bluuebunny/crossref_metadata_2025 huggingface dataset:
A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii
Authors: Gupta Purav , Hiller Aiden , Chowdhury Jawad , Lim Declan , Lim Dillon Yee , Saeij Jeroen P.J. , Babaian Artem , Rodriguez Felipe , Pereira Luke , Morales Alex
Published: September 2023

We are entering a “Platinum Age of Virus Discovery”, an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally-assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health.

From a computational viral screen of human neuronal datasets, we identified a novel narnavirusApocryptovirus odysseus(Ao) which likely infects the neurotropic parasiteToxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we presentin silicoevidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected byT. gondii.T. gondiiinfects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically-proximal viruses to Ao and discovered 19Apocryptovirusspecies, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While the Narnavirus samples making up this genus-like clade are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic (Apicomplexa) nucleic acid co-occurrence, supporting that these are a clade of parasite-infecting viruses.

This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict this highly diverged Ao RNA virus is biologically aT. gondiiinfection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.
A meta-analysis of bulk RNA-seq datasets identifies potential biomarkers and repurposable therapeutics against Alzheimer’s disease
Authors: Lamisa Anika Bushra , Ahammad Ishtiaque , Bhattacharjee Arittra , Hossain Mohammad Uzzal , Ishtiaque Ahmed , Chowdhury Zeshan Mahmud , Das Keshob Chandra , Salimullah Md , Keya Chaman Ara
Published: September 2023

Alzheimer’s disease (AD) poses a major challenge due to its impact on the elderly population and the lack of effective early diagnosis and treatment options. In an effort to address this issue, a study focused on identifying potential biomarkers and therapeutic agents for AD was carried out. Using RNA-Seq data from AD patients and healthy individuals, 12 differentially expressed genes (DEGs) were identified, with 9 expressing upregulation (ISG15, HRNR, MTATP8P1, MTCO3P12, DTHD1, DCX, ST8SIA2, NNAT,andPCDH11Y) and 3 expressing downregulation (LTF, XIST,andTTR). Among them,TTRexhibited the lowest gene expression profile. Interestingly, functional analysis tiedTTRto amyloid fiber formation and neutrophil degranulation through enrichment analysis. These findings suggested the potential ofTTRas a diagnostic biomarker for AD. Additionally, druggability analysis revealed that the FDA-approved drug Levothyroxine might be effective against the Transthyretin protein encoded by theTTRgene. Molecular docking and dynamics simulation studies of Levothyroxine and Transthyretin suggested that this drug could be repurposed to treat AD. However, additional studies using in vitro and in vivo models are necessary before these findings can be applied in clinical applications.
Field performance and cost-effectiveness of a point-of-care triage test for HIV virological failure in Southern Africa
Authors: Saura-Lázaro Anna , Bock Peter , van den Bogaart Erika , van Vliet Jessie , Granés Laura , Nel Kerry , Naidoo Vikesh , Scheepers Michelle , Saunders Yvonne , Leal Núria , Ramponi Francesco , Paulussen René , de Wit Tobias Rinke , Naniche Denise , López-Varela Elisa
Published: September 2023

Introduction

Antiretroviral therapy (ART) monitoring using viral load (VL) testing is challenging in high-burden, limited-resources settings. Chemokine IP-10 (interferon gamma-induced protein 10) strongly correlates with human immunodeficiency virus (HIV) VL. Its determination could serve to predict virological failure (VF) and to triage patients requiring VL testing. We assessed the field performance of a semi-quantitative IP-10 lateral flow assay (LFA) for VF screening in South Africa, and the cost-effectiveness of its implementation in Mozambique.

Methods

A cross-sectional study was conducted between June and December 2021 in three primary health clinics in the Western Cape. Finger prick capillary blood was collected from adults on ART for ≥1 year for direct application onto the IP-10 LFA (index test) and compared with a plasma VL result ≤1 month prior (reference test). We estimated the area under the receiver operating characteristic curves (AUC), sensitivity and specificity, to evaluate IP-10 LFA prediction of VF (VL>1,000 copies/mL). A decision tree model was used to investigate the cost-effectiveness of integrating IP-10 LFA combined with VL testing into the current Mozambican ART monitoring strategy. Averted disability-adjusted life years (DALYs) and HIV infections, and incremental cost-effectiveness ratios were estimated.

Results

Among 209 participants (median age 38 years and 84% female), 18% had VF. Median IP-10 LFA values were higher among individuals with VF compared to those without (24.0 vs. 14.6; p<0.001). The IP-10 LFA predicted VF with an AUC=0.76 (95% confidence interval (CI) 0.67–0.85), 91.9% sensitivity (95%CI 78.1%–98.3%) and 35.1% specificity (95%CI 28.0%– 42.7%). Integrating the IP-10 LFA in a setting with 20% VF prevalence and 61% VL testing coverage could save 13.0% of costs and avert 14.9% of DALYs and 55.7% new HIV infections. Furthermore, its introduction was estimated to reduce the total number of routine VL tests required for ART monitoring by up to 68%.

Conclusions

The IP-10 LFA is an effective VF triage test for routine ART monitoring. Combining a highly sensitive, low-cost IP-10 LFA-based screening with targeted VL confirmatory testing could result in significant healthcare quality improvements and cost savings in settings with limited access to VL testing.
Improved Detection of Decreased Glucose Handling Capacities via Novel Continuous Glucose Monitoring-Derived Indices: AC_Mean and AC_Var
Authors: Sugimoto Hikaru , Hironaka Ken-ichi , Nakamura Tomoaki , Yamada Tomoko , Miura Hiroshi , Otowa-Suematsu Natsu , Fujii Masashi , Hirota Yushi , Sakaguchi Kazuhiko , Ogawa Wataru , Kuroda Shinya
Published: September 2023

Background

Efficiently detecting impaired glucose control abilities is a pivotal challenge in public health. This study assessed the utility of relatively easy-to-measure continuous glucose monitoring (CGM)-derived indices in estimating glucose handling capacities calculated from resource-intensive clamp tests.

Methods

We conducted a prospective, single-center, observational cohort study of 64 individuals without prior diabetes diagnosis. The study utilized CGM, oral glucose tolerance test, and hyperglycemic and hyperinsulinemic-euglycemic clamp tests. We validated CGM-derived indices characteristics using an independent dataset and mathematical model with simulated data.

Findings

A novel CGM-derived index, AC_Var, was significantly correlated with insulin sensitivity (r = –0.31; 95% CI: –0.52 to –0.06), insulin clearance (r = –0.31; 95% CI: –0.54 to –0.06), and disposition index (DI) (r = –0.31; 95% CI: –0.52 to –0.07) calculated from clamp tests.

AC_Var was also significantly correlated with insulin resistance (r = 0.48; 95% CI: 0.23 to 0.68) in an independent dataset. Multivariate analyses indicated AC_Var’s contribution to predicting reduced blood glucose control abilities independent from conventional CGM-derived indices. The prediction model’s accuracy utilizing CGM-measured glucose standard deviation and AC_Var as input variables, with clamp-derived DI as the outcome, closely matched that of predicting clamp- from OGTT-derived DI. Mathematical simulations also underscored AC_Var’s association with insulin clearance and DI.

Interpretation

CGM-derived indices, including AC_Var, can be useful for screening decreased blood glucose control ability. We developed a web application that calculates these indices (https://cgm-ac-mean-std.streamlit.app/).

Funding

The Japan Society for the Promotion of Science KAKENHI, CREST, Japan Science and Technology Agency, and Uehara Memorial Foundation.
A Breath-Based In Vitro Diagnostics for Lower Respiratory Tract Infection
Authors: Chen Dapeng , Mirski Marek A , Caton Emily R , Kiser Kiana M , Haddaway Caroline R , Cetta Maximilian S , Chen Shuo , Bryden Wayne A , McLoughlin Michael
Published: September 2023

Lower Respiratory Tract Infections (LRTIs) represent the leading cause of death due to infectious diseases. Current diagnostic modalities primarily depend on clinical symptoms and lack specificity, especially in light of common colonization without overt infection. To address this, we developed a noninvasive diagnostic approach that employs BreathBiomicsTM, an advanced human breath sampling system, to detect protease activities induced by bacterial infection in the lower respiratory tract. Specifically, we engineered a high-sensitivity and high-specificity molecular sensor for human neutrophil elastase (HNE). The sensor undergoes cleavage in the presence of HNE, an event that is subsequently detected via Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS). Application of this methodology to clinical samples, breath specimens collected from intubated patients with LRTIs, demonstrated the detection of the cleaved sensor by MALDI-TOF MS. Our findings indicate that this novel approach offers a noninvasive and specific diagnostic strategy for people with LRTIs.
Southern Ethiopian skilled birth attendant variations and maternal mortality: a multilevel study of a population-based cross-sectional household survey
Authors: Kea Aschenaki Zerihun , Lindtjorn Bernt , Tekle Achamyelesh Gebretsadik , Hinderaker Sven Gudmund
Published: September 2023

Introduction

Studies examining skilled birth attendants (SBA) use and its correlation with maternal mortality at lower administrative levels are scarce. This study assessed the coverage and variations of SBA, the physical accessibility of health facilities for SBA, and the association of SBA with maternal mortality.

Materials and methods

A cross-sectional study using a population-based household survey was conducted in six Sidama National Regional State, southern Ethiopia districts, from July 2019 to May 2020. Women who had given birth in the past two years prior to the study were included. Stata 15 and ArcGIS 10.4.1 were used for data analysis. A multilevel logistic regression analysis was conducted to assess the effect of the sampling units and identify factors independently associated with SBA. The association between SBA and maternal mortality was examined using data from a maternal mortality household survey.

Results

A total of 3191 women were interviewed. The coverage of SBA was 46.7%, with high variations in the districts. Thirty percent of SBA use was accounted for by the differences among the districts. One-third of the women travel more than two hours to access the nearest hospital. Districts with low coverage of SBA and located far away from the regional referral centre had high maternal mortality. Education of the mother, occupation of the husband, pregnancy-related complications, use of antenatal care, parity, and distance to the nearest hospital and health centre were associated with the use of SBA.

Conclusions

The coverage of SBA in the Sidama Region was low, with high variations in the districts. Low SBA use was associated with high maternal mortality. Due attention should be given to districts with low coverage of SBA and those located far away from the referral centre. Access to hospitals has to improve. All women should be encouraged to get antenatal care services.
NeuroMechFly v2, simulating embodied sensorimotor control in adultDrosophila
Authors: Wang-Chen Sibo , Stimpfling Victor Alfred , Lam Thomas Ka Chung , Özdil Pembe Gizem , Genoud Louise , Hurtak Femke , Ramdya Pavan
Published: September 2023

Discovering principles underlying the control of animal behavior requires a tight dialogue between experiments and neuromechanical models. Until now, such models, including NeuroMechFly for the adult fly,Drosophila melanogaster, have primarily been used to investigate motor control. Far less studied with realistic body models is how the brain and motor systems work together to perform hierarchical sensorimotor control. Here we present NeuroMechFly v2, a framework that expandsDrosophilaneuromechanical modeling by enabling visual and olfactory sensing, ascending motor feedback, and complex terrains that can be navigated using leg adhesion. We illustrate its capabilities by first constructing biologically inspired locomotor controllers that use ascending motor feedback to perform path integration and head stabilization. Then, we add visual and olfactory sensing to this controller and train it using reinforcement learning to perform a multimodal navigation task in closed loop. Finally, we illustrate more biorealistic modeling in two ways: our model navigates a complex odor plume using aDrosophilaodor taxis strategy, and it uses a connectome-constrained visual system network to follow another simulated fly. With this framework, NeuroMechFly can be used to accelerate the discovery of explanatory models of the nervous system and to develop machine learning-based controllers for autonomous artificial agents and robots.
The sterol transporter STARD3 transports sphingosine at ER-lysosome contact sites
Authors: Hempelmann Pia , Lolicato Fabio , Graziadei Andrea , Brown Ryan D. R. , Spiegel Sarah , Rappsilber Juri , Nickel Walter , Höglinger Doris , Jamecna Denisa
Published: September 2023

Sphingolipids are important structural components of membranes. Additionally, simple sphingolipids such as sphingosine are highly bioactive and participate in complex subcellular signaling. Sphingolipid deregulation is associated with many severe diseases including diabetes, Parkinson’s and cancer. Here, we focus on how sphingosine, generated from sphingolipid catabolism in late endosomes/lysosomes, is reintegrated into the biosynthetic machinery at the endoplasmic reticulum (ER). We characterized the sterol transporter STARD3 as a sphingosine transporter acting at lysosome-ER contact sites. Experiments featuring crosslinkable sphingosine probes, supported by unbiased molecular dynamics simulations, exposed how sphingosine binds to the lipid-binding domain of STARD3. Following the metabolic fate of pre-localized lysosomal sphingosine showed the importance of STARD3 and its actions at contact sites for the integration of sphingosine into ceramide in a cellular context. Our findings provide the first example of inter-organellar sphingosine transfer and pave the way for a better understanding of sphingolipid – sterol co-regulation.
Reconstructing creative thoughts: Hopfield Neural Networks
Authors: Checiu Denisa , Bode Mathias , Khalil Radwa
Published: September 2023

From a brain processing perspective, the perception of creative thinking is rooted in the underlying cognitive process, which facilitates exploring and cultivating novel avenues and problem-solving strategies. However, it is challenging to emulate the intricate complexity of how the human brain presents a novel way to uncover unique solutions. One potential approach to mitigate this complexity is incorporating creative cognition within the evolving artificial intelligence systems and associated neural models. Hopfield Neural Networks (HNN) are commonly acknowledged as a simplified neural model, renowned for their biological plausibility to store and retrieve information, specifically patterns of neurons. Therefore, we propose for the first time using HNN to generate a potential model that emulates specific cognitive processes of creative thinking based on generating meaningful links between seemingly disparate concepts.
Human brain state dynamics reflect individual neuro-phenotypes
Authors: Lee Kangjoo , Ji Jie Lisa , Fonteneau Clara , Berkovitch Lucie , Rahmati Masih , Pan Lining , Repovš Grega , Krystal John H. , Murray John D. , Anticevic Alan
Published: September 2023

Neural activity and behavior vary within an individual (states) and between individuals (traits). However, the mapping of state-trait neural variation to behavior is not well understood. To address this gap, we quantify moment-to-moment changes in brain-wide co-activation patterns derived from resting-state functional magnetic resonance imaging. In healthy young adults, we identify reproducible spatio-temporal features of co-activation patterns at the single subject level. We demonstrate that a joint analysis of state-trait neural variations and feature reduction reveal general motifs of individual differences, en-compassing state-specific and general neural features that exhibit day-to-day variability. The principal neural variations co-vary with the principal variations of behavioral phenotypes, highlighting cognitive function, emotion regulation, alcohol and substance use. Person-specific probability of occupying a particular co-activation pattern is reproducible and associated with neural and behavioral features. This combined analysis of statetrait variations holds promise for developing reproducible neuroimaging markers of individual life functional outcome.
Kappa opioid receptor activation induces epigenetic silencing of brain-derived neurotropic factor via HDAC5 in depression
Authors: Yadav Anubhav , Dogra Shalini , Kumar Boda Arun , Kumari Poonam , Kumar Ajeet , Dash Manish K , Yadav Prem N
Published: September 2023

Treatment-resistant depression (TRD) occurs in almost 50% of depressed patients. Central kappa opioid receptor (KOR) agonism has been demonstrated to induce depression and anxiety, while KOR antagonism alleviate depression like symptoms in rodent models and TRD in clinical studies. Previously, we have shown that sustained KOR activation leads to TRD-like phenotype in mice, and modulation of brain-derived neurotrophic factor (BDNF) expression in the prefrontal cortex (PFC) appears to be one of the molecular determinants of the antidepressant response. In the present study, we observed that sustained KOR activation by a selective agonist, U50488, selectively reduced theBdnftranscriptsII, IV, andBdnf CDS(protein-codingExon IX) in the PFC and cultured primary cortical neurons, which was blocked by selective KOR antagonist, norbinaltorphimine. Considering the crucial role of epigenetic pathways inBDNFexpression, we further investigated the role of various epigenetic markers in KOR induced BDNF downregulation in mice. We observed that treatment with U50488 resulted in selective and specific downregulation of acetylation at the 9th lysine residue of the histone H3 protein (H3K9ac) and upregulation of HDAC5 expression in the PFC. Further, using anti-H3K9ac and anti-HDAC5 antibodies in chromatin immune precipitation assay, we detected decreased enrichment of H3K9ac and increased HDAC5 binding atBdnf IIandIVtranscripts after U50488 treatment, which were blocked by a selective KOR antagonist, norbinaltorphimine. Further mechanistic studies using HDAC5 selective inhibitor, LMK235, in primary cortical neurons, and adeno-associated viral shRNA mediated HDAC5-knockdown in the PFC of mice, we demonstrated an essential role of HDAC5 in KOR-mediated reduction ofBdnfexpression in the PFC and depression-like symptoms in mice. These results suggest that KOR engages multiple pathways to induce depression-like symptoms in mice, and provide novel insights into the mechanisms by which activation of KOR regulates major depressive disorders.
A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin
Authors: Ho William , Seneviratne Janith A. , Glancy Eleanor , Eckersley-Maslin Melanie A.
Published: September 2023

Background

Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome occurs predominantly at promoters where it poises them for future transcriptional upregulation or terminal silencing. We know little of the dynamics, resolution, and regulation of this chromatin state outside of embryonic stem cells where it was first described. This is partly due to the technical challenges distinguishing bone-fide bivalent chromatin, where both marks are on the same nucleosome, from allelic or sample heterogeneity where there is a mix of H3K4me3-only and H3K27me3-only mononucleosomes.

Results

Here, we present a robust and sensitive method to accurately map genome-wide bivalent chromatin along with all necessary controls from as little as 2 million cells. We optimised and refined the sequential ChIP protocol which uses two sequential overnight immunoprecipitation reactions to robustly purify nucleosomes that are truly bivalent and contain both H3K4me3 and H3K27me3 modifications. Our method generates high quality genome-wide maps with strong peak enrichment and low background which can be analysed using standard bioinformatic packages. Using this method, we detect twice as many bivalent regions in mouse embryonic stem cells as previously identified, bringing the total number of bivalently marked gene promoters to 8,373. Furthermore, profiling Dppa2/4 knockout mouse embryonic stem cells which lose both H3K4me3 and H3K27me3 at approximately 10% of bivalent promoters, demonstrated the ability of our method to capture bivalent chromatin dynamics.

Conclusions

Our optimised sequential reChIP method enables high-resolution genome-wide assessment of bivalent chromatin together with all required controls in as little as 2 million cells. We share a detailed protocol and guidelines that will enable bivalent chromatin landscapes to be generated in a range of cellular contexts, greatly enhancing our understanding of bivalent chromatin and epigenetic plasticity beyond embryonic stem cells.
ESR1fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes
Authors: Yates Megan E. , Li Zheqi , Li Yiting , Guzolik Hannah , Wang Xiaosong , Liu Tiantong , Hooda Jagmohan , Atkinson Jennifer M. , Lee Adrian V. , Oesterreich Steffi
Published: September 2023

Breast cancer is a leading cause of female mortality and despite advancements in diagnostics and personalized therapeutics, metastatic disease largely remains incurable due to drug resistance. Fortunately, identification of mechanisms of therapeutic resistance have rapidly transformed our understanding of cancer evasion and is enabling targeted treatment regimens. When the druggable estrogen receptor (ER,ESR1), expressed in two-thirds of all breast cancer, is exposed to endocrine therapy, there is risk of somatic mutation development in approximately 30% of cases and subsequent treatment resistance. A more recently discovered mechanism of ER mediated endocrine resistance is the expression of ER fusion proteins. ER fusions, which retain the protein’s DNA binding domain, harborESR1exons 1-6 fused to an in-frame gene partner resulting in loss of the 3’ ER ligand binding domain (LBD). In this report we demonstrate that in no-special type (NST) and invasive lobular carcinoma (ILC) cell line models, ER fusion proteins exhibit robust hyperactivation of canonical ER signaling pathways independent of the ligand estradiol or anti-endocrine therapies such as Fulvestrant and Tamoxifen. We employ cell line models stably overexpressing ER fusion proteins with concurrent endogenous ER knockdown to minimize the influence of endogenous wildtype ER. Cell lines exhibited shared transcriptomic enrichment in pathways known to be drivers of metastatic disease, notably the MYC pathway. The heterogeneous 3’ fusion partners, particularly transcription factorsSOX9andYAP1, evoked varying degrees of transcriptomic and cistromic activity that translated into unique phenotypic readouts. Herein we report that cell line activity is subtype-, fusion-, and assay-specific suggesting that the loss of the LBD, the 3’ fusion partner, and the cellular landscape all influence fusion activity. Therefore, it will be critical to generate additional data on frequency of the ER fusions, in the context of the clinicopathological features of the tumor.

Significance

ER fusion proteins exhibit diverse mechanisms of endocrine resistance in breast cancer cell lines representing the no special type (NST) and invasive lobular cancer (ILC) subtypes. Our emphasize upon both the shared and unique cellular adaptations imparted by ER fusions offers the foundation for further translational research and clinical decision making.
Hatcheries to high seas: climate change connections to salmon marine survival
Authors: Kitada Shuichi , Myers Katherine W. , Kishino Hirohisa
Published: September 2023

We investigated variations in the marine survival of Japanese hatchery chum salmon (Oncorhynchus keta) during 25 years of climate change (1998-2023). Japan is the world largest producer of hatchery salmon, and is located near the global southern distribution limit of chum salmon. Our goal was to identify local and context-specific metrics related to salmon marine survival for use in the adaptive management of hatchery salmon resources. We hypothesized multiple metrics in three categories of stressors: hatchery carryovers, ocean conditions, and predators and competitors. The hatchery carryovers are stressors related to hatchery rearing that affect survival at a different life stage. We collected, processed, and collated large publicly available datasets of metrics into a comprehensive open-access database encompassing the life cycle of Japanese chum salmon, from eggs to adult spawners. Multivariate regression models showed associations between stressor metrics and adult salmon return rate (marine survival) varied by coastal management region, salmon life stage, and seasonal high seas distribution area. Generalized additive models identified a shift to younger age at maturity and egg size decline in all management regions. Our analysis suggested that maternal traits (egg size, fecundity) and the quality of fry hatchery salmon (body size at release) are particularly important for survival at later ocean stages. Our results support the hypothesis that whole life-cycle processes from anthropogenic selection in hatcheries to climate-driven changes in coastal predation, inter- and intra-specific high seas competition, and maternal effects during egg maturation at sea are responsible for the observed coastwide decline in survival of Japanese hatchery chum salmon over the past two decades. Our study highlights the need for an experimental approach to hatchery practices, including monitoring and analyses with updated information, leading to effective management decisions and policies for future sustainability and conservation of salmon resources.
Community coalescence altered the potential of horizontal gene transfers within the native soil microbiome
Authors: Liu Xipeng , Hackl Thomas , Salles Joana Falcão
Published: September 2023

Microbial community coalescence, which refers to the mixing of microbial communities, frequently shapes the assemblage of soil microbiomes in natural ecosystems. It can exert selective pressure on the coalescent taxa, leading to ecological changes in microbial community structure or microbial evolutionary changes via horizontal gene transfer (HGT). However, the influence of community coalescence on the potential of HGTs within native communities, particularly in soil ecosystems, remains poorly understood. Here, we experimentally quantified the potential evolutionary consequences of soil coalescence. We achieved that by subjecting microcosms containing natural soil to invasion by several microbial communities and profiling mobile genetic elements (MGEs) and adaptive genes of microbial communities up to 60 days after coalescence. Our findings revealed both specific and common responses of MGEs to coalescences over time. Specific effects differed across invasive communities and were particularly pronounced in the early stages. Common effects were associated with an increased abundance of insertion sequences (ISs) across different treatments, suggesting that ISs played a crucial role in promoting diversification at the community level. In summary, we showed that changing MGE profiles are an intrinsic response of the soil microbial community to coalescence-imposed pressure. Our study provides new insights into the modulation of adaptability in soil microbial communities by utilizing community coalescences to address global challenges.
Revealing principles of autonomous thermal soaring in windy conditions using vulture-inspired deep reinforcement-learning
Authors: Flato Yoav , Harel Roi , Tamar Aviv , Nathan Ran , Beatus Tsevi
Published: September 2023

Thermal soaring, a technique used by birds and gliders to utilize updrafts of hot air, is an appealing model-problem for studying motion control and how it is learned by animals and engineered autonomous systems. Thermal soaring has rich dynamics and nontrivial constraints, yet it uses few control parameters and is becoming experimentally accessible. Following recent developments in applying reinforcement learning methods for training deep neural-network (deep-RL) models to soar autonomously both in simulation and real gliders, here we develop a simulation-based deep-RL system to study the learning process of thermal soaring. We find that this process has learning bottlenecks, we define a new efficiency metric and use it to characterize learning robustness, we compare the learned policy to data from soaring vultures, and find that the neurons of the trained network divide into function clusters that evolve during learning. These results pose thermal soaring as a rich yet tractable model-problem for the learning of motion control.
Parallel evolution of local adaptation inLittorina saxatilisinferred with whole-genome pool-seq data
Authors: Carvalho João , Faria Rui , Butlin Roger K. , Sousa Vítor C.
Published: September 2023

Parallel evolution of phenotypic divergence offers compelling evidence supporting the influence of natural selection on the divergence process. However, the existence of ecotypes adapted to different habitats in separate locations is not a definitive proof of parallel evolution. Here, we leverage a large pool-seq dataset of the rocky-shore gastropod,Littorina saxatilisto compare and contrast two explicit scenarios of ecotype formation. Populations of this species inhabit contrasting habitats, where the main selective pressure is either wave action or crab predation. Using approximate Bayesian computation to jointly infer demographic parameters and account for pool-seq specific sources of uncertainty, our analysis reveals that ecotype formation at a large geographical scale has occurred in parallel. Parameter estimates provide strong support for a demographic history marked by the spatial separation of the ancestral populations that later gave rise to parallel evolution of ecotypes in Spain and Sweden. Additionally, ecotype formation occurred in the face of continuous gene flow between the diverging ecotypes. These results shed new light on a important model of speciation driven by ecological factors and emphasize the effectiveness of combining pool-seq with ABC for studying parallel evolution across diverse geographical regions.
Heterologous naringenin production in the filamentous fungusPenicillium rubens
Authors: Peng Bo , Dai Lin , Iacovelli Riccardo , Driessen Arnold J. M. , Haslinger Kristina
Published: September 2023

Naringenin is a natural product with several reported bioactivities and is the key intermediate for the entire class of plant flavonoids. The translation of flavonoids into modern medicine as pure compounds is often hampered by their low abundance in nature and difficult chemical synthesis. Here, we investigated new avenues toward producing high levels of naringenin in microbial hosts.Penicillium rubensis a well characterized and highly engineered traditional “workhorse” for the production of β-lactam antibiotics and cholesterol-lowering statins. We explored a secondary metabolite deficientP. rubensstrain,P. rubens4xKO, that was derived from an earlier industrial production strain as a promising microbial host for a recombinant flavonoid pathway. By integrating two plant genes encoding for enzymes in the naringenin biosynthesis pathway into the genome of this strain, we achieved a high naringenin titer in flask fermentations 36 h after feeding the precursorp-coumaric acid. Along with the rapid product accumulation of up to an 88% molar yield, we also observed rapid degradation of naringenin. Based on high-resolution mass spectrometric analysis, we identified the degradation products and proposed a naringenin degradation pathway inP. rubens4xKO, which is distinct from other flavonoid-converting pathways reported in fungi. Our approach combines fundamental research with application-oriented microbial engineering, and our findings will pave the way to the more sustainable and economically feasible production of flavonoids for pharmaceutical and nutraceutical applications.
The Neural Correlates of Novelty and Variability in Human Decision-Making under an Active Inference Framework
Authors: Zhang Shuo , Tian Yan , Liu Quanying , Wu Haiyan
Published: September 2023

Active inference integrates perception, decision-making, and learning into a united theoretical frame-work, providing an efficient way to trade off exploration and exploitation by minimizing (expected) free energy. In this study, we asked how the brain represents values and uncertainties (novelty and variability), and resolves these uncertainties under the active inference framework in the exploration-exploitation trade-off. 25 participants performed a contextual two-armed bandit task, with electroen-cephalogram (EEG) recordings. By comparing the model evidence for active inference and rein-forcement learning models of choice behavior, we show that active inference better explains human decision-making under novelty and variability, which entails exploration or information seeking. The EEG sensor-level results show that the activity in the frontal, central, and parietal regions is associated with novelty, while activity in the frontal and central brain regions is associated with variability. The EEG source-level results indicate that the expected free energy is encoded in the frontal pole and middle frontal gyrus and uncertainties are encoded in different brain regions but with overlap. Our study dissociates the expected free energy and uncertainties in active inference theory and their neural correlates, speaking to the construct validity of active inference in characterizing cognitive processes of human decisions. It provides behavioral and neural evidence of active inference in decision processes and insights into the neural mechanism of human decisions under uncertainties.
Adaptive HD-sEMG decomposition: Towards robust real-time decoding of neural drive
Authors: Yeung Dennis , Negro Francesco , Vujaklija Ivan
Published: September 2023

Neural interfacing via decomposition of high-density surface electromyography (HD-sEMG) should be robust to signal non-stationarities incurred by changes in joint pose and contraction intensity. We present an adaptive real-time motor unit (MU) decoding algorithm and test it on HD-sEMG collected from the extensor carpi radialis brevis during isometric contractions over a range of wrist angles and contraction intensities. The performance of the algorithm was verified using high-confidence benchmark decompositions derived from concurrently recorded intramuscular electromyography (iEMG). In trials where contraction conditions between the initialization and testing data differed, the adaptive decoding algorithm maintained significantly higher decoding accuracies when compared to static decoding methods. Using ‘gold standard’ verification techniques, we demonstrate the limitations of filter re-use decoding methods and show the necessity of parameter adaptation to achieve robust neural decoding.
Mobile barrier mechanisms for Na+-coupled symport in an MFS sugar transporter
Authors: Hariharan Parameswaran , Shi Yuqi , Katsube Satoshi , Willibal Katleen , Burrows Nathan D. , Mitchell Patrick , Bakhtiiari Amirhossein , Stanfield Samantha , Pardon Els , Kaback H. Ronald , Liang Ruibin , Steyaert Jan , Viner Rosa , Guan Lan
Published: September 2023

While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of the Na+-coupled major facilitator superfamily transporters. With a conformational nanobody (Nb), we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. Collectively with the available outward-facing sugar-bound structures, both the outer and inner barriers were localized. The N-and C-terminal residues of the inner barrier contribute to the sugar selectivity pocket. When the inner barrier is broken as shown in the inward-open conformation, the sugar selectivity pocket is also broken. The binding assays by isothermal titration calorimetry revealed that this inward-facing conformation trapped by the conformation-selective Nb exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for the substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is also supported by molecular dynamics simulations. Furthermore, the use of this Nb in combination with the hydron/deuterium exchange mass spectrometry allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
Dynamic Functional Hyperconnectivity after Psilocybin Intake is Primarily Associated with Oceanic Boundlessness
Authors: Mortaheb Sepehr , Fort Larry D. , Mason Natasha L. , Mallaroni Pablo , Ramaekers Johannes G. , Demertzi Athena
Published: September 2023

To provide insights into neurophenomenological richness after psilocybin intake, we investigated the link between dynamical brain patterns and the ensuing phenomenological pattern after psilocybin intake. Healthy participants received either psilocybin (n=22) or placebo (n=27) while in ultra-high field 7T MRI scanning. Changes in the phenomenological patterns were quantified using the 5-Dimensional Altered States of Consciousness (5D-ASC) Rating Scale, revealing alterations across all dimensions under psilocybin. Changes in the neurobiological patterns displayed that psilocybin induced widespread increases in averaged functional connectivity. Time-varying connectivity analysis unveiled a recurrent hyperconnected pattern characterized by low BOLD signal amplitude, suggesting heightened cortical arousal. In terms of neurophenomenology, canonical correlation analysis primarily linked the transition probabilities of the hyperconnected pattern with feelings of oceanic boundlessness (OBN), and secondly with visionary restructuralization. We suggest that the brain’s tendency to enter a hyperconnected-hyperarousal pattern under psilocybin represents the potential to entertain variant mental associations. For the first time, these findings link brain dynamics with phenomenological alterations, providing new insights into the neurophenomenology and neurophysiology of the psychedelic state.
The circadian clock regulates PIF3 protein stability in parallel to red light
Authors: Liu Wei , Lowrey Harper , Leung Chun Chung , Adamchek Christopher , Du Juan , He Jiangman , Chen Meng , Gendron Joshua M.
Published: September 2023

The circadian clock is an endogenous oscillator, but its importance lies in its ability to impart rhythmicity on downstream biological processes or outputs. Focus has been placed on understanding the core transcription factors of the circadian clock and how they connect to outputs through regulated gene transcription. However, far less is known about posttranslational mechanisms that tether clocks to output processes through protein regulation. Here, we identify a protein degradation mechanism that tethers the clock to photomorphogenic growth. By performing a reverse genetic screen, we identify a clock-regulated F-box type E3 ubiquitin ligase,CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1(CFH1), that controls hypocotyl length. We then show that CFH1 functions in parallel to red light signaling to target the transcription factor PIF3 for degradation. This work demonstrates that the circadian clock is tethered to photomorphogenesis through the ubiquitin proteasome system and that PIF3 protein stability acts as a hub to integrate information from multiple environmental signals.
Single-cell Herpes Simplex Virus type-1 infection of neurons using drop-based microfluidics reveals heterogeneous replication kinetics
Authors: Fredrikson Jacob P. , Domanico Luke F. , Pratt Shawna L. , Loveday Emma K. , Taylor Matthew P. , Chang Connie B.
Published: September 2023

Single-cell analyses of viral infections often reveal heterogeneity that is not detected by traditional population-level studies. This study applies drop-based microfluidics to investigate the dynamics of HSV-1 infection of neurons at the single-cell level. We used micron-scale Matrigel beads, termed microgels, to culture individual murine Superior Cervical ganglia (SCG) neurons or epithelial cells. Microgel-cultured cells are subsequently enclosed in individual media-in-oil droplets with a dual fluorescent-reporter HSV-1, enabling real-time observation of viral gene expression and replication. Infection within drops revealed that the kinetics of initial viral gene expression and replication were dependent on the inoculating dose. Notably, increasing inoculating doses led to earlier onset of viral gene expression and more frequent productive viral replication. These observations provide crucial insights into the complexity of HSV-1 infection in neurons and emphasize the importance of studying single-cell outcomes of viral infection. The innovative techniques presented here for cell culture and infection in drops provide a foundation for future virology and neurobiology investigations.
Age-specific and compartment-dependent changes in mitochondrial homeostasis and cytoplasmic viscosity in mouse peripheral neurons
Authors: Sleigh James N. , Mattedi Francesca , Richter Sandy , Annuario Emily , Ng Kristal , Emilie Steinmark I. , Ivanova Iveta , Darabán István L. , Joshi Parth P. , Rhymes Elena R. , Awale Shirwa , Yahioglu Gokhan , Mitchell Jacqueline C. , Suhling Klaus , Schiavo Giampietro , Vagnoni Alessio
Published: September 2023

Mitochondria are dynamic bioenergetic hubs that become compromised with age. In neurons, declining mitochondrial axonal transport has been associated with reduced cellular health. However, it is still unclear to what extent the decline of mitochondrial transport and function observed during ageing are coupled, and if somal and axonal mitochondria display compartment-specific features that make them more susceptible to the ageing process. It is also not known whether the biophysical state of the cytoplasm, thought to affect many cellular functions, changes with age to impact mitochondrial trafficking and homeostasis. Focusing on the mouse peripheral nervous system, we show that age-dependent decline in mitochondrial trafficking is accompanied by reduction of mitochondrial membrane potential and intra-mitochondrial viscosity, but not calcium buffering, in both somal and axonal mitochondria. Intriguingly, we observe a specific increase in cytoplasmic viscosity in the neuronal cell body, where mitochondria are most polarised, which correlates with decreased cytoplasmic diffusiveness. Increasing cytoplasmic crowding in the somatic compartment of DRG neurons grown in microfluidic chambers reduces mitochondrial axonal trafficking, suggesting a mechanistic link between the regulation of cytoplasmic viscosity and mitochondrial dynamics. Our work provides a reference for studying the relationship between neuronal mitochondrial homeostasis and the viscoelasticity of the cytoplasm in a compartment-dependent manner during ageing.
Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics
Authors: Hsiung CC , Wilson CM , Sambold NA , Dai R , Chen Q , Misiukiewicz S , Arab A , Teyssier N , O’Loughlin T , Cofsky JC , Shi J , Gilbert LA
Published: September 2023

Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order (>3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered anAcidaminococcusCas12a variant -- referred to asmultiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
The use of cultured human alveolar basal cells to mimic honeycomb formation in idiopathic pulmonary fibrosis
Authors: Blumer Sabrina , Khan Petra , Artysh Nataliia , Plappert Linda , Savic Spasenija , Knudsen Lars , Jonigk Danny , Kuehnel Mark P. , Prasse Antje , Hostettler Katrin E.
Published: September 2023

Honeycomb cysts (HC) within the alveolar region are distinct histopathological features in the lungs of idiopathic pulmonary fibrosis (IPF) patients. HC are lined with basal cells (BC), or with a bronchiolar-like epithelium composed of basal-, ciliated- and secretory epithelial cells. By using cultured IPF patient-derived alveolar BC, we aimed to establishin vitro- andin vivomodels to mimic HC formation in IPF. In order to do so, we cultured the cells (1) on an air liquid interface (ALI) or (2) in a three dimensional (3D) organoid modelin vitro, and (3) investigated the cells’ behavior after instillation into bleomycin-challenged micein vivo. Under the here testedin vitro- andin vivoconditions, alveolar BC differentiate and formed HC-like structures, which closely resemble HC within the IPF lung. These models therefore represent powerful tools to study HC formation, and its potential therapeutic inhibition in IPF.