bluuebunny/crossref_metadata_2025 huggingface dataset:
How attaining the goals of a stroke care pathway is related to functional outcome after stroke. A nationwide study
Authors: Bergh Elin , Askim Torunn , Rønning Ole Morten , Fjærtoft Hild , Thommessen Bente
Published: March 2023

Background and purpose

In 2018 a stroke care pathway (SCP) was introduced in Norway. The goal of the pathway was to improve acute stroke care by reducing time-delay. We aimed to evaluate if achieving the target times of the SCP was associated with a better functional outcome at 3 months post-stroke and to identify characteristics of patients attaining the goals.

Methods

We performed a register-based study with data from the Norwegian stroke register (NSR). Patients registered with acute stroke in 2019 were included. Functional outcome at 3 months in the patients with “achievement” was compared to patients with “non-achievement”. Achievement was defined as attaining three important goals in the SCP; 1) time from symptom onset to contact with the emergency medical service, 2) time from symptom onset to arrival in hospital, 3) time from arrival in hospital to admission to a stroke unit. Additionally, we evaluated time from arrival in hospital to treatment with intravenous thrombolysis. Modified Rankin Scale (mRS) was used to measure functional outcome at 3 months post-stroke and functional independence was defined as mRS 0-2. Characteristics of the “achievers” were analysed by univariate and multivariate logistic regression analyses.

Results

In total 2818 patients were included, 460 (16%) were in the achievement group. The mean (SD) age was 72.5 (12.6) years and 1201 (43%) were women. The probability of being independent at 3 months post-stroke was significantly higher in the achievement group versus the non-achievement group (OR 1.36, 95% CI 1.04-1.79, p=0.026). The “achievers” were significantly younger, less likely to be living alone, less likely to have diabetes, more often had an ischemic stroke and were admitted with more severe strokes than the “non-achievers”.

Conclusion

Goal achievement in the SCP was significantly associated with independence 3 months post-stroke.
AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors
Authors: Danneskiold-Samsøe Niels Banhos , Kavi Deniz , Jude Kevin M. , Nissen Silas Boye , Wat Lianna W. , Coassolo Laetitia , Zhao Meng , Santana-Oikawa Galia Asae , Broido Beatrice Blythe , Garcia K. Christopher , Svensson Katrin J.
Published: March 2023

Secreted proteins play crucial roles in paracrine and endocrine signaling; however, identifying novel ligand-receptor interactions remains challenging. Here, we benchmarked AlphaFold as a screening approach to identify extracellular ligand-binding pairs using a structural library of single-pass transmembrane receptors. Key to the approach is the optimization of AlphaFold input and output for screening ligands against receptors to predict the most probable ligand-receptor interactions. Importantly, the predictions were performed on ligand-receptor pairs not used for AlphaFold training. We demonstrate high discriminatory power and a success rate of close to 90 % for known ligand-receptor pairs and 50 % for a diverse set of experimentally validated interactions. These results demonstrate proof-of-concept of a rapid and accurate screening platform to predict high-confidence cell-surface receptors for a diverse set of ligands by structural binding prediction, with potentially wide applicability for the understanding of cell-cell communication.
A Weakly Supervised U-Net Model for Precise Whole Brain Immunolabeled Cell Detection
Authors: Wang Li-Wen , Wu Ya-Lun , Lee Chih-Lin , Cheng Ching-Chuan , Lu Kuan-Yi , Tsai Jyun-Huei , Lin Ya-Hui , Hsu Ching-Han , Kuo Tsung-Han , Chu Li-An
Published: March 2023

Cell segmentation’s low precision due to the intensity differences hinders widespread use of whole brain microscopy imaging. Previous studies used ResNet or CNN to account for this problem, but are unapplicable to immunolabeled signals across samples. Here we present a semiauto ground truth generation and weakly-supervised U-Net-based Deep-learning precise segmentation pipeline for whole brain immunopositive c-FOS signals, which reveals the distinct neural activity maps with different social motivations.
Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics
Authors: Weinreb Caleb , Pearl Jonah , Lin Sherry , Osman Mohammed Abdal Monium , Zhang Libby , Annapragada Sidharth , Conlin Eli , Hoffman Red , Makowska Sofia , Gillis Winthrop F. , Jay Maya , Ye Shaokai , Mathis Alexander , Mathis Mackenzie Weygandt , Pereira Talmo , Linderman Scott W. , Datta Sandeep Robert
Published: March 2023

Keypoint tracking algorithms have revolutionized the analysis of animal behavior, enabling investigators to flexibly quantify behavioral dynamics from conventional video recordings obtained in a wide variety of settings. However, it remains unclear how to parse continuous keypoint data into the modules out of which behavior is organized. This challenge is particularly acute because keypoint data is susceptible to high frequency jitter that clustering algorithms can mistake for transitions between behavioral modules. Here we present keypoint-MoSeq, a machine learning-based platform for identifying behavioral modules (“syllables”) from keypoint data without human supervision. Keypoint-MoSeq uses a generative model to distinguish keypoint noise from behavior, enabling it to effectively identify syllables whose boundaries correspond to natural sub-second discontinuities inherent to mouse behavior. Keypoint-MoSeq outperforms commonly used alternative clustering methods at identifying these transitions, at capturing correlations between neural activity and behavior, and at classifying either solitary or social behaviors in accordance with human annotations. Keypoint-MoSeq therefore renders behavioral syllables and grammar accessible to the many researchers who use standard video to capture animal behavior.
Antigen receptor signaling and cell death resistance controls intestinal humoral response zonation
Authors: Raso Fiona , Liu Shuozhi , Willett Mikala JoAnn , Barton Gregory , Mayer Christian Thomas , Bannard Oliver , Acharya Mridu , Muppidi Jagan R. , Marshak-Rothstein Ann , Reboldi Andrea
Published: March 2023

Immunoglobulin A (IgA), the main antibody isotype found in the intestine, has evolved to maintain the stability of commensal communities, and prevent dysbiosis. In stark contrast to systemic antibody response against pathogens, the generation of IgA against intestinal resident microbes assures the simultaneous binding to multiple and diverse commensal-derived antigens. However, the exact mechanisms by which B cells mount such broadly reactive IgA response to the gut microbiome at the mucosal barrier remain elusive. Here we show surface IgA B cell receptor (BCR) is required to confer enhanced B cell fitness during the germinal center reaction in Peyer’s patches and to mediate selection of gut-homing plasma cells with higher efficiency. We demonstrate that, upon antigen stimulation, IgA+ BCR drives greater intracellular signaling in mouse and human B cells and as consequence, IgA+ B cells received higher positive selection cues in the germinal center. Mechanistically,in vivoIgA BCR signaling offsets Fas-mediated cell death to rescue low affinity B cell clones and redirects the humoral response to an increased variety of commensal strains at the intestinal interface. Our findings revealed a new mechanism linking tissue-specific antigen receptor signaling with B cell fate and localization of antibody production; and have implications for understanding how intestinal antigen recognition shapes humoral immunity in health and disease.
Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14
Authors: Zhang Chi , Tunes Luiza , Hsieh Meng-Hsiung , Wang Ping , Kumar Ashwani , Khadgi Brijesh B. , Yang YenYu , Doxtader Katelyn A. , Herrell Emily , Koczy Oliwia , Setlem Rohit , Zhang Xunzhi , Evers Bret , Wang Yinsheng , Xing Chao , Zhu Hao , Nam Yunsun
Published: March 2023

Chemical modification of RNAs is important for post-transcriptional gene regulation. The METTL3-METTL14 complex generates mostN6-methyladenosine (m6A) modifications in mRNAs, and dysregulated methyltransferase expression has been linked to numerous cancers. Here we show that changes in m6A modification location can impact oncogenesis. A gain-of-function missense mutation found in cancer patients, METTL14R298P, promotes malignant cell growth in culture and in transgenic mice. The mutant methyltransferase preferentially modifies noncanonical sites containing a GGAU motif and transforms gene expression without increasing global m6A levels in mRNAs. The altered substrate specificity is intrinsic to METTL3-METTL14, helping us to propose a structural model for how the METTL3-METTL14 complex selects the cognate RNA sequences for modification. Together, our work highlights that sequence-specific m6A deposition is important for proper function of the modification and that noncanonical methylation events can impact aberrant gene expression and oncogenesis.
Draft Genome Assembly of the Ancient Tetraploid Orphan Legume Marama Bean (Tylosema esculentum) with PacBio HiFi data
Authors: Li Jin , Cullis Christopher
Published: March 2023

Tylosema esculentum(marama bean), an underutilized orphan legume, has long been considered to have the potential to be domesticated as a crop to improve local food security due to the nutrient-rich seeds. As a plant species that grows naturally in the deserts of southern Africa, marama also serves as a good model for studying plant adaptation to extreme environments. In this study, HMW leaf DNA samples were prepared to generate 21.6 Gb PacBio HiFi data, which was assembled into to a raw tetraploid genome assembly of 1.24 Gb using Canu and into a partially phased assembly of 564.8 Mb by Hifiasm. The N50 values were 1.28 Mb and 2.75 Mb, respectively, and the BUSCO completeness were all above 99%. Repeats were found to account for 27.35% of the genome. The k-mer analysis indicated that marama was likely to be an autotetraploid plant with an estimated haplotype genome size of only 277 Mb. The current assembly was aligned with the genome ofBauhinia variegata, the closest species to marama whose genome has been sequenced, with an overall alignment rate of only 20.36% indicating a significant divergence between the two. This is the first high-quality genome assembly of marama bean, albeit unphased and still fragmented. However, some of the long contigs, which can be close to half the chromosome length, can serve as good references for studying the genes underlying the traits of interest. This will greatly facilitate the molecular breeding of the bean.
Hardwired to attack: Transcriptionally defined amygdala subpopulations play distinct roles in innate social behaviors
Authors: Lischinsky Julieta E. , Yin Luping , Shi Chenxi , Prakash Nandkishore , Burke Jared , Shekaran Govind , Grba Maria , Corbin Joshua G. , Lin Dayu
Published: March 2023

Social behaviors are innate and supported by dedicated neural circuits, but it remains unclear whether these circuits are developmentally hardwired or established through social experience. Here, we revealed distinct response patterns and functions in social behavior of medial amygdala (MeA) cells originating from two embryonically parcellated developmental lineages. MeA cells in male mice that express the transcription factor Foxp2 (MeAFoxp2) are specialized for processing male conspecific cues even before puberty and are essential for adult inter-male aggression. In contrast, MeA cells derived from theDbx1-lineage (MeADbx1) respond broadly to social cues and are non-essential for male aggression. Furthermore, MeAFoxp2and MeADbx1cells show differential anatomical and functional connectivity. Altogether, our results support a developmentally hardwired aggression circuit at the level of the MeA and we propose a lineage-based circuit organization by which a cell’s embryonic transcription factor profile determines its social information representation and behavior relevance during adulthood.

Highlights

MeAFoxp2cells in male mice show highly specific responses to male conspecific cues and during attack while MeADbx1cells are broadly tuned to social cues.

The male-specific response of MeAFoxp2cells is present in naïve adult males and adult social experience refines the response by increasing its trial-to-trial reliability and temporal precision.

MeAFoxp2cells show biased response to males even before puberty.

Activation of MeAFoxp2, but not MeADbx1, cells promote inter-male aggression in naïve male mice.

Inactivation of MeAFoxp2, but not MeADbx1, cells suppresses inter-male aggression.

MeAFoxp2and MeADbx1cells show differential connectivity at both the input and output levels.
Ultra-high throughput mapping of genetic design space
Authors: O’Connell Ronan W. , Rai Kshitij , Piepergerdes Trenton C. , Wang Yiduo , Samra Kian D. , Wilson Jack A. , Lin Shujian , Zhang Thomas H. , Ramos Eduardo M. , Sun Andrew , Kille Bryce , Curry Kristen D. , Rocks Jason W. , Treangen Todd J. , Mehta Pankaj , Bashor Caleb J.
Published: March 2023

Massively parallel genetic screens have been used to map sequence-to-function relationships for a variety of genetic elements. However, because these approaches only interrogate short sequences, it remains challenging to perform high throughput (HT) assays on constructs containing combinations of multiple sequence elements arranged across multikb length scales. Overcoming this barrier could accelerate synthetic biology; by screening diverse gene circuit designs, “composition-to-function” mappings could be created that reveal genetic part composability rules and enable rapid identification of behavior-optimized variants. Here, we introduce CLASSIC, a genetic screening platform that combines long– and short-read next-generation sequencing (NGS) modalities to quantitatively assess pools of constructs of arbitrary length containing diverse part compositions. We show that CLASSIC can measure expression profiles of >105 drug-inducible gene circuit designs (from 6-9 kb) in a single experiment in human cells. Using statistical inference and machine learning (ML) approaches, we demonstrate that data obtained with CLASSIC enables accurate predictive modeling of an entire circuit design landscape, offering critical insight into underlying design principles. Our work shows that by expanding the throughput and understanding gained with each design-build-test-learn (DBTL) cycle, CLASSIC dramatically augments the pace and scale of synthetic biology and establishes an experimental basis for data-driven design of complex genetic systems.
RHINO restricts MMEJ activity to mitosis
Authors: Brambati Alessandra , Sacco Olivia , Porcella Sarina , Heyza Joshua , Kareh Mike , Schmidt Jens C. , Sfeir Agnel
Published: March 2023

DNA double-strand breaks (DSBs) are toxic lesions that can lead to genome instability if not properly repaired. Breaks incurred in G1 phase of the cell cycle are predominantly fixed by non-homologous end-joining (NHEJ), while homologous recombination (HR) is the primary repair pathway in S and G2. Microhomology-mediated end-joining (MMEJ) is intrinsically error-prone and considered a backup DSB repair pathway that becomes essential when HR and NHEJ are compromised. In this study, we uncover MMEJ as the major DSB repair pathway in M phase. Using CRISPR/Cas9-based synthetic lethal screens, we identify subunits of the 9-1-1 complex (RAD9A-HUS1-RAD1) and its interacting partner, RHINO, as critical MMEJ factors. Mechanistically, we show that the function of 9-1-1 and RHINO in MMEJ is inconsistent with their well-established role in ATR signaling. Instead, RHINO plays an unexpected and essential role in directing mutagenic repair to M phase by directly binding to Polymerase theta (Polθ) and promoting its recruitment to DSBs in mitosis. In addition, we provide evidence that mitotic MMEJ repairs persistent DNA damage that originates in S phase but is not repaired by HR. The latter findings could explain the synthetic lethal relationship betweenPOLQandBRCA1/2and the synergistic effect of Polθ and PARP inhibitors. In summary, our study identifies MMEJ as the primary pathway for repairing DSBs during mitosis and highlights an unanticipated role for RHINO in directing mutagenic repair to M phase.
The Major-Minor mode Dichotomy in Music Perception: A Systematic Review and Meta-Analysis on its Behavioural, Physiological, and Clinical Correlates
Authors: Carraturo Giulio , Pando-Naude Victor , Costa Marco , Vuust Peter , Bonetti Leonardo , Brattico Elvira
Published: March 2023

Since ancient Greece, major and minor modes in Western tonal music have been identified as the primary responsible musical feature for eliciting emotional states. As such, the underlying correlates of the major-minor mode dichotomy in music perception have been extensively investigated through decades of psychological and neuroscientific research, providing plentiful yet often discordant results. Specifically, crucial questions remain about the several factors contributing to the affective perception of major and minor modes, at times very different among individuals. Moreover, major and minor mode perception has never been quantitatively compared in literature. This comprehensive systematic review and meta-analysis aimed to provide a qualitative and quantitative synthesis of musical mode perception and its behavioural and neural correlates. The qualitative synthesis resulted in 69 studies, showing great diversity in how the major-minor dichotomy has been empirically approached. Most studies reviewed were conducted on adults, considered participants’ expertise, employed real-life musical stimuli, performed behavioural evaluations, and were carried out among Western listeners. Behavioural, electroencephalography, and neuroimaging meta-analyses (36 studies) consistently showed that major and minor mode elicit distinct neural and emotional responses. Based on our findings, a framework to describe aMajor-Minor Mode(l)of music perception and its behavioural and physiological correlates is proposed, incorporating individual factors such as age, expertise, cultural background, and emotional disorders. Limitations, implications, and suggestions for future research are discussed, including putative clinical applications of major-minor dichotomy and best practices regarding stimulation paradigms for musical mode investigation.

Public Significance Statement

This study provides qualitative and quantitative evidence of the distinct behavioral and neural responses elicited by major and minor mode, while also highlighting the influence of factors such as age, culture, personality, and health. Results offers a detailed overview of the major-minor dichotomy in music, putting forward an integrated and critical discussion of methodologies, paradigms, and clinical implications of this pivotal musical feature.
Ingestion ofBacillus cereusspores dampens the immune response to favor bacterial persistence
Authors: Hachfi Salma , Brun-Barale Alexandra , Munro Patrick , Nawrot-Esposito Marie-Paule , Michel Gregory , Fichant Arnaud , Bonis Mathilde , Ruimy Raymond , Boyer Laurent , Gallet Armel
Published: March 2023

Spores are considered as dormant entities highly resistant to extreme conditions. Among them,Bacillus cereusspores are commonly associated with foodborne outbreaks. Nevertheless, the pathological processes associated with spore ingestion and germination remain poorly understood. Here, we show that while ingestion of vegetative bacteria leads to their elimination from the midgut and small intestines ofDrosophilaand mice, respectively, a single ingestion of spores leads to the persistence of bacteria for at least 10 days. UsingDrosophilagenetics, we demonstrate that spores escape the innate immune response of the anterior midgut. Once in the posterior midgut, spores germinate, and the vegetative cells dampen the immune signaling through the induction of amidases which are negative regulators of the immune response. This study provides evidence for howB. cereusspores hijack the intestinal immune defenses allowing the localized birth of vegetative bacteria responsible for the digestive symptoms associated with foodborne illness outbreaks.
TCR/CD3-based synthetic antigen receptors (TCC) convey superior antigen sensitivity combined with high fidelity of activation
Authors: Peters Timo , Mühlgrabner Vanessa , Cárdenas Rubí M.-H. Velasco , Platzer René , Göhring Janett , Salzer Benjamin , Plach Angelika , Höhrhan Maria , Perez Iago Doel , Goncalves Vasco Dos Reis , Farfán Jesús Siller , Lehner Manfred , Stockinger Hannes , Schamel Wolfgang W. , Schober Kilian , Busch Dirk H. , Hudecek Michael , Dushek Omer , Minguet Susanna , Huppa Johannes B.
Published: March 2023

Low antigen sensitivity and a gradual loss of effector functions limit the clinical applicability of chimeric antigen receptor (CAR)-modified T-cells and call for alternative antigen receptor designs for effective T-cell-based cancer immunotherapy. Here we applied advanced microscopy to demonstrate that TCR/CD3-based synthetic constructs (TCC) outperform second-generation CAR formats with regard to conveyed antigen sensitivities by up to a thousand-fold. TCC-based antigen recognition occurred without adverse non-specific signaling, which is typically observed in CAR-T-cells, and did not depend - unlike sensitized peptide/MHC detection by conventional T-cells - on CD4- or CD8- coreceptor engagement. TCC-endowed signaling properties may prove critical when targeting antigens in low abundance and aiming for a durable anti-cancer response.
Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models
Authors: Schmid-Siegert Emanuel , Qin Mengting , Tian Huan , Arpat Bulak , Chen Bonnie , Xenarios Ioannis
Published: March 2023

Mouse xenograft models play a vital role in tumor studies for research as well as for screening of drugs for the pharmaceutical industry. In particular, models with compromised immunity are favorable to increase the success of transplantation, such as e.g. NOD/SCID and BALB/c Nude strains. The genomic sequence and alterations of many of these models still remain elusive and might hamper a model’s further optimization or proper adapted usage. This can be in respect to treatments (e.g. NOD/SCID sensitivity to radiation), experiments or analysis of derived sequencing data of such models. Here we present the genome assemblies for the NOD/SCID and BALB/c nude strains to overcome this short-coming for the future and improve our understanding of these models in the process. We highlight as well first insights into observed genomic differences for these models compared to the C57BL/6 reference genome. Genome assemblies for both are close to full chromosome representations and provided with liftover annotations from the GRCm39 reference genome.
Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior
Authors: Barron Jerika J. , Mroz Nicholas M. , Taloma Sunrae E. , Dahlgren Madelene W. , Ortiz-Carpena Jorge , Dorman Leah C. , Vainchtein Ilia D. , Escoubas Caroline C. , Molofsky Ari B. , Molofsky Anna V.
Published: March 2023

The innate immune system plays essential roles in brain synaptic development, and immune dysregulation is implicated in neurodevelopmental diseases. Here we show that a subset of innate lymphocytes (group 2 innate lymphoid cells, ILC2s) is required for cortical inhibitory synapse maturation and adult social behavior. ILC2s expanded in the developing meninges and produced a surge of their canonical cytokine Interleukin-13 (IL-13) between postnatal days 5-15. Loss of ILC2s decreased cortical inhibitory synapse numbers in the postnatal period where as ILC2 transplant was sufficient to increase inhibitory synapse numbers. Deletion of the IL-4/IL-13 receptor (Il4ra) from inhibitory neurons phenocopied the reduction inhibitory synapses. Both ILC2 deficient and neuronalIl4radeficient animals had similar and selective impairments in adult social behavior. These data define a type 2 immune circuit in early life that shapes adult brain function.

One sentence summary

Type 2 innate lymphoid cells and Interleukin-13 promote inhibitory synapse development.
Atlas of Fetal Metabolism During Mid-To-Late Gestation and Diabetic Pregnancy
Authors: Perez-Ramirez Cesar A , Nakano Haruko , Law Richard C , Matulionis Nedas , Thompson Jennifer , Pfeiffer Andrew , Park Junyoung O , Nakano Atsushi , Christofk Heather R
Published: March 2023

Mounting evidence supports an instructive role for metabolism in stem cell fate decisions. However, much is yet unknown about how fetal metabolism changes during mammalian development and how altered maternal metabolism shapes fetal metabolism. Here, we present a descriptive atlas ofin vivofetal murine metabolism during mid-to-late gestation in normal and diabetic pregnancy. Using13C-glucose and LC-MS, we profiled the metabolism of fetal brains, hearts, livers, and placentas harvested from pregnant dams between embryonic days (E)10.5 and 18.5. Comparative analysis of our large metabolomics dataset revealed metabolic features specific to fetal tissues developed under a hyperglycemic environment as well as metabolic signatures that may denote developmental transitions during euglycemic development. We observed sorbitol accumulation in fetal tissues and altered neurotransmitter levels in fetal brains isolated from dams with maternal hyperglycemia. Tracing13C-glucose revealed disparate nutrient sourcing in fetuses depending on maternal glycemic states. Regardless of glycemic state, histidine-derived metabolites accumulated during late development in fetal tissues and maternal plasma. Our rich dataset presents a comprehensive overview ofin vivofetal tissue metabolism and alterations occurring as a result of maternal hyperglycemia.
Guide-specific loss of efficiency and off-target reduction with Cas9 variants
Authors: Zhang Liang , He Wei , Fu Rongjie , Xu Han
Published: March 2023

High-fidelity Cas9 variants have been developed to reduce the off-target effects of CRISPR systems at a cost of efficiency loss. To systematically evaluate the efficiency and off-target tolerance of Cas9 variants in complex with different single guide RNAs (sgRNAs), we applied high-throughput viability screens and a synthetic paired sgRNA-target system to assess thousands of sgRNAs in combination with two high-fidelity Cas9 variants HiFi and LZ3. Comparing these variants against WT SpCas9, we found that ~20% of sgRNAs are associated with a significant loss of efficiency when complexed with either HiFi or LZ3. The loss of efficiency is dependent on the sequence context in the seed region of sgRNAs, as well as at positions 15-18 in the non-seed region that interacts with the REC3 domain of Cas9, suggesting that the variant-specific mutations in REC3 domain account for the loss of efficiency. We also observed various degrees of sequencedependent off-target reduction when different sgRNAs are used in combination with the variants. Given these observations, we developed GuideVar, a transfer-learning-based computational framework for the prediction of on-target efficiency and off-target effect with high-fidelity variants. GuideVar facilitates the prioritization of sgRNAs in the applications with HiFi and LZ3, as demonstrated by the improvement of signal-to-noise ratios in high-throughput viability screens using these high-fidelity variants.
Discovery of an endogenous DNA virus in the amphibian killing fungus and its association with pathogen genotype and virulence
Authors: Clemons Rebecca , Yacoub Mark , Faust Evelyn , Toledo L. Felipe , Jenkinson Thomas S. , Carvalho Tamilie , Simmons D. Rabern , Kalinka Erik , Fritz-Laylin Lillian K. , James Timothy Y. , Stajich Jason E.
Published: March 2023

The Global Panzootic Lineage (GPL) of the pathogenic fungusBatrachochytrium dendrobatidis(Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly availableBdgenome sequences, we identified multiple non-GPLBdisolates that contain a circular Rep-encoding single stranded DNA (CRESS)-like virus which we named BdDV-1. We further sequenced and constructed genome assemblies with long read sequences to find that the virus is integrated into the nuclear genome in some strains. Attempts to cure virus positive isolates were unsuccessful, however, phenotypic differences between naturally virus positive and virus negativeBdisolates suggested that BdDV-1 decreases the growth of its hostin vitrobut increases the virulence of its hostin vivo. BdDV-1 is the first described CRESS DNA mycovirus of zoosporic true fungi with a distribution inversely associated with the emergence of the panzootic lineage.
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA andin situsequencing
Authors: Zhang Aixin , Jin Lei , Yao Shenqin , Matsuyama Makoto , Velthoven Cindy van , Sullivan Heather , Sun Na , Kellis Manolis , Tasic Bosiljka , Wickersham Ian R. , Chen Xiaoyin
Published: March 2023

Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactionsin vivoand synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell andin situsequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4,130 retrogradely labeled cells and 2,914 transsynaptically labeled cellsin situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq andin situsequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combiningin situsequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
The microglia receptor protein TREM2 is essential for protective innate immune responses against herpesvirus infection in the brain
Authors: Fruhwürth Stefanie , Reinert Line S. , Öberg Carl , Sakr Marcelina , Henricsson Marcus , Zetterberg Henrik , Paludan Søren R.
Published: March 2023

Immunological control of viral infection in the brain is essential for immediate protection, but also for long-term maintenance of brain integrity. As the primary resident immune cell of the brain, microglia protect against viral infections through key macrophage functions, including release of the antiviral type I interferons (IFN-I) and clearance of infected cells. Microglia express the cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS), which can bind viral DNA leading to signaling through stimulator of interferon genes (STING), and downstream immune activation. Here we report that herpes simplex virus (HSV) 1 infection of microglia leads to activation of IFN-I genes and pro-inflammatory cytokines. However, HSV1 also down-regulated expression of a subset of genes, including genes in the pathway engaged by the microglial receptor triggering receptor expressed on myeloid cells-2 (TREM2). Knockdown experiments revealed that TREM2 is important for viral activation of cGAS-STING signaling in microglia, induction of IFN-I, and phagocytosis of HSV1 infected neurons. Consequently, TREM2 depletion increased susceptibility to HSV1 infection in human microglia-neuron co-cultures and micein vivo. Mechanistically, we show that TREM2 is essential for phosphorylation of STING, and downstream activation of the IFN-inducing transcription factor IRF3. We conclude that TREM2 is a novel component of the antiviral immune response in microglia, crucial for immediate host defense against HSV1 in the brain. Since bothTREM2loss-of-function mutations and HSV1 serological status are linked to development of Alzheimeŕs disease (AD), this work opens the question whether defects in TREM2 could predispose to impaired viral clearance and post-infection pathological neurological changes.
Correlates of time to first citation in ecology and taxonomy
Authors: Guedes Jhonny J. M. , Melo Isabella , Bione Igor , Nunes Matheus
Published: March 2023

Several metrics exists to evaluate the impact of publications and researchers, but most are based on citation counts, which usually fail to capture the temporal aspect of citations. Time to first citation represents a useful metric for research evaluation, and informs the speed at which scientific knowledge is disseminated through the scientific community. Understanding which factors affect such metrics is important as they impact resource allocation and career progression, besides influencing knowledge promotion across disciplines. Many ecological works rely on species identity, which is the ‘coin’ of taxonomy. Despite its importance, taxonomy is a discipline in crisis lacking staff, funds and prestige, which ultimately may affect the evaluation and dissemination of taxonomic works. We used a time-to-event analysis to investigate whether taxonomic, socioeconomic, and scientometric factors influence first citation speed across hundreds of ecological and taxonomic articles. Time to first citation differed greatly between these areas. Ecological studies were first cited much faster than taxonomic studies. Multitaxa articles received first citations earlier than studies focused on single major taxonomic groups. Article length andh-index among authors were negatively correlated with time to first citation, while the number of authors, number of countries, and Gross Domestic Product was unimportant. Knowledge dissemination is faster for lengthy, multitaxa, and ecological articles relative to their respective counterparts, as well as for articles with highly prolific authors. We stress that using several unrelated metrics is desirable when evaluating research from different–and even related–disciplines, particularly in the context of professional progression and grant allocation.
New PALM-compatible integration vectors for use in the Gram-positive model bacteriumBacillus subtilis
Authors: Altinoglu Ipek , Carballido-Lopez Rut
Published: March 2023

Improvements in super-resolution and single-molecule techniques together with the development of new fluorescent proteins and labelling methods have allowed super-resolution microscopy to be applied to bacterial cells. Cloning vectors remain important tools for researchers to perform efficient labelling. Here, we describe the creation of four PhotoActivated Localization Microscopy (PALM)-compatible integration plasmids for the Gram-positive model organismBacillus subtilis. These plasmids carry either the photoswitchable green fluorescent protein dronPA or the photoactivatable red fluorescent protein PAmCherry1, codon-optimized or not forB. subtilis. For fast and interchangeable cloning, we have inserted multi cloning sites at both the C-terminal and the N-terminal end of the fluorophores. The plasmids replicate inEscherichia coliand allow integration at the ectopicamyEorthrCloci ofB. subtilisvia double homologous recombination, for stable chromosomal insertions of dronPA and PAmCherry1 protein fusions respectively. Dual color imaging is accessible with the simultaneous use of the two vectors. Insertion of the gene encoding the LacI repressor under control of a constitutive promoter in each of the four plasmids yielded four derivative vectors that, combined with an array oflacOoperator sites, allow Fluorescent Repressor-Operator System (FROS) localization studies. We demonstrated the successful photoactivation of the LacI-dronPA or PAmCherry1 fusions, and used them to report with nanoscale precision the subcellular localization of bacteriophage SPP1 DNA in infectedB. subtiliscells as proof of concept. Our PALM-compatible integration vectors expand the genetic toolbox for single molecule localization microscopy studies inB. subtilis.
Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ: explained by strain energy
Authors: Banerjee Souradeep , Chowdhury Debojyoti , Chakraborty Soham , Haldar Shubhasis
Published: March 2023

Polypeptide chains experiences mechanical tension while translocating through cellular tunnel. In this scenario, interaction of tunnel-associated chaperones with the emerging polypeptide occurs under force; however, this force-regulated chaperone behaviour is not fully understood.

We studied the mechanical chaperone activity of two tunnel-associated chaperones BiP and ERdj3 both in the absence and presence of force; and compared to their respective cytoplasmic homologs DnaK and DnaJ. We found that BiP/ERdj3 shows strong foldase activity under force; whereas their cytoplasmic homolog DnaK/DnaJ behave as holdase. Importantly, these tunnel-associated chaperones (BiP/ERdj3) revert to holdase in the absence of force, suggesting that mechanical chaperone activity differs depending on the presence or absence of force. This tunnel-associated chaperone-driven folding event generates additional mechanical energy of up to 54 zJ that could help protein translocation. The mechanical-chaperone behaviour can be explained by strain theory: chaperones with higher intrinsic deformability function as mechanical foldase (BiP, ERdj3), while chaperones with lower intrinsic deformability act as holdase (DnaK and DnaJ). Our study thus unveils the underlying mechanism of mechanically regulated chaperoning activity and provides a novel mechanism of co-translocational protein folding.

Significance

The mechanical-activity of chaperones, located at the edge of a tunnel, could be different from their cytoplasmic homologs. Translocating substrates within the tunnel are known to experience mechanical constraints, whereas the cytosolic substrates interact with the chaperones in the absence of force.

To understand this phenomenon, we investigated two tunnel-associated chaperones BiP/ERdj3 and their cytosolic homologs-DnaK/DnaJ. We observed that BiP/ERdj3 possess strong foldase activity while their substrates are under force; whereas DnaK/DnaJ possess holdase function. Notably all these chaperones function as holdase in the absence of force, which suggest that mechanical chaperone activity is different with and without force. We explained this mechanical behaviour using strain theory, providing a physical mechanism of chaperone-assisted co-translocational protein folding.
Can a bulky glycocalyx promote catch bonding in early integrin adhesion? Perhaps a bit
Authors: Blanchard Aaron
Published: March 2023

Many types of cancer overexpress bulky glycoproteins to form a thick glycocalyx layer. The glycocalyx physically separates the cell from its surroundings, but recent work has shown that the glycocalyx can paradoxically increase adhesion to soft tissues and therefore promote the metastasis of cancer cells. This surprising phenomenon occurs because the glycocalyx forces adhesion molecules (called integrins) on the cell’s surface into clusters. These integrin clusters have cooperative effects that allow them to form stronger adhesions to surrounding tissues than would be possible with equivalent numbers of un-clustered integrins. These cooperative mechanisms have been intensely scrutinized in recent years; a more nuanced understanding of the biophysical underpinnings of glycocalyx-mediated adhesion could uncover therapeutic targets, deepen our general understanding of cancer metastasis, and elucidate general biophysical processes that extend far beyond the realm of cancer research.

This work examines the hypothesis that the glycocalyx has the additional effect of increasing mechanical tension experienced by clustered integrins. Integrins function as mechanosensors that undergo catch bonding – meaning the application of moderate tension increases integrin bond lifetime relative to the lifetime of integrins experiencing low tension. In this work, a three-state chemomechanical catch bond model of integrin tension is used to investigate catch bonding in the presence of a bulky glycocalyx.

This modeling suggests that a bulky glycocalyx can lightly trigger catch bonding, increasing the bond lifetime of integrins at adhesion edges by up to 100%. The total number of integrin-ligand bonds within an adhesion is predicted to increase by up to ~60% for certain adhesion geometries. Catch bonding is predicted to decrease the activation energy of adhesion formation by ~1-4 kBT, which translates to a ~3-50× increase in the kinetic rate of adhesion nucleation. This work reveals that integrin mechanic and clustering likely both contribute to glycocalyx-mediated metastasis.

Graphical Abstract
Respiration shapes sleep-oscillations and memory reactivation in humans
Authors: Schreiner Thomas , Petzka Marit , Staudigl Tobias , Staresina Bernhard P.
Published: March 2023

The beneficial effect of sleep on memory consolidation relies on the precise interplay of slow oscillations (SOs) and spindles. However, whether these rhythms are orchestrated by an underlying pacemaker has remained elusive. Here, we tested whether respiration, which has been shown to impact brain rhythms and cognition during wake, shapes memory reactivation by modulating sleep-related oscillations and their interplay in humans. We recorded scalp EEG and respiration throughout an experiment in which participants acquired associative memories before taking a nap. Our results reveal that respiration strongly modulates the emergence of sleep oscillations. Specifically, SOs, spindles as well as their interplay (i.e., coupled SO_spindle complexes) systematically increase towards inhalation peaks. Moreover, the strength of respiration-SO_spindle coupling is linked to the extent of memory reactivation during SO_spindles. Our results identify respiration as a potential pacemaker for memory consolidation in humans and highlight the critical role of brain-body interactions during sleep.
Statistical analyses of motion-corrupted MRI relaxometry data
Authors: Corbin Nadège , Oliveira Rita , Raynaud Quentin , Domenicantonio Giulia Di , Draganski Bogdan , Kherif Ferath , Callaghan Martina F. , Lutti Antoine
Published: March 2023

Consistent noise variance across data points (i.e. homoscedasticity) is required to ensure the validity of statistical analyses of MRI data conducted using linear regression methods. However, head motion leads to degradation of image quality, introducing noise heteroscedasticity into ordinary-least square analyses. The recently introduced QUIQI method restores noise homoscedasticity by means of weighted least square analyses in which the weights, specific for each dataset of an analysis, are computed from an index of motion-induced image quality degradation. QUIQI was first demonstrated in the context of brain maps of the MRI parameter R2*, which were computed from a single set of images with variable echo time. Here, we extend this framework to quantitative maps of the MRI parameters R1, R2*, and MTsat, which are computed from multiple sets of images. QUIQI allows for optimization of the noise model by using metrics quantifying heteroscedasticity and free energy. QUIQI restores homoscedasticity more effectively than insertion of an image quality index in the analysis design and yields higher sensitivity than simply removing the datasets most corrupted by head motion from the analysis. In sum, QUIQI provides an optimal approach to group-wise analyses of a range of quantitative MRI parameter maps that is robust to inherent homoscedasticity.
General and specific patterns of cortical gene expression as spatial correlates of complex cognitive functioning
Authors: Moodie Joanna E. , Harris Sarah E. , Harris Mathew A. , Buchanan Colin R. , Davies Gail , Taylor Adele , Redmond Paul , Liewald David , del C Valdés Hernández Maria , Shenkin Susan , Russ Tom C. , Maniega Susana Muñoz , Luciano Michelle , Corley Janie , Stolicyn Aleks , Shen Xueyi , Steele Douglas , Waiter Gordon , Sandu-Giuraniuc Anca , Bastin Mark E. , Wardlaw Joanna M. , McIntosh Andrew , Whalley Heather , Tucker-Drob Elliot M. , Deary Ian J. , Cox Simon R.
Published: March 2023

Gene expression varies across the brain. This spatial patterning denotes specialised support for particular brain functions. However, the way that a given gene’s expression fluctuates across the brain may be governed by general rules. Quantifying patterns of spatial covariation across genes would offer insights into the molecular characteristics of brain areas supporting, for example, complex cognitive functions. Here, we use principal component analysis to separate general and unique gene regulatory associations with cortical substrates of cognition. We find that the region-to-region variation in cortical expression profiles of 8235 genes covaries across two major principal components : gene ontology analysis suggests these dimensions are characterised by downregulation and upregulation of cell-signalling/modification and transcription factors. We validate these patterns out-of-sample and across different data processing choices. Brain regions more strongly implicated in general cognitive functioning (g; 3 cohorts, total meta-analyticN =39,519) tend to be more balanced between downregulation and upregulation of both major components (indicated by regional component scores). We then identify a further 41 genes as candidate cortical spatial correlates ofg, beyond the patterning of the two major components (|β| range = 0.15 to 0.53). Many of these genes have been previously associated with clinical neurodegenerative and psychiatric disorders, or with other health-related phenotypes. The results provide insights into the cortical organisation of gene expression and its association with individual differences in cognitive functioning.