bluuebunny/crossref_metadata_2025 huggingface dataset:
Inflammatory profiles are associated with long COVID up to 6 months after illness onset: a prospective cohort study of individuals with mild to critical COVID-19
Authors: Wynberg Elke , Han Alvin X. , van Willigen Hugo D.G. , Verveen Anouk , van Pul Lisa , Maurer Irma , van Leeuwen Ester M. , van den Aardweg Joost G. , de Jong Menno D. , Nieuwkerk Pythia , Prins Maria , Kootstra Neeltje A. , de Bree Godelieve J.
Published: June 2023

Background

After initial COVID-19 disease, immune dysregulation may persist and drive post-acute sequelae of COVID-19 (PASC). We described longitudinal trajectories of cytokines in adults up to 6 months following SARS-CoV-2 infection and explored early predictors of PASC.

Methods

RECoVERED is a prospective cohort of individuals with laboratory-confirmed SARS-CoV-2 infection between May 2020 and June 2021 in Amsterdam, the Netherlands. Serum was collected at weeks 4, 12 and 24 of follow-up. Monthly symptom questionnaires were completed from month 2 after illness onset onwards; lung diffusion capacity (DLCO) was tested at 6 months. Cytokine concentrations were analysed by human magnetic Luminex screening assay. We used a linear mixed-effects model to study log-concentrations of cytokines over time, assessing their association with socio-demographic and clinical characteristics that were included in the model as fixed effects.

Results

186/349 (53%) participants had ≥2 serum samples and were included. Of these, 101 (54%: 45/101[45%] female, median age 55 years [IQR=45-64]) reported PASC at 12 and 24 weeks after illness onset. We included 37 reference samples (17/37[46%] female, median age 49 years [IQR=40-56]). PASC was associated with raised CRP and abnormal diffusion capacity with raised IL10, IL17, IL6, IP10 and TNFα at 24 weeks in the multivariate model. Early (0-4 week) IL-1βand BMI at illness onset were predictive of PASC at 24 weeks.

Conclusions

Our findings indicate that immune dysregulation plays an important role in PASC pathogenesis, especially among those individuals with reduced pulmonary function. Early IL-1βshows promise as predictors of PASC.
Not only a matter of age: Machine learning-based characterization of the differential effect of brain stimulation on skill acquisition
Authors: Maceira-Elvira Pablo , Popa Traian , Schmid Anne-Christine , Cadic-Melchior Andéol , Müller Henning , Schaer Roger , Cohen Leonardo G. , Hummel Friedhelm C.
Published: June 2023

Brain stimulation shows potential at enhancing cognitive and motor functions in humans. However, multiple studies assessing its effects on behavior show heterogeneous results, especially in healthy older subjects. We propose a new method to predict an individual’s likelihood and the magnitude of the benefit from stimulation, based on the baseline performance of a sequential motor task, framed in the context of their age. Our results show a differential effect of stimulation, in which individuals with less efficient learning mechanisms benefit from stimulation, while those possessing optimal learning strategies resent a detrimental effect. Importantly, this differential effect was determined by one’s ability to integrate task-relevant information at the early stages of training, and not the age. This study paves the way towards the personalized application of stimulation to maximize its effects, and constitutes the first steps to implement an individualized translational clinical intervention, based on the state of the neural system.

Teaser

Age notwithstanding, brain stimulation is most effective in deficient neural systems, while being detrimental to optimal systems

Visual abstract

Main finding

Anodal transcranial direct current stimulation (atDCS), applied over the hand representation of the motor cortex concomitant to the training of a sequential motor sequence, has differential effects as a function of the recipient’s ability to integrate task-relevant information at the early stages of training. Stimulation benefits individuals with seemingly less efficient learning mechanisms, enabling the rapid storage of the spatial coordinates of the motor sequence and an accelerated optimization of the accuracy of execution. In contrast, individuals possessing optimal learning mechanisms experience detrimental effects of stimulation, leading to drops in the accuracy of execution.
A Functional Data Analysis Approach to RuBisCO Engineering
Authors: McCormack Adam C.
Published: June 2023

Mitigating and adapting to climate change requires carbon emission control and effective technologies for drawing greenhouse gases from the atmosphere. Here we propose an effective strategy for guiding the rubisco engineering problem, which seeks to improve photosynthesis and carbon sequestration in crops by minimizing photorespiration, a major impediment to crop yields. Photorespiration occurs when rubisco oxygenates rather than carboxylates, thus reducing carbohydrate synthesis to eliminate toxic byproducts. Most plants, including most agricultural crops, exhibit a C3 photosynthetic pathway and have not developed adaptive mechanisms to combat rubisco’s tradeoff. The span of low activity rubiscos opens the possibility of engineering less productive crops to express higher activity enzymes. The main experimental challenges in bypassing rubisco’s biochemical limitations include its molecular size and complexity, lack of empirical data, and costs of acquiring new data, but recent advances in machine learning and data analytics could allow us to overcome these challenges. In particular, we propose a novel computational approach to inform experimental research into rubisco engineering by employing recently developed techniques from functional data analysis. We show that the separation between high and low activity enzymes can be modeled within the sequence space of rubisco’s primary structure, and we further discuss how our approach can guide deeper investigation into the rubisco engineering problem. Future empirical success would simultaneously address major global issues such as rising atmospheric CO2levels and food insecurity.
NG2 Glia Reprogramming Induces Robust Axonal Regeneration After Spinal Cord Injury
Authors: Tai Wenjiao , Du Xiaolong , Chen Chen , Xu Xiao-Ming , Zhang Chun-Li , Wu Wei
Published: June 2023

Spinal cord injury (SCI) often leads to neuronal loss, axonal degeneration and behavioral dysfunction. We recently show that in vivo reprogramming of NG2 glia produces new neurons, reduces glial scaring, and ultimately leads to improved function after SCI. By examining endogenous neurons, we here unexpectedly uncover that NG2 glia reprogramming also induces robust axonal regeneration of the corticospinal tract and serotonergic neurons. Such reprogramming-induced axonal regeneration may contribute to the reconstruction of neural networks essential for behavioral recovery.
A Synthetic Protein Secretion System for Living Bacterial Therapeutics
Authors: Ahan Recep Erdem , Ozcelik Cemile Elif , Cagil Irem Niran , Seker Urartu Ozgur Safak
Published: June 2023

Bacteria species can thrive and colonize different parts of the human body. Those naturally residing at disease sites e.g., tumors and gut can be designed for targeted protein delivery which can provide better clinical profiles for protein-based therapies. Therefore, a generalizable, efficient, and safe protein secretion system would a be valuable tool to engineer therapeutically active microbes, especially for gram-negative species due to the presence of the second cell wall. Here, we propose an approach called iLOM-SS, an acronym forinducibleLeakyOuterMembrane basedSecretionSystem, to secrete proteins in gram-negative bacteria (GNB). In iLOM-SS, the outer membrane of GNB is made permeable by transient suppression of structural protein(s) to enable free diffusion of cargo proteins expressed at the periplasm. To validate this approach, an iLOM-SS is constructed inEscherichia coliNissle 1917 (EcN) strain. Proteins including enzymes and a human cytokine were proven to be secreted with iLOM-SS by EcNin vitro. Further characterizations of iLOM-SS in ECN showed that fast and titratable secretion, a stop switch design for secretion, and functional implementation of the secretion system in different genetic circuit architectures were possible. We foresee that this work will pave the way for designing GNB to secrete proteins for diverse arrays of applications including but not limited to the development of sentinel cells for therapeutic purposes.
Live-cell invasive phenotyping uncovers the ALK2/BMP6 iron homeostasis pathway as a therapeutic vulnerability in LKB1-mutant lung cancer
Authors: Koo Junghui , Seong Chang-Soo , Parker Rebecca E. , Dwivedi Bhakti , Arthur Robert A. , Dinasarapu Ashok Reddy , Johnston H. Richard , Claussen Henry , Tucker-Burden Carol , Ramalingam Suresh S. , Fu Haian , Zhou Wei , Marcus Adam I. , Gilbert-Ross Melissa
Published: June 2023

The acquisition of invasive properties is a prerequisite for tumor progression and metastasis. Molecular subtypes of KRAS-driven lung cancer exhibit distinct modes of invasion that likely contribute to unique growth properties and therapeutic susceptibilities. Despite this, pre-clinical discovery strategies designed to exploit invasive phenotypes are lacking. To address this, we designed an experimental system to screen for targetable signaling pathways linked to active early invasion phenotypes in the two most prominent molecular subtypes, TP53 and LKB1, of KRAS-driven lung adenocarcinoma (LUAD). By combining live-cell imaging of human bronchial epithelial cells in a 3D invasion matrix with RNA transcriptome profiling, we identified the LKB1-specific upregulation of bone morphogenetic protein 6 (BMP6). Examination of early-stage lung cancer patients confirmed upregulation of BMP6 in LKB1-mutant lung tumors. At the molecular level, we find that the canonical iron regulatory hormone Hepcidin is induced via BMP6 signaling upon LKB1 loss, where intact LKB1 kinase activity is necessary to maintain signaling homeostasis. Furthermore, pre-clinical studies in a novel Kras/Lkb1-mutant syngeneic mouse model show that potent growth suppression was achieved by inhibiting the ALK2/BMP6 signaling axis with single agents that are currently in clinical trials. We show that alterations in the iron homeostasis pathway are accompanied by simultaneous upregulation of ferroptosis protection proteins. Thus, LKB1 is sufficient to regulate both the ‘gas’ and ‘breaks’ to finely tune iron-regulated tumor progression.
UniSpec: A Deep Learning Approach for Predicting Energy-Sensitive Peptide Tandem Mass Spectra and Generating Proteomics-Wide In-Silico Spectral Libraries
Authors: Lapin Joel , Yan Xinjian , Dong Qian
Published: June 2023

In this report, we present UniSpec, an attention-based deep neural network designed to predict complete collision-induced fragmentation of tryptic peptides, aimed at enhancing peptide and protein identification in shotgun proteomics studies. We preprocessed spectral data from peptide tandem mass spectral libraries, compiled by the National Institute of Standards and Technology (NIST), utilizing a data approach tailored for model development, resulting in high-quality, energy-consistent spectral datasets. By analyzing all the annotated fragment ions present in these libraries, we constructed an extensive peptide fragment dictionary containing 7919 isotopic ions from sequence ions, neutral loss, internal, iminium, and amino acid fragment ions. The streamlined dictionary-based spectral training data enables UniSpec to efficiently learn the complex intensity patterns of various product ions, resulting in reliable spectral predictions for a wide range of unmodified and modified peptides. We evaluated the model’s accuracy by comparing its performance across training and testing data, considering diverse peptide characteristics like peptide classes, charge states, and sequence lengths. Our model attained a median cosine similarity score of 0.951 and 0.923 on the training and test data respectively. Contrary to existing deep learning models that often overlook a substantial part of peptide tandem mass spectra beyond the sequence b and y ion series, UniSpec can predict up to 75% of all measured fragment intensities (including unknown signals) in the raw experimental spectra. This represents a marked advancement from the 43.5% coverage achieved solely by b and y sequence ions in the NIST library spectra. For the evaluation of our model’s practical utility in predicting proteome-wide in-silico spectral libraries, we executed a benchmark test using a dataset of HeLa cells. UniSpec displayed a significant overlap of peptide identifications with the widely used search engine MS-GF+ and the NIST experimental spectral library, demonstrating its robust performance as a standalone peptide identification tool.
Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by minor groove anchor competition
Authors: Kobayashi Wataru , Sappler Anna , Bollschweiler Daniel , Kümmecke Maximilian , Basquin Jérôme , Arslantas Eda Nur , Ruangroengkulrith Siwat , Hornberger Renate , Duderstadt Karl , Tachibana Kikuë
Published: June 2023

Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors, which bind nucleosomal DNA and initiate gene expression from closed chromatin. How pioneer factors perform this function is poorly understood. Nr5a2 is a pioneer factor that is critical for zygotic genome activation (ZGA) in totipotent embryos, pluripotency in embryonic stem cells and metabolic regulation in adult tissues. To study how Nr5a2 functions as a pioneer factor, we used cryo-electron microscopy to determine a structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved C-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA at a ∼50° angle. Residue aspartic acid 159 of the CTE loop induces the rearrangement by shifting a histone H2A α2 helix towards the nucleosome center. Mutational analysis showed that NR5A2 D159 is largely dispensable for DNA binding but required for stable nucleosome association and persistent DNA unwrapping. These findings suggest that NR5A2 belongs to a previously unknown class of pioneer factors that can use minor groove anchor competition to destabilize nucleosomes and facilitate gene expression changes during reprogramming.
Comparison of genomic diversity between single and pooledStaphylococcus aureuscolonies isolated from human colonisation cultures
Authors: Raghuram Vishnu , Gunoskey Jessica J. , Hofstetter Katrina S. , Jacko Natasia F. , Shumaker Margot J. , Hu Yi-Juan , Read Timothy D. , David Michael Z.
Published: June 2023

The most common approach to sampling the bacterial populations within an infected or colonised host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. An alternative is to sequence a mixture containing multiple colonies (“pool-seq”), but this has the disadvantage that it is a non-homogeneous sample, making it difficult to perform specific experiments. We compared differences in measures of genetic diversity between eight single-colony isolates (singles) and pool-seq on a set of 2286S. aureusculture samples. The samples were obtained by swabbing three body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistantS. aureusskin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple Multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.

Graphical Abstract
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plantNepenthes gracilis
Authors: Saul Franziska , Scharmann Mathias , Wakatake Takanori , Rajaraman Sitaram , Marques André , Freund Matthias , Bringmann Gerhard , Channon Louisa , Becker Dirk , Carroll Emily , Low Yee Wen , Lindqvist Charlotte , Gilbert Kadeem J. , Renner Tanya , Masuda Sachiko , Richter Michaela , Vogg Gerd , Shirasu Ken , Michael Todd P. , Hedrich Rainer , Albert Victor A. , Fukushima Kenji
Published: June 2023

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plantNepenthes gracilisto analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype with five complete sets of syntenic chromosomes (2n= 10x= 80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbor three transcription factors involved in flower and pollen development, including a likely neofunctionalizedLEAFYduplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent because duplicates were enriched withNepenthes-specific genes with tissue-specific expression, including those expressed in trapping pitchers. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes experiencing relaxed purifying selection to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.
Neural manifolds in V1 change with top-down signals from V4 targeting the foveal region
Authors: Morales-Gregorio Aitor , Kurth Anno C. , Ito Junji , Kleinjohann Alexander , Barthélemy Frédéric V. , Brochier Thomas , Grün Sonja , van Albada Sacha J.
Published: June 2023

High-dimensional brain activity is often organized into lower-dimensional neural manifolds. However, the neural manifolds of the visual cortex remain understudied. Here, we study large-scale multielectrode electrophysiological recordings of macaque (Macaca mulatta) areas V1, V4 and DP with a high spatio-temporal resolution. We find, for the first time, that the population activity of V1 contains two separate neural manifolds, which correlate strongly with eye closure (eyes open/closed) and have distinct dimensionalities. Moreover, we find strong top-down signals from V4 to V1, particularly to the foveal region of V1, which are significantly stronger during the eyes-open periods, a previously unknown effect. Finally,in silicosimulations of a balanced spiking neuron network qualitatively reproduce the experimental findings. Taken together, our analyses and simulations suggest that top-down signals modulate the population activity of V1, causing two distinct neural manifolds. We postulate that the top-down modulation during the eyes-open periods prepares V1 for fast and efficient visual responses, resulting in a type of visual stand-by state.
Temporal segmentation and ‘look ahead’ simulation: Physical events structure visual perception of intuitive physics
Authors: Yates Tristan S. , Yasuda Shannon , Yildirim Ilker
Published: June 2023

How we perceive the physical world is not only organized in terms of objects, but also structured in time as sequences of events. This is especially evident in intuitive physics, with temporally bounded dynamics such as falling, occlusion, and bouncing demarcating the continuous flow of sensory inputs. While the spatial structure and attentional consequences of physical objects have been well-studied, much less is known about the temporal structure and attentional consequences of physical events in visual perception. Previous work has recognized physical events as units in the mind, and used pre-segmented object interactions to explore physical representations. However, these studies did not address whether and how perception imposes the kind of temporal structure that carves these physical events to begin with, and the attentional consequences of such segmentation during intuitive physics. Here, we use performance-based tasks to address this gap. In Experiment 1, we find that perception not only spontaneously separates visual input in time into physical events, but also, this segmentation occurs in a nonlinear manner within a few hundred milliseconds at the moment of the event boundary. In Experiment 2, we find that event representations, once formed, use coarse ‘look ahead’ simulations to selectively prioritize those objects that are predictively part of the unfolding dynamics. This rich temporal and predictive structure of physical events, formed during vision, should inform models of intuitive physics.
Mechanisms of cilia regeneration inXenopusmulticiliated epitheliumin vivo
Authors: Rao Venkatramanan G. , Subramanianbalachandar Vignesharavind , Magaj Magdalena M. , Redemann Stefanie , Kulkarni Saurabh S.
Published: June 2023

Cilia regeneration is a physiological event, and while studied extensively in unicellular organisms, it remains poorly understood in vertebrates. In this study, usingXenopusmulticiliated cells (MCCs) as a model, we demonstrate that, unlike unicellular organisms, deciliation removes the transition zone (TZ) and the ciliary axoneme. While MCCs immediately begin the regeneration of the ciliary axoneme, surprisingly, the assembly of TZ is delayed. However, ciliary tip proteins, Sentan and Clamp, localize to regenerating cilia without delay. Using cycloheximide (CHX) to block new protein synthesis, we show that the TZ protein B9d1 is not a component of the cilia precursor pool and requires new transcription/translation, providing insights into the delayed repair of TZ. Moreover, MCCs in CHX treatment assemble fewer (∼ 10 vs. ∼150 in controls) but near wild-type length (ranging between 60 to 90%) cilia by gradually concentrating ciliogenesis proteins like IFTs at a select few basal bodies. Using mathematical modeling, we show that cilia length compared to cilia number influences the force generated by MCCs more. In summary, our results question the requirement of TZ in motile cilia assembly and provide insights into how cells determine organelle size and number.
Structure Reveals Homology in Elevator Transporters
Authors: Trebesch Noah , Tajkhorshid Emad
Published: June 2023

The elevator transport mechanism is one of the handful of canonical mechanisms by which transporters shuttle their substrates across the semi-permeable membranes that surround cells and organelles. Studies of molecular function are naturally guided by evolutionary context, but until now this context has been limited for elevator transporters because established evolutionary classification methods have organized them into several apparently unrelated families. Through comprehensive examination of the pertinent structures available in the Protein Data Bank, we show that 62 elevator transporters from 18 families share a conserved architecture in their transport domains consisting of 10 helices connected in 8 topologies. Through quantitative analysis of the structural similarity, structural complexity, and topologically-corrected sequence similarity among the transport domains, we provide compelling evidence that these elevator transporters are all homologous. Using our analysis, we have constructed a phylogenetic tree to enable quantification and visualization of the evolutionary relationships among elevator transporters and their families. We also report several examples of functional features that are shared by elevator transporters from different families. Our findings shed new light on the elevator transport mechanism and allow us to understand it in a far deeper and more nuanced manner.
Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells
Authors: Pulecio Julian , Tayyebi Zakieh , Liu Dingyu , Wong Wilfred , Luo Renhe , Damodaran Jeyaram R , Kaplan Samuel , Cho Hyunwoo , Yan Jielin , Murphy Dylan , Rickert Robert W. , Shukla Abhijit , Zhong Aaron , González Federico , Yang Dexin , Li Wenbo , Zhou Ting , Apostolou Effie , Leslie Christina S. , Huangfu Danwei
Published: June 2023

The mechanisms underlying the ability of embryonic stem cells (ESCs) to rapidly activate lineage-specific genes during differentiation remain largely unknown. Through multiple CRISPR-activation screens, we discovered human ESCs have pre-established transcriptionally competent chromatin regions (CCRs) that support lineage-specific gene expression at levels comparable to differentiated cells. CCRs reside in the same topological domains as their target genes. They lack typical enhancer-associated histone modifications but show enriched occupancy of pluripotent transcription factors, DNA demethylation factors, and histone deacetylases. TET1 and QSER1 protect CCRs from excessive DNA methylation, while HDAC1 family members prevent premature activation. This “push and pull” feature resembles bivalent domains at developmental gene promoters but involves distinct molecular mechanisms. Our study provides new insights into pluripotency regulation and cellular plasticity in development and disease.

One sentence summary

We report a class of distal regulatory regions distinct from enhancers that confer human embryonic stem cells with the competence to rapidly activate the expression of lineage-specific genes.
Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes
Authors: Hippen Ariel A. , Davidson Natalie R. , Barnard Mollie E. , Weber Lukas M. , Gertz Jason , Doherty Jennifer A. , Hicks Stephanie C. , Greene Casey S.
Published: June 2023

Ovarian cancer is a deadly disease with few effective therapies. The most common form is high-grade serous ovarian cancer (HGSOC). Transcriptomic subtypes of HGSOC have shown promise in characterizing tumor heterogeneity and are associated with survival. Gene expression signatures for the subtypes suggest variation in stromal cell types in the tumor microenvironment (TME). Here, we characterize the TME composition of HGSOC on a population scale by performing deconvolution on bulk transcriptomic data. We use comprehensive cell type profiles from 164 HGSOC tumor samples from two independent reference datasets, in order to compare cell type proportions across and within bulk transcriptomic datasets, and assess their alignment to the subtypes proposed by The Cancer Genome Atlas. We also assess the relationship between tumor composition and clinical outcomes. Our results suggest that HGSOC transcriptomic subtypes are driven by TME composition, specifically fibroblast and immune cell content, and we propose a modified HGSOC subtype model informed by cell composition.
Striatal integration of inverse dopamine and serotonin signals gates learning
Authors: Pinto Daniel F. Cardozo , Pomrenze Matthew B. , Guo Michaela Y. , Bentzley Brandon S. , Eshel Neir , Malenka Robert C.
Published: June 2023

The neuromodulators dopamine (DA) and serotonin (5-hydroxytryptamine; 5HT) are powerful regulators of associative learning1–9. Similarities in the activity and connectivity of these neuromodulatory systems have inspired competing models of how DA and 5HT interact to drive the formation of new associations10–13. However, these hypotheses have yet to be tested directly because it has not been possible to precisely interrogate and manipulate multiple neuromodulatory systems in a single subject. Here, we establish a double transgenic mouse model enabling simultaneous genetic access to the brain’s DA and 5HT systems. Anterograde axon tracing revealed the nucleus accumbens (NAc) to be a putative hotspot for the integration of convergent DA and 5HT signals. Simultaneous recordings of DA and 5HT input activity in the NAc posterior medial shell revealed that DA axons are excited by rewards while 5HT axons are inhibited. Optogenetically blunting DA and 5HT reward responses simultaneously blocked learning about a reward-predictive cue. Optogenetically reproducing both DA and 5HT responses to reward, but not either one alone, was sufficient to drive the acquisition of new associations. Altogether, these results demonstrate that striatal integration of inverse DA and 5HT signals is a crucial mechanism gating associative learning.
JMnorm: a novel Joint Multi-feature normalization method for integrative and comparative epigenomics
Authors: Xiang Guanjue , Guo Yuchun , Bumcrot David , Sigova Alla
Published: June 2023

Combinatorial patterns of epigenetic features reflect transcriptional states and functions of genomic regions. While many epigenetic features have correlated relationships, most existing data normalization approaches analyze each feature independently. Such strategies may distort relationships between functionally correlated epigenetic features and hinder biological interpretation. We present a novel approach named JMnorm that simultaneously normalizes multiple epigenetic features across cell types, species, and experimental conditions by leveraging information from partially correlated epigenetic features. We demonstrate that JMnorm-normalized data can better preserve cross-epigenetic-feature correlations across different cell types and enhance consistency between biological replicates than data normalized by other methods. Additionally, we show that JMnorm-normalized data can consistently improve the performance of various downstream analyses, which include candidate cis-regulatory element clustering, cross-cell-type gene expression prediction, detection of transcription factor binding and changes upon perturbations. These findings suggest that JMnorm effectively minimizes technical noise while preserving true biologically significant relationships between epigenetic datasets. We anticipate that JMnorm will enhance integrative and comparative epigenomics.

GRAPHICAL ABSTRACT

JMnorm can jointly normalize multiple epigenetic features between the target sample and the reference.
BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets
Authors: Nuhamunada Matin , Mohite Omkar S. , Phaneuf Patrick V. , Palsson Bernhard O. , Weber Tilmann
Published: June 2023

Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as; i) data selection, ii) functional annotation, iii) phylogenetic analysis, iv) genome mining, and v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of theSaccharopolysporagenus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge in the ever-growing genomic datasets of biotechnologically relevant bacterial species. BGCFlow is available for downloading athttps://github.com/NBChub/bgcflow.
Structural organisation of perisomatic inhibition in the mouse medial prefrontal cortex
Authors: Nagy-Pál Petra , Veres Judit M. , Fekete Zsuzsanna , Karlócai Mária R. , Weisz Filippo , Barabás Bence , Reéb Zsófia , Hájos Norbert
Published: June 2023

Perisomatic inhibition profoundly controls neural function. However, the structural organisation of inhibitory circuits giving rise to the perisomatic inhibition in the higher-order cortices is not completely known. Here, we performed a comprehensive analysis of those GABAergic cells in the medial prefrontal cortex (mPFC) that provide inputs onto the somata and proximal dendrites of pyramidal neurons. Our results show that most GABAergic axonal varicosities contacting the perisomatic region of superficial (layer 2/3) and deep (layer 5) pyramidal cells express parvalbumin (PV) or cannabinoid receptor type 1 (CB1). Further, we found that the ratio of PV/CB1 GABAergic inputs is larger on the somatic membrane surface of pyramidal tract neurons in comparison to those projecting to the contralateral hemisphere. Our morphological analysis of in vitro labelled PV+ basket cells (PVBC) and CCK/CB1+ basket cells (CCKBC) revealed differences in many features. PVBC dendrites and axons arborized preferentially within the layer where their soma was located. In contrast, the axons of CCKBCs expanded throughout layers, though their dendrites were found preferentially either in superficial or deep layers. Finally, using anterograde trans-synaptic tracing we observed that PVBCs are preferentially innervated by thalamic and basal amygdala afferents in layer 5a and 5b, respectively. Thus, our results suggest that PVBCs can control the local circuit operation in a layer-specific manner via their characteristic arborization, while CCKBCs rather provide cross-layer inhibition in the mPFC.

Significance Statement

Inhibitory cells in cortical circuits are crucial for the precise control of local network activity. Nevertheless, in higher-order cortical areas that are involved in cognitive functions like decision making, working memory and cognitive flexibility, the structural organisation of inhibitory cell circuits is not completely understood. In this study we show that perisomatic inhibitory control of excitatory cells in the medial prefrontal cortex is performed by two types of basket cells endowed with different morphological properties that provide inhibitory inputs with distinct layer specificity on cells projecting to disparate areas. Revealing this difference in innervation strategy of the two basket cell types is a key step towards understanding how they fulfil their distinct roles in cortical network operations.
The paradox of extremely fast evolution driven by genetic drift in multi-copy gene systems
Authors: Wang Xiaopei , Ruan Yongsen , Zhang Lingjie , Chen Xiangnyu , Shi Zongkun , Wang Haiyu , Chen Bingjie , Tracy Miles , Huang Liying , Wu Chung-I , Wen Haijun
Published: June 2023

Multi-copy gene systems that evolve within, as well as between, individuals are common. They include viruses, mitochondrial DNAs, multi-gene families etc. The paradox is that neutral evolution in two stages should be far slower than single-copy systems but the opposite is often true, thus leading to the suggestion of natural selection. We now apply the new Generalized Haldane (GH) model to quantify genetic drift in the mammalian ribosomal RNA genes (or rDNAs). On average, rDNAs haveC∼ 150 - 300 copies. A neutral mutation in rDNA should take 4NC*generations to become fixed (N, the population size;C*, the effective copy number). WhileC>C*>> 1 is expected, the observed fixation time in mouse and human is < 4N, hence the paradox ofC*< 1. Genetic drift thus appears as much as 100 times stronger for rRNA genes as for single-copy genes. The large increases in genetic drift are driven by a host of molecular mechanisms such as gene conversion and unequal crossover. Although each mechanism of drift has been extremely difficult to quantify, the GH model permits the estimation of their total effects on genetic drift. In conclusion, the GH model can be generally applicable to multi-copy gene systems without being burdened by tracking the diverse molecular mechanisms individually.
Universal Dynamic Fitting of Magnetic Resonance Spectroscopy
Authors: Clarke William T , Ligneul Clémence , Cottaar Michiel , Ip I Betina , Jbabdi Saad
Published: June 2023

Dynamic (2D) magnetic resonance spectroscopy is a collection of techniques where acquisitions of spectra are repeated under varying experimental or physiological conditions. Dynamic MRS comprises a rich set of contrasts, including diffusion-weighted, relaxation-weighted, functional, edited, or hyperpolarized spectroscopy, leading to quantitative insights into multiple physiological or microstructural processes. Conventional approaches to dynamic MRS analysis ignore the shared information between spectra, and instead proceed by independently fitting noisy individual spectra before modelling temporal changes in the parameters. Here we propose a universal dynamic MRS toolbox which allows simultaneous fitting of dynamic spectra of arbitrary type. A simple interface allows information to be shared and precisely modelled across spectra to make inferences on both spectral and dynamic processes. We demonstrate and thoroughly evaluate our approach in three types of dynamic MRS techniques. Simulations of functional and edited MRS are used to demonstrate the advantages of dynamic fitting. Analysis of synthetic functional 1H-MRS data shows a marked decrease in parameter uncertainty as predicted by prior work. Analysis with our tool replicates the results of two previously published studies using the original in vivo functional and diffusion-weighted data. Finally, joint spectral fitting with diffusion orientation models is demonstrated in synthetic data. The toolbox is shared as a fully open-source software with comprehensive documentation, example data, and tutorials.
Characterization of the genetic composition and establishment of a core collection for the INERA Robusta coffee (Coffea canephora) field genebank from the Democratic Republic of the Congo
Authors: Verleysen Lauren , Bollen Robrecht , Kambale Jean-Léon , Tshimi Ebele , Ntumba Katshela Benjamin , Depecker Jonas , Poncet Valérie , Assumani Dieu-Merci , Vandelook Filip , Stoffelen Piet , Honnay Olivier , Ruttink Tom
Published: June 2023

Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope, but substantial effort must be made to improve its cupping quality and other agronomic traits. Robusta coffee genetic resources conserved in field genebanks can play an important role in this context, but many of them are limited and poorly characterized. In this study, we aimed to characterize the genetic composition of the historically important but until recently neglected INERA Coffee Collection in Yangambi (Democratic Republic of the Congo) and to propose a Robusta core collection. We combined genome-wide GBS marker sets with a novel versatile multiplex amplicon sequencing (HiPlex) screening assay, for the genetic screening of the INERA Coffee Collection and created tools for future genetic screening. A set of 730 coffee shrubs in the collection were genotyped at 86 HiPlex loci and 263 unique genetic fingerprints were identified. Representative fingerprints were compared to ‘Lula’ cultivars, ‘Luki’ cultivars, Congolese subgroup A, and wild genotypes growing in the rainforest of the Yangambi region. The majority of the unique genetic fingerprints were identified as ‘Lula’ cultivars but also four Congolese subgroup A and nine wild genotypes were found in the collection. Twenty-five percent of the unique genetic fingerprints had a hybrid identity which could result from seed-based propagation of the collection or natural cross-pollination. Moreover, eight unique genetic fingerprints were frequently identified as a parent and these may correspond to the ancient selected mother plants, or direct descendants thereof, of which seed material was widely distributed from 1930 to 1960 for the creation of coffee plantations. Finally, to delineate core collections we tested the maximization strategy and genetic distance method for the INERA Coffee Collection, and proposed i) a core collection conserving the loci diversity of the collection,i.e.100 accessions and ii) a core collection holding the highest genetic distances between the accessions,i.e.10 accessions. Our study provides a method for the genetic characterization of Robusta coffee collections in general and contributes to the revaluation and exploitation of the Robusta coffee genetic resources in the Democratic Republic of the Congo in particular.
The structure of the OmpA/Pal protein ofAnaplasma phagocytophilum
Authors: Cadby I.T.
Published: June 2023

Peptidoglycan associated lipoprotein (Pal) and Outer Membrane Protein A (OmpA), interact with the outer membrane and peptidoglycan in Gram-negative bacteria, conferring structural integrity to the bacterial cell and functioning in cell division. Both OmpA and Pal proteins have moonlighting roles as virulence factors, facilitating infection and host-pathogen interactions in a range of bacteria. The OmpA-like protein ofAnaplasma phagocytophilum, a tick-borne pathogen that infects a wide range of hosts, seems to function primarily as a virulence factor, since this bacterium lacks a peptidoglycan cell wall. Here we present crystal structures of the OmpA-like protein ofA. phagocytophilum, demonstrating that this protein has amino acid insertions that confer flexibility. This insertion is also found in the OmpA-like proteins of other pathogens, related toA. phagocytophilum. Whether this flexibility is reflective of any adaptations for host-pathogen interactions remains to be determined but, since the OmpA-like proteins ofAnaplasmaspecies are current targets for vaccine development, might have importance for these efforts.
Molecular basis of Progressive Familial Intrahepatic Cholestasis 3. A proteomics study
Authors: Guerrero Laura , Carmona-Rodríguez Lorena , Santos Fátima Millhano , Ciordia Sergio , Stark Luiz , Hierro Loreto , Vicent David , Corrales Fernando J.
Published: June 2023

Background and aims

Progressive familiar intrahepatic cholestasis type 3 (PFIC3) is a severe rare liver disease which affects between 1/50,000 to 1/100,000 children. In physiological conditions, bile is produced by the liver and stored in the gallbladder, then it flows to the small intestine to play its role in fat digestion. To prevent tissue damage, bile acids are kept into phospholipid micelles. Mutations in phosphatidyl choline transporter ABCB4 (MDR3) lead to intrahepatic accumulation of free bile acids that results in liver damage. PFIC3 onset occurs usually at early ages, progress rapidly and the prognosis is poor. Currently, besides the palliative use of ursodeoxycholate, the only available treatment for this disease is liver transplantation, which is really challenging for short-aged patients.

Methods

To gain insight into the pathogenesis of PFIC3 we have performed an integrated proteomics and phosphoproteomics study in human liver samples to then validate the emerging functional hypotheses in a PFIC3 murine model.

Results

We identified 6,246 protein groups, 324 proteins among them showing differential expression between control and PFIC3. The phosphoproteomic analysis allowed the identification of 5,090 phosphopeptides, from which 215 corresponding to 157 protein groups, were differentially phosphorylated in PFIC3, including MDR3. Regulation of essential cellular processes and structures, such as inflammation, metabolic reprograming, cytoskeleton and extracellular matrix remodeling and cell proliferation were identified as main drivers of the disease.

Conclusion

Our results provide a strong molecular background that significantly contributes to a better understanding of PFIC3 and provides new concepts that might prove useful in the clinical management of patients.

Lay Summary/Key Points

PFIC3 is a rare disease that affect 1/50,000 to 1/100,000 children that present severe symptoms in the first years of life and have scarce therapeutic options. We identified a panel of proteins that recapitulate some of the main cellular processes associated to the progression of liver injury in PFIC3 patients and suggest alternative treatment options.
Comparative analysis of PDZ-binding motifs in the diacylglycerol kinase family
Authors: Zambo Boglarka , Gogl Gergo , Morlet Bastien , Eberling Pascal , Negroni Luc , Moine Hervé , Travé Gilles
Published: June 2023

Diacylglycerol kinases (DGKs) control local and temporal amounts of diacylglycerol (DAG) and phosphatidic acid (PA) by converting DAG to PA through phosphorylation in cells. Certain DGK enzymes possess C-terminal sequences that encode potential PDZ-binding motifs (PBMs), which could be involved in their recruitment into supramolecular signaling complexes. In this study, we used two different interactomic approaches, quantitative native holdup (nHU) and qualitative affinity purification (AP), both coupled to mass spectrometry (MS) to investigate the PDZ partners associated with the potential PBMs of DGKs. Complementing these results with site-specific affinity interactomic data measured on isolated PDZ domain fragments and PBM motifs, as well as evolutionary conservation analysis of the PBMs of DGKs, we explored functional differences within different DGK groups. All our results indicate that putative PBM sequences of type II enzymes are likely to be nonfunctional. In contrast, type IV enzymes possess highly promiscuous PBMs that interact with a set of PDZ proteins with very similar affinity interactomes. The combination of various interactomic assays and evolutionary analyses provides a useful strategy for identifying functional domains and motifs within diverse enzyme families.