bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape
Authors: Batjargal Taivan , Zappa Francesca , Grant Ryan J , Piscopio Robert A , Chialastri Alex , Dey Siddharth S , Acosta-Alvear Diego , Wilson Maxwell Z 
Published: May 2022

AbstractThe Integrated Stress Response (ISR) is a conserved signaling network that detects cellular damage and computes adaptive or terminal outcomes. Understanding the mechanisms that underly these computations has been difficult because natural stress inputs activate multiple parallel signaling pathways and classical ISR inducers have pleiotropic effects. To overcome this challenge, we engineered photo-switchable control over the ISR stress sensor kinase PKR (opto-PKR), which allows virtual control of the ISR. Using controlled light inputs to activate opto-PKR we traced information flow in the ISR both globally, in the transcriptome, and for key ISR effectors. Our analyses revealed a biphasic, input-proportional transcriptional response with two dynamic modes, transient and gradual, that correspond to adaptive and terminal ISR outcomes. Using this data, we constructed an ordinary differential equation (ODE) model of the ISR which predicted system hysteresis dependent on prior stress durations and that stress memory encoding may lead to resilience. Our results demonstrate that the input dynamics of the ISR encode information in stress levels, durations, and the timing between stress encounters.
Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type
Authors: O’Connor D , Mandino F , Shen X , Horien C , Ge X , Herman P , Crair M , Papademetris X , Lake EMR , Constable RT 
Published: May 2022

AbstractTo improve ‘bench-to-bedside’ translation, it is integral that knowledge flow bidirectionally—from animal models to humans, and vice versa. This requires common analytical frameworks, as well as open software and data sharing practices. We share a new pipeline (and test dataset) for the preprocessing of wide-field optical fluorescence imaging data—an emerging mode applicable in animal models—as well as results from a functional connectivity and graph theory analysis inspired by recent work in the human neuroimaging field. The approach is demonstrated using a dataset comprised of two test-cases: (1) data from animals imaged during awake and anesthetized conditions with excitatory neurons labeled, and (2) data from awake animals with different genetically encoded fluorescent labels that target either excitatory neurons or inhibitory interneuron subtypes. Both seed-based connectivity and graph theory measures (global efficiency, transitivity, modularity, and characteristic path-length) are shown to be useful in quantifying differences between wakefulness states and cell populations. Wakefulness state and cell type show widespread effects on canonical network connectivity with variable frequency band dependence. Differences between excitatory neurons and inhibitory interneurons are observed, with somatostatin expressing inhibitory interneurons emerging as notably dissimilar from parvalbumin and vasoactive polypeptide expressing cells. In sum, we demonstrate that our pipeline can be used to examine brain state and cell-type differences in mesoscale imaging data, aiding translational neuroscience efforts. In line with open science practices, we freely release the pipeline and data to encourage other efforts in the community.
Online Forays for Macrofungi: Expediting the Rate of Documenting Biodiversity
Authors: Russell Stephen D. 
Published: May 2022

AbstractA citizen-science oriented mushroom collecting event was organized online and held across the state of Indiana from October 23-29, 2017. Utilizing iNaturalist as the observational reporting platform, 30 members of the Hoosier Mushroom Society made over 1,300 observations of macrofungi during the week of the event. More importantly, the associated specimens were saved for more than 800 of the observations. Over 400 of the specimens were retained and received DNA barcodes, resulting in novel genotypes for 73 putative species being added to public databases. A full set of administrator and participant protocols has been compiled to aid others in conducting this style of biodiversity research for macrofungi. Methods include volunteer recruitment, participant protocols, specimen shipment, triage, and storage. Data management is also a key administrative aspect. Methodologies for integrating iNaturalist observational data with DNA sequence data and herbarium collection information are outlined for the MycoMap platform. Traditional mushroom collecting events have a number of limitations when compared to the online foray model. These advantages are discussed and key considerations for hosting online forays are examined.
Adaptation of cyanobacteria to the endolithic light spectrum in hyper-arid deserts
Authors: Murray Bayleigh , Ertekin Emine , Dailey Micah , Soulier Nathan T. , Shen Gaozhong , Bryant Donald A. , Perez-Fernandez Cesar , DiRuggiero Jocelyne 
Published: May 2022

AbstractIn hyper-arid deserts, endolithic microbial communities survive in the pore spaces and cracks of rocks, an environment that enhances water retention and filters UV radiation. The rock colonization zone is enriched in far-red light (FRL) and depleted in visible light. This poses a challenge to cyanobacteria, which are the primary producers of endolithic communities. Many species of cyanobacteria are capable of Far-Red Light Photoacclimation (FaRLiP), a process in which FRL induces the synthesis of specialized chlorophylls and remodeling of the photosynthetic apparatus, providing the ability to grow in FRL. While FaRLiP has been reported in cyanobacteria from various low-light environments, our understanding of light adaptations for endolithic cyanobacteria remains limited. Here, we demonstrated that endolithic Chroococidiopsis isolates from deserts around the world synthesize chlorophyll f, an FRL-specialized chlorophyll when FRL is the sole light source. The metagenome-assembled genomes of these isolates encoded chlorophyll f synthase and all the genes required to implement the FaRLiP response. We also present evidence of FRL-induced changes to the major light-harvesting complexes of a Chroococidiopsis isolate. These findings indicate that endolithic cyanobacteria from hyper-arid deserts use FRL photo-acclimation as an adaptation to the unique light transmission spectrum of their rocky habitat.
Coenzyme A binding sites induce proximal acylation across protein families
Authors: Carrico Chris , Cruz Andrew , Walter Marius , Meyer Jesse , Wehrfritz Cameron , Shah Samah , Wei Lei , Schilling Birgit , Verdin Eric 
Published: May 2022

AbstractLysine Nε-acylations, such as acetylation or succinylation, are post-translational modifications that regulate protein function. In mitochondria, lysine acylation is predominantly non-enzymatic, and only a specific subset of the proteome is acylated. Coenzyme A (CoA) can act as an acyl group carrier via a thioester bond, but what controls the acylation of mitochondrial lysines remains poorly understood. Using published datasets, here we found that proteins with a CoA-binding site are more likely to be acetylated, succinylated, and glutarylated. Using computational modeling, we show that lysine residues near the CoA-binding pocket are highly acylated compared to those farther away. We hypothesized that acyl-CoA binding enhances acylation of nearby lysine residues. To test this hypothesis, we co-incubated enoyl-CoA hydratase short chain 1 (ECHS1), a CoA-binding mitochondrial protein, with succinyl-CoA and CoA. Using mass spectrometry, we found that succinyl-CoA induced widespread lysine succinylation and that CoA competitively inhibited ECHS1 succinylation. CoA-induced inhibition at a particular lysine site correlated inversely with the distance between that lysine and the CoA-binding pocket. Our study indicated that CoA acts as a competitive inhibitor of ECHS1 succinylation by binding to the CoA-binding pocket. Together, this suggests that proximal acylation at CoA-binding sites is a primary mechanism for lysine acylation in the mitochondria.
Increasing computational protein design literacy through cohort-based learning for undergraduate students
Authors: Yang Erin C. , Divine Robby , Kang Christine S. , Chan Sidney , Arenas Elijah , Subol Zoe , Tinker Peter , Manninen Hayden , Feichtenbiner Alicia , Mustafa Talal , Hallowell Julia , Orr Isiac , Haddox Hugh , Koepnick Brian , O’Connor Jacob , Haydon Ian C. , Herpoldt Karla-Luise , Van Wormer Kandise , Abell Celine , Baker David , Khmelinskaia Alena , King Neil P. 
Published: May 2022

AbstractUndergraduate research experiences can improve student success in graduate education and STEM careers. During the COVID-19 pandemic, undergraduate researchers at our institution and many others lost their work-study research positions due to interruption of in-person research activities. This imposed a financial burden on the students and eliminated an important learning opportunity. To address these challenges, we created a paid, fully-remote, cohort-based research curriculum in computational protein design. Our curriculum used existing protein design methods as a platform to first educate and train undergraduate students and then to test research hypotheses. In the first phase, students learned computational methods to assess the stability of designed protein assemblies. In the second phase, students used a larger dataset to identify factors that could improve the accuracy of current protein design algorithms. This cohort-based program created valuable new research opportunities for undergraduates at our institute and enhanced the undergraduates’ feeling of connection with the lab. Students learned transferable and useful skills such as literature review, programming basics, data analysis, hypothesis testing, and scientific communication. Our program provides a model of structured computational research training opportunities for undergraduate researchers in any field for organizations looking to expand educational access.Graphical Abstract
A robust and efficient DNA storage architecture based on modulation encoding and decoding
Authors: Zan Xiangzhen , Xie Ranze , Yao Xiangyu , Xu Peng , Liu Wenbin 
Published: May 2022

AbstractThanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution to the data explosion problem. However, due to the large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable data recovery remains a critical challenge, which hinders its large-scale application. Here, we propose a modulation-based DNA storage architecture. Experiments on simulation and real datasets demonstrate that it has two distinct advantages. First, modulation encoding provides a simple way to ensure the encoded DNA sequences comply with biological sequence constraints (i.e., GC balanced and no homopolymers); Second, modulation decoding is highly efficient and extremely robust for the detection of insertions and deletions, which can correct up to ~40% errors. These two advantages pave the way for future high-throughput and low-cost techniques, and will kickstart the actualization of a viable, large-scale system for DNA data storage.
Genomic surveillance of carbapenem-resistant Klebsiella in Wales reveals persistent spread of K. pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids
Authors: David Sophia , Mentasti Massimo , Sands Kirsty , Portal Edward , Graham Lee , Watkins Joanne , Williams Catie , Healy Brendan , Spiller Owen B. , Aanensen David M. , Wootton Mandy , Jones Lim 
Published: May 2022

AbstractRising rates of multi-drug resistant Klebsiella infections necessitate a comprehensive understanding of the major strains and plasmids driving spread of resistance elements. Here we analysed 540 Klebsiella isolates recovered from patients across Wales between 2007 and 2020 using combined short- and long-read sequencing approaches. We identified resistant clones that have spread within and between hospitals including the high-risk strain, sequence type (ST) 307, which acquired the blaOXA-244 carbapenemase gene on a pOXA-48-like plasmid. We found evidence that this strain, which caused an acute outbreak largely centred on a single hospital in 2019, had been circulating undetected across South Wales for several years prior to the outbreak. In addition to clonal transmission, our analyses revealed evidence for substantial plasmid spread, mostly notably involving blaKPC-2 and blaOXA-48-like (including blaOXA-244) carbapenemase genes that were found among many species and strain backgrounds. Two thirds (20/30) of the blaKPC-2 genes were carried on the Tn4401a transposon and associated with IncF plasmids. These were mostly recovered from patients in North Wales, reflecting an outward expansion of the plasmid-driven outbreak of blaKPC-2-producing Enterobacteriaceae in North-West England. 92.1% (105/114) of isolates with a blaOXA-48-like carbapenemase carried the gene on a pOXA-48-like plasmid. While this plasmid family is highly conserved, our analyses revealed novel accessory variation including integrations of additional resistance genes. We also identified multiple independent deletions involving the tra gene cluster among pOXA-48-like plasmids in the ST307 outbreak lineage. These resulted in loss of conjugative ability and signal adaptation of the plasmids to carriage by the host strain. Altogether, our study provides the first high resolution view of the diversity, transmission and evolutionary dynamics of major resistant clones and plasmids of Klebsiella in Wales and forms an important basis for ongoing surveillance efforts.Data SummaryAll raw short read sequence data and hybrid assemblies are available in the European Nucleotide Archive (ENA) under project accession PRJEB48990.
Laboratory study ofFritillarialifecycle reveals larvacean commonalities and key morphogenetic events leading to genus-specific anatomy
Authors: Henriet Simon , Aasjord Anne , Chourrout Daniel 
Published: May 2022

ABSTRACTA fascinating variety of adult body plans can be found in the Tunicates, the closest existing relatives of vertebrates. A distinctive feature of the larvacean class of pelagic tunicates is the presence of a highly specialized surface epithelium that produces a cellulose test, the “larvacean house”. While substantial differences exist between the anatomy of larvacean families, most of the ontogeny is derived from the observations of a single genus,Oikopleura. We present the first study ofFritillariadevelopment based on the observation of individuals reproduced in the laboratory. Like the other small epipelagic speciesOikopleura dioica, the larvae ofFritillaria borealisgrow rapidly in the laboratory, and they acquire the adult form within a day. We could show that major morphological differences exhibited byFritillariaandOikopleuraadults originate from a key developmental stage during larval organogenesis. Here, the surface epithelium progressively retracts from the posterior digestive organs ofFritillarialarvae, and it establishes house-producing territories around the pharynx. Our results show that the divergence between larvacean genera was associated with a profound rearrangement of the mechanisms controlling the differentiation of the larval ectoderm.
Dysbiosis of the larval gut microbiota of Spodoptera frugiperda Strains feeding on different host-plants
Authors: de Oliveira Nathalia Cavichiolli , Cônsoli Fernando Luis 
Published: May 2022

AbstractThe gut microbiota plays important roles in the bioecology of insects, including host plant adaptation and speciation. Spodoptera frugiperda has two well-established host-adapted strains with marked differences at the genetic and host plant utilization levels. We investigated whether differences in the gut microbiota would occur between the “corn” (CS) and “rice” (RS) strains of S. frugiperda when feeding on different crops. The gut microbiota of larvae fed on corn and millet was predominantly represented by Firmicutes followed by Proteobacteria, with an opposite pattern in larvae fed on cotton. No differences were observed between the CS and RS using PERMANOVA. PCoA analyses resulted in distinct bacterial clusters based on the host plant. Comparisons of strains gut microbiota at the phylum level resulted in differences only for larvae fed on cotton, but differences in the relative abundance of minor representatives at the genus level between strains were observed regardless of the food source used. We also found differences in the potential functional contribution of bacteria between the strains. In conclusion the gut microbiota of S. frugiperda is strongly modulated by the host plant while strains seemed to play a minor role in changing the abundance of members of the gut bacterial community.
The selection of antibiotic- and bacteriophage-resistant Pseudomonas aeruginosa is prevented by their combination
Authors: Ferran Aude A , Lacroix Marlène Z. , Gourbeyre Ophélie , Huesca Alicia , Gaborieau Baptiste , Debarbieux Laurent , Bousquet-Mélou Alain 
Published: May 2022

AbstractObjectivesBacteria developing resistance compromise the efficacy of antibiotics or bacteriophages (phages). We tested the association of these two antibacterials to circumvent resistance.MethodsWith the Hollow Fiber Infection Model (HFIM), we mimicked the concentration profile of ciprofloxacin in the lungs of patients treated orally for Pseudomonas aeruginosa infections and independently, mimicked a single inhaled administration of phages (one or two phages).ResultsEach treatment selects for antibiotic-or phage-resistant clones in less than 30 h. By contrast, no bacteria were recovered from the HFIM at 72 h when ciprofloxacin was started 4 h post-phage administration, even when increasing the initial bacterial concentration by a 1000 fold.ConclusionThe combination of phages with antibiotics used according to clinical regimens prevents the growth of resistant clones, providing opportunities to downscale the use of multiple antibiotics.
Identification of the Branching Order within the Kingdom Bamfordvirae
Authors: Kotsinyan Armen , Sahakyan Harutyun , Zakaryan Hovakim 
Published: May 2022

AbstractThe kingdom Bamfordvirae comprises the majority of the realm Varidnaviria and, according to the 2021 release of Virus Taxonomy by the International Committee on Taxonomy of Viruses, consists of the phyla Nucleocytoviricota and Preplasmiviricota. There are several fundamental unresolved issues related to the evolution of Bamfordvirae. These are questions concerning Bamfordvirae taxonomy including the branching order of Nucleocytoviricota and the question of the monophyly of Preplasmiviricota. Here, based on the analyses of the individual core protein phylogenies, supertree, concatenated trees, dendrograms, as well as superdendrogram, we have refined the branching order of major groups within phylum Nucleocytoviricota using the rooting of the entire phylum on the cellular outgroups. These efforts resulted in several major changes in Bamfordvirae phylogeny. In particular, we showed that Nucleocytoviricota consists of two sister clades, consisting of Phycodnaviridae sensu lato on the one hand and Mimiviridae sensu lato, Iridoviridae/Ascoviridae, Marseilleviridae, pithoviruses including Cedratvirus, Solumvirus, Solivirus, and Orpheovirus, Mininucleoviridae, Asfarviridae sensu lato, and Poxviridae on the other hand. According to our data, Asfarviridae sensu lato and Poxviridae have likely originated from within the class Megaviricetes. We gave evidence for polyphyly of the phylum Preplasmiviricota and argued for a transfer of the families Lavidaviridae, Adintoviridae, and Adenoviridae from the phylum Preplasmiviricota into the phylum Nucleocytoviricota. We also argued for the origin of the Nucleocytoviricota from small prokaryotic viruses and gave arguments against the origin of Nucleocytoviricota from the Adintoviridae/Polinton-like viruses.ImportanceThe monophyly of Varidnaviria, consisting of the Bamfordvirae and Helvetiavirae kingdoms, remains a matter of debate. To confirm or refute the monophyly of Varidnaviria, it is important to identify the sources of origin and phylogenetic relationships common to all Varidnaviria genes, such as the FtsK-HerA superfamily ATPases, major and minor capsid proteins. However, such studies are relevant only if the direction of evolution of both kingdoms was firmly established. Thus, our work, by clarifying the phylogenetic relationships within the Bamfordvirae kingdom, provided a solid basis for studying the evolutionary relationships of this kingdom with a vast diversity of supposedly related viruses outside of Bamfordvirae, including Helvetiavirae (Varidnaviria).
Crystal structure, absolute configuration and characteristic temperatures of SmFe3(BO3)4 in the temperature range 11–400 K
Authors: Smirnova Ekaterina S. , Alekseeva Olga A. , Dudka Alexander P. , Sorokin Timofei A. , Khmelenin Dmitry N. , Yapaskurt Vasily O. , Lyubutina Marianna V. , Frolov Kirill V. , Lyubutin Igor S. , Gudim Irina A. 
Published: May 2022

The crystal structure of samarium iron borate was analyzed with regard to growth conditions and temperature. The inclusion of about 7% Bi atoms in the crystals grown using the Bi2Mo3O12-based flux was discovered and there were no impurities in the crystals grown using the Li2WO4-based flux. No pronounced structural features associated with Bi inclusion were observed. The different absolute configurations of the samples grown using both fluxes were demonstrated. Below 80 K, a negative thermal expansion of the c unit-cell parameter was found. The structure of (Sm0.93Bi0.07)Fe3(BO3)4 belongs to the trigonal space group R32 in the temperature range 90–400 K. A decrease in the (Sm,Bi)—O, Sm—B, Sm—Fe, Fe—O, Fe—B and Fe—Fe distances is observed with a lowering of the temperature, B1—O does not change, B2—O increases slightly and the B2O3 triangles deviate from the ab plane. The strongest decrease in the equivalent isotropic atomic displacement parameters (U
eq) with decreasing temperature is observed for atoms Sm and O2, and the weakest is observed for B1. The O2 atoms have the highest U
eq values, the most elongated atomic displacement ellipsoids of all the atoms and the smallest number of allowed vibrational modes of all the O atoms. The largest number of allowed vibrational modes and the strongest interactions with neighbouring atoms is seen for the B atoms, and the opposite is seen for the Sm atoms. The quadrupole splitting Δ(T) of the paramagnetic Mössbauer spectra increases linearly with cooling. The Néel temperature [T
N = 31.93 (5) K] was determined from the temperature dependence of the hyperfine magnetic field B
hf(T), which has a non-Brillouin character. The easy-plane long-range magnetic ordering below T
N was confirmed.