bluuebunny/crossref_metadata_2025 huggingface dataset:
Causal Estimands for Analyses of Averted and Avertible Outcomes due to Infectious Disease Interventions
Authors: Jia Katherine M , Boyer Christopher B , Wallinga Jacco , Lipsitch Marc
Published: January 2025

During the coronavirus disease (COVID-19) pandemic, researchers attempted to estimate the number of averted and avertible outcomes due to vaccination campaigns to quantify public health impact. However, the estimands used in these analyses have not been previously formalized. It is also unclear how these analyses relate to the broader framework of direct, indirect, total, and overall causal effects under interference. Here, using potential outcome notation, we adjust the direct and overall effects to accommodate analyses of averted and avertible outcomes. We use this framework to interrogate the commonly held assumption that vaccine-averted outcomes via direct impact among vaccinated individuals (or vaccine-avertible outcomes via direct impact among unvaccinated individuals) is a lower bound on vaccine-averted (or -avertible) outcomes overall. To do so, we describe a susceptible-infected-recovered-death model stratified by vaccination status. When vaccine efficacies wane, the lower bound fails for vaccine-avertible outcomes. When transmission or fatality parameters increase over time, the lower bound fails for both vaccine-averted and -avertible outcomes. Only in the simplest scenario where vaccine efficacies, transmission, and fatality parameters are constant over time, outcomes averted via direct impact among vaccinated individuals (or outcomes avertible via direct impact among unvaccinated individuals) is a lower bound on overall impact. In conclusion, the lower bound can fail under common violations to assumptions on time-invariant vaccine efficacy, pathogen properties, or behavioral parameters. In real data analyses, estimating what seems like a lower bound on overall impact through estimating direct impact may be inadvisable without examining the directions of indirect effects.
A quasi-experimental study of general practices’ referral to mammography in the post-trials treatment era
Authors: Lousdal Mette Lise , Lash Timothy L , Flanders W Dana , Brookhart M Alan , Kristiansen Ivar Sønbø , Vedsted Peter , Støvring Henrik
Published: January 2025

Background:

Improvements in breast cancer therapy since the randomized controlled trials of mammography screening might have reduced the screening benefit. Most observational studies of mammography effectiveness would be confounded by these improvements and other factors. Using a design resistant to this confounding, we evaluated whether mammography in asymptomatic women reduces breast cancer mortality during the treatment era succeeding the trials.

Methods:

We designed a quasi-experimental cohort study in regions of Denmark without organized screening. We predicted the number of expected mammograms for each general practice based on observed numbers of mammograms and individual risk factors. Regardless of a woman’s individual exposure to mammography, we assigned her the ratio of observed to expected mammograms of her general practice as her instrumental variable. We employed this potential instrumental variable as mammography exposure status and followed women from January 1, 2006 until death, emigration, or December 31, 2014, whichever came first.

Results:

We included 169,197 women aged 50–66 from 738 general practices and without previous breast cancer as of January 1, 2006. Women affiliated with a practice referring more women than expected, compared with less, had a lower hazard of breast cancer death (hazard ratio 0.80, 95% confidence interval 0.68, 0.95). Negative control associations were near null, suggesting no confounding bias.

Conclusions:

This quasi-experimental study estimated a continued protective effect of mammography in women where most were presumably asymptomatic. In contrast to conventional observational studies, the use of practice referral ratio as an instrumental variable may avoid bias from uncontrolled confounding.
Point-of-Care Ultrasound of a Pediatric Mediastinal Mass
Authors: Greenwald Phoebe , Rabiner Joni E.
Published: January 2025

Point-of-care ultrasound may be used for identification of thoracic pathology, including mediastinal masses. In this case report, we describe the case of an otherwise healthy 17-year-old boy who presented with generalized pruritis. Point-of-care ultrasound was useful in identifying a complex cystic and solid mediastinal mass extending into the thoracic cavities as well as an associated pericardial effusion.
Genetic Analysis ofArabidopsisAutophagy-Related 8 Family Proteins
Reveals Their Redundant and Regulatory Roles in Plant Autophagy
Authors: Dong Kuntian , Deng Guiling , Liu Yilin , Wei Huan , Chen Kuo-En , Huang Xiner , Huang Wanying , Zheng Ping , Ueda Takashi , Vierstra Richard D. , Huang Xiao , Li Faqiang
Published: January 2025

Autophagy, a critical process for the vacuolar degradation of proteins and
organelles, is governed by multiple conserved autophagy-related (ATG) proteins.
The central component of the ATG machinery is the ubiquitin-like protein ATG8,
which is essential for multiple steps of the autophagy process, including
phagophore expansion, autophagosome closure, trafficking and fusion with the
lysosome/vacuole, and selective cargo recruitment. Currently, our understanding
of the roles of ATG8 in plant autophagy and the functional specialization of
ATG8 family members is limited due to genetic redundancy. To assess the roles
ofATG8genes in plant autophagy, here we used
CRISPR/Cas9 technology to systematically knockout theArabidopsis
ATG8genes. By analyzing
theatg8mutants, we found that in contrast to
mammalian ATG8s, in which the LC3s and GABARAP subfamilies play distinct roles
in the autophagic process,ArabidopsisATG8s perform an
overlapping function in controlling autophagic flux. Combinatorial mutations of
Clade I and Clade II ATG8s resulted in severely impaired autophagy under
nutrient-starved conditions. Furthermore, we found that RABG3 proteins, members
of the RAB7/RABG GTPase family, interact with ATG8s through AIM-LDS interfaces,
and that such interaction is essential for the association of RABG3 proteins
with the autophagosomal membrane and probably for the fusion of autophagosome
with the vacuole, but is not required for endosomal trafficking. With the
collection of multiple high-orderatg8mutants
generated in this study, we now provide a venue to study the roles
ofATG8genes in canonical autophagy and
non-canonical autophagy inArabidopsis.
Lower cortical activation and altered functional connectivity characterize passive auditory spatial attention in ASD
Authors: Osorio Sergio , Tan Jasmine , Levine Grace , Ahlfors Seppo P , Graham Steven , Mamashli Fahimeh , Khan Sheraz , Joseph Robert M , Nayal Zein , Losh Ainsley , Pawlyszyn Stephanie , McGuiggan Nicole M , Hamalainen Matti S , Bharadwaj Hari , Kenet Tal
Published: January 2025

Autism Spectrum Disorder (ASD) is a developmental condition characterized by difficulties in social interaction, communication and sensory processing. The ability to orient towards sounds is a key component of social interactions, yet auditory spatial attention remains relatively understudied in ASD, despite some prior research indicating differences in this domain. Here, we investigate the neural signatures associated with passive auditory spatial attention in children with ASD (n = 21, ages 6-17) relative to age- and IQ-matched typically developing (TD) children (n = 31), using source-localized magnetoencephalography (MEG). Participants listened passively, while watching a silenced movie, to non-social auditory stimuli designed to either remain lateralized to one hemifield (stay trials), or to change in location from one side to the contralateral hemifield (jump trials). Linear mixed effect modeling showed lower cortical activation in the auditory cortex in the ASD group in response to jump trials, relative to the TD group. Additionally, functional connectivity analyses showed higher alpha-band functional connectivity in the ASD group between auditory cortex seeds and frontoparietal regions known to be recruited during auditory spatial attention. Right prefrontal alpha-band connectivity estimates were associated with worse behaviorally assessed auditory processing scores and increased ASD symptomatology. Our results align with the hypothesis that auditory spatial attention generally, and specifically orientation to sounds even when experienced passively, differs in ASD individuals.
Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starvingBacillus subtilis
Authors: Zhang Yujia , Palma Cristina S.D. , Chen Zhuo , Zarazúa-Osorio Brenda , Fujita Masaya , Igoshin Oleg
Published: January 2025

In starvingBacillus subtilisbacteria, the initiation of two survival programs – biofilm formation and sporulation – is both controlled by the same phosphorylated master regulator Spo0A∼P. Its gene,spo0A, is transcribed from two promoters, Pvand Ps, that are respectively regulated by RNAP holoenzymes bearing σAand σH. Notably, transcription is directly autoregulated by Spo0A∼P binding sites known as 0A1, 0A2, and 0A3 box, located in between the two promoters. It remains unclear whether, at the onset of starvation, these boxes activate or repressspo0Aexpression, and whether the Spo0A∼P transcriptional feedback plays a role in the increase inspo0Aexpression. Based on the experimental data of the promoter activities under systematic perturbation of the promoter architecture, we developed a biophysical model of transcription regulation ofspo0Aby Spo0A∼P binding to each of the 0A boxes. The model predicts that Spo0A∼P binding to its boxes does not affect the RNA polymerase recruitment to the promoters but instead affects the transcriptional initiation rate. Moreover, the effects of Spo0A∼P binding to 0A boxes are mainly repressive and saturated early at the onset of starvation. Therefore, the increase inspo0Aexpression is mainly driven by the increase in RNAP holoenzyme levels. Additionally, we reveal that Spo0A∼P affinity to 0A boxes is strongest at 0A3 and weakest at 0A2 and that there are attractive forces between the occupied 0A boxes. Our findings, in addition to clarifying how the sporulation master regulator is controlled, offer a framework to predict regulatory outcomes of complex gene-regulatory mechanisms.

Importance

Cell differentiation is often critical for survival. In bacteria, differentiation decisions are controlled by transcriptional master regulators under transcriptional feedback control. Therefore, understanding how master regulators are transcriptionally regulated is required to understand differentiation. However, in many cases, underlying regulation is complex with multiple transcription factor binding sites and multiple promoters, making it challenging to dissect the exact mechanisms. Here, we address this problem for theB. subtilismaster regulator Spo0A. Using a biophysical model, we quantitatively characterize the effect of individual transcription factor binding sites on eachspo0Apromoter. Further, the model allows to identify the specific transcription step that is affected by transcription factor binding. Such model is promising for the quantitative study of a wide range of master regulators involved in transcriptional feedback.
Psychedelic-mediated Reversal of General Anesthesia and Restoration of Brain Dynamics in Rat
Authors: Huels Emma R. , Kolbman Nicholas , Fields Christopher W. , Nelson Amanda G. , Jackson Hazel , Liu Tiecheng , Mashour George A. , Pal Dinesh
Published: January 2025

Serotonergic psychedelics enhance neurophysiological complexity and the repertoire of brain states, whereas general anesthetics produce opposite effects. Serotonergic psychedelics are also known to increase wakefulness and reduce sleep time in rodents. Therefore, we hypothesized that 2,5-dimethoxy-4-iodopamphetamine (DOI), a serotonergic psychedelic, will reverse general anesthesia and restore neurophysiological conditions associated with normal wakefulness. We demonstrate that intravenous administration of DOI in rats under general anesthesia induced wakefulness despite ongoing delivery of the anesthetics, propofol or isoflurane. Behavioral arousal was accompanied by recovery of directional and non-directional high gamma (125-165Hz) functional connectivity and restoration of functional brain network structure. These behavioral and neurophysiological effects were blocked by a 5-HT2A antagonist, volinanserin. Intravenous administration of a non-psychedelic 5-HT2A agonist, lisuride, failed to restore wakefulness or brain dynamics in anesthetized rats. To our knowledge, these results provide the first evidence of psychedelic-mediated reversal of general anesthesia and concurrent restoration of brain dynamics associated with normal wakefulness.
Hybrid sequencing reveals the genome of aChrysochromulina parvavirus and highlight its distinct replication strategy
Authors: Nash Delaney , Palermo Christine N. , Inamoto Ichiro , Charles Trevor C. , Nissimov Jozef I. , Short Steven M.
Published: January 2025

Chrysochromulina parva(C. parva) is a eukaryotic freshwater haptophyte algae found in lakes and rivers worldwide. It is known to be infected by viruses, yet knowledge of the diversity and activity of these viruses is still very limited. Based on sequences of PCR-amplifiedpolBgene fragments,Chrysochromulina parvavirus BQ1 (CpV-BQ1) was the first known lytic agent ofC. parva, and was considered a member of the virus familyPhycodnaviridae,orderAlgavirales. However, the genome of a differentC. parva-infecting virus (CpV-BQ2, orTethysvirus ontarioense) from another virus family, theMesomimiviridae, orderImitervirales,was the first sequenced. Here, we report the complete genome sequence of the putative phycodnavirus CpV-BQ1, accessionPQ783904. The complete CpV-BQ1 genome sequence is 165,454 bp with a GC content of 32.32% and it encodes 193 open reading frames. Phylogenetic analyses of several virus hallmark genes including the DNA polymerase (polB), the late gene transcription factor (VLTF-3), and the putative A32-like virion packaging ATPase (Viral A32) all demonstrate that CpV-BQ1 is most closely related to other viruses in the phylumMegaviriceteswithin the orderAlgavirales, familyPhycodnaviridae.
mzQuality: A tool for quality monitoring and reporting of targeted mass spectrometry measurements
Authors: van der Peet Marielle , Maas Pascal , Wegrzyn Agnieszka , Lamont Lieke , Fleming Ronan , Harms Amy , Hankemeier Thomas , Kindt Alida
Published: January 2025

Analyzing metabolites using mass spectrometry can offer valuable insight into an individual’s health or disease status. However, various sources of experimental variation can affect the data, making robust quality control essential. In this context, we introduce mzQuality, a user-friendly software tool designed to evaluate and correct technical variations in mass spectrometry-based metabolomics data. MzQuality offers key quality control features, such as batch correction, outlier identification, and analysis of signal-to-noise ratios. It supports any peak-integrated processed data independent of vendor software and does not require the user to have any programming skills. We demonstrate the functionality of mzQuality with a data set of 419 samples measured across six batches, in which mzQuality effectively minimized experimental variation, ensuring the data’s readiness for statistical analysis and biological interpretation. With customizable settings, mzQuality can be seamlessly integrated into research workflows to produce more accurate and reproducible metabolomics data.
Multi-scale simulations of membrane adhesion mediated by CD47-SIRPαcomplexes
Authors: Hou Ruihan , Ren Shuanglong , Wang Rong , Różycki Bartosz , Hu Jinglei
Published: January 2025

Adhesion of biological cells is essential for various processes, including tissue formation, immune responses, and signaling. It involves multiple length scales, ranging from nanometers to micrometers, which are characteristic of (a) the intercellular receptor-ligand binding that mediates the cell adhesion, (b) the spatial distribution of the receptor and lignad proteins in the membranes of adhering cells, (c) adhesion-induced deformations and thermal undulations of the membranes, (d) the overall size of the interface between adhering cells. Therefore, computer simulations of cell membrane adhesion require multi-scale modeling and suitable approximations that capture the essential physics of the system under study. Here, we introduce such a multi-scale approach to study membrane adhesion mediated by the CD47-SIRPαbinding, which is an immunologically relevant process. The synergetic use of coarse-grained molecular dynamics simulations and mesoscale kinetic Monte Carlo simulations allows us to explore both equilibrium properties and dynamical behavior of adhering membranes on the relevant length scales between 1 nm and 1 µm on time scales ranging from 0.1 ns all the way up to about 20 s. The multi-scale simulations not only reproduce available experimental data but also give quantitative predictions on binding-induced conformational changes of SIRPαand membrane-mediated cooperativity of the CD47-SIRPαbinding as well as fluctuation-induced interactions between the CD47-SIRPαcomplexes. Our approach is applicable to various membrane proteins and provides invaluable data for comparison with experimental findings.
Regionally specific resting-state beta neural power predicts brain injury and symptom recovery in adolescents with concussion: a longitudinal study
Authors: Edgar J. Christopher , Blaskey Lisa , Chen Yuhan , Podolak Olivia E. , Murray Drayton L. , McNamee Marybeth , Konka Kimberly , Berman Jeffrey I. , Roberts Timothy P.L. , Huang Mingxiong , Arbogast Kristy B. , Master Christina L.
Published: January 2025

Mild traumatic brain injury (mTBI) is common in adolescents. Magnetoencephalography (MEG) studies (primarily reporting on adult males) have demonstrated abnormal resting-state (RS) brain activity in mTBI. The present study sought to identify RS abnormalities in male and female adolescents with mTBI (no previous mTBI and no previous DSM-5 diagnosis) identified from an outpatient specialty care concussion program setting as a basis for evaluating potential clinical utility. Visit 1 MEG RS data were obtained from 46 adolescents with mTBI (mean age: 15.4 years, 25 females) within 4 months of a mTBI (mTBI acute to sub-acute period) as well as from 34 typically developing (TD) controls (mean age: 14.8 years; 17 females) identified from the local community. Visit 2 RS data (follow-up ∼4.3 months after Visit 1; mTBI sub-chronic period) were obtained from 36 mTBI (19 females) and 29 TD (14 females) of those participants. Source-space RS neural activity was examined from 4 to 56 Hz. Visit 1 t-tests showed that group differences were largest in the beta range (16-30 Hz; mTBI < TD), with Visit 2 whole-brain linear mixed model (LMM) analyses examining beta-band group differences as a function of Visit. A main effect of Group indicated Visit 1 and 2 beta-band group differences in midline superior frontal gyrus, right temporal pole, and right central sulcus (all mTBI < TD). The group effects were large (Cohen’sdvalues 0.75 to 1.31). Of clinical significance in the mTBI group, a decrease in mTBI symptoms from Visit 1 to 2 was associated with an increase in beta power in 4 other brain regions. Present findings suggest that RS beta power has potential as a measure and perhaps as a mechanism of clinical recovery in adolescents with mTBI.
3D dynamic multiscale force and shape analysis ofin-vivoelastic stress sensors
Authors: Jurado Alejandro , Isensee Jonas , Hofemeier Arne , Krüger Lea Johanna , Wittkowski Raphael , Golestanian Ramin , Bittihn Philip , Betz Timo
Published: January 2025

The measurement of stresses and forces at the tissue level has proven to be an indispensable tool for the understanding of complex biological phenomena such as cancer invasion, embryo development or wound healing. One of the most versatile tools for force inference at the cell and tissue level are elastic force sensors, whose biocompatibility and tunable material properties make them suitable for many different experimental scenarios. The evaluation of those forces, however, is still a bottleneck due to the numerical methods seen in literature until now, which are usually slow and render low experimental yield. Here we present Bead-Buddy, a ready-to-use platform for the evaluation of deformation and stresses from fluorescently labelled sensors within seconds. The strengths of BeadBuddy lie in the pre-computed analytical solutions of the elastic problem, the abstraction of data into Spherical Harmonics, and a simple user interface that creates a smooth workflow for force inference.

Abstract Figure
Extrachromosomal circular DNA promotes inflammation and hepatocellular carcinoma development
Authors: Chan Lap Kwan , Shan Juanjuan , Rodriguez-Fos Elias , Healy Marc Eamonn , Leary Peter , Parrotta Rossella , Desboeufs Nina , Semere Gabriel , Wittstruck Nadine , Henssen Anton G. , Weber Achim
Published: January 2025

Two decades after the initial report on increased micronuclei in human chronic liver disease (CLD) and hepatocellular carcinoma (HCC), their role in HCC development is still poorly understood. Here we show that micronuclei in hepatocytes trigger hepatic immune response and promote HCC development via an increased level of extrachromosomal circular DNA (eccDNA). Livers from a CLD model (Mcl1Δhepmice) show increased micronuclei in parallel to eccDNA. Circular sequencing confirms higher eccDNA levels in micronuclei compared to primary nuclei. We developed nuclei-segregated DNA fiber (NuSeF) assay to show that micronuclei are more susceptible to replication stress, showing increased replication fork slowing. By comparing different murine liver disease models, high eccDNA is correlated with increased tumor incidence. EccDNA is a strong immunostimulant and promotes a crosstalk between hepatocytes and immune cells through the cGAS-STING pathway. Deletion ofSting1inMcl1Δhepmice reduces immune cell chemotaxis, as well as tumor incidence. Our findings suggest that eccDNA from micronuclei mediates inflammation-driven liver carcinogenesis in CLD.
Cell Painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes
Authors: Ewald Jessica D. , Titterton Katherine L. , Bäuerle Alex , Beatson Alex , Boiko Daniil A. , Cabrera Ángel A. , Cheah Jaime , Cimini Beth A. , Gorissen Bram , Jones Thouis , Karczewski Konrad J. , Rouquie David , Seal Srijit , Weisbart Erin , White Brandon , Carpenter Anne E. , Singh Shantanu
Published: January 2025

High-throughput, human-relevant approaches for predicting chemical toxicity are urgently needed for better decision-making in human health. Here, we apply image-based profiling (the Cell Painting assay) and two cytotoxicity assays (metabolic and membrane damage readouts) to primary human hepatocytes after exposure to eight concentrations of 1085 compounds that include pharmaceuticals, pesticides, and industrial chemicals with known liver toxicity-related outcomes. Three computational methods (CellProfiler, a Cell Painting-specific convolutional neural network, and a pretrained vision transformer) were compared to extract morphology features from single cells or entire images. We used these morphology features to predict activity in the measured cytotoxicity assays, as well as in 412 curated ToxCast assays that span cytotoxicity, cell-based, and cell-free categories. We found that the morphological profiles detect compound bioactivity at lower concentrations than standard cytotoxicity assays. In supervised analyses, they predict cytotoxicity and targeted cell-based assay readouts, but not cell-free assay readouts. We also found that the various feature extraction methods performed relatively similarly and that filtering out non-bioactive or cytotoxic concentrations did not boost supervised assay prediction performance for any assay endpoint category, although it did have a large influence on unsupervised cluster analysis. We envision that image-based profiling could serve as a key component of modern safety assessment.
Evolution of chronic lymphocytic leukemia after allogeneic stem cell transplant
Authors: Garber Haven R. , Wang Danwei , Kerros Celine , Beird Hannah C. , Mao Xizeng , Howard Nina G. , Zhang Jianhua , Roszik Jason , Miller John P. , Leonard Paul , Cao Yu , Zhao Li , Song Xingzhi , Seth Sahil , Lin Pei , Sun Huandong , St John Lisa S. , Lu Sijie , Wierda William , Khouri Issa F. , Clise-Dwyer Karen , Im Jin S. , Alatrash Gheath , Futreal P. Andrew , Liang Shoudan , Koppikar Priya , Gu Shengqing (Stan) , Molldrem Jeffrey J.
Published: January 2025

Allogeneic stem cell transplant (alloSCT) for patients with relapsed/refractory chronic lymphocytic leukemia (CLL) can result in cure in some patients. Analogous to chemotherapy and targeted therapy, we hypothesized that allogeneic cellular immunotherapies, including alloSCT and donor lymphocyte infusion (DLI), would impact malignant evolution through the application of selective immunologic pressure with reciprocal changes in the T cell compartment. We tested a cohort of 24 patients treated with HLA-matched alloSCT +/− DLI, two mediators of the graft versus leukemia (GVL) effect. Comparison of pre-alloSCT samples revealed that a key difference between responders (n=13) and non-responders (n=11) is the cellularity of leukemic cells. We further mapped mutational trajectories of tumor cells by whole exome sequencing (WES) of sort-purified CLL in 11 post-transplant relapsed patients and found evidence of subclonal leukemic evolution in 8/11 patients after nonmyeloablative human leukocyte antigen (HLA)-matched alloSCT. Different patterns of CLL evolution were observed, and these changes included putative CLL drivers in every case. To investigate the presence of immune-related variants in patients, we collected 19 T cell co-culture CRISPR datasets and identified the top positive and negative regulators of cancer cell’s response to T-cell-dependent killing. We found that most mutations linked to T-cell killing emerged after allo-SCT treatment, suggesting that selective pressures from the GVL effect may drive the evolution of these mutations. Together, these data identify cellular homogeneity as a key biomarker for susceptibility to GVL-driven immunity in CLL and illustrate how the leukemic cells further evolve to evade immunosurveillance.

SIGNIFICANCE

The impact of allogeneic stem cell transplant (alloSCT) on subclonal leukemia evolution remains poorly understood. By performing whole exome sequencing (WES) on pre- and post-alloSCT patient samples, we reveal different patterns of CLL evolution and potential immune-related driver genes influencing CLL relapse and refractory disease post-alloSCT.
Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes
Authors: Janeva Ana , Penfold Christopher A , Llorente-Armijo Sara , Li Huiwen , Zikmund Tomas , Stock Marco , Jullien Jerome , Straub Tobias , Forne Ignasi , Imhof Axel , Vaquerizas Juan M , Gurdon John B , Hoermanseder Eva B
Published: January 2025

Fates of differentiated cells in our body can be induced to change by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling can be produced. However, the efficiency of this process is low, partly due to the properties of somatic donor nuclei which stabilize their differentiated fate but also act as barriers reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood. Here, we developed an artificial intelligence-based approach to model nuclear reprogramming and used it to identify the chromatin modification H3K27ac as a novel epigenetic barrier to reprogramming-induced cell fate changes. Using reprogramming by nuclear transfer (NT) to eggs of Xenopus laevis as a model system, we profiled chromatin modifications in different cell types alongside gene expression patterns before and after reprogramming. Our model integrated the data to accurately predict reprogramming outcomes on a transcriptome level. By leveraging model predictions, we find that genes resisting inactivation during reprogramming display specific chromatin modification barcodes, including the known reprogramming barrier H3K4me3 alongside a novel candidate barrier, H3K27ac. Accordingly, reducing H3K27ac levels using p300/CBP inhibitors before reprogramming led to an improved downregulation of genes linked to H3K27ac-modified enhancers after reprogramming. Importantly, these effects were accompanied by improved embryonic development of the resulting nuclear transfer embryos. In summary, our study developed Digital Reprogramming, an artificial intelligence approach capable of predicting resistance to cell-fate reprogramming, which led to the identification of H3K27ac as a critical barrier to reprogramming-associated cell-fate changes. Keywords: machine learning, predictive modeling, SCNT, nuclear reprogramming, H3K27ac, p300/CBP, epigenetic memory, cell fate stability.
JNK regulates GABAAR expression at the cell surface via the receptor clustering protein GIT1 (ArfGAP1)
Authors: Varidaki Artemis , Deshpande Prasannakumar , Nagaeva Elina , Sino Valentina , Schäfer Annika , Sourander Christel , Lagerholm Christoffer , James Peter , Korpi Esa R. , Coffey Eleanor
Published: January 2025

GABA type A receptors (GABAARs) receive inhibitory neurotransmitter input and control excitatory/inhibitory balance in the nervous system. Loss of GABAergic function leads to maladaptive changes in circuit dynamics associated with neuropsychiatric disorders, yet the adaptive mechanisms used by cells to regulate GABAAR availability are poorly understood. Previously, we identified that the stress-sensing kinase JNK1 promotes anxiety-like behaviours in mice. Here, we show that genetic deletion or inhibition of JNK1 increases GABAAR β3 subunit surface expression at extrasynaptic sites and at excitatory synapses. We also identify that JNK1 phosphorylates the signalling scaffold GIT1 on S371. Accordingly, GIT1 enriches in dendritic spines inJnk1-/-mice or JNK inhibitor-treated neurons, and GIT1-S371D is excluded. Furthermore, GIT1 is required for JNK-dependent regulation of GABAAR β3 surface expression. Consistent with these findings, the amplitude of spontaneous inhibitory post-synaptic potentials and tonic inhibitory currents are increased in neurons fromJnk1-/-mice. These results suggest that JNK1 activity represses GABAAR complex stability and function.

Significance statement

In this study we identify that the stress-sensing kinase JNK1 regulates the amount of GABAARs that are at the plasma membrane both at synapses and at extrasynaptic sites. When JNK activity is blocked, there is more GABAAR detected at the cell surface and GABAAR current is increased. The mechanism involves the receptor clustering protein GIT1 (ArfGAP1), which when dephosphorylated on S371 is enriched at dendritic spines and its binding to a receptor complex including β3-GABAAR, paxillin and 14-3-3ζ also increases. These results are significant because they provide a mechanism whereby cells can rapidly regulate GABAAR availability in response to stress.
Root Cap-Specific Transcriptomics Identify the NAC Transcription Factor SOMBRERO as a Versatile Regulator of Auxin Gradients
Authors: Wang Pengfei , Liu Zhongyuan , Zhou Yuling , He Junxian , Kang Byung-Ho
Published: January 2025

Auxin gradients in the root cap play a crucial role in the root cap development and root tropism. In the central root cap, meristematic cells in the columella initial differentiate into gravity-sensing columella cell, and mature into border-like cells that eventually separate from the root cap. Golgi stacks exhibit distinct ultrastructural features in each cell type across the central root cap, serving as effective cell markers. This cell type-specific Golgi remodeling was inhibited insmb-3mutant root cap. When we carried out transcriptomic analyses of isolated root cap from Col-0 andsmb-3, transcript levels of numerous auxin-related genes, including those involved in auxin synthesis, transport, and signaling, were significantly altered insmb-3mutant root caps. The auxin gradient was suppressed within the central root cap ofsmb-3mutant lines and they displayed decreased sensitivity to N-1-naphthylphthalamic acid (NPA) in comparison to Col-0. Furthermore, we demonstrated that the SMB binds to the promoter regions of auxin-related genes displaying large changes insmb-3root cap cells. Our findings suggest that SMB functions as a versatile transcription factor that regulates the expression of genes critical for local auxin distribution and responses in the root cap, thereby coordinating root cap cell differentiation and controlling root growth directions in response to external stimuli.
Chemistry-based vectors map the chemical space of natural biomes from untargeted mass spectrometry data
Authors: Peets Pilleriin , Litos Aristeidis , Dührkop Kai , Garza Daniel R. , van der Hooft Justin J.J. , Böcker Sebastian , Dutilh Bas E.
Published: January 2025

Untargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (<10%). We used chemistry-based vectors, consisting of molecular fingerprints or chemical compound classes, predicted from mass spectrometry data, to characterize compounds and samples. These chemical characteristics vectors (CCVs) estimate the fraction of compounds with specific chemical properties in a sample. Unlike the aligned MS1 data with intensity information, CCVs incorporate actual chemical properties of compounds, offering deeper insights into sample comparisons. Thus, we identified key compound classes differentiating biomes, such as ethers which are enriched in environmental biomes, while steroids enriched in animal host-related biomes. In biomes with greater variability, CCVs revealed key clustering compound classes, such as organonitrogen compounds in animal distal gut and lipids in animal secretions. CCVs thus enhance the interpretation of untargeted metabolomic data, providing a quantifiable and generalizable understanding of the chemical space of natural biomes.
In Silico Analysis of Non-Coding RNA Regulation in Human Gene Expression: A Systematic Computational Approach to Understanding Regulatory Networks
Authors: Akbar Arshiya
Published: January 2025

The regulatory networks of miRNAs, lncRNAs, and their target genes play a crucial role in controlling various cellular processes, including cell growth, apoptosis, and immune responses. In this study, we performed an in silico analysis to explore the interactions between miRNAs, lncRNAs, and their target genes in the context of disease mechanisms. We utilized multiple computational approaches, including miRNA-target interaction prediction, lncRNA-target network analysis, differential expression analysis using RNA-seq data, and validation of interactions using miRNA target prediction tools. Our results highlight key genes involved in apoptosis, cell cycle regulation, and tumorigenesis, providing valuable insights into the molecular mechanisms underlying disease progression.

Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have emerged as pivotal regulators of gene expression in human cells. Despite substantial research into their roles, there remains a critical gap in understanding how these molecules interact within complex regulatory networks. In this study, we employed a comprehensive bioinformatics approach to systematically identify and analyze ncRNA-mediated gene regulation in human cells. We utilized publicly available datasets from the ENCODE and GEO repositories, combined with computational tools such as miRBase, LNCipedia, TargetScan, and Cytoscape, to predict ncRNA-gene interactions and construct regulatory networks. Our analysis reveals several novel ncRNA regulators and their associated gene targets, which were further explored through pathway enrichment analysis. This study provides new insights into the regulatory networks of ncRNAs in human gene expression, offering a foundation for future functional studies and potential therapeutic applications.
Detection of low pre-existing humoral immunity against influenza virus H5N1 clade 2.3.4.4b in unexposed individuals
Authors: Daniel Katharina , Ullrich Leon , Ruchnewitz Denis , Meijers Matthijs , Halwe Nico Joel , Wild Ursula , Eberhardt Jan , Stumpf Ricarda , Schlotz Maike , Wunsch Marie , Lessa Luana Girao , Dietrich Christopher , Pinger Andreas , Schumacher Anna-Lena , Germer Maximilian , Rohde Malena , Kukat Christian , Gieselmann Lutz , Gruell Henning , Hoffmann Donata , Beer Martin , Erren Thomas , Lässig Michael , Kreer Christoph , Klein Florian
Published: January 2025

The repeated spill-over of Influenza A virus H5N1 clade 2.3.4.4b from cattle to humans highlights the risk of a human H5N1 pandemic. Given the impact of pre-existing immunity on the course and severity of viral infections, we assessed in detail the humoral immunity against the H5N1 A/Texas/37/2024 isolate in H5N1-naïve individuals. To this end, we performed complementary binding and neutralization assays on 66 subjects and ranked activities among a panel of 76 influenza A virus isolates. We detected low but distinct cross-neutralizing titers against A/Texas/37/2024 with a 3.9 to 15.6-fold reduction compared to selected H1N1 or H3N2 strains. Moreover, by cloning and evaluating 136 monoclonal antibodies from single memory B cells, we identified potent A/Texas/37/2024-neutralizing monoclonal antibodies in five out of six investigated individuals. These antibodies predominantly utilize VH1-69 gene segments, cross-neutralize H1, and compete with antibodies targeting the HA stem. Our findings demonstrate partial pre-existing humoral immunity to A/Texas/37/2024 in H5N1-naïve individuals.
CD226 identifies effector CD8+T cells during tuberculosis and costimulates recognition ofMycobacterium tuberculosis-infected macrophages
Authors: Shinkawa Tomoyo , Chang Evelyn , Rakib Tasfia , Cavallo Kelly , Lai Rocky , Behar Samuel M.
Published: January 2025

CD8+T cells defend againstMycobacterium tuberculosis(Mtb) infection but variably recognize Mtb-infected macrophages. To define how the diversity of lung parenchymal CD8+T cells changes during chronic infection, cells from C57BL/6J mice infected for 6- and 41-weeks were analyzed by scRNA-seq. We identified an effector lineage, including a cluster that expresses high levels of cytotoxic effectors and cytokines, and dysfunctional lineage that transcriptionally resembles exhausted T cells. The most significant differentially expressed gene between two distinct CD8+T cell lineages is CD226. Mtb-infected IFNγ-eYFP reporter mice revealed IFNγ production is enriched in CD226+CD8+T cells, confirming these as functional T cells in vivo. Purified CD226+but not CD226−CD8+T cells recognize Mtb-infected macrophages, and CD226 blockade inhibits IFNγ and granzyme B production. Thus, CD226 costimulation is required for efficient CD8+T cell recognition of Mtb-infected macrophages, and its expression identifies CD8+T cells that recognize Mtb-infected macrophages.

One Sentence Summary

Shinkawa et al. discover that CD226 is a functional marker that distinguishes effector from dysfunctional CD8+T cells in theMycobacterium tuberculosis(Mtb)-infected lung and has a crucial role in costimulating CD8+T cell recognition of Mtb-infected macrophages.
Exploring Genomic Signatures of Selection in Guineafowl and Chicken Populations Across Diverse Climatic Zones: A Comparative Analysis of Africa, Asia, and Europe Research Article
Authors: Moraa Grace , Ogada Stephen , Kuria Stephen , Lichoti Jacqueline , Ommeh Sheila
Published: January 2025

This study aimed to investigate the signatures of selection in guineafowl and chicken genomes adapted to divergent climatic conditions across Africa, Asia, and Europe. We used whole genome sequence data of guineafowls and chicken from selected countries in these continents. To identify the signatures of selection, we employed three population genomics methods: FST,integrated Haplotype Score (iHS), and Cross-Population Extended Haplotype Homozygosity (XP-EHH). Our findings revealed enriched terms related to metabolic processes, response to stimulus, signaling, and developmental processes, all of which play a role in the stress response for both guineafowls and chickens. Several candidate genes such asCRYGN,BRAF,MAP3K2,ANGPT2,COL1A1,ATP13A4, andSLC66A1, were among the positively selected candidate genes. Most of the candidate genes selected and the significant pathways identified play various roles in stress response in these two poultry species. Examination of divergent populations has provided new insights into genes potentially under selection for tolerance to the population’s indigenous environment, serving as a baseline for examining the genomic contributions to tolerance adaption. The knowledge gained from this research establishes a valuable foundation and guide for molecular breeding and conservation.
Temperature and precipitation interactively shape the plant microbiome by regulating the start of the growing season
Authors: in 't Zandt Dina , Florianová Anna , urinová Mária , in 't Zandt Michiel , Klanderud Kari , Vandvik Vigdis , Münzbergová Zuzana
Published: January 2025

Climate change is altering associations between plants and soil microbiota, threatening ecosystem functioning and stability. Predicting these effects requires understanding how concomitant changes in temperature and precipitation influence plant-soil microbiota associations. We identify the pathways via which temperature and precipitation shape prokaryote and fungal rhizosphere and root-associated communities of the perennial grass Festuca rubra in cold-climate ecosystems. We found that interactive effects of temperature and precipitation are key in shaping plant-soil microbiota associations, with the start of the growing season as a critical mediating factor. Specifically, the start of the growing season is advanced by increasing temperature, but delayed by increasing precipitation. This interactive pathway particularly shaped rhizosphere organic matter degrading microbiota, and root-associated plant pathogen and beneficial microbiota. We conclude that understanding local temperature, precipitation, and seasonal changes is crucial to accurately predict how the unique plant-microbiota interactions shaping cold-climate ecosystems are evolving with the ongoing change in climate.
CAR T-cell and oncolytic virus dynamics and determinants of combination therapy success for glioblastoma
Authors: Conte Martina , Xella Agata , Woodall Ryan T. , Cassady Kevin A. , Branciamore Sergio , Brown Christine E. , Rockne Russell C.
Published: January 2025

Glioblastoma is a highly aggressive and treatment-resistant primary brain cancer. While chimeric antigen receptor (CAR) T-cell therapy has demonstrated promising results in targeting these tumors, it has not yet been curative. An innovative approach to improve CAR T-cell efficacy is to combine them with other immune modulating therapies. In this study, we investigatein vitrocombination of IL-13Rα2 targeted CAR T-cells with an oncolytic virus (OV) and study the complex interplay between tumor cells, CAR T-cells, and OV dynamics with a novel mathematical model. We fit the model to data collected from experiments with each therapy individually and in combination to reveal determinants of therapy synergy and improved efficacy. Our analysis reveals that the virus bursting size is a critical parameter in determining the net tumor infection rate and overall combination treatment efficacy. Moreover, the model predicts that administering the oncolytic virus simultaneously with, or prior to, CAR T-cells could maximize therapeutic efficacy.
Characterization of nuclear genome size and variation in a freshwater snail model system featuring a recent whole-genome duplication
Authors: Neiman Maurine , Pichler Maria , Haase Martin , Lamatsch Dunja K.
Published: January 2025

Species are defined by unique nuclear genome characteristics like nucleotide composition, genomic structure, and genome size. These fundamental aspects of the nuclear genome can themselves be the object of natural selection. We here provide the first high-quality direct measurements of nuclear genome DNA content in a representative diverse sample ofPotamopyrgus antipodarum, an Aotearoa New Zealand freshwater snail that is a textbook example of the maintenance of sexual reproduction in nature and is invasive worldwide. We used propidium-iodide-based flow cytometry to characterize nuclear DNA content, and its variation, in nearly 100P. antipodarumfrom multiple populations representing both sexual and asexual individuals. We also estimated nuclear DNA content in multipleP. estuarinus, a closely related obligately sexual species. These data confirmed and extended earlier lines of evidence for polyploidy and variable genome size within asexualP. antipodarumand provided the first direct evidence for distinctly higher nuclear genome content in diploid (sexual)P. antipodarumrelative to diploid sexualP. estuarinus. These data are consistent with genomic evidence for a recent whole-genome duplication (WGD) and subsequent and in-process rediploidization inP. antipodarum, setting the stage for use ofPotamopyrgusas a model for WGD and its consequences.
Unified meta regression models for rare variant association studies
Authors: Lauer Larissa , Rivas Manuel A.
Published: January 2025

Rare variant association studies (RVAS) of complex traits have emerged as a powerful approach to advance drug discovery and diagnostics. Missense pathogenicity predictions from AlphaMissense based on structural context and protein language models improve the differentiation between benign and deleterious variants. Constraint metrics, on the other hand, allow researchers to pinpoint genomic regions under selective pressure that may not directly impact protein structure, but are more likely to contain functionally important mutations. Loss-of-function (LoF) variants, which result in the complete or partial loss of protein function, are particularly informative, as it is more straightforward to assess their downstream functional consequences. In this study, we present a unified meta regression model approach that incorporates the probability of pathogenicity, probability of constraint, and indicator whether a variant is a predicted loss-of-function or missense variant as features to model the observed effect size and uncertainty of effect size obtained from single-variant genetic analysis. We applied the unified meta regression model to 1,144 continuous phenotypes from UK Biobank using single variant summary statistics obtained from Genebass. We replicated our findings using the AllofUS cohort. For each gene discovery, we make available a characterization of whether constrained sites are associated with the phenotype, whether pathogenic sites determined by structural based predictions are associated with phenotype, and whether broader loss-of-function or missense variant annotation better explains the summary statistics observed. Our results are publicly available at Global Biobank Engine (https://biobankengine.shinyapps.io/phenome-wide-unified-model/).