bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between Non-Dietary Cardiovascular Health and Expenditures Related to Acute Coronary Syndrome in the US between 2008–2018
Authors: Enyeji Abraham , Barengo Noël C. , Ibrahimou Boubakari , Ramirez Gilbert , Arrieta Alejandro
Published: April 2023

Background

Acute Coronary Syndrome (ACS) causes the most deaths in the United States and accounts for the highest amount of healthcare spending. Cardiovascular Health (CVH) metrics have been widely used in primary prevention, but their benefits in secondary prevention on total healthcare expenditures related to ACS are largely unknown. This study aims to quantify the potential significance of ideal CVH scores as a tool in secondary cardiovascular disease prevention.

Methods

In a cross-sectional analytical study, ten years of Medical Expenditure Panel Survey (MEPS) data from 2008 to 2018 were pooled, comparing ACS to non-ACS subgroups, utilizing a Two-part model with log link and gamma distribution, since our sample had both positive and zero costs. Conditional on positive expenditure, healthcare expenditure amounts were measured as a function of ACS status, socio-demographics, and CVH while controlling for relevant covariates. Finally, interactions of ACS with CVH metrics and other key variables were included to allow for variations in the effect of these variables on the two subgroups.

Results

Improvements in CVH scores tended to reduce annual expenditures to a greater degree percentage-wise among ACS subjects compared to non-ACS groups, even though subjects with an ACS diagnosis tended to have approximately twice as big expenditures as similar subjects without an ACS diagnosis. Meanwhile, the financial impact of an ACS event on total expenditure would be approximately $88,500 ([95% CI, $70,200–106,900;p< 0.001]), and a unit improvement in CVH management score would generate savings of approximately $4160 ([95% CI, $5390–2950;p< 0.001]) in total health expenditures.

Conclusion

Effective secondary preventive measures through targeted behavioral endeavors and improved health factors, especially the normalization of hypertension, diabetes mellitus, body mass index, and smoking cessation, have the potential to reduce medical spending for ACS subgroups.
Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Dual-Functional CRISPR-Cas12a
Authors: Tian Zimu , Yan He , Zeng Yong
Published: April 2023

Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advance in CRISPR-based biosensing promises the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. Currently prevailing strategy of developing CRISPR assays exploits only the non-specific trans-cleavage function of a CRISPR-Cas12a/Cas13a system for detection and combines it with an additional pre-amplification reaction to enhance the sensitivity. In contrast to this single-function strategy, here we present a new approach that collaboratively integrates the dual functions of CRISPR-Cas12a: sequence-specific binding and trans-cleavage activity. With this approach, we developed a POC nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection assay Integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with the fluorogenic detection by the activated Cas12a on beads. Our proof-of-concept study demonstrated that the SPEEDi-CRISPR assay affords an improved detection sensitivity for human papillomavirus (HPV)-18 with a LOD of 2.3 fM and excellent specificity to discriminate HPV-18 from HPV-16, Parvovirus B19, and scramble HPV-18. Furthermore, this robust assay was readily coupled with a portable smartphone-based fluorescence detector and a lateral flow assay for quantitative detection and visualized readout, respectively. Overall, these results should suggest that our dual-function strategy could pave a new way for developing the next-generation CRISPR diagnostics and that the SPEEDi-CRISPR assay provides a potentially useful tool for point-of-care testing.
Unsupervised representation learning improves genomic discovery and risk prediction for respiratory and circulatory functions and diseases
Authors: Yun Taedong , Cosentino Justin , Behsaz Babak , McCaw Zachary R. , Hill Davin , Luben Robert , Lai Dongbing , Bates John , Yang Howard , Schwantes-An Tae-Hwi , Zhou Yuchen , Khawaja Anthony P. , Carroll Andrew , Hobbs Brian D. , Cho Michael H. , McLean Cory Y. , Hormozdiari Farhad
Published: April 2023

High-dimensional clinical data are becoming more accessible in biobank-scale datasets. However, effectively utilizing high-dimensional clinical data for genetic discovery remains challenging. Here we introduce a general deep learning-based framework, REpresentation learning for Genetic discovery on Low-dimensional Embeddings (REGLE), for discovering associations between genetic variants and high-dimensional clinical data. REGLE uses convolutional variational autoencoders to compute anon-linear, low-dimensional, disentangled embeddingof the data with highly heritable individual components. REGLE can incorporate expert-defined or clinical features and provides a framework to create accurate disease-specific polygenic risk scores (PRS) in datasets which have minimal expert phenotyping. We apply REGLE to both respiratory and circulatory systems: spirograms which measure lung function and photoplethysmograms (PPG) which measure blood volume changes. Genome-wide association studies on REGLE embeddings identify more genome-wide significant loci than existing methods and replicate known loci for both spirograms and PPG, demonstrating the generality of the framework. Furthermore, these embeddings are associated with overall survival. Finally, we construct a set of PRSs that improve predictive performance of asthma, chronic obstructive pulmonary disease, hypertension, and systolic blood pressure in multiple biobanks. Thus, REGLE embeddings can quantify clinically relevant features that are not currently captured in a standardized or automated way.
Altered Functional Networks during Gain Anticipation in Fibromyalgia
Authors: Park Su Hyoun , Michael Andrew M. , Baker Anne K. , Lei Carina , Martucci Katherine T.
Published: April 2023

Reward motivation is essential in shaping human behavior and cognition. Previous studies have shown altered reward motivation and reward brain circuitry in chronic pain conditions, including fibromyalgia. Fibromyalgia is a chronic disorder characterized by widespread musculoskeletal pain, fatigue, cognitive problems, and mood-related symptoms. In this study, we analyzed brain reward networks in patients with fibromyalgia by using a data-driven approach with task-based fMRI data. fMRI data from 24 patients with fibromyalgia and 24 healthy controls were acquired while subjects performed a monetary incentive delay (MID) reward task. Functional networks were derived using independent component analysis (ICA) focused on the gain anticipation phase of the reward task. Functional activity in the motor, value-driven attention, and basal ganglia networks was evaluated during gain anticipation in both patient and healthy control groups. Compared to controls, the motor network was more engaged during gain anticipation in patients with fibromyalgia. Our findings suggest that reward motivation may lead to hyperactivity in the motor network, possibly related to altered motor processing, such as restricted movement or dysregulated motor planning in fibromyalgia. As an exploratory analysis, we compared levels of motor network engagement during early and late timepoints of the gain anticipation phase. Both groups showed greater motor network engagement during the late timepoint (i.e., closer to response), which reflected motor preparation prior to target response. Importantly, compared to controls and consistent with the initial findings described above, patients exhibited greater engagement of the motor network during both early and late timepoints. In summary, by using a novel data-driven ICA approach to analyze task-based fMRI data, we identified elevated motor network engagement during gain anticipation in fibromyalgia.
Language experience shapes predictive coding of rhythmic sound sequences
Authors: Morucci Piermatteo , Nara Sanjeev , Lizarazu Mikel , Martin Clara , Molinaro Nicola
Published: April 2023

Perceptual systems heavily rely on prior knowledge and predictions to make sense of the environment. Predictions can originate from multiple sources of information, including contextual short-term priors, based on isolated temporal situations, and context-independent long-term priors, arising from extended exposure to statistical regularities. While the effects of short-term predictions on auditory perception have been well-documented, how long-term predictions shape early auditory processing is poorly understood. To address this, we recorded magnetoencephalography data from native speakers of two languages with different word orders (Spanish: functor-initial versus Basque: functor-final) listening to simple sequences of binary sounds alternating in duration with occasional omissions. We hypothesized that, together with contextual transition probabilities, the auditory system uses the characteristic prosodic cues (duration) associated with the native language’s word order as an internal model to generate long-term predictions about incoming non-linguistic sounds. Consistent with our hypothesis, we found that the amplitude of the mismatch negativity elicited by sound omissions varied orthogonally depending on the speaker’s linguistic background and was most pronounced in the left auditory cortex. Importantly, listening to binary sounds alternating in pitch instead of duration did not yield group differences, confirming that the above results were driven by the hypothesized long-term “duration” prior. These findings show that experience with a given language can shape a fundamental aspect of human perception – the neural processing of rhythmic sounds – and provides direct evidence for a long-term predictive coding system in the auditory cortex that uses auditory schemes learned over a lifetime to process incoming sound sequences.
Long-Run Olfactory Enrichment Promotes Non-Olfactory Cognition, Noradrenergic Plasticity And Remodeling Of Brain Functional Connectivity In Aged Mice
Authors: Terrier Claire , Greco-Vuilloud Juliette , Cavelius Matthias , Thévenet Marc , Mandairon Nathalie , Didier Anne , Richard Marion
Published: April 2023

Normal brain aging is accompanied by functional and structural changes, leading to cognitive decline. A high level of cognitive stimulation during life is associated with improved cognitive performances in elderly, forming the so-called cognitive reserve whose cellular mechanisms remain largely unknown. Noradrenaline has been proposed as a molecular link between environmental stimulation and the constitution of the cognitive reserve. Taking advantage of the ability of olfactory stimulation to trigger noradrenaline release, we used repeated olfactory enrichment sessions distributed over the mouse lifespan to enable the cognitive reserve buildup. Mice submitted to lifelong olfactory enrichment whether started in early or late adulthood, displayed improved olfactory discrimination at late ages. Interestingly, benefits extended to spatial memory and cognitive flexibility and olfactory and non-olfactory cognitive performances correlated with increased noradrenergic innervation in the olfactory bulb and dorsal hippocampus. Finally, using c-Fos mapping and connectivity analysis, we reported task-specific remodeling of functional neural networks in aged mice with increased network specialization or enlargement in an olfactory discrimination or a spatial memory task respectively. We thus propose long-run olfactory enrichment as a mouse model of the cognitive reserve buildup relying on plasticity of the noradrenergic system and network remodeling to promote better cognitive aging.
Cholinergic activation of corticofugal circuits in the adult mouse prefrontal cortex
Authors: Gulledge Allan T.
Published: April 2023

In layer 5 of the neocortex, ACh promotes cortical output to the thalamus and brainstem by preferentially enhancing the postsynaptic excitability of pyramidal tract (PT) neurons relative to neighboring intratelencephalic (IT) neurons. Less is known about how ACh regulates the excitatory synaptic drive of IT and PT neurons. To address this question, spontaneous excitatory postsynaptic potentials (sEPSPs) were recorded in pairs of IT and PT neurons in slices of prelimbic cortex from adult female and male mice. ACh (20 µM) enhanced sEPSP amplitudes, frequencies, rise-times, and half-widths preferentially in PT neurons. These effects were blocked by the muscarinic acetylcholine receptor antagonist atropine (1 µM). When challenged with pirenzepine (1 µM), an antagonist selective for M1-type muscarinic receptors, ACh instead reduced sEPSP frequencies. The cholinergic increase in sEPSP amplitudes and frequencies in PT neurons was not sensitive to blockade of GABAergic receptors with gabazine (10 µM) and CGP52432 (2.5 µM), but was blocked by tetrodotoxin (1 µM), suggesting that ACh enhances action-potential-dependent excitatory synaptic transmission in PT neurons. ACh also preferentially promoted the occurrence of synchronous sEPSPs in pairs of PT neurons relative to IT-PT and IT-IT pairs. Finally, selective chemogenetic silencing of hM4Di-expressing PT, but not IT, neurons with clozapine-N-oxide (5 µM) blocked cholinergic enhancement of sEPSP amplitudes and frequencies in PT neurons. These data suggest that, in addition to enhancing the postsynaptic excitability of PT neurons, M1 receptor activation promotes corticofugal output by preferentially amplifying recurrent excitation within networks of PT neurons.
Prospective role of PAK6 and 14-3-3γ as biomarkers for Parkinson’s disease
Authors: Giusto Elena , Maistrello Lorenza , Iannotta Lucia , Giusti Veronica , Iovino Ludovica , Bandopadhyay Rina , Antonini Angelo , Bubacco Luigi , Barresi Rita , Plotegher Nicoletta , Greggio Elisa , Civiero Laura
Published: April 2023

2.

Background

Parkinson’s disease is a progressive neurodegenerative disorder mainly distinguished by sporadic aetiology, although a genetic component is also well established. Variants in theLRRK2gene are associated with both familiar and sporadic disease. We have previously shown that PAK6 and 14-3-3γ protein interact with and regulate the activity of LRRK2.

Objectives

The aim of this study is to quantify PAK6 and 14-3-3γ in plasma as a reliable biomarker strategy for the diagnosis of both sporadic and LRRK2-linked Parkinson’s disease.

Methods

After an initial quantification of PAK6 and 14-3-3γ expression by means of Western blot in post-mortem human brains, we verified the presence of the two proteins in plasma by using quantitative ELISA tests. We analysed samples obtained from 39 healthy subjects, 40 patients with sporadic Parkinson’s disease, 50 LRRK2-G2019S non-manifesting carriers and 31 patients with LRRK2-G2019S Parkinson’s disease.

Results

The amount of PAK6 and 14-3-3γ is significantly different in patients with Parkinson’s disease compared to healthy subjects. Moreover, the amount of PAK6 also varies with the presence of the G2019S mutation in the LRRK2 gene. Although the generalized linear models show a low association between the presence of PD and PAK6, the kinase can be added in a broader panel of biomarkers for the diagnosis of Parkinson’s disease.

Conclusions

Changes of PAK6 and 14-3-3γ amount in plasma represent a shared readout for patients affected by sporadic and LRRK2-linked Parkinson’s disease. Overall, they can contribute to the establishment of an extended panel of biomarkers for the diagnosis of Parkinson’s disease.
Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex
Authors: Piet Alex , Ponvert Nick , Ollerenshaw Douglas , Garrett Marina , Groblewski Peter A. , Olsen Shawn , Koch Christof , Arkhipov Anton
Published: April 2023

In complex environments, animals can adopt diverse strategies to find rewards. How distinct strategies differentially engage brain circuits is not well understood. Here we investigate this question, focusing on the cortical Vip-Sst disinhibitory circuit. We characterize the behavioral strategies used by mice during a visual change detection task. Using a dynamic logistic regression model we find individual mice use mixtures of a visual comparison strategy and a statistical timing strategy. Separately, mice also have periods of task engagement and disengagement. Two-photon calcium imaging shows large strategy dependent differences in neural activity in excitatory, Sst inhibitory, and Vip inhibitory cells in response to both image changes and image omissions. In contrast, task engagement has limited effects on neural population activity. We find the diversity of neural correlates of strategy can be understood parsimoniously as increased activation of the Vip-Sst disinhibitory circuit during the visual comparison strategy which facilitates task appropriate responses.
Repeated MRI scans of the human brain: diurnal oscillations in healthy adults and bipolar disorder patients
Authors: Carlucci Matthew , Lett Tristram , Chavez Sofia , Malinowski Alexandra , Lobaugh Nancy J. , Petronis Art
Published: April 2023

Regulation of biological processes according to a 24-hr rhythm is essential for the normal functioning of an organism. Temporal variation in brain MRI data has often been attributed to circadian or diurnal oscillations; however, it is not clear if such oscillations exist. We provide the first evidence that diurnal oscillations indeed govern multiple MRI metrics. We recorded cerebral blood flow, diffusion-tensor metrics, T1 relaxation, and cortical structural features every three hours over a 24-hr period in each of 16 male controls and eight male bipolar disorder patients. Diurnal oscillations were detected in numerous MRI metrics at the whole-brain level, and regionally. Rhythmicity parameters in the bipolar disorder patients were similar to the controls for most metrics, except for a larger phase variation in cerebral blood flow. The ubiquitous nature of diurnal oscillations has broad implications for neuroimaging studies and furthers our understanding of the dynamic nature of the human brain.
Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning
Authors: Castellani Marco , Zhang Meng , Thangavel Gokilavani , Mata Sucre Yennifer , Lux Thomas , Campoy José A. , Marek Magdalena , Huettel Bruno , Sun Hequan , Mayer Klaus F. X. , Schneeberger Korbinian , Marques André
Published: April 2023

Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics influencing the overall distribution and frequency of crossovers. Here, we studied how recombination is regulated and distributed in the holocentric plantRhynchospora breviuscula, a species lacking localised centromeres. Combining immunocytochemistry, chromatin analysis and high-throughput single-pollen sequencing, we discovered that crossover frequency is higher at ends related to centred chromosomal regions. Contrasting the diffused distribution of (epi)genetic features and hundreds of repeat-based centromeric units. Remarkably, we found that crossovers were abolished at core centromeric units but not at their vicinity indicating the absence of a centromere effect across repeat-based holocentromeres. We further show that telomere-led pairing and synapsis of homologous chromosomes appear to be the primary force determining the observed U-shaped recombination landscape. While centromere and (epi)genetic properties only affect crossover positioning locally. Our results suggest that the conserved U-shaped crossover distribution of eukaryotes is independent of chromosome compartmentalisation and centromere organisation.
Basolateral amygdala oscillations enable fear learning in a biophysical model
Authors: Cattani Anna , Arnold Don B , McCarthy Michelle , Kopell Nancy
Published: April 2023

The basolateral amygdala (BLA) is a key site where fear learning takes place through synaptic plasticity. Rodent research shows prominent low theta (∼3-6 Hz), high theta (∼6-12 Hz), and gamma (>30 Hz) rhythms in the BLA local field potential recordings. However, it is not understood what role these rhythms play in supporting the plasticity. Here, we create a biophysically detailed model of the BLA circuit to show that several classes of interneurons (PV, SOM, and VIP) in the BLA can be critically involved in producing the rhythms; these rhythms promote the formation of a dedicated fear circuit shaped through spike-timing-dependent plasticity. Each class of interneurons is necessary for the plasticity. We find that the low theta rhythm is a biomarker of successful fear conditioning. The model makes use of interneurons commonly found in the cortex and, hence, may apply to a wide variety of associative learning situations.

Significance

Our paper accounts for the experimental evidence showing that amygdalar rhythms exist, suggests network origins for these rhythms, and points to their central role in the mechanisms of plasticity involved in associative learning. It is one of the few papers to address high-order cognition with biophysically detailed models, which are sometimes thought to be too detailed to be adequately constrained. Our paper provides a template for how to use information about brain rhythms to constrain biophysical models. It shows in detail, for the first time, how multiple interneurons help to provide time scales necessary for some kinds of spike-timing-dependent plasticity (STDP). It spells out the conditions under which such interactions between interneurons are needed for STDP and why. Finally, our work helps to provide a framework by which some of the discrepancies in the fear learning literature might be reevaluated. In particular, we discuss issues about Hebbian plasticity in fear learning; we show in the context of our model how neuromodulation might resolve some of those issues. The model addresses issues more general than that of fear learning since it is based on interactions of interneurons that are prominent in the cortex, as well as the amygdala.
Data-based large-scale models provide a window into the organization of cortical computations
Authors: Chen Guozhang , Scherr Franz , Maass Wolfgang
Published: April 2023

The neocortex of the brain is one of the most powerful computing devices that exists, but it remains largely open how its computations are organized. Since the neocortex is a 2D tapestry consisting of repeating stereotypical local cortical microcircuits, a key step for solving this problem is to understand how cortical microcircuits compute. We know by now a lot about their connectivity structure and their neuron types, but we are lacking tools for elucidating causal relations between this structure and their computational function. We present a new tool for elucidating this relation: We train large-scale models of cortical microcircuits, which integrate most current knowledge about their structure, for carrying out similar computational tasks as in the brain. We show that the trained model achieves a similar computational performance as the brain, and that it reproduces experimentally found traits of cortical computation and coding that do not appear in neural network models from AI. Furthermore, we reverse-engineer how computations are organized in the model, thereby producing specific hypotheses that can be tested in experimental neuroscience. Altogether we show that cortical microcircuits provide a distinct new neural network paradigm that is of particular interest for neuromorphic engineering because it computes with highly energy-efficient sparse activity.

Teaser

Reverse engineering of cortical computations
Brucellatargets host USP8 through the effector protein TcpB to facilitate infection of macrophages
Authors: Radhakrishnan Girish , Joshi Kiranmai , Mujumdar Varad
Published: April 2023

Brucellaspecies are Gram-negative intracellular bacterial pathogens that cause the worldwide zoonotic disease brucellosis.Brucellacan infect many mammals, including humans and domestic and wild animals.Brucellamanipulates various host cellular processes to invade and multiply in professional and non-professional phagocytic cells. However, the host targets and their modulation byBrucellato facilitate the infection process remain obscure. Here, we report that the host Ubiquitin Specific Protease, USP8 negatively regulates the invasion ofBrucellainto macrophages through the plasma membrane receptor, CXCR4.Brucellasuppressed the expression of USP8 at its early stage of infection in the infected macrophages. Subsequent studies revealed that theBrucellaeffector protein, TIR-domain containing protein fromBrucella, TcpB plays a significant role in downregulating the expression of USP8 by targeting the CREB pathway. Treatment of mice with USP8 inhibitor resulted in enhanced survival ofB. melitensis,whereas mice treated with CXCR4 or 14-3-3 antagonist showed a diminished bacterial load. Our experimental data demonstrate a novel role of USP8 in the host defence against microbial intrusion and microbial subversion of host defences.
Cerebellar state estimation enables resilient coupling across behavioural domains
Authors: Palacios Ensor Rafael , Chadderton Paul , Friston Karl , Houghton Conor
Published: April 2023

Cerebellar computations are necessary for fine behavioural control and are thought to rely on internal probabilistic models performing state estimation. We propose that the cerebellum infers how states contextualise (i.e., interact with) each other, and coordinates extra-cerebellar neuronal dynamics underpinning a range of behaviours. To support this claim, we describe a cerebellar model for state estimation that includes states interactions, and link the underlying inference with the neuronal architecture and dynamics observed empirically. This is formalised using the free energy principle, which provides a dual perspective on a system in terms of both the dynamics of its physical – in this case neuronal – states, and the inference process they entail. As a proof of principle, we simulate cerebellar-dependent synchronisation of whisking and respiration, which are known to be tightly coupled in rodents. In summary, we suggest that cerebellar-dependent contextualisation of behaviour can explain its ubiquitous involvement in most aspects of behaviour.
Sensorimotor Confidence for Tracking Eye Movements
Authors: Goettker Alexander , Locke Shannon M. , Gegenfurtner Karl R. , Mamassian Pascal
Published: April 2023

For successful interactions with the world, we often have to evaluate our own performance. Such metacognitive evaluations have been studied with perceptual decisions, but much less with respect to the evaluation of our own actions. While eye movements are one of the most frequent actions we perform, we are typically unaware of them. Here, we investigated if there is any evidence for metacognitive sensitivity for the accuracy of eye movements. Participants tracked a dot cloud as it followed an unpredictable sinusoidal trajectory for six seconds, and then reported if they thought their performance was better or worse than their average tracking performance. Our results show above chance identification of better tracking behavior across all trials and also for repeated attempts of the same target trajectories. While the sensitivity in discriminating performance between better and worse trials was stable across sessions, for their judgements participants relied more on performance in the final seconds of each trial. This behavior matched previous reports when judging the quality of hand movements, although overall metacognitive sensitivity for eye movements was significantly lower. Together, these results provide an additional piece of evidence for sensorimotor confidence, and open interesting questions about why it differs across actions and how it could be related to other instances of confidence.

Statement of Relevance

In everyday life, it is often critical to be able to evaluate the quality of our own cognitive decisions and actions. However, one of our most frequent actions often does not even reach our awareness: eye movements. We investigated whether observers were able to successfully judge the accuracy of their eye movements when tracking a cloud of dots that followed an unpredictable trajectory. We found that observers were able to distinguish good from bad trials, although sensitivity was lower compared to equivalent previous reports when judging the quality of hand movements. These results add an item to the growing list of our metacognitive abilities, but critically for eye movements that we are typically unaware of. They lead to important novel questions about why metacognitive abilities differ across decisions or different types of actions, and what the potential components of metacognitive abilities might be.
Replication elongates short DNA, reduces sequence bias, and develops trimer structure
Authors: Serrão Adriana Calaça , Dänekamp Felix T. , Meggyesi Zsófia , Braun Dieter
Published: April 2023

The origin of molecular evolution required the replication of short oligonucleotides to form longer polymers. Prebiotically plausible oligonucleotide pools tend to contain more of some nucleotide bases than others. It has been unclear whether this initial bias persists and how it affects replication. To investigate this, we examined the evolution of 12 mer biased short DNA pools during enzymatic templated polymerization. Our analysis using next-generation sequencing from different time points revealed that the initial nucleotide bias of the pool disappeared in the elongated pool after isothermal replication. In contrast, the nucleotide composition at each position in the elongated sequences remained biased and varied with both position and initial bias. Furthermore, we observed the emergence of highly periodic dimer and trimer motifs in the rapidly elongated sequences. This shift in nucleotide composition and the emergence of structure through templated replication could help explain how biased prebiotic pools could undergo molecular evolution and lead to complex functional nucleic acids.
Fluctuation dominated ligand binding in molten globule protein
Authors: Moulick Abhik Ghosh , Chakrabarti J.
Published: April 2023

A molten globule (MG) state is an intermediate state of protein observed during the unfolding of the native structure. In MG states, milk proteinα-Lactalbumin (aLA) binds to oleic acid (OLA). This MG-aLA-OLA complex, popularly known as XAM-LET performs cytotoxic activities against cancer cell lines. However, the microscopic understanding of ligand recognition ability in MG state of protein is not yet explored. Motivated by this, we explore binding of bovine aLA with OLA (BAMLET) using all atom molecular dynamics(MD) simulations. We find the binding mode between MG-aLA and OLA using the conformational thermodynamics method. We also estimate the binding free energy using the umbrella sampling (US) method for both MG state and neutral state. We find that the binding free energy obtained from US is comparable with earlier experimental results. We characterize the dihedral fluctuations as the ligand is liberated from the active site of the protein using steered molecular dynamics. The long-live fluctuations occur near the ligand binding site, which eventually transfers towards Ca2+binding site as the ligand is taken away from the protein.

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Removal of a genomic duplication by double-nicking CRISPR restores synaptic transmission and behavior in the MyosinVA mutant mouse Flailer
Authors: Bustos Fernando J , Pandian Swarna , Haensgen Henny , Zhao Jian-Ping , Strouf Haley , Heidenreich Matthias , Swiech Lukasz , Deverman Benjamin , Gradinaru Viviana , Zhang Feng , Constantine-Paton Martha
Published: April 2023

Copy number variations, and particularly duplications of genomic regions, have been strongly associated with various neurodegenerative conditions including autism spectrum disorder (ASD). These genetic variations have been found to have a significant impact on brain development and function, which can lead to the emergence of neurological and behavioral symptoms. Developing strategies to target these genomic duplications has been challenging, as the presence of endogenous copies of the duplicate genes often complicates the editing strategies. Using the ASD and anxiety mouse model Flailer, that contains a duplication working as a dominant negative for MyoVa, we demonstrate the use of DN-CRISPRs to remove a 700bp genomic duplicationin vitroandin vivo. Importantly, DN-CRISPRs have not been used to remove more gene regions <100bp successfully and with high efficiency. We found that editing theflailergene in primary cortical neurons reverts synaptic transport and transmission defects. Moreover, long-term depression (LTD), disrupted in Flailer animals, is recovered after gene edition. Delivery of DN-CRISPRsin vivoshows that local delivery to the ventral hippocampus can rescues some of the mutant behaviors, while intracerebroventricular delivery, completely recovers Flailer animal phenotype associated to anxiety and ASD. Our results demonstrate the potential of DN-CRISPR to efficiently (>60% editingin vivo) removelarge genomic duplications, working as a new gene therapy approach for treating neurodegenerative diseases.
Post-translational modification of SPATULA by SECRET AGENT and SPINDLY promotes organ symmetry transition at the gynoecium apex
Authors: Jiang Yuxiang , Curran-French Seamus , Koh Samuel W.H. , Jamil Iqra , Argirò Luca , Lopez Sergio , Martins Carlo , Saalbach Gerhard , Moubayidin Laila
Published: April 2023

The establishment of organ symmetry during multicellular development is a fundamental process shared by most living organisms. Here, we investigated how twoO-glycosyltransferases ofArabidopsis thaliana, SPINDLY (SPY) and SECRET AGENT (SEC) synergistically promote a rare bilateral-to-radial symmetry transition during patterning of the plant reproductive organ, the gynoecium. SPY and SEC modify N-terminal residues of the bHLH transcription factor SPATULA (SPT)in vivoandin vitroby attachingO-fucose andO-linked-β-N-Acetylglucosamine (O-GlcNAc), to promote style development. This post-translational regulation does not impact SPT homo- and hetero-dimerisation events with INDEHISCENT (IND) and HECATE 1 (HEC1), although it enhances the affinity of SPT for the kinasePINOID(PID) gene locus to promote transcriptional repression. Our findings reveal a previously unrecognized mechanism forO-GlcNAc andO-fucose post-translational decorations in controlling style development and offer the first molecular example of a synergistic role for SEC and SPY in plant post-embryonic organ patterning.
Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease
Authors: Choi Doo Eun , Shin Jun Wan , Zeng Sophia , Hong Eun Pyo , Jang Jae-Hyun , Loupe Jacob M. , Wheeler Vanessa C. , Stutzman Hannah E. , Kleinstiver Benjamin P. , Lee Jong-Min
Published: April 2023

An expanded CAG repeat in the huntingtin gene (HTT) causes Huntington’s disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and gRNAs efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without alteringHTTmRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion base editing strategies in HD and potentially other repeat expansion disorders.
Tasting to preserve: An educational activity to promote children’s positive attitudes towards intraspecific diversity conservation
Authors: Pessoa Patrícia , Aboim Sara , Afonso Lisa , Lopes J. Bernardino , Sá-Pinto Xana
Published: April 2023

On the edge of causing the sixth big mass extinction event, the development of positive attitudes towards the conservation of intraspecific diversity from early ages is essential to overcome the biodiversity crisis we currently face. However, there is no information available on elementary school students’ attitudes toward intraspecific diversity conservation nor is there a framework available to perform such analysis. For this study we designed, implemented, and evaluated an educational activity planned for third graders (8 to 13 years old) to explore the intraspecific diversity of vegetables and to promote healthy eating habits. Additionally, a framework was developed to evaluate students’ attitudes towards intraspecific diversity conservation and applied to semi-structured interviews conducted with students before and after engaging in the educational activity. In this paper we present a reliable framework, developed aligned with the ABC model of attitudes, based on literature, and adapted to elementary school students’ responses, to evaluate students’ attitudes toward intraspecific diversity. Our results show that, before the educational activity, most students choose a non-biodiverse option, justifying this choice with the affective component of attitudes: mostly emotional factors but also aesthetic and social/cultural factors. After the educational activity, we observed a significant increase in the frequency of students that choose the biodiverse option and that justified it with the cognitive component of attitudes: mainly with biology and health knowledge factors, but also with economic and ethical knowledge factors. Our findings support the positive impact of educational activities that explore vegetable varieties on students’ attitudes toward intraspecific diversity conservation.
Tryptophan-based motifs in the LLP3 Region of the HIV-1 envelope glycoprotein cytoplasmic tail direct trafficking to the endosomal recycling compartment and mediate particle incorporation
Authors: Lerner Grigoriy , Ding Lingmei , Spearman Paul
Published: April 2023

The HIV-1 envelope glycoprotein complex (Env) is incorporated into developing particles at the plasma membrane (PM). The cytoplasmic tail (CT) of Env is known to play an essential role in particle incorporation, while the exact mechanisms underlying this function of the CT remain uncertain. Upon reaching the PM, trafficking signals in the CT interact with host cell endocytic machinery, directing Env into endosomal compartments within the cell. Prior studies have suggested that Env must traffic through the endosomal recycling compartment (ERC) in order for Env to return to the plasma membrane (PM) site of particle assembly. Expression of a truncated form of the ERC-resident trafficking adaptor Rab11-Family Interacting Proteins C (FIP1C) resulted in CT-dependent sequestration of Env in the condensed ERC, preventing recycling of Env to the PM. In this work, the motifs within the CT responsible for ERC localization of Env were systematically mapped. A small deletion encompassing the N-terminal portion of LLP3 eliminated ERC localization. Site-directed mutagenesis identified two tryptophan-based motifs (WE790-791and WW796-797) within the N-terminus of LLP3 that were essential for ERC localization of Env. Mutant viruses bearing substitutions in these motifs were deficient in Env incorporation, with a corresponding loss of particle infectivity and a significant defect in replication in a spreading infection assay. These results identify two tryptophan-based motifs at the N-terminal portion of LLP3 that mediate ERC localization and Env incorporation, providing additional supporting evidence for the importance of cellular recycling pathways in HIV-1 particle assembly.

IMPORTANCE

The HIV-1 envelope glycoprotein (Env) is an essential component of the virus, and has an exceedingly long cytoplasmic tail (CT). Previous studies have suggested that trafficking signals in the CT interact with host factors to regulate the incorporation of Env into particles. One particular area of interest is termed lentiviral lytic peptide 3 (LLP3), as small deletions in this region have been shown to disrupt Env incorporation. In this study, we identify a small region within LLP3 that regulates how Env associates with cellular recycling compartments. Mutants that reduced or eliminated Env from the recycling compartment also reduced Env incorporation into particles. These findings emphasize the importance of two tryptophan motifs in LLP3 to the incorporation of Env into particles, and provide additional support for the idea that the CT interacts with host recycling pathways to determine particle incorporation.
Functional redundancy revealed by the deletion of the mimivirus GMC-oxidoreductase genes
Authors: Alempic Jean-Marie , Bisio Hugo , Villalta Alejandro , Santini Sébastien , Lartigue Audrey , Schmitt Alain , Bugnot Claire , Notaro Anna , Belmudes Lucid , Adrait Annie , Poirot Olivier , Ptchelkine Denis , De Castro Cristina , Couté Yohann , Abergel Chantal
Published: April 2023

The mimivirus 1.2Mb genome was shown to be organized into a nucleocapsid-like genomic fiber encased in the nucleoid compartment inside the icosahedral capsid (1). The genomic fiber protein shell is composed of a mixture of two GMC-oxidoreductase paralogs, one of them being the main component of the glycosylated layer of fibrils at the surface of the virion (2). In this study, we determined the effect of the deletion of each of the corresponding genes on the genomic fiber and the layer of surface fibrils. First, we deleted the GMC-oxidoreductase the most abundant in the genomic fiber, and determined its structure and composition in the mutant. As expected, it was composed of the second GMC-oxidoreductase and contained 5- and 6-start helices similar to the wild-type fiber. This result led us to propose a model explaining their coexistence. Then, we deleted the GMC-oxidoreductase the most abundant in the layer of fibrils to analyze its protein composition in the mutant. Second, we showed that the fitness of single mutants and the double mutant were not decreased compared to the wild-type viruses in laboratory conditions. Third, we determined that deleting the GMC-oxidoreductase genes did not impact the glycosylation or the glycan composition of the layer of surface fibrils, despite modifying their protein composition. Since the glycosylation machinery and glycan composition of members of different clades are different (3, 4), we expanded the analysis of the protein composition of the layer of fibrils to members of the B and C clades and showed that it was different among the three clades and even among isolates within the same clade. Taken together, the results obtained on two distinct central processes (genome packaging and virion coating) illustrate an unexpected functional redundancy in members of the familyMimiviridae, suggesting this may be the major evolutionary force behind their giant genomes.

One-Sentence Summary

Functional redundancy preserves mimivirus genomic fiber and layer of fibrils formation.
Genetic context controls early microglia-synaptic interactions in mouse models of Alzheimer’s disease
Authors: Heuer Sarah E. , Keezer Kelly J. , Hewes Amanda A. , Onos Kristen D. , Graham Kourtney C. , Howell Gareth R. , Bloss Erik B.
Published: April 2023

Common features of Alzheimer’s disease (AD) include amyloid pathology, microglia activation and synaptic dysfunction, however, the causal relationships amongst them remains unclear. Further, human data suggest susceptibility and resilience to AD neuropathology is controlled by genetic context, a factor underexplored in mouse models. To this end, we leveraged viral strategies to label an AD-vulnerable neuronal circuit in CA1 dendrites projecting to the frontal cortex in genetically diverse C57BL/6J (B6) and PWK/PhJ (PWK)APP/PS1mouse strains and used PLX5622 to non-invasively deplete brain microglia. Reconstructions of labeled neurons revealed microglia-dependent changes in dendritic spine density and morphology in B6 wild-type (WT) andAPP/PS1yet a marked stability of spines across PWK mice. We further showed that synaptic changes depend on direct microglia-dendrite interactions in B6.APP/PS1but not PWK.APP/PS1mice. Collectively, these results demonstrate that microglia-dependent synaptic alterations in a specific AD-vulnerable projection pathway are differentially controlled by genetic context.
The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities
Authors: Wang Miaoxiao , Chen Xiaoli , Fang Yuan , Zheng Xin , Huang Ting , Nie Yong , Wu Xiao-Lei
Published: April 2023

In microbial systems, a metabolic pathway can be either completed by one autonomous population or alternatively be distributed among a consortium performing metabolic division of labor (MDOL), where several specialized populations cooperate to complete the pathway. MDOL facilitates the system’s function by reducing the metabolic burden; however, it may also hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the metabolic efficiency of a community is influenced by trade-offs between the metabolic specialization and versatility of individuals, with the latter potentially introducing metabolic redundancy into the community. However, it remains unclear how metabolic specialization and versatility of the individuals involved can be controlled in order to optimize the function of the community. In this study, we deconstructed the metabolic pathway of naphthalene degradation into four specialized steps and introduced them individually or combinatorically into different strains, with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia with varying levels of metabolic redundancy and tested their naphthalene degradation efficiency. We found that 74 consortia possessing metabolic redundancy exhibited higher degradation efficiency than both the autonomous population and the rigorous MDOL community. Quantitative modeling derived from our experiments provides general strategies for identifying the most effective MDOL consortium with functional redundancy (MCFR) from a range of possible MCFRs. Our large-scale genomic analysis suggests that natural communities for hydrocarbon degradation are mostly functionally redundant. In summary, our study provides critical insights into the engineering of high-performance microbial systems and explains why functional redundancy is prevalent in natural microbial communities.