bluuebunny/crossref_metadata_2025 huggingface dataset:
Tillage homogenizes soil bacterial communities in microaggregate fractions by facilitating dispersal
Authors: West Jaimie R. , Lauer Joseph G. , Whitman Thea
Published: March 2023

Soil aggregation physically protects soil organic matter and promotes soil carbon persistence through microaggregate formation and organo-mineral associations. Tillage is a ubiquitous disturbance to arable soil that disrupts aggregation, thus affecting microbial resource availability, soil microhabitat conditions, and microbial interactions. We investigated how tillage affects bacterial community composition of soil microaggregate fractions (53–250 µm), specifically the free microaggregate fraction in bulk soil, and the occluded microaggregate fraction from within macroaggregates, using two long-term tillage vs. no-tillage experiments in southern WI, U.S., that represent two different silt loam soils (Alfisol and Mollisol). We applied 16S rRNA gene amplicon sequencing to characterize the effects of tillage on microaggregate bacterial communities by relating compositional changes and ecological community assembly patterns to various tillage-driven changes in the soil environment, including aggregate size distribution and carbon content. Tillage homogenized soil bacterial communities, as quantified by increased compositional similarity at both within-plot and between-plot scales, and community assembly was increasingly influenced by homogenizing dispersal with tillage. We did not identify major distinctions between bacterial communities of the free and occluded microaggregate fractions, thus highlighting how soil microaggregates readily shift between these operationally defined fractions in temperate annual cropping systems, where the soil environment is subject to drastic seasonal changes that are exacerbated by tillage. With this study, we improve our understanding of the microbial response to soil disturbance, and thus the potential mechanisms through which disturbances like tillage affect soil carbon persistence.

Highlights

Tillage homogenized soil bacterial communities, within and between plots

Homogenizing dispersal drove community assembly under tillage

Free and occluded microaggregate fractions hosted similar communities
Molecular Weight-dependent Diffusion, Biodistribution, and Clearance Behavior of Tetra-armed Poly(ethylene glycol) Subcutaneously Injected into the Back of Mice
Authors: Ishikawa Shohei , Kato Motoi , Si Jinyan , Yu Lin Chen , Kimura Kohei , Katashima Takuya , Naito Mitsuru , Kurita Masakazu , Sakai Takamasa
Published: March 2023

Four-armed poly(ethylene glycol) (PEG)s are essential hydrophilic polymers extensively utilized to prepare PEG hydrogels, which are valuable tissue scaffolds. When hydrogels are usedin vivo, they eventually dissociate due to the cleavage of the backbone structure. When the cleavage occurs at the cross-linking point, the hydrogel elutes as an original polymer unit, i.e., four-armed PEG. Although four-armed PEGs have been utilized as subcutaneously implanted biomaterials, the diffusion, biodistribution, and clearance behavior of four-armed PEG from the skin are essential. This paper investigates time-wise diffusion from the skin, biodistribution to distant organs, and clearance of fluorescence-labeled four-armed PEGs with molecular weight (Mw) ranging from 5–40 kg/mol subcutaneously injected into the back of mice. Changes over time indicated that the fate of subcutaneously injected PEGs isMw-dependent. Four-armed PEGs withMw≤ 10 kg/mol gradually diffused to deep adipose tissue beneath the injection site and distributed dominantly to distant organs, such as the kidney. PEGs withMw≥ 20 kg/mol stagnated in the skin and deep adipose tissue, and were mainly delivered to the heart, lung, and liver. The fundamental understanding of theMw-dependent behavior of four-armed PEGs is beneficial for preparing biomaterials using PEGs, providing a reference in the field of tissue engineering.
Transgenerational effects of exercise on mouse brain and cognition
Authors: Cintado Elisa , Tezanos Patricia , De las Casas Manuela , Muela Pablo , McGreevy Kerry R. , Fontán-Lozano Ángela , Sacristán-Horcajada Eva , Pignatelli Jaime , de Ceballos María L. , del Hierro María Jesús , Fernández-Punzano Julia , Montoliu Lluis , Trejo José Luis
Published: March 2023

Lifestyle induces long lasting effects on brain and cognition, with some interventions like stress including transgenerational inheritance mediated by epigenetic mechanisms. Physical exercise is one lifestyle intervention driving robust improvements of cognition, including intergenerational transmission to the litter. However, little is known about whether exercise effects are transgenerationally transmitted. Here we analyzed adult hippocampal neurogenesis (AHN) and behavioral phenotype of sedentary adult male mice of F2 generation of exercised grandfathers (F0). Both F1 and F2 were sedentary, while F0 performed moderate exercise. We found F2 mice from exercised F0 acquired and recalled both spatial and non-spatial information better than F2 from sedentary F0. Contextual fear conditioning was not affected, together with no differences in AHN markers. Hippocampal smallRNAseq analysis revealed 35 significant differentially expressed (sDE) microRNAs (miRNAs) associated to relevant brain function families. Moreover, 11 of the 35 miRNAs target gene sets were found also enriched in F0 and F1, as well as target genes of 6 of them were differentially expressed also in F0 or F1. One of these 6 is miRNA-144, that together with miRNA-298 were found inversely correlated to cognitive index in F2. These results demonstrate that transgenerational transmission of the effects of exercise on specific cognitive tasks persists after two generations, even though some cellular changes induced in F1 vanish in F2. Thus, they suggest moderate exercise training has longer-lasting effects than previously thought, probably mediated by a small group of miRNAs acting across generations, and this is worth taking into account in public health programs.
Membrane and glycocalyx tethering of DNA nanostructures for enhanced uptake
Authors: Wang Weitao , Chopra Bhavya , Walawalkar Vismaya , Liang Zijuan , Adams Rebekah , Deserno Markus , Ren Xi , Taylor Rebecca E.
Published: March 2023

DNA nanostructures (DNs) have been increasingly utilized in biosensing, drug delivery, diagnostics and therapeutics, because of their programmable assembly, control over size and shape, and ease of functionalization. However, the low cellular uptake of DNs has limited their effectiveness in these biomedical applications. Here we demonstrate the potential of membrane and glycocalyx binding as general strategies to enhance the cellular uptake of DNs. By targeting the plasma membrane and cell-surface glycocalyx, the uptake of all three distinct DNs is significantly enhanced as compared to uptake of bare DNs. We also demonstrate the viability of single-step membrane labeling by cholesterol-DNs as competitive with previous multistep approaches. Further, we show that the endocytic pathway of membrane-bound DNs is an interdependent process that involves scavenger receptors, clathrin-, and caveolinmediated endocytosis. Our findings may potentially expand the toolbox for effective cellular delivery of DNA nanostructured systems.
ReCo: automated NGSread-counting of single and combinatorial CRISPR gRNAs
Authors: Wegner Martin , Kaulich Manuel
Published: March 2023

CRISPR screens are increasingly performed to associate genotypes with genotypes. So far, however, their analysis required specialized computational knowledge to transform high-throughput next-generation sequencing (NGS) data into sequence formats amenable for downstream analysis. We developed ReCo, a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data. Together with cutadapt and bowtie2 for rapid sequence trimming and alignment, ReCo enables the automated generation of read count tables from staggered NGS reads for the downstream identification of gRNA-induced phenotypes.

Availability and implementation

ReCo is published under the MIT license and available at:https://github.com/KaulichLab/ReCo.

Supplementary information

Supplementary data are available at Bioinformatics online.
Discovery of 1,3,4-oxadiazoles with slow-action activity againstPlasmodium falciparummalaria parasites
Authors: Andrews Katherine T. , Fisher Gillian M. , Firmin Meaghan , Liepa Andris J. , Wilson Tony , Gardiner James , Mohri Yacine , Rai Anjana , Davey Andrew K. , Masurier Antoine , Delion Alix , Mouratidis Alexandos A. , Hutt Oliver , Burrows Jeremy N. , Ryan John H. , Riches Andrew G. , Skinner-Adams Tina S.
Published: March 2023

To achieve malaria eradication, new preventative agents that act differently to front-line treatment drugs are needed. To identify potential chemoprevention starting points we screened a sub-set of the CSIRO Australia Compound Collection for compounds with slow-actionin vitroactivity againstPlasmodium falciparum. This work identifiedN,N-dialkyl-5-alkylsulfonyl-1,3,4-oxadiazol-2-amines as a new antiplas-modial chemotype (e.g.,196 h IC50550 nM) with a different action to delayed-death slow-action drugs. Structure activity relationship analysis of analogues identified multiple compounds with potent and selectivein vitroactivity against drug-sensitive and multi-drug resistantPlasmodiumparasites (e.g.,31and3296 h IC50<40 nM; SI >2,500). However subsequent studies in mice with lead compound1, which had the best microsomal stability of the compounds assessed, demonstrated rapid clearance (T1/2<1.6 h) and poor oralin vivoefficacy. This indicates that improvements in the pharmacokinetic profile ofN,N-dialkyl-5-alkylsulfonyl-1,3,4-oxadiazol-2-amines would be needed for the development of this chemotype for malaria chemoprophylaxis.
Real-time tractography-assisted neuronavigation for TMS
Authors: Aydogan Dogu Baran , Souza Victor H. , Matsuda Renan H. , Lioumis Pantelis , Ilmoniemi Risto J.
Published: March 2023

Background

State-of-the-art navigated transcranial magnetic stimulation (nTMS) systems can display the TMS coil position relative to the structural magnetic resonance image (MRI) of the subject’s brain and calculate the induced electric field. However, the local effect of TMS propagates via the white-matter network to different areas of the brain, and currently there is no commercial or research neuronavigation system that can highlight in real time the brain’s structural connections during TMS.

Objective

To develop a real-time tractography-assisted TMS neuronavigation system and investigate its feasibility.

Method

We propose a modular framework that seamlessly integrates offline (preparatory) analysis of diffusion MRI data with online (real-time) tractography. For tractography and neuronavigation we combine our custom software Trekker and InVesalius, respectively. We evaluate the feasibility of our system by comparing online and offline tractography results in terms of streamline count and their overlap.

Results

A real-time tractography-assisted TMS neuronavigation system is developed. Key features include the application of state-of-the-art tractography practices, the ability to tune tractography parameters on the fly, and the display of thousands of new streamlines every few seconds using a novel uncertainty visualization technique. We demonstrate in a video the feasibility and quantitatively show the agreement with offline filtered streamlines.

Conclusion

Real-time tractography-assisted TMS neuronavigation is feasible. With our system, it is possible to target specific brain regions based on their structural connectivity, and to aim for the fiber tracts that make up the brain’s networks.
Neural mechanisms of costly helping in the general population and mirror-pain synesthetes
Authors: Ioumpa Kalliopi , Gallo Selene , Keysers Christian , Gazzola Valeria
Published: March 2023

Helping others often comes with a cost to ourselves. It has been argued that experiencing the pain of others motivates helping. Here we investigate how individuals that report somatically feeling the pain of others (mirror-pain synesthetes) differ from those that do not, when deciding to help and reduce someone’s pain conveyed through different modalities. Mirror-pain synesthetes and participants who do not report such everyday life experiences witnessed a confederate expressing pain and could decide to reduce the intensity by donating money. Measuring brain activity using fMRI confirmed our initial hypothesis: self-reported mirror-pain synesthetes increased their donation more steeply, as the intensity of the observed pain increased, and their somatosensory brain activity (in SII and the adjacent IPL) activity was more tightly associated with donation when the pain of other was conveyed by the reactions of the pain-receiving hand. For all participants, in a condition where the pain was conveyed by facial expressions, activation in insula, SII and MCC correlated with the trial by trial donation made, while SI and MTG activation was correlated with the donation in the Hand condition. These results further inform us about the role of empathy in costly helping, the underlying neural mechanism, and individual variability.
RNA allelic frequencies of somatic mutations encode substantial functional information in cancers
Authors: Black James R.M. , Jones Thomas P. , Martínez-Ruiz Carlos , Litovchenko Maria , Puttick Clare , McGranahan Nicholas
Published: March 2023

A central goal of cancer research is the identification of cancer genes that drive tumour growth and progression. Existing approaches to this problem typically leverage frequentist approaches based on patterns of somatic mutagenesis in DNA. Here, we interrogate RNA variant allele frequencies to identify putative cancer genes with a novel computational tool,RVdriver, from bulk genomic-transcriptomic data within 7,948 paired exomes and transcriptomes across 30 cancer types. An elevated RNA VAF reflects a signal from multiple biological features: clonal mutations; mutations retained or gained during somatic copy-number alterations; mutations favoured by allele-specific expression; and mutations in genes expressed preferentially by the tumour compartment of admixed bulk samples.RVdriver, a statistical approach that classifies RNA VAFs of nonsynonymous mutations relative to a synonymous mutation background, leverages this information to identify known, as well as putatively novel, cancer genes, with comparable performance to DNA-based approaches. Furthermore, we demonstrate RNA VAFs of individual mutations are able to distinguish ‘driver’ from ‘passenger’ mutations within established cancer genes. Low-RNA VAFEGFRmutations otherwise annotated as drivers of glioblastoma by DNA tools harbour a phenotype of reduced EGFR signalling, whilst high-RNA VAFKDM6Amutations otherwise annotated as passengers exhibit a driver-like H3K27me3 expression profile, demonstrating the value of our approach in phenotyping tumours. Overall, our study showcases a novel approach for cancer gene discovery, and highlights the potential value of multi-omic and systems-biology approaches in finding novel therapeutic vulnerabilities in cancer to bring about patient benefit.
Topographical similarity of cortical thickness represents generalized anxiety symptoms in adolescence
Authors: Yoo Chaebin , Kim M. Justin
Published: March 2023

Generalized anxiety disorder (GAD) is a common condition characterized by excessive, uncontrollable worry. Despite increasing efforts to identify the neural underpinnings of GAD, neuroimaging research using cortical thickness have yielded largely inconsistent results. To address this, we adopted an inter-subject representational similarity analysis framework and utilized a sample of 120 adolescents (13 to 18 years of age) from the Healthy Brain Network dataset. We found greater topographical resemblance among participants with heightened generalized anxiety symptoms in the left caudal anterior cingulate and pericalcarine cortex. Such associations were not observed when including a group of younger participants (11 to 12 years of age), highlighting the importance of age range selection when considering the link between cortical thickness and anxiety. Our findings reveal a novel cortical thickness topography that represents generalized anxiety in adolescents, which is embedded within the shared geometries between generalized anxiety symptoms and cortical thickness.
Erythrocyte ghosts and Plasma beads as Antigen peptide delivery systems in animals and humans
Authors: Jameel M. Rizwan , Jameel Hina , Mustafa Saad , Khan Mohd Faisal , Misbah Mohammad
Published: March 2023

Erythrocytes are the most plentiful cells of the human body with desirable morphologic and physiologic characteristics and their function in drug delivery has been exploited comprehensively. These cellular carriers, containing significant biodegradability, biocompatibility, and duration in circulation, can be burdened by a wide spectrum of compounds of therapeutic interest Carrier erythrocytes holding drugs, enzymes or peptides, Cas, and Nanoparticles can be used as a delivery system that approval to changes in the kinetic behavior and selective bio-distribution of the substances encapsulated. Carrier erythrocytes have been exploited for numerous potential applications, including the intravenous slow release of drug targeting, therapeutic agents and enzyme therapy to a reticuloendothelial system (RES). Hypotonic dialysis is the process most usually utilized in the formation of erythrocytes of carrier, however many features concern the give up and the erythrocytes ghost characteristics obtained with this technique. Attempt was also completed observe but erythrocyte regular release entrapped substances/antigens with additional entrapment in the plasma beads, improves the protein immunogenicity. The glycoenzyme invertase of large molecular weight was utilized a model substance and entrapment of invertase consummate with the dialysis method. Enzyme entrapment was examined in derived erythrocytes from rabbits, goats and human. Intended for the immunological studies were used in the rabbits. Invertase entrapped erythrocytes rabbit, where point out was additional encapsulated in the plasma beads and a contrast of immunogenicity of lose invertase, entrapped invertase in erythrocytes and that entrapped in RBCs and additional in encapsulated the plasma beads were examined. Antibodies production was investigated are different periods such as 12, 20, 20 and 35 days.
Neurons from pre-motor areas to the Mushroom bodies can orchestrate latent visual learning in navigating insects
Authors: Wystrach Antoine
Published: March 2023

Spatial learning is peculiar. It can occur continuously and stimuli of the world need to be encoded according to some spatial organisation. Recent evidence showed that insects categorise visual memories as whether their gaze is facing left vs. right from their goal, but how such categorisation is achieved during learning remains unknown. Here we analysed the movements of ants exploring the world around their nest, and used a biologically constrained neural model to show that such parallel, lateralized visual memories can be acquired straightforwardly and continuously as the agent explore the world. During learning, ‘left’ and ‘right’ visual memories can be formed in different neural comportments (of the mushroom bodies lobes) through existing lateralised dopaminergic neural feedback from pre-motor areas (the lateral accessory lobes) receiving output from path integration (in the central complex). As a result, path integration organises visual learning ‘internally’, without the need to be expressed through behaviour; and therefore, views can be learnt continuously (without suffering memory overload) while the insect is free to explore the world randomly or using any other navigational mechanism. After learning, this circuit produces robust homing performance in a 3D reconstructed natural habitat despite a noisy visual recognition performance. Overall this illustrates how continuous bidirectional relationships between pre-motor areas and visual memory centres can orchestrate latent spatial learning and produce efficient navigation behaviour.
Ontology for Cellular Senescence Mechanisms
Authors: Yamagata Yuki , Fukuyama Tsubasa , Onami Shuichi , Masuya Hiroshi
Published: March 2023

Although cellular senescence is a key factor in organismal aging, with both positive and negative effects on individuals, its mechanisms remain largely unknown. Thus, integrating knowledge is essential to explain how cellular senescence manifests in tissue damage and age-related diseases. Here, we propose an ontological model that organizes knowledge of cellular senescence in a computer-readable form. We manually annotated and defined cellular senescence processes, molecules, anatomical structures, phenotypes, and other entities based on the Homeostasis Imbalance Process ontology. We described the mechanisms as causal relationships of processes and modeled a homeostatic imbalance between stress and stress response in cellular senescence for a unified framework. HoIP was assessed formally, and the relationships between cellular senescence and disease were inferred for higher-order knowledge processing. We visualized cellular senescence processes to support knowledge utilization. Our study provides a knowledge base to help elucidate mechanisms linking cellular and organismal aging.
RNA transcripts suppress G-quadruplex structures through G-loop formation
Authors: Sato Koichi , Hendrikx Aiko G.M. , Knipscheer Puck
Published: March 2023

The eukaryotic genome contains numerous guanine-rich sequences that regulate DNA replication and transcription by folding into non-canonical structures called G-quadruplexes (G4s)1. Compromised G4 resolution causes genomic instability and diseases linked to cancer susceptibility and aging2. However, how G4s are resolved is poorly understood. G4 structures are found in genomic regions containing DNA:RNA hybrids, also referred to as R-loops3, 4. When an R-loop and G4 structure form exactly opposite to each other, a G-loop structure is formed. G-loops have been observed directly in prokaryotes5but their function is unknown. Using theXenopusegg extract system, we show that G-loop structures act in suppressing mutagenic G4 structures thereby preventing genomic instability. Mechanistically, the RAD51 recombinase binds to the G4-opposing strand and promotes hybridization of RNA transcripts supplied by the hnRNPA1 ribonucleoprotein complex independently of ongoing transcription. The resulting G-loop then induces FANCI-FANCD2 monoubiquitination that triggers site-specific incision of the hybrid strand by the SLX4-XPF-ERCC1 complex. G-loop incision requires prior G4 unwinding by the DHX36 and FANCJ helicases and allows immediate DNA synthesis past the G4 motif. This resynthesis step impacts local chromatin states. This work establishes a G-loop-dependent mechanism that prevents mutagenic consequences of both G4 and R-loop structures.
Individual similarities and differences in eye-movement-related eardrum oscillations (EMREOs)
Authors: King Cynthia D , Lovich Stephanie N , Murphy David LK , Landrum Rachel , Kaylie David , Shera Christopher A , Groh Jennifer M
Published: March 2023

We recently discovered a unique type of low-frequency otoacoustic emission (OAE) time-locked to the onset (and offset) of saccadic eye movements and occurring in the absence of external sound (Gruters et al., 2018). How and why these eye-movement-related eardrum oscillations (EMREOs) are generated is unknown, with a role in visual-auditory integration being the likeliest candidate. Clues to both the drivers of EMREOs and their purpose can be gleaned by examining responses in normal hearing human subjects. Do EMREOs occur in all individuals with normal hearing? If so, what components of the response occur most consistently? Understanding which attributes of EMREOs are similar across participants and which show more variability will provide the groundwork for future comparisons with individuals with hearing abnormalities affecting the ear’s various motor components. Here we report that in subjects with normal hearing thresholds and normal middle ear function, all ears show (a) measurable EMREOs (mean: 58.7 dB SPL; range 45-67 dB SPL for large contralateral saccades), (b) a phase reversal for contra-versus ipsilaterally-directed saccades, (c) a large peak in the signal occurring soon after saccade onset, (d) an additional large peak time-locked to saccade offset and (e) evidence that saccade duration is encoded in the signal. We interpret the attributes of EMREOs that are most consistent across subjects as the ones that are most likely to play an essential role in their function. The individual differences likely reflect normal variation in individuals’ auditory system anatomy and physiology, much like traditional measures of auditory function such as auditory-evoked OAEs, tympanometry and auditory-evoked potentials. Future work will compare subjects with different types of auditory dysfunction to population data from normal hearing subjects. Overall, these findings provide important context for the widespread observations of visual-and eye-movement related signals found in cortical and subcortical auditory areas of the brain.
Diverse mutant selection windows shape spatial heterogeneity in evolving populations
Authors: King Eshan S. , Pierce Beck , Hinczewski Michael , Scott Jacob G.
Published: March 2023

Mutant selection windows (MSWs), the range of drug concentrations that select for drug-resistant mutants, have long been used as a model for predicting drug resistance and designing optimal dosing strategies in infectious disease. The canonical MSW model offers comparisons between two subtypes at a time: drug-sensitive and drug-resistant. In contrast, the fitness landscape model withNalleles, which maps genotype to fitness, allows comparisons betweenNgenotypes simultaneously, but does not encode continuous drug response data. In clinical settings, there may be a wide range of drug concentrations selecting for a variety of genotypes. Therefore, there is a need for a more robust model of the pathogen response to therapy to predict resistance and design new therapeutic approaches. Fitness seascapes, which model genotype-by-environment interactions, permit multiple MSW comparisons simultaneously by encoding genotype-specific dose-response data. By comparing dose-response curves, one can visualize the range of drug concentrations where one genotype is selected over another. In this work, we show howN-allele fitness seascapes allow forN ∗2N−1unique MSW comparisons. In spatial drug diffusion models, we demonstrate how fitness seascapes reveal spatially heterogeneous MSWs, extending the MSW model to more accurately reflect the selection fo drug resistant genotypes. Furthermore, we find that the spatial structure of MSWs shapes the evolution of drug resistance in an agent-based model. Our work highlights the importance and utility of considering dose-dependent fitness seascapes in evolutionary medicine.

Author Summary

Drug resistance in infectious disease and cancer is a major driver of mortality. While undergoing treatment, the population of cells in a tumor or infection may evolve the ability to grow despite the use of previously effective drugs. Researchers hypothesize that the spatial organization of these disease populations may contribute to drug resistance. In this work, we analyze how spatial gradients of drug concentration impact the evolution of drug resistance. We consider a decades-old model called the mutant selection window (MSW), which describes the drug concentration range that selects for drug-resistant cells. We show how extending this model with continuous dose-response data, which describes how different types of cells respond to drug, improves the ability of MSWs to predict evolution. This work helps us understand how the spatial organization of cells, such as the organization of blood vessels within a tumor, may promote drug resistance. In the future, we may use these methods to optimize drug dosing to prevent resistance or leverage known vulnerabilities of drug-resistant cells.
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an Integer Programming framework
Authors: Loyer Gabriel , Reinharz Vladimir
Published: March 2023

Motivation

The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of non-canonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops.

Results

We previously developed the integer programming framework RNAMoIP (RNA Motifs over Integer Programming) to reconcile RNA secondary structure and local 3D motif information available in databases. We further develop our model to now simultaneously predict the canonical base pairs (with pseudoknots) from base pair probability matrices with or without alignment. We benchmarked our new method over the all non-redundant RNAs below 150 nucleotides. We show that the joined prediction of canonical base pairs structure and local conserved motifs (i) improves the ratio of well-predicted interactions in the secondary structure, (ii) predicts well canonical and Wobble pairs at the location where motifs are inserted, (iii) is greatly improved with evolutionary information and (iv) non-canonical motifs at kink-turn locations.

Availability

The source code of the framework is available athttps://gitlab.info.uqam.ca/cbe/RNAMoIPand an interactive web server athttps://rnamoip.cbe.uqam.ca/
Salactin, a dynamically unstable actin homolog in Haloarchaea
Authors: Zheng Jenny , Lammers Alex , Mallon John , Litschel Thomas , Moody Edmund R.R. , Ramirez-Diaz Diego A. , Schmid Amy , Williams Tom A. , Bisson-Filho Alexandre W. , Garner Ethan
Published: March 2023

Across the domains of life, actin homologs are integral components of many essential processes such as DNA segregation, cell division, and cell shape determination. Archaea genomes, like those of bacteria and eukaryotes, also encode actin homologs, but much less is known about these proteins’ in vivo dynamics and cellular functions. We identified and characterized the function and dynamics of Salactin, an actin homolog in the hypersaline archaeon Halobacterium salinarum. Despite Salactin’s homology to bacterial MreB proteins, we find it does not function as a MreB ortholog in H. salinarum. Rather, live-cell imaging revealed that Salactin forms dynamically unstable filaments that grow and shrink out of the cell poles. Like other dynamically unstable polymers, Salactin monomers add at the growing filament end and its ATP-bound critical concentration is substantially lower than the ADP-bound form. When H. salinarum’s chromosomal copy number becomes limiting under low phosphate growth conditions, cells lacking Salactin show perturbed DNA distributions. Taken together, we propose that Salactin is part of a previously unknown chromosomal segregation apparatus required during low-ploidy conditions.
ATF4 Expression in Thermogenic Adipocytes is Required for Cold-Induced Thermogenesis in Mice via FGF21-Independent Mechanisms
Authors: Bjorkman Sarah H. , Marti Alex , Jena Jayashree , Garcia Pena Luis M , Weatherford Eric T. , Kato Kevin , Koneru Jivan , Chen Jason , Sood Ayushi , Potthoff Matthew J. , Adams Christopher M. , Abel E. Dale , Pereira Renata O.
Published: March 2023

In brown adipose tissue (BAT), short-term cold exposure induces the activating transcription factor 4 (ATF4), and its downstream target fibroblast growth factor 21 (FGF21). Induction of ATF4 in BAT in response to mitochondrial stress is required for thermoregulation, partially via upregulation of FGF21. In the present study, we tested the hypothesis thatAtf4andFgf21induction in BAT are both required for BAT thermogenesis by generating mice selectively lacking eitherAtf4 (ATF4 BKO)orFgf21(FGF21 BKO) in UCP1-expressing adipocytes. After 3 days of cold exposure, core body temperature was significantly reduced inad-libitum-fed ATF4 BKO mice, which correlated withFgf21downregulation in brown and beige adipocytes, and impaired browning of white adipose tissue (WAT). Conversely, despite having reduced browning, FGF21 BKO mice had preserved core body temperature after cold exposure. Mechanistically, ATF4, but not FGF21, regulates amino acid import and metabolism in response to cold, likely contributing to BAT thermogenic capacity underad libitum-fed conditions. Importantly, under fasting conditions, both ATF4 and FGF21 were required for thermogenesis in cold-exposed mice. Thus, ATF4 regulates BAT thermogenesis by activating amino acid metabolism in BAT in a FGF21-independent manner.

Graphical Abstract
Knockout of cardiolipin synthase disrupts postnatal cardiac development by inhibiting the maturation of mitochondrial cristae
Authors: Ren Mindong , Xu Yang , Phoon Colin K. L. , Erdjument-Bromage Hediye , Neubert Thomas A. , Schlame Michael
Published: March 2023

Background

Cardiomyocyte maturation requires a massive increase in respiratory enzymes and their assembly into long-lived complexes of oxidative phosphorylation (OXPHOS). The molecular mechanisms underlying the maturation of cardiac mitochondria have not been established.

Methods

To determine whether the mitochondria-specific lipid cardiolipin is involved in cardiac maturation, we created a cardiomyocyte-restricted knockout (KO) of cardiolipin synthase (Crls1) in mice and studied the postnatal development of the heart. We also measured the turnover rates of proteins and lipids in cardiolipin-deficient flight muscle from Drosophila, a tissue that has mitochondria with high OXPHOS activity like the heart.

Results

Crls1KOmice survived the prenatal period but failed to accumulate OXPHOS proteins during postnatal maturation and succumbed to heart failure at the age of 2 weeks. Turnover measurements showed that the exceptionally long half-life of OXPHOS proteins is critically dependent on cardiolipin.

Conclusions

Cardiolipin is essential for the postnatal maturation of cardiomyocytes because it allows mitochondrial cristae to accumulate OXPHOS proteins to a high concentration and to shield them from degradation.
Functional diversity of theTP53mutome revealed by saturating CRISPR mutagenesis
Authors: Funk Julianne , Klimovich Maria , Pavlakis Evangelos , Neumann Michelle , Drangenstein Daniel , Noeparast Maxim , Hunold Pascal , Borowek Anna , Balourdas Dimitrios-Ilias , Kochhan Katharina , Merle Nastasja , Bullwinkel Imke , Wanzel Michael , Elmshäuser Sabrina , Nist Andrea , Procida Tara , Bartkuhn Marek , Humpert Katharina , Mernberger Marco , Savai Rajkumar , Joerger Andreas C. , Stiewe Thorsten
Published: March 2023

The tumor suppressor geneTP53is the most frequently mutated gene in various cancers. Unlike other tumor suppressors,TP53is mostly hit by missense mutations, of which more than 2,000 have been described in cancer patients. To take advantage ofTP53mutation status for personalized therapy, a deeper knowledge of the functional ramifications of specific mutations is required as evidence of the functional heterogeneity of mutant p53 proteins mounts. Here, we report on a CRISPR-based saturation mutagenesis screen of 9,225 variants expressed from the endogenousTP53gene locus of a cancer cell. By tracking changes in the abundance of individual variants in response to specific p53-pathway stimulation, we were able to construct high-resolution functional activity maps of theTP53mutome, covering ∼94.5% of all cancer-associated missense mutations. The results demonstrate the impact of individual mutations on tumor cell fitness with unprecedented precision and coverage, even revealing underlying mechanisms such as apoptosis. The high discriminatory power also resolves subtle loss-of-function phenotypes and highlights a subset of mutants as particularly promising targets for pharmacological reactivation. Moreover, the data offer intriguing insight into the role of aberrant splicing and nonsense-mediated mRNA decay in clearing truncated proteins due to not only nonsense, frameshift, and splice-site mutations but also missense and synonymous mutations. Surprisingly, no missense mutation provided an immediate proliferative advantage over a null mutation. Nonetheless, cells with a missense, but not null mutations, acquired pro-metastatic properties after prolonged growth in mice, emphasizing the significance of mutant p53-directed clonal evolution in the progression of tumors towards metastasis.
Natural language processing models reveal neural dynamics of human conversation
Authors: Cai Jing , Hadjinicolaou Alex E. , Paulk Angelique C. , Soper Daniel J. , Xia Tian , Williams Ziv M. , Cash Sydney S.
Published: March 2023

Through conversation, humans relay complex information through the alternation of speech production and comprehension. The neural mechanisms that underlie these complementary processes or through which information is precisely conveyed by language, however, remain poorly understood. Here, we used pretrained deep learning natural language processing models in combination with intracranial neuronal recordings to discover neural signals that reliably reflect speech production, comprehension, and their transitions during natural conversation between individuals. Our findings indicate that neural activities that encoded linguistic information were broadly distributed throughout frontotemporal areas across multiple frequency bands. We also find that these activities were specific to the words and sentences being conveyed and that they were dependent on the word’s specific context and order. Finally, we demonstrate that these neural patterns partially overlapped during language production and comprehension and that listener-speaker transitions were associated with specific, time-aligned changes in neural activity. Collectively, our findings reveal a dynamical organization of neural activities that subserve language production and comprehension during natural conversation and harness the use of deep learning models in understanding the neural mechanisms underlying human language.
Comparative 3D ultrastructure ofPlasmodium falciparumgametocytes
Authors: Evers Felix , Roverts Rona , Boshoven Cas , Kea-te Lindert Mariska , Verhoef Julie M.J. , Sinden Robert E. , Akiva Anat , Kooij Taco W.A.
Published: March 2023

Despite the enormous significance of malaria parasites for global health, some basic features of their ultrastructure remain obscure. In this study, we apply high-resolution volumetric electron microscopy to examine and compare the ultrastructure ofPlasmodium falciparumgametocytes of both genders and in different stages of development as well as the more intensively studied asexual blood stages revisiting previously described phenomena in 3D. In doing so, we challenge the widely accepted notion of a single mitochondrion by demonstrating the presence of multiple mitochondria in gametocytes. We also provide evidence for a gametocyte-specific cytostome variant. Furthermore, we generate, among other organelles, the first 3D reconstructions of endoplasmic reticulum (ER), Golgi apparatus, and extraparasitic structures in gametocytes. Assessing interconnectivity between organelles, we find frequent structural appositions between the nucleus, mitochondria, and apicoplast. We provide evidence that the ER is a promiscuous interactor with numerous organelles and the trilaminar membrane of the gametocyte. Public availability of these volumetric electron microscopy resources of wild-type asexual and sexual blood-stage malaria parasites will facilitate reinterrogation of this global dataset with different research questions and expertise. Taken together, we reconstruct the 3D ultrastructure ofP. falciparumgametocytes in high detail and shed light on the unique organellar biology of these deadly parasites.
Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease
Authors: Sullivan Patrick F. , Meadows Jennifer R. S. , Gazal Steven , Phan BaDoi N. , Li Xue , Genereux Diane P. , Dong Michael X. , Bianchi Matteo , Andrews Gregory , Sakthikumar Sharadha , Nordin Jessika , Roy Ananya , Christmas Matthew J. , Marinescu Voichita D. , Wallerman Ola , Xue James R. , Li Yun , Yao Shuyang , Sun Quan , Szatkiewicz Jin , Wen Jia , Huckins Laura M. , Lawler Alyssa J. , Keough Kathleen C. , Zheng Zhili , Zeng Jian , Wray Naomi R. , Johnson Jessica , Chen Jiawen ,   Zoonomia Consortium, Paten Benedict , Reilly Steven K. , Hughes Graham M. , Weng Zhiping , Pollard Katherine S. , Pfenning Andreas R. , Forsberg-Nilsson Karin , Karlsson Elinor K. , Lindblad-Toh Kerstin
Published: March 2023

Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores
Authors: Stuber Annina , Douaki Ali , Hengsteler Julian , Buckingham Denis , Momotenko Dmitry , Garoli Denis , Nakatsuka Nako
Published: March 2023

Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces, is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with a serotonin sensor fabricated with the same methodology. When sensing these two neurotransmitters with comparable mass and equal charge, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates to the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments, but will also drive further innovations in biomimetic nanopore technologies.
Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition
Authors: Berns H. Matthew , Watkins-Chow Dawn E. , Lu Sizhu , Louphrasitthiphol Pakavarin , Zhang Tongwu , Brown Kevin M. , Moura-Alves Pedro , Goding Colin R. , Pavan William J.
Published: March 2023

The human Red Hair Color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. WhileMC1Rvariants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to reveal a Pheomelanin Gene Signature (PGS) comprising genes implicated in melanogenesis and oncogenic transformation. We show that TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, is part of the PGS and binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into mechanisms by which MC1R signaling regulates pigmentation and how individuals with the RHC phenotype are predisposed to melanoma.
Diverse Phosphoserine Phosphatases Exhibit Maximum Activity at an Intermediate Binding Affinity in Accord with the Sabatier Principle of Catalysis
Authors: Chiba Yoko , Ooka Hideshi , Wintzer Marie , Tsunematsu Nao , Suzuki Takehiro , Dohmae Naoshi , Nakamura Ryuhei
Published: March 2023

A unified framework to rationalize enzymatic activity is essential to understand cellular function and metabolic evolution. Recent studies have shown that the activity of several hydrolases is maximized when the substrate binding affinity (Michaelis-Menten constant: Km) is neither too strong nor too weak. This is because an intermediate Km resolves the trade-off between Km and kcat, in accord with the Sabatier principle of artificial catalysis. However, it remains unclear whether this concept is applicable to enzymes in general, especially for those which catalyze the same reaction but have evolved under different selection pressures due to the phylogeny or physiology of the host organism. Here, we demonstrate that the activity of 10 distinct wild-type phosphoserine phosphatases (PSP) exhibits a maximum at an intermediate binding affinity (Km approximately 0.5 mM), indicating that they also follow the Sabatier principle. Furthermore, by considering not only Km but also the equilibrium rate constant (k20) of each enzyme, we have succeeded in rationalizing the PSP activity quantitatively. k20 is the rate constant of product release (ES to E + P) in the absence of any driving force, and a large k20 allows kcat to be increased without increasing Km. Although the traditional Sabatier principle considers only the binding affinity (Km), we show that the additional contribution of k20 drastically improves the consistency between experiments and theory. Our expanded framework which quantitatively explains the activity of phylogenetically and physiologically diverse enzymes with respect to their physicochemical parameters may lead to the rational design of highly active enzymes.