bluuebunny/crossref_metadata_2025 huggingface dataset:
The structure of the human LACTB filament reveals the mechanisms of assembly and membrane binding
Authors: Bennett Jeremy A. , Steward Lottie R. , Rudolph Johannes , Voss Adam P. , Aydin Halil
Published: May 2022

Mitochondria are complex organelles that play a central role in metabolism. Dynamic membrane-associated processes regulate mitochondrial morphology and bioenergetics in response to cellular demand. In tumor cells, metabolic reprogramming requires active mitochondrial metabolism for providing key metabolites and building blocks for tumor growth and rapid proliferation. To counter this, the mitochondrial serine beta-lactamase-like protein (LACTB) alters mitochondrial lipid metabolism and potently inhibits the proliferation of a variety of tumor cells. Mammalian LACTB is localized in the mitochondrial intermembrane space, where it assembles into filaments to regulate the efficiency of essential metabolic processes. However, the structural basis of LACTB polymerization and regulation remains incompletely understood. Here, we describe how human LACTB self-assembles into micron-scale filaments that increase their catalytic activity. The electron cryo-microscopy (cryoEM) structure defines the mechanism of assembly and reveals how highly ordered filament bundles stabilize the active state of the enzyme. We identify and characterize residues that are located at the filament-forming interface, and further show that mutations that disrupt filamentation reduce enzyme activity. Furthermore, our results provide evidence that LACTB filaments can bind lipid membranes. These data reveal the detailed molecular organization and polymerization-based regulation of human LACTB and provide new insights into the mechanism of mitochondrial membrane organization that modulates lipid metabolism.
METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance
Authors: Hashimoto-Roth Emily , Surendra Anuradha , Lavallée-Adam Mathieu , Bennett Steffany A. L. , Čuperlović-Culf Miroslava
Published: May 2022

Motivation

Class imbalance, or unequal sample sizes between classes, is an increasing concern in machine learning for metabolomic and lipidomic data mining, which can result in overfitting for the over-represented class. Numerous methods have been developed for handling class imbalance, but they are not readily accessible to users with limited computational experience. Moreover, there is no resource that enables users to easily evaluate the effect of different over-sampling algorithms.

Results

METAbolomics data Balancing with Over-sampling Algorithms (META-BOA) is a web-based application that enables users to select between four different methods for class balancing, followed by data visualization and classification of the sample to observe the augmentation effects. META-BOA outputs a newly balanced dataset, generating additional samples in the minority class, according to the user’s choice of Synthetic Minority Over-sampling Technique (SMOTE), Borderline-SMOTE (BSMOTE), Adaptive Synthetic (ADASYN), or Random Over-Sampling Examples (ROSE). META-BOA further displays both principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) visualization of data pre- and post-over-sampling. Random forest classification is utilized to compare sample classification in both the original and balanced datasets, enabling users to select the most appropriate method for their analyses.

Availability and implementation

META-BOA is available at https://complimet.ca/meta-boa.

Supplementary Information

Supplementary material is available at Bioinformatics online.
ACSS2 Regulates HIF-2α Degradation through the E3-Ubiquitin Ligase MUL1 in Clear Cell Renal Cell Carcinoma
Authors: Bacigalupa Zachary A. , Brown Whitney A. , Krystofiak Evan S. , Wolf Melissa M. , Hongo Rachel A. , Landis Madelyn , Amason Edith K. , Beckermann Kathryn E. , Rathmell Jeffrey C. , Rathmell W. Kimryn
Published: May 2022

Clear cell renal cell carcinoma (ccRCC) is an aggressive kidney cancer driven by VHL loss and aberrant HIF-2α signaling. Acetate metabolism may contribute to this axis by ACSS2-dependent acetylation of HIF-2α and may provide opportunities to intervention. Here we tested the effects of pharmacological and genetic manipulation of ACSS2 on HIF-2α, ccRCC cells, and tumors. ACSS2 inhibition led to HIF-2α degradation and suppressed ccRCC growth in vitro, in vivo, and in primary cell cultures of ccRCC patient tumors. This treatment resulted in reduced glucose and cholesterol metabolism, mitochondrial biogenesis and altered cristae deformation, that are consistent with loss of HIF-2α. Mechanistically, HIF-2α protein levels are regulated through proteolytic degradation and we found, in parallel to VHL, HIF-2α stability was dependent on ACSS2 activity to prevent direct interaction with the E3 ligase MUL1. These findings highlight ACSS2 as a critical upstream regulator of HIF-2α that may be exploited to overcome resistance to HIF-2α inhibitor therapies.

STATEMENT OF SIGNIFICANCE

We have unveiled ACSS2 as a critical upstream regulator of HIF-2α in ccRCC. Targeting ACSS2 potently promotes HIF-2α degradation via MUL1 to effectively deplete mitochondrial activity and block ccRCC primary tumor models and growth models resistant to HIF-2α inhibitor therapy.
Characterization of human immunodeficiency virus (HIV-1) envelope glycoprotein variants selected for resistance to a CD4-mimetic compound
Authors: Anang Saumya , Richard Jonathan , Bourassa Catherine , Goyette Guillaume , Chiu Ta-Jung , Chen Hung-Ching , Smith Amos B. , Madani Navid , Finzi Andrés , Sodroski Joseph
Published: May 2022

Binding to host cell receptors, CD4 and CCR5/CXCR4, triggers conformational changes in the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer that promote virus entry. CD4 binding allows the gp120 exterior Env to bind CCR5/CXCR4 and induces a pre-hairpin intermediate conformation in the gp41 transmembrane Env. Small-molecule CD4-mimetic compounds (CD4mcs) bind within the conserved Phe-43 cavity of gp120, near the binding site for CD4. CD4mcs inhibit HIV-1 infection by competing with CD4 and by prematurely activating Env, leading to irreversible inactivation. BNM-III-170 is a CD4mc that inhibits the infection of approximately 70% of HIV-1 strains at micromolar concentrations. We selected and analyzed variants of the primary HIV-1AD8 strain resistant to BNM-III-170. Two changes (S375N and I424T) in gp120 residues that flank the Phe-43 cavity each conferred ∼5-fold resistance to BNM- III-170 with minimal fitness cost. A third change (E64G) in Layer 1 of the gp120 inner domain resulted in ∼100-fold resistance to BNM-III-170, ∼2-3-fold resistance to soluble CD4-Ig, and a moderate decrease in viral fitness. The gp120 changes additively or synergistically contributed to BNM-III-170 resistance. The sensitivity of the Env variants to BNM-III-170 inhibition of virus entry correlated with their sensitivity to BNM-III-170- induced Env activation and shedding of gp120. The S375N and I424T changes, but not the E64G change, conferred resistance to BMS-806, a potent HIV-1 entry inhibitor that blocks Env conformational transitions. These studies identify pathways whereby HIV-1 can develop resistance to CD4mcs and BMS-806 conformational blockers, two classes of entry inhibitors that target the conserved gp120 Phe-43 cavity.

IMPORTANCE

CD4-mimetic compounds (CD4mcs) and BMS-806 are small-molecule inhibitors of human immunodeficiency virus (HIV-1) entry into host cells. Although CD4mcs and BMS-806 inhibit HIV-1 entry by different mechanisms, they both target a pocket on the viral envelope glycoprotein (Env) spike that is used for binding to the receptor, CD4, and is highly conserved among HIV-1 strains. Our study identifies changes near this pocket that can confer various levels of resistance to the antiviral effects of both a CD4mc and BMS-806. We relate the antiviral potency of a CD4mc against this panel of HIV-1 variants to the ability of the CD4mc to activate changes in Env conformation and to induce the shedding of the gp120 exterior Env from the spike. These findings will guide efforts to improve the potency and breadth of small-molecule HIV-1 entry inhibitors.
Disruption of long-term psychological distress trajectories during the COVID-19 pandemic: evidence from three British birth cohorts
Authors: Moreno-Agostino Darío , Fisher Helen L. , Goodman Alissa , Hatch Stephani L , Morgan Craig , Richards Marcus , Das-Munshi Jayati , Ploubidis George B.
Published: May 2022

Importance

Mental health disorders were among the leading global contributors to years lived with disability prior to the COVID-19 pandemic onset, and growing evidence suggests that population mental health outcomes have worsened since the pandemic started. The extent that these changes have altered common age-related trends in psychological distress, where distress typically rises until mid-life and then falls in both sexes, is unknown.

Objective

To analyse whether long-term pre-pandemic psychological distress trajectories have altered during the pandemic, and whether these changes have been different across generations and by sex.

Design

Cross-cohort study with prospective data collection over a 40-year period (earliest time point: 1981; latest time point: February/March 2021).

Setting

Population-based (adult general population), Great Britain.

Participants

Members of three nationally representative birth cohorts which comprised all people born in Great Britain in a single week of 1946, 1958, or 1970, and who participated in at least one of the data collection waves conducted after the start of the pandemic (40.6%, 42.8%, 39.4%, respectively).

Exposure(s)

Time, COVID-19 pandemic.

Main Outcome(s) and Measure(s)

Psychological distress factor scores, as measured by validated self-reported questionnaires.

Results

16,389 participants (2,175 from the 1946 birth cohort, 52.8% women; 7,446 from the 1958 birth cohort, 52.4% women; and 6,768 from the 1970 birth cohort, 56.2% women) participated in the study. By September/October 2020, psychological distress levels had reached or exceeded the levels of the peak in the pre-pandemic life-course trajectories, with larger increases in younger cohorts: Standardised Mean Differences (SMD) and 95% confidence intervals (CIs) of -0.02 [-0.07, 0.04], 0.05 [0.02, 0.07], and 0.09 [0.07, 0.12] for the 1946, 1958, and 1970 birth cohorts, respectively. Increases in distress were larger among women than men, widening the pre-existing inequalities observed in the pre-pandemic peak and in the most recent pre-pandemic assessment.

Conclusions and Relevance

Pre-existing long-term psychological distress trajectories of adults born between 1946 and 1970 were disrupted during the COVID-19 pandemic, particularly among women, who reached the highest levels ever recorded in up to 40 years of follow-up data. This may impact future trends of morbidity, disability, and mortality due to common mental health problems.
Unhealthy lifestyle mediates the adverse effect of childhood traumas on acceleration of aging: analysis of 110,596 UK Biobank participants
Authors: Yang Gan , Cao Xingqi , Li Xueqin , Zhang Jingyun , Ma Chao , Zhang Ning , Lu Qingyun , Crimmins Eileen M. , Gill Thomas M. , Chen Xi , Liu Zuyun
Published: May 2022

Background

Accelerated aging makes adults more vulnerable to chronic diseases and death. This study evaluates the association of childhood traumas with a phenotypic aging measure that captures mortality and morbidity risk, and the role of unhealthy lifestyle in mediating these associations.

Methods

We assembled data from 110,596 members of the UK Biobank aged 40-69 years who participated in the baseline survey (2006-2010) and online mental health questionnaire (2016). A phenotypic aging measure—Phenotypic Age Acceleration (PhenoAgeAccel) was calculated, with the higher value indicating the acceleration of aging. Body mass index, smoking status, alcohol consumption, physical activity, and diet were combined to construct an unhealthy lifestyle score (range: 0-5). Childhood traumas including physical neglect, emotional neglect, sexual abuse, physical abuse, and emotional abuse were assessed. General linear regression and formal mediation analysis were performed.

Results

Each individual childhood trauma and cumulative childhood traumas were significantly associated with PhenoAgeAccel. For instance, compared with participants who did not experience childhood traumas, those who experienced four (β=0.292, standard error [SE]: 0.091) or five childhood traumas had higher PhenoAgeAccel (β=0.669, SE: 0.169) in fully adjusted models. The formal mediation analysis revealed that unhealthy lifestyle partially mediated the associations of childhood traumas with PhenoAgeAccel (26.1%-42.6%).

Conclusions

In a large sample from UKB, childhood traumas were positively associated with acceleration of aging; and more importantly, unhealthy lifestyle partially mediated these associations. These findings reveal a novel pathway from childhood traumas to late-life health through lifestyle and underscore the potential of more psychological strategies beyond lifestyle interventions to promote healthy aging.
Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform
Authors: Wing Kevin , Grint Daniel J , Mathur Rohini , Gibbs Hamish P , Hickman George , Nightingale Emily , Schultze Anna , Forbes Harriet , Nafilyan Vahé , Bhaskaran Krishnan , Williamson Elizabeth , House Thomas , Pellis Lorenzo , Herrett Emily , Gautam Nileesa , Curtis Helen J , Rentsch Christopher T , Wong Angel YS , MacKenna Brian , Mehrkar Amir , Bacon Seb , Douglas Ian J , Evans Stephen JW , Tomlinson Laurie , Goldacre Ben , Eggo Rosalind M
Published: May 2022

Ethnic differences in the risk of severe COVID-19 may be linked to household composition. We quantified the association between household composition and risk of severe COVID-19 by ethnicity for older individuals. With the approval of NHS England, we analysed ethnic differences in the association between household composition and severe COVID-19 in people aged 67 or over in England. We defined households by number of generations living together, and used multivariable Cox regression stratified by location and wave of the pandemic and accounted for age, sex, comorbidities, smoking, obesity, housing density and deprivation. We included 2 692 223 people over 67 years in wave 1 (01/02/2020-31/08/2020) and 2 731 427 in wave 2 (01/09/2020-31/01/2021). Multigenerational living was associated with increased risk of severe COVID-19 for White and South Asian older people in both waves (e.g. wave 2, 67+ living with 3 other generations vs 67+ year olds only: White HR 1·61 95% CI 1·38-1·87, South Asian HR 1·76 95% CI 1·48-2·10), with a trend for increased risks of severe COVID-19 with increasing generations in wave 2. Multigenerational living was associated with severe COVID-19 in older adults. Older South Asian people are over-represented within multigenerational households in England, especially in the most deprived settings. The number of generations in a household, number of occupants, ethnicity and deprivation status are important considerations in the continued roll-out of COVID-19 vaccination and targeting of interventions for future pandemics.

Funding

This research was funded in part, by the Wellcome Trust. For the purpose of open access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
Crosslinker design determines microtubule network organization by opposing motors
Authors: Henkin Gil , Chew Wei-Xiang , Nédélec François , Surrey Thomas
Published: May 2022

During cell division, crosslinking motors determine the architecture of the spindle, a dynamic microtubule network that segregates the chromosomes. It is unclear how motors with opposite directionality coordinate to drive both contractile and extensile behaviors in the spindle. Particularly, the impact of different crosslinker designs on network self-organization is not understood, limiting our understanding of self-organizing structures in cells, but also our ability to engineer new active materials. Here, we use experiment and theory to examine active microtubule networks driven by mixtures of motors with opposite directionality and different crosslinker design. We find that although the kinesin-14 HSET causes network contraction when dominant, it can also assist the opposing kinesin-5 KIF11 to generate extensile networks. This bifunctionality results from HSET’s asymmetric design, distinct from symmetric KIF11. These findings expand the set of rules underlying patterning of active microtubule assemblies and allow a better understanding of motor cooperation in the spindle.

SIGNIFICANCE STATEMENT

During cell division, the spindle apparatus segregates duplicated chromosomes for their inheritance by the daughter cells. The spindle is a highly interconnected network of microtubule filaments that are crosslinked by different types of molecular motors. How the different motors cooperate to organize the spindle network is not understood. Here, we show that an asymmetric crosslinker design can confer bifunctionality to a mitotic motor in the presence of other motors. The asymmetric motor supports both extensile and contractile microtubule network behaviors as observed in different parts of the spindle. These findings define new rules controlling the generation of active microtubule networks and allow us to better understand how motors cooperate to organize the correct spindle architecture when a cell divides.
Spt4 drives cellular senescence by activating non-coding RNA transcription in ribosomal RNA gene clusters
Authors: Yokoyama Masaaki , Sasaki Mariko , Kobayashi Takehiko
Published: May 2022

Genome instability can drive aging in many organisms. The ribosomal RNA gene (rDNA) cluster is one of the most unstable regions in the genome. Replicative lifespan in budding yeast is correlated to rDNA stability, suggesting that the rDNA locus produces an aging signal. To understand the underlying mechanism, we looked for yeast mutants with more stable rDNA and longer lifespan than wild-type cells. We reveal that absence of a transcription elongation factor, Spt4, resulted in an increased rDNA stability, a reduced activity of the regulatory E-pro promoter in the rDNA, and extended replicative lifespan in a SIR2-dependent manner. Spt4-dependent lifespan restriction was abolished in the absence of non-coding RNA transcription at the E-pro locus. The amount of Spt4 increases and its function becomes more important as cells age. These findings suggest that Spt4 is a promising aging factor that accelerates cellular senescence through rDNA instability driven by non-coding RNA transcription
Targeting diverse operational regimes in recurrent spiking networks
Authors: Ekelmans Pierre , Kraynyukova Nataliya , Tchumatchenko Tatjana
Published: May 2022

Neural computations emerge from recurrent neural circuits that comprise hundreds to a few thousand neurons. Continuous progress in connectomics, electrophysiology, and calcium imaging require tractable spiking network models that can consistently incorporate new information about the network structure and reproduce the recorded neural activity features. However, it is challenging to predict which spiking network connectivity configurations and neural properties can generate fundamental operational states and specific experimentally reported nonlinear cortical computations. Theoretical descriptions for the computational state of cortical spiking circuits are diverse, including the balanced state where excitatory and inhibitory inputs balance almost perfectly or the inhibition stabilized state (ISN) where the excitatory part of the circuit is unstable. It remains an open question whether these states can co-exist with experimentally reported nonlinear computations and whether they can be recovered in biologically realistic implementations of spiking networks. Here, we show how to identify spiking network connectivity patterns underlying diverse nonlinear computations such as XOR, bistability, inhibitory stabilization, supersaturation, and persistent activity. We established a mapping between the stabilized supralinear network (SSN) and spiking activity which allowed us to pinpoint the location in parameter space where these activity regimes occur. Notably, we found that biologically-sized spiking networks can have irregular asynchronous activity that does not require strong excitation-inhibition balance or large feedforward input and we showed that the dynamic firing rate trajectories in spiking networks can be precisely targeted without error-driven training algorithms.
Enhanced Mirror Neuron Network Activity and Effective Connectivity during Live Interaction Among Female Subjects
Authors: Hsu Chun-Ting , Sato Wataru , Kochiyama Takanori , Nakai Ryusuke , Asano Kohei , Abe Nobuhito , Yoshikawa Sakiko
Published: May 2022

Facial expressions are indispensable in daily human communication. Previous neuroimaging studies investigating facial expression processing have presented pre-recorded stimuli and lacked live face-to-face interaction. Our paradigm alternated between presentations of real-time model performance and pre-recorded videos of dynamic facial expressions to participants. Simultaneous functional magnetic resonance imaging (fMRI) and facial electromyography activity recordings, as well as post-scan valence and arousal ratings were acquired from 44 female participants. Live facial expressions enhanced the subjective valence and arousal ratings as well as facial muscular responses. Live performances showed greater engagement of the right posterior superior temporal sulcus (pSTS), right inferior frontal gyrus (IFG), right amygdala and right fusiform gyrus, and modulated the effective connectivity within the right mirror neuron system (IFG, pSTS, and right inferior parietal lobule). A support vector machine algorithm could classify multivoxel activation patterns in brain regions involved in dynamic facial expression processing in the mentalizing networks (anterior and posterior cingulate cortex). These results indicate that live social interaction modulates the activity and connectivity of the right mirror neuron system and enhances spontaneous mimicry, further facilitating emotional contagion.

Highlights

We alternately presented real-time and pre-recorded dynamic facial expressions.

Live facial expressions enhanced emotion contagion and spontaneous facial mimicry.

Live conditions modulated mirror neuron system activity and effective connectivity.

The mentalizing network showed distinctive multivoxel patterns in live conditions.

The results support the validity of second-person design in social neuroscience.
Paracrine factors of stressed peripheral blood mononuclear cells activate pro-angiogenic and anti-proteolytic processes in whole blood cells and protect the endothelial barrier
Authors: Copic Dragan , Direder Martin , Schossleitner Klaudia , Laggner Maria , Klas Katharina , Bormann Daniel , Ankersmit Hendrik Jan , Mildner Michael
Published: May 2022

Tissue regenerative properties have been attributed to secreted paracrine factors derived from stem cells and other cell types. Especially, the secretome of γ-irradiated peripheral blood mononuclear cells (PBMCsec) has been shown to possess high tissue-regenerative and pro-angiogenic capacities in a variety of preclinical studies. In the light of future therapeutic intravenous applications of PBMCsec, we investigated possible effects of PBMCsec on circulating white blood cells and endothelial cells lining the vasculature.

Methods

To identify changes in the transcriptional profile of white blood cells treated with PBMCSec, whole blood was drawn from healthy individuals and stimulated with PBMCsec for 8 hours ex vivo before further processing for single cell RNA sequencing (scRNAseq). In addition, we performed in vitro assay to confirm findings arising from the transcriptional profiling.

Results

Addition of PBMCsec to whole blood significantly altered the gene signature of granulocytes (17 genes), T-cells (45 genes), B-cells (72 genes) and most prominently monocytes (322 genes). We detected a strong upregulation of several tissue-regenerative and pro-angiogenic cyto- and chemokines in monocytes, including VEGFA, CXCL1 and CXCL5. Intriguingly, inhibitors of endopeptidase activity, such as SERPINB2, were also strongly induced. Measurement of the trans-endothelial electrical resistance of primary human microvascular endothelial cells revealed a strong barrier-protective effect of PBMCsec after barrier disruption.

Conclusion

Together, we show that PBMCsec induces angiogenic and proteolytic processes in the blood and is able to attenuate endothelial barrier damage. These regenerative properties suggest that systemic application of PBMCsec might be a promising novel strategy to restore damaged organs.
CASK and FARP localize two classes of post-synaptic ACh receptors thereby promoting cholinergic transmission
Authors: Li Lei , Liu Haowen , Qian Kang-Ying , Nurrish Stephen , Zeng Xian-Ting , Zeng Wan-Xin , Wang Jiafan , Kaplan Joshua M , Tong Xia-Jing , Hu Zhitao
Published: May 2022

Changes in neurotransmitter receptor abundance at post-synaptic elements play a pivotal role in regulating synaptic strength. For this reason, there is significant interest in identifying and characterizing the scaffolds required for receptor localization at different synapses. Here we analyze the role of two C. elegans post-synaptic scaffolding proteins (LIN-2/CASK and FRM-3/FARP) at cholinergic neuromuscular junctions. Constitutive knockouts or muscle specific inactivation of lin-2 and frm-3 dramatically reduced spontaneous and evoked post-synaptic currents. These synaptic defects resulted from the decreased abundance of two classes of post-synaptic ionotropic acetylcholine receptors (ACR-16/CHRNA7 and levamisole-activated AChRs). LIN-2’s AChR scaffolding function is mediated by its SH3 and PDZ domains, which interact with AChRs and FRM-3/FARP, respectively. Thus, our findings show that post-synaptic LIN-2/FRM-3 complexes promote cholinergic synaptic transmission by recruiting AChRs to post-synaptic elements.
Multisite imaging of neural activity using a genetically encoded calcium sensor in the honey bee
Authors: Carcaud Julie , Otte Marianne , Grünewald Bernd , Haase Albrecht , Sandoz Jean-Christophe , Beye Martin
Published: May 2022

Understanding of the neural bases for complex behaviors in Hymenoptera insect species has been limited by a lack of tools that allow measuring neuronal activity simultaneously in different brain regions. Here, we developed the first pan-neuronal genetic driver in a Hymenopteran model organism, the honey bee, and expressed the calcium indicator GCaMP6f under the control of the honey beesynapsinpromoter. We show that GCaMP6f is widely expressed in the honey bee brain, allowing to record neural activity from multiple brain regions. To assess the power of this tool, we focused on the olfactory system, recording simultaneous responses from the antennal lobe, and from the more poorly investigated lateral horn and mushroom body calyces. Neural responses to 16 distinct odorants demonstrate that odorant quality (chemical structure) and quantity are faithfully encoded in the honey bee antennal lobe. In contrast, odor coding in the lateral horn departs from this simple physico-chemical coding, supporting the role of this structure in coding the biological value of odorants. We further demonstrate robust neural responses to several bee pheromone odorants, key drivers of social behavior, in the lateral horn. Combined, these brain recordings represent the first use of a neurogenetic tool for recording large-scale neural activity in a eusocial insect, and will be of utility in assessing the neural underpinnings of olfactory and other sensory modalities and of social behaviors and cognitive abilities.
VelcroVax: a ‘bolt-on’ vaccine platform technology improves antibody titres against a viral glycoprotein in mice
Authors: Kingston Natalie J , Grehan Keith , Snowden Joseph S , Hassall Mark , Alzahrani Jehad , Paesen Guido C , Sherry Lee , Hayward Connor , Roe Amy , Stephen Sam , Tomlinson Darren , Zeltina Antra , Doores Katie J , Ranson Neil A , Stacey Martin , Page Mark , Rose Nicola J , Bowden Thomas A , Rowlands David J , Stonehouse Nicola J
Published: May 2022

Having varied approaches to the design and manufacture of vaccines is critical in being able to respond to worldwide needs and to newly emerging pathogens. Virus-like particle (VLP) vaccines form the basis of two of the most successful licensed vaccines (against hepatitis B virus (HBV) and human papillomavirus). They are produced by recombinant expression of viral structural proteins, which self-assemble into immunogenic nanoparticles. VLPs can also be modified to present unrelated antigens, and here we describe a universal ‘bolt-on’ vaccine platform (termed VelcroVax) where the capturing VLP and the target antigen (hapten) are produced separately. We utilise a modified HBV core (HBcAg) VLP, with surface expression of a high-affinity binding sequence (Affimer) directed against a SUMO tag and use this to capture SUMO-tagged gp1 glycoprotein from the arenavirus, Junín virus (JUNV). Using this model system, we have solved high-resolution structures of VelcroVax VLPs, and shown that the VelcroVax-JUNV gp1 complex induces superior humoral immune responses compared to the non-complexed viral protein. We propose that this system could be modified to present a range of haptens and therefore form the foundation of future rapid-response vaccination strategies.
Biomolecular condensates can both accelerate and suppress aggregation of α-synuclein
Authors: Lipiński Wojciech P. , Visser Brent S. , Robu Irina , Fakhree Mohammad A. A. , Lindhoud Saskia , Claessens Mireille M. A. E. , Spruijt Evan
Published: May 2022

Biomolecular condensates present in cells can fundamentally affect the aggregation of amyloidogenic proteins and play a role in the regulation of this process. While liquid-liquid phase separation of amyloidogenic proteins by themselves can act as an alternative nucleation pathway, interaction of partly disordered aggregation-prone proteins with pre-existing condensates that act as localization centers could be a far more general mechanism of altering their aggregation behavior. Here, we show that so-called host biomolecular condensates can both accelerate and slow down amyloid formation. We study the amyloidogenic protein α-synuclein and two truncated α-synuclein variants in the presence of three types of condensates composed of non-aggregating peptides, RNA or ATP. Our results demonstrate that condensates can dramatically speed up amyloid formation when proteins localize to their interface. However, condensates can also significantly suppress aggregation by sequestering and stabilizing amyloidogenic proteins, thereby providing living cells with a possible protection mechanism against amyloid formation.
MME+ fibro-adipogenic progenitors are the dominant adipogenic population during fatty infiltration in human skeletal muscle
Authors: Fitzgerald Gillian , Turiel Guillermo , Gorski Tatiane , Soro-Arnaiz Inés , Zhang Jing , Casartelli Nicola C , Masschelein Evi , Maffiuletti Nicola A , Sutter Reto , Leunig Michael , Farup Jean , De Bock Katrien
Published: May 2022

Summary/Abstract

Fatty infiltration, the ectopic deposition of adipose tissue within skeletal muscle, is mediated via the adipogenic differentiation of fibro-adipogenic progenitors (FAPs). We used single-nuclei and single- cell RNA sequencing to characterize FAP heterogeneity in patients with fatty infiltration. We identified an MME+ FAP subpopulation which, based on ex vivo characterization as well as transplantation experiments, exhibits high adipogenic potential. MME+ FAPs are characterized by low activity of WNT, known to control adipogenic commitment, and are refractory to the inhibitory role of WNT activators. Using preclinical models for muscle damage versus fatty infiltration, we show that many MME+ FAPs undergo apoptosis during muscle regeneration and differentiate into adipocytes under pathological conditions, leading to their depletion. Finally, we utilized the varying fat infiltration levels in human hip muscles to show the depletion of MME+ FAPs in fatty infiltrated human muscle. Altogether, we have identified the dominant adipogenic FAP subpopulation in skeletal muscle.
Cluster-Based Inference for Memory-Based Cognition
Authors: Penny Will , Menghi Nicho , Renoult Louis
Published: May 2022

This paper proposes a model of hippocampal-based category learning using a cluster-based inference framework which produces two systems (i) an extendable cluster-based memory module (CMM) that provides representations of learning episodes with strong pattern separation, and supports online decision making during that learning, (ii) cluster-based task modules (CTMs) which consolidate clusters learnt by CMM to support higher-accuracy decision making in the mid-term. Learning in CMMs optimises the joint probability of stimuli and category labels, whereas learning in CTMs optimises the probability of categories given stimuli. The latter system learns from the former via a process of “cluster consolidation”. We apply the model to data from a behavioral learning task and find that, as well as improving categorisation performance, cluster consolidation decreases recognition scores for old cues but increases them for novel cues. This model-based perspective explains forgetting and false memory effects as serving future categorisation performance. The paper also expresses a view that models of memorybased cognition should provide human-level performance on complex categorisation tasks, and do so with minimal labelled data. In working toward this goal we therefore compared the accuracy of CMM- and CTM-based decision making to standard Softmax Regression approaches on benchmark machine learning datasets. This produced mixed results. We found some significant improvements of CMM over Softmax Regression and of CTM over CMM. Overall, our framework reconciles complementary learning systems theory with more recent findings from cognitive neuroscience of generative replay and hippocampal-based generalisation.
Adenine base editing is an efficient approach to restore function in FA patient cells without double-stranded DNA breaks
Authors: Siegner Sebastian M. , Clemens Alexandra , Ugalde Laura , Garcia-Garcia Laura , Bueren Juan A. , Rio Paula , Karasu Mehmet E. , Corn Jacob E.
Published: May 2022

Fanconi Anemia (FA) is a debilitating genetic disorder with a wide range of severe symptoms including bone marrow failure and predisposition to cancer. CRISPR-Cas genome editing manipulates genotypes by harnessing DNA repair and has been proposed as a potential cure for FA. But FA is caused deficiencies in DNA repair itself, preventing the use of editing strategies such as homology directed repair. Recently developed base editing (BE) systems do not rely on double stranded DNA breaks and might be used to target mutations in FA genes, but this remains to be tested. Here we develop a proof of concept therapeutic base editing strategy to address two of the most prevalent FANCA mutations in patient cells. We find that optimizing adenine base editor construct, vector type, guide RNA format, and delivery conditions lead to very effective genetic modification in multiple FA patient backgrounds. Optimized base editing restored FANCA expression, molecular function of the FA pathway, and phenotypic resistance to crosslinking agents. ABE8e mediated editing in primary hematopoietic stem and progenitor cells from an FA patient was both genotypically effective and restored FA pathway function, indicating the potential of base editing strategies for future clinical application in FA.
Simple within-stride changes in treadmill speed can drive selective changes in human gait symmetry
Authors: Browne Michael G. , Stenum Jan , Padmanabhan Purnima , Roemmich Ryan T.
Published: May 2022

Background

Millions of people worldwide are affected by clinical conditions that result in gait asymmetry (e.g., stroke, cerebral palsy, lower limb amputation). There is a need for customizable rehabilitation approaches that can flexibly target different aspects of gait asymmetry with minimal need for specialized equipment. Here, we studied how simple within-stride changes in treadmill speed could drive selective, predictable changes in human gait symmetry.

Methods

In Experiment 1, ten healthy young adults walked on an instrumented treadmill with and without a closed-loop controller engaged. The controller changed the treadmill speed to 1.50 m/s or 0.75 m/s depending on whether the right or left leg generated propulsive (i.e., forward-directed) ground reaction forces, respectively. In Experiment 2, a separate group of ten healthy young adults walked on the treadmill with and without an open-loop controller engaged. This controller changed the treadmill speed to 1.50 m/s or 0.75 at a prescribed time interval. We used a metronome to guide the participants to step at a series of different time points relative to the controller-driven speed change. We collected kinematic and kinetic data in Experiments 1 and 2.

Results

In Experiment 1, participants walked with asymmetric kinematics and ground reaction forces when the closed-loop controller was engaged. The leg that accelerated during propulsion (right leg) showed a smaller leading limb angle and a larger trailing limb angle than the leg that decelerated during propulsion (left leg). The right leg also generated smaller propulsive forces than the left leg. In Experiment 2, the patterns of asymmetry in spatiotemporal gait parameters, kinematics, and ground reaction forces depended on the timing of the speed change within the gait cycle. Step times, leading limb angles, and peak propulsion became asymmetric when the treadmill speed changed early in stance. When the treadmill speed changed later in stance, step lengths, step times, and propulsion impulses became asymmetric.

Conclusions

Simple manipulations of treadmill speed can drive predictable, selective changes in human gait symmetry. Future work will explore this customizable technique as a potential approach for restoring gait symmetry in clinical populations.
Locomotion control during curb descent: Bilateral ground reaction variables covary consistently during the double support phase regardless of future foot placement constraints
Authors: Cui Chuyi , Kulkarni Ashwini , Rietdyk Shirley , Ambike Satyajit
Published: May 2022

During community ambulation, anticipatory adaptations in gait are key for navigating built, populated and natural environments. It has been argued that some instability in gait can be functionally beneficial in situations demanding high maneuverability, and while the mechanisms utilized to maintain locomotor balance are well understood, relatively less is known about how the control of gait stability changes to facilitate upcoming maneuvers in challenging environments. The double support phase may be important in this regard; since both feet can push off the ground simultaneously, there is greater control authority over the body’s movement during this phase. Our goal was to identify how this control authority is exploited to prepare for upcoming maneuvers in challenging environments. We used synergy indices to quantify the degree of coordination between the ground reaction forces and moments under the two feet for stabilizing the resultant force and moment on the body during the double support phase of curb descent. In contrast to our expectations, we observed that the kinetic synergy indices during curb descent were minimally influenced by expected foot targeting maneuvers for the subsequent step. Only the resultant moment in the frontal plane showed reduced stability when targeting was required, but the synergy index was still high, indicating that the resultant moment was stable. Furthermore, the synergy indices indicated that the main function of the ground reaction variables is to maintain stability of whole-body rotations during double support, and this prerogative was minimally influenced by the subsequent foot targeting tasks, likely because the cost of losing balance while descending a curb would be higher than the cost of mis-stepping on a visual target. Our work demonstrates the salience of stabilizing body rotations during curb negotiation and improves our understanding of locomotor control in challenging environments.
A rapid and universal liquid chromatograph-mass spectrometry-based platform, refmAb-Q nSMOL, for monitoring monoclonal antibody therapeutics
Authors: Iwamoto Noriko , Koguchi Yoshinobu , Yokoyama Kotoko , Hamada Akinobu , Yonezawa Atsushi , Piening Brian D. , Tran Eric , Fox Bernard A. , Redmond William L. , Shimada Takashi
Published: May 2022

Accurate quantitation of antibody is critical for development of monoclonal antibody therapeutics (mAbs). Therapeutic drug monitoring has been applied to measure levels of mAbs in clinics for dose adjustment for autoimmune disease. Trough levels of mAbs can be a biomarker for cancer immunotherapy. Thus, the deployment of a rapid and universal platform for mAb monitoring may benefit processes ranging from drug development to clinical practice for a wide spectrum of diseases. However, mAb monitoring often requires development and conduct of an individual ligand binding assay such as ELISA, which is impractical to scale. We streamlined quantitation of antibody therapeutics by a nano-surface and molecular-orientation limited (nSMOL) proteolysis assay using LC-MS with a universal reference antibody (refmAb-Q), for accurate multiplexed quantitation of unique signature peptides derived from mAbs. This innovative refmAb-Q nSMOL platform may provide a practical solution for quantitating an ever-increasing number of mAbs from developmental to clinical use settings.
TFIIFα interacts with the Topoisomerase VI complex and selectively controls the expression of genes encoding PPR proteins involved in organellar RNA editing in Arabidopsis
Authors: Dimnet Laura , Vriet Cécile , Achard Dorine , Lecampion Cécile , Breuer Christian , Soubigou-Taconnat Ludivine , Sugimoto Keiko , Delannoy Etienne , Laloi Christophe
Published: May 2022

Communication between organelles and the nucleus is referred to as anterograde (nucleus to organelle) and retrograde (organelle to nucleus) signalling. In plants, the pentatricopeptide repeat (PPR) proteins represent a large family of nuclear-encoded proteins that are required for post-transcriptional control of chloroplast and mitochondria gene expression, and hence play a central role in the nuclear anterograde control of organelle genome expression. How PPR gene expression is controlled and regulated by retrograde signals is, however, still unknown. Here, we report a significant role for the general transcription factor TFIIF α-subunit (TFIIFα) in controlling PPR gene expression in Arabidopsis. First, we found that TFIIFα interacts with the BIN4 subunit of the Topoisomerase VI (Topo VI). Transcriptome analysis of TFIIF and Topo VI mutant lines then revealed that many PLS-type PPR genes involved in RNA editing are reciprocally controlled by TFIIF and Topo VI. The misexpression of CLB19 and DYW1 genes in two allelic tfIIfα mutants was associated with editing impairments in their plastid target RNAs rpoA and ndhD, respectively. Interestingly, we also detected a change in NDH activity in tfIIfα plants. We also show that TFIIFα and Topo VI coordinate the expression of NDH subunits encoded by the nuclear and plastid genomes. These results reveal the crucial role of the nuclear TFIIFα and Topo VI complexes in controlling plastid genome expression at multiple levels of regulation, including the particular regulation of PPR gene expression.
5′ transgenes drive leaky expression of 3′ transgenes in inducible bicistronic vectors
Authors: Osanai Yasuyuki , Xing Yao Lulu , Kobayashi Kenta , Homman-Ludiye Jihane , Cooray Amali , Poh Jasmine , Ohno Nobuhiko , Merson Tobias D.
Published: May 2022

Molecular cloning techniques enabling contemporaneous expression of two or more protein-coding sequences in a cell type of interest provide an invaluable tool for understanding the molecular regulation of cellular functions. DNA recombination employing the Cre-lox system is commonly used as a molecular switch for inducing the expression of recombinant proteins encoded within a bicistronic cassette. In such an approach, the two protein-coding sequences are separated by a 2A peptide or internal ribosome entry site (IRES), and expression is designed to be strictly Cre-dependent by using a lox-STOP-lox cassette or flip-excision (FLEX) switch. However, low-level or ‘leaky’ expression of recombinant proteins is often observed in the absence of Cre activity, potentially compromising the utility of this approach. To investigate the mechanism of leaky gene expression, we generated pCAG-lox-GFP-STOP-lox-Transgene A-2A-Transgene B vectors, which are designed to express nuclear-targeted GFP in the absence of Cre, and express both transgenes A and B after Cre-mediated recombination. We found that cells transfected with these bicistronic vectors exhibited low-level Cre-independent expression specifically of the transgene positioned 3′ of the 2A peptide. We observed similar results in vivo by viral transduction of the adult mouse cerebral cortex with AAV-mutagenesis of putative transcription factor binding sites that the 5′ transgene confers promoter-like activity that drives expression of the 3′ transgene. Finally, we demonstrate that inclusion of an additional lox-STOP-lox cassette between the 2A sequence and 3′ transgene dramatically reduces the extent of Cre-independent leaky gene expression. Our findings highlight that caution should be applied to the use of Cre-dependent bicistronic constructs when tight regulation of transgene expression is desired and provide a guide to preventing leaky gene expression when the expression of more than one protein is required.
Proteostatic regulation of caveolins avoids premature oligomerisation and preserves ER homeostasis
Authors: Morales-Paytuví Frederic , Ruiz-Mirapeix Carles , Fajardo Alba , Rae James , Bosch Marta , Enrich Carlos , Collins Brett M. , Parton Robert G. , Pol Albert
Published: May 2022

Caveolin-1 (CAV1) and CAV3 are membrane sculpting proteins driving formation of plasma membrane caveolae. Caveola formation is unique as it requires oligomerisation of newly synthesised caveolins through the biosynthetic-secretory pathway. Here, we combine structural, biochemical, and microscopy analyses to examine the early proteostasis of caveolin family members and mutants. We describe striking trafficking differences between newly synthesised caveolins, with CAV1 rapidly exported to the Golgi but CAV3 showing ER retention and targeting to lipid droplets. Only monomeric/low oligomeric caveolins are efficiently exported from the ER, with oligomers assembling beyond the cis-Golgi and disease-causing mutations leading to detrimental non-functional complexes. Caveolins in the ER are maintained at low levels by active proteasomal degradation, avoiding premature oligomerisation and ER stress. Increasing lipid availability, cholesterol for CAV1 and fatty acids for CAV3, enhances trafficking and reduces proteasomal degradation. In conclusion, we identify proteostatic mechanisms that modulate stability and trafficking of newly synthesised caveolins, protecting cells against ER stress but perturbed in caveolin-related disease.

Understanding the unique proteostasis of caveolins has important implications for cell biology and physiopathology. Combining structural, microscopy, and biochemical analyses, we uncover new insights into the mechanisms that differentiate the early biosynthetic steps of caveolin family members, isoforms, and pathogenic mutants.