bluuebunny/crossref_metadata_2025 huggingface dataset:
Msh3 and Pms1 Set Neuronal CAG-repeat Migration Rate to Drive Selective Striatal and Cortical Pathogenesis in HD Mice
Authors: Wang Nan , Zhang Shasha , Langfelder Peter , Ramanathan Lalini , Plascencia Mary , Gao Fuying , Vaca Raymond , Gu Xiaofeng , Deng Linna , Dionisio Leonardo E. , Prasad Brinda C. , Vogt Thomas , Horvath Steve , Aaronson Jeffrey S. , Rosinski Jim , Yang X. William
Published: July 2024

Modifiers of Huntington’s disease (HD) include mismatch repair (MMR) genes; however, their underlying disease-altering mechanisms remain unresolved. Knockout (KO) alleles for 9 HD GWAS modifiers/MMR genes were crossed to the Q140 Huntingtin (mHtt) knock-in mice to probe such mechanisms. Four KO mice strongly (Msh3andPms1) or moderately (Msh2andMlh1) rescue a triad of adult-onset, striatal medium-spiny-neuron (MSN)-selective phenotypes: somaticHttDNA CAG-repeat expansion, transcriptionopathy, and mHtt protein aggregation. Comparatively, Q140 cortex also exhibits an analogous, but later-onset, pathogenic triad that isMsh3-dependent. Remarkably, Q140/homozygous Msh3-KO lacks visible mHtt aggregates in the brain, even at advanced ages (20-months). Moreover,Msh3-deficiency prevents striatal synaptic marker loss, astrogliosis, and locomotor impairment in HD mice. Purified Q140 MSN nuclei exhibit highly linear age-dependent mHtt DNA repeat expansion (i.e. repeat migration), with modal-CAG increasing at +8.8 repeats/month (R2=0.98). This linear rate is reduced to 2.3 and 0.3 repeats/month in Q140 with Msh3 heterozygous and homozygous alleles, respectively. Our study defines somaticHttCAG-repeat thresholds below which there are no detectable mHtt nuclear or neuropil aggregates. Mild transcriptionopathy can still occur in Q140 mice with stabilizedHtt140-CAG repeats, but the majority of transcriptomic changes are due to somatic repeat expansion. Our analysis reveals 479 genes with expression levels highly correlated with modal-CAG length in MSNs. Thus, our study mechanistically connects HD GWAS genes to selective neuronal vulnerability in HD, in whichMsh3andPms1set the linear rate of neuronal mHtt CAG-repeat migration to drive repeat-length dependent pathogenesis; and provides a preclinical platform for targeting these genes for HD suppression across brain regions.

One Sentence Summary

Msh3 and Pms1 are genetic drivers of sequential striatal and cortical pathogenesis in Q140 mice by mediating selective CAG-repeat migration in HD vulnerable neurons.
Dynamics and Activation of Membrane-Bound B Cell Receptor Assembly
Authors: Do Hung N. , Zhao Mingfei , Munir Alam S. , Gnanakaran S.
Published: July 2024

B-cell receptor complexes (BCR) are expressed on the surface of a B-cell and are critical in antigen recognition and modulating the adaptive immune response. Even though the relevance of antibodies has been known for almost a hundred years, the antigen-dependent activation mechanism of B-cells has remained elusive. Several models have been proposed for BCR activation, including cross-linking, conformation-induced oligomerization, and dissociation activation models. Recently, the first cryo-EM structures of the human B-cell antigen receptor of the IgM and IgG isotypes were published that validated the asymmetric organization of the BCR complex. Here, we have carried out extensive molecular dynamics simulations to probe the conformational changes upon antigen binding and the influence of the membrane lipids. We identified two critical dynamical events that could be associated with antigen-dependent activation of BCR. First, antigen binding caused increased flexibility in regions distal to the antigen binding site. Second, antigen binding altered the rearrangement of IgM transmembrane helices, including the relative interaction of Igα/Igβ that mediates intracellular signaling. Furthermore, these transmembrane rearrangements led to changes in localized lipid composition.
From resting state to inactivation: the dynamic journey of the inactivation peptide in Shaker Kv channels
Authors: Pandey Roshan , Kalstrup Tanja , Blunck Rikard
Published: July 2024

Shaker Kv channels inactivate rapidly to culminate the action potential and maintain the homeostasis of excitable cells. The so-called N-type inactivation is caused by the first 46 amino acids of the N-terminus of the channel, known as the inactivation peptide. Numerous mutational studies have characterized N-type inactivation functionally, however, the position of the inactivation peptide in the resting state and its transition during inactivation is still debated. Here, we tracked the movement of the inactivation peptide during inactivation using voltage clamp fluorometry. By inserting an unnatural amino acid, 3-[(6-acetyl-2-naphthalenyl) amino]-L-alanine (Anap), which is sensitive to changes in environment, we identified the movements of ball and chain separately. Our data suggests that N-type inactivation occurs in a biphasic movement by first releasing the IP, which then blocks the pore from the cytoplasmic side. To further narrow down the resting position of the inactivation peptide, we used Lanthanide-based Resonance Energy transfer and transition metal (tm)FRET. We propose that the inactivation peptide is located in the window formed by the channel and the T1 domain, interacting with the acidic residues of the T1 domain.
Enhancing Retrieval Capacity of the Predictive Brain through Dorsolateral Prefrontal Cortex Intervention
Authors: Szücs-Bencze Laura , Vékony Teodóra , Pesthy Orsolya , Kocsis Krisztián , Kincses Zsigmond Tamás , Szabó Nikoletta , Nemeth Dezso
Published: July 2024

The ability to extract spatial or temporal regularities across experiences is crucial for skill development and predictive processes. The prefrontal cortex (PFC) plays a key role in modulating competitive memory systems, supporting declarative/episodic memory as opposed to statistical learning. This regulatory role may explain findings of improved acquisition and consolidation of statistical regularities following the suppression of dorsolateral PFC (DLPFC) by repetitive transcranial magnetic stimulation (rTMS). This raises a key question: Is access to models and prior statistical knowledge also modulated by the DLPFC? This preregistered study provides new insights by examining the role of the DLPFC in retrieving pre-existing knowledge of temporally distributed statistical regularities. Using a probabilistic learning task, healthy participants engaged in implicit statistical learning for 25 minutes. After a 24-hour consolidation period, participants received either 1 Hz rTMS or sham stimulation over the left, right, or bilateral DLPFC for 10 minutes before retesting. We found more effective access to statistical regularities in the bilateral DLPFC group compared to the sham group. Our results suggest that DLPFC suppression enhances the retrieval of statistical knowledge, particularly when interhemispheric compensatory mechanisms are prevented. These findings contribute to understanding competitive memory systems and offer implications for cognitive enhancement strategies.
On the validity of electric brain signal predictions based on population firing rates
Authors: Ness Torbjørn V. , Tetzlaff Tom , Einevoll Gaute T. , Dahmen David
Published: July 2024

Neural activity at the population level is commonly studied experimentally through measurements of electric brain signals like local field potentials (LFPs), or electroencephalography (EEG) signals. To allow for comparison between observed and simulated neural activity it is therefore important that simulations of neural activity can accurately predict these brain signals. Simulations of neural activity at the population level often rely on point-neuron network models or firing-rate models. While these simplified representations of neural activity are computationally efficient, they lack the explicit spatial information needed for calculating LFP/EEG signals. Different heuristic approaches have been suggested for overcoming this limitation, but the accuracy of these approaches has not fully been assessed. One such heuristic approach, the so-called kernel method, has previously been applied with promising results and has the additional advantage of being well-grounded in the bio-physics underlying electric brain signal generation. It is based on calculating rate-to-LFP/EEG kernels for each synaptic pathway in a network model, after which LFP/EEG signals can be obtained directly from population firing rates. This amounts to a massive reduction in the computational effort of calculating brain signals because the brain signals are calculated for each population instead of for each neuron. Here, we investigate how and when the kernel method can be expected to work, and present a theoretical framework for predicting its accuracy. We show that the relative error of the brain signal predictions is a function of the single-cell kernel heterogeneity and the spike-train correlations. Finally, we demonstrate that the kernel method is most accurate for the dominating brain signal contributions. We thereby further establish the kernel method as a promising approach for calculating electric brain signals from large-scale neural simulations.
How cells align to structured collagen fibrils: A hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions
Authors: Keijzer Koen A.E. , Tsingos Erika , Merks Roeland M.H.
Published: July 2024

Many mammalian cells, including endothelial cells and fibroblasts, tend to align and elongate with the orientation of extracellular matrix (ECM) fibers in a gel when cultured in vitro. During cell elongation, clusters of focal adhesions (FAs) form near the poles of the elongating cells. FAs are mechanosensitive clusters of adhesions that grow under mechanical tension due to the cells’ pulling on the ECM, and shrink when the tension is released. Using a mathematical modeling approach, we study the hypothesis that reciprocity between cells and the ECM drives cell shape changes. We show that FAs are preferentially stabilized along the orientation of ECM fibers, where the cells can generate more tension than perpendicular to the ECM fibers. We present a hybrid cellular Potts model that represents the ECM as an off-the-lattice network of cross-linked deformable fibers, whereas the cell is represented on the lattice. Multiple FAs are modeled individually by an independent rate of FA assembly and a mechanoresponsive FA disassembly. The resulting computational model predicts stiffness-dependent cell spreading and local ECM remodelling, and ECM-alignment dependent cell elongation. The effects combined suffice to explain how cell morphology is determined by local ECM structure and mechanics.
Exercise training at different intensities induces heat stress, disrupts barrier function and alters microbiota in the gut of mice
Authors: Lian Puqiao , Kovynev Artemiy , Wang Lei , Pronk Amanda C. M. , Verhoeven Aswin , Giera Martin , Thijssen Suzan , Martínez Téllez Borja , Kooijman Sander , Rensen Patrick C. N. , Timmerman Harro , Wichers Harry J. , Henricks Paul A. J. , Folkerts Gert , Schönke Milena , Braber Saskia
Published: July 2024

Exercise is generally beneficial for health but strenuous exercise can have detrimental effects on the gastrointestinal tract. The combination of ischemia and heat shock during exercise is a crucial contributor to intestinal epithelial damage. Growing evidence points towards an important regulatory role of gut microbes in intestinal homeostasis. Here, we characterize and compare the effects of moderate and vigorous exercise training on intestinal epithelial damage, stress response, inflammatory response, and gut microbiota alterations in mice and investigate the mechanisms underlying exercise-induced intestinal injury. Exercise training for six weeks caused heat stress in the intestine, resulting in the disruption of the intestinal epithelial barrier and local inflammation. This was characterized by increased colonic HSP-70 and HSF-1 protein expression, increased epithelial permeability, decreased colonic expression of tight junction proteins ZO-1 and occludin and intestinal morphological changes. Daily moderate exercise training caused hereby more severe injury than vigorous training on alternating days. Furthermore, exercise training altered the gut microbiota profile. The abundance ofLactobacillaceaewas reduced, potentially contributing to the deteriorated intestinal status, while the abundance of short-chain fatty acid-producingLachnospiraceaewas increased, especially following vigorous training. This increase in short-chain fatty acid-producing bacteria following vigorous training possibly counteracted the impairment of the intestinal barrier function. In summary, exercise disrupts the intestinal barrier function, with vigorous exercise training with intermittent rest days being less damaging than daily moderate exercise training.
CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply
Authors: Jeong Tae-Kyeong , Frater Robert Ciaran MacKenzie , Yoon Jongha , Groth Anja , Song Ji-Joon
Published: July 2024

ASF1 is a major histone chaperone that regulates the supply of histone H3-H4 and facilitates nucleosome assembly to maintain chromatin structure during DNA replication and transcription. CODANIN-1 negatively regulates the function of ASF1. However, the molecular mechanism by which CODANIN-1 inhibits the ASF1-mediated histone supply remains elusive. Here, we present the electron microscopy (cryo-EM) structure of a human CODANIN-1_ASF1A complex at 3.75 Å resolution. The structure reveals that CODANIN-1 forms a dimer where each monomer holds two ASF1 molecules, utilizing two B-domains and two histone H3 mimic helices (HMHs). The interaction of CODANIN-1 with ASF1 via the HMH and B domains inhibits the formation of an ASF1/H3-H4 complex and sequesters ASF1 in the cytoplasm. Our study provides a structural and molecular basis for the function of CODANIN-1 as a unique negative regulator that highjacks ASF1 interaction sites with histones and downstream chaperones to inhibit nucleosome assembly.
Animacy semantic network supports implicit causal inferences about illness
Authors: Hauptman Miriam , Bedny Marina
Published: July 2024

Inferring the causes of illness is a culturally universal example of causal thinking. We tested the hypothesis that implicit causal inferences about biological processes (e.g., illness) depend on the animacy semantic network. Participants (n=20) undergoing fMRI read two-sentence vignettes that elicited causal inferences across sentences, either about the emergence of illness or about the mechanical breakdown of inanimate objects, in addition to noncausal control vignettes. All vignettes were about people and were linguistically matched. The same participants performed localizer tasks: language, logical reasoning, and mentalizing. Inferring illness causes, relative to all control conditions, selectively engaged a portion of the precuneus (PC) previously implicated in the semantic representation of animates (e.g., people, animals). Neural responses to causal inferences about illness were adjacent to but distinct from responses to mental state inferences, suggesting a neural mind/body distinction. We failed to find evidence for domain-general responses to causal inference. Implicit causal inferences are supported by content-specific semantic networks that encode causal knowledge.
Lipid Organization by the Caveolin-1 Complex
Authors: Liebl Korbinian , Voth Gregory A.
Published: July 2024

Caveolins are lipid-binding proteins that can organize membrane remodeling and oligomerize into the 8S-complex. The CAV1 8S-complex comprises a disk-like structure, about 15nm in diameter, with a central beta barrel. Further oligomerization of 8S-complexes remodels the membrane into caveolae vessels, with a dependence on cholesterol concentration. However, the molecular mechanisms behind membrane remodeling and cholesterol filtering are still not understood. Performing atomistic Molecular Dynamics simulations in combination with advanced sampling techniques, we describe how the CAV1-8S complex bends the membrane and accumulates cholesterol. Here, our simulations show an enhancing effect by the palmitoylations of CAV1, and we predict that the CAV1-8S complex can extract cholesterol molecules from the lipid bilayer and accommodate them in its beta barrel. Through backmapping to the all-atom level we also conclude that the Martini v2 coarse-grained forcefield overestimates membrane bending, as the atomistic simulations exhibit only very localized bending.
Enhancing the accuracy of genome-scale metabolic models with kinetic information
Authors: Lázaro Jorge , Wongprommoon Arin , Júlvez Jorge , Oliver Stephen G.
Published: July 2024

Metabolic models can be used to analyze and predict cellular features such as growth, gene essentiality, and product formation. There are several metabolic models but two of the main types are the constraint-based models and the kinetic models. Constraint-based models usually account for a large subset of the metabolic reactions of the organism and, in addition to the reaction stoichiometry, these models can accommodate gene regulation and constant flux bounds of the reactions. Constraint-based models are mostly limited to the steady state and it is challenging to optimize competing objective functions. On the other hand, kinetic models contain detailed kinetic information of a relatively small subset of metabolic reactions; thus, they can only provide precise predictions of a reduced part of an organism’s metabolism. We propose an approach that combines these two types of modeling to enrich metabolic genome-scale constraint-based models by re-defining their flux bounds. We apply our approach to the constraint-based model ofE. coli, both as a wild-type and when genetically modified to produce citramalate. We show that the enriched model has more realistic reaction flux boundaries. We also resolve a bifurcation of fluxes between growth and citramalate production present in the genetically modified model by fixing the growth rate to the value computed according to kinetic information, enabling us to predict the rate of citramalate production.

IMPORTANCE

The investigation addressed in this manuscript is crucial for biotechnology and metabolic engineering, as it enhances the predictive power of metabolic models, which are essential tools in these disciplines. Constraint-based metabolic models, while comprehensive, are limited by their steady-state assumption and difficulty in optimizing competing objectives, whereas kinetic models, though detailed, only cover a small subset of reactions. By integrating these two approaches, our novel methodology refines flux bounds in genome-scale models, leading to more accurate and realistic metabolic predictions. Key highlights include improved predictive accuracy through more realistic flux boundaries, application to both wild-type and genetically modifiedE. colifor citramalate production, successful resolution of the bifurcation between growth and product formation, and broad applicability to other organisms and metabolic engineering projects, paving the way for more efficient bioproduction processes.
Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer
Authors: McPherson Andrew , Vázquez-García Ignacio , Myers Matthew A. , Zatzman Matthew , Al-Rawi Duaa , Weiner Adam , Freeman Samuel , Mohibullah Neeman , Satas Gryte , Williams Marc J. , Ceglia Nicholas , Zhang Allen W. , Li Jun , Lim Jamie L.P. , Wu Michelle , Choi Seongmin , Havasov Eliyahu , Grewal Diljot , Shi Hongyu , Kim Minsoo , Schwarz Roland , Kaufmann Tom , Dinh Khanh Ngoc , Uhlitz Florian , Tran Julie , Wu Yushi , Patel Ruchi , Ramakrishnan Satish , Kim DooA , Clarke Justin , Green Hunter , Ali Emily , DiBona Melody , Varice Nancy , Kundra Ritika , Broach Vance , Gardner Ginger J. , Roche Kara Long , Sonoda Yukio , Zivanovic Oliver , Kim Sarah H. , Grisham Rachel N. , Liu Ying L. , Viale Agnes , Rusk Nicole , Lakhman Yulia , Ellenson Lora H. , Tavaré Simon , Aparicio Samuel , Chi Dennis S. , Aghajanian Carol , Abu-Rustum Nadeem R. , Friedman Claire F. , Zamarin Dmitriy , Weigelt Britta , Bakhoum Samuel F. , Shah Sohrab P.
Published: July 2024

Whole-genome doubling (WGD) is a critical driver of tumor development and is linked to drug resistance and metastasis in solid malignancies. Here, we demonstrate that WGD is an ongoing mutational process in tumor evolution. Using single-cell whole-genome sequencing, we measured and modeled how WGD events are distributed across cellular populations within tumors and associated WGD dynamics with properties of genome diversification and phenotypic consequences of innate immunity. We studied WGD evolution in 65 high-grade serous ovarian cancer (HGSOC) tissue samples from 40 patients, yielding 29,481 tumor cell genomes. We found near-ubiquitous evidence of WGD as an ongoing mutational process promoting cell-cell diversity, high rates of chromosomal missegregation, and consequent micronucleation. Using a novel mutation-based WGD timing method,doubleTime, we delineated specific modes by which WGD can drive tumor evolution: (i) unitary evolutionary origin followed by significant diversification, (ii) independent WGD events on a pre-existing background of copy number diversity, and (iii) evolutionarily late clonal expansions of WGD populations. Additionally, through integrated single-cell RNA sequencing and high-resolution immunofluorescence microscopy, we found that inflammatory signaling and cGAS-STING pathway activation result from ongoing chromosomal instability and are restricted to tumors that remain predominantly diploid. This contrasted with predominantly WGD tumors, which exhibited significant quiescent and immunosuppressive phenotypic states. Together, these findings establish WGD as an evolutionarily ‘active’ mutational process that promotes evolvability and dysregulated immunity in late stage ovarian cancer.
“Micro-offline gains” convey no benefit for motor skill learning
Authors: Das Anwesha , Karagiorgis Alexandros , Diedrichsen Jörn , Stenner Max-Philipp , Azañón Elena
Published: July 2024

While practising a new motor skill, resting for a few seconds can improve performance immediately after the rest. This improvement has been interpreted as rapid offline learning1,2(“micro-offline gains”, MOG), supported by neural replay of the trained movement sequence during rest3. Here, we provide evidence that MOG reflect transient performance benefits, partially mediated by motor planning, and not replay-mediated offline learning. In five experiments, participants trained to produce a sequence of finger movements as many times as possible during fixed-duration practice periods. When participants trained during 10-second practice periods, each followed by a 10-second rest period, they produced more correct keypresses during training than participants who trained without taking breaks. However, this benefit vanished within seconds after the end of training, when both groups performed under comparable conditions, revealing similar levels of skill acquisition. This challenges the idea that MOG reflect offline learning, which, if present, should result in sustained performance benefits, compared to training without breaks. Furthermore, sequence-specific replay was not necessary for MOG, given that we observed persistent MOG when participants produced random sequences that never repeated, preventing any effect of (sequence-specific) replay on the performance. Importantly, we observed diminished MOG when participants could not pre-plan the first few movements of an upcoming practice period. We conclude that “micro-offline gains” represent short-lived performance benefits that are partially driven by motor pre-planning, rather than replay-mediated offline learning.
An extreme mutational hotspot innlpDdepends on transcriptional induction ofrpoS
Authors: Farr Andrew D. , Vasileiou Christina , Lind Peter A. , Rainey Paul B.
Published: July 2024

Mutation rate varies within and between genomes. Within genomes, tracts of nucleotides, including short sequence repeats and palindromes, can cause localised elevation of mutation rate. Additional mechanisms remain poorly understood. Here we report an instance of extreme mutational bias inPseudomonas fluorescensSBW25 associated with a single base-pair change innlpD.These mutants frequently evolve in static microcosms, and have a cell-chaining (CC) phenotype. Analysis of 153 replicate populations revealed 137 independent instances of a C565T loss-of-function mutation at codon 189 (CAG to TAG (Q189*)). Fitness measures of alternativenlpDmutants showed molecular parallelism to be unconnected to selective advantage. Recognising that transcription can be mutagenic, and that codon 189 overlaps with a predicted promoter (rpoSp) for the adjacent stationary phase sigma factor,rpoS, transcription across this promoter region was measured. This confirmedrpoSpis induced in stationary phase and that C565T mutation caused significant elevation of transcription. The latter provided opportunity to determine the C565T mutation rate using a reporter-gene fused torpoSp. Fluctuation assays demonstrate the C565T mutation rate to be 5,700-fold higher than expected. InPseudomonas, transcription ofrpoSrequires the positive activator PsrA, which we show also holds for SBW25. Fluctuation assays performed in a ΔpsrAbackground showed a 60-fold reduction in mutation rate confirming that the elevated rate of mutation at C565T mutation rate is dependent on induction of transcription. This hotspot suggests a generalisable phenomenon where the induction of transcription causes elevated mutation rates within defining regions of promoters.
Accurate isoform quantification by joint short- and long-read RNA-sequencing
Authors: Apostolides Michael , Choi Benedict , Navickas Albertas , Saberi Ali , Soto Larisa M. , Goodarzi Hani , Najafabadi Hamed S.
Published: July 2024

Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing RNA sequencing methods have significant limitations: short-read (SR) sequencing provides high depth but struggles with isoform deconvolution, whereas long-read (LR) sequencing offers isoform resolution at the cost of lower depth, higher noise, and technical biases. Addressing this gap, we introduce Multi-Platform Aggregation and Quantification of Transcripts (MPAQT), a generative model that combines the complementary strengths of different sequencing platforms to achieve state-of-the-art isoform-resolved transcript quantification, as demonstrated by extensive simulations and experimental benchmarks. By applying MPAQT to an in vitro model of human embryonic stem cell differentiation into cortical neurons, followed by machine learning-based modeling of transcript abundances, we show that untranslated regions (UTRs) are major determinants of isoform proportion and exon usage; this effect is mediated through isoform-specific sequence features embedded in UTRs, which likely interact with RNA-binding proteins that modulate mRNA stability. These findings highlight MPAQT’s potential to enhance our understanding of transcriptomic complexity and underline the role of splicing-independent post-transcriptional mechanisms in shaping the isoform and exon usage landscape of the cell.
DNA supercoiling enhances DNA condensation by ParB proteins
Authors: Martin Gonzalez Alejandro , Tišma Miloš , Analikwu Brian T. , Barth Anders , Janissen Richard , Antar Hammam , Kemps Gianluca , Gruber Stephan , Dekker Cees
Published: July 2024

The ParABS system plays a critical role in bacterial chromosome segregation. The key component of this system, ParB, loads and spreads along DNA to form a local protein-DNA condensate known as a partition complex. As bacterial chromosomes are heavily supercoiled due to the continuous action of RNA polymerases, gyrases, and nucleoid-associated proteins, it is important to study the impact of DNA supercoiling on the ParB-DNA partition complex formation. Here, we use anin vitrosingle- molecule assay to visualize ParB on supercoiled DNA. Unlike most DNA-binding proteins, individual ParB proteins are found to not pin plectonemes on supercoiled DNA, but freely diffuse along supercoiled DNA. We find that DNA supercoiling enhances ParB-DNA condensation which initiates at lower ParB concentrations than on DNA that is torsionally relaxed. ParB proteins induce a DNA- protein condensate that strikingly absorbs all supercoiling writhe. Our findings provide mechanistic insights that have important implications for our understanding of bacterial chromosome organization and segregation.
Sex-specific DNA methylation signatures of autism spectrum disorder in newborn blood
Authors: Mouat Julia S. , Krigbaum Nickilou Y. , Hakam Sophia , Thrall Emily , Kuodza George E. , Mellis Julia , Yasui Dag H. , Cirillo Piera M. , Ludena Yunin , Schmidt Rebecca J. , La Merrill Michele A. , Hertz-Picciotto Irva , Cohn Barbara A. , LaSalle Janine M.
Published: July 2024

Background

Autism spectrum disorder(ASD)comprises a group of neurodevelopmental conditions currently diagnosed by behavioral assessment in childhood, although neuropathology begins during gestation. A poorly understood male bias for ASD diagnosis is thought to be due to both biological sex differences and cultural biases against female diagnosis of ASD. Identification of molecular biomarkers of ASD likelihood in newborns would provide more objective screening and early intervention. Epigenetic dysregulation has been reported in multiple tissues from newborns who are later diagnosed with ASD, but this is the first study to investigate sex-specific DNA methylation signatures for ASD in newborn blood, an accessible and widely banked tissue.

Methods

DNA methylation was assayed from ASD and typically developing(TD)newborn blood (discovery setn= 196, replication setn= 90) using whole genome bisulfite sequencing(WGBS). Sex-stratified differentially methylated regions(DMRs)were assessed for replication, comparisons by sex, overlaps with DMRs from other tissues, and enrichment for biological processes and SFARI ASD-risk genes.

Results

We found that newborn blood ASD DMRs from both sexes significantly replicated in an independent cohort and were enriched for hypomethylation in ASD compared to TD samples, as well as location in promoters, CpG islands and CpG shores. Comparing females and males, we found that most DMRs with sex differences amongst TD individuals were also found in ASD individuals, plus many additional DMRs with sex differences that were only found in those with ASD. Newborn blood DMRs from females were enriched for the X chromosome and both sexes showed significant overlap with DMRs from umbilical cord blood and placenta but not post-mortem cortex. DMRs from all tissues were enriched for neurodevelopmental processes (females) and SFARI ASD-risk genes (females and males).

Limitations

This study is primarily limited by sample sizes, particularly amongst females.

Conclusions

Overall, we found a highly replicated sex-specific DNA methylation signature of ASD in newborn blood that showed support for the female protective effect and convergence with epigenetic and genetic signatures of ASD in newborns. These results demonstrate the utility of newborn blood in ASD screening and emphasizes the importance of sex-stratification in future studies.
Previously unknown regulatory role of extracellular RNA on bacterial directional migration
Authors: Tetz Victor , Kardava Kristina , Vecherkovskaya Maria , Khodadadi-Jamayran Alireza , Tsirigos Aristotelis , Tetz George
Published: July 2024

Bacterial directional migration plays a significant role in bacterial adaptation. However, the regulation of this process, particularly in young biofilms, remains unclear.

Here, we demonstrated the critical role of extracellular RNA as part of the Universal Receptive System in bacterial directional migration using a multidisciplinary approach, including bacterial culture, biochemistry, and genetics.

We found that the destruction or inactivation of extracellular RNA with RNase or RNA-specific antibodies in the presence of the chemoattractant triggered the formation of bacterial “runner cells» in what we call a “panic state” capable of directional migration. These cells quickly migrated even on the surface of 1.5% agar and formed evolved colonies that were transcriptionally and biochemically different from the ancestral cells. We have also shown that cell-free DNA from blood plasma can act as a potent bacterial chemoattractant. Our data revealed a previously unknown role of bacterial extracellular RNA in the regulation of bacterial migration and have shown that its destruction or inhibition triggered the directional migration of developing and mature biofilms towards the chemoattractant.
Seasonal influenza A virus lineages exhibit divergent abilities to antagonize interferon induction and signaling
Authors: Rivera-Cardona Joel , Kakuturu Neeha , Rowland Elizabeth F , Teo Qi Wen , Thayer Elizabeth A , Tan Timothy J.C. , Sun Jiayi , Kieffer Collin , Wu Nicholas C. , Brooke Christopher B
Published: July 2024

The circulation of seasonal influenza A viruses (IAVs) in humans relies on effective evasion and subversion of the host immune response. While the evolution of seasonal H1N1 and H3N2 viruses to avoid humoral immunity is well characterized, relatively little is known about the evolution of innate immune antagonism phenotypes in these viruses. Numerous studies have established that only a small subset of infected cells is responsible for initiating the type I and type III interferon (IFN) response during IAV infection, emphasizing the importance of single cell studies to accurately characterize the IFN response during infection. We developed a flow cytometry-based method to examine transcriptional changes in IFN and interferon stimulated gene (ISG) expression at the single cell level. We observed that NS segments derived from seasonal H3N2 viruses are more efficient at antagonizing IFN signaling but less effective at suppressing IFN induction, compared to the pdm2009 H1N1 lineage. We compared a collection of NS segments spanning the natural history of the current seasonal IAV lineages and demonstrate long periods of stability in IFN antagonism potential, punctuated by occasional phenotypic shifts. Altogether, our data reveal significant differences in how seasonal and pandemic H1N1 and H3N2 viruses antagonize the human IFN response at the single cell level.
Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities
Authors: Morimoto Juliano , Pietras Zuzanna
Published: July 2024

Background

Amino acids are the building blocks of proteins and enzymes, which are pivotal for life on Earth. Amino acid usage provides critical insights into the functional constraints acting on proteins and illuminates molecular mechanisms underpinning traits. Despite this, we have limited knowledge of the genome-wide signatures of amino acid usage across domains of life, precluding new genome and proteome patterns to being discovered.

Results

Here, we analysed the proteomes of 5,590 species across four domains of life and found that only a small subset of amino acids is most and least frequently used across proteomes. This creates a ubiquitous ‘edge effect’ on amino acid usage diversity by rank that arises from protein secondary structural constrains. This edge effect was not driven by the evolutionary chronology of amino acids, showing that functional rather than evolutionary constrains shape amino acid usage in the proteome. We also tested contemporary hypotheses about similarities in amino acid usage profiles and the relationship between amino acid usage and growth temperature, and found that, contrary to previous beliefs, amino acid usage varies across domains of life and temperature only weakly contributes to variance in amino acid usage.

Conclusion

We have described a novel and ubiquitous pattern of amino acid usage signature across genomes, which reveals how structural constrains shape amino acid usage at the proteome level. This can ultimately influence the way in which we probe deep evolutionary relationships of protein families across the tree of life and engineer biology in synthetic biology.
Ribosomal DNA arrays are the most H-DNA rich element in the human genome
Authors: Chantzi Nikol , Patsakis Michail , Nayak Akshatha , Montgomery Austin , Mouratidis Ioannis , Georgakopoulos-Soares Ilias
Published: July 2024

Repetitive DNA sequences can form non-canonical structures such as H-DNA which is an intramolecular triplex DNA structure. The new Telomere-to-Telomere (T2T) genome assembly for the human genome has eliminated gaps, enabling the examination of highly repetitive regions including centromeric and pericentromeric repeats and ribosomal DNA arrays. This gapless assembly allows for the examination of the distribution of H-DNA sequences in parts of the human genome that were not previously annotated. We find that H-DNA appears once every 30,000 bps in the human genome. Its distribution is highly inhomogeneous with H-DNA motif hotspots being detectable in acrocentric chromosomes. Ribosomal DNA arrays in acrocentric chromosomes are the genomic element with the highest H-DNA enrichment, with 13.22% of total H-DNA motifs being found in ribosomal DNA arrays, representing a 42.65-fold enrichment over what would be expected by chance. Across the acrocentric chromosomes we report that 55.87% of all H-DNA motifs found in these chromosomes are in rDNA array loci. The H-DNA motifs are primarily found in the intergenic spacer regions of the ribosomal DNA arrays, generating repeated clusters. We also discover that binding sites for PRDM9, a protein that regulates the formation of double-strand breaks and determines the meiotic recombination hotspots in humans and most mammals, are over 5-fold enriched for H-DNA motifs. Finally, we provide evidence that our findings are consistent in other non-human great ape genomes. We conclude that ribosomal DNA arrays are the most enriched genomic loci for H-DNA sequences in human and other great ape genomes.
The mitochondrial Na+/Ca2+exchanger NCLX is implied in the activation of hypoxia-inducible factors
Authors: Choya-Foces Carmen , Hernansanz-Agustín Pablo , Navarro Elisa , López Manuela G. , Egea Javier , Martínez-Ruiz Antonio
Published: July 2024

Eukaryotic cells and organisms depend on oxygen for basic living functions, and they display a panoply of adaptations to situations in which oxygen availability is diminished (hypoxia). A number of these responses in animals are mediated by changes in gene expression programs directed by hypoxia-inducible factors (HIFs), whose main mechanism of stabilization and functional activation in response to decreased cytosolic oxygen concentration was elucidated two decades ago. Human acute responses to hypoxia have been known for decades, although their precise molecular mechanism for oxygen sensing is not fully understood. It is already known that a redox component, linked with reactive oxygen species (ROS) production of mitochondrial origin, is implied in these responses. We have recently described a mechanism by which the mitochondrial sodium/calcium exchanger, NCLX, participates in mitochondrial electron transport chain regulation and ROS production in response to acute hypoxia.

Here we show that NCLX is also implied in the response to hypoxia mediated by the HIFs. By using a NCLX inhibitor and interference RNA we show that NCLX activity is necessary for HIF-α subunits stabilization in hypoxia and for HIF-1-dependent transcriptional activity. We also show that hypoxic mitochondrial ROS production is not required for HIF-1α stabilization under all circumstances, suggesting that other mechanism(s) could be operating in the NCLX-mediated response to hypoxia that operates through HIF-α stabilization. This finding provides a link between acute and medium-term responses to hypoxia, reinforcing a central role of mitochondrial cell signalling in the response to hypoxia.
The association between metabolite concentrations and wellbeing in adults
Authors: Azcona-Granada Natalia , Geijsen Anne J.M.R. , Pool René , Pelt Dirk H. M. , Bartels Meike
Published: July 2024

The biological complexity of wellbeing is studied from various perspectives, including genetics and epigenetics. However, there is a knowledge gap concerning other layers, such as metabolomics, which is dynamic and changes throughout life. This study explores the association between metabolites and wellbeing in a sample (N = 4748) drawn from the Netherlands Twin Register. A latent factor score for wellbeing was constructed based on: Quality of Life, Life Satisfaction, and Subjective Happiness. A total of 231 blood metabolites were analyzed using1HNMR technique. Linear regression models were performed for each metabolite, while correcting for family clustering, relevant covariates, and multiple testing. None of the metabolites were significantly associated with wellbeing after multiple testing correction. Despite the lack of significant findings, the 34 metabolites with the lowestp-value (0.25) pointed to the same metabolic pathway: endogenous lipid metabolism. This pathway has previously been linked to wellbeing in a GWAS and associated with related phenotypes in other metabolomic studies. In conclusion, this study confirms the biological complexity of wellbeing and speculates on a potential role of lipids. Further research is needed to confirm these hypotheses.
Exploring Anatomical Links Between the Crow’s Nidopallium Caudolaterale and its Song System
Authors: Moll Felix W. , Kersten Ylva , Erdle Saskia , Nieder Andreas
Published: July 2024

Crows are corvid songbirds that exhibit remarkable cognitive control over their actions, including their vocalizations. They can learn to vocalize on command and the activity of single neurons from the crow’s associative telencephalic structure nidopallium caudolaterale (NCL) is correlated with the execution of this vocal and many non-vocal skilled behaviors. However, it remains unknown if specific anatomical adaptations that directly link the crow NCL to any of the nuclei of the crow’s “song system” exist. To address this issue, we used fluorescent tracers along with histological staining methods (Nissl-, myelin-, and anti tyrosine hydroxylase) to characterize the connectivity of the crow’s NCL in relation to its song system nuclei. We found that the NCL sends dense projections into the dorsal intermediate arcopallium (AID) directly adjacent to and engulfing the robust nucleus of the arcopallium (RA), which is the telencephalic motor output of the song system. Similarly, we demonstrate dense NCL projections into the striatum surrounding the basal ganglia song nucleus “area X”. Both of these descending projections mirror the projections of the nidopallial song nucleus HVC (proper name) into RA and area X, with extremely sparse NCL fibers extending into area X. Furthermore, we characterized the distribution of cells projecting from the lateral part of the magnocellular nucleus of the anterior nidopallium (MAN) to NCL. Notably, a separate medial population of MAN cells projects to HVC. These two sets of connections—MAN to NCL and MAN to HVC—run in parallel but do not overlap. Taken together, our findings support the hypothesis that the NCL is part of a “general motor system” that parallels the song system but exhibits only minimal monosynaptic interconnections with it.
Fromin vitrotoin silico: a pipeline for generating virtual tissue simulations from real image data
Authors: Nürnberg Elina , Vitacolonna Mario , Bruch Roman , Reischl Markus , Rudolf Rüdiger , Sauer Simeon
Published: July 2024

3D cell culture models replicate tissue complexity, aiming to study cellular interactions and responses in a more physiologically relevant environment compared to traditional 2D cultures. However, the spherical structure of these models makes it difficult to extract meaningful data, necessitating advanced techniques for proper analysis. In silico simulations enhance research by predicting cellular behaviors and therapeutic responses, providing a powerful tool to complement experimental approaches. Despite their potential, these simulations often require advanced computational skills and significant resources, creating a barrier for many researchers.

To address these challenges, we developed an accessible pipeline using open-source software to facilitate virtual tissue simulations. Our approach employs the Cellular Potts Model, a versatile framework for simulating cellular behaviors in tissues. The simulations are constructed from real world 3D image stacks of cancer spheroids, ensuring the virtual models are rooted in experimental data. By introducing a new metric for parameter optimization, we enable the creation of realistic simulations without requiring extensive computational expertise. This pipeline benefits researchers wanting to incorporate computational biology into their methods, even if they do not possess extensive expertise in this area. By reducing the technical barriers associated with advanced computational modeling, our pipeline allows more researchers to utilize these powerful tools. Our approach aims to foster broader use ofin silicomethods in disease research, contributing to a deeper understanding of disease biology and the refinement of therapeutic interventions.
Rep structures comprise metastable intermediates between open and closed states whose transitional kinetics are tuned by the ionic environment
Authors: Howard Jamieson A L , Ambrose Benjamin , Abdelhamid Mahmoud A S , Alevropoulos-Borrill Antoinette , Ejaz Ayesha , Dresser Lara , Dienerowitz Maria , Quinn Steven D , Squires Allison H , Noy Agnes , Craggs Timothy David , Leake Mark C
Published: July 2024

Helicases undergo conformational changes in the presence or absence of the DNA substrate and cofactors, however, the forces driving these structural dynamics are poorly understood. Here, we study single molecules of Rep, an accessory helicase which undergoes conformational transitions during bacterial DNA replication, repair and recombination. We use time-correlated single-photon counting, fluorescence correlation spectroscopy, rapid single-molecule Förster resonance energy transfer, Anti-Brownian ELectrokinetic trapping and molecular dynamics simulations to provide unparalleled temporal and spatial resolution of Rep's domain movement. Our rapid measurements reveal hitherto hidden intermediates between open and closed conformations, several of which are strongly dependent on sodium chloride concentration. Our findings suggest that the transition between open and closed conformations is not a simple single arm-swing mechanism but comprises different salt-dependent metastable states. They also support an alternative binding model for accessory helicases that utilises conformational plasticity to explore a multiplicity of structures whose landscape can be tuned by the ionic environment prior to locking-in upon DNA binding.