bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconfiguration of Functional Brain Hierarchy in Schizophrenia
Authors: Acero-Pousa Irene , Escrichs Anira , Dagnino Paulina Clara , Perl Yonatan Sanz , Kringelbach Morten L. , Uhlhass Peter J. , Deco Gustavo
Published: August 2024

The multidimensional nature of schizophrenia requires a comprehensive exploration of the functional and structural brain networks. While prior research has provided valuable insights into these aspects, our study goes a step further to investigate the reconfiguration of the hierarchy of brain dynamics, which can help understand how brain regions interact and coordinate in schizophrenia. We applied an innovative thermodynamic framework, which allows for a quantification of the degree of functional hierarchical organization by analysing resting state fMRI-data. Our findings reveal increased hierarchical organization at the whole-brain level and within specific resting-state networks in individuals with schizophrenia, which correlated with negative symptoms, positive formal thought disorder and apathy. Moreover, using a machine learning approach, we showed that hierarchy measures allow a robust diagnostic separation between healthy controls and schizophrenia patients. Thus, our findings provide new insights into the nature of functional connectivity anomalies in schizophrenia, suggesting that they could be caused by the breakdown of the functional orchestration of brain dynamics.
Focused Ultrasound Augments the Delivery and Penetration of Model Therapeutics into Cerebral Cavernous Malformations
Authors: Fisher Delaney G. , Hoch Matthew R. , Gorick Catherine M. , Huchthausen Claire , Breza Victoria R. , Sharifi Khadijeh A. , Tvrdik Petr , Miller G. Wilson , Price Richard J.
Published: August 2024

BACKGROUND

Cerebral cavernous malformations (CCMs) are vascular neoplasms in the brain that can cause debilitating symptoms. Current treatments pose significant risks to some patients, motivating the development of new nonsurgical options. We recently discovered that focused ultrasound-microbubble treatment (FUS) arrests CCM formation and growth. Here, we build on this discovery and assess the ability of FUS to deliver model therapeutics into CCMs.

METHODS

Quantitative T1 mapping MRI sequences were used with 1 kDa (MultiHance; MH) and 17 kDa (GadoSpin D; GDS) contrast agents to assess the FUS-mediated delivery and penetration of model small molecule drugs and biologics, respectively, into CCMs of Krit1 mutant mice.

RESULTS

FUS elevated the rate of MH delivery to both the lesion core (4.6-fold) and perilesional space (6.7-fold). Total MH delivery more than doubled in the lesion core and tripled in the perilesional space when FUS was applied immediately prior to MH injection. For the model biologic drug (i.e. GDS), FUS was of greater relative benefit, resulting in 21.7-fold and 3.8-fold delivery increases to the intralesional and perilesional spaces, respectively

CONCLUSIONS

FUS augments the delivery and penetration of therapeutics into the complex and disorganized CCM microenvironment. Benefits to small molecule drug delivery are more evident in the perilesional space, while benefits to biologic delivery are more evident in CCM cores. These findings, when combined with ability of FUS alone to control CCMs, highlight the potential of FUS to serve as a powerful non-invasive therapeutic platform for CCM.
Neuronal heterogeneity in the medial septum and diagonal band of Broca: classes and continua
Authors: Kuhn Felix , Mocellin Petra , Pupe Stefano , Wang Lihua , Lemire Andrew L. , Sosulina Liudmila , Barnstedt Oliver , Spruston Nelson , Cembrowski Mark S. , Remy Stefan
Published: August 2024

The medial septum and diagonal band of Broca (MSDB) is known for its diverse populations of cholinergic, GABAergic, and glutamatergic neurons, each contributing to various cognitive processes. However, cell-specific manipulations within this region often result in incongruous behavioral outcomes and reach conflicting conclusions, likely because of a hitherto unknown molecular complexity in its cellular landscape. In this study, we employed single-cell RNA sequencing to thoroughly describe the heterogeneity of MSDB neurons. We confirmed previously established neuronal classes, found gene expression gradients within them and revealed genetically defined subclusters. Moreover, we characterized the genetic profiles of these neuronal subclusters and mapped their spatial distribution. Our analysis presents a comprehensive description of the heterogeneity of MSDB neurons, provides marker genes to target them, explains previous paradoxical results, and opens unexplored avenues to study the impact of neuromodulators in the basal forebrain.
Birth order specified recruitment of motor circuits during spontaneous neural activity in zebrafish embryo
Authors: Abi Younes Maroun , Rima Mohamad , Coutanceau Jean-Pierre , Peysson Ninon , Hoseinkhani Fatemeh , Rodrigues Edson , Bullier Erika , Legendre Pascal , Mangin Jean-Marie , Hong Elim
Published: August 2024

Modular organization of spinal neural circuits control dynamic regulation of locomotion. However, it is unknown when or how the distinct microcircuits emerge during development. We carried out high-resolution calcium imaging of neural activity driving the first motor behavior in one day old zebrafish embryo. During this period, at least two waves of neurogenesis occur to generate primary and secondary motoneurons. We found that embryos first display a single highly synchronized rhythmic neuronal circuit containing interneurons and motoneurons. Later, two distinct interneuron-motoneuron circuits emerge with one containing early-born motoneurons displaying low-frequency activity and the other containing later-born motoneurons with high-frequency activity. The results indicate a mode of birth order determined microcircuits where neurons that are born together are recruited together. Nicotine affected neuronal activity frequency, revealing a functional role for cholinergic signaling in the emergence of patterned spinal circuits. Indeed, we found aberrant arrhythmic synchronized activity in mutants forcholineacetyltransferase-awhere acetylcholine is no longer synthesized. Overall, we reveal the sequential recruitment of birth order specified microcircuits during the emergence of the earliest motor behavior and highlight a conserved role for cholinergic signaling in regulating rhythmic neural activity in the embryonic spinal cord.
Phylogenetic diversity of light dependent phosphorylation of Thr78 in Rca
Authors: Bhatnagar Nikita , Chung Sarah S. , Hodge John , Boyd Ryan A , Kim Sang Yeol , Sands Mia , Leakey Andrew D. B. , Ort Donald R. , Burgess Steven
Published: August 2024

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of ribulose-1,5-bisphosphate carboxylase/oxygenase during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of threonine 78. The prevalence of threonine 78 in Rubisco activase was investigated across sequences from 91 plant species, finding 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a threonine 78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of threonine 78 was observed only in Arabidopsis. Further, phosphorylation of threonine 78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of threonine 78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. This provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.
Beyond bacterial paradigms: uncovering the functional significance and first biogenesis machinery of archaeal lipoproteins
Authors: Hong Yirui , Makarova Kira S. , Xu Rachel , Pfeiffer Friedhelm , Pohlschroder Mechthild
Published: August 2024

Lipoproteins are major constituents of prokaryotic cell surfaces. In bacteria, lipoprotein attachment to membrane lipids is catalyzed by prolipoprotein diacylglyceryl transferase (Lgt). However, no Lgt homologs have been identified in archaea, suggesting the unique archaeal membrane lipids require distinct enzymes for lipoprotein lipidation. Here, we performedin silicopredictions for all major archaeal lineages and revealed a high prevalence of lipoproteins across the domain Archaea. Using comparative genomics, we identified the first set of candidates for archaeal lipoprotein biogenesis components (Ali). Genetic and biochemical characterization confirmed two paralogous genes,aliAandaliB, are important for lipoprotein lipidation in the archaeonHaloferax volcanii. Disruption of AliA- and AliB-mediated lipoprotein lipidation results in severe growth defects, decreased motility, and cell-shape alterations, underscoring the importance of lipoproteins in archaeal cell physiology. AliA and AliB also exhibit different enzymatic activities, including potential substrate selectivity, uncovering a new layer of regulation for prokaryotic lipoprotein lipidation.
Temporally discordant chromatin accessibility and DNA demethylation define short and long-term enhancer regulation during cell fate specification
Authors: Guerin Lindsey N. , Scott Timothy J. , Yap Jacqueline A. , Johansson Annelie , Puddu Fabio , Charlesworth Tom , Yang Yilin , Simmons Alan J. , Lau Ken S. , Ihrie Rebecca A. , Hodges Emily
Published: August 2024

Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand this paradox, we established a highly-resolved timeline of DNA demethylation, chromatin accessibility, and transcription factor occupancy during neural progenitor cell differentiation. We show thousands of enhancers undergo rapid, transient accessibility changes associated with distinct periods of transcription factor expression. However, most DNA methylation changes are unidirectional and delayed relative to chromatin dynamics, creating transiently discordant epigenetic states. Genome-wide detection of 5-hydroxymethylcytosine further revealed active demethylation begins ahead of chromatin and transcription factor activity, while enhancer hypomethylation persists long after these activities have dissipated. We demonstrate that these timepoint specific methylation states predict past, present and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to mediate short and long-term enhancer regulation during cell fate specification.
Machine learning and data-driven inverse modeling of metabolomics unveil key process of active aging
Authors: Li Jiahang , Brenner Martin , Pierides Iro , Wessner Barbara , Franzke Bernhard , Strasser Eva-Maria , Waldherr Steffen , Wagner Karl-Heinz , Weckwerth Wolfram
Published: August 2024

Physical inactivity and a weak fitness status have become a global health concern. Metabolomics, as an integrative systematic approach, might link to individual’s fitness at the molecular level. In this study, we performed blood samples metabolomics analysis of a cohort of elderly people with different treatments. By defining two groups of fitness and corresponding metabolites profiles, we tested several machine learning classification approaches to identify key metabolite biomarkers, which showed robustly aspartate as a dominant negative marker of fitness. Following, the metabolomics data of the two groups were analyzed by a novel approach for metabolic network interaction termed COVRECON. Where we identified the enzyme AST as the most important metabolic regulation between the fit and the less fit groups. Routine blood tests in these two cohorts validated significant differences in AST and ALT. In summary, we combine machine learning classification and COVRECON to identify metabolomics biomarkers and causal processes for fitness of elderly people.
Yes, they’re all individuals: Hierarchical models from repeat measurement data improve estimates of tree growth and size
Authors: O’Brien Theresa , Warton David , Falster Daniel
Published: August 2024

Abstract

Repeat measurement surveys of tree size are used in forests to estimate growth be-haviour, biomass, and population dynamics. Although size is measured with error, and individuals vary in their growth trajectories, current size-based growth modelling approaches do not usually or fully account for both of these features, and therefore under-utilise available data.

We present a new method that leverages the auto-correlation structure of repeat surveys into a hierarchical Bayesian longitudinal growth model. This new structure allows users to correct for measurement error and capture individual-level variation in growth trajectories and parameters.

To demonstrate the new method we applied it to a sample of tropical tree survey data from long-term monitoring sites at Barro Colorado Island. We were able to reduce estimated error in size and growth, and extract individual-and population-level growth parameter estimates. We used simulation to evaluate the ability of the new method to improve estimates of growth rate and size, and estimate individual and species-level parameters. Our method substantially improved RMSE for growth by an average of 61% compared to existing approaches using pairwise differences; and reduced RMSE in estimated size RMSE compared to ‘observed’ values in simulated data. Better numerical integration methods (Runge-Kutta 4th order in comparison to Euler and midpoint) provided better estimates of parameters, but did not improve the estimation of size and growth. The choice of a positive growth function eliminated all negative increments without data exclusion.

Overall, this study shows how we can gain new and improved insights on growth, using repeat forest surveys. Our new method offers improved biomass dynamics estimation through reduced error in sizes over time, coupled with novel information about within-species variation in growth behaviour that is inaccessible with species average models, such as individual parameters for the growth function which allows for relationships between parameters to be considered for the first time.
Time-resolved, integrated multi-omic analysis reveals central role of amino acid pathways for defense responses inArabidopsis thaliana
Authors: Joller Charlotte , Schläppi Klaus , Sasse Joelle
Published: August 2024

Plants respond to biotic stresses by altering gene expression and metabolism. However, how fast different tissues respond to microbial presence, and how similar these responses are is mostly unresolved. Here, we treatArabidopsis thalianawith elicitors and investigate time-resolved changes in shoot, root, and root-derived (exudate) metabolite profiles. We find that root responses precede shoots and that first metabolite changes take place after 1.5 h and persist for 3 d. Exudates respond within 4 h (earliest timepoint available) to elicitor presence. This response diminishes when plants are pulse-treated but persists for continuously treated plants. Defense compounds such as phenylpropanoids increase after 1.5-4 h. Amino acids were iden6fied as central players in defense: they increase after 1.5 h in shoots, roots, and exudates. Transcriptome analysis at 4 h and 1 d and integrated, multi-omic analysis of transcription and metabolome suggest that aromatic and aliphatic amino acids are central players in defense responses. As their transcriptional and metabolite increases are fast and persisting over days for most amino acids, we propose amino acids as early indicators for biotic stress monitoring.
Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls
Authors: Ali Zahin Mohd , Tan Qiao Wen , Lim Peng Ken , Chen Hengchi , Pfeifer Lukas , Julca Irene , Lee Jia Min , Classen Birgit , Vries Sophie de , Vries Jan de , Koh Teng Seah , Chin Li Li , Vinter Fanny , Alvarado Camille , Layens Amandine , Mizrachi Eshchar , Motawie Mohammed Saddik , Joergensen Bodil , Ulvskov Peter , de Peer Yves van , Ho Boon Chuan , Sibout Richard , Mutwil Marek
Published: August 2024

Despite ferns being crucial to understanding plant evolution, their large and complex genomes has kept their genetic landscape largely uncharted, with only a handful of genomes sequenced and sparse transcriptomic data. Addressing this gap, we generated extensive RNA-sequencing data for multiple organs across 22 representative species over the fern phylogeny, assembling high-quality transcriptomes. These data facilitated the construction of a time-calibrated fern phylogeny covering all major clades, revealing numerous whole-genome duplications and highlighting the uniqueness of fern genetics, with half of the uncovered gene families being fern-specific. Our investigation into fern cell walls through biochemical and immunological analyses identified occurrences of the lignin syringyl unit and its independent evolution in ferns. Moreover, the discovery of an unusual sugar in fern cell walls hints at a divergent evolutionary path in cell wall biochemistry, potentially driven by gene duplication and sub-functionalization. We provide an online database preloaded with genomic and transcriptomic data for ferns and other land plants, which we used to identify an independent evolution of lignocellulosic gene modules in ferns. Our data provide a framework for the unique evolutionary path that ferns have navigated since they split from the last common ancestor of euphyllophytes more than 360 million years ago.
Near-infrared MINFLUX imaging enabled by suppression of fluorophore blinking
Authors: Srambickal C Venugopal , Esmaeeli H , Piguet J , Reinkensmeier L , Siegmund R , Bates M , Egner A , Widengren J
Published: August 2024

MINimal photon FLUXes (MINFLUX) offers super-resolution microscopy (SRM) with nanometer localization precision, with more relaxed fluorophore brightness and photostability requirements than for other SRM techniques. Nonetheless, low localization probabilities have been reported in several MINFLUX studies, and a broader use of less bright and photostable fluorophores, including near-infrared (NIR) fluorophores has been difficult to realize. In this work, we identified fluorophore blinking as a main cause of erroneous (and dismissed) fluorophore localizations in MINFLUX imaging and devised strategies to overcome these effects. We systematically studied the blinking/switching properties of cyanine fluorophores emitting in the far-red or NIR range, and over typical time scales (µs-10ms), sample and excitation conditions used in MINFLUX imaging. By subsequent simulations of representative MINFLUX localization procedures, we found that trans-cis isomerization, and in particular photo-reduction of the fluorophores, can generate significant localization errors. However, these localization errors could be suppressed by balanced redox buffers and repetitive excitation beam scans. Implementing these strategies, and replacing the slower, intrinsic switching of the fluorophores needed for the localization by transient binding of fluorophore-labelled DNA strands to complementary DNA strands attached to the targets (DNA-PAINT), we could for the first time demonstrate NIR-MINFLUX imaging with nanometer localization precision. This work presents an overall strategy, where fluorophore blinking characterization and subsequent simulations make it possible to design optimal sample and excitation conditions, opening for NIR-MINFLUX imaging, as well as for a broader use of fluorophores in MINFLUX and related SRM studies.
Rapid resistance evolution against phage cocktails
Authors: van der Steen Baltus A , Gralka Matti , Mulla Yuval
Published: August 2024

When bacteria are treated with multiple antibiotics simultaneously, resistance is exceedingly unlikely to evolve. In stark contrast, resistance against multiple phages frequently arises during therapy. Why does resistance against multi-phage cocktails evolve so easily? Using a mathematical model, we show how the bacterial evolutionary dynamics and phage replicative dynamics uniquely intertwine, facilitating the rapid evolution of multi-phage resistance. As different phages replicate and become inhibitory at varying time points, bacteria can sequentially acquire resistance rather than simultaneously – increasing the chance of multi-resistance by orders of magnitude. Additionally, we identify a regime where multi-phage resistance is robustly prevented. Our findings provide a framework for the rational design of phage cocktails to minimize resistance development.
A novel chemogenomic screening platform for scalable antimalarial drug target identification
Authors: Bower-Lepts Christopher , Rawat Mukul , Keith William Collins , Girling Gareth , Luth Madeline R , Carolino Krypton , Boroviak Katharina , Coyle Rachael , Schwach Frank , Smidt Cindy , Bushell Ellen , Moliner-Cubel Sonia , Gomez-Lorenzo Maria D , Gamo Francisco-Javier , Winzeler Elizabeth A. , Billker Oliver , Lee Marcus C.S. , Rayner Julian C.
Published: August 2024

Large-scale chemical-genetic screening, or chemogenomics, can faciliate rapid and scalable drug target identification. To establish a chemogenomic screen for antimalarial drug target identification, we leveraged ∼600Plasmodium bergheiartificial chromosomes (PbACs) encoding potential drug targets to generate a systematic overexpression library. PbACs were engineered with DNA barcodes, enabling their quantification within mixed pools using next generation sequencing (barcode sequencing or BarSeq). Pooled transfection of PbACs into the highly genetically tractablePlasmodium knowlesidemonstrated efficient vector uptake and transcription of encodedP. bergheigenes. Parasite pools were exposed to antimalarial candidates, with pilot screens probing for known gene-compound associations identifying their targets with high sensitivity. Screening antimalarial inhibitors with unknown mechanisms of action successfully identifiedpi4kas the target for one novel compound, which was subsequently validated usingin vitroevolution inPlasmodium falciparumparasites. This sensitive and scalable chemogenomics platform therefore represents a valuable early-stage tool for antimalarial target identification.
HIRA-dependent provision of histone H3.3 in active chromatin ensures genome compartmentalisation
Authors: Karagyozova Tina , Gatto Alberto , Forest Audrey , Quivy Jean-Pierre , Marti-Renom Marc A. , Mirny Leonid , Almouzni Geneviève
Published: August 2024

The mammalian genome, organised into chromatin, adopts a three-dimensional (3D) folding within the cell nucleus with spatially segregated active and repressed compartments, termed A and B. However, how nucleosome deposition impacts these levels of organisation is unknown. Here, we monitored changes in 3D genome folding by Hi-C after impairing the chaperone HIRA, involved in histone H3.3 deposition. In the absence of HIRA, H3.3 enrichment decreases in compartment A that also shows weaker interactions. At this scale, histone post-translational modifications (PTMs) do not follow H3.3 changes. In line with impaired H3.3 nucleosome maintenance, compartment A accessibility measured by ATAC-seq increases. Specifically, at active genes, accessibility increases in gene bodies but decreases at promoters where compensation by H3.1 reduces nucleosome turnover. Notably, regions flanking active genes show reduced insulation. We conclude that the HIRA-dependent pathway involved in H3.3 deposition is key to maintain higher order organisation in active regions and impact compartmentalisation independently of histone PTMs.
Engineering of ATP synthase for enhancement of proton-to-ATP ratio
Authors: Ueno Hiroshi , Yasuda Kiyoto , Hamaguchi-Suzuki Norie , Marui Riku , Adachi Naruhiko , Senda Toshiya , Murata Takeshi , Noji Hiroyuki
Published: August 2024

FoF1-ATP synthase (FoF1) interconverts the energy of the proton motive force (pmf) and that of ATP via mechanical rotation of the rotor complex. The H+/ATP ratio, one of the most crucial parameters in bioenergetics, varies among species due to the different number of H+-bindingc-subunits, resulting in H+/ATP ratios ranging from 2.7 to 5. The present study attempted to enhance the H+/ATP ratio significantly by employing a novel approach that differs from that of nature. We engineered FoF1to form multiple peripheral stalks, each bound to a proton-conductinga-subunit. Engineered FoF1showed an H+/ATP ratio of 5.9, beyond the highest among naturally occurring FoF1s, enabling ATP synthesis at a lowpmf, at which wild-type enzymes are unable to synthesize ATP. Structural analysis showed that the engineered FoF1formed up to three peripheral stalks and thea-subunits. This study not only provides important insights into the H+-transport mechanism of FoF1but also opens the possibility of engineering the foundation of cell bioenergetics.
Optimization of screening methods leads to the discovery of new viruses in black soldier flies (Hermetia illucens)
Authors: Pienaar Robert D. , Herrero Salvador , de Araujo Alexandra Cerqueira , Krupa Frank , Abd-Alla Adly M. M. , Herniou Elisabeth A.
Published: August 2024

Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the ordersGhabriviralesandBunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. In this study, we describe five newly discovered viruses from the familiesDicistroviridae,Iflaviridae,Rhabdoviridae,Solinviviridae, andInseviridae. These viruses were detected in BSF from multiple origins, outlining a diversity of naturally occurring viruses associated with BSF. This viral community may also include BSF pathogens. The growing list of viruses found in BSF allowed the development of molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.
QuICSeedR: An R package for analyzing fluorophore-assisted seed amplification assay data
Authors: Li Manci , Bryant Damani N. , Gresh Sarah , Milstein Marissa , Christenson Peter R. , Lichtenberg Stuart S. , Larsen Peter A. , Oh Sang-Hyun
Published: August 2024

Fluorophore-assisted seed amplification assays (F-SAAs), such as real-time quaking-induced conversion (RT-QuIC) and fluorophore-assisted protein misfolding cyclic amplification (F-PMCA), have become indispensable tools for studying protein misfolding in neurodegenerative diseases. However, analyzing data generated by these techniques often requires complex and time-consuming manual processes. Additionally, the lack of standardization in F-SAA data analysis presents a significant challenge to the interpretation and reproducibility of F-SAA results across different laboratories and studies. Here, we present QuICSeedR (pronounced as “quick seeder”), an R package that addresses these challenges by providing a comprehensive toolkit for the automated processing, analysis, and visualization of F-SAA data. Importantly, QuICSeedR also sets up the foundation for building an F-SAA data management and analysis framework, enabling more consistent and comparable results across different research groups.

Availability and implementation

QuICSeedR source code is freely available at:https://github.com/mancili/QuICSeedR. Data and code used in this manuscript are provided in Supplementary Materials.

Supplementary information

Supplementary Materials are available with the manuscript.
Plasmid-bornemcr-1and Replicative Transposition of Episomal and Chromosomal blaNDM-1, blaOXA-69, and blaOXA-23 Carbapenemases in a ClinicalAcinetobacter baumanniiIsolate
Authors: Mmatli Masego , Mbelle Nontombi Marylucy , Osei Sekyere John
Published: August 2024

Background

A multidrug-resistant clinical A. baumannii isolate with resistance to most antibiotics was isolated from a patient at an intensive care unit. The genetic environment, transcriptome, mobile, and resistome were characterized.

Method

The MicroScan system, disc diffusion, and broth microdilution were used to determine the resistance profile of the isolate. A multiplex PCR assay was also used to screen for carbapenemases and mcr-1 to -5 resistance genes. Efflux-pump inhibitors were used to evaluate efflux activity. The resistome, mobilome, epigenome, and transcriptome were characterized.

Results & conclusion

There was phenotypic resistance to 22 of the 25 antibiotics tested, intermediate resistance to levofloxacin and nalidixic acid, and susceptibility to tigecycline, which corresponded to the 27 resistance genes found in the genome, most of which occurred in multiple copies through replicative transposition. A plasmid-borne (pR-B2.MM_C3)mcr-1 and chromosomalblaPER-7, blaOXA-69, blaOXA-23(three copies),blaADC-25,blaTEM-1B, andblaNDM-1were found within composite transposons, ISs, and/or class 1 and 2 integrons on genomic islands. Types I and II methylases and restriction endonucleases were in close synteny to these resistance genes within the genomic islands; chromosomal genomic islands aligned with known plasmids. There was a closer evolutionary relationship between the strain and global strains but not local or regional strains; the resistomes also differed. Significantly expressed/repressed genes (6.2%) included resistance genes, hypothetical proteins, mobile elements, methyltransferases, transcription factors, membrane and efflux proteins.

The genomic evolution observed in this strain explains its adaptability and pandrug resistance and shows its genomic plasticity on exposure to antibiotics.
Gene expression and chromatin accessibility comparison in iPSC-derived microglia in African, European, and Amerindian genomes in Alzheimer’s patients and controls
Authors: Moura Sofia , Nasciben Luciana Bertholim , Ramirez Aura M. , Coombs Lauren , Rivero Joe , Van Booven Derek J. , DeRosa Brooke A. , Hamilton-Nelson Kara L. , Whitehead Patrice L. , Adams Larry D. , Starks Takiyah D. , Mena Pedro R. , Illanes-Manrique Maryenela , Tejada Sergio , Byrd Goldie S. , Cornejo-Olivas Mario R. , Feliciano-Astacio Briseida E. , Nuytemans Karen , Wang Liyong , Pericak-Vance Margaret A. , Dykxhoorn Derek M. , Rajabli Farid , Griswold Anthony J. , Young Juan I. , Vance Jeffery M.
Published: August 2024

Alzheimer’s disease (AD) risk differs between population groups, with African Americans and Hispanics being the most affected groups compared to non-Hispanic Whites. Genetic factors contribute significant risk to AD, but the genetic regulatory architectures (GRA) have primarily been studied in Europeans. Many AD genes are expressed in microglia; thus, we explored the impact of genetic ancestry (Amerindian (AI), African (AF), and European (EU)) on the GRA in iPSC-derived microglia from 13 individuals (∼4 each with high global ancestry, AD and controls) through ATAC-seq and RNA-seq analyses. We identified several differentially accessible and expressed genes (2 and 10 AD-related, respectively) between ancestry groups. We also found a high correlation between the transcriptomes of iPSC-derived and brain microglia, supporting their use in human studies. This study provides valuable insights into genetically diverse microglia beyond the analysis of AD.
Training Experimentally Naive Seals for Vocal Learning Experiments
Authors: Duengen Diandra , Ravignani Andrea
Published: August 2024

Harbor seals (Phoca vitulina) are a common zoo species that show a scientifically valuable propensity for vocal learning. Under human care, the seals can be trained to associate vocalizations with cues. This ability is termed vocal usage learning and is characterized by learning to use a vocalization in a specific context. Among mammals, seals are prime candidates to investigate vocal learning. Yet, only a handful of reports exist on harbor seal vocal learning abilities and even less document how these were trained or tested. Here, we investigate how, and if, two experimentally naive harbor seals under human care, can be trained to participate in scientific experiments. We describe the training and testing of two seals in two basic vocal learning experiments. We trained the animals to vocalize upon the presentation of a discriminative stimuli (SD) through operant conditioning methods and tested their abilities to i) vocalize and refrain from vocalizing on two distinct SD’s, and ii) produce two different vocalizations upon the presentation of two different SD’s. Both seals learned the tasks: the first task was achieved within 118 trials (22 errors to criterion) and 220 trials (40 errors to criterion), the second task within 480 trials (158 errors to criterion) and 380 trials (94 errors to criterion), respectively. Our results confirm that harbor seals are capable of vocal usage learning and further suggest that associating individually distinct vocalizations with different SD’s may be more cognitively demanding than vocalizing and being silent on SD.
Bronchopulmonary Dysplasia with Pulmonary Hypertension Associates with Loss of Semaphorin Signaling and Functional Decrease in FOXF1 Expression
Authors: Shirazi Shawyon P. , Negretti Nicholas M. , Jetter Christopher S. , Sharkey Alexandria L. , Garg Shriya , Kapp Meghan E. , Wilkins Devan , Fortier Gabrielle , Mallapragada Saahithi , Banovich Nicholas E. , Wright Christopher V. E. , Frank David B. , Kropski Jonathan A. , Sucre Jennifer M. S.
Published: August 2024

Lung injury in preterm infants leads to structural and functional respiratory deficits, with a risk for bronchopulmonary dysplasia (BPD) that in its most severe form is accompanied by pulmonary hypertension (PH). To examine cellular and molecular dynamics driving evolving BPD in humans, we performed single-cell RNA sequencing of preterm infant lungs in early stages of BPD and BPD+PH compared to term infants. Analysis of the endothelium revealed a unique aberrant capillary cell-state primarily in BPD+PH marked byANKRD1expression. Predictive signaling analysis identified deficits in the semaphorin guidance-cue signaling pathway and decreased expression of pro-angiogenic transcription factorFOXF1within the alveolar parenchyma in neonatal lung samples with BPD/BPD+PH. Loss of semaphorin signaling was replicated in a murine BPD model and in humans with alveolar capillary dysplasia (ACDMPV), suggesting a mechanistic link between the developmental programs underlying BPD and ACDMPV and a critical role for semaphorin signaling in normal lung development.
Missing links connect the phylogeographic structure of endangered red pandas, remaining as one species –Ailurus fulgens, and expediting conservation
Authors: Dueck Lucy A. , Uluer Deniz Aygören
Published: August 2024

Monitoring biodiversity depends on well-informed taxonomy, reflecting the underlying biology of organisms critical for appropriate conservation management. The taxonomy of red pandas, endangered mammals distributed along a ∼2500km montane range fringing the southern Tibetan Plateau, has been perplexing. Finally resolved as evolutionarily unique Musteloidea, further division ofAilurusinto two geographic variants remains contentious. Red pandas are threatened by extinction from anthropogenic disturbances with consequent population decline; continued gene flow is therefore crucial to maintain adaptive potential. A recent phylogenomic study from sampling range ends and a constrictive species concept split red pandas into two species. Subsequent studies supplied additional data missing from their midrange. We evaluated GenBank mtDNA sequences from 393 animals, plotted sampling locations, and analyzed with and without midrange samples. Two sublineages of monophyleticAiluruswere weakly supported by one method when the midrange was excluded, but not when it was included. Using more stringent analyses,Ailuruswas strongly confirmed as a single species in all circumstances, although the western sublineage (A. f. fulgens) was weakly supported within. Four haplogroups associated with specific regions, suggesting broad phylogeographic patterning and gene flow, with sympatric crossover and a cline bracketing unsampled Bhutan in the midrange. Red pandas are due for IUCN Red List reassessment in 2025; unwarranted taxonomic revision would delay and imperil action needed to prevent extinction. We recommend maintainingAilurusas one species, recognizing and protecting biodiversity at one intraspecific level, allowing for gene flow in conservation management, and extensively investigating intergradation of midrange red pandas.
Cold and lonely: low-abundance microbiota and no core microbiome across a broad geographic sampling of a mosquito species in Greenland
Authors: Rojas-Guerrero Diana , Kolasa Michał , Buczek Mateusz , Prus-Frankowska Monika , Nowak Karol H. , Roslin Tomas , Łukasik Piotr
Published: August 2024

Microbial symbionts play a crucial role in the biology of their insect hosts. In recent years, the mosquito microbiome has emerged as a promising tool for controlling mosquito populations and altering their capacity to transmit diseases. However, while mosquitoes are widespread, most microbiome research focuses on a few model species, leaving many others understudied. In this study, we investigated how temporal and spatial variations influence the microbial abundance and diversity associated withOchlerotatusmosquitoes in Greenland. We did this by conducting high-throughput sequencing of insect and bacterial marker gene amplicons and quantifying bacterial abundance across a large collection of mosquitoes sampled systematically from four regions of Greenland between 2009 and 2023.

Analysis of COI data identified two species within our collection: the widely distributedO. nigripesand the less commonO. impiger. Quantitative 16S rRNA amplicon sequencing revealed a highly variable number of bacterial rRNA gene copies per mosquito, with overall microbiota abundance typically lower (Avg = ∼1.2×105, Mdn = 1.04×104) than that estimated for both lab-rearedAedes aegyptiand wildCulex pipiensfrom Poland. Despite identifying diverse bacterial taxa, includingPseudomonas, Wolbachia, andBartonella, we observed significant microbiome variability between individual mosquitoes. Notably, there were no consistent patterns of microbiota distribution across sexes, geographic locations, or sampling years. These findings suggest thatOchlerotatusmosquitoes from the surveyed populations in Greenland may not rely on abundant or specialized microbiota for their reproduction or nutrition, indicating a flexible or minimal relationship with their associated bacterial communities.
The cytokinetic midbody mediates asymmetric fate specification at mitotic exit during neural stem cell division
Authors: LaFoya Bryce , Penkert Rhiannon R , Prehoda Kenneth E.
Published: August 2024

Asymmetric cell division (ACD) is a broadly used mechanism for generating cellular diversity. Molecules known as fate determinants are segregated during ACD to generate distinct sibling cell fates, but determinants should not be activated until fate can be specified asymmetrically. Determinants could be activated after cell division but many animal cells complete division long after mitosis ends, raising the question of how activation could occur at mitotic exit taking advantage of the unique state plasticity at this time point. Here we show that the midbody, a microtubule-rich structure that forms in the intercellular bridge connecting nascent siblings, mediates fate determinant activation at mitotic exit in neural stem cells (NSCs) of theDrosophilalarval brain. The fate determinants Prospero (Pros) and Brain tumor (Brat) are sequestered at the NSC membrane at metaphase but are released immediately following nuclear division when the midbody forms, well before cell division completes. The midbody isolates nascent sibling cytoplasms, allowing determinant release from the membrane via the cell cycle phosphatase String, without influencing the fate of the incorrect sibling. Our results identify the midbody as a key facilitator of ACD that allows asymmetric fate determinant activation to be initiated before division.
Association Between Relational Mobility and DNA Methylation in Oxytocin Receptor Gene: A Social Epigenetic Study
Authors: Li Shubing , Yamada Junko , Ishihara Toru , Nishina Kuniyuki , Nishitani Shota , Sasaki Tetsuhiko , Matsuda Tetsuya , Inoue-Murayama Mino , Takagishi Haruto
Published: August 2024

DNA methylation is a type of epigenetic modification known to exhibit fluctuations in response to environmental factors. The association of macrosocial factors, such as interpersonal mobility, on methylation has seldom been investigated. This study aimed to examine the association of relational mobility, defined as the extent to which individuals can form and replace social relationships, on the DNA methylation of oxytocin receptor genes. DNA was extracted from the buccal cells of 95 adult participants (50 men and 45 women) and subjected to microarray analysis of DNA methylation using Illumina EPIC v2.0. The findings indicate that the oxytocin receptor gene’s methylation level was higher in individuals residing in low relational mobility social environments. The CpG site associated with relational mobility is an enhancer region, indicating that social environments with low relational mobility exert a suppressive effect on the transcriptional efficiency of the oxytocin receptor gene.

Significance Statement

The association between DNA methylation of the oxytocin receptor gene and relational mobility was examined in 95 adults in their 20s to 60s, and found that those living in social environments with lower levels of relationship mobility had higher rates of DNA methylation of the oxytocin receptor gene. This study is a novel approach to a problem discussed in the social sciences using new analytical techniques in epigenomics.
Running on empty: Mitochondria without DNA exhibit differential motility and connectivity
Authors: Chustecki Joanna M. , Schneider Alora Q. , Faber Madeleine H. , Christensen Alan C.
Published: August 2024

Plant mitochondria are in continuous motion. While providing ATP to other cellular processes, they also constantly consume ATP to move rapidly within the cell. This movement is in part related to taking up, converting and delivering metabolites and energy to and from different parts of the cell. Plant mitochondria have varying amounts of DNA even within a single cell, from none to the full mitochondrial genome. Because mitochondrial dynamics are altered in anArabidopsismutant with disrupted DNA maintenance, we hypothesised that exchanging DNA templates for repair is one of the functions of their movement and interactions. Here, we image mitochondrial DNA by two distinct methods while tracking mitochondrial position to investigate differences in the behaviour of mitochondria with and without DNA inArabidopsis thaliana. In addition to staining mitochondrial DNA with SYBR Green, we have developed and implemented a fluorescent mitochondrial DNA binding protein that will also enable future understanding of mitochondrial dynamics, genome maintenance and replication. We demonstrate that mitochondria without mtDNA have altered physical behaviour and have a lower immediate connectivity to the rest of the population, further supporting a link between the physical and genetic dynamics of these complex organelles.
NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks
Authors: Koonce Noelle L. , Emerson Sarah E. , Bhaskar Dhananjay , Kuchroo Manik , Moyle Mark W. , Arroyo-Morales Pura , Martínez Nabor Vázquez , Krishnaswamy Smita , Mohler William , Colón-Ramos Daniel
Published: August 2024

Volume electron microscopy (vEM) datasets such as those generated for connectome studies allow nanoscale quantifications and comparisons of the cell biological features underpinning circuit architectures. Quantifications of cell biological relationships in the connectome result in rich multidimensional datasets that benefit from data science approaches, including dimensionality reduction and integrated graphical representations of neuronal relationships. We developed NeuroSCAN, an online open-source platform that bridges sophisticated graph analytics from data science approaches with the underlying cell biological features in the connectome. We analyze a series of publishedC. elegansbrain neuropils and demonstrate how these integrated representations of neuronal relationships facilitate comparisons across connectomes, catalyzing new insights on the structure-function relationships of the circuits and their changes during development. NeuroSCAN is designed for intuitive examination and comparisons across connectomes, enabling synthesis of knowledge from high-level abstractions of neuronal relationships derived from data science techniques to the detailed identification of the cell biological features underpinning these abstractions.
Nuclear actin is a critical regulator ofDrosophilafemale germline stem cell maintenance
Authors: Green Nicole M. , Talbot Danielle , Tootle Tina L.
Published: August 2024

Nuclear actin has been implicated in regulating cell fate, differentiation, and cellular reprogramming. However, its roles in development and tissue homeostasis remain largely unknown. Here we uncover the role of nuclear actin in regulating stemness usingDrosophilaovarian germline stem cells (GSCs) as a model. We find that the localization and structure of nuclear actin is dynamic in the early germ cells. Nuclear actin recognized by anti-actin C4 is found in both the nucleoplasm and nucleolus of GSCs. The polymeric nucleoplasmic C4 pool is lost after the 2-cell stage, whereas the monomeric nucleolar pool persists to the 8-cell stage, suggesting that polymeric nuclear actin may contribute to stemness. To test this idea, we overexpressed nuclear targeted actin constructs to alter nuclear actin polymerization states in the GSCs and early germ cells. Increasing monomeric nuclear actin, but not polymerizable nuclear actin, causes GSC loss that ultimately results in germline loss. This GSC loss is rescued by simultaneous overexpression of monomeric and polymerizable nuclear actin. Together these data reveal that GSC maintenance requires polymeric nuclear actin. This polymeric nuclear actin likely plays numerous roles in the GSCs, as increasing monomeric nuclear actin disrupts nuclear architecture causing nucleolar hypertrophy, distortion of the nuclear lamina, and heterochromatin reorganization; all factors critical for GSC maintenance and function. These data provide the first evidence that nuclear actin, and in particular, its ability to polymerize, are critical for stem cell function and tissue homeostasisin vivo.