetracyclines, carbapenems, cephalosporins, fluoroquinolone, and aminoglycosides. Whole-genome analysis was performed by long- and short-read sequencing, resulting in the complete genome sequence consisting of one chromosome and five plasmid sequences. ARGs and plasmid replicons in the genome were detected using ResFinder with the custom ARG database, including all known tigecycline resistance genes, and PlasmidFinder, respectively. A 152.2-kb IncC plasmid, pNUITM-VS2_2, co-carried two mobile tigecycline resistance genes, tet(X4) and tmexC3.2D3.2-toprJ1. In addition, a 24.8-kb untypeable plasmid, pNUITM-VS2_4, carried the carbapenemase gene blaNDM-1. pNUITM-VS2_2 was transferred to Escherichia coli by conjugation, which simultaneously conferred high-level resistance against many antimicrobials, including tigecycline. To the best of our knowledge, this is the first report of the detection of the mobile RND-type efflux pump gene cluster tmexCD-toprJ in Shewanella species. Our results provide genetic evidence of the complexity of the dynamics of clinically important ARGs among aquatic bacteria, which could be important reservoirs for ARGs in the natural environment.