bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary history of Euteliidae (Lepidoptera, Noctuoidea)
Authors: Zahiri Reza , Holloway Jeremy D. , Rota Jadranka , Schmidt B. Christian , Pellinen Markku J. , Kitching Ian J. , Miller Scott E. , Wahlberg Niklas
Published: September 2022

The Euteliidae stand apart in the Noctuoidea as the second smallest family, but most highly specialized in terms of larval hostplant relationships, favouring plant families with high levels of resin or latex, including the family dominant in Oriental lowland forests, the Dipterocarpaceae. Given the proportionally large foliage biomass represented by dipterocarps, exploitation of this abundant resource by lepidopteran defoliators is surprisingly low, and the Euteliidae may have achieved this through pre-adaption to dipterocarp chemical defences. Therefore, to assess this, we performed a molecular phylogenetic analysis on the family Euteliidae to clarify deep divergences and elucidate evolutionary relationships at the level of the subfamily, tribe, and genus. Our dataset consists of 6.3 kbp of one mitochondrial and seven nuclear DNA loci and was analyzed using model-based phylogenetic methods, i.e., maximum likelihood and Bayesian inference. We attempted to diagnose apomorphic morphological character states for Euteliidae and each monophyletic group within the family. Additionally, the evolution of hostplant use was reconstructed and a molecular-dating approach was conducted to assess the ages of major lineages within Euteliidae. We present an updated phylogenetic hypothesis for Euteliidae consisting of two strongly supported subfamilies: Euteliinae and Stictopterinae. Within Stictopterinae there are two tribes: Stictopterini and Odontodini. Several genera (e.g.,Targalla, Paectes, Marathyssa, Eutelia) were found to be polyphyletic and require taxonomic revision. Two new genera (NiklasteliaandPellinentelia) are described and several taxonomic changes (e.g., new combinations and new synonymies) are made. The Neotropical genusThyriodes, currently included in Euteliidae, is found to be associated with Erebinae (Erebidae). The divergence time estimate for the split between the Euteliidae and Noctuidae is at 53 my, and the Euteliidae split into the subfamilies Euteliinae and Stictopterinae at 42 my. In Stictopterinae, the tribes Stictopterini and Odontodini split at 31 my and the Euteliinae began a much more complex diversification at 34 my. Ancestral hostplant reconstruction identified Malpighiales (e.g., Clusiaceae) as the ancestral larval hostplant order for the family Euteliidae. The ancestors of Stictopterinae also appear to have been Malpighiales feeders, but then split into exclusive specialisms on Malvales (Odontodini) and Malpighiales (Stictopterini) hostplants. Larvae of Stictopterini appear to be restricted to Clusiaceae, apart from a few records from Dipterocarpaceae. In Euteliinae, Anacardiaceae are predominant as larval hosts. Thus, all hosts in the family are lactiferous, possibly providing some degree of pre-adaptation for exploiting Dipterocarpaceae.
A conserved role for stomatin domain genes in olfactory behavior
Authors: Liang Xiaoyu , Taylor Morgan , Napier-Jameson Rebekah , Calovich-Benne Canyon , Norris Adam
Published: September 2022

The highly-conserved stomatin domain has been identified in genes throughout all classes of life. In animals, different stomatin domain-encoding genes have been implicated in the function of the kidney, red blood cells, and specific neuron types, though the underlying mechanisms remain unresolved. In one well-studied example of stomatin domain gene function, theC. elegansgenemec-2and its mouse homologueStoml3are required for the function of mechanosensory neurons, where they modulate the activity of mechanosensory ion channels on the plasma membrane. Here we identify an additional shared function formec-2andStoml3in a very different sensory context, that of olfaction. In worms, we find that a subset of stomatin domain genes are expressed in olfactory neurons, but onlymec-2is strongly required for olfactory behavior.mec-2acts cell-autonomously and does not have any observable effect on olfactory neuron development or morphology, but modestly reduces olfactory neuron activity. We generate aStoml3knockout mouse and demonstrate that, like its worm homologuemec-2, it is required for olfactory behavior. In mice,Stoml3is not required for odor detection, but is required for odor discrimination. Therefore, in addition to their shared roles in mechanosensory behavior,mec-2andStoml3also have a shared role in olfactory behavior.
Positive, negative and engineered durotaxis
Authors: Sáez P. , Venturini C.
Published: September 2022

Cell migration is a physical process central to life. Among others, it regulates embryogenesis, tissue regeneration and tumor growth. Therefore, understanding and controlling cell migration represent fundamental challenges in science. Specifically, the ability of cells to follow stiffness gradients, known as durotaxis, is ubiquitous across most cell types. Even so, certain cells follow positive stiffness gradients while others move along negative gradients. How the physical mechanisms involved in cell migration works to enable a wide range of durotactic responses is still poorly understood. Here, we provide a mechanistic rationale of durotaxis by integrating stochastic clutch models for cell adhesion with an active gel theory of cell migration. We show that positive and negative durotaxis found across cell types are explained by asymmetries in the cell adhesion dynamics. We rationalize durotaxis by an asymmetric mechanotransduction in the cell adhesion behavior that further polarizes the intracellular retrograde flow and the protruding velocity at the cell membrane. Our theoretical framework confirms previous experimental observations and explains positive and negative durotaxis. Moreover, we show how durotaxis can be engineer to manipulate cell migration, which has important implications in biology, medicine and bioengineering.
Neuronal activity-related transcription is blunted in immature compared to mature dentate granule cells
Authors: Parylak Sarah L , Qiu Fan , Linker Sara B , Gallina Iryna S , Lim Christina K , Preciado David , McDonald Aidan H , Gage Fred H
Published: September 2022

Immature dentate granule cells (DGCs) generated in the hippocampus during adulthood are believed to play a unique role in dentate gyrus function. Although immature DGCs have hyperexcitable membrane properties in vitro, the consequences of this hyperexcitability in vivo remain unclear. In particular, the relationship between experiences that activate the dentate gyrus, such as exploration of a novel environment (NE), and downstream molecular processes that modify dentate gyrus circuitry in response to cellular activation are unknown in this cell population. We first performed quantification of immediate early gene proteins in immature (5-week-old) and mature (13-week-old) DGCs from mice exposed to a NE. Paradoxically, we observed lower immediate early gene protein expression in hyperexcitable immature DGCs. We then isolated nuclei from active and inactive immature DGCs and performed single nuclei RNA-Sequencing. Compared to mature nuclei collected from the same animal, immature DGC nuclei showed less activity-induced transcriptional change, even though they were classified as active based on expression of ARC protein. These results demonstrate that the coupling of spatial exploration, cellular activation, and transcriptional change differs between immature and mature DGCs, with blunted activity-induced changes in immature cells.
DomainRank: Improving Biological Data Sets With Domain Knowledge and Google’s PageRank
Authors: Schneider Michael , Rappsilber Juri , Brock Oliver
Published: September 2022

Motivation

The quality of biological data crucially affects progress in science. This quality can be improved with better measurement devices, more sophisticated experimental designs, or repetitious measurements. Each of these options is associated with substantial costs. We present a simple computational tool as an alternative. This algorithmic tool, called DomainRank, leverages simple domain knowledge and overlapping information content in biological network data to improve measurement quality at a negligible cost. Following the simple computational template of Domain-Rank, researchers can boost the confidence of their own data with little effort.

Results

We demonstrate the performance of DomainRank in three test cases: DomainRank finds 14.9% more interactions in quantitative proteomics experiments, improves the precision of predicted residue-residue contacts from co-evolutionary data by up to 11.6% (averaged over 882 proteins), and identifies 89.2% more cross-links in photo-crosslinking/mass spectrometry (photo-CLMS) experiments. Although our proposed template is specialized on biological network data, we view this approach as an universal computational tool for data improvement that could be routinely applied in many disciplines.

Availability

An implementation of DomainRank is freely available: https://github.com/Rappsilber-Laboratory/pagerank-refine
ROCKETS - a novel one-for-all toolbox for light sheet microscopy in drug discovery
Authors: Mueller Joerg PJ , Dobosz Michael , O’Brien Nils , Giusti Anna Maria , Lechmann Martin , Osl Franz , Wolf Ann-Katrin , Sauer Markus , Herting Frank , Umana Pablo , Colombetti Sara , Pöschinger Thomas , Beilhack Andreas
Published: September 2022

Advancing novel immunotherapy strategies requires refined tools in preclinical research to thoroughly assess drug targets, biodistribution, safety, and efficacy. Light sheet fluorescence microscopy (LSFM) offers unprecedented fast volumetric ex vivo imaging of large tissue samples in high resolution. Yet, to date laborious and unstandardized tissue processing procedures have limited throughput and broader applications in immunological research. Therefore, we have developed a simple and harmonized protocol for processing, clearing and imaging of all mouse organs and even entire mouse bodies. Applying this Rapid Optical Clearing Kit for Enhanced Tissue Scanning (ROCKETS) in combination with LSFM allowed us to comprehensively study the in vivo biodistribution of an antibody targeting Epithelial Cell Adhesion Molecule (EpCAM) in 3D. Quantitative high-resolution scans of whole organs did not only reveal known EpCAM expression patterns but, importantly, uncovered several new EpCAM-binding sites. We identified choroid plexi in the brain and duodenal papillae as unexpected locations of high EpCAM-expression. These tissue locations may be considered as particularly sensitive sites due their importance for liquor production or as critical junctions draining bile and digestive pancreatic enzymes into the small bowel, respectively. These newly gained insights appear highly relevant for clinical translation of EpCAM-addressing immunotherapies. Thus, ROCKETS in combination with LSFM may help to set new standards for preclinical evaluation of immunotherapeutic strategies. Conclusively, we propose ROCKETS as an ideal platform for a broader application of LSFM in immunological research optimally suited for quantitative co-localization studies of immunotherapeutic drugs and defined cell populations in the microanatomical context of organs or even whole mice.
Biomimetic S-Adenosylmethionine Regeneration Starting from Different Byproducts Enables Biocatalytic Alkylation with Radical SAM Enzymes
Authors: Gericke Lukas , Mhaindarkar Dipali , Karst Lukas , Jahn Sören , Kuge Marco , Mohr Michael K. F. , Gagsteiger Jana , Cornelissen Nicolas V. , Wen Xiaojin , Mordhorst Silja , Jessen Henning J. , Rentmeister Andrea , Seebeck Florian P. , Layer Gunhild , Loenarz Christoph , Andexer Jennifer N.
Published: September 2022

S-Adenosylmethionine (SAM) is an enzyme cofactor involved in methylation, aminopropyl transfer, and radical reactions. This versatility renders SAM-dependent enzymes of great interest in biocatalysis. The usage of SAM analogues adds to this diversity. However, high cost and instability of the cofactor impedes the investigation and usage of these enzymes. While SAM regeneration protocols from the methyltransferase (MT) byproductS-adenosylhomocysteine are available, aminopropyl transferases and radical SAM enzymes are not covered. Here, we report an efficient one-pot system to supply or regenerate SAM and SAM analogues for all three enzyme classes. The system’s flexibility is showcased by the transfer of an ethyl group with a cobalamin-dependent radical SAM MT usingS-adenosylethionine as a cofactor. This shows the potential of SAM (analogue) supply and regeneration for the application of diverse chemistry, as well as for mechanistic studies using cofactor analogues.
Reprogramming Adeno-Associated Virus Tropism Via Displayed Peptides Tiling Receptor-Ligands
Authors: Portell Andrew , Ford Kyle M. , Suhardjo Amanda , Rainaldi Joseph , Bublik Mark N. , Sanghvi Milan , Kumar Aditya , Wing Madeleine K. , Palmer Nathan D. , Le Duy An , Kalahasti Nikitha , Dailamy Amir , Mali Prashant
Published: September 2022

Adeno-associated viruses (AAVs) are common gene therapy vectors, however, their effectiveness is hindered by poor target tissue transduction and off-target delivery. Hypothesizing that naturally occurring receptor-ligand interactions could be repurposed to engineer tropism, we fragmented all annotated protein ligands known to bind human receptors into tiling 20-mer peptides and displayed these onto the surface loops of AAV5 and AAV9 capsids at two sites. The resulting four capsid libraries, comprising >1 million AAV variants, were screened across 9 tissues in C57BL/6 mice. Tracking variant abundance, we identified >250,000 variants which packaged into capsids, and >15,000 variants which efficiently transduced at least one mouse organ. We individually validated 21 AAV variants with 74.3% of the organ tropism predictions accurately reproducing, confirming overall screen efficacy. Systematic ligand tiling enabled prediction of putative AAV-receptor interactions, which we successfully validated by targeted genetic perturbations. Comprehensive peptide tiling also enabled examination of homologous peptide activity. Interestingly, we observed functional peptides tended to be derived from specific domains on ligands. Notably, certain peptides also displayed consistent activity across mice strains, capsid insertion contexts, and capsid serotypes, including novel immune orthogonal serotypes. Further analyses of displayed peptides revealed that biophysical attributes were highly predictive of AAV variant packaging, and there was a machine learnable relationship between peptide sequence and tissue tropism. We anticipate this comprehensive ligand peptide tiling and display approach will enable engineering of tropism across diverse viral, viral-like, and non-viral delivery platforms, and shed light into basic receptor-ligand biology.
Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper
Authors: Sharma Anuj , Li Jian , Wente Rebecca , Minsavage Gerald V. , Gill Upinder S. , Ortega Arturo , Vallejos C. Eduardo , Hart John P. , Staskawicz Brian J. , Mazourek Michael R. , Stall Robert E. , Jones Jeffrey B. , Hutton Samuel F.
Published: September 2022

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregant populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6 of pepper. We also identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. Mapping of bs5 and bs6 will facilitate their use in breeding programs through marker-assisted selection and is also a crucial step towards understanding the mechanisms of resistance.

Key message

Two recessive bacterial spot resistance genes were mapped in the pepper genome, which will facilitate their advancement in commercial pepper for management of all races of Xanthomonas euvesicatoria.
Placental nanoparticle gene therapy normalizes gene expression changes in the fetal liver associated with fetal growth restriction in a fetal sex-specific manner
Authors: Wilson Rebecca L , Stephens Kendal K , Jones Helen N
Published: September 2022

Fetal growth restriction (FGR) is associated with increased risk of developing Non-Communicable Diseases. We have a placenta-specific nanoparticle gene therapy protocol that increases placental expression of human insulin-like growth factor 1 (hIGF-1), for the treatment of FGR in utero. We aimed to characterize the effects of FGR on hepatic gluconeogenesis pathways during early stages of FGR establishment, and determine whether treatment of the placenta with nanoparticle mediated hIGF-1 therapy could resolve differences in the FGR fetus. Female Hartley guinea pigs (dams) were fed either a control or maternal nutrient restriction (MNR) diet using established protocols. At GD30-33, dams underwent ultrasound guided, transcutaneous, intra-placental injection of hIGF-1 nanoparticle or PBS (sham), and were sacrificed 5 days post-injection. Fetal liver tissue was fixed and snap frozen for morphology and gene expression analysis. In female and male fetuses, liver weight as a percentage of body weight was reduced by MNR, and not changed with hIGF-1 nanoparticle treatment. In female fetal livers, expression of hypoxia inducible factor 1 (Hif1α) and tumor necrosis factor (Tnfα) were increased in MNR compared to Control, but reduced towards Control in MNR + hIGF-1 livers. In male fetal liver, MNR increased expression of Igf-1, and decreased expression of Igf-2 compared to Control. Igf-1 and Igf-2 expression was restored to Control levels in the MNR + hIGF-1 group. This data provides further insight into the sex-specific mechanistic adaptations seen in FGR fetuses, and demonstrates that disruption to fetal developmental mechanisms may be returned to normal by treatment of the placenta.
A circadian-like gene network regulates heterochronic miRNA transcription inC. elegans
Authors: Kinney Brian , Sahu Shubham , Stec Natalia , Hills-Muckey Kelly , Adams Dexter W. , Wang Jing , Jaremko Matt , Joshua-Tor Leemor , Keil Wolfgang , Hammell Christopher M.
Published: September 2022

Developmental robustness relies on precise control of the timing and order of cellular events. InC. elegans, the invariant sequence of post-embryonic cell fate specification is controlled by oscillatory patterns of heterochronic microRNA transcription that are phase-locked with the larval molting cycle1-4. How these transcriptional patterns are generated and how microRNA dosage is controlled is unknown. Here we show that transcriptional pulses of thelin-4heterochronic microRNA are produced by two nuclear hormone receptors, NHR-85 and NHR-23, whose mammalian orthologs, Rev-Erb and ROR, function in the circadian clock. While Rev-Erb and ROR play antagonistic roles in regulating once-daily transcription5-7, we find that NHR-85 and NHR-23 bind cooperatively as heterodimers tolin-4regulatory elements to induce a single brief pulse of expression during each larval stage. We demonstrate that the timing and duration oflin-4transcriptional pulses are programmed by the phased overlap of NHR-85 and NHR-23 protein expression and that these regulatory interactions are post-transcriptionally controlled by LIN-42, the circadian Period ortholog inC. elegans. These findings suggest that an evolutionary rewiring of the circadian clock machinery is co-opted in nematodes to generate periodic transcriptional patterns that define cell fate progression.
Structural foundations of potassium selectivity in channelrhodopsins
Authors: Govorunova Elena G. , Sineshchekov Oleg A. , Brown Leonid S. , Bondar Ana-Nicoleta , Spudich John L.
Published: September 2022

Kalium channelrhodopsins (KCRs) are light-gated K+ channels recently found in the stramenopile protist Hyphochytrium catenoides. When expressed in neurons, KCRs enable high-precision optical inhibition of spiking (optogenetic silencing). KCRs are capable of discriminating K+ from Na+ without the conventional K+-selectivity filter found in classical K+ channels. The genome of H. catenoides also encodes a third paralog that is more permeable for Na+ than for K+. To identify structural motifs responsible for the unusual K+ selectivity of KCRs, we systematically analyzed a series of chimeras and mutants of this protein. We found that mutations of three critical residues in the paralog convert its Na+ selective channel into a K+ selective one. Our characterization of homologous proteins from other protists (Colponema vietnamica, Cafeteria burkhardae and Chromera velia) and metagenomic samples confirmed the importance of these residues for K+ selectivity. We also show that Trp102 and Asp116, conserved in all three H. catenoides orthologs, are necessary, although not sufficient, for K+ selectivity. Our results provide the foundation for further engineering of KCRs for optogenetic needs.

IMPORTANCE

Recently discovered microbial light-gated ion channels (channelrhodopsins) with a higher permeability for K+ than for Na+ (kalium channelrhodopsins, or KCRs) demonstrate an alternative K+ selectivity mechanism, unrelated to well-characterized “selectivity filters” of voltage- and ligand-gated K+ channels. KCRs can be used for optogenetic inhibition of neuronal firing, and potentially for the development of gene therapies to treat neurological and cardiovascular disorders. In this study we identify structural motifs that determine the K+ selectivity of KCRs that provide the foundation for that provide the foundation for elucidating their K+ selectivity mechanism and for their further engineering as optogenetic tools.
SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3
Authors: Schindewolf Craig , Lokugamage Kumari , Vu Michelle N. , Johnson Bryan A. , Scharton Dionna , Plante Jessica A. , Kalveram Birte , Crocquet-Valdes Patricia A. , Sotcheff Stephanea , Jaworski Elizabeth , Alvarado R. Elias , Debbink Kari , Daugherty Matthew D. , Weaver Scott C. , Routh Andrew L. , Walker David H. , Plante Kenneth S. , Menachery Vineet D.
Published: September 2022

Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2’-O methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2’-O MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2’-O methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, a methyltransferase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a possible target for future antiviral therapies.

Importance

Similar to other coronaviruses, disruption of SARS-CoV-2 NSP16 function attenuates viral replication in a type I interferon-dependent manner. In vivo, our results show reduced disease and viral replication at late times in the hamster lung, but an earlier titer deficit for the NSP16 mutant (dNSP16) in the upper airway. In addition, our results confirm a role for IFIT1, but also demonstrate the necessity of IFIT3 in mediating dNSP16 attenuation. Finally, we show that targeting NSP16 activity with a 2’-O methyltransferase inhibitor in combination with type I interferon offers a novel avenue for antiviral development.
A natural history of networks: Modeling higher-order interactions in geohistorical data
Authors: Rojas Alexis , Holmgren Anton , Neuman Magnus , Edler Daniel , Blöcker Christopher , Rosvall Martin
Published: September 2022

Paleobiologists are increasingly employing network-based methods to analyze the complex data retrieved from geohistorical records, including stratigraphic sections, sediments, and fossil collections. However, the lack of a common framework for designing, performing, evaluating, and communicating these studies, leads to issues of reproducibility and communicability. The high-dimensional geohistorical data also raises questions about the limitations of standard network approaches, which assume independent interactions between pairs of components. Higher-order network models better suited for the complex relational structure of the geohistorical data provide an opportunity to overcome these challenges. These models can represent temporal and spatial constraints inherent to the biosedimentary record and describe higher-order interactions, capturing more accurate biogeographical, biostratigraphic, and macroevolutionary patterns. Here we describe how to use the Map Equation framework for designing higher-order network models of geohistorical data, address some practical decisions involved in modeling complex dependencies, and discuss critical methodological and conceptual issues that currently make it difficult to compare results across studies in the growing body of network-based paleobiology research. We illustrate different higher-order network representations and models, including multilayers, hypergraphs, and varying Markov times models, using case studies on gradient analysis, bioregionalization, and macroevolution, and delineate future research directions for current challenges in the emerging field of network paleobiology.
Somatostatin slows Aβ plaque deposition in aged APPNL-F/NL-F mice by blocking Aβ aggregation in a neprilysin-independent manner
Authors: Williams Declan , Yan Bei Qi , Wang Hansen , Negm Logine , Sackmann Christopher , Verkuyl Claire , Rezai-Stevens Vanessa , Eid Shehab , Sato Christine , Watts Joel C. , Wille Holger , Schmitt-Ulms Gerold
Published: September 2022

The molecular underpinnings that govern the endoproteolytic release of the amyloid beta peptide (Aβ) from the amyloid precursor protein (APP) are now quite well understood. The same cannot be said for the events that precipitate the aggregation and amyloid deposition of Aβ in Alzheimer’s disease (AD). The 14-amino-acid cyclic neuroendocrine peptide somatostatin (SST-14) has long been thought of as playing a role, foremost by controlling the expression of the Aβ clearing enzyme neprilysin, and more recently by directly interacting with Aβ oligomers. Missing have been in vivo data in a relevant Aβ amyloidosis model. Here we addressed this shortcoming by crossing AppNL-F/NL-F mice with Sst-deficient mice of identical genetic background to assess if and how the presence of Sst influences key pathological hallmarks of Aβ amyloidosis that develop in AppNL-F/NL-F mice after 10 months of age. Surprisingly, we found that Sst had no influence on whole brain neprilysin transcript, protein or activity levels, an observation that cannot be accounted for by a compensatory upregulation of the Sst paralog, cortistatin (Cort), that we observed in 15-month-old Sst-deficient mice. The absence of Sst did lead to a subtle but significant increase in the density of cortical Aβ amyloid plaques. Follow-on western blot analyses of whole brain extracts indicated that Sst interferes with early steps of Aβ assembly that manifest in Sst null brains through the appearance of SDS-stable smears of 55- 150 kDa. As expected, no effect of Sst on tau steady-state levels or its phosphorylation were observed. Results from this study are easier reconciled with an emerging body of data that point toward Sst affecting Aβ amyloid plaque formation through direct interference with Aβ aggregation rather than through its effects on neprilysin expression.
3D Ground Truth Annotations of Nuclei in 3D Microscopy Volumes
Authors: Chen Alain , Wu Liming , Winfree Seth , Dunn Kenneth W. , Salama Paul , Delp Edward J.
Published: September 2022

In this paper we describe a set of 3D microscopy volumes we have partially manually annotated. We describe the volumes annotated and the tools and processes we use to annotate the volumes. In addition, we provide examples of annotated subvolumes. We also provide synthetically generated 3D microscopy volumes that can be used for training segmentation methods. The full set of annotations, synthetically generated volumes, and original volumes can be accessed as described in the paper.
Evaluating user experience with immersive technology in simulation-based education: a modified Delphi study with qualitative analysis
Authors: Jacobs Chris , Foote Georgia , Williams Michael
Published: September 2022

Background

Immersive technology is becoming more widespread in simulation-based medical education with applications that both supplement and replace traditional teaching methods. There is a lack of validated measures that capture user experience to inform of the technology utility. We aimed to establish a consensus of items and domains that different simulation experts would include in a measure for immersive technology use.

Methods

A 3-stage modified Delphi using online software was conducted to support the conceptual framework for the proposed measure. The first round was informed by prior work on immersive technology in simulation. In the first round, participants were asked to describe what we could measure in simulation-based education and technology. Thematic analysis generated key themes that were presented to the participants in the second round. Ranking of importance in round 2 was determined by mean rank scores. The final round was an online meeting for final consensus discussion and most important domains by experts were considered.

Results

A total of 16 simulation experts participated in the study. A consensus was reached on the ideal measure in immersive technology simulation that would be a user questionnaire and domains of interest would be: what was learnt, the degree of immersion experienced, fidelity provided, debrief, psychological safety and patient safety. No consensus was reached with the barriers that this technology introduces in education.

Conclusions

There is varied opinion on what we should prioritise in measuring the experience in simulation practice. Importantly, this study identified key areas that aids our understanding on how we can measure new technology in educational settings. Synthesising these results in to a multidomain instrument requires a systematic approach to testing in future research
Genome-scale mRNA transcriptomic insights into the mature growth dynamic of Cigar tobacco leaves
Authors: Yang Jinpeng , Wan Di , Qiao Baoming , Yu Jun , Li Zongping , Liu Daisong , Lv Peijun , Hu Jinwen , Rao Xiongfei , Xu Fangsen , Wang Sheliang , Yang Chunlei
Published: September 2022

The harvest time is a key factor for cigar leaves with high quality, which varies greatly depending on the environment. Here, we performed a genome-scale mRNA transcriptomic analysis on the cigar cultivar CX-26 (Nicotiana tabacum L.) to evaluate the relationship between gene expression and growth state. The leaves were harvested with 67 (T1), 71(T2) and 75 (T3)-day growth. A total of 80,502 genes were detected in the CX-26 leaves, of which 64,611 genes were annotated on the reference genome. Principal component analysis showed that T1 and T2 leaves had a high overlapping pattern, while T3 leaves were distinct. Indeed, T1 and T2 leaves had fewer differential expressing genes (DEGs), while T3 leaves had 26,456 DGEs from T2 leaves, supporting the distinct growth of T3 leaves. GO annotations mainly enriched the photosynthesis-related metabolic process, catalytic activity and binding biological processes. KEEG analysis identified the key pathways including photosynthesisantenna proteins, plant hormone/MAPK signaling pathway and plant-pathogen interaction. The maturity regulation and defense response-associated hormones abscisic acid and jasmonate acid were higher in the T3 leaves than that in T1 and T2 leaves confirming the KEEG analysis. Furthermore, several photosynthesis-related enzymes and a transcription factor were highlighted in the gene regulatory network, which might regulate the dynamics of carbohydrate metabolism, lipid metabolism and energy metabolism. In summary, our study provides insight into the growth state of CX-26 cigar leaves.
Updated site concordance factors minimize effects of homoplasy and taxon sampling
Authors: Mo Yu K. , Lanfear Robert , Hahn Matthew W. , Minh Bui Quang
Published: September 2022

Motivation

Site concordance factors (sCFs) have become a widely used way to summarize discordance in phylogenomic datasets. However, the original version of sCFs were calculated by sampling a quartet of tip taxa and then applying parsimony-based criteria for discordance. This approach has the potential to be strongly affected by multiple hits at a site (homoplasy), especially when substitution rates are high or taxa are not closely related.

Results

Here, we introduce a new method for calculating site concordance factors. The updated version uses likelihood to generate probability distributions of ancestral states at internal nodes of the phylogeny. By sampling from the states at internal nodes adjacent to a given branch, this approach substantially reduces—but does not completely abolish—the effects of homoplasy and taxon sampling.

Availability and implementation

Updated sCFs are implemented in IQ-TREE 2.2.2. The software is freely available at https://github.com/iqtree/iqtree2/releases.

Contact

moyu@iu.edu
An Aurora B-RPA signaling axis secures chromosome segregation fidelity
Authors: Roshan Poonam , Kuppa Sahiti , Mattice Jenna R. , Kaushik Vikas , Chadda Rahul , Pokhrel Nilisha , Tumala Brunda , Bothner Brian , Antony Edwin , Origanti Sofia
Published: September 2022

Errors in chromosome segregation underlie genomic instability associated with cancers. Resolution of replication and recombination intermediates and protection of vulnerable single-stranded DNA (ssDNA) intermediates during mitotic progression requires the ssDNA binding protein Replication Protein A (RPA). However, the mechanisms that regulate RPA specifically during unperturbed mitotic progression are poorly resolved. RPA is a heterotrimer composed of RPA70, RPA32 and RPA14 subunits and is predominantly regulated through hyperphosphorylation of RPA32 in response to DNA damage. Here, we have uncovered a mitosis-specific regulation of RPA by Aurora B kinase. Aurora B phosphorylates Ser-384 in the DNA binding domain B of the large RPA70 subunit and highlights a mode of regulation distinct from RPA32. Disruption of phosphorylation markedly affects cell viability and causes defects in chromosome segregation with hypersensitivity to DNA damaging agents. Phosphorylation at Ser-384 remodels the protein interaction domains of RPA and facilitates formation of higher density filaments. Furthermore, phosphorylation impairs RPA binding to DSS1 that likely suppresses homologous recombination during mitosis by preventing recruitment of DSS1-BRCA2 to exposed ssDNA. We showcase a critical RPA-Aurora B signaling axis in mitosis that is essential for maintaining genomic integrity.
Perturbation variance suppresses error sensitivity in the implicit learning system
Authors: Albert Scott , Shadmehr Reza
Published: September 2022

When variability is added to a sensorimotor perturbation, total adaptation is impaired. In Albert et al.1 we explored this phenomenon, and observed that it is the brain’s implicit, i.e., subconscious learning system that is most affected by perturbation variance. We observed that perturbation variability impaired implicit learning by downregulating its sensitivity to error. Recently, Wang et al.2 present an alternate viewpoint: implicit error sensitivity does not change with experience, only the errors observed by the implicit system change. Here we evaluated this alternate view by empirically measuring error sensitivity as a function of error size. We found that perturbation variability strongly downregulates implicit error sensitivity when controlling for error size, consistent with our original results, counter to the inflexible model argued by Wang et al. With that said, a pre-existing relationship between error sensitivity and error magnitude noted by Wang et al. can contribute at least in part to implicit behavior. State-space models that start with this pre-existing error sensitivity curve and then update it with training according to a ‘memory of errors’ most accurately tracked measured behavior.
A scalable implementation of the recursive least-squares algorithm for training spiking neural networks
Authors: Arthur Benjamin J. , Kim Christopher M. , Chen Susu , Preibisch Stephan , Darshan Ran
Published: September 2022

Training spiking recurrent neural networks on neuronal recordings or behavioral tasks has become a popular way to study computations performed by the nervous system. As the size and complexity of neural recordings increase, there is a need for efficient algorithms that can train models in a short period of time using minimal resources. We present optimized CPU and GPU implementations of the recursive least-squares algorithm in spiking neural networks. The GPU implementation can train networks of one million neurons, with 100 million plastic synapses and a billion static synapses, about 1000 times faster than an unoptimized reference CPU implementation. We demonstrate the code’s utility by training a network, in less than an hour, to reproduce the activity of > 66, 000 recorded neurons of a mouse performing a decision-making task. The fast implementation enables a more interactivein-silicostudy of the dynamics and connectivity underlying multi-area computations. It also admits the possibility to train models asin-vivoexperiments are being conducted, thus closing the loop between modeling and experiments.
Fine-scale sampling uncovers the complexity of migrations in 5th-6th century Pannonia
Authors: Vyas Deven N. , Koncz István , Modi Alessandra , Mende Balázs Gusztáv , Tian Yijie , Francalacci Paolo , Lari Martina , Vai Stefania , Straub Péter , Gallina Zsolt , Szeniczey Tamás , Hajdu Tamás , Radzevičiūtė Rita , Hofmanová Zuzana , Évinger Sándor , Bernert Zsolt , Pohl Walter , Caramelli David , Vida Tivadar , Geary Patrick J. , Veeramah Krishna R.
Published: September 2022

As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving “barbarian” groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.1,2To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5th century cemeteries3–5at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site6and analyzed them alongside data from over 550 penecontemporaneous individuals7–19. The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial representation and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artefacts and genetic ancestry among 5th century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.
Comparison Of New and emerging SARS-CoV-2 variant Transmissibility through Active Contact Testing. A comparative cross-sectional household seroprevalence study
Authors: Gaskell KM , Kheir N El , Mirfendesky M , Rampling T , Marks M , Houlihan C F , Lemonge N , Bristowe H , Aslam S , Kyprianou D , Nastouli E , Goldblatt D , Fielding K , Moore DAJ ,   CONTACT team (field team)
Published: September 2022

Historically SARS-CoV-2 secondary attack rates (SAR) have been based on PCR positivity on screening symptomatic contacts, this misses transmission events and identifies only symptomatic contacts who are PCR positive at the time of sampling. We used serology to detect the relative transmissibility of Alpha Variant of Concern (VOC) to non-VOC SARS-CoV-2 to calculate household secondary attack rates. We identified index patients diagnosed with Alpha and non-VOC SARS-CoV-2 across two London Hospitals between November 2020 and January 2021 during a prolonged and well adhered national lockdown. We completed a household seroprevalence survey and found that 61.8% of non-VOC exposed household contacts were seropositive compared to 82.1% of Alpha exposed household contacts. The odds of infection doubled with exposure to an index diagnosed with Alpha. There was evidence of transmission events in almost all households. Our data strongly support that estimates of SAR should include serological data to improve accuracy and understanding.

Key Messages

Secondary attack rates (SAR) in SARS-CoV-2 were previously calculated using PCR positive samples only, it is more accurate to use a household transmission model and screen contacts using serology, as done in this study. SAR should include serological data to improve accuracy and understanding. All households in this study had transmission events. SAR were 61.8% in non-VOC SARS-CoV-2 exposed household contacts compared to 82.1% in Alpha SARS-CoV-2 exposed household contacts.
Crystal structure of chlorido[diphenyl(thiophen-2-yl)phosphine-κP]gold(I)
Authors: Neils Thomas , LaDuca Andrew , Bender John E. , Staples Richard J. , Biros Shannon M.
Published: September 2022

The crystal structure of the title compound, [AuCl(C16H13PS)], is reported. The molecular structure features a nearly linear arrangement of the chloride and phosphino ligands around the gold(I) center, with a P—Au—Cl bond angle of 179.42 (9)°. The Au—P and Au—Cl bond lengths are 2.226 (2) and 2.287 (2) Å, respectively. The geometry of the groups bonded to the phosphorus atom of the ligand is a slightly distorted tetrahedron. The phenyl and thienyl rings of the ligand are extensively disordered, with the thienyl refined over all three possible positions on the phosphorus atom. The relative occupancy ratio between these positions was found to be 0.406 (3):0.406 (2):0.188 (2). One of the major thienyl ring positions with the relative occupancy of 0.406 was modeled as two rotational isomers around the C—P bond with a relative occupancy ratio of 0.278 (3):0.128 (3). Intermolecular C—H...π interactions present in the crystal lattice link molecules of the title compound together to form a complex three-dimensional network.
Crystal structure of the monoglycidyl ether of isoeugenol
Authors: Cattey Hélène , Boni Gilles , Pourchet Sylvie , Plasseraud Laurent
Published: September 2022

The title compound, C13H16O3 [GE-isoEu; systematic name: 2-({2-methoxy-4-[(E)-1-propen-1-yl]phenoxy}methyl)oxirane], which crystallizes in the triclinic P\overline{1} space group, was synthesized in one step from iso-eugenol, a bio-based phenylpropanoid, with an excess of epichlorohydrin. Colourless prismatic crystals suitable for X-ray diffraction were obtained from a mixture of ethyl acetate and cyclohexane, during purification by column chromatography on silica gel. GE-isoEu, which corresponds to the trans isomer of the monoglycidyl ether of iso-eugenol, is based on a 1,2,4-trisubstituted benzene ring by diglycidyl ether, methoxy and 1-(E)-propenyl groups, respectively. In the crystal, molecules are organized through offset π-stacking interactions. Chemically, GE-isoEu constitutes an intermediate in the synthesis protocol of 2-[3-methoxy-4-(2-oxiranylmethoxy)phenyl]-3-methyloxirane (GEEp-isoEu), a diepoxydized monomer used in the manufacturing of thermosetting resins and intended for the elaboration of bio-composites.
Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element
Authors: Verdonk Callum J. , Marshall Andrew C. , Ramsay Joshua P. , Bond Charles S.
Published: September 2022

The recombination directionality factors from Mesorhizobium spp. (RdfS) are involved in regulating the excision and transfer of integrative and conjugative elements. Here, solution small-angle X-ray scattering, and crystallization and preliminary structure solution of RdfS from Mesorhizobium japonicum R7A are presented. RdfS crystallizes in space group P212121, with evidence of eightfold rotational crystallographic/noncrystallographic symmetry. Initial structure determination by molecular replacement using ab initio models yielded a partial model (three molecules), which was completed after manual inspection revealed unmodelled electron density. The finalized crystal structure of RdfS reveals a head-to-tail polymer forming left-handed superhelices with large solvent channels. Additionally, RdfS has significant disorder in the C-terminal region of the protein, which is supported by the solution scattering data and the crystal structure. The steps taken to finalize structure determination, as well as the scattering and crystallographic characteristics of RdfS, are discussed.
Bis(4-hydroxyphenyl) 1,4-phenylenebiscarbamate
Authors: Martínez-de la Luz Isabel , López-Velázquez Delia , Bernès Sylvain , Varela Caselis Jenaro L.
Published: September 2022

The title compound, C20H16N2O6 (systematic name: 4-hydroxyphenyl N-{4-[(4-hydroxyphenoxycarbonyl)amino]phenyl}carbamate), contains two urethane groups substituting the central benzene ring in para positions. The molecule is centrosymmetric, and displays a twisted conformation for the three aromatic rings [the dihedral angle between central benzene ring and the urethane group is 33.4 (6)°, and that between the latter and the terminal ring is 65.1 (1)°]. In the crystal, a three-dimensional framework is formed through O—H...O and N—H...O hydrogen bonds involving the hydroxy and urethane functional groups, respectively.