bluuebunny/crossref_metadata_2025_split huggingface dataset:
Head and eye movement planning differ in access to information during visual search
Authors: Durant Szonya , Watson Tamara 
Published: May 2022

AbstractTo characterize the process of visual search, reaction time is measured relative to stimulus onset, when the whole search field is presented in view simultaneously. Salient objects are found faster, suggesting that they are detected using peripheral vision (rather than each object being fixated in turn). This work investigated how objects are detected in the periphery when onset in the visual field is due to head movement. Is the process of target detection similarly affected by salience? We test this in 360 degree view with free head and eye movement, using a virtual reality headset with eye tracking. We presented letters and Gabor patches as stimuli in separate experiments. Four clusters were arranged horizontally such that two clusters were visible at onset either side of a fixation cross (near location) while the other two entered the field of view (FoV) when the participant made an appropriate head movement (far location). In both experiments we varied whether the target was less or more salient. We found an interesting discrepancy in that across both tasks and locations the first eye movement to land near a cluster was closer to the salient target, even though salience did not lead to a faster head movement towards a cluster at the far locations. We also found that the planning of head movement changed the landing of gaze position to be targeted more towards the centres of the clusters at the far locations, leading to more accurate initial gaze positions relative to target, regardless of salience. This suggests that the spatial information available for targeting of eye movements within a given FoV is not always available for the planning of head movements and how a target appears in view affects gaze targeting accuracy.
Determinants of hyena participation in risky collective action
Authors: Montgomery Tracy M. , Lehmann Kenna D.S. , Gregg Samantha , Keyser Kathleen , McTigue Leah E. , Beehner Jacinta C. , Holekamp Kay E. 
Published: May 2022

ABSTRACTMany species engage in risky cooperative behaviors, which pose a challenge to evolutionary theory: participants take on all the costs of cooperation, yet even non-participants benefit from success in these encounters. So, why participate in these risky behaviors? We address this question using data from spotted hyenas fighting with lions. Lions are much larger, and kill many hyenas, so these fights require cooperative mobbing by hyenas for them to succeed. We identify factors that predict: (1) when hyena groups engage in cooperative fights with lions, (2) which individuals choose to participate, and (3) how the benefits of victory are distributed among cooperators and non-cooperators. We find that cooperative mobbing is more strongly influenced by lower costs (no male lions, more hyenas) than higher benefits (need for food). Individual participation is facilitated by social factors, both over the long term (close kin, social bond strength) and the short term (greeting interactions prior to cooperation). Finally, we find some direct benefits of participation; after cooperation, participants were more likely to feed at contested carcasses than non-participants. Overall, these results suggest that, when animals play dangerous cooperative games, selection favors flexible strategies that are sensitive to dynamic factors emerging over multiple time-scales.
Mapping the temporal transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Authors: Gupta Anushka , Shamsi Farnaz , Patti Mary Elizabeth , Tseng Yu-Hua , Streets Aaron 
Published: May 2022

ABSTRACTAdipogenesis is key to maintaining organism-wide energy balance and healthy metabolic phenotype, making it critical to thoroughly comprehend its molecular regulation in humans. By single-nuclei RNA-sequencing (snRNA-seq) of over 20,000 differentiating white and brown preadipocytes, we constructed a high-resolution temporal transcriptional landscape of human white and brown adipogenesis. White and brown preadipocytes were isolated from a single individual’s neck region, thereby eliminating inter-subject variability across two distinct lineages. These preadipocytes were also immortalized to allow for controlled, in vitro differentiation, allowing sampling of distinct cellular states across the spectrum of adipogenic progression. Pseudotemporal cellular ordering revealed the dynamics of ECM remodeling during early adipogenesis, and lipogenic/thermogenic response during late white/brown adipogenesis. Comparison with adipogenic regulation in murine models revealed several targets for potential adipogenic/thermogenic drivers in humans. Key adipogenic and lipogenic markers revealed in our analysis were applied to analyze publicly available scRNA-seq datasets; these confirmed unique cell maturation features in recently discovered murine preadipocytes, and revealed inhibition of adipogenic expansion in humans with obesity. Overall, our study presents a comprehensive molecular description of both white and brown adipogenesis in humans and provides an important resource for future studies of adipose tissue development and function in both health and metabolic disease state.
Generation of Functional Human T Cell Development in NOD/SCID/IL2rγnull Humanized Mice Without Using Fetal Tissue: Application as a Model of HIV Infection and Persistence
Authors: Colas Chloé , Volodina Olga , Béland Kathie , Pham Tram N.Q. , Li Yuanyi , Dallaire Frédéric , Soulard Clara , Lemieux William , Colamartino Aurélien B.L. , Tremblay-Laganière Camille , Dicaire Renée , Guimond Jean , Patey Natasha , Vobecky Suzanne , Poirier Nancy , Cohen Éric A. , Haddad Elie 
Published: May 2022

AbstractGenerating humanized mice with fully functional T cells currently relies on co-implantation of hematopoietic stem cells from fetal liver and autologous fetal thymic tissue (BLT mouse). However, access to such tissues has ethical and logistical challenges. Herein, we show that NOD/SCID/IL2rγnull mice humanized with cord blood-derived CD34+ cells and implanted in quadriceps with pediatric thymic tissues excised during cardiac surgeries (CCST mice) are an alternative to BLT mice. Our data revealed a strong immune reconstitution in CCST mice, with T cells originating from CD34+ progenitor cells, proliferating efficiently in response to mitogenic stimulation ex vivo and capable of rejecting allogeneic human leukemic cells in vivo. Despite having less T cells than BLT mice, CCST mice were equally susceptible to mucosal or intraperitoneal HIV infection. Importantly, HIV-specific T cell responses were significantly higher in CCST-mice (median: 10.4% vs. 0.7%; p<0.0001 for CD8+cells and 3.9% vs. 0.7%; p<0.01 for CD4+ cells). As well, antiretroviral therapy (ART) robustly suppressed viremia and reduced the frequencies of cells carrying integrated HIV DNA by up to 2 logs in various CCST mouse tissues. As in BLT mice, we observed a complete viral rebound in 67% of the animals by 2-4 weeks following ART interruption, suggesting the presence of HIV reservoirs. In conclusion, CCST mice represent an ethical and practical alternative to BLT mice, broadening the feasibility of utilizing humanized mice for research on HIV and other human diseases.One Sentence SummaryWe herein report a new humanized mouse model implanted with human cord blood hematopoietic stem cells and allogenic pediatric thymic tissue that develops a functional T cell compartment and supports efficient HIV infection and persistence during antiretroviral therapy.
DNA passes through cohesin’s hinge as well as its Smc3-kleisin interface
Authors: Collier James E , Nasmyth Kim A 
Published: May 2022

SummaryThe ring model (Haering et al. 2002) proposes that sister chromatid cohesion is mediated by co-entrapment of sister DNAs inside a tripartite cohesin ring created by a pair of rod-shaped proteins (Smc1 and Smc3) whose two ends are connected through dimerization of their hinges at one end and by association of their ATPase domains at the other end with the N- and C-terminal domains of a kleisin subunit (Scc1). The model explains how Scc1 cleavage triggers anaphase (Uhlmann, Lottspeich, and Nasmyth 1999) but has hitherto only been rigorously tested using small circular mini-chromosomes in yeast, where crosslinking the ring’s three interfaces, creating a covalent circular molecule, induces catenation of individual sister DNAs (Haering et al. 2008; Srinivasan et al. 2018). If the model applies to real chromatids, then the ring must have a DNA entry gate essential for mitosis. Whether this is situated at the Smc3/Scc1 (Murayama and Uhlmann 2015; Murayama et al. 2018) or Smc1/Smc3 hinge (Gruber et al. 2006) interface is an open question. Using an in vitro system (Collier et al. 2020), we show that cohesin in fact possesses two DNA gates, one at the Smc3/Scc1 interface and a second at the Smc1/3 hinge. Unlike the Smc3/Scc1 interface, passage of DNAs through SMC hinges depends on both Scc2 and Scc3, a pair of regulatory subunits necessary for entrapment in vivo (Srinivasan et al. 2018). This property together with the lethality caused by locking this interface but not that between Smc3 and Scc1 in vivo (Gruber et al. 2006) suggests that passage of DNAs through the hinge is essential for building sister chromatid cohesion. Passage of DNAs through the Smc3/Scc1 interface is necessary for cohesin’s separase-independent release from chromosomes (Chan et al. 2012) and may therefore largely serve as an exit gate.
SARS-CoV-2 Helicase might interfere with cellular nonsense-mediated RNA decay, insights from a bioinformatics study
Authors: Akbari Behnia , Ahmadi Ehsan , Zamir Mina Roshan , Shaker Mina Sadeghi , Noorbakhsh Farshid 
Published: May 2022

AbstractUnraveling molecular interactions between viral proteins and host cells is key to understanding the pathogenesis of viral diseases. We hypothesized that potential sequence and structural similarities between SARS-CoV2 proteins and proteins of infected cells might influence host cell biology and antiviral defense. Comparing the proteins of SARS-CoV-2 with human and mammalian proteins revealed sequence and structural similarities between viral helicase with human UPF1. The latter is a protein that is involved in nonsense mediated RNA decay (NMD), an mRNA surveillance pathway which also acts as a cellular defense mechanism against viruses. Protein sequence similarities were also observed between viral nsp3 and human Poly ADP-ribose polymerase (PARP) family of proteins. Gene set enrichment analysis on transcriptomic data derived from SARS-CoV-2 positive samples illustrated the enrichment of genes belonging to the NMD pathway compared with control samples. Moreover, comparing transcriptomic data from SARS-CoV2-infected samples with transcriptomic data derived from UPF1 knockout cells demonstrated a significant overlap between datasets. These findings suggest that helicase/UPF1 sequence and structural similarity might have the ability to interfere with the NMD pathway with pathogenic and immunological implications.
A universal system for streamlined genome integrations with CRISPR-associated transposases
Authors: Wang Megan , Sanfiorenzo Charles , Zhang Raymond J. , Wang Kaihang 
Published: May 2022

AbstractGenome engineering tools in bacteria are limited by their targeting abilities, cargo size capacities, and integration efficiencies. Programmable Cas-directed transposons have been shown to bypass these constraints; however, genome integrations with these Cas-directed transposons require a cargo plasmid carrying the desired DNA payload flanked by directed repeat transposon arms. This cloning pre-requisite significantly hinders the modularity and streamlining capabilities of Cas-directed transposon systems, diminishing their utility for genome engineering. Here, we present a system that can robustly integrate a linear DNA payload into the genome ofE. coliby employing a Type I-F CRISPR-associated transposon fromVibrio cholerae. This system bypasses the traditional limiting factors of Cas-directed transposons by leveraging oligonucleotide design and nested polymerase chain reactions to reconstitute the transposon arms onto a designated cargo. Our findings demonstrate that this programmable linear integration method has high efficiencies in integrating large DNA payloads across multiple genomic loci.
Calcium transport by the Mycobacterium tuberculosis PE15/PPE20 proteins
Authors: Boradia Vishant , Frando Andrew , Grundner Christoph 
Published: May 2022

ABSTRACTMany aspects of eukaryotic physiology are regulated by calcium ions (Ca2+). Whether bacteria have similar Ca2+ systems for transport, storage, binding, and response to Ca2+ is not well understood. To identify components of Ca2+ signaling in Mycobacterium tuberculosis, we determined its transcriptional response to Ca2+. Overall, only few genes changed expression, suggesting a limited role of Ca2+ as a transcriptional regulator. However, two of the most strongly downregulated genes were the pe15 and ppe20 genes that code for members of a large family of proteins that localizes to the outer membrane. PE15 and PPE20 formed a complex and PPE20 directly bound Ca2+. Ca2+-associated phenotypes such as an increase in ATP consumption and increase in biofilm formation were reversed in a pe15/ppe20 knockout strain, suggesting a direct role in Ca2+ homeostasis. To test whether the complex has a role in Ca2+ transport across the outer membrane, we created a fluorescence resonance energy transfer (FRET)-based Ca2+ reporter strain. A pe15/ppe20 knockout in the FRET background showed a specific and selective loss of Ca2+ influx that was dependent on the presence of an intact outer cell wall. These data show that PE15/PPE20 form a Ca2+-binding protein complex that selectively imports Ca2+ and support the emerging idea of a general family-wide role of PE/PPE proteins in transport across the outer membrane.
Stochastic inference of clonal dominance in gene therapy studies
Authors: Core L. Del , Grzegorczyk M. A. , Wit E. C. 
Published: May 2022

AbstractClonal dominance is a wake-up-call for adverse events in gene therapy applications. This phenomenon has mainly been observed as a consequence of a malignancy progression, and, in some rare cases, also during normal haematopoiesis. We propose here a random-effects stochastic model that allows for a quick detection of clonal expansions that possibly occur during a gene therapy treatment.Starting from the Ito-type equation, the dynamics of cells duplication, death and differentiation at clonal level without clonal dominance can be described by a local linear approximation. The parameters of the base model, which are inferred using a maximum likelihood approach, are assumed to be shared across the clones. In order to incorporate the possibility of clonal dominance, we extend the base model by introducing random effects for the clonal parameters. This extended model is estimated using a tailor-made expectation maximization algorithm. The main idea of this paper is to compare the base and the extended models in high dimensional clonal tracking datasets by means of Akaike Information Criterion in order to detect the presence of clonal dominance. The method is evaluated using a simulation study, and is applied to investigating the dynamics of clonal expansion in a in-vivo model of rhesus macaque hematopoiesis.Author summaryPreventing or quickly detecting clonal dominance is an important aspect in gene therapy applications. Over the past decades, clonal tracking has proven to be a cutting-edge analysis capable to unveil population dynamics and hierarchical relationships in vivo. For this reason, clonal tracking studies are required for safety and long-term efficacy assessment in preclinical and clinical studies. In this work we propose a random-effects stochastic framework that allows to investigate events of clonal dominance using high-dimensional clonal tracking data. Our framework is based on the combination between stochastic reaction networks and mixed-effects generalized linear models. We have shown in a simulation study and in a real world application that our method is able to detect the presence of clonal expansions. Our tool can provide statistical support to biologists in gene therapy surveillance analyses.
Double trouble or a blessing in disguise? Co-infection of potato with the causal agents of late and early blight
Authors: Brouwer S.M. , Wolters P.J. , Andreasson E. , Liljeroth E. , Vleeshouwers V.G.A.A. , Grenville-Briggs L.J. 
Published: May 2022

AbstractThe simultaneous occurrence of multiple diseases is an understudied area in plant pathology; however, studies of animal and human diseases have shown that the presence of multiple pathogens can impact virulence, and the course of disease development. Furthermore, they also present an important driver of epidemiological dynamics. Global potato production is plagued by multiple pathogens, amongst which are Phytophthora infestans and Alternaria solani, the causal agents of potato late and early blight respectively. Both these pathogens have different lifestyles and are successful pathogens of potato, but despite observations of both pathogens infecting potato simultaneously in field conditions, the tripartite interactions between potato and these two pathogens are so far, poorly understood. Here we studied the interaction of A. solani and P. infestans first in vitro and subsequently in planta both in laboratory and field settings. We found that A. solani can inhibit P. infestans both in terms of growth in vitro and infection of potato, both in laboratory experiments and in an agriculturally relevant field setting.
Gene editing and super-resolution microscopy reveal multiple distinct roles for ARF GTPases in cellular membrane organization
Authors: Wong-Dilworth Luis , Rodilla-Ramirez Carmen , Fox Eleanor , Restel Steffen D. , Stockhammer Alexander , Adarska Petia , Bottanelli Francesca 
Published: May 2022

AbstractADP-ribosylation factor (ARF) GTPases are major regulators of cellular membrane homeostasis. High sequence similarity and multiple, possible redundant functions of the five human ARFs make investigating their function a challenging task. To shed light on the roles of the different Golgi-localized ARF members in membrane trafficking, we generated CRISPR-Cas9 knock ins (KIs) of type I (ARF1 and ARF3) and type II ARFs (ARF4 and ARF5) and mapped their nanoscale localization with stimulated emission depletion (STED) super-resolution microscopy. We find ARF1, ARF4 and ARF5 on segregated nano-domains on the cis-Golgi and ER-Golgi intermediate compartments (ERGIC), revealing distinct roles in COPI recruitment on early secretory membranes. Interestingly, ARF4 and ARF5 define Golgi-tethered ERGIC elements decorated by COPI and devoid of ARF1. Differential localization of ARF1 and ARF4 on distal ERGICs suggests the presence of functionally different classes of intermediate compartments that could regulate bi-directional transport between the ER and the Golgi. Furthermore, ARF1 and ARF3 localize to segregated nano-domains on the trans-Golgi network (TGN) and TGN-derived post-Golgi tubules, strengthening the idea of distinct roles in post-Golgi sorting. This work provides the first map of the nanoscale organization of human ARF GTPases on cellular membranes and sets the stage to dissect their numerous cellular roles.
Specificity and overlap in the genetic architectures of functional and structural connectivity within cerebral resting-state networks
Authors: Tissink E.P. , Werme J. , de Lange S.C. , Savage J.E. , Wei Y. , de Leeuw C.A. , Nagel M. , Posthuma D. , van den Heuvel M.P. 
Published: May 2022

AbstractThe functional connectivity and dynamics of resting-state networks (RSN-FC) are vital for cognitive functioning. RSN-FC is heritable and partially translates to the anatomical architecture of white matter, but the genetic component of structural connections of RSNs (RSN-SC) and their potential genetic overlap with RSN-FC remains unknown. Here we perform genome-wide association studies (Ndiscovery=24,336; Nreplication=3,412) and in silico annotation on RSN-SC and RSN-FC. We identify the first genes for visual network-SC, that are involved in axon guidance and synaptic functioning and show that genetic variation in RSN-FC impacts biological processes related to brain disorders that have previously been associated with FC alterations in those same RSNs. Correlations of the genetic components of RSNs are mostly observed within the functional domain, whereas less overlap is observed within the structural domain and between the functional and structural domains. This study advances the understanding of the complex functional organization of the brain and its structural underpinnings from a genetics viewpoint.
Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3’ end biogenesis
Authors: Muckenfuss Lena M. , Migenda Herranz Anabel C. , Boneberg Franziska M. , Clerici Marcello , Jinek Martin 
Published: May 2022

ABSTRACT3’ end formation of most eukaryotic mRNAs is dependent on the assembly of a ∼1.5 megadalton multiprotein complex, that catalyzes the coupled reaction of pre-mRNA cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) constitutes the core of the 3’ end processing machinery onto which the remaining factors, including cleavage stimulation factor (CstF) and poly(A) polymerase (PAP), assemble. These interactions are mediated by Fip1, a CPSF subunit characterized by high degree of intrinsic disorder. Here, we report two crystal structures revealing the interactions of human Fip1 (hFip1) with CPSF30 and CstF77. We demonstrate that CPSF contains two copies of hFip1, each binding to the zinc finger (ZF) domains 4 and 5 of CPSF30. Using polyadenylation assays we show that the two hFip1 copies are functionally redundant in recruiting one copy of PAP, thereby increasing the processivity of RNA polyadenylation. We further show that the interaction between hFip1 and CstF77 is mediated via a short motif in the N-terminal “acidic” region of hFip1. In turn, CstF77 competitively inhibits CPSF-dependent PAP recruitment and 3’ polyadenylation. Taken together, these results provide a structural basis for the multivalent scaffolding and regulatory functions of hFip1 in 3’ end processing.