bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimenter sex modulates mouse biobehavioural and pharmacological responses
Authors: Georgiou Polymnia , Zanos Panos , Mou Ta-Chung M. , An Xiaoxian , Gerhard Danielle M. , Dryanovski Dilyan I. , Potter Liam E. , Highland Jaclyn N. , Jenne Carleigh E. , Stewart Brent W. , Pultorak Katherine , Yuan Peixiong , Powels Chris F. , Lovett Jacqueline , Pereira Edna F. , Clark Sarah M. , Tonelli Leonardo H. , Moaddel Ruin , Zarate Carlos A. , Duman Ronald S. , Thompson Scott M. , Gould Todd D.
Published: January 2022

Differential rodent responses to the sex of human experimenters could have far reaching consequences in preclinical studies. Here, we show that the sex of human experimenters affects mouse behaviours and responses to the rapid-acting antidepressant ketamine and its bioactive metabolite (2R,6R)-hydroxynorketamine. We found that mice manifest aversion to human male odours, preference to female odours, and increased susceptibility to stress when handled by male experimenters. This male induced aversion and stress susceptibility is mediated by the activation of brain corticotropin-releasing factor (CRF) neurons projecting from the entorhinal cortrex to hippocampal area CA1. We further establish that exposure to male scent prior to ketamine administration activates CRF neurons projecting from the entorhinal cortex to hippocampus, and that CRF is necessary and sufficient for ketamine’s in vivo and in vitro actions. Further understanding of the specific and quantitative contributions of the sex of human experimenters to different experimental outcomes in rodents may lead not only to reduced heterogeneity between studies, but also increased capability to uncover novel biological mechanisms.
Chronic Ca2+ imaging of cortical neurons with long-term expression of GCaMP-X
Authors: Geng Jinli , Li Wenxiang , Tang Yingjun , Gao Yunming , Lu Yitong , Li Ping , Li Xiaomei , Wang Ping , Fan Yubo , Yang Yaxiong , Guo Zengcai V. , Liu Xiaodong
Published: January 2022

Dynamic Ca2+ signals reflect acute changes in membrane excitability (e.g. sensory response), and also mediate intracellular signaling cascades normally of longer time scales (e.g., Ca2+-dependent neuritogenesis). In both cases, chronic Ca2+ imaging has been often desired, but largely hindered by unexpected cytotoxicity intrinsic to GCaMP, a popular series of genetically-encoded Ca2+ indicators. Here, we demonstrate that the recently developed GCaMP-X outperforms GCaMP in long-term probe expression and/or chronic Ca2+ imaging. GCaMP-X shows much improved compatibility with neurons and thus more reliable than GCaMP as demonstrated in vivo by acute Ca2+ responses to whisker deflection or spontaneous Ca2+ fluctuations over an extended time frame. Chronic Ca2+ imaging data (≥1 month) are acquired from the same set of cultured cortical neurons, unveiling that spontaneous/local Ca2+ activities would progressively develop into autonomous/global Ca2+ oscillations. Besides the morphological indices of neurite length or soma size, the major metrics of oscillatory Ca2+, including rate, amplitude, synchrony among different neurons or organelles have also been examined along with the developmental stages. Both neuritogenesis and Ca2+ signals are dysregulated by GCaMP in virus-infected or transgenic neurons, in direct contrast to GCaMP-X without any noticeable side-effect. Such in vitro data altogether consolidate the unique importance of oscillatory Ca2+ to activity-dependent neuritogenesis, as one major factor responsible for the distinctions between GCaMP vs GCaMP-X in vivo. For the first time with GCaMP-X of long-term expression in neurons, spontaneous and sensory-evoked Ca2+ activities are imaged and evaluated both in vitro and in vivo, providing new opportunities to monitor neural development or other chronic processes concurrently with Ca2+ dynamics.
Impact of Nosema ceranae invasion on sucrose solution consumption, midgut epithelial cell structure, and lifespan of Apis cerana cerana workers
Authors: Long Qi , Sun Minghui , Fan Xiaoxue , Zhang Wende , Zhou Dingding , Hu Ying , Wang Zixin , Zhang Kaiyao , Yu Kejun , Zhao Haodong , Song Yuemei , Fu Zhongmin , Chen Dafu , Guo Rui
Published: January 2022

Nosema ceranae is an intracellular fungal parasite for honeybees, leading to chronic disease named bee nosemosis with worldwide distribution. Asian honeybee (Apis cerana) is the original host for N. ceranae, but the impact of N. ceranae infection on A. cerana physiology is largely unknown. In this current work, workers of Apis cerana cerana, a subspecies of Asian honeybee, were artificially inoculated with N. ceranae spores and reared under lab conditions, followed by detection of fungal spore load as well as host sucrose solution consumption, midgut epithelial cell structure, and lifespan. The result of spore counting suggested that the spore load in the host midgut decreased significantly during 1 dpi-2 dpi, whereas that displayed an elevated trend among 2 dpi-13 dpi. The sucrose solution consumption of workers in N. ceranae-inoculated groups among 1 dpi-20 dpi was always higher than that of workers in un-inoculated groups; additionally, the difference of sucrose solution consumption between these two groups at 4 dpi, 5 dpi, and 13 dpi was of significance. Based on microscopic observation of paraffin sections, darkly stained parasites were clearly detected in the midgut epithelial cells of N. ceranae-inoculated workers at 7 dpi-10 dpi, whereas no parasite was observed in those of un-inoculated workers. In addition, the boundaries of un-inoculated host epithelial cells were intact and the darkly stained nucleus were clear, while the boundaries of midgut epithelial cells of N. ceranae-inoculated workers were blurred, the nucleus were almost disappeared, and the nucleic acid substances were diffused. Moreover, the survival rates of workers in both N. ceranae-inoculated groups and un-inoculated groups at 1 dpi-5 dpi were pretty high and then started to decrease at 5 dpi; the survival rate of workers in N. ceranae-inoculated groups was always lower than that in un-inoculated groups, with significant difference between these two groups during 11 dpi-20 dpi. These results together indicate that the quantity of fungal spores continuously elevated with the microsporidian multiplication, causing energetic stress for workers and host cell structure damage, which further negatively affected the host lifespan. Our findings offer a solid basis not only for exploring the molecular mechanism underlying N. ceranae infection but also for investigating the interaction between N. ceranae and eastern honeybee.
Reexamining Waddington: Canalization and new mutations are not required for the evolution of genetic assimilation
Authors: Marzec Sarah Ruth , Pelletier Katharine , Chang Amy Hui-Pin , Dworkin Ian
Published: January 2022

Over 65 years ago, Waddington demonstrated ancestrally phenotypically plastic traits can evolve to become constitutive, a process he termed genetic assimilation. Genetic assimilation evolves rapidly, assumed to be in large part due to segregating genetic variation only expressed in rare/novel environments, but otherwise phenotypically cryptic. Despite previous work suggesting a substantial role of cryptic genetic variation contributing to the evolution of genetic assimilation, some have argued for a prominent role for new mutations of large effect concurrent with selection. Interestingly, Waddington was less concerned by the relative contribution of CGV or new variants, but aimed to test the role of canalization, an evolved form of robustness. While canalization has been extensively studied, its role in the evolution of genetic assimilation is disputed, in part because explicit tests of evolved robustness are lacking. To address these questions, we recreated Waddington’s selection experiments on an environmentally sensitive change in Drosophila wing morphology (crossvein development), using many independently evolved replicate lineages. Using these, we show that 1) a polygenic CGV, but not new variants of large effect are largely responsible for the evolved response demonstrated using both genomic and genetic approaches. 2) Using both environmental manipulations and mutagenesis of the evolved lineages that there is no evidence for evolved changes in canalization contributing to genetic assimilation. Finally, we demonstrate that 3) CGV has potentially pleiotropic and fitness consequences in natural populations and may not be entirely “cryptic”.
A unique Thy-1-negative immunofibroblast population emerges as a key determinant of fibrotic outcomes to biomaterials
Authors: Abebayehu Daniel , Pfaff Blaise N. , Bingham Grace C. , Ghatti Surabhi , Miller Andrew , Griffin Donald R. , Barker Thomas H.
Published: January 2022

Microporous annealed particle (MAP) hydrogels are an exciting new development in biomaterial design. They regulate innate and acquired immunity which has been linked to their ability to evade normal host-material fibrosis. Yet, resident stromal fibroblasts, not immune cells, are the arbiters of the extracellular matrix assembly that characterizes fibrosis. In other idiopathic fibrotic disorders, a fibroblast subpopulation defined by its loss of cell surface Thy-1 expression is strongly correlated with degree of fibrosis. We have previously shown that Thy-1 is a critical αvβ3 integrin regulator that enables normal fibroblast mechanosensing and here, leveraging non-fibrosing MAP gels, we demonstrate that Thy-1-/- mice mount a robust response to MAP gels that remarkably resembles a classical foreign body response. We further find that within the näive, Thy-1+ fibroblast population exists a distinct and cryptic αSMA+ Thy-1- population that emerges in response to IL-1β and TNFα. Employing single-cell RNA sequencing, we find that IL-1β/TNFα-induced Thy-1- fibroblasts actually consist of two distinct subpopulations, both of which are strongly pro-inflammatory. These findings illustrate the emergence of a unique pro-inflammatory, pro-fibrotic fibroblast subpopulation that is central to material-associated fibrosis likely through amplifying local inflammatory signaling.

Significance Statement

Despite decades of research, implanted biomaterials are still significantly hampered by the foreign body response and fibrotic encapsulation.

Advancements in material design and immunomodulation have made positive impacts, yet, a fuller mechanistic understanding of aberrant ECM remodeling in the biomaterial microenvironment could improve approaches in biomaterial-host interactions. Here, we leverage anti-fibrotic MAP hydrogels and demonstrate that their ability to evade fibrosis is linked to fibroblast Thy-1 (CD90) surface expression. Thy-1-/- mice exhibit elevated NFκB signaling and elevated fibrosis in response to MAP gel implantation. Interestingly, pro-inflammatory cytokines elicit a Thy-1-/αSMA+ myofibroblast subpopulation. Single-cell RNA-Seq more fully identifies an ‘immunofibroblast’ subpopulation defined by Thy-1 loss and a pro-inflammatory/fibrotic cytokine, chemokine, and cytokine receptor expression profile, suggesting a self-perpetuating pro-fibrotic subpopulation.
Integrated cyto-physiological and proteomic analyses reveal new insight into CMS mechanism in a novel upland cotton CMS line LD6A
Authors: Jie Zheng , Khan Aziz , Bujin Zhou , Qiong Zhou , Ullah Najeeb , Xiangjun Kong , Yiding Liu , Fang Liu , Ruiyang Zhou
Published: January 2022

Cytoplasmic male sterile (CMS) system has extensively been exploited for hybrid vigor in plant breeding programs. However, its application in many crops is limited due to poor understanding of molecular mechanism of fertility restoration. Using advanced analytical approaches, we elucidated molecular pathways regulating CMS induction and fertility restoration in cotton. Reproductive structures of a novel CMS (LD6A) and its maintainer (LD6B) line were analyzed for physiological and proteomic changes during the development process. Significant differential expression of proteins, such as Abrin, malate dehydrogenase, malic enzyme, isocitrate dehydrogenase, histone acetyltransferase was observed in CMS and its maintainer line. Transmission electron micrographs of anther tapetum showed that inner ridge of CMS mitochondria was relatively indistinct than that of LD6B with narrower membranous space at tetrad stage. Further, relatively higher reactive oxygen species were accumulated in the anther of CMS than its maintainer line at pollen mother cell and tetrad stage. We suggest that abnormal sequence of mitochondrial ribosome gene rps4 and rpl10 and high expression of ribosome-inactivating protein gene Abrin in CMS line damaged mitochondrial membrane and consequently induced pollen sterility. These data provide new insight into CMS mechanism in cotton crops and a tool to develop new CMS germplasm resources.
Quantifying behavior change during the first year of the COVID-19 pandemic in the United States
Authors: Chao Dennis L , Cho Victor , Izzo Amanda S , Proctor Joshua L , Zimmermann Marita
Published: January 2022

Background

During the first year of the COVID-19 pandemic, the most effective way to reduce transmission and to protect oneself was to reduce contact with others. However, it is unclear how behavior changed, despite numerous surveys about peoples’ attitudes and actions during the pandemic and public health efforts to influence behavior.

Methods

We used two sources of data to quantify changes in behavior at the county level during the first year of the pandemic in the United States: aggregated mobile device (smartphone) location data to approximate the fraction of people staying at home each day and digital invitation data to capture the number and size of social gatherings.

Results

Between mid-March to early April 2020, the number of events fell and the fraction of devices staying at home peaked, independently of when states issued emergency orders or stay-at-home recommendations. Activity began to recover in May or June, with later rebounds in counties that suffered an early spring wave of reported COVID-19 cases. Counties with high incidence in the summer had more events, higher mobility, and less stringent state-level COVID-related restrictions the month before than counties with low incidence. Counties with high incidence in early fall stayed at home less and had less stringent state-level COVID-related restrictions in October, when cases began to rise in some parts of the US. During the early months of the pandemic, the number of events was inversely correlated with the fraction of devices staying at home, but after the fall of 2020 mobility appeared to stay constant as the number of events fell. Greater changes in behavior were observed in counties where a larger fraction voted for Biden in the 2020 US Presidential election. The number of people invited per event dropped gradually throughout the first year of the pandemic.

Conclusions

The mobility and events datasets uncovered different kinds of behavioral responses to the pandemic. Our results indicate that people did in fact change their behavior in ways that likely reduced COVID exposure and transmission, though the degree of change appeared to be affected by political views. Though the mobility data captured the initial massive behavior changes in the first months of the pandemic, the digital invitation data, presented here for the first time, continued to show large changes in behavior later in the first year of the pandemic.
Plasma sgp130 is an independent predictor of non-alcoholic fatty liver disease severity
Authors: Gunes Aysim , Bilodeau Laurent , Huet Catherine , Belblidia Assia , Baldwin Cindy , Giard Jeanne-Marie , Biertho Laurent , Lafortune Annie , Couture Christian Yves , Nguyen Bich N , Galun Eithan , Bémeur Chantal , Bilodeau Marc , Laplante Mathieu , Tang An , Faraj May , Estall Jennifer L.
Published: January 2022

Background

Interleukin-6 (IL-6) plays important and dynamic roles in inflammation associated with fatty liver disease over all stages, from simple steatosis to steatohepatitis, cirrhosis and cancer. IL-6 signals locally, but also circulates with multiple co-factors that control paracrine and endocrine signaling. As inflammation is a main driver of liver fibrosis, we investigated relationships between circulating components of the interleukin-6 signaling pathway (IL-6, sIL-6R and sgp130) and liver pathology in subjects with metabolically associated fatty liver disease (MAFLD) or steatohepatitis (MASH).

Methods

Predictive performances of plasma IL-6, sIL-6R and sgp130 were investigated in two independent cohorts: 1) patients with biopsy-confirmed MASH (n=49), where magnetic resonance spectroscopy (MRS), imaging (MRI) and elastography (MRE) assessed liver fat, volume and stiffness; and 2) patients with morbid obesity (n=245) undergoing bariatric surgery where histological staging of steatosis, activity, and fibrosis determined MASH severity. Correlations were evaluated between IL-6, sIL-6R and sgp130 and anthropomorphic characteristics, plasma markers of metabolic disease or liver pathology.

Results

In patients with MASH, plasma IL-6 and sgp130 strongly correlated with liver stiffness, which for sgp130 was independent of age, sex, BMI, diabetes, hyperlipidemia, hypertension or history of HCC. Plasma sgp130 was the strongest predictor of liver stiffness compared to common predictors and risk scores. Plasma sIL-6R correlated with liver volume independent of age, sex, and BMI. In patients with morbid obesity, circulating sgp130 correlated with advanced liver fibrosis.

Conclusion

Levels of circulating sgp130 can predict progressing MASH and may be used alone or in combination with other predictors as a non-invasive measure of liver disease severity.

GRAPHICAL ABSTRACT
Geospatial modeling of pre-intervention prevalence of Onchocerca volvulus infection in Ethiopia as an aid to onchocerciasis elimination
Authors: Shrestha Himal , McCulloch Karen , Hedtke Shannon M , Grant Warwick N
Published: January 2022

Background
Onchocerciasis is a neglected tropical and filarial disease transmitted by the bites of blackflies, causing blindness and severe skin lesions. The change in focus for onchocerciasis management from control to elimination requires thorough mapping of pre-control endemicity to identify areas requiring interventions and to monitor progress. Onchocerca volvulus infection prevalence in sub-Saharan Africa is spatially continuous and heterogeneous, and highly endemic areas may contribute to transmission in areas of low endemicity or vice-versa. Ethiopia is one such onchocerciasis-endemic country with heterogeneous O. volvulus infection prevalence, and many districts are still unmapped despite their potential for O. volvulus infection transmission.
Methodology/Principle findings
A Bayesian geostatistical model was fitted for retrospective pre-intervention nodule prevalence data collected from 916 unique sites and 35,077 people across Ethiopia. We used multiple environmental, socio-demographic, and climate variables to estimate the pre-intervention prevalence of O. volvulus infection across Ethiopia and to explore their relationship with prevalence. Prevalence was high in southern and northwestern Ethiopia and low in Ethiopia's central and eastern parts. Distance to the nearest river (-0.015, 95% BCI: -0.025 - -0.005), precipitation seasonality (-0.017, 95% BCI: -0.032 - -0.001), and flow accumulation (-0.042, 95% BCI: -0.07 - -0.019) were negatively associated with O. volvulus infection prevalence, while soil moisture (0.0216, 95% BCI: 0.014 - 0.03) was positively associated.
Conclusions/Significance
Infection distribution was correlated with habitat suitability for vector breeding and associated biting behavior. The modeled pre-intervention prevalence can be used as a guide for determining priority for intervention in regions of Ethiopia that are currently unmapped, most of which have comparatively low infection prevalence.
A Coupled Experimental and Statistical Approach for an Assessment of the Airborne Infection Risk in Event Locations
Authors: Siebler Lukas , Rathje Torben , Calandri Maurizio , Stergiaropoulos Konstantinos , Richter Bernhard , Nusseck Manfred , Spahn Claudia
Published: January 2022

Operators of event locations are particularly affected by a pandemic. Resulting restrictions may cause uneconomical business. With previous models, only an incomplete quantitative risk assessments is possible, whereby no suitable restrictions can be derived. Hence, a mathematical and statistical model has been developed in order to link measurement data of substance dispersion in rooms with epidemiological data like incidences, reproduction numbers, vaccination rates and test qualities. This allows a first time overall assessment of airborne infection risks in large event locations. In these venues displacement ventilation concepts are often implemented. In this case simplified theoretical assumptions fail for the prediction of relevant airflows for infection processes. Thus, with locally resolving trace gas measurements and specific data of infection processes, individual risks can be computed more detailed. Via inclusion of many measurement positions, an assessment of entire event locations is possible. Embedding the overall model in a flexible application, daily updated epidemiological data allow latest calculations of expected new infections and individual risks of single visitors for a certain event. With this model, an instrument has been created that can help policymakers and operators to take appropriate measures and to check restrictions for their effect.
A simple bypass assay for DNA polymerases shows hypermutating variants associated with cancer show mechanistic differences in vitro
Authors: Crevel Gilles , Kearsey Stephen , Cotterill Sue
Published: January 2022

Errors made by DNA polymerases contribute to both natural variation and, in extreme cases, to genome instability and its associated diseases. Recently the importance of polymerase misincorporation in disease has been highlighted by the identification of cancer-associated polymerase variants and the recognition that a subgroup of these variants have a hypermutation phenotype in tumours. We have developed a bypass assay to rapidly determine the tendency of a polymerase to misincorporate in vitro. We have used the assay to compare misincorporation by wild-type, exonuclease defective and two hypermutating DNA polymerase e variants, P286R and V411L. The assay clearly distinguished between the misincorporation rates of wild type, exonuclease dead and P286R polymerases. However, the V411L polymerase showed different misincorporation characteristics to P286R, suggesting that these variants cause hypermutation by different mechanisms. Using this assay misincorporation opposite a templated C nucleotide was consistently higher than for other nucleotides, and this caused predominantly C to T transitions. This is consistent with the observation that C to T transitions are commonly seen in POLE mutant tumours.
Membrane interactions and uncoating of Aichi virus, a picornavirus that lacks a VP4
Authors: Kelly James T. , Swanson Jessica , Newman Joseph , Groppelli Elisabetta , Stonehouse Nicola J. , Tuthill Tobias J.
Published: January 2022

Kobuviruses are an unusual and poorly characterised genus within the picornavirus family, and can cause gastrointestinal enteric disease in humans, livestock and pets. The human Kobuvirus, Aichi virus (AiV) can cause severe gastroenteritis and deaths in children below the age of five years, however this is a very rare occurrence. During the assembly of most picornaviruses (e.g. poliovirus, rhinovirus and foot-and-mouth disease virus), the capsid precursor protein VP0 is cleaved into VP4 and VP2. However, Kobuviruses retain an uncleaved VP0. From studies with other picornaviruses, it is known that VP4 performs the essential function of pore formation in membranes, which facilitates transfer of the viral genome across the endosomal membrane and into the cytoplasm for replication. Here, we employ genome exposure and membrane interaction assays to demonstrate that pH plays a critical role in AiV uncoating and membrane interactions. We demonstrate that incubation at low pH alters the exposure of hydrophobic residues within the capsid, enhances genome exposure and enhances permeabilisation of model membranes. Furthermore, using peptides we demonstrate that the N-terminus of VP0 mediates membrane pore formation in model membranes, indicating that this plays an analogous function to VP4.

Importance

To initiate infection, viruses must enter a host cell and deliver their genome into the appropriate location. The picornavirus family of small non-enveloped RNA viruses includes significant human and animal pathogens and are also models to understand the process of cell entry. Most picornavirus capsids contain the internal protein VP4, generated from cleavage of a VP0 precursor. During entry, VP4 is released from the capsid. In enteroviruses this forms a membrane pore, which facilitates genome release into the cytoplasm. Due to high levels of sequence similarity, it is expected to play the same role for other picornaviruses. Some picornaviruses, such as Aichi virus, retain an intact VP0, and it is unknown how these viruses re-arrange their capsids and induce membrane permeability in the absence of VP4. Here we have used Aichi virus as a model VP0 virus to test for conservation of function between VP0 and VP4. This could enhance understanding of pore function and lead to development of novel therapeutic agents that block entry.
Sex-specific regulation of metabolic health and vertebrate lifespan by AMP biosynthesis
Authors: Astre Gwendoline , Atlan Tehila , Goshtchevsky Uri , Shapira Kobi , Oron-Gottesman Adi , Levy Tomer , Velan Ariel , Smirnov Margarita , Deelen Joris , Levanon Erez Y. , Harel Itamar
Published: January 2022

Energy homeostasis is disrupted with age, which then fuels multiple age-related pathologies. The AMP-activated protein kinase (AMPK) is the primary sensor of cellular energy in eukaryotes. However, the genetic regulation of vertebrate aging by AMPK remains poorly understood. Here, we manipulate energy levels in the turquoise killifish by mutatingAPRT, a key enzyme in AMP biosynthesis. These manipulations produced a male-specific lifespan extension and restored metabolic plasticity. Exploring the observed sex differences using an integrated omics approach implicated the mitochondria as an important player. Mechanistically, APRT regulated mitochondrial functions and AMPK activity, mimicking energy starvation in heterozygous cells. A fasting-like state was also detected, particularly in heterozygous males, which leads to resistance to high-fat diet. Finally, life-long intermittent fasting eliminated the male-specific longevity benefits mediated by theAPRTmutation. These observations identify the AMP/AMPK axis as a sex-specific regulator of vertebrate longevity and metabolic health.
Molecular basis of SARS-CoV-2 Omicron variant receptor engagement and antibody evasion and neutralization
Authors: Hong Qin , Han Wenyu , Li Jiawei , Xu Shiqi , Wang Yifan , Li Zuyang , Wang Yanxing , Zhang Chao , Huang Zhong , Cong Yao
Published: January 2022

The SARS-CoV-2 Omicron variant exhibits striking immune evasion and is spreading globally at an unprecedented speed. Understanding the underlying structural basis of the high transmissibility and greatly enhanced immune evasion of Omicron is of high importance. Here through cryo-EM analysis, we present both the closed and open states of the Omicron spike, which appear more compact than the counterparts of the G614 strain, potentially related to the Omicron substitution induced enhanced protomer-protomer and S1-S2 interactions. The closed state showing dominant population may indicate a conformational masking mechanism of immune evasion for Omicron spike. Moreover, we capture two states for the Omicron S/ACE2 complex with S binding one or two ACE2s, revealing that the substitutions on the Omicron RBM result in new salt bridges/H-bonds and more favorable electrostatic surface properties, together strengthened interaction with ACE2, in line with the higher ACE2 affinity of the Omicron relative to the G614 strain. Furthermore, we determine cryo-EM structures of the Omicron S/S3H3 Fab, an antibody able to cross-neutralize major variants of concern including Omicron, elucidating the structural basis for S3H3-mediated broad-spectrum neutralization. Our findings shed new lights on the high transmissibility and immune evasion of the Omicron variant and may also inform design of broadly effective vaccines against emerging variants.
Uncertainty-guided learning with scaled prediction errors in the basal ganglia
Authors: Moeller Moritz , Manohar Sanjay , Bogacz Rafal
Published: January 2022

To accurately predict rewards associated with states or actions, the variability of observations has to be taken into account. In particular, when the observations are noisy, the individual rewards should have less influence on tracking of average reward, and the estimate of the mean reward should be updated to a smaller extent after each observation. However, it is not known how the magnitude of the observation noise might be tracked and used to control prediction updates in the brain reward system. Here, we introduce a new model that uses simple, tractable learning rules that track the mean and standard deviation of reward, and leverages prediction errors scaled by uncertainty as the central feedback signal. We provide a normative analysis, comparing the performance of the new model with that of conventional models in a value tracking task. We find that the new model has an advantage over conventional models when tested across various levels of observation noise. Further, we propose a possible biological implementation of the model in the basal ganglia circuit. The scaled prediction error feedback signal is consistent with experimental findings concerning dopamine prediction error scaling relative to reward magnitude, and the update rules are found to be consistent with many features of striatal plasticity. Our results span across the levels of implementation, algorithm, and computation, and might have important implications for understanding the dopaminergic prediction error signal and its relation to adaptive and effective learning.

Author Summary

The basal ganglia system is a collection of subcortical nuclei in the mammalian brain. This system and its dopaminergic inputs are associated with learning from rewards. Here, dopamine is thought to signal errors in reward prediction. The structure and function of the basal ganglia system are not fully understood yet—for example, the basal ganglia are split into two antagonistic pathways, but the reason for this split and the role of the two pathways are unknown. Further, it has been found that under some circumstances, rewards of different sizes lead to dopamine responses of similar size, which cannot be explained with the reward prediction error theory. Here, we propose a new model of learning in the basal ganglia—the scaled prediction error model. According to our model, both reward average and reward uncertainty are tracked and represented in the two basal ganglia pathways. The learned reward uncertainty is then used to scale dopaminergic reward prediction errors, which effectively renders learning adaptive to reward noise. We show that such learning is more robust than learning from unscaled prediction errors and that it explains several physiological features of the basal ganglia system.
Nrf2 attenuates the innate immune response after experimental myocardial infarction
Authors: Bromage Daniel I. , Trevelin Silvia , Huntington Josef , Yang Victoria X. , Muthukumar Ananya , Mackie Sarah J. , Sawyer Greta , Zhang Xiaohong , Santos Celio X.C. , Safinia Niloufar , Smyrnias Ioannis , Giacca Mauro , Ivetic Alex , Shah Ajay M.
Published: January 2022

Objectives

We aimed to investigate the contribution of the transcription factor nuclear factor erythroid-derived 2-like 2 (Nrf2) to the inflammatory response after experimental myocardial infarction (MI).

Background

There is compelling evidence implicating dysregulated inflammation in the mechanism of ventricular remodeling and heart failure (HF) after MI. The transcription factor Nrf2 (encoded by Nfe2l2) is a promising target in this context. It impedes transcriptional upregulation of pro-inflammatory cytokines and is anti-inflammatory in various murine models.

Methods

We subjected Nrf2-/- mice and wild type (WT) controls to permanent left coronary artery (LCA) ligation. The inflammatory response was investigated with fluorescence-activated cell sorting (FACS) analysis of peripheral blood and heart cell suspensions, together with qRT-PCR of infarcted tissue for chemokines and their receptors. To investigate whether Nrf2-mediated transcription is a dedicated function of leukocytes, we interrogated publicly available RNA-sequencing (RNA-seq) data from mouse hearts after permanent LCA ligation for Nrf2-regulated gene (NRG) expression.

Results

FACS analysis demonstrated a profoundly inflamed phenotype in the hearts of global Nrf2-/- mice as compared to WT mice after MI. Moreover, infarcted tissue from Nrf2-/- mice displayed higher expression of inflammatory cytokines, chemokines, and their receptors, including IL6, Ccl2, and Cxcr4. RNA-seq analysis showed upregulated NRG expression in WT mice after MI compared to untreated mice, which was significantly higher in bioinformatically isolated CCR2+ cells.

Conclusions

Taken together, the results suggest that Nrf2 signalling in leukocytes, and possibly CCR2+ monocyte-derived cardiac resident macrophages, may be potential targets to prevent post-MI ventricular remodeling.
Strong SARS-CoV-2 N-specific CD8+ T immunity induced by engineered extracellular vesicles associates with protection from lethal infection in mice
Authors: Ferrantelli Flavia , Chiozzini Chiara , Manfredi Francesco , Leone Patrizia , Spada Massimo , Virgilio Antonio Di , Giovannelli Andrea , Sanchez Massimo , Cara Andrea , Michelini Zuleika , Federico Maurizio
Published: January 2022

SARS-CoV-2-specific CD8+ T cell immunity is expected to counteract viral variants in both efficient and durable ways. We recently described a way to induce a potent SARS-CoV-2 CD8+ T immune response through the generation of engineered extracellular vesicles (EVs) emerging from muscle cells. This method relies on intramuscular injection of DNA vectors expressing different SARS-CoV-2 antigens fused at their N-terminus with Nefmut protein, i.e., a very efficient EV-anchoring protein. However, quality, tissue distribution, and efficacy of these SARS-CoV-2-specific CD8+ T cells remained uninvestigated. To fill the gaps, antigen-specific CD8+ T lymphocytes induced by the immunization through the Nefmut-based method were characterized in terms of their polyfunctionality and localization at lung airways, i.e., the primary targets of SARS-CoV-2 infection. We found that injection of vectors expressing Nefmut/S1 and Nefmut/N generated polyfunctional CD8+ T lymphocytes in both spleens and bronchoalveolar lavage fluids (BALFs). When immunized mice were infected with 4.4 lethal doses 50% of SARS-CoV-2, all S1-immunized mice succumbed, whereas those developing the highest percentages of N-specific CD8+ T lymphocytes resisted the lethal challenge. We also provide evidence that the N-specific immunization coupled with the development of antigen-specific CD8+ T-resident memory cells in lungs, supporting the idea that the Nefmut- based immunization can confer a long-lasting, lung-specific immune memory. In view of the limitations of current anti-SARS-CoV-2 vaccines in terms of antibody waning and efficiency against variants, our CD8+ T cell-based platform could be considered for a new combination prophylactic strategy.
Actin-microtubule dynamic composite forms responsive active matter with memory
Authors: Kučera Ondřej , Gaillard Jérémie , Guérin Christophe , Théry Manuel , Blanchoin Laurent
Published: January 2022

Active cytoskeletal materials in vitro demonstrate self-organising properties similar to those observed in their counterparts in cells. However, the search to emulate phenomena observed in the living matter has fallen short of producing a cytoskeletal network that would be structurally stable yet possessing adaptive plasticity. Here, we address this challenge by combining cytoskeletal polymers in a composite, where self-assembling microtubules and actin filaments collectively self-organise due to the activity of microtubules-percolating molecular motors. We demonstrate that microtubules spatially organise actin filaments that in turn guide microtubules. The two networks align in an ordered fashion using this feedback loop. In this composite, actin filaments can act as structural memory and, depending on the concentration of the components, microtubules either write this memory or get guided by it. The system is sensitive to external stimuli suggesting possible autoregulatory behaviour in changing mechanochemical environment. We thus establish artificial active actin-microtubule composite as a system demonstrating architectural stability and plasticity.
Choice of medium affects PBMC quantification, cell size, and downstream respiratory analysis
Authors: Christensen Ida Bager , Ribas Lucas , Larsen Steen , Dela Flemming , Gillberg Linn
Published: January 2022

High-resolution respirometry (HRR) can assess PBMC bioenergetics, but no standardized medium for PBMC preparation and HRR analysis exist. Here, we study the effect of four different media (MiR05, PBS, RPMI, Plasmax) on quantification, size, and HRR analysis (Oxygraph-O2k) of intact PBMCs. Remarkably, PBMC quantification was 21% higher in MiR05 than PBS and Plasmax, and 28% higher than in RPMI, causing O2flux underestimation during HRR due to inherent adjustments. Moreover, smaller cell size of PBMCs and aggregation was observed in MiR05. We suggest optimization of HRR with a standardized, plasma-like medium for future HRR analysis of intact PBMCs.
TRF2 rescues telomere attrition and prolongs cell survival in Duchenne muscular dystrophy cardiomyocytes derived from human iPSCs
Authors: Eguchi Asuka , Torres-Bigio Sofía I. , Koleckar Kassie , Gonzalez Adriana Fernanda G. S. , Birnbaum Foster , Blau Helen M.
Published: January 2022

Duchenne muscular dystrophy (DMD) is a severe muscle wasting disease caused by the lack of dystrophin. Heart failure, driven by cardiomyocyte death, fibrosis, and the development of dilated cardiomyopathy, is the leading cause of death in DMD patients. Current treatments decrease the mechanical load on the heart, but do not address the root cause of dilated cardiomyopathy: cardiomyocyte death. Previously, we showed that telomere shortening is a hallmark of cardiomyocytes in DMD patient cardiac tissues and in a mouse model of DMD we generated that manifests dilated cardiomyopathy. We also found that this telomere shortening is recapitulated in DMD cardiomyocytes differentiated from patient-derived induced pluripotent stem cells (iPSCs). Here we further characterize that DMD cardiomyocytes exhibit reduced cell size, nuclear size, and sarcomere density compared to healthy isogenic controls. The telomere-binding protein, TRF2, is a core component of the shelterin complex, which protects chromosome ends and is expressed at lower levels in DMD cardiomyocytes compared to controls. We investigated whether preservation of telomere length could be achieved with upregulation of TRF2. We found that TRF2 upregulation in DMD cardiomyocytes increased telomere lengths, cell size, nuclear size, sarcomere density, and cell survival. These data suggest TRF2 gene therapy has the potential to delay the onset of dilated cardiomyopathy.
Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells
Authors: Barnada Samantha M. , Isopi Andrew , Tejada-Martinez Daniela , Goubert Clément , Patoori Sruti , Pagliaroli Luca , Tracewell Mason , Trizzino Marco
Published: January 2022

Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ∼3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that ∼750 SVAs are co-opted as functional cis-regulatory elements in human induced pluripotent stem cells. These SVAs are significantly closer to genes and harbor more transcription factor binding sites than non-co-opted SVAs. We show that a long DNA motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs and that these two transcription factors bind consecutively on the TE sequence. We used CRISPRi to epigenetically repress active SVAs in stem cell-like NCCIT cells. Epigenetic perturbation of active SVAs strongly attenuated YY1/OCT4 binding and influenced neighboring gene expression. Ultimately, SVA repression resulted in ∼3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA. In summary, we demonstrated that SVAs modulate human gene expression, and uncovered that location and sequence composition contribute to SVA domestication into gene regulatory networks.
Strong Aversive Conditioning Triggers a Long-Lasting Generalized Aversion
Authors: Ramos Raul , Wu Chi-Hong , Turrigiano Gina G.
Published: January 2022

Generalization is an adaptive mnemonic process in which an animal can leverage past learning experiences to navigate future scenarios, but overgeneralization is a hallmark feature of anxiety disorders. Therefore, understanding the synaptic plasticity mechanisms that govern memory generalization and its persistence is an important goal. Here, we demonstrate that strong CTA conditioning results in a long-lasting generalized aversion that persists for at least two weeks. Using brain slice electrophysiology and activity-dependent labeling of the conditioning-active neuronal ensemble within the gustatory cortex, we find that strong CTA conditioning induces a long-lasting increase in synaptic strengths that occurs uniformly across superficial and deep layers of GC. Repeated exposure to salt, the generalized tastant, causes a rapid attenuation of the generalized aversion that correlates with a reversal of the CTA-induced increases in synaptic strength. Unlike the uniform strengthening that happens across layers, reversal of the generalized aversion results in a more pronounced depression of synaptic strengths in superficial layers. Finally, the generalized aversion and its reversal do not impact the acquisition and maintenance of the aversion to the conditioned tastant (saccharin). The strong correlation between the generalized aversion and synaptic strengthening, and the reversal of both in superficial layers by repeated salt exposure, strongly suggests that the synaptic changes in superficial layers contribute to the formation and reversal of the generalized aversion. In contrast, the persistence of synaptic strengthening in deep layers correlates with the persistence of CTA. Taken together, our data suggest that layer-specific synaptic plasticity mechanisms separately govern the persistence and generalization of CTA memory.
The dorsal hippocampus’ role in context-based timing in rodents
Authors: De Corte Benjamin J. , Farley Sean J. , Heslin Kelsey A. , Parker Krystal L. , Freeman John H.
Published: January 2022

To act proactively, we must predict when future events will occur. Individuals generate temporal predictions using cues that indicate an event will happen after a certain duration elapses. Neural models of timing focus on how the brain represents these cue-duration associations. However, these models often overlook the fact that situational factors frequently modulate temporal expectations. For example, in realistic environments, the intervals associated with different cues will often covary due to a common underlying cause. According to the ‘common cause hypothesis,’ observers anticipate this covariance such that, when one cue’s interval changes, temporal expectations for other cues shift in the same direction. Furthermore, as conditions will often differ across environments, the same cue can mean different things in different contexts. Therefore, updates to temporal expectations should be context-specific. Behavioral work supports these predictions, yet their underlying neural mechanisms are unclear. Here, we asked whether the dorsal hippocampus mediates context-based timing, given its broad role in context-conditioning. Specifically, we trained rats with either hippocampal or sham lesions that two cues predicted reward after either a short or long duration elapsed (e.g., tone-8s / light-16s). Then, we moved rats to a new context and extended the long-cue’s interval (e.g., light-32s). This caused rats to respond later to the short cue, despite never being trained to do so. Importantly, when returned to the initial training context, sham rats shifted back toward both cues’ original intervals. In contrast, lesion rats continued to respond at the long cue’s newer interval. Surprisingly, they still showed contextual modulation for the short cue, responding earlier like shams. These data suggest the hippocampus only mediates context-based timing if a cue is explicitly paired and/or rewarded across distinct contexts. Furthermore, as lesions did not impact timing measures at baseline or acquisiton for the long cue’s new interval, our data suggests that the hippocampus only modulates timing when context is relevant.
TrpA1 is a shear stress mechanosensing channel regulating intestinal homeostasis in Drosophila
Authors: Gong Jiaxin , Nirala Niraj K. , Chen Jiazhang , Wang Fei , Gu Pengyu , Wen Qi , Ip Y. Tony , Xiang Yang
Published: January 2022

Adult stem cells are essential for maintaining normal tissue homeostasis and supporting tissue repair. Although genetic and biochemical programs controlling adult stem cell behavior have been extensively investigated, how mechanosensing regulates stem cells and tissue homeostasis is not well understood. Here, we show that shear stress can activate enteroendocrine cells, but not other gut epithelial cell types, to regulate intestine stem cell-mediated gut homeostasis. This shear stress sensing is mediated by transient receptor potential A1 (TrpA1), a Ca2+-permeable ion channel that expressed only in enteroendocrine cells among all gut epithelial cells. Genetic depletion of TrpA1 or modification of its shear stress sensing function causes reduced intestine stem cell proliferation and intestine growth. We further show that among the TrpA1 splice variants, only select isoforms are activated by shear stress. Altogether, our results suggest the naturally occurring mechanical force such as fluid passing generated shear stress regulates intestinal stem cell-mediated tissue growth by activating enteroendocrine cells, and Drosophila TrpA1 as a new shear stress sensor.