bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements
Authors: Eppley John M. , Biller Steven J. , Luo Elaine , Burger Andrew , DeLong Edward F. 
Published: July 2022

AbstractPhage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many of the marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage interference and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, and bacteriophage-induced cell mortality and host and virus productivity. These previously unrecognized marine phage satellites therefore have potential to impact the ecology and evolution of bacteria and their bacteriophages in the ocean, and similar phage parasites likely thrive in many other microbial habitats as well.Significance statementPhage satellites are mobile genetic elements that parasitize bacteriophage, thereby exerting profound biological and ecological impacts. To date however, phage satellites have been found primarily in Gram-positive cocci and a few Gram-negative bacteria, many of which are human pathogens. Direct inspection of “wild” marine virus particles however, revealed that phage satellites are widely distributed in the sea, and that their genetic diversity, gene repertoires, and host ranges are much greater than previously supposed. Our analyses provide insight into their parasitic life cycles, potential satellite-helper-phage interactions, and reproductive strategies of these newly recognized phage-parasitizing mobile elements. Their properties, diversity and environmental distributions suggest they exert pervasive influence on marine plankton ecology and bacterial and virus evolution in the sea.
A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals
Authors: Martynowycz Michael W. , Shiriaeva Anna , Clabbers Max T. B. , Nicolas William J. , Weaver Sara J. , Hattne Johan , Gonen Tamir 
Published: July 2022

AbstractCrystallization of membrane proteins, such as G protein-coupled receptors (GPCRs), is challenging and frequently requires the use of lipidic cubic phase (LCP) crystallization methods. These typically yield crystals that are too small for synchrotron X-ray crystallography, but ideally suited for the cryogenic electron microscopy (cryoEM) method microcrystal electron diffraction (MicroED). However, the viscous nature of LCP makes sample preparation challenging. The LCP layer is often too thick for transmission electron microscopy (TEM), and crystals buried in LCP cannot be identified topologically using a focused ion-beam and scanning electron microscope (FIB/SEM). Therefore, the LCP needs to either be converted to the sponge phase or entirely removed from the path of the ion-beam to allow identification and milling of these crystals. Unfortunately, conversion of the LCP to sponge phase can also deteriorate the sample. Methods that avoid LCP conversion are needed. Here, we employ a novel approach using an integrated fluorescence light microscope (iFLM) inside of a FIB/SEM to identify fluorescently labelled crystals embedded deep in a thick LCP layer. The crystals are then targeted using fluorescence microscopy and unconverted LCP is removed directly using a plasma focused ion beam (pFIB). To assess the optimal ion source to prepare biological lamellae, we first characterized the four available gas sources on standard crystals of the serine protease, proteinase K. However, lamellae prepared using either argon and xenon produced the highest quality data and structures. Fluorescently labelled crystals of the human adenosine receptor embedded in thick LCP were placed directly onto EM grids without conversion to the sponge phase. Buried microcrystals were identified using iFLM, and deep lamellae were created using the xenon beam. Continuous rotation MicroED data were collected from the exposed crystalline lamella and the structure was determined using a single crystal. This study outlines a robust approach to identifying and milling LCP grown membrane protein crystals for MicroED using single microcrystals, and demonstrates plasma ion-beam milling as a powerful tool for preparing biological lamellae.
Investigating Predictive Coding in Younger and Older Children Using MEG and a Multi-Feature Auditory Oddball Paradigm
Authors: Rapaport Hannah , Seymour Robert A. , Benikos Nicholas , He Wei , Pellicano Elizabeth , Sowman Paul F. 
Published: July 2022

AbstractThere is mounting evidence for predictive coding theory from computational, neuroimaging, and psychological research. However there remains a lack of research exploring how predictive brain function develops across childhood. To address this gap, we used paediatric magnetoencephalography (MEG) to record the evoked magnetic fields of 18 younger children (M = 4.1 years) and 19 older children (M = 6.2 years) as they listened to a 12-minute auditory oddball paradigm. For each child, we computed a mismatch field ‘MMF’: an electrophysiological component that is widely interpreted as a neural signature of predictive coding. Consistent with our hypotheses, the older children showed significantly larger MMF amplitudes relative to the younger children. Furthermore, the older children showed a significantly larger MMF amplitude in the right inferior frontal gyrus (IFG; 0.312 to 0.33 s) relative to the younger children, p < .05. These findings support the idea that predictive brain function develops during childhood, with increasing involvement of the frontal cortex in response to prediction errors. These findings contribute to a deeper understanding of the brain function underpinning child cognitive development.HighlightsThis is the first paediatric MEG study to examine the sources underlying the MMF.Older children showed larger MMF amplitudes in the right inferior frontal gyrus.Results support the idea that predictive brain function develops during childhood.
Transcriptomic classification of pituitary neuroendocrine tumors causing acromegaly
Authors: Rymuza Julia , Kober Paulina , Rusetska Natalia , Mossakowska Beata J. , Maksymowicz Maria , Nyc Aleksandra , Baluszek Szymon , Zieliński Grzegorz , Kunicki Jacek , Bujko Mateusz 
Published: July 2022

AbstractAcromegaly results from growth hormone hypersecretion caused by somatotroph pituitary neuroendocrine tumor (PitNET). Our molecular profiling revealed that acromegaly-causing tumors form three distinct transcriptomic subgroups with different histological/clinical features. Transcriptomic subtypes of somatotroph tumors differ in the expression levels of numerous genes including those involved in hormone secretion and genes with known prognostic value. They can be distinguished by determining the expression of marker genes. Transcriptomic group 1 includes ∼20% of acromegaly patients with GNAS mutations-negative, mainly densely granulated tumors with NR5A1 (SF-1) and GIPR co-expression. Group 2 tumors are the most common (46%) and include mainly GNAS-mutated, densely granulated somatotroph and mixed PitNETs. They have significantly smaller size and express favorable prognosis-related genes. Group 3 includes predominantly sparsely granulated somatotroph PitNETs with low GNAS mutations frequency causing ∼35% of acromegaly cases. Ghrelin signaling is implied in their pathogenic mechanism, they have unfavorable gene expression profile, and invasive growth rate. Since a subgroup of somatotroph tumors have high NR5A1 expression, using SF-1 as classification marker specific to gonadotroph PitNETs could be reconsidered.
Bacterial cell widening alters periplasmic size and activates envelope stress responses
Authors: Zietek Matylda , Miguel Amanda , Khusainov Iskander , Shi Handuo , Asmar Abir T , Ram Sri , Wartel Morgane , Sueki Anna , Schorb Martin , Goulian Mark , Collet Jean-François , Beck Martin , Huang Kerwyn Casey , Typas Athanasios 
Published: July 2022

AbstractThe Rcs signal transduction system is a phosphorelay responsible for sensing a wide variety of enterobacterial cell envelope stresses. In Escherichia coli, the Rcs system is required to survive A22 and mecillinam treatment, two drugs that perturb cell size. To test whether cell size changes might be correlated with envelope damage and thereby sensed by the Rcs system, we tuned E. coli cell size via drug inhibition with A22, point mutations to the cell-shape determinant MreB, and mechanically confined growth. In all conditions, cell width was strongly correlated with Rcs activation, with wider cells exhibiting more activation than wild-type. In all conditions, RcsF, the outer membrane-localized upstream component of the Rcs system, was essential for responding to cell width changes. Consistently, several envelope gene deletions known to induce the Rcs system via RcsF resulted in cells that were wider than wild-type. Cryo- electron microscopy revealed that the periplasm of a wide MreB mutant was on average ∼3 nm thinner than wild-type, thereby bringing RcsF closer to the downstream components of the signaling cascade in the inner membrane. Conversely, extending the flexible linker region of RcsF by ∼3 nm increased Rcs activity in wild-type cells. In summary, we propose that the Rcs system responds to changes in cell width because of altered periplasmic thickness.
Modulation of bacterial cell size and growth rate via activation of a cell envelope stress response
Authors: Miguel Amanda , Zietek Matylda , Shi Handuo , Sueki Anna , Maier Lisa , Verheul Jolanda , Blaauwen Tanneke den , Valen David Van , Typas Athanasios , Huang Kerwyn Casey 
Published: July 2022

AbstractFluctuating conditions and diverse stresses are typical in natural environments. In response, cells mount complex responses across multiple scales, including adjusting their shape to withstand stress. In enterobacteria, the Rcs phosphorelay is activated by cell envelope damage and by changes to periplasmic dimensions and cell width. Here, we investigated the physiological and morphological consequences of Rcs activation in Escherichia coli in the absence of stresses, using an inducible version of RcsF that mislocalizes to the inner membrane, RcsFIM. Expression of RcsFIM immediately reduced cellular growth rate and the added length per cell cycle in a manner that was directly dependent on induction levels, but independent of Rcs-induced capsule production. At the same time, cells increased intracellular concentration of the cell division protein FtsZ, and decreased the distance between division rings in filamentous cells. Depletion of the Rcs negative regulator IgaA phenocopied RcsFIM induction, indicating that IgaA is essential due to growth inhibition in its absence. However, A22 treatment did not affect growth rate or FtsZ intracellular concentration, despite activating the Rcs system. These findings suggest that the effect of Rcs activation on FtsZ levels is mediated indirectly through growth-rate changes, and highlight feedbacks among the Rcs stress response, growth dynamics, and cell-size control.
Age-related seroprevalence trajectories of seasonal coronaviruses in children
Authors: Luo Yasha , Lv Huibin , Zhao Shilin , Sun Yuanxin , Liu Chengyi , Chen Chunke , Liang Weiwen , Kwok Kin-on , Teo Qi Wen , So Ray TY , Lin Yihan , Deng Yuhong , Li Biyun , Dai Zixi , Zhu Jie , Zhang Dengwei , Fernando Julia , Wu Nicholas C , Tun Hein M. , Bruzzone Roberto , Mok Chris KP , Mu Xiaoping 
Published: July 2022

AbstractFour seasonal coronaviruses, including HCoV-NL63 and HCoV-229E, HCoV-OC43 and HCoV-HKU1 cause approximately 15–30% of common colds in adults. However, the frequency and timing of early infection with four seasonal coronaviruses in the infant are still not well studied. Here, we evaluated the serological response to four seasonal coronaviruses in 1886 children under 18-year-old to construct the viral infection rates. The antibody levels were also determined from the plasma samples of 485 pairs postpartum women and their newborn babies. This passive immunity waned at one year after birth and the resurgence of the IgGs were found thereafter with the increase of the age. Taken together, our results show the age-related seroprevalence trajectories of seasonal coronaviruses in children and provide useful information for deciding vaccine strategy for coronaviruses in the future.
Proteins with multiple G protein-coupled receptor domains
Authors: Isildayancan Kilic , Kessel Amit , Solan Ron , Kolodny Rachel , Ben-Tal Nir 
Published: July 2022

AbstractCurrently known G protein-coupled receptors (GPCRs) have a single transmembrane domain. Many GPCRs form dimers that have two transmembrane domains (one per protein), and there are indications that this dimeric interaction is functionally meaningful. Here, based on sequence analysis and structure predictions, we report the existence of 57 proteins with two, three, or four GPCR domains within the same protein chain. We analyze the structures of these multi-GPCRs and show that almost all have DRY/NPxxY motifs, a strong indication of signaling activity. By homology, most of the multi-GPCRs that we identified are olfactory-related; a few are chemokine-related. Multi-GPCR candidates are found in various Chordata species including fish, camel, marmite, Chinese hamster, and new world monkeys. The discovery of receptors with multiple transmembrane domains suggests the possibility for signal regulation and amplification within an individual receptor, revealing another step in GPCR evolution and a new layer of complexity in signal transduction.
Honokiol inhibits SARS-CoV-2 replication in cell culture
Authors: Salgado-Benvindo Clarisse , Leijs Anouk A. , Thaler Melissa , Tas Ali , Arbiser Jack L. , Snijder Eric J. , van Hemert Martijn J. 
Published: July 2022

SUMMARYSARS-CoV-2 emerged in 2019 and since its global spread has caused the death of over 6 million people. There are currently few antiviral options for treatment of COVID-19. Repurposing of known drugs can be a fast route to obtain molecules that inhibit viral infection and/or modulate pathogenic host responses. Honokiol is a small molecule fromMagnoliatrees, for which several biological effects have been reported,, including anticancer and anti-inflammatory activity. Honokiol has also been shown to inhibit several viruses in cell culture. In this study, we show that honokiol protected Vero E6 cells from SARS-CoV-2-mediated cytopathic effect with an EC50 of 7.8 µM. In viral load reduction assays we observed that honokiol decreased viral RNA copies as well as viral infectious progeny titers. The compound also inhibited SARS-CoV-2 replication in the more relevant A549 cells, expressing ACE2 and TMPRSS2. A time-of-addition assay showed that honokiol inhibited virus replication even when added post infection, suggesting it acts at a post-entry step of the replication cycle. Honokiol was also effective against more recent variants of SARS-CoV-2, including omicron and it inhibited other human coronaviruses as well. Our study suggests that honokiol is an interesting molecule to evaluate in animal studies and clinical trials to investigate its effect on virus replication and pathogenic (inflammatory) host responses.
The Insulin receptor and Insulin like growth factor receptor 5’ UTRs support translation initiation independently of eIF4G1
Authors: Clark Nicholas K. , Harris Meghan T. , Marr Michael T. 
Published: July 2022

ABSTRACTProtein synthesis is tightly regulated under stress conditions where energy may be scarce. Despite global repression of translation, some transcripts remain actively translated in order for the cell to be able to respond to the insult or prepare to quickly return normal cellular function after the stress ends. For the insulin receptor (Insr) and insulin-like growth factor receptor (Igf1r) transcripts this translation is mediated by an internal ribosome entry site (IRES) in their 5’UTRs that functions independently of eukaryotic initiation factor 4A (eIF4A) and eIF4E. Here we show that these cellular IRESes are also able to promote translation independently of the scaffolding protein eIF4G1 both in vitro and in the cell.BackgroundIRES mediated translation initiation requires a different repertoire of factors than canonical cap-dependent translation.ResultsTreatments that inhibit the canonical translation factor eIF4G1 have little or no effect on the ability of the Insr and Igf1r cellular IRESes to promote translation.ConclusionTranscripts for two cellular receptors contain RNA elements that facilitate translation initiation without intact eIF4G1SignificanceCellular IRES mechanisms may resemble viral type III IRESes allowing them to promote translate with a limited number of initiation factors allowing them to work under stress conditions when canonical translation is repressed.
Risk of BA.5 infection in individuals exposed to prior SARS-CoV-2 variants
Authors: Malato João , Ribeiro Ruy M. , Leite Pedro Pinto , Casaca Pedro , Fernandes Eugénia , Antunes Carlos , Fonseca Válter R. , Gomes Manuel Carmo , Graca Luis 
Published: July 2022

AbstractThe SARS-CoV-2 omicron BA.5 subvariant is progressively displacing earlier subvariants, BA.1 and BA.2, in many countries. One possible explanation is the ability of BA.5 to evade immune responses elicited by prior BA.1 and BA.2 infections. The impact of BA.1 infection on the risk of reinfection with BA.5 is a critical issue because adapted vaccines under current clinical development are based on BA.1.We used the national Portuguese COVID-19 registry to analyze the risk of BA.5 infection in individuals without a documented infection or previously infected during periods of distinct variants’ predominance (Wuhan-Hu-1, alpha, delta, BA.1/BA.2). National predominance periods were established according to the national SARS-CoV-2 genetic surveillance data (when one variant represented >90% of the sample isolates).We found that prior SARS-CoV-2 infection reduced the risk for BA.5 infection. The protection effectiveness, related to the uninfected group, for a first infection with Wuhan-Hu-1 was 52.9% (95% CI, 51.9 – 53.9%), for Alpha 54.9% (51.2 – 58.3%), for Delta 62.3% (61.4 – 63.3%), and for BA.1/BA.2 80.0% (79.7 – 80.2%).The results ought to be interpreted in the context of breakthrough infections within a population with a very high vaccine coverage (>98% of the study population completed the primary vaccination series).In conclusion, infection with BA.1/BA.2 reduces the risk for breakthrough infections with BA.5 in a highly vaccinated population. This finding is critical to appraise the current epidemiological situation and the development of adapted vaccines.
The anatomy of transcriptionally active chromatin loops inDrosophilaprimary spermatocytes using super-resolution microscopy
Authors: Ball Madeleine L. , Koestler Stefan A. , Muresan Leila , Rehman Sohaib Abdul , O’Holleran Kevin , White Robert 
Published: July 2022

AbstractWhile the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase.For this analysis, we have used super-resolution microscopy to image theDrosophila melanogasterY loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops.These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription.
Modular Pooled Discovery of Synthetic Knockin Sequences to Program Durable Cell Therapies
Authors: Blaeschke Franziska , Chen Yan Yi , Apathy Ryan , Li Zhongmei , Mowery Cody T. , Nyberg William A. , To Angela , Yu Ruby , Bueno Raymund , Kim Min Cheol , Schmidt Ralf , Goodman Daniel B. , Feuchtinger Tobias , Eyquem Justin , Ye Chun Jimmie , Shifrut Eric , Roth Theodore L. , Marson Alexander 
Published: July 2022

SUMMARYChronic stimulation can cause T cell dysfunction and limit efficacy of cellular immunotherapies. CRISPR screens have nominated gene targets for engineered T cells, but improved methods are required to compare large numbers of synthetic knockin sequences to reprogram cell functions. Here, we developed Modular Pooled Knockin Screening (ModPoKI), an adaptable platform for modular construction of DNA knockin libraries using barcoded multicistronic adaptors. We built two ModPoKI libraries of 100 transcription factors (TFs) and 129 natural and synthetic surface receptors. Over 20 ModPoKI screens across human TCR and CAR T cells in diverse conditions identified a transcription factor AP4 (TFAP4) construct to enhance long-term T cell fitness and anti-cancer functionin vitroandin vivo. ModPoKI’s modularity allowed us to generate a ∼10,000-member library of TF combinations. Non-viral knockin of a combined BATF-TFAP4 polycistronic construct further enhanced functionin vivo. ModPoKI facilitates discovery of complex gene constructs to program cellular functions.HighlightsModular pooled knockins of hundreds of TF and surface receptor constructs combined with different antigen receptorsChronic stimulation screens discover programs to improve T cell persistenceCombinatorial knockin screens with ∼10,000 transcription factor combinationsBATF-TFAP4 dual knockin construct improves CAR T cell functionin vitroandin vivo