bluuebunny/crossref_metadata_2025 huggingface dataset:
ROCK2 Knockout Improves Proliferation Rate in a Cellular Model of Down Syndrome
Authors: LeBlanc-Straceski Janine , Williams Riley , Ward Kylie , Bates Autumn , Duran Catherine , Anderson Lordina , Murray Morgan , Pereira-Badji Jennifer , Shoushani Christina , Thibault Jacob
Published: October 2022

In a cellular model of Down Syndrome, hTERT immortalized RPE-1 (human retinal pigment epithelial-1) cells carrying an extra copy of chromosome 21 exhibit reduced fitness, in part, as an increase in doubling time (or a reduction in cell proliferation rate) in culture. ROCK2 (Rho associated coiled-coil containing kinase 2) was identified in a whole genome CRISPR knockout (KO) screen designed to identify genes and pathways that could be therapeutically targeted to improve cell proliferation (Replogle JM, et al. manuscript in preparation). ROCK2 KO cell lines of both RPE-1 euploid and trisomy 21 aneuploid cells were created using CRISPR. Trisomy 21 ROCK2 KO cell lines showed a modest increase in cell proliferation rate compared to the parental aneuploid cells, similar to the relative effect that ROCK2 knockout had in the whole genome CRISPR screen. Euploid ROCK2 KO cell lines showed no difference in growth rate vs their ROCK2 expressing counterparts. Changes in doubling time in response to two pharmaceutical ROCK inhibitors, Fasudil and Y27632, also showed the same modest increase in cell proliferation rate in the trisomy 21 cells. The actin cytoskeleton, a target of ROCK2 regulation, exhibited long stress fibers that aligned across multiple contiguous cells in confluent trisomy 21 ROCK2 KO cells compared to the disorganized stress fibers of the parental trisomy 21 cells with normal ROCK2 expression.
Dynamics of BMP signaling in the earlyDrosophilaembryo
Authors: Al Asafen Hadel Y. , Beseli Aydin , Hiremath Sharva , Williams Cranos M. , Reeves Gregory T.
Published: October 2022

In developing tissues, morphogen gradients are thought to initialize gene expression patterns. However, the relationship between the dynamics of morphogen-encoded signals and gene expression decisions are largely unknown. Here we examine the dynamics of the Bone Morphogenetic Protein (BMP) pathway inDrosophilablastoderm-stage embryos. In this tissue, the BMP pathway is highly dynamic: it begins as a broad and weak signal on the dorsal half of the embryo, then 20-30 min later refines into a narrow, intense peak centered on the dorsal midline. This dynamical progression of the BMP signal raises questions of how it stably activates target genes. Therefore, we performed live imaging of the BMP signal and found that dorsal-lateral cells experience only a short transient in BMP signaling, after which the signal is lost completely. Moreover, we measured the transcriptional response of the BMP target genepannierin live embryos and found it to remain activated in dorsal-lateral cells, even after the BMP signal is lost. Our findings may suggest that the BMP pathway activates a memory, or “ratchet” mechanism that may sustain gene expression.
Condensin dysfunction is a reproductive isolating barrier in mice
Authors: Yakoubi Warif El , Akera Takashi
Published: October 2022

Reproductive isolation occurs when the genomes of two populations accumulate genetic incompatibilities that prevent inter-breeding. Cell biological understanding of such hybrid incompatibility is limited, especially for hybrid female sterility. Here we find that species divergence in condensin regulation and centromere organization between two mouse species,Mus musculusandMus spretus, drives chromosome de-condensation and mis-segregation in their F1 hybrid oocytes, reducing female fertility. The chromosome condensation defects in hybrid oocytes were especially prominent atMus musculuscentromeres due to their highly abundant major satellite DNA, leading to species-specific chromosome mis-segregation. This study provides the first mechanistic insights into hybrid incompatibility in female meiosis and demonstrates that condensin mis-regulation can be a reproductive isolating barrier in mammals.
Insights into H2O2-induced signaling in Jurkat cells from analysis of gene expression
Authors: Taylor Megan F. , Black Michael A. , Hampton Mark B. , Ledgerwood Elizabeth C.
Published: October 2022

Hydrogen peroxide (H2O2) is a ubiquitous oxidant produced in a regulated manner by various enzymes in mammalian cells. H2O2reversibly oxidises thiol groups of cysteine residues to mediate intracellular signalling. Whilst examples of H2O2dependent signalling have been reported, the exact molecular mechanism(s) of signalling and the pathways affected are not well understood. Here, the transcriptomic response of Jurkat T cells to H2O2was investigated to determine global effects on gene expression. With a low H2O2concentration (10 μM) that did not induced an oxidative stress response or cell death, extensive changes in gene expression occurred after 4 hours (6803 differentially expressed genes). Of the genes with greater then 2-fold change in expression, 85% were upregulated suggesting that in a physiological setting H2O2predominantly activates gene expression. Pathway analysis identified gene expression signatures associated with FOXO and NTRK signalling. These signatures were associated with an overlapping set of transcriptional regulators. Overall, our results provide a snapshot of gene expression changes in response to H2O2, which, along with further studies, will lead to new insights into the specific pathways that are activated in response to endogenous production of H2O2, and the molecular mechanisms of H2O2signalling.
Mitotic chromosomes scale to nucleo-cytoplasmic ratio and cell size inXenopus
Authors: Zhou Coral Y. , Dekker Bastiaan , Liu Ziyuan , Cabrera Hilda , Ryan Joel , Dekker Job , Heald Rebecca
Published: October 2022

During the rapid and reductive cleavage divisions of early embryogenesis, subcellular structures such as the nucleus and mitotic spindle scale to decreasing cell size. Mitotic chromosomes also decrease in size during development, presumably to coordinately scale with mitotic spindles, but underlying mechanisms are unclear. Here we combinein vivoandin vitroapproaches using eggs and embryos from the frogXenopus laevisto show that mitotic chromosome scaling is mechanistically distinct from other forms of subcellular scaling. We found that mitotic chromosomes scale continuously with cell, spindle and nuclear sizein vivo. However, unlike for spindles and nuclei, mitotic chromosome size cannot be re-set by cytoplasmic factors from earlier developmental stages.In vitro, increasing nucleo-cytoplasmic (N/C) ratio is sufficient to recapitulate mitotic chromosome scaling, but not nuclear or spindle scaling, through differential loading of maternal factors during interphase. An additional pathway involving importin α scales mitotic chromosomes to cell surface area/volume (SA/V) during metaphase. Finally, single-chromosome immunofluorescence and analysis of Hi-C data suggest that mitotic chromosomes scale through decreased recruitment of condensin I, resulting in major rearrangements of DNA loop architecture to accommodate the same amount of DNA on a shorter axis. Together, our findings demonstrate how mitotic chromosome size is set by spatially and temporally distinct developmental cues in the early embryo.
Neural predictors of subjective fear depend on the situation
Authors: Wang Yiyu , Kragel Philip A. , Satpute Ajay B.
Published: October 2022

ABSTRSCT

The extent to which neural representations of fear experience depend on or generalize across the situational context has remained unclear. We systematically manipulated variation within and across three distinct fearevocative situations including fear of heights, spiders, and social threats. Participants (n=21, 10 females and 11 males) viewed 20 second clips depicting spiders, heights, or social encounters, and rated fear after each video. Searchlight multivoxel pattern analysis (MVPA) was used to identify whether and which brain regions carry information that predicts fear experience, and the degree to which the fear-predictive neural codes in these areas depend upon or generalize across the situations. The overwhelming majority of brain regions carrying information about fear did so in a situation dependent manner. These findings suggest that local neural representations of fear experience are unlikely to involve a singular pattern, but rather a collection of multiple heterogeneous brain states
MdrDB: Mutation-induced drug resistance DataBase
Authors: Yang Ziyi , Ye Zhaofeng , Qiu Jiezhong , Feng Rongjun , Li Danyu , Hsieh Changyu , Allcock Jonathan , Zhang Sheng-Yu
Published: October 2022

Abstract

Mutation-induced drug resistance – where the efficacy of drugs is diminished by structural changes in proteins – presents a significant challenge to drug development and the clinical treatment of disease. Understanding the effects of mutation on protein-ligand binding affinities is a key step in developing more effective drugs and therapies, but as a research community we are currently hindered by the lack of a comprehensive database of relevant information. To address this issue, we have developed MdrDB, a database of information related to changes in protein-ligand affinity caused by mutations in protein structure. MdrDB combines data from seven publicly available datasets with calculated biochemical features, as well as 3D structures computed with PyMOL and AlphaFold 2.0, to form the largest database of its kind. With 3D structural information provided for all samples, MdrDB was specifically created to have the size, breadth, and complexity to be useful for practical protein mutation studies and drug resistance modeling. The database brings together wild type and mutant protein-ligand complexes, binding affinity changes upon mutation (ΔΔG), and biochemical features calculated from complexes to advance our understanding of mutation-induced drug resistance, the development of combination therapies, and the discovery of novel chemicals. In total, MdrDB contains 100,537 samples generated from 240 proteins (5,119 total PDB structures), 2,503 mutations, and 440 drugs. Of the total samples, 95,971 are based on available PDB structures, with the remaining 4,566 based on AlphaFold 2.0 predicted structures.
Perceptions of COVID-19 risk, vaccine access, and confidence: a qualitative analysis of South Asians in Canada
Authors: Kandasamy Sujane , Manoharan Baanu , Khan Zainab , Stennett Rosain , Desai Dipika , Nocos Rochelle , Wahi Gita , Banner Davina , de Souza Russell J. , Lear Scott A. , Anand Sonia S.
Published: October 2022

VISUAL ABSTRACT CAN BE FOUNDHERE

Objectives

In the first full year of the COVID-19 pandemic (2020), South Asians living in the Greater Toronto Hamilton and Vancouver Areas experienced specific barriers to accessing SARS-CoV-2 testing and receiving reliable health information. However, between June 2021 and February 2022, the proportion of people having received at least 1 dose of a COVID-19 vaccine was higher among this group (96%) than among individuals who were not visible minorities (93%). A better understanding of successful approaches and the challenges experienced by those who remain unvaccinated among this highly vaccinated group may improve public health outreach in subsequent waves of the current pandemic or for future pandemic planning. Using qualitative methods, we sought to explore the perceptions of COVID-19 risk, vaccine access, uptake, and confidence among South Asians living in Canada.

Methods

In this qualitative study, we interviewed 25 participants between July 2021 and January 2022 in the Greater Toronto Hamilton and Greater Vancouver Areas (10 community members, 9 advocacy group leaders, 6 public health staff). We conducted initial and focused coding in duplicate and developed salient themes. Throughout this process, we held frequent discussions with members of the study’s advisory group to guide data collection as it relates to community engagement, recruitment, and data analysis.

Results

Access to and confidence in the COVID-19 vaccine was impacted by individual risk perceptions; sources of trusted information (ethnic and non-ethnic); impact of COVID-19 and the pandemic on individuals, families, and society; and experiences with COVID-19 mandates and policies (including temporal and generational differences). Approaches that include community-level awareness and tailored outreach as it relates to language and cultural context were considered successful.

Conclusion

Understanding factors and developing strategies that build vaccine confidence can guide our approach to increase vaccine acceptance in the current and future pandemics.
Pre-MEASURE:FLT3-ITD and mutatedNPM1measurable residual disease before allogeneic transplant in adults with AML in first remission
Authors: Dillon Laura W , Gui Gege , Ravindra Niveditha , Wong Zoë , Andrew Georgia , Mukherjee Devdeep , Zeger Scott L. , El Chaer Firas , Spellman Stephen , Howard Alan , Chen Karen , Auletta Jeffery , Devine Steven M. , Jimenez Jimenez Antonio Martin , De Lima Marcos J.G. , Litzow Mark Robert , Kebriaei Partow , Saber Wael , Weisdorf Daniel Jordan , Page Kristin M. , Hourigan Christopher S.
Published: October 2022

Background

Prevention of relapse for adults with Acute Myeloid Leukemia (AML) in first remission (CR1) is the most common indication for allogeneic hematopoietic cell transplantation (alloHCT). Measurable residual disease (MRD) detection has been associated with higher relapse rates, but testing is not standardized. Establishment of validated AML MRD criteria would allow harmonization across centers facilitating clinical trials and generalizable practice guidelines.

Methods

Patients aged 18 or older who underwent first alloHCT forFLT3, NPM1, IDH1, IDH2and/orKITmutated AML in CR1 were eligible for this multicenter study. Residual mutations detected in remission using ultra-deep error-corrected next-generation DNA-sequencing (NGS-MRD) associated with increased relapse risk were validated in a second independent cohort. The impact of baseline characteristics on NGS-MRD results was evaluated.

Results

Pre-conditioning CR1 blood samples from 1075 patients were tested. Detection of residualNPM1and/orFLT3-ITD mutations before alloHCT was associated with worse outcomes after transplantation in both discovery (patients transplanted 2013-2017) and validation (patients transplanted 2018-2019) cohorts. In multivariate Cox regression analysis detection of residualNPM1m (relapse; HR: 4.9, 3.5-7.0, P<0.0001, survival; HR: 2.9, 2.2-4.0, P<0.0001), residualFLT3-ITD (relapse: HR: 4.2, 3.1-5.7, P<0.0001, survival; HR: 2.6, 2.0-3.6, P<0.0001), and receipt of non-melphalan containing reduced intensity conditioning were associated with inferior clinical outcomes.

Conclusions

Detection of residualNPM1and/orFLT3-ITD mutations in the blood of patients undergoing alloHCT for AML in CR1 is associated with increased relapse and worse survival. In those undergoing reduced intensity conditioning, melphalan may reduce the risk associated with testing NGS-MRD positive prior to transplantation.
Population serum proteomics uncovers prognostic protein classifier and molecular mechanisms for metabolic syndrome
Authors: Cai Xue , Xue Zhangzhi , Zeng Fang-Fang , Tang Jun , Yue Liang , Wang Bo , Ge Weigang , Xie Yuting , Miao Zelei , Gou Wanglong , Fu Yuanqing , Li Sainan , Gao Jinlong , Shuai Menglei , Zhang Ke , Xu Fengzhe , Tian Yunyi , Xiang Nan , Zhou Yan , Shan Peng-Fei , Zhu Yi , Chen Yu-ming , Zheng Ju-Sheng , Guo Tiannan
Published: October 2022

Metabolic syndrome (MetS) is a complex metabolic disorder with a global prevalence of 20-25%. Early identification and intervention would help minimize the global burden on healthcare systems. Here, we measured over 400 proteins from ∼20,000 proteomes using data-independent acquisition mass spectrometry for 7890 serum samples from a longitudinal cohort of 3840 participants with two follow-up time points over ten years. We then built a machine learning model for predicting the risk of developing MetS within ten years. Our model, composed of 11 proteins and the age of the individuals, achieved an area under the curve of 0.784 in the discovery cohort (n=855) and 0.774 in the validation cohort (n=242). Using linear mixed models, we found that apolipoproteins, immune-related proteins, and coagulation-related proteins best correlated with MetS development. This population-scale proteomics study broadens our understanding of MetS, and may guide the development of prevention and targeted therapies for MetS.
Intergenic regions of Saccharomycotina yeasts are enriched in potential to form transmembrane domains
Authors: Tassios Emilios , Nikolaou Christoforos , Vakirlis Nikolaos
Published: October 2022

Intergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins, also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously non-coding sequences has now been established as a potent force for genomic novelty. Recently, it was shown that intergenic regions in the genome ofS. cerevisiaeharbor pervasive cryptic potential to, if theoretically translated, form transmembrane domains (TM domains) more frequently than expected by chance, a property that we refer to as TM-forming enrichment. The source and biological relevance of this property is unknown. Here we expand the investigation into the TM-forming potential of intergenic regions to the entire Saccharomycotina budding yeast subphylum, in an effort to explain this property and understand its importance. We find pervasive but variable enrichment in TM-forming potential across the subphylum, regardless of the composition and average size of intergenic regions. This cryptic property is evenly spread across the genome, cannot be explained by the hydrophobic content of the sequence, and does not appear to localize to regions containing regulatory motifs. This TM-forming enrichment specifically, and not the actual TM-forming potential, is associated, across genomes, with more TM domains in evolutionarily young genes. Our findings shed light on this newly discovered feature of yeast genomes and constitute a first step towards understanding its evolutionary importance.
Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements
Authors: Garcia-Alles Luis F. , Soldan Vanessa , Custovic Irma , Castaño-Cerezo Sara , Balor Stéphanie , Fuentes-Cabrera Miguel , Truan Gilles , Lesniewska Eric , Reguera David
Published: October 2022

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate to varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of trends of self-assembly of BMC hexamers (BMC-H), the most abundant shell constituents. Published and new microscopy data show that some BMC-H, likeβ-carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved-implying objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the disposition adopted by BMC-H that form curved objects experimentally, conducting to almost identical arrangements to those found in structures of recomposed BMC shells. Simulations on ensembles of planar-behaving hexamers, which were previously reconfigured to comply with such disposition, confirmed that bending is defined by assembly details, rather than by BMC-H identity. Finally, although no common atomic determinants could be identified as responsible of BMC-H spontaneous curvature, an inter-hexamer ionic pair was pinpointed as contributor to hold a subset of BMC-H in low bending dispositions. These results are expected to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.
Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques
Authors: Hoang Timothy N. , Viox Elise G. , Upadhyay Amit A. , Strongin Zachary , Tharp Gregory K. , Pino Maria , Nchioua Rayhane , Hirschenberger Maximilian , Gagne Matthew , Nguyen Kevin , Harper Justin L. , Marciano Shir , Boddapati Arun K. , Pellegrini Kathryn L. , Tisoncik-Go Jennifer , Whitmore Leanne S. , Karunakaran Kirti A. , Roy Melissa , Kirejczyk Shannon , Curran Elizabeth H. , Wallace Chelsea , Wood Jennifer S. , Connor-Stroud Fawn , Kasturi Sudhir P. , Levit Rebecca D. , Gale Michael , Vanderford Thomas H. , Silvestri Guido , Busman-Sahay Kathleen , Estes Jacob D. , Vaccari Monica , Douek Daniel C. , Sparrer Konstantin M.J. , Kirchhoff Frank , Johnson R. Paul , Schreiber Gideon , Bosinger Steven E. , Paiardini Mirko
Published: October 2022

Type-I interferons (IFN-I) are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, and for the first time, IFN-I signaling was modulated in rhesus macaques (RMs) prior to and during acute SARS-CoV-2 infection using a mutated IFNα2 (IFN-modulator; IFNmod), which has previously been shown to reduce the binding and signaling of endogenous IFN-I. In SARS-CoV-2-infected RMs, IFNmod reduced both antiviral and inflammatory ISGs. Notably, IFNmod treatment resulted in a potent reduction in (i) SARS-CoV-2 viral load in Bronchoalveolar lavage (BAL), upper airways, lung, and hilar lymph nodes; (ii) inflammatory cytokines, chemokines, and CD163+MRC1-inflammatory macrophages in BAL; and (iii) expression of Siglec-1, which enhances SARS-CoV-2 infection and predicts disease severity, on circulating monocytes. In the lung, IFNmod also reduced pathogenesis and attenuated pathways of inflammasome activation and stress response during acute SARS-CoV-2 infection. This study, using an intervention targeting both IFN-α and IFN-β pathways, shows that excessive inflammation driven by type 1 IFN critically contributes to SARS-CoV-2 pathogenesis in RMs, and demonstrates the potential of IFNmod to limit viral replication, SARS-CoV-2 induced inflammation, and COVID-19 severity.
Gene Gain and Loss from the Asian Corn Borer W Chromosome
Authors: Dai Wenting , Mank Judith E. , Ban Liping
Published: October 2022

We built a chromosome-level genome assembly of the Asian corn borer,Ostrinia furnacalisGuenée (Lepidoptera: Pyralidae, Pyraloidea), an economically important pest in corn, from a female, including both the Z and W chromosome. Despite deep conservation of the Z chromosome across Lepidoptera, our chromosome-level W assembly reveals little conservation with available W chromosome sequence in related species or with the Z chromosome, consistent with a non-canonical origin of the W chromosome. The W chromosome has accumulated significant repetitive elements and experienced rapid gene gain from the remainder of the genome, with most genes exhibiting pseudogenization after duplication to the W. The genes that retain significant expression are largely enriched for functions in DNA recombination, the nucleosome, chromatin and DNA binding, likely related to meiotic and mitotic processes within the female gonad.
The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling
Authors: Alexander Kellianne D , Ramachandran Shankar , Biswas Kasturi , Lambert Christopher M , Russell Julia , Oliver Devyn B , Armstrong William , Rettler Monika , Doitsidou Maria , Bénard Claire , Francis Michael M
Published: October 2022

An important step in brain development is the remodeling of juvenile neural circuits to establish mature connectivity. The elimination of juvenile synapses is a critical step in this process; however, the molecular mechanisms directing synapse elimination activities and their timing are not fully understood. We identify here a conserved transcriptional regulator, DVE-1, that shares homology with mammalian special AT-rich sequence-binding (SATB) family members and directs the elimination of juvenile synaptic inputs onto remodelingC. elegansGABAergic neurons. Dorsally localized juvenile acetylcholine receptor clusters and apposing presynaptic sites are eliminated during maturation of wild type GABAergic neurons but persist into adulthood indve-1mutants. The persistence of juvenile synapses indve-1mutants does not impede synaptic growth during GABAergic remodeling and therefore produces heightened motor connectivity and a turning bias during movement. DVE-1 is localized to GABAergic nuclei prior to and during remodeling and DVE-1 nuclear localization is required for synapse elimination to proceed, consistent with DVE-1’s function as a transcriptional regulator. Pathway analysis of DVE-1 targets and proteasome inhibitor experiments implicate transcriptional control of the ubiquitin-proteasome system in synapse elimination. Together, our findings demonstrate a new role for a SATB family member in the control of synapse elimination during circuit remodeling through transcriptional regulation of ubiquitin-proteasome signaling.

Contributions Summary

KDA generated strains, transgenic lines, molecular constructs, confocal microscopy images and analysis, performed optogenetic behavioral experiments, photoconversion experiments, modencode ChIP-seq analysis and pathway analysis. SR performed all calcium imaging experiments/analysis and conducted single worm tracking. KB performed all Bortezomib inhibitor experiments and analysis. CL generated most vectors and constructs. JR assisted with generation of CRISPR/Cas9 generated strains. WA and MR assisted with aldicarb behavioral assay. DO assisted with EMS screen and isolation ofdve-1mutant. CB and MD aided in CloudMap bioinformatic analysis of theuf171mutant. MMF and KDA designed and interpreted results of all experiments and wrote the manuscript.
The line bisection bias stems from left-side underawareness, not from right-side hyperattention
Authors: Smaczny S. , Klein E. , Jung S. , Moeller K. , Karnath H.-O.
Published: October 2022

It is still a matter of scientific debate whether the line bisection bias frequently observed in patients with spatial neglect is due to attentional underawareness of the left end of the line, attentional hyperattention towards the right end, or a logarithmically compressed perception of the line. To address this question, neglect patients who showed a line bisection bias were administered additional tasks involving horizontal lines (e.g., number line estimation tasks). Their performance was compared to neglect patients not showing a line bisection bias, patients with right hemisphere damage without neglect, and healthy controls. Results indicated that patients with a line bisection bias tended to overestimate lefthand segments when they had to dissect lines into three or four equal parts. This is congruent with both the notions of an underawareness of lefthand segments as well as a logarithmic compression of the line. However, when these patients had to imagine the lines as bounded fraction number lines ranging from 0-1, the results were mixed. When the number lines ranged from 0-10, these patients showed rightward overestimation biases for the numbers 4 and 5. Additionally, all patient groups, but not healthy controls, tended to place number 1 too far to the left and number 9 too far to the right, suggesting a general bias towards endpoints. In sum, this seems more congruent with attentional accounts than a perceptual one. Spatial-numerical associations could be ruled out, as all participants showed a verbal number bisection bias towards smaller numbers (i.e., the ‘left’ of the mental number line). Therefore, these findings seem to indicate that the line bisection bias is most likely due to underawareness of the left end rather than hyperattention towards the right or a logarithmic perception of the line.
Vector-clustering Multiple Sequence Alignment: Aligning into the twilight zone of protein sequence similarity with protein language models
Authors: McWhite Claire D. , Singh Mona
Published: October 2022

Multiple sequence alignment is a critical step in the study of protein sequence and function. Typically, multiple sequence alignment algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tree. These alignment algorithms use scoring systems based on substitution matrices to measure amino-acid similarities. While successful, standard methods struggle on sets of proteins with low sequence identity - the so-called twilight zone of protein alignment. For these difficult cases, another source of information is needed. Protein language models are a powerful new approach that leverage massive sequence datasets to produce high-dimensional contextual embeddings for each amino acid in a sequence. These embeddings have been shown to reflect physicochemical and higher-order structural and functional attributes of amino acids within proteins. Here, we present a novel approach to multiple sequence alignment, based on clustering and ordering amino acid contextual embeddings. Our method for aligning semantically consistent groups of proteins circumvents the need for many standard components of multiple sequence alignment algorithms, avoiding initial guide tree construction, intermediate pairwise alignments, gap penalties, and substitution matrices. The added information from contextual embeddings leads to higher accuracy alignments for structurally similar proteins with low amino-acid similarity. We anticipate that protein language models will become a fundamental component of the next generation of algorithms for generating MSAs.

Software availability:https://github.com/clairemcwhite/vcmsa
Macrophage phenotype transitions in a stochastic gene-regulatory network model
Authors: Frank Anna-Simone , Larripa Kamila , Ryu Hwayeon , Röblitz Susanna
Published: October 2022

Polarization is the process by which a macrophage cell commits to a phenotype based on external signal stimulation. To know how this process is affected by random fluctuations and events within a cell is of utmost importance to better understand the underlying dynamics and predict possible phenotype transitions. For this purpose, we develop a stochastic modeling approach for the macrophage polarization process. We classify phenotype states using the Robust Perron Cluster Analysis and quantify transition pathways and probabilities by applying Transition Path Theory. Depending on the model parameters, we identify four bistable and one tristable phenotype configuration. We find that bistable transitions are fast but their states less robust. In contrast, phenotype transitions in the tristable situation have a comparatively long time duration, which reflects the robustness of the states. The results indicate parallels in the overall transition behavior of macrophage cells with other heterogeneous and plastic cell types, such as cancer cells. Our approach allows for a probabilistic interpretation of macrophage phenotype transitions and biological inference on phenotype robustness. In general, the methodology can easily be adapted to other systems where random state switches are known to occur.
Monopolization at the cost of desiccation: Reduced waterproofing cuticular hydrocarbons impairs nestmate discrimination in an ant
Authors: Pierre-André Eyer , Helms Anjel M. , Moran Megan N. , Vargo Edward L.
Published: October 2022

After humans, social insects represent one of the most complex groups of social organisms, relying on a well-organized communication system among colony members. The transfer of information among individuals is primarily based on cuticular hydrocarbons (CHC). These chemical compounds, produced by all insects, initially evolved to prevent water loss1. They were subsequently co-opted as semiochemicals to communicate various types of information. This includes nestmate recognition in social insects2,3, enabling different colonies to partition resources by ousting conspecific competitors. In this study, we report the near complete loss of CHC production by workers of the antNylanderia fulva. This absence of CHCs is a double-edged sword. It represents a causative agent in the ecological success of this ant species — enabling the development of a large supercolony in its invasive range through limited ability to differentiate nestmates— but increases the risk of suffering ecological stress through desiccation.
FANCJ DNA helicase is recruited to the replisome by AND-1 to ensure genome stability
Authors: Boavida Ana , Napolitano Luisa M. R. , Santos Diana , Cortone Giuseppe , Onesti Silvia , Jegadesan Nanda K. , Branzei Dana , Pisani Francesca M.
Published: October 2022

FANCJ is a DNA helicase linked to Fanconi anemia and frequently mutated in breast and ovarian cancers. If and how FANCJ is recruited to the replisome is unknown. Here, we report that FANCJ directly binds to AND-1 (the vertebrate ortholog of budding yeast Ctf4), a homo-trimeric protein adaptor that connects the CDC45/MCM2-7/GINS replicative DNA helicase with DNA polymerase α and several factors at DNA replication forks. We find that the interaction between FANCJ and AND-1 requires the integrity of an evolutionarily conserved Ctf4-interacting protein (CIP) box located between the FANCJ helicase motifs IV and V. Disruption of the FANCJ CIP box significantly reduces FANCJ association with the replisome, causing enhanced DNA damage, decreased replication fork recovery and fork asymmetry in stressful conditions. Cancer-relevant FANCJ CIP box variants display reduced AND-1-binding, a finding that suggests a potential role of the mutatedFANCJalleles in cancer predisposition.
Molecular early burst associated with the diversification of birds at the K–Pg boundary
Authors: Berv Jacob S. , Singhal Sonal , Field Daniel J. , Walker-Hale Nathanael , McHugh Sean W. , Shipley J. Ryan , Miller Eliot T. , Kimball Rebecca T. , Braun Edward L. , Dornburg Alex , Parins-Fukuchi C. Tomomi , Prum Richard O. , Winger Benjamin M. , Friedman Matt , Smith Stephen A.
Published: October 2022

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K– Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds [1-9]. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade [10]. Our approach identifies distinct and contrasting regimes of molecular evolution across exons, introns, untranslated regions, and mitochondrial genomes. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds [11-13]. Using simulation and machine learning techniques, we show that shifts in developmental mode [14] or adult body mass [4] best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass [15, 16]. In agreement with theoretical predictions, this scaling relationship appears to have weakened across the end-Cretaceous transition. Overall, our study provides evidence that the Chicxulub bolide impact [17] triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.
Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting
Authors: Torino Stefania , Dhurandhar Mugdha , Stroobants Annelore , Claessens Raf , Efremov Rouslan G.
Published: October 2022

Using single particle cryogenic electron microscopy (cryo-EM) high-resolution structures of proteins in different conformations can be reconstructed. Protein function often involves transient functional conformations, which can be resolved using time-resolved cryo-EM (trEM). In trEM, reactions are arrested after a defined delay time by rapid vitrification of protein solution on the EM grid. Despite the increasing interest in trEM among the cryo-EM community, making trEM samples with a time resolution below 100 ms remains challenging. Here we report the design and the realization of a time-resolved cryo-plunger that combines a droplet-based microfluidic mixer with a laser-induced generator of microjets that allows rapid initiation of reaction and rapid plunge-freezing of cryo-EM grids. Using this approach, a time resolution of 5 ms was achieved and the protein density map was reconstructed to a spatial resolution of 2.1 Å. We performed trEM experiments on GroEL:GroES chaperonin complex, these resolved the kinetics of the complex formation and visualized putative short-lived conformations of GroEL-ATP complex.
A spatial-attentional mechanism underlies action-related distortions of time judgement
Authors: Cao Liyu
Published: October 2022

Temporal binding has been understood as an illusion in timing judgement. When an action triggers an outcome (e.g. a sound) after a brief delay, the action is reported to occur later than if the outcome does not occur, and the outcome is reported to occur earlier than a similar outcome not caused by an action. We show here that an attention mechanism underlies the seeming illusion of timing judgement. In one method, participants watch a rotating clock hand and report event times by noting the clock hand position when the event occurs. We find that visual spatial attention is critically involved in shaping event time reports made in this way. This occurs because action and outcome events result in shifts of attention around the clock rim, thereby biasing the perceived location of the clock hand. Using a probe detection task to measure attention, we show a difference in the distribution of visual spatial attention between a single-event condition (sound only or action only) and a two-event agency condition (action plus sound). Participants accordingly report the timing of the same event (the sound or the action) differently in the two conditions: spatial attentional shifts masquerading as temporal binding. Furthermore, computational modelling based on the attention measure can reproduce the temporal binding effect. Studies that use time judgement as an implicit marker of voluntary agency should first discount the artefactual changes in event timing reports that actually reflect differences in spatial attention. The study also has important implications for related results in mental chronometry obtained with the clock-like method since Wundt, as attention may well be a critical confounding factor in the interpretation of these studies.
The annotation and function of the Parkinson’s and Gaucher disease-linked geneGBA1has been concealed by its protein-coding pseudogeneGBAP1
Authors: Gustavsson Emil K. , Sethi Siddharth , Gao Yujing , Brenton Jonathan W. , García-Ruiz Sonia , Zhang David , Garza Raquel , Reynolds Regina H. , Evans James R. , Chen Zhongbo , Grant-Peters Melissa , Macpherson Hannah , Montgomery Kylie , Dore Rhys , Wernick Anna I. , Arber Charles , Wray Selina , Gandhi Sonia , Esselborn Julian , Blauwendraat Cornelis , Douse Christopher H. , Adami Anita , Atacho Diahann A.M. , Kouli Antonina , Quaegebeur Annelies , Barker Roger A. , Englund Elisabet , Platt Frances , Jakobsson Johan , Wood Nicholas W. , Houlden Henry , Saini Harpreet , Bento Carla F. , Hardy John , Ryten Mina
Published: October 2022

The human genome contains numerous duplicated regions, such as parent-pseudogene pairs, causing sequencing reads to align equally well to either gene. The extent to which this ambiguity complicates transcriptomic analyses is currently unknown. This is concerning as many parent genes have been linked to disease, includingGBA1,causally linked to both Parkinson’s and Gaucher disease. We find that most of the short sequencing reads that map toGBA1, also map to its pseudogene,GBAP1. Using long-read RNA-sequencing in human brain, where all reads mapped uniquely, we demonstrate significant differences in expression compared to short-read data. We identify novel transcripts from bothGBA1andGBAP1, including protein-coding transcripts that are translatedin vitroand detected in proteomic data, but that lack GCase activity. By combining long-read with single-nuclear RNA-sequencing to analyse brain-relevant cell types we demonstrate that transcript expression varies by brain region with cell-type-selectivity. Taken together, these results suggest a non-lysosomal function for both GBA1 and GBAP1 in brain. Finally, we demonstrate that inaccuracies in annotation are widespread among parent genes, with implications for many human diseases.
Npr3 regulates neural crest and cranial placode progenitors formation through its dual function as clearance and signaling receptor
Authors: Devotta Arun , Juraver-Geslin Hugo , Griffin Casey , Saint-Jeannet Jean-Pierre
Published: October 2022

Natriuretic peptide signaling has been implicated in a broad range of physiological processes, regulating blood volume and pressure, ventricular hypertrophy, fat metabolism, and long bone growth. Here we describe a completely novel role for natriuretic peptide signaling in the control of neural crest (NC) and cranial placode (CP) progenitors formation. Among the components of this signaling pathway, we show that natriuretic peptide receptor 3 (Npr3) plays a pivotal role by differentially regulating two developmental programs through its dual function as clearance and signaling receptor. Using a combination of MO-based knockdowns, pharmacological inhibitors and rescue assays we demonstrate that Npr3 cooperate with guanylate cyclase natriuretic peptide receptor 1 (Npr1) and natriuretic peptides (Nppa/Nppc) to regulate NC and CP formation, pointing at a broad requirement of this signaling pathway in early embryogenesis. We propose that Npr3 acts as a clearance receptor to regulate local concentrations of natriuretic peptides for optimal cGMP production through Npr1 activation, and as a signaling receptor to control cAMP levels through inhibition of adenylyl cyclase. The intracellular modulation of these second messengers therefore participates in the segregation of NC and CP cell populations.
VStrains: De Novo Reconstruction of Viral Strains via Iterative Path Extraction From Assembly Graphs
Authors: Luo Runpeng , Lin Yu
Published: October 2022

With the high mutation rate in viruses, a mixture of closely related viral strains (called viral quasispecies) often co-infect an individual host. Reconstructing individual strains from viral quasispecies is a key step to characterizing the viral population, revealing strain-level genetic variability, and providing insights into biomedical and clinical studies. Reference-based approaches of reconstructing viral strains suffer from the lack of high-quality references due to high mutation rates and biased variant calling introduced by a selected reference. De novo methods require no references but face challenges due to errors in reads, the high similarity of quasispecies, and uneven abundance of strains.

In this paper, we propose VStrains, a de novo approach for reconstructing strains from viral quasispecies. VStrains incorporates contigs, paired-end reads, and coverage information to iteratively extract the strain-specific paths from assembly graphs. We benchmark VStrains against multiple state-of-the-art de novo and reference-based approaches on both simulated and real datasets. Experimental results demonstrate that VStrains achieves the best overall performance on both simulated and real datasets under a comprehensive set of metrics such as genome fraction, duplication ratio, NGA50, error rate,etc.

Availability

VStrains is freely available athttps://github.com/MetaGenTools/VStrains.
Identification of two novel heterodimeric ABC transporters in melanoma: ABCB5β/B6 and ABCB5β/B9
Authors: Gerard Louise , Duvivier Laurent , Fourrez Marie , Salazar Paula , Sprimont Lindsay , Xia Di , Ambudkar Suresh V. , Gottesman Michael M. , Gillet Jean-Pierre
Published: October 2022

ABCB5 is a member of the ABC transporter superfamily composed of 48 transporters, which have been extensively studied for their role in cancer multidrug resistance and, more recently, in tumorigenesis. ABCB5 has been identified as a marker of skin progenitor cells, melanoma, and limbal stem cells. It has also been associated with multidrug resistance in several cancers. The unique feature of ABCB5 is that it exists as both a full transporter (ABCB5FL) and a half transporter (ABCB5β). Several studies have shown that the ABCB5β homodimer does not confer multidrug resistance, in contrast to ABCB5FL. In this study, using three complementary techniques; (1) nanoluciferase-based bioluminescence resonance energy transfer, (2) co-immunoprecipitation, and (3) proximity ligation assay, we identified two novel heterodimers in melanoma: ABCB5β/B6 and ABCB5β/B9. Both heterodimers could be expressed in high-five insect cells and ATPase assays revealed that they have a basal ATPase activity. These results are an important step toward untangling the functional role of ABCB5β in melanocytes and melanoma.
Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation and virulence
Authors: Sun Wei-Sheng , Lassinantti Lena , Järvå Michael , Schmitt Andreas , Beek Josy ter , Berntsson Ronnie P-A
Published: October 2022

Type 4 Secretion Systems are a main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. In Gram-positives, these secretion systems often rely on surface adhesins to enhance cellular aggregation and mating pair formation. One of the best studied adhesins is PrgB from the conjugative plasmid pCF10 ofEnterococcus faecalis,which has been shown to play major roles in conjugation, biofilm formation and importantly also in bacterial virulence. SinceprgBorthologs exist on a large number of conjugative plasmids in various different species, this makes PrgB a model protein for this widespread virulence factor. After characterizing the polymer adhesin domain of PrgB previously, we here report the structure for almost the entire remainder of PrgB, which reveals that PrgB contains four immunoglobulin-like domains. Based on this new insight, we re-evaluate previously studied variants and present newin vivodata where specific domains or conserved residues have been removed. For the first time, we can show a decoupling of cellular aggregation from biofilm formation and conjugation inprgBmutant phenotypes. Based on the presented data, we propose a new functional model to explain how PrgB mediates its different functions. We hypothesize that the Ig-like domains act as a rigid stalk that presents the polymer adhesin domain at the right distance from the cell wall.