bluuebunny/crossref_metadata_2025 huggingface dataset:
oskaracts with the transcription factor Creb to regulate long-term memory in crickets
Authors: Kulkarni Arpita , Ewen-Campen Ben , Terao Kanta , Matsumoto Yukihisa , Li Yaolong , Watanabe Takayuki , Kao Jonchee A. , Parhad Swapnil S. , Ylla Guillem , Mizunami Makoto , Extavour Cassandra G.
Published: October 2022

Novel genes have the potential to drive the evolution of new biological mechanisms, or to integrate into pre-existing regulatory circuits and contribute to the regulation of older, conserved biological functions. One such gene, the novel insect-specific geneoskar, was first identified based on its role in establishing theDrosophila melanogastergerm line. We previously showed that this gene likely arose through an unusual domain transfer event involving bacterial endosymbionts, and played a somatic role before evolving its well-known germ line function. Here, we provide empirical support for this hypothesis in the form of evidence for a novel neural role foroskar. We show thatoskaris expressed in the adult neural stem cells of a hemimetabolous insect, the cricketGryllus bimaculatus. In these stem cells, called neuroblasts,oskaris required together with the ancient animal transcription factorCrebto regulate long-term (but not short-term) olfactory memory. We provide evidence thatoskarpositively regulatesCreb, which plays a conserved role in long-term memory across animals, and thatoskarin turn may be a direct target of Creb. Together with previous reports of a role foroskarin nervous system development and function in crickets and flies, our results are consistent with the hypothesis thatoskar’s original somatic role may have been in the insect nervous system. Moreover, its co-localization and functional cooperation with the conserved pluripotency genepiwiin the nervous system may have facilitatedoskar’s later co-option to the germ line in holometabolous insects.
Residue-based correlation between equilibrium and rate constants is an experimental formulation of the consistency principle for smooth structural changes of proteins
Authors: Kohda Daisuke , Hayashi Seiichiro , Fujinami Daisuke
Published: October 2022

The consistency principle represents a physicochemical condition requisite for ideal protein folding. It assumes that any pair of amino acid residues in partially folded structures has an attractive short-range interactiononly ifthe two residues are in contact within the native structure. The residue-specific equilibrium constant,K, and the residue-specific rate constant,k(forward and backward), can be determined by NMR and hydrogen-deuterium exchange studies. Linear free energy relationships (LFER) in the rate-equilibrium free energy relationship (REFER) plots (i.e., logkvs. logK) are widely seen in protein-related phenomena, but our REFER plot differs from them in that the data points are derived from one polypeptide chain under a single condition. Here, we examined the theoretical basis of the residue-based LFER. First, we derived a basic equation, ρij= ½(ϕi+ ϕj), from the consistency principle, where ρijis the slope of the line segment that connects residues i and j in the REFER plot, and ϕiand ϕjare the local fractions of the native state in the transient state ensemble (TSE). Next, we showed that the general solution is the alignment of the (logK, logk) data points on a parabolic curve in the REFER plot. Importantly, unlike LFER, the quadratic free energy relationship (QFER) is compatible with the heterogenous formation of local structures in the TSE. Residue-based LFER/QFER provides a unique insight into the TSE: A foldable polypeptide chain consists of several folding units, which are consistently coupled to undergo smooth structural changes.
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population
Authors: Saubin Méline , Tellier Aurélien , Stoeckel Solenn , Andrieux Axelle , Halkett Fabien
Published: October 2022

Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering the full trajectory compared to few time samples. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetics changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.
Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data
Authors: Pellecchia Simona , Viscido Gaetano , Franchini Melania , Gambardella Gennaro
Published: October 2022

Although an essential step, the functional annotation of cells often proves particularly challenging in the analysis of single-cell transcriptional data. Several methods have been developed to accomplish this task. However, in most cases, these rely on techniques initially developed for bulk RNA sequencing or simply make use of marker genes identified from cell clustering followed by supervised annotation. To overcome these limitations and automatise the process, we have developed two novel methods, the single-cell gene set enrichment analysis (scGSEA) and the single cell mapper (scMAP). scGSEA combines latent data representations and gene set enrichment scores to detect coordinated gene activity at single-cell resolution. scMAP uses transfer learning techniques to repurpose and contextualise new cells into a reference cell atlas. Using both simulated and real datasets, we show that scGSEA effectively recapitulates recurrent patterns of pathways’ activity shared by cells from different experimental conditions. At the same time, we show that scMAP can reliably map and contextualise new single cell profiles on a breast cancer atlas we recently released. Both tools are provided in an effective and straightforward workflow providing a framework to determine cell function and significantly improve annotation and interpretation of scRNA-seq data.
Functional ultrasound imaging reveals an aberrant developmental trajectory of functional connectivity in a mouse model of the 15q13.3 copy number variant microdeletion
Authors: Grohs-Metz Gillian , Hengerer Bastian , Cruces Solis Hugo
Published: October 2022

The developmental nature of many neuropsychiatric disorders such as schizophrenia necessitates the detection of functional biomarkers during the prodromal phase of disease that can predict symptomatic conversion and outcomes. Structural chromosomal aberrations, such as copy number variants, confer high risk and penetrance of neuropsychiatric disorders. We used functional ultrasound imaging (fUS) to characterize the functional connectivity profile of the 15q13.3+/−copy number variant mouse model during major developmental milestones on post-natal day (p)35, 42, 60, and 90 in comparison to wild type littermates. We identified divergent trajectories for 15q13.3+/−mice and WT littermate controls where functional connectivity was reduced for both genotypes with age, but to a lesser extent for 15q13.3+/−mice. We were then able to isolate the distinct differences between genotypes to identify a large-scale network where 15q13.3+/−mice displayed global cortical hyperconnectivity and elevated intra-connectivity within the hippocampus and amygdala, in particular. In order to determine the stage of development where the connectivity trajectories bifurcated, we used machine learning to predict genotype. We found that the connectivity profile from p42, but not p35, predicted the genotype of individual mice at p90 with 82% accuracy. All together, these results suggest a crucial period of network maturation from early to late pubescence that is pivotal in the transition of healthy network connectivity into adulthood. This novel application of fUS longitudinally through development shows promise in improving the understanding of the disease biology of mouse models of psychiatric diseases.
Proteogenomic Characterization Reveals Therapeutic Opportunities Related to Mitochondrial Function in Melanoma
Authors: Gil Jeovanis , Kim Yonghyo , Doma Viktória , Çakır Uğur , Kuras Magdalena , Betancourt Lazaro Hiram , Parada Indira Pla , Sanchez Aniel , Sugihara Yutaka , Appelqvist Roger , Oskolas Henriett , Lee Boram , de Siqueira Guedes Jéssica , Monnerat Gustavo , Alves Carneiro Gabriel Reis , Nogueira Fábio CS , Domont Gilberto B. , Malm Johan , Baldetorp Bo , Wieslander Elisabet , Balázs Németh István , Szász A. Marcell , Kwon Ho Jeong , Hong Runyu , Pawłowski Krzysztof , Rezeli Melinda , Tímár József , Fenyö David , Kárpáti Sarolta , Marko-Varga György
Published: October 2022

The dynamics of more than 1900 mitochondrial proteins was explored through quantitative proteomics in 151 melanoma-related tissue samples of both surgical and autopsy origin. Dysregulation of mitochondrial pathways in primary tumors, metastases, and peritumoral tissues was correlated with age and survival of patients, as well as with tumor cell proliferation and the BRAF mutation status of the tumors. The outlined proteomic landscape confirmed the central role of a pathologically upregulated mitochondrial translation machinery and oxidative phosphorylation (OXPHOS) in the development, proliferation, and progression of melanomas. Our results from different melanoma cell lines confirmed our findings and we could document that treatments with selected OXPHOS inhibitors and antibiotics successfully impaired tumor cell proliferation. In addition, we provided proteomic evidence on the mechanism-of-action of the different treatments. These observations could contribute to the development of therapeutic approaches targeting the mitochondrial pathology in melanoma.

TOC figure

Highlights

Mitochondrial proteome landscape outlined in 151 melanoma-related samples

Mitochondrial Translation and OXPHOS impact disease severity and survival

BRAF V600E mutation correlates with upregulation of mitochondrial energy production

Targeting the mitochondrial OXPHOS and ribosomes impairs tumor cell proliferation

Therapeutic opportunities complementary to the standard of care are proposed

In brief

Mitochondrial proteome profiling of melanomas reveals dysregulation in major metabolic pathways, suggesting a central role of the mitochondria within the development and progression of melanoma. Targeting mitochondrial pathways has the potential to impact the course of the disease, which provides opportunities for complementary drug interventions.
Comprehensive cell atlas of the first-trimester developing human brain
Authors: Braun Emelie , Danan-Gotthold Miri , Borm Lars E. , Vinsland Elin , Lee Ka Wai , Lönnerberg Peter , Hu Lijuan , Li Xiaofei , He Xiaoling , Andrusivová Žaneta , Lundeberg Joakim , Arenas Ernest , Barker Roger A. , Sundström Erik , Linnarsson Sten
Published: October 2022

The adult human brain likely comprises more than a thousand kinds of neurons, and an unknown number of glial cell types, but how cellular diversity arises during early brain development is not known. Here, in order to reveal the precise sequence of events during early brain development, we used single-cell RNA sequencing and spatial transcriptomics to uncover cell states and trajectories in human brains at 5 – 14 post-conceptional weeks (p.c.w.). We identified twelve major classes and over 600 distinct cell states, which mapped to precise spatial anatomical domains at 5 p.c.w. We uncovered detailed differentiation trajectories of the human forebrain, and a surprisingly large number of region-specific glioblasts maturing into distinct pre-astrocytes and pre-oligodendrocyte precursor cells (pre-OPCs). Our findings reveal the emergence of cell types during the critical first trimester of human brain development.
Spatiotemporal tissue maturation of thalamocortical pathways in the human fetal brain
Authors: Wilson Siân , Pietsch Maximilian , Cordero-Grande Lucilio , Christiaens Daan , Uus Alena , Karolis Vyacheslav , Kyriakopoulou Vanessa , Colford Kathleen , Price Anthony N. , Hutter Jana , Rutherford Mary A. , Hughes Emer J. , Counsell Serena J. , Tournier Jacques-Donald , Hajnal Joseph V , Edwards A. David , O’Muircheartaigh Jonathan , Arichi Tomoki
Published: October 2022

The development of connectivity between the thalamus and maturing cortex is a fundamental process in the second half of human gestation, establishing the neural circuits that are the basis for several important brain functions. In this study, we acquired high-resolutionin uterodiffusion MRI from 140 fetuses as part of the Developing Human Connectome Project, to examine the emergence of thalamocortical white matter over the second to third trimester. We delineate developing thalamocortical pathways and parcellate the fetal thalamus according to its cortical connectivity using diffusion tractography. We then quantify microstructural tissue components along the tracts in the fetal compartments that are critical substrates for white matter maturation, such as the subplate and intermediate zone. We identify patterns of change in the diffusion metrics that reflect critical neurobiological transitions occurring in the second to third trimester, such as the disassembly of radial glial scaffolding and the lamination of the cortical plate. These maturational trajectories of MR signal in transient fetal compartments provide a normative reference to complement histological knowledge, facilitating future studies to establish how developmental disruptions in these regions contribute to pathophysiology.
Causes and consequences of linkage disequilibrium among transposable elements within eukaryotic genomes
Authors: Roze Denis
Published: October 2022

Sex and recombination can affect the dynamics of transposable elements (TEs) in various ways: while sex is expected to help TEs to spread within populations, the deleterious effect of ectopic recombination among transposons represents a possible source of purifying selection limiting their number. Furthermore, recombination may also increase the efficiency of selection against TEs by reducing selective interference among loci. In order to better understand the effects of recombination and reproductive systems on TE dynamics, this article provides analytical expressions for the linkage disequilibrium (LD) among TEs in a classical model in which TE number is stabilized by synergistic purifying selection. The results show that positive LD is predicted in infinite populations despite negative epistasis, due to the effect of the transposition process. Positive LD may substantial inflate the variance in the number of elements per genome in the case of partially selfing or partially clonal populations. Finite population size tends to generate negative LD (Hill-Robertson effect), the relative importance of this effect increasing with the degree of linkage among loci. The model is then extended in order to explore how TEs may affect selection for recombination. While positive LD generated by transposition generally disfavors recombination, the Hill-Robertson effect may represent a non-negligible source of indirect selection for recombination when TEs are abundant. However, the direct fitness cost imposed by ectopic recombination among elements generally drives the population towards low-recombination regimes, at which TEs cannot be maintained at a stable equilibrium.
scifAI: Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
Authors: Boushehri Sayedali Shetab , Essig Katharina , Chlis Nikolaos-Kosmas , Herter Sylvia , Bacac Marina , Theis Fabian J , Glasmacher Elke , Marr Carsten , Schmich Fabian
Published: October 2022

Therapeutic antibodies are widely used to treat severe diseases. Most of them alter immune cells and act within the immunological synapse; an essential cell-to-cell interaction to direct the humoral immune response. Although many antibody designs are generated and evaluated, a high-throughput tool for systematic antibody characterization and prediction of function is lacking. Here, we introduce the first comprehensive open-source framework, scifAI (single-cell imaging flow cytometry AI), for preprocessing, feature engineering and explainable, predictive machine learning on imaging flow cytometry (IFC) data. Additionally, we generate the largest publicly available IFC data set of the human immunological synapse containing over 2.8 million images. Using scifAI, we analyze class frequency- and morphological changes under different immune stimulation. T cell cytokine production across multiple donors and therapeutic antibodies is quantitatively predictedin vitro,linking morphological features with function and demonstrating the potential to significantly impact antibody design. scifAI is universally applicable to IFC data. Given its modular architecture it is straightforward to incorporate into existing workflows and analysis pipelines, e.g. for rapid antibody screening and functional characterization.
Heavy metal pollution characteristics of soil around a copper-nickel mine tailings pond in the northwest arid area of China and evaluation of desert phytoremediation potential
Authors: Shi Jianfei , Jin Zhengzhong , Zhou Zhibin , Wang Xin , Yang Xiaoliang , Qian Wenting
Published: October 2022

Phytoextraction and phytostabilization are two mechanisms used by plants to remove and stabilize heavy metals in soil. However, there has been little research on the extraction/stabilization of heavy metals by desert plants in arid areas. This study analyzed eight heavy metals (Cr, Ni, Cu, Zn, Cd, Pb, Mn, and As) in 10 desert plants and their growth matrices. In addition, the single factor pollution index and Nemerow comprehensive pollution index were used to evaluate soil pollution. Based on the biological accumulation factor and the biological concentration factor, the fuzzy evaluation method was used to evaluate plant extraction/stability potentials for heavy metals. The results showed that Cd, Cu, Ni, and Cr in the soil around the tailings pond were at the heavy pollution level, Mn and Pb pollution was moderate, and Zn and As pollution was light. The matrix factorization model showed that Cu and Ni came from industrial pollution; Cd and Cr came from atmospheric deposition and agricultural pollution; Pb came from traffic pollution; and Mn, Zn, and As came from natural sources. The metal contents of the desert plants exceeded the standard for normal plants, of which Cr contents in theAtriplex patensandAmmophila breviligulataFernald aboveground parts were 35.63 and 53.77 mg/kg respectively, and the Ni contents in theKlasea centauroidessubsp.polycephala(Iljin) L. Martins underground parts and theA. breviligulataFernald aboveground parts were 102.67 and 101.67 mg/kg, respectively, exceeding the maximum toxicity threshold for Cr and Ni.Ammophila breviligulataFernald had the highest plant comprehensive extraction coefficient (CEI) and plant comprehensive stability coefficient (CSI) at 0.81 and 0.83 respectively, indicating that it has strong heavy metal extraction and stabilization abilities. Therefore,A. breviligulataFernald can be selected as a remediation species for heavy metal pollution in the soil around tailings reservoir areas.
Episodic long-term memory formation during slow-wave sleep
Authors: Schmidig Flavio J. , Ruch Simon , Henke Katharina
Published: October 2022

We are unresponsive during slow-wave sleep but continue monitoring external events for survival. Our brain wakens us when danger is imminent. If events are non-threatening, our brain might store them for later consideration to improve decision-making. To test this hypothesis, we examined whether novel vocabulary consisting of simultaneously played pseudowords and translation words are encoded/stored during sleep, and which neural-electrical events facilitate encoding/storage. An algorithm for brain-state dependent stimulation selectively targeted word pairs to slow-wave peaks or troughs. Retrieval tests were given 12 and 36 hours later. These tests required decisions regarding the semantic category of previously sleep-played pseudowords. The sleep-played vocabulary influenced awake decision-making 36 hours later, if targeted to troughs. The words’ linguistic processing raised neural complexity. The words’ semantic-associative encoding was supported by increased theta power during the ensuing peak. Fast-spindle power ramped up during a second peak likely aiding consolidation. Hence, new vocabulary played during slow-wave sleep was stored and influenced decision-making days later.
SDRAP for annotating scrambled or rearranged genomes
Authors: Braun Jasper , Neme Rafik , Feng Yi , Landweber Laura F. , Jonoska Nataša
Published: October 2022

DNA rearrangements are important in various contexts, such as in vertebrate immunity, and cancer genome instability. The single-celled eukaryoteOxytricha trifallaxundergoes massive and reproducible genome rearrangement during post-zygotic development, making it a compelling model organism to study DNA rearrangements. To date, computational tools for the extraction and analysis of rearrangement annotations lack transparency and rely on assumptions that may not hold for all analyzed data, leading to irreproducibility of results and loss of information through data filtering or misrepresentation.

An implementation of a procedure for the annotation and analysis of DNA rearrangement as a web application is discussed and tested. The resulting annotations provide an improvement over previous annotations in the following manner. (a) SDRAP achieves more complete precursor-product mappings than previous software (b) the software allows for full transparency of all parameters used during the annotation and therefore facilitates reproducible results, and (c) this parameter transparency makes SDRAP suitable for comparison of genomic data from different sources, including cancer genomes.

This work introduces a theoretical framework and software to systematically extract and analyze annotations from pairs of genome assemblies corresponding to precursor and product rearrangement data. The software makes no assumptions about the structure of the rearrangements, and permits the user to select parameters to suit the data.
Reward modulates visual responses in the superficial superior colliculus of mice
Authors: Baruchin Liad J. , Alleman Matteo , Schröder Sylvia
Published: October 2022

The superficial layers of the superior colliculus (SC) are highly visual and receive direct input from the retina. Nonetheless, neural activity in the superficial SC (sSC) is modulated by locomotion and pupil-linked arousal. Here we show that visual responses of neurons in the sSC are additionally modulated by reward delivered prior to the visual stimulus. We trained mice to perform a visual detection task and recorded the activity of neurons in the SC using two-photon calcium imaging and electrophysiological recordings using high-density silicone probes (Neuropixels). Neurons across all layers of the SC responded to various task events, including reward delivery. However, responses to events like licking or movements did not explain the visual response modulation by reward. Electrophysiological recordings showed that most of the reward modulation occurred in the superficial rather than the deeper layers of the SC. Neurons also exhibited modulation by pupil-linked arousal, which was independent of the reward modulation. Performance of a population decoder to detect visual stimuli improved significantly by reward modulation but not by pupil-linked arousal modulation. Our results indicate that behavioural factors other than locomotion and arousal modulate visual activity in the SC.
Part-night exposure to artificial light at night has more detrimental effects on aphid colonies than fully lit nights
Authors: Heinen Robin , Sanchez-Mahecha Oriana , Bezemer T. Martijn , Dominoni Davide M. , Knappe Claudia , Kollmann Johannes , Kopatsch Anton , Pfeiffer Zoë A. , Schloter Michael , Sturm Sarah , Schnitzler Jörg-Peter , Vlot A. Corina , Weisser Wolfgang W.
Published: October 2022

Artificial light at night (ALAN) threatens natural ecosystems globally. While ALAN research is increasing, little is known about how ALAN affects plants and interactions with other organisms. We explored the effects of ALAN on plant defence and plant–insect interactions using barley (Hordeum vulgare) and the English grain aphid (Sitobion avenae). Plants were exposed to ‘full’ or ‘part’ nights of 15–20 lux ALAN, or no ALAN ‘control’ nights, to test the effects of ALAN on plant growth and defence. Although plant growth was only minimally affected by ALAN, aphid colony growth and aphid maturation were reduced significantly by ALAN treatments. Importantly, we found strong differences between full-night and part-night ALAN treatments. Contrary to our expectations, part ALAN had stronger negative effects on aphid colony growth than full ALAN. Defence-associated gene expression was affected in some cases by ALAN, but also positively correlated with aphid colony size, suggesting that the effects of ALAN on plant defences are indirect, and regulated via direct disruption of aphid colonies, rather than via ALAN-induced upregulation of defences. Mitigating ecological side effects of ALAN is a complex problem, as reducing exposure to ALAN increased its negative impact on insect herbivores.
ISPRED-SEQ: Deep neural networks and embeddings for predicting interaction sites in protein sequences
Authors: Manfredi Matteo , Savojardo Castrense , Martelli Pier Luigi , Casadio Rita
Published: October 2022

The knowledge of protein-protein interaction sites (PPIs) is crucial for protein functional annotation. Here we address the problem focusing on the prediction of putative PPIs having as input protein sequences. The problem is important given the huge volume of sequences compared to experimental and/or computed protein structures. Taking advantage of recently developed protein language models and Deep Neural networks here we describe ISPRED-SEQ, which overpasses state-of-the-art predictors addressing the same problem. ISPRED-SEQ is freely available for testing athttps://ispredws.biocomp.unibo.it.
Eliminate false positives in metagenomic profiling based on type IIB restriction sites
Authors: Sun Zheng , Liu Jiang , Zhang Meng , Wang Tong , Huang Shi , Weiss Scott T. , Liu Yang-Yu
Published: October 2022

Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome shotgun sequencing (WMS) data. Numerous computational methods, broadly referred to as metagenomic profilers, have been developed to identify species in microbiome samples by classification of sequencing reads and quantification of their relative abundances. Yet, existing metagenomic profilers typically suffer from false positive identifications and consequently biased relative abundance estimation (as false positives can be accounted for more than 90% of total identified species). Here, we present a new metagenomic profiler MAP2B (MetAgenomicProfiler based on typeIIBrestriction site) to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives. By benchmarking the performance in metagenomic profiling using data from CAMI2 (Critical Assessment of Metagenome Interpretation: second round of challenge), we illustrate the superior performance of MAP2B (F1 score ~ 0.93) over existing metagenomic profilers (F1 score ranges from 0.18 to 0.58). We further tested the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior performance and robustness against sequencing depth. In addition, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features obtained by MAP2B can better discriminate disease status and predict metabolomic profiles.
Single-cell analysis of prenatal and postnatal human cortical development
Authors: Velmeshev Dmitry , Perez Yonatan , Yan Zihan , Valencia Jonathan E. , Castaneda-Castellanos David R. , Wang Li , Schirmer Lucas , Mayer Simone , Wick Brittney , Wang Shaohui , Nowakowski Tomasz Jan , Paredes Mercedes , Huang Eric J , Kriegstein Arnold R
Published: October 2022

We analyze more than 700,000 single-nucleus RNA-seq profiles from 106 donors during prenatal and postnatal developmental stages and identify lineage-specific programs that underlie the development of specific subtypes of excitatory cortical neurons, interneurons, glial cell types and brain vasculature. By leveraging single-nucleus chromatin accessibility data, we delineate enhancer-gene regulatory networks and transcription factors that control commitment of specific cortical lineages. By intersecting our results with genetic risk factors for human brain diseases, we identify the cortical cell types and lineages most vulnerable to genetic insults of different brain disorders, especially autism. We find that lineage-specific gene expression programs upregulated in female cells are especially enriched for the genetic risk factors of autism. Our study captures the molecular progression of cortical lineages across human development.

One Sentence Summary

Single-cell transcriptomic atlas of human cortical development identifies lineage and sex-specific programs and their implication in brain disorders.
Jag1 Insufficiency Disrupts Neonatal T Cell Differentiation and Impairs Hepatocyte Maturation, Leading to Altered Liver Fibrosis
Authors: Mašek Jan , Filipovic Iva , Hul Noémi Van , Belicová Lenka , Jiroušková Markéta , Oliveira Daniel V. , Frontino Anna Maria , Hankeova Simona , He Jingyan , Turetti Fabio , Iqbal Afshan , Červenka Igor , Sarnová Lenka , Verboven Elisabeth , Brabec Tomáš , Björkström Niklas K. , Gregor Martin , Dobeš Jan , Andersson Emma R.
Published: October 2022

Fibrosis is a physiological tissue repair mechanism, but excessive fibrosis can disrupt organ function. Alagille syndrome (ALGS), which is caused by mutations in the Notch ligandJAGGED1, results in bile duct paucity, neonatal cholestasis, and a characteristic fibrotic response. Here, we show thatJag1Ndr/Ndrmice, a model for ALGS, recapitulates ALGS-like pericellular fibrosis. Single-cell RNA-seq and multi-color flow cytometry characterization of the liver and spleen revealed immature hepatocytes and paradoxically low intrahepatic T cell infiltration in cholestaticJag1Ndr/Ndrmice, despite an enrichment in extrahepatic (thymic and splenic) regulatory T cells (Tregs).Jag1Ndr/Ndrlymphocyte immune and fibrotic capacity was tested with adoptive immune cell transplantation intoRag1-/-mice, challenged with dextran sulfate sodium (DSS) or bile duct ligation (BDL). TransplantedJag1Ndr/Ndrlymphocytes were less inflammatory with fewer activated T cells thanJag1+/+lymphocytes, in response to DSS. Cholestasis induced by BDL inRag1-/-mice withJag1Ndr/Ndrlymphocytes resulted in periportal Treg accumulation and three-fold less periportal fibrosis than inRag1-/-mice withJag1+/+lymphocytes. Finally, we show that theJag1Ndr/Ndrhepatocyte expression profile and Treg overrepresentation are corroborated by transcriptomic data from children with ALGS. In sum, these data lead to a model in which Jag1-driven developmental hepatic and immune defects interact to determine the fibrotic process in ALGS.
State-dependent, visually-guided behaviors in the nudibranchBerghia stephanieae
Authors: Quinlan Phoenix D. , Katz Paul S.
Published: October 2022

Nudibranch molluscs have structurally simple eyes whose behavioral roles have not been established. We tested the effects of visual stimuli on the behavior of the nudibranchBerghia stephanieaeunder different food and hunger conditions. In an arena that was half shaded, animals spent most of their time in the dark, where they also decreased their speed and made more changes in heading. These behavioral differences between the light and dark were less evident in uniformly illuminated or darkened arenas, suggesting that they were not caused by the level of illumination.Berghiaresponded to distant visual targets; animals approached a stripe that was at least 15° wide and 50% darker than the background. They did not approach a stripe that was lighter than the background but approached a stripe that was isoluminant with the background, suggesting the detection of spatial information. Animals travelled in convoluted paths in a featureless arena but straightened their paths when a visual target was present even if they did not approach it, suggesting that visual cues were used for navigation. Individuals were less responsive to visual stimuli when food-deprived or in the presence of a food odor. Furthermore, when given a food odor, they had a weaker preference for the dark and behaved similarly in the light and dark. Thus,Berghiaexhibits visually-guided behaviors that are influenced by odors and hunger state.

Summary statement

Behavioral analyses demonstrate that the nudibranchBerghia stephanieaeis capable of spatial vision and has visually-guided behaviors that are influenced by olfactory information and hunger state.
3D Digitizing An Animal Organ Could Make It Possible To Work With Anatomy Classes In The Metaverse Or With A 3D-Printed Real-Scale Organ On Demand
Authors: Sumer Dogasav , Ozten Onat , Gungor Mert , Yilmaz Meryem , Nart Ismail , Tastan Cihan
Published: October 2022

Organ scanning is not a novel technology but the unique part of this study is to eliminate the need for expensive devices by using free iOS/Android applications. The apps allow users to create high-quality 3D models from photos taken with a phone or tablet. Metaverse and 3D digitization are the future of technology. Implementation of these approaches into the anatomy can change education style. Also, 3D printing technology along with the digitization of real-sized organs enables researchers and clinicians to study with 3D printed organs in class, even with augmented reality glasses. In this study, we first aimed to 3D digitized an animal organ with its real sizes to print in a 3D printer. Next, we wanted to digitize decellularized form of the organ, which suggests researchers study extracellular matrix and vascularization. This digitization of the different organ forms can improve the progression of artificial organ studies. Free and easy-to-use iOS or Android applications for 3D digitization enable medical students to study not only animal organs but cadavers. Hereby, we are suggesting organ scanning can be done on a daily basis in a standard laboratory. It is aimed to enable medical students to work effectively in anatomy lessons in Metaverse or in real cases, thanks to the anatomical library created with the accessibility brought by easy usability.
Cell cycle alterations associate with a redistribution of mutation rates across chromosomal domains in human cancers
Authors: Salvadores Marina , Supek Fran
Published: October 2022

Somatic mutations in human cells have a highly heterogeneous genomic distribution, with increased burden in late-replication time (RT), heterochromatic domains of chromosomes. This regional mutation density (RMD) landscape is known to vary between cancer types, in association with tissue-specific RT or chromatin organization. Here, we hypothesized that regional mutation rates additionally vary between individual tumors in a manner independent of cell type, and that recurrent alterations in DNA replication programs and/or chromatin organization may underlie this. Here, we identified various RMD signatures that describe a global genome-wide mutation redistribution across many megabase-sized domains in >4000 tumors. We identified two novel global RMD signatures of somatic mutation landscapes that were universally observed across various cancer types. First, we identified a mutation rate redistribution preferentially affecting facultative heterochromatin, Polycomb-marked domains, and enriched in subtelomeric regions. This RMD signature strongly reflects regional plasticity in DNA replication time and in heterochromatin domains observed across tumors and cultured cells, which was linked with a stem-like phenotype and a higher expression of cell cycle genes. Consistently, occurrence of this global mutation pattern in cancers is associated with altered cell cycle control via loss of activity of theRB1tumor suppressor gene. Second, we identified another independant global RMD signature associated with loss-of-function of theTP53pathway, mainly affecting the redistribution of mutation rates away from late RT regions. The local mutation supply towards 26%-75% cancer driver genes is altered in the tumors affected by the global RMD signatures detected herein, including additionally a known pattern of a general loss of mutation rate heterogeneity due to DNA repair failures that we quantify. Our study highlights that somatic mutation rates at the domain scale are variable across tumors in a manner associated with loss of cell cycle control viaRB1orTP53, which may trigger the local remodeling of chromatin state and the RT program in cancers.
Genes vary greatly in their propensity for collateral fitness effects of mutations
Authors: Mehlhoff Jacob D. , Ostermeier Marc
Published: October 2022

Mutations can have deleterious fitness effects when they decrease protein specific activity or decrease active protein abundance. Mutations will also be deleterious when they cause misfolding or misinteractions that are toxic to the cell (i.e., independent of whether the mutations affect specific activity and abundance). The extent to which protein evolution is shaped by these and other collateral fitness effects is unclear in part because little is known of their frequency and magnitude. Using deep mutational scanning (DMS), we previously found at least 42% of missense mutations in theTEM-1β-lactamase antibiotic resistance gene cause deleterious collateral fitness effects. Here, we used DMS to comprehensively determine the collateral fitness effects of missense mutations in three genes encoding the antibiotic resistance proteins New Delhi metallo-β-lactamase (NDM-1), chloramphenicol acetyltransferase I (CAT-I), and 2”-aminoglycoside nucleotidyltransferase (AadB).AadB(20%),CAT-I(0.9%), andNDM-1 (0.2%) were less susceptible to deleterious collateral fitness effects thanTEM-1(42%) indicating that genes have different propensities for these effects. As was observed withTEM-1, all the studied deleteriousaadBmutants increased aggregation. However, aggregation did not correlate with collateral fitness effects for many of the deleterious mutants ofCAT-IandNDM-1. Select deleterious mutants caused unexpected phenotypes to emerge. The introduction of internal start codons inCAT-1caused loss of the episome and a mutation inaadBmade its cognate antibiotic essential for growth. Our study illustrates how the complexity of the cell provides a rich environment for collateral fitness effects and new phenotypes to emerge.
Development of Scaffold-free 3D Cholangiocyte Organoids to Study the Progression of Primary Sclerosing Cholangitis
Authors: Zhang Wenjun , Kyritsi Konstantina , Isidan Abdulkadir , Park Yujin , Li Ping , Cross-Najafi Arthur A , Lopez Kevin , Kennedy Lindsey , Sato Keisaku , Glaser Shannon , Francis Heather , Alpini Gianfranco , Ekser Burcin
Published: October 2022

Organoids are novelin vitromodels to study intercellular crosstalk between the different types of cells in the pathophysiology of disease. To better understand the underlying mechanisms driving the progression of primary sclerosing cholangitis (PSC), we developed scaffold-free multi-cellular 3D cholangiocyte organoids (3D-CHO) using ‘primary’ liver cell lines derived from normal and PSC patients. Human liver samples from healthy donors and late-stage PSC patients were used to isolate ‘primary’ cholangiocytes (EPCAM+/CK-19+), liver endothelial cells (LECs, CD31+), and hepatic stellate cells (HSCs, CD31−/CD68−/Desmin+/Vitamin A+). 3D-CHOs were formed using cholangiocytes:HSCs:LECs and kept viable for up to 1 month. Isolated primary cell lines and 3D-CHOs were further characterized by immunofluorescence (IF), qRT-PCR, and transmission electron microscopy. Gene expressions for cholangiocytes (SOX9, CFTR, EpCAM, AE, SCT, SCTR), fibrosis (ACTA2, COL1A1, DESMIN, TGFβ1), angiogenesis (PECAM, VEGF, CDH5, vWF), and inflammation (IL-6, TNF-α) confirmed PSC phenotypes of 3D-CHOs. Since cholangiocytes develop a neuroendocrine phenotype and express neuromodulators, confocal-IF demonstrated that neurokinin-1 receptor (NK-1R, expressed by cholangiocytes and upregulated in PSC), was localized within CK-19+cholangiocytes. Moreover, 3D-CHOs from PSC patients confirmed PSC phenotypes with upregulated NK-1R, tachykinin precursor 1, and downregulated membrane metalloendopeptidase. Our viable scaffold-free multiple-cell 3D-CHOs showed superiority as anin vitromodel in mimicking PSCin vivophenotypes compared to 2D cell culture, which can be used in PSC disease-related research.
Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2
Authors: Kim Dong Gun , Kim Hak Sung , Choi Yoonjoo , Stan Razvan C.
Published: October 2022

Fever is a typical symptom of most infectious diseases. While prolonged fever may be clinically undesirable, mild reversible fever (< 39°C, 312K) can potentiate the immune responses against pathogens. Here, using molecular dynamics, we investigated the effect of febrile temperatures (38°C to 40°C, 311K to 313K) on the immune complexes formed by the SARS-CoV-2 spike protein with two neutralizing antibodies. We found that, at mild fever temperatures (311-312K), the binding affinities of the two antibodies improve when compared to the physiological body temperature (37°C, 310K). Furthermore, only at 312K, antibodies exert distinct mechanical effects on the receptor binding domains of the spike protein that may hinder SARS-CoV-2 infectivity. Enhanced antibody binding affinity may thus be obtained using appropriate temperature conditions.
Novel estimators for family-based genome-wide association studies increase power and robustness
Authors: Guan Junming , Nehzati Seyed Moeen , Benjamin Daniel J. , Young Alexander I.
Published: October 2022

A goal of genome-wide association studies (GWASs) is to estimate the causal effects of alleles carried by an individual on that individual (‘direct genetic effects’). Typical GWAS designs, however, are susceptible to confounding due to gene-environment correlation and non-random mating (population stratification and assortative mating). Family-based GWAS, in contrast, is robust to such confounding since it uses random, within-family genetic variation. When both parents are genotyped, a regression controlling for parental genotype provides the most powerful approach. However, parental genotypes are often missing. We have previously shown that imputing the genotypes of missing parent(s) can increase power for estimation of direct genetic effects over using genetic differences between siblings. We extend the imputation method, which previously only applied to samples with at least one genotyped sibling or parent, to ‘singletons’ (individuals without any genotyped relatives). By including singletons, the effective sample size for estimation of direct effects can be increased by up to 50%. We apply this method to 408,254 ‘White British’ individuals from the UK Biobank, obtaining an effective sample size increase of between 25% and 43% (depending upon phenotype) by including 368,629 singletons. While this approach maximizes power, it can be biased when there is strong population structure. We therefore introduce an imputation based estimator that is robust to population structure and more powerful than other robust estimators. We implement our estimators in the software package snipar using an efficient linear-mixed model (LMM) specified by a sparse genetic relatedness matrix. We examine the bias and variance of different family-based and standard GWAS estimators theoretically and in simulations with differing levels of population structure, enabling researchers to choose the appropriate approach depending on their research goals.
Capturing differences in the regulation of LRRK2 dynamics and conformational states by small molecule kinase inhibitors
Authors: Weng Jui-Hung , Ma Wen , Wu Jian , Silletti Steve , McCammon J. Andrew , Taylor Susan
Published: October 2022

Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinson’s Disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. We showed previously that in addition to influencing intrinsic kinase activity, the global conformation of the LRRK2 protein plays a vital role in regulating LRRK2 signaling pathways. Deciphering the allosteric regulation in LRRK2 provides novel strategies for drug discovery. In this study, we combined enhanced sampling simulations with HDX-MS to analyze the inhibitor-induced dynamic changes and the allosteric communications in the C-terminal half of LRRK2, LRRK2RCKW. We find that a type I inhibitor (MLi-2) locks the kinase into a closed, active-like configuration, whereas a type II inhibitor (Rebastinib) shifts the kinase to an open, inactive configuration. While both type I and type II inhibitors reduce the kinase activity effectively, they have distinct effects on the LRRK2 conformational dynamics. Specifically, binding of MLi-2 stabilizes the kinase domain in a closed conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKWstructure. In contrast, binding of Rebastinib stabilizes an open conformation where communication between the N- and C-lobe is severed, which promotes a more extended LRRK2RCKWstructure. Rebastinib, based on HDX-MS, creates a more dynamic kinase domain especially at domain interfaces associated with the C-lobe. Our results also reveal the importance of the Dk-helix, which plays a crucial role in propagating communication between the kinase domain and the GTPase domain.