bluuebunny/crossref_metadata_2025 huggingface dataset:
The anthropogenic fingerprint on emerging infectious diseases
Authors: Gibb Rory , Ryan Sadie J. , Pigott David , Fernandez Maria del Pilar , Muylaert Renata L. , Albery Gregory F. , Becker Daniel J. , Blackburn Jason K. , Caceres-Escobar Hernan , Celone Michael , Eskew Evan A. , Frank Hannah K. , Han Barbara A. , Hulland Erin N. , Jones Kate E. , Katz Rebecca , Kucharski Adam , Limmathurotsakul Direk , Lippi Catherine A. , Longbottom Joshua , Martinez Juan Fernando , Messina Jane P. , Nsoesie Elaine O. , Redding David W. , Romero-Alvarez Daniel , Schmid Boris V. , Seifert Stephanie N. , Sinchi Anabel , Trisos Christopher H. , Wille Michelle , Carlson Colin J.
Published: May 2024

Emerging infectious diseases are increasingly understood as a hallmark of the Anthropocene1–3. Most experts agree that anthropogenic ecosystem change and high-risk contact among people, livestock, and wildlife have contributed to the recent emergence of new zoonotic, vector-borne, and environmentally-transmitted pathogens1,4–6. However, the extent to which these factors also structure landscapes of human infection and outbreak risk is not well understood, beyond certain well-studied disease systems7–9. Here, we consolidate 58,319 unique records of outbreak events for 32 emerging infectious diseases worldwide, and systematically test the influence of 16 hypothesized social and environmental drivers on the geography of outbreak risk, while adjusting for multiple detection, reporting, and research biases. Across diseases, outbreak risks are widely associated with mosaic landscapes where people live alongside forests and fragmented ecosystems, and are commonly exacerbated by long-term decreases in precipitation. The combined effects of these drivers are particularly strong for vector-borne diseases (e.g., Lyme disease and dengue fever), underscoring that policy strategies to manage these emerging risks will need to address land use and climate change10–12. In contrast, we find little evidence that spillovers of directly-transmitted zoonotic diseases (e.g., Ebola virus disease and mpox) are consistently associated with these factors, or with other anthropogenic drivers such as deforestation and agricultural intensification13. Most importantly, we find that observed spatial outbreak intensity is primarily an artefact of the geography of healthcare access, indicating that existing disease surveillance systems remain insufficient for comprehensive monitoring and response: across diseases, outbreak reporting declined by a median of 32% (range 1.2%-96.7%) for each additional hour’s travel time from the nearest health facility. Our findings underscore that disease emergence is a multicausal feature of social-ecological systems, and that no one-size-fits-all global strategy can prevent epidemics and pandemics. Instead, ecosystem-based interventions should follow regional priorities and system-specific evidence, and be paired with investment in One Health surveillance and health system strengthening.
Effect of Machine Learning on Anaesthesiology Clinician Prediction of Postoperative Complications: The Perioperative ORACLE Randomised Clinical Trial
Authors: Fritz Bradley A , King Christopher R , Abdelhack Mohamed , Chen Yixin , Kronzer Alexander , Abraham Joanna , Tripathi Sandhya , Ben Abdallah Arbi , Kannampallil Thomas , Budelier Thaddeus P , Helsten Daniel , Montes de Oca Arianna , Mehta Divya , Sontha Pratyush , Higo Omokhaye , Kerby Paul , Gregory Stephen H , Wildes Troy S , Avidan Michael S
Published: May 2024

Background: Anaesthesiology clinicians can implement risk mitigation strategies if they know which patients are at greatest risk for postoperative complications. Although machine learning models predicting complications exist, their impact on clinician risk assessment is unknown. Methods: This single-centre randomised clinical trial enrolled patients age ≥18 undergoing surgery with anaesthesiology services. Anaesthesiology clinicians providing remote intraoperative telemedicine support reviewed electronic health records with (assisted group) or without (unassisted group) also reviewing machine learning predictions. Clinicians predicted the likelihood of postoperative 30-day all-cause mortality and postoperative acute kidney injury within 7 days. Area under the receiver operating characteristic curve (AUROC) for the clinician predictions was determined. Results: Among 5,071 patient cases reviewed by 89 clinicians, the observed incidence was 2% for postoperative death and 11% for acute kidney injury. Clinician predictions agreed with the models more strongly in the assisted versus unassisted group (weighted kappa 0.75 versus 0.62 for death [difference 0.13, 95%CI 0.10-0.17] and 0.79 versus 0.54 for kidney injury [difference 0.25, 95%CI 0.21-0.29]). Clinicians predicted death with AUROC of 0.793 in the assisted group and 0.780 in the unassisted group (difference 0.013, 95%CI -0.070 to 0.097). Clinicians predicted kidney injury with AUROC of 0.734 in the assisted group and 0.688 in the unassisted group (difference 0.046, 95%CI -0.003 to 0.091). Conclusions: Although there was evidence that the models influenced clinician predictions, clinician performance was not statistically significantly different with and without machine learning assistance. Further work is needed to clarify the role of machine learning in real-time perioperative risk stratification. Trial Registration: ClinicalTrials.govNCT05042804
High-throughput competitive binding assay for targeting RNA with small molecules: discovery of new PreQ1riboswitch ligands
Authors: Wintermans Sophie E.L. , Hoffmann Jana S. , Tacoma Mariska D. , Broekhuizen Indy , van Doodewaerd Bjorn R. , Geurink Paul P. , Janssen Antonius P.A. , Artola Marta , Olsthoorn René R.C.L.
Published: May 2024

In the evolving landscape of RNA targeting, there is an indisputable need for new screening methodologies to find small molecules targeting relevant tertiary RNA structures, like viral pseudoknots or bacterial riboswitches. Here, we developed a competitive binding high-throughput screening assay to identify ligands for the bacterial PreQ1-I riboswitch. In this assay, ligands compete with a rationally designed quencherlabeled antisense for binding to the riboswitch. The method is validated for theFusobacterium nucleatum(Fnu),Thermoanaerobacter tengcongensis(Tte),Bacillus subtilis(Bsu) andEnterococcus faecalis(Efa) PreQ1riboswitches, using the natural riboswitch ligand PreQ1 and various analogues. A commercial RNA-focused library consisting of ∼15,000 compounds was then screened against theFnuriboswitch, leading to the identification of 4 hits exhibiting competitive binding activity. These hits were evaluated in in vitro translation assays against several PreQ1riboswitches. The most promising hit4494showed competitive binding activity to theFnu,Tte,BsuandEfariboswitches, and was able to inhibit translation of aTteriboswitch-regulated reporter gene, making it an interesting starting point for the development of new antibiotics. In essence, this HTS assay has the potential to discover highly sought-after RNA targeting small molecules for complex and clinically relevant RNA structures.

Graphical abstract
Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data
Authors: Chi L. América , Barnes Jonathan E. , Suresh Patel Jagdish , Ytreberg F. Marty
Published: May 2024

Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and antibody-based therapies. The ability to predict these escape mutations with computer simulations would allow us to detect threats early and develop effective countermeasures, but a lack of large-scale experimental data has hampered the validation of these calculations. In this study, we evaluate the ability of the MD+FoldX molecular modeling method to predict escape mutations by leveraging a large deep mutational scanning dataset, focusing on the SARS-CoV-2 receptor binding domain. Our results show a positive correlation between predicted and experimental data, indicating that mutations with reduced predicted binding affinity correlate moderately with higher experimental escape fractions. We also demonstrate that better performance can be achieved using affinity cutoffs tailored to distinct antibody-antigen interactions rather than a one-size-fits-all approach. We find that 70% of the systems surpass the 50% precision mark, and demonstrate success in identifying mutations present in significant variants of concern and variants of interest. Despite promising results for some systems, our study highlights the challenges in comparing predicted and experimental values. It also emphasizes the need for new binding affinity methods with improved accuracy that are fast enough to estimate hundreds to thousands of antibody-antigen binding affinities.
Diurnal variations in digestion and luminal flow determine microbial population dynamics along the human large intestine
Authors: Salari Alinaghi , Cremer Jonas
Published: May 2024

The human large intestine harbors a highly dynamic microbial ecosystem in which growing microbes regularly replenish biomass lost via feces. Understanding this population dynamics is biomedically important but remains a significant challenge due to rapid changes in microbial biomass and intestinal fluid flows. Leveraging experimental data on fluid turnover, nutrient supply, and microbial growth, we here derive a biophysical model of population dynamics. We show how the digestion of meals in batches triggers strong fluctuations in fluid movement and bacteria growth along the proximal large intestine. Comparing different model scenarios, we further analyze how the expandable nature of the proximal large intestine, the presence of a pouch-like cecum off major flow paths, and the periodic exit of luminal content via ‘mass movements’ are required in combination to maintain the high microbial population observed in the proximal large intestine. Since the microbial population undergoes several bottlenecks followed by rapid growth each day, the effective population size in the proximal large intestine is small,Ne∼ 107− 1011, promoting the fast evolution of microbes. The diurnal fluctuations in flow also hamper the accumulation of slower-growing bacteria and lead to substantial variations in the uptake of fermentation products by the host. Our findings underscore the highly intertwined population dynamics of the gut microbiota, determined by the physics of fluid flow and growth with strong consequences for the microbiome and the host.

Significance statement

The density of microbial biomass within the large intestine is a key determinant of microbiome-host interactions and their impact on the human body. Studies with animal models have suggested highly intertwined population dynamics with strong variations of microbial densities over time and space. To elucidate the physiological drivers of these spatiotemporal dynamics along the human large intestine, we introduce a biophysical modeling framework that considers at its core the diurnal variation of digestion and fluid flow. Our analysis reveals how nutrient supply and the rapid movement of luminal content cause strong fluctuations in microbial biomass turnover throughout the day. The intertwined dynamics provide the host with ample mechanisms to control the microbiota, suppressing, for example, the emergence of slow-growing cross-feeding microbes.
Strong pairwise interactions do not drive interactions in a plant leaf associated microbial community
Authors: Höhn Franziska , Chaudhry Vasvi , Bagci Caner , Mahmoudi Maryam , Klenk Elke , Berg Lara , Stincone Paolo , Hughes Chambers C. , Petras Daniel , Brötz-Oesterhelt Heike , Kemen Eric , Ziemert Nadine
Published: May 2024

Microbial communities that promote plant growth show promise in reducing the impacts of climate change on plant health and productivity. Understanding microbe-microbe interactions in a community context is paramount for designing effective microbial consortia that enhance plant resilience. In this study, we investigated the dynamics of a synthetic microbial community (SynCom) assembled fromArabidopsis thalianaleaves to elucidate factors shaping community composition and stability. We found notable disparities betweenin vitropairwise interactions and those inferred from correlation networksin planta. Our findings suggested that secondary metabolites, particularly antimicrobials, might mediate interactionsin vitro, but fade into the background in the community context. Through co-cultivation experiments, we identified the siderophore pseudobactin as a potent antimicrobial agent against several SynCom members, but its impact on community compositionin plantawas negligible. Notably, dominant SynCom members, such asPseudomonas koreensis, Flavobacterium pectinovorum, andSporobolomyces roseus, exhibited only positive correlations, suggesting synergism based on for example exopolysaccharides and biotransformation might drive community dynamics rather than competition. Two correlations between SynCom members in the co-abundance network corresponded with their pairwisein vitrointeractions, highlighting the potential for further research, and demonstrating the usefulness of correlation networks in identifying key microbe-microbe interactions. Our findings highlight the importance of considering microbiome-wide interaction studies and synthetic communities in understanding and manipulating plant microbiomes.
Autonomous Shaping of the piRNA Sequence Repertoire by Competition between Adjacent Ping-Pong Sites
Authors: Yu Jie , Izumi Natsuko , Tomari Yukihide , Shoji Keisuke
Published: May 2024

PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements (TEs). In many species, piRNAs are generated via a complex process known as the ping-pong pathway, which couples TE cleavage with new piRNA amplification. However, the biological significance of this complexity and its impact on the piRNA sequence repertoire remain unclear. Here, we systematically compared piRNA production patterns in two closely related silkworm cell lines and found significant changes in their piRNA sequence repertoire. Importantly, the changeability of this repertoire showed a strong negative correlation with the efficiency of piRNA biogenesis. This can be explained by competition between adjacent ping-pong sites, as supported by our mathematical modeling. Moreover, this competition can rationalize how piRNAs autonomously avoid deleterious mismatches to target TEs. These findings unveil the intrinsic plasticity and adaptability of the piRNA system to combat diverse TE sequences and highlight the universal power of competition and self-amplification to drive autonomous optimization.
Differential biological effect of low doses of ionizing radiation depending on the radiosensitivity in a cell line model
Authors: Palma-Rojo Elia , Barquinero Joan-Francesc , Pérez-Alija Jaime , González Juan R , Armengol Gemma
Published: May 2024

Purpose

Exposure to low doses (LD) of ionizing radiation (IR), such as the ones employed in computed tomography (CT) examination, can be associated with cancer risk. However, not all individuals respond the same to IR, and cancer development could depend on the individual radiosensitivity. Notably, inter-individual differences in the response to IR have been very well studied for high and medium doses, but not for LD. In the present study, we wanted to evaluate the differences in the response to a CT-scan radiation dose of 20 mGy in two lymphoblastoid cell lines with different radiosensitivity.

Materials and Methods

Several parameters were studied: gene expression, DNA damage, and its repair (by analyzing gamma-H2AX foci, chromosome breaks, and sister chromatid exchange), as well as cell viability, proliferation, and death.

Results

After 20 mGy of IR, the radiosensitive (RS) cell line showed an increase in DNA damage, and higher cell proliferation and apoptosis, whereas the radioresistant (RR) cell line was insensitive to this LD. Interestingly, gene expression analysis showed a higher expression of an antioxidant gene in the RR cell line, which could be used by the cells as a protective mechanism. After a dose of 500 mGy, both cell lines were affected by IR but with significant differences. The RS cells presented an increase in DNA damage and apoptosis, but a decrease in cell proliferation and cell viability, as well as less antioxidant response.

Conclusions

A differential biological effect was observed between two cell lines with different radiosensitivity, and these differences are especially interesting after a CT scan dose. If this is confirmed by further studies, one could think that individuals with radiosensitivity-related genetic variants may be more vulnerable to long-term effects of IR, potentially increasing cancer risk after LD exposure.
Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements
Authors: Mateo-Cáceres Víctor , Redrejo-Rodríguez Modesto
Published: May 2024

Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against viruses and other genetic mobile elements. Here, we disclose pipolins, previously found in diverse bacterial phyla and encoding a primer-independent PolB, as a new category of widespread defense islands. The analysis of the occurrence and structure of pipolins revealed that they are commonly integrative elements flanked by direct repeats in Gammaproteobacteria genomes, mainlyEscherichia,VibrioorAeromonas, often taking up known mobile elements integration hotspots. Remarkably, integrase dynamics correlates with alternative integration spots and enables diverse lifestyles, from integrative to mobilizable and plasmid pipolins, such as in members of the generaLimosilactobacillus,PseudosulfitobacterorStaphylococcus.

Pipolins harbor a minimal core and a large cargo module enriched for defense factors. In addition, analysis of the weighted gene repertoire relatedness revealed that many of these defense factors are actively exchanged with other mobile elements. These findings indicate pipolins and, potentially other defense islands, act as orthogonal reservoirs of defense genes, potentially transferable to immune autonomous MGEs, suggesting complementary exchange mechanisms for defense genes in bacterial populations.
SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling
Authors: Evans Daniel , Sheraz Samreen , Lau Albert
Published: May 2024

In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state-of-the-art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein’s C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedrals angles in transmitting allosteric signals.
Super-enhancer-driven ZFP36L1 promotes PD-L1 expression in infiltrative gastric cancer
Authors: Wei Xujin , Liu Jie , Cheng Jia , Cai Wangyu , Xie Wen , Wang Kang , Lin Lingyun , Hou Jingjing , Cai Jianchun , Zhuo Huiqin
Published: May 2024

Gastric cancer (GC) is a major cause of cancer-related mortality worldwide. Despite the widespread recognition of tumor immunotherapy in treating unresectable GC, challenges, including ineffective immunotherapy and drug resistance, persist. Therefore, understanding the regulatory mechanisms of PD-L1, particularly in the context of super-enhancers (SEs) and zinc finger protein 36 ring finger protein-like 1 (ZFP36L1) RNA-binding protein, is crucial.

Methods

In this study, we performed H3K27ac CUT&Tag sequencing, investigated the heterogeneity of SEs between two GC subtypes with differential growth patterns, and revealed the immune escape signatures driven by ZFP36L1-SE in infiltrative GC through SEs inhibitors treatment. The regulation of ZFP36L1 to PD-L1 was evaluated by quantitative PCR, western blot, flow cytometry and immunohistochemistry. Furthermore, we explored its regulatory mechanisms using a combination of molecular biology techniques, including luciferase reporter assay, GST/RNA pull-down, ChIP/RIP experiments, and in vivo functional assays.

Results

We demonstrated that ZFP36L1, driven by an SE, enhances IFN-γ-induced PD-L1 expression, with SPI1 identified as the specific transcription factor binding to ZFP36L1-SE. Mechanistically, ZFP36L1 binds to the adenylate uridylate-rich element in the 3’UTR ofHDAC3mRNA, exacerbating its mRNA decay, and thereby facilitating PD-L1 abnormal transcriptional activation.

Conclusions

Collectively, our findings provide mechanistic insights into the role of the SPI1– ZFP36L1–HDAC3–PD-L1 signaling axis in orchestrating immune escape mechanisms in GC, thereby offering valuable insights into the potential targets for immune checkpoint therapy in GC management.
Therapeutic potential of SOX9 dysruption in Combined Hepatocellular Carcinoma-Cholangiocarcinoma
Authors: Park Yoojeong , Hu Shikai , Kim Minwook , Oertel Michael , Singhi Aatur , Monga Satdarshan P. , Liu Silvia , Ko Sungjin
Published: May 2024

Combined hepatocellular carcinoma-cholangiocarcinoma (cHCC-CCA) represents a challenging subtype of primary liver cancer with limited treatment options and a poor prognosis. Recently, we and others have highlighted the context-dependent roles of the biliary-specific transcription factor SOX9 in the pathogenesis of liver cancers using variousCreapplications inSox9(flox/flox)strains, to achieve elimination for exon 2 and 3 of theSox9gene locus as a preventive manner. Here, we reveal the contrasting responses of developmentalSox9elimination usingAlb-Cre;Sox9(flox/flox)(Sox9LKO) versusCRISPR/Cas9-based tumor specific acuteSox9CKO in SB-HDTVI-basedAkt-YAP1andAkt-NRAScHCC-CCA formation.Sox9LKO specifically abrogates theAkt-YAP1CCA region while robustly stimulating the proliferation of remaining poorly differentiated HCC pertaining liver progenitor cell characteristics, whereasSox9CKO potently preventsAkt-YAP1andAkt-NRAScHCC-CCA development irrespective of fate of tumor cells compared to respective controls. Additionally, we find thatAkt-NRAS, but notAkt-YAP1, tumor formation is partially dependent on theSox9-Dnmt1cascade. Pathologically, SOX9 is indispensable forAkt-YAP1-mediated HC-to-BEC/CCA reprogramming but required for the maintenance of CCA nodules. Lastly, therapeutic elimination ofSox9using theOPN-CreERT2strain combined with an inducibleCRISPR/Cas9-basedSox9iKO significantly reducesAkt-YAP1cHCC-CCA tumor burden, similar toSox9CKO. Thus, we contrast the outcomes of acuteSox9deletion with developmentalSox9knockout models, emphasizing the importance of considering adaptation mechanisms in therapeutic strategies. This necessitates the careful consideration of genetic liver cancer studies using developmental Cre and somatic mutant lines, particularly for genes involved in hepatic commitment during development. Our findings suggest that SOX9 elimination may hold promise as a therapeutic approach for cHCC-CCA and underscore the need for further investigation to translate these preclinical insights into clinical applications.
Flexible males, proactive females: personality tests show increased boldness/exploration in colonists damping with time in males but not in females
Authors: Tchabovsky Andrey V. , Surkova Elena N. , Savinetskaya Ludmila E. , Khropov Ivan S.
Published: May 2024

Individuals colonizing new areas at expanding ranges encounter challenging and unfamiliar environments, suggesting that colonists should differ in behavioural traits from the residents of the source populations. The colonizer syndrome is supposed to be associated with boldness, exploration, activity, and low sociability. We assessed spatial and temporal variation in the colonizer syndrome in the expanding population of midday gerbils (Meriones meridianus). Male first colonists tended to be faster and bolder than residents, although the difference was not significant. Female first colonists were bolder, faster and more explorative than residents. These findings support boldness/exploration syndrome as a typical colonizer trait, which appears to be restricted to females in midday gerbils. Males and females also differed in the behavioural dynamics post-colony establishment. In males, boldness/exploration/sociability peaked in newly founded colonies, then sharply decreased in subsequent generations following decreasing environmental uncertainty in aging colonies. In females, increased boldness/exploration did not lower with time post-colonization, i.e. female colonists retained bold/explorative phenotype in subsequent generations despite facing a less challenging environment. Thus, female colonists, unlike males, carry a specialized behavioural colonizer phenotype corresponding to a proactive behavioural coping strategy. We link sex differences in behavioural traits of colonists to the sex-specific life-history strategies.
Coupled phylogenetic and functional enrichment in the tomato rhizosphere microbiome
Authors: Talavera-Marcos Silvia , Gallego Ramón , Chaboy Rubén , Rastrojo Alberto , de Cárcer Daniel Aguirre
Published: May 2024

Plant-microbe interactions occur mainly in the rhizosphere, a hot spot of microbial activity and diversity. Given that the outcome of such interactions can significantly impact plant productivity, we require a better understanding of the rhizosphere microbiome if knowledge-based microbiome modification strategies are to be successfully deployed in the future. Here, we aimed to gain a better understanding of the assembly process of the tomato rhizosphere microbiome and its potential composition-function relationships. Among other things, we studied community assembly through the lens of a conceptual framework for the phylogenetically constrained assembly of microbial communities, while assessing community function based on the predicted minimal metagenome of the microbial ecosystem. We observed a systematic enrichment in terms of phylogeny and predicted functional content in the rhizosphere and were able to delimit phylogenetic signal in the ecosystem with 12 functionally coherent phylogenetic groups present in all samples which together accounted for a large fraction of the total community. Our analyses indicated that these groups included a significantly larger content of the ecosystem’s minimal metagenome than expected by chance. Thus, our study suggests that community assembly followed coupled phylo-functional selection independent of host genetics, and we expect the same phenomenon to occur in other rhizosphere microbiomes. This knowledge provides a thrust in our understanding of how community composition-phylogeny-function relationships drive the assembly process of the rhizosphere microbiome and should help guide the design of synthetic rhizosphere microbiomes for both research and commercial purposes.
Phenotypic and genetic heterogeneity ofAcinetobacter baumanniiin the course of a chronic infection
Authors: Bednarczuk Léa , Chassard Alexandre , Plantade Julie , Charpentier Xavier , Laaberki Maria-Halima
Published: May 2024

Acinetobacter baumanniiis a nosocomial pathogen associated with various infections, including urinary tract infections (UTIs). In the course of an infection,A. baumanniiis known to rapidly become resistant to antibiotic therapy, but much less is known about possible adaptation without antibiotic pressure. Through a retrospective study, we investigated within-host genetic diversity during a subclinical five-year UTI in an animal-patient after withdrawal of colistin treatment. We conducted whole-genome sequencing and phenotypic assays on seventeen clonally related isolates from the Sequence Type 25 lineage. Phylogenomic analysis revealed their proximity with animal and human strains from the same country suggesting zoonotic transmission (France). In this case study, the clonally related strains presented variations in genome sizes and nucleotide sequences. Over the course of the infection,A. baumanniiunderwent genome reduction through insertion sequence (IS) recombination, phage excision, or plasmid curing. Alongside this global genome reduction, we observed an expansion of IS17, initially located on the endogenous large plasmid. Genetic variations were mainly located in biofilm formation and metabolism genes. We observed repeated variation affecting three biofilm genes and two adhesion operons associated with weak biofilm-forming capacity. Conversely, only two metabolic genes were recurrently affected and phenotypic assays indicated a rather stable metabolism profile between the isolates suggesting minor adaptations to its host. Lastly, an overall decreased antibiotic resistance, expected in the absence of antibiotic treatment, contrasted with a conserved colistin resistance due to apmrBmutation among the isolates.
A simple active fluid model unites cytokinesis, cell crawling, and axonal outgrowth
Authors: Craig Erin M. , Oprea Francesca , Alam Sajid , Grodsky Ania , Miller Kyle E.
Published: May 2024

Axonal outgrowth, cell crawling, and cytokinesis utilize actomyosin, microtubule-based motors, cytoskeletal dynamics, and substrate adhesions to produce traction forces and bulk cellular motion. While it has long been appreciated that growth cones resemble crawling cells and that the mechanisms that drive cytokinesis help power cell crawling, they are typically viewed as unique processes. To better understand the relationship between these modes of motility, here, we developed a unified active fluid model of cytokinesis, amoeboid migration, mesenchymal migration, neuronal migration, and axonal outgrowth in terms of cytoskeletal flow, adhesions, viscosity, and force generation. Using numerical modeling, we fit subcellular velocity profiles of the motions of cytoskeletal structures and docked organelles from previously published studies to infer underlying patterns of force generation and adhesion. Our results indicate that, during cytokinesis, there is a primary converge zone at the cleavage furrow that drives flow towards it; adhesions are symmetric across the cell, and as a result, cells are stationary. In mesenchymal, amoeboid, and neuronal migration, the site of the converge zone shifts, and differences in adhesion between the front and back of the cell drive crawling. During neuronal migration and axonal outgrowth, the primary convergence zone lies within the growth cone, which drives actin retrograde flow in the P-domain and bulk anterograde flow of the axonal shaft. They differ in that during neuronal migration, the cell body is weakly attached to the substrate and thus moves forward at the same velocity as the axon. In contrast, during axonal outgrowth, the cell body strongly adheres to the substrate and remains stationary, resulting in a decrease in flow velocity away from the growth cone. The simplicity with which cytokinesis, cell crawling, and axonal outgrowth can be modeled by varying coefficients in a simple model suggests a deep connection between them.
The contribution of epigenetic variation to evolution in crows
Authors: Merondun Justin , Wolf Jochen B. W.
Published: May 2024

Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation to evolution we leveraged genome and methylome sequencing data from an incipient avian species: all-black carrion crows, grey-coated hooded crows and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone we show that 5mC methylation variation was almost exclusively explained by genome properties and ontogenetic program of the organism. Evidence for an environmental contribution was minor, and all methylation variation of potential importance to speciation clustered in intergenic space within a genomic region of elevated genetic differentiation encoding the diagnostic color-contrast between taxa. We conclude that methylation variation may aid in phenotypic translation of genetic polymorphism, but provides little scope for an autonomous contribution to evolution in this system.
Consistency of resting-state correlations between fMRI networks and EEG band-power
Authors: Xavier Marta , Esteves Inês , Jorge João , Abreu Rodolfo , Giraud Anne-Lise , Sadaghiani Sepideh , Wirsich Jonathan , Figueiredo Patrícia
Published: May 2024

Several simultaneous EEG-fMRI studies have aimed to identify the relationship between EEG band power and fMRI resting state networks (RSNs) to elucidate their neurobiological significance. Although common patterns have emerged, inconsistent results have also been reported. This study examines the consistency of these correlations across subjects and to understand how factors such as the hemodynamic response delay and the use of different EEG data spaces (source/scalp) influence them. Using three distinct EEG-fMRI datasets, acquired independently on 1.5T, 3T and 7T MRI scanners (comprising 42 subjects in total), we evaluate the generalizability of our findings across different acquisition conditions. We found consistent correlations between fMRI RSN and EEG band-power time-series across subjects in the three datasets studied, with systematic variations with RSN, EEG frequency-band, and HRF delay, but not with EEG space. Qualitatively, the majority of these correlations were similar across the three datasets, despite important differences in field strength, number of subjects and resting-state conditions. Our findings support consistent correlations across specific fMRI RSNs and EEG bands and highlight the importance of methodological considerations in interpreting them that may explain conflicting reports in existing literature.
MINFLUX Reveals Dynein Stepping in Live Neurons
Authors: Schleske Jonas M. , Hubrich Jasmine , Wirth Jan Otto , D’Este Elisa , Engelhardt Johann , Hell Stefan W.
Published: May 2024

Dynein is the primary molecular motor responsible for retrograde intracellular transport of a variety of cargoes, performing successive nanometer-sized steps within milliseconds. Due to the limited spatiotemporal precision of established methods for molecular tracking, current knowledge of dynein stepping is essentially limited to slowed-down measurements in vitro. Here, we use MINFLUX fluorophore localization to directly track CRISPR/Cas9-tagged endogenous dynein with nanometer/millisecond precision in living primary neurons. We show that endogenous dynein primarily takes 8 nm steps, including frequent sideways steps but few backward steps. Strikingly, the majority of direction reversals between retrograde and anterograde movement occurred on the time scale of single steps (16 ms), suggesting a rapid regulatory reversal mechanism. Tug-of-war-like behavior during pauses or reversals was unexpectedly rare. By analyzing the dwell time between steps, we concluded that a single rate-limiting process underlies the dynein stepping mechanism whereby dynein consumes one adenosine 5’-triphosphate (ATP) per step. Our study underscores the power of MINFLUX localization to elucidate the spatiotemporal changes underlying protein function in living cells.
Identification of a new cell cycle variant during multiciliated cell differentiation
Authors: Serizay Jacques , Damaa Michella Khoury , Boudjema Amélie-Rose , Balagué Rémi , Faucourt Marion , Delgehyr Nathalie , Noûs Camille , Zaragosi Laure-Emmanuelle , Barbry Pascal , Spassky Nathalie , Koszul Romain , Meunier Alice
Published: May 2024

2

A complex and conserved regulatory network drives the cell cycle. Individual components of this network are sometimes used in differentiated cells, i.e. to control organelle destruction in mammalian lens cells or light response in land plants. Some differentiated cells co-opt cell-cycle regulators more largely, to increase their ploidy using a cell cycle variant named endoreplication. Using single-cell RNA-seq profiling and functional assays in differentiating multiciliated cells, we identified a novel type of cell cycle variant that supports cytoplasmic organelle, rather than nuclear content amplification. This variant operates in post-mitotic, centriole-amplifying differentiating multiciliated cells and is characterized by (i) a circular trajectory of the transcriptome, (ii) sequential expression of more than 70% of the genes involved in S, G2 and M-like progression along this trajectory, and (iii) successive waves of cyclins. This cell cycle variant is tailored by the expression of the non-canonical cyclins O and A1 – which replace the transcriptionally silent cyclins E2 and A2 – and by the silencing of the APC/C inhibitor Emi1, two switches also detected in male meiosis, another variant of the canonical cell cycle where centriole and DNA replications are uncoupled. Re-expressing Cyclin E2, cyclin A2 or Emi1 is sufficient to induce partial replication and mitosis, suggesting that change in the regulation of expression of a few cell cycle key players drives a qualitative and quantitative tuning of Cdk activity, allowing the diversion of the cell cycle in the multiciliation variant. We also propose that this new cell cycle variant relies on the existence of a cytoplasmic – or centriolar – Cdk threshold, lower than the S-phase threshold, which affects only the cytoplasmic reorganization.

One-Sentence Summary

MCC progenitors undergo a final, tailored iteration of the cell cycle during differentiation, to drive centriole amplification without DNA replication or mitosis.
The salivary virome during childhood dental caries
Authors: Tang Jonah , Baker Jonathon L.
Published: May 2024

While many studies have examined the bacterial taxa associated with dental caries, the most common chronic infectious disease globally, little is known about the caries-associated virome. In this study, the salivary viromes of 21 children with severe caries (>2 dentin lesions) and 23 children with healthy dentition were examined. 2,485 viral metagenome-assembled genomes (vMAGs) were identified, binned, and quantified from the metagenomic assemblies. These vMAGs were mostly phage, and represented 1,547 unique species-level vOTUs, 247 of which appear to be novel. The metagenomes were also queried for all 3,835 unique species-level vOTUs of DNA viruses with a human host on NCBI Virus, however all butHuman betaherpesvirus 7were at very low abundance in the saliva. The oral viromes of the children with caries exhibited significantly different beta diversity compared to the oral virome of the children with healthy dentition; several vOTUs predicted to infectPauljenseniaandNeisseriawere strongly correlated with health, and two vOTUs predicted to infect Saccharibacteria andPrevotella histicola, respectively, were correlated with caries. Co-occurrence analysis indicated that phage typically co-occurred with both their predicted hosts and with bacteria that were themselves associated with the same disease status. Overall, this study provided the sequences of 53 complete or nearly complete novel oral phages and illustrated the significance of the oral virome in the context of dental caries, which has been largely overlooked. This work represents an important step towards the identification and study of phage therapy candidates which treat or prevent caries pathogenesis.

Importance

Dental caries is the most common chronic infectious disease, worldwide, and is caused by a dysbiosis of the oral microbiome featuring an increased abundance of acid-tolerant, acid-producing, and biofilm-forming bacteria. The oral microbiome also contains viruses; however, very little is known about the the caries-associated virome. In this study, the salivary virome of children with severe caries was compared to the salivary virome of children with healthy dentition. The metagenomes contained a total of 1,547 unique species-level vOTUs, 247 of which appeared to be novel. The viromes from the children with caries were significantly different than the viromes from the children with healthy teeth, and several health- and disease-associated vOTUs were identified. This study illustrated the importance of the oral virome in the context of dental caries, and serves as a step towards a better understanding of oral inter-kingdom interactions and identification of potential phage-based caries therapeutics.
Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation
Authors: DeGroat William , Inoue Fumitaka , Ashuach Tal , Yosef Nir , Ahituv Nadav , Kreimer Anat
Published: May 2024

Background

Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of regulatory programs this variation affects can shed light on the apparatuses of human diseases.

Results

We collected epigenetic and gene expression datasets from seven early time points during neural differentiation. Focusing on this model system, we constructed networks of enhancer-promoter interactions, each at an individual stage of neural induction. These networks served as the base for a rich series of analyses, through which we demonstrated their temporal dynamics and enrichment for various disease-associated variants. We applied the Girvan-Newman clustering algorithm to these networks to reveal biologically relevant substructures of regulation. Additionally, we demonstrated methods to validate predicted enhancer-promoter interactions using transcription factor overexpression and massively parallel reporter assays.

Conclusions

Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes. This includes a comprehensive approach to studying the effects of disease-associated variation on transcriptional networks. The techniques applied to our networks have been published alongside our findings as a computational tool, E-P-INAnalyzer. Our procedure can be utilized across different cellular contexts and disorders.
Mathematical Modeling Unveils Optimization Strategies for Targeted Radionuclide Therapy of Blood Cancers
Authors: Kuznetsov Maxim , Adhikarla Vikram , Caserta Enrico , Wang Xiuli , Shively John E. , Pichiorri Flavia , Rockne Russell C.
Published: May 2024

Targeted radionuclide therapy is based on injections of cancer-specific molecules conjugated with radioactive nuclides. Despite the specificity of this treatment, it is not devoid of side-effects limiting its use and is especially harmful for rapidly proliferating organs well perfused by blood, like bone marrow. Optimization of radioconjugates administration accounting for toxicity constraints can increase treatment efficacy. Based on our experiments on disseminated multiple myeloma mouse model treated by225Ac-DOTA-daratumumab, we developed a mathematical model which investigation highlighted the following principles for optimization of targeted radionuclide therapy. 1) Nuclide to antibody ratio importance. The density of radioconjugates on cancer cells determines the density of radiation energy deposited in them. Low labeling ratio as well as accumulation of unlabeled antibodies and antibodies attached to decay products in the bloodstream can mitigate cancer radiation damage due to excessive occupation of specific receptors by antibodies devoid of radioactive nuclides. 2) Cancer binding capacity-based dosing. The rate of binding of drug to cancer cells depends on the total number of their specific receptors, which therefore can be estimated from the pharmacokinetic curve of diagnostic radioconjugates. Injection of doses significantly exceeding cancer binding capacity should be avoided since radioconjugates remaining in the bloodstream have negligible efficacy to toxicity ratio. 3) Particle range-guided multi-dosing. The use of short-range particle emitters and high-affinity antibodies allows for robust treatment optimization via initial saturation of cancer binding capacity, enabling redistribution of further injected radioconjugates and deposited dose towards still viable cells that continue expressing specific receptors.

Significance

Mathematical modeling yields general principles for optimization of targeted radionuclide therapy in mouse models of multiple myeloma that can be extrapolated on another cancer models and on clinical setting.
Formation of vimentin biomolecular condensate-like structures under oxidative stress
Authors: Martínez-Cenalmor Paula , Martínez Alma E. , Moneo-Corcuera Diego , Jiménez Patricia González- , Pérez-Sala Dolores
Published: May 2024

The intermediate filament protein vimentin performs a key role in cytoskeletal interplay and dynamics, and in cellular responses to stress. The vimentin monomer possesses a central α-helical rod domain flanked by N- and C-terminal low complexity domains. Interactions between this type of domains play an important function in the formation of phase-separated biomolecular condensates, which in turn are critical for the organization of cellular components. Vimentin filaments undergo distinct and versatile reorganizations in response to diverse stimuli. Here we show that certain oxidants and electrophiles, including hydrogen peroxide and diamide, elicit the remodeling of vimentin filaments into small particles. Diamide in particular, induces a fast conversion of filaments into circular, motile dots, for which the presence of the single vimentin cysteine residue, C328, is critical. This effect is reversible, and filament reassembly can be noticed within minutes of removal of the oxidant. Diamide-elicited structures can recover fluorescence after photobleaching. Moreover, fusion of cells expressing differentially tagged vimentin allows the detection of dots positive for both tags, suggesting that vimentin dots can merge upon cell fusion. The aliphatic alcohol 1,6-hexanediol, known to alter interactions between low complexity domains, readily dissolves diamide-elicited vimentin dots at low concentrations, whereas at high concentrations it disrupts vimentin filaments. Taken together, these results indicate that vimentin oxidation can promote a fast and reversible filament remodeling into biomolecular condensate-like structures. Moreover, we hypothesize that this reorganization into droplet-like structures could play a protective role against irreversible damage by oxidative stress.