bluuebunny/crossref_metadata_2025 huggingface dataset:
Stroke and Motor Recovery are Associated with Regional and Age-Specific Changes in Periodic and Aperiodic Cortical Activity
Authors: Albertson Asher J. , Landsness Eric. C. , Eisfelder Margaret , Young Brittany M , Judge Bradley , Brier Matthew R. , Euler Matthew J. , Cramer Steven C. , Lee Jin-Moo , Lohse Keith R
Published: November 2024

Normal aging is associated with widespread changes in neuronal structure, function, and activity. The consequences of focal brain injury on global neuronal activity in aged individuals are poorly understood. Historically, stroke and aging have been associated with changes in narrow-band periodic neuronal activity, however recent work has highlighted the importance of broad-band aperiodic activity. Aperiodic activity is represented by the 1/f slope of power spectral density generated by cortical activity.

Abnormalities in aperiodic activity have been identified in psychiatric disorders and stroke, are associated with cognitive dysfunction in aging, and have been hypothesized to reflect changes in excitation/inhibition balance. Here we sought to further explore changes in both periodic and aperiodic cortical activity in neurotypical intact young and aged healthy individuals and individuals with stroke. We compared “resting state” electroencephalograms from all participants after applying thespecparamalgorithm, which decomposes the power spectrum into aperiodic and periodic components. We also correlated stroke outcomes using previously obtained tests of motor outcome (box and block) to average whole cortex spectral slopes within the stroke group. Consistent with prior work we found a significant flattening (decrease in exponent) of power spectral slope with normal aging. We also found that both aging and stroke were associated with fewer periodic peaks within the power spectrum. Interestingly, we found that stroke was associated with a significant increase in spectral slope, but age moderated this effect. Younger stroke patients showed minimal difference in slope while older stroke patients had significantly steeper slopes (opposite to the direction in normal aging). Using MRIs from stroke participants we investigated the lesion locations most associated with changes in slope. Interestingly deep lesions were observed to have the greatest influence on cortical spectral slope. Finally, slope in the stroke group was correlated with performance on a test of manual dexterity, however this correlation was much more significant in aged individuals. Our data suggest that stroke in the aged brain has unique effects on aperiodic activity possibly reflecting unique influence of injury on cerebral excitation/inhibition balance in aged individuals and that the degree of these changes may be related to stroke outcomes.
Language model generatescis-regulatory elements across prokaryotes
Authors: Xia Yan , Sun Jinyuan , Du Xiaowen , Liang Zeyu , Shi Wenyu , Guo Shuyuan , Huo Yi-Xin
Published: November 2024

Deep learning had succeeded in designingCis-regulatory elements (CREs) for certain species, but necessitated training data derived from experiments. Here, we present Promoter-Factory, a protocol that leverages language models (LM) to design CREs for prokaryotes without experimental prior. Millions of sequences were drawn from thousands of prokaryotic genomes to train a suite of language models, named PromoGen2, and achieved the highest zero-shot promoter strength prediction accuracy among tested LMs. Artificial CREs designed with Promoter-Factory achieved a 100% success rate to express gene inEscherichia coli,Bacillus subtilis, andBacillus licheniformis. Furthermore, most of the promoters designed targetingJejubactersp. L23, a halophilic bacterium without available CREs, were active and successfully drove lycopene overproduction. The generation of 2 million putative promoters across 1,757 prokaryotic genera, along with the Promoter-Factory protocol, will significantly expand the sequence space and facilitate the development of an extensive repertoire of prokaryotic CREs.
Unpacking fitness differences between invaders in a multispecies context
Authors: Freire Tomas , Madec Sten , Gjini Erida
Published: November 2024

Ecosystems are constantly exposed to new strains of a given species. Which strain will be able to invade a resident multi-species community depends on the strain’s relative fitness. Here we develop an approach to quantify fitness differences between two co-invading strains based on the replicator equation. By assuming that the resident species’ frequencies remain constant during the initial phase of invasion, we are able to determine the invasion fitness differential between the two strains, which drives growth rate differences post-invasion. We then apply our approach to a critical current global problem: invasion of the gut microbiota by antibiotic resistant strains of the pathobiontEscherichia coli. Our results underscore the context-dependent nature of fitness and demonstrate how species frequencies in a host environment can explicitly modulate the selection coefficient between two strains. This framework can predict relative fitness in new environments and may contribute to design strategies to lower resistance levels in microbiomes.
Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation
Authors: Dong Zheng (Joe) , Schaffner Samantha , Fu Maggie , Whitehead Joanne , MacIsaac Julia L. , Rehkopf David H. , Boyce W. Thomas , Rosero-Bixby Luis , Quintana-Murci Lluis , Patin Etienne , Miller Gregory E. , Korthauer Keegan , Kobor Michael S.
Published: November 2024

DNA methylation (DNAm) is a key epigenetic mark that modulates regulatory elements and gene expression, playing a crucial role in mammalian development and physiological function. Despite extensive characterization of DNAm profiles across species, little is known about its evolutionary conservation. Here, we conducted a comparative epigenome-wide analysis of great apes to identify and characterize sequence- and methylation-conserved CpGs (MCCs). Using 202 DNAm arrays, alongside 6 matched genotype and 13 matched transcriptomic datasets, we identified 11,500 MCCs for which methylation was evolutionarily related to sequences of CpGs and methylation quantitative trait loci. MCCs were the most stable across healthy human tissues and exhibited weaker genetic associations than other CpGs. Moreover, MCCs showed minimal associations with demographic, environmental factors, and noncancer diseases, yet demonstrated stronger associations with certain cancers than other CpGs, particularly gastrointestinal cancers. Functional enrichment analysis revealed that genes associated with MCC methylation in cancer were enriched for cancer driver genes and canonical cancer pathways, highlighting a significant regulatory role for MCCs in tumorigenesis. Collectively, our findings reveal the extent of DNAm conservation in great ape evolution, its association with genetic conservation, and its relevance to human diseases. These integrative analyses offer evolutionary insights into epigenetic variation and its functional implications in human populations.
Computational Modeling and Analysis of the TGF-β-induced ERK and SMAD Pathways
Authors: Chung Seung-Wook , Cooper Carlton R. , Farach-Carson Mary C. , Ogunnaike Babatunde A.
Published: November 2024

TGF-β, an important cytokine that plays a key role in many diseases regulates a wide array of cellular and physiologic processes via several TGF-β-driven signaling cascades, including the SMAD and non-SMAD-driven pathways. However, the detailed mechanisms by which TGF-β induces such diverse responses remain poorly understood. In particular, compared to the SMAD-dependent pathway, SMAD-independent pathways such as the ERK/MAPK pathway, which is critical in cancer progression, are less characterized. Here, we develop an integrated mechanistic model of the TGF-β-triggered ERK activation pathway and its crosstalk with the SMAD pathway, an analysis of which demonstrates how SMAD dynamics can be significantly modulated and regulated by the ERK pathway. In particular, SMAD-mediated transcription can be altered and delayed due to expedited phosphorylation of the linker of SMAD by TGF-β-activated ERK; and enhanced ERK activity, but attenuated SMAD activity, can be achieved simultaneously by fast turnover of TGF-β receptors via lipid-rafts. Also,in silicomutations of the TGF-β pathways reveal that the dynamic characteristics of both SMAD and ERK signaling may change significantly during cancer development. Specifically, normal cells may exhibit enhanced and sustained SMAD signaling with transient ERK activation, whereas cancerous cells may produce elevated and prolonged ERK signaling with enervated SMAD activation. These distinctive differences between normal and cancerous signaling behavior provide clues concerning, and potential explanations for, the seemingly contradictory roles played by TGF-β during cancer progression. We demonstrate how crosstalk among various branch pathways of TGF-β can influence overall cellular behavior. Based on model analysis, we hypothesize that aberrant molecular alterations drive changes in the intensity and duration of SMAD and ERK signaling during cancer progression and ultimately lead to an imbalance between the SMAD and ERK pathways in favor of tumor promotion. Thus, to treat cancer patients with a genetic signature of oncogenic Ras effectively may requireat leasta combination therapy to restoreboththe expression of TGF-β receptors and the GTPase activity of Ras.
Morpho-molecular features of Epithelial Mesenchymal Transition associate with clinical outcome in patients with rectal cancer
Authors: Gwerder Mauro , Demir Cansaran Saygili , Williams Hannah L. , Lugli Alessandro , Martinez Cristina Graham , Kowal Joanna , Khan Amjad , Kirchner Philipp , Koessler Thibaud , Berger Martin D. , Weigert Martin , Zlobec Inti
Published: November 2024

In rectal cancer, where part of the patients undergoes chemoradiotherapy, there is a need for improved pretreatment biomarkers applicable to biopsies. Tumor budding (TB) is a biomarker used in colon cancer, and due to its link to epithelial-mesenchymal transition (EMT), is hypothesized to be a potential marker for therapy resistance. Assessment of the utility of tumor buds in rectal biopsies is challenging due to their rarity. As EMT-related processes are also seen in other morphological features beyond tumor buds, we investigated EMT in tumor tissue including morphological features such as tumorcluster sizeand fibril-like structures. To do so, we leveraged a cohort of colon cancer whole-slide images and another cohort consisting of rectal cancer biopsies, visualized using hyperplex immunofluorescence to identify tumor and EMT-associated proteins. We built a custom image analysis pipeline to detect and segment tumor buds and other morphological features and correlated them with molecular expression intensities. We found strong correlations of EMT up-regulation and morphological transition states, both at the invasive margin and the tumor center. We furthermore observed a link between morpho-molecular transitions and histological growth patterns, which in turn can inform novel biomarkers. Finally, quantification of these morpho-molecular transition states in rectal biopsies showed their impact on survival after neoadjuvant chemoradiotherapy.
Bayesian nonparametric analysis of residence times for protein-lipid interactions in Molecular Dynamics simulations
Authors: Sexton Ricky , Fazel Mohamadreza , Schweiger Maxwell , Pressé Steve , Beckstein Oliver
Published: November 2024

Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid-protein binding kinetics has remained challenging due to considerable noise and low frequency of long binding events, even in hundreds of microseconds of simulation data. Here we apply Bayesian nonparametrics to compute residue-resolved residence time distributions from MD trajectories. Such an analysis characterizes binding processes at different timescales (quantified by their kinetic off-rate) and assigns to each trajectory frame a probability of belonging to a specific process. In this way, we classify trajectory frames in an unsupervised manner and obtain, for example, different binding poses or molecular densities based on the timescale of the process. We demonstrate our approach by characterizing interactions of cholesterol with six different G-protein coupled receptors (A2AAR,β2AR, CB1R, CB2R, CCK1R, CCK2R) simulated with coarse-grained MD simulations with the MARTINI model. The nonparametric Bayesian analysis allows us to connect the coarse binding time series data to the underlying molecular picture and, thus, not only infers accurate binding kinetics with error distributions from MD simulations but also describes molecular events responsible for the broad range of kinetic rates.
RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling
Authors: Lim Chun Shen , Brown Chris M.
Published: November 2024

Ribosome profiling is a high-throughput sequencing technique that captures the positions of translating ribosomes on RNAs. Recent advancements in ribosome profiling include achieving highly-phased ribosome footprints for plant translatomes and more recently for bacterial translatomes. This substantially increases the specificity of detecting open reading frames (ORFs) that can be translated, such as small ORFs located upstream and downstream of the annotated ORFs. However, most genomes (e.g. bacterial genomes) lack the annotations for the transcription start and termination sites. This hinders the systematic discovery of novel ORFs in the ‘untranslated’ regions in ribosome profiling data. Here we develop a new computational pipeline called RIBOSS. We use RIBOSS to leverage long-read and short-read data forde novotranscriptome assembly, and highly-phased ribosome profiling data for detecting novel translational events in the newly assembled transcriptome. We demonstrate the capability of RIBOSS using recently published metatranscriptome and translatome data forSalmonella entericaserovar Typhimurium. The RIBOSS Python modules are versatile and can be used to analyse prokaryotic or eukaryotic data. In sum, RIBOSS is the first computational pipeline to integrate long- and short-read sequencing technologies to investigate translation. RIBOSS is freely available athttps://github.com/lcscs12345/riboss.
Neural Context Reinstatement of Recurring Events
Authors: Broitman Adam W. , Kahana Michael J.
Published: November 2024

Episodic recollection involves retrieving context information bound to specific events. However, autobiographical memory largely comprises recurrent, similar experiences that become integrated into joint representations. In the current study, we extracted a neural signature of temporal context from scalp electroencephalography (EEG) to investigate whether recalling a recurring event accompanies the reinstatement of one or multiple instances of its occurrence. We asked 52 young adults to study and recall lists of words that included both once-presented and repeated items. Participants recalled repeated items in association with neighboring list items from each occurrence, but with stronger clustering around the repetition’s initial occurrence. Furthermore, multivariate spectral EEG analyses revealed that neural activity from just prior to the recall of these words resembled patterns of activity observed near the item’s first occurrence, but not its second. Together, these results suggest that the initial occurrence of an event carries stronger temporal context associations than later repetitions.

Research Transparency Statement

The authors report no conflicts of interest with respect to the authorship or publication of this article. This research was conducted with support from National Institutes of Health grant MH55687. The current study was not preregistered. Data are available upon reasonable request and with proper approval from the University of Pennsylvania research and ethics entities. Requests should be directed to Adam Broitman. Key EEG and behavioral data analysis scripts are available for download at https://github.com/awb99cu/repFRcode.Studymaterialsareavailablefordownloadathttps://memory.psych.upenn.edu/PEERS.
Tidyplots empowers life scientists with easy code-based data visualization
Authors: Engler Jan Broder
Published: November 2024

Code-based data visualization is a crucial tool for understanding and communicating experimental findings while ensuring scalability and reproducibility. However, complex programming interfaces pose a significant barrier for life scientists. To address this challenge, tidyplots provides a user-friendly code-based interface for creating customizable and insightful plots. With its consistent and intuitive syntax, tidyplots empowers researchers to leverage automated data visualization pipelines while minimizing required programming skills.

Tidyplots is available on CRAN athttps://CRAN.R-project.org/package=tidyplotsand GitHub athttps://github.com/jbengler/tidyplots. The full documentation is available athttps://tidyplots.org.
A bacterial cell wall repair and modification system to resist host antibacterial factors
Authors: Burnier Jessica , Gallay Clement , Bruce Kevin , Bjånes Elisabet , Martin Louise , Jim Kinki , Tsui Ho-Ching Tiffany , Cremers Amelieke , Mignolet Johann , Vollmer Daniela , Biboy Jacob , Nizet Victor , Vollmer Waldemar , Winkler Malcolm E. , Veening Jan-Willem
Published: November 2024

Pathogenic bacteria have acquired the ability to resist antibacterial defense mechanisms of the host. Streptococci are common in animal microbiota and include opportunistic pathogens like Group A Streptococcus (GAS) andStreptococcus pneumoniae(pneumococcus). While the conserved streptococcal S protein has been identified as a key factor in GAS virulence, its exact function is unclear. Here, we show that the pneumococcal S protein is crucial for resisting against host-derived antimicrobials by coordinating cell wall modification and repair. Specifically, we show that S proteins are septally localized through their transmembrane domain and contain an extracellular peptidoglycan (PG) binding LysM domain which is required for its function. Protein-protein and genetic interaction studies demonstrate that the pneumococcal S protein directly interacts with a PG synthase, class A penicillin binding protein PBP1a, and the PG deacetylase PgdA. Single-molecule experiments reveal that the fraction of circumferentially moving PBP1a molecules is reduced in the absence of S protein. Consistent with an impaired PBP1a function, streptococci lacking S protein exhibit increased susceptibility to cell wall targeting antibiotics and altered cell morphologies. PG analysis showed reduced N-deacetylation of glycans in theS. pneumoniaeS protein mutant, indicating reduced PgdA activity. We show that pneumococci lacking the S protein cannot persist transient penicillin treatment, are more susceptible to the human antimicrobial peptide LL-37 and to lysozyme, and show decreased virulence in zebrafish and mice. Our data support a model in which S proteins regulate PBP1a activity and play a key role in coordinating PG repair and modification. This cell wall ‘sentinel’ control system provides defense against host-derived and environmental antimicrobial attack.
Risk factors, prognostic factors, and nomograms for distant metastasis in patients with triple-negative breast cancer: a population-based study
Authors: Guo Hongguo , Qiao Song , Cheng Cai , Liu Jun , Yang Shangzhen , Lu Wanling
Published: November 2024

Background

Triple-negative breast cancer (TNBC) is associated with a poor prognosis, higher invasiveness compared to other breast cancer variants, and limited treatment options. Due to the lack of conventional treatment methods, TNBC patients are prone to distant metastasis. The purpose of this study is to evaluate the clinical and pathological characteristics of TNBC patients, predict the impact of risk factors on their prognosis, and establish a predictive model to assist doctors in treating TNBC patients and improving their outcomes.

Methods

We conducted a retrospective study on patients with TNBC from 2010 to 2015 in the Surveillance, Epidemiology, and End Results (SEER) database. We gathered tumor characteristics and treatment data from these patients. Univariate and multivariate logistic regression analyses were employed to identify independent risk factors for distant metastasis in TNBC patients, while univariate and multivariate Cox proportional hazards regression analyses were utilized to determine independent prognostic factors for TNBC patients with distant metastasis. Based on these factors, a new nomogram was constructed, and patients were categorized into high and low-risk groups using the nomogram scores. The prognosis of the patients was analyzed using Kaplan-Meier (K-M) survival analysis.

Results

This study enrolled a total of 16,959 patients with TNBC, among whom 730 (4.3%) had distant metastasis at the time of diagnosis. Independent risk factors for distant metastasis in TNBC patients encompass being married, having an invasive lobular carcinoma (ILC) pathology, advanced T stage, advanced N stage, no radiotherapy, no surgery, and tumor size exceeding 50mm. The area under the curve (AUCs) for the training set and validation set were 0.892 and 0.907, respectively. The independent prognostic factors for patients with distant metastasis were being unmarried (P < 0.001), not undergoing surgery (P < 0.001), and not receiving chemotherapy (P < 0.001). The AUCs for the training set at 12, 36, and 60 months were 0.751, 0.709, and 0.691, respectively, while the AUCs for the validation set at 12, 36, and 60 months were 0.690, 0.690, and 0.732, respectively. The AUCs for the extended test set at 12, 36, and 60 months were 0.741, 0.727, and 0.718 respectively. The results of the calibration curve, decision curve analysis (DCA), and K-M survival curve confirm that both nomograms can accurately predict the occurrence of distant metastasis and prognosis in TNBC patients.

Conclusion

We constructed two nomograms to predict distant metastasis risk in TNBC patients and prognosis in patients with distant metastasis. Our findings suggest that they could serve as effective predictive tools and may assist in clinical decision-making.
Geographic-specific Diversification of Vaginal Microbiota in China
Authors: Yang Hua , Liu Yina , Liu Zimo , Zhou Chuanya , Hu Lingjie , He Jintao , Lv Lingling , Zhou Zhemin , Zhu Lan
Published: November 2024

The vaginal microbiota is pivotal to women's reproductive health, with significant geographic and ethnic heterogeneity suggesting evolutionary adaptations to environmental, climatic, and lifestyle factors. In this multi-centric study, we analyzed vaginal microbiome samples from women across five provinces in China, each characterized by distinct climatic, ethnic, and lifestyle traits. Our results indicate that the vaginal microbiota among Chinese women is characterized by low alpha diversity, withLactobacillus crispatusbeing the dominant species in Community State Type (CST) I, especially in the northern regions. While most participants exhibited stable CSTs throughout their menstrual cycles, fluctuations were observed in some individuals. We also detected low-abundance bacterial species such asFannyhesea vaginaeandSneathia vaginalis. Comparative genomic analysis of high-quality metagenome-assembled genomes ofL. crispatusrevealed minimal single nucleotide polymorphism (SNP) variations within individuals but substantial diversity between individuals, delineating a distinct separation between vaginal-associated populations (VAP) and gut-associated populations (GAP). These findings highlight the intricate dynamics of the vaginal microbiome, which are markedly influenced by geographic and individual determinants. This study offers an in-depth phylogenetic and genomic analysis of the vaginal microbiota among Chinese women, underscoring the imperative for further research into the impact of regional and individual variations on microbial community composition. Such knowledge could facilitate the development of personalized vaginal health management strategies that accommodate the unique microbiome profiles specific to different geographical regions.
Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes
Authors: Stevenson Zachary C. , Laufer Eleanor , Estevez Annette O. , Robinson Kristin , Phillips Patrick C.
Published: November 2024

A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system inCaenorhabditis elegans(Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode experimental evolution animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels,avr-14,avr-15, andglc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, yielding the largest animal experimental evolution study to date. The frequency of each barcode was determined at multiple time points via sequencing at deep coverage and then used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate thatC. eleganscan be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.
Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mtDNA copy number in songbird blood and sperm cells
Authors: Bagdonaitė Laima , Leder Erica H. , Lifjeld Jan T. , Johnsen Arild , Mauvisseau Quentin
Published: November 2024

Mitochondrial DNA copy number varies across species, individuals and cell types. Two avian cell types carrying a relatively low number of mitochondria are the red blood cells and spermatozoa. While previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), this method shows potential limitations when quantifying low abundant targets. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. Using synthetic DNA, we found that both dPCR and ddPCR displayed lower Limit of Detection and Limit of Quantification than qPCR. Using DNA extracted from blood and sperm cells of Eurasian Siskin, we found that qPCR, dPCR and ddPCR reliably quantified mitochondrial DNA in sperm samples, but showed significant differences when analyzing typically lower levels of mtDNA in blood. We found that ddPCR consistently showed lower variation among replicates. These analyses provide critical insights and recommendations for future studies aiming to quantify target mtDNA. Our study indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA.
A Systematic Review of the Impacts of El Niño-Driven Drought, Fire, and Smoke on Non-Human Primates in Southeast Asia
Authors: Barrow Elizabeth J. , Erb Wendy M.
Published: November 2024

During the El Niño phase of the El Niño-Southern Oscillation (ENSO), much of Southeast Asia experiences intense droughts and surging temperatures, exacerbating wildfires and creating a blanket of hazardous haze across much of the region. These patterns are predicted to worsen with climate change, further exacerbating the vulnerability of the regions’ primate species, 94% of which are threatened with extinction. Here, we report findings from a systematic search of the literature and synthesise the current state of knowledge regarding the impacts of El Niño-driven drought, fire, and smoke on non-human primates in Southeast Asia. Our review shows that habitat loss and degradation driven by El Niño-induced drought and fire causes changes to diet, activity patterns, social interactions, and physical condition, and leads to population crowding, reduced group sizes, increased infant mortality, displacement of individuals, and even local extirpation. Further, prolonged exposure to smoke alters behaviour and worsens the health of primates. Notably, two studies presented evidence for the recovery of primate populations in habitats damaged by fire if forest is allowed to regenerate. We highlight significant gaps in our understanding of the impacts of El Niño on non-human primates, particularly the need for research that encompasses the interconnected factors of rainfall, temperature, fire, and smoke, as well as long-term effects on reproduction and mortality. Due to the unpredictable nature of El Niño, we acknowledge the difficulties of planning research in this area and emphasise the potential of long-term research sites to add to our understanding of this key conservation issue.
Generation of a novel constitutive smooth muscle cell-specificMyh11-driven Cre mouse model
Authors: Dong Kunzhe , Bai Zhixia , He Xiangqin , Zhang Lu , Hu Guoqing , Yao Yali , Cai Chen-Leng , Zhou Jiliang
Published: November 2024

Dysfunction in either embryonic or postnatal vascular smooth muscle cells (SMCs) significantly contributes to the progression of various cardiovascular diseases. Therefore, elucidating the molecular mechanisms governing VSMC development and homeostasis is crucial.MYH11is the most reliable lineage gene for SMCs and has been utilized to develop tamoxifen-inducible Cre driver lines for achieving SMC-specific gene manipulation by crossing with mice carrying the loxP-flanked gene, particularly in adult mice. For studies involving SMCs during embryogenesis, the commonly used constitutive Cre driver is controlled by theTagln(Sm22α) promoter. However, this Cre driver exhibits activity in multiple non-SMC populations, including cardiomyocytes and skeletal muscle precursors, introducing confounding effects. Additionally, most existing SMC-specific Cre drivers are generated using a transgenic approach, raising concerns about random site integration and variable gene copy numbers. To address these limitations, we report a novel Cre mouse model generated by knock-in (KI) of a nuclear-localized Cre recombinase into theMyh11gene locus using homologous recombination. We confirmed that the Cre activity precisely recapitulates endogenousMyh11expression by crossing withRosa26mTmG or tdTomato reporter mice. Moreover,Myh11-driven Cre can efficiently delete the floxed allele of the transcription factorTead1specifically in SMCs. TheTead1SMC-specific knockout mice did not exhibit an overt phenotype, thereby circumventing the embryonic lethal phenotype mediated byTagln-driven Cre, as we previously reported. These findings establish this novel Cre driver line as a robust tool for tracing theMyh11-positive SMC lineage and manipulating gene function specifically in SMCs during embryonic development in mice.
Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1
Authors: Arkinson Connor , Gee Christine L. , Zhang Zeyuan , Dong Ken C. , Martin Andreas
Published: November 2024

The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting cofactors thereby modulates these functions and aids in substrate degradation. Here, we solved several high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and sub-stoichiometric concentrations by time resolved cryo-EM. We identified distinct binding modes of TXNL1 that depend on the proteasome conformational and ATPase motor states. Together with biophysical and biochemical experiments, our structural studies reveal that the resting-state proteasome prior to substrate engagement with the ATPase motor binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, the actively degrading proteasome shows additional interactions leading to high-affinity TXNL1 binding, whereby TXNL1’s C-terminal tail covers the catalytic groove of the Rpn11 deubiquitinase and coordinates the active-site Zn2+. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in all registers of spiral-staircase arrangements and thus visualize the complete ATP-hydrolysis cycle of the AAA+ motor, indicating temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the beta-barrel mEos3.2 substrate while the ATPase hexamer is in a particular spiral staircase register. Our findings challenge current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct but broad range of conformational states to coordinate cofactor binding and substrate processing.

Highlights

High resolution structures of the redox active cofactor TXNL1 in complex with the human 26S proteasome solved by time-resolved cryo-EM.

TXNL1 binds the catalytic groove of the main proteasomal deubiquitinase Rpn11 and coordinates its active-site Zinc specifically in substrate-degrading states of the proteasome.

Visualizing a partially unfolded intermediate of the mEos model substrate during processing.

Structures of the actively degrading human proteasome reveal all spiral-staircase registers of the AAA+ ATPase hexamer with unexpected nucleotide occupancies that indicate asymmetric ATP hydrolysis mechanisms, conformational changes with burst phases, and thus new models for hand-over-hand substrate translocation.
Commonalities and differences in the Cryptococcus neoformans response to ingestion by protozoal and mammalian phagocytic cells suggests host cell metabolism as a target for intracellular survival
Authors: Dragotakes Quigly , Jacobs Ella , Gerbig Gracen , Greengo Seth , Jedlicka Anne , Dziedzic Amanda , Casadevall Arturo
Published: November 2024

The outcome of the interaction between Cryptococcus neoformans and infected hosts can be determined by whether the fungal cell survives ingestion by phagocytic cells. This applies to both unicellular and multicellular hosts such as amoeba and animals, respectively. Ingestion by phagocytic cells results in the formation of the cryptococcal phagosome but this structure has proved difficult to isolate. In this study, we report the successful isolation of cryptococcal phagosomes from murine and human phagocytes, followed by their characterization using proteomic and transcriptional analysis. Comparison of cryptococcal proteins from Acanthamoeba castellanii, Mus musculus, and Homo sapiens phagocytes revealed the existence of a shared set suggesting a conserved fungal response to ingestion by phagocytic cells. Given that the cryptococcal intracellular pathogenic strategy is ancient, dating to at least to the cretaceous epoch, these results are consistent with the notion that the fungal response to ingestion reflects the result of selection pressures by environmental ameboid predators over eons of evolutionary time. We propose the existence of a conserved cryptococcal toolkit for intracellular survival that includes metabolic enzymes. We propose that host cell metabolic disruption provides a common strategy for the cryptococcal survival after ingestion by phylogenetically distant phagocytic hosts.
Drospondin, a novel glial-secreted glycoprotein, controls the development and function of theDrosophilanervous system
Authors: Rojo-Cortés Francisca , Roa-Siegfried Candy B. , Fuenzalida-Uribe Nicolás , Amado-Hinojosa Paula , González-Ramírez María-Constanza , Almonacid-Torres Isidora , Birman Serge , Goodman Lindsey D. , Kanca Oguz , Oliva Carlos , Marzolo María Paz , Campusano Jorge M.
Published: November 2024

Reelin is a secreted glycoprotein with roles in the development of the mammalian neocortex, hippocampus and cerebellum. This vertebrate signaling molecule also contributes to adult brain function. Mammalian Reelin increases the complexity ofDrosophilaMushroom Body (MB) neurites, an effect mediated by LpR1 and LpR2, the orthologs of mammalian Reelin receptors. Paradoxically, to date, no Reelin ortholog has been described inDrosophila. Here, we report that the protein product of the uncharacterizedDrosophila CG17739gene, which we named Drospondin, shares sequence homology with vertebrate F-spondin and Reelin. We show that Drospondin is expressed in glial cells and is crucial for MB development. Our results also show that Drospondin genetically interacts with LpRs and that human Reelin rescues structural defects in Drospondin-deficient flies. Furthermore, Drospondin-deficient flies exhibit altered sleep homeostasis, locomotion, and social behaviors. Our results reveal that flies express a functional homolog of mammalian Reelin that controls the development and function of theDrosophilanervous system.
Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display
Authors: Wang Sijie , Faucher Franco F. , Bertolini Matilde , Kim Heeyoung , Yu Bingchen , Cao Li , Roeltgen Katharina , Lovell Scott , Shanker Varun , Boyd Scott D. , Wang Lei , Bartenschlager Ralf , Bogyo Matthew
Published: November 2024

Peptide macrocycles are promising therapeutics for a variety of disease indications due to their overall metabolic stability and potential to make highly selective binding interactions with targets. Recent advances in covalent macrocycle peptide discovery, driven by phage and mRNA display methods, have enabled the rapid identification of highly potent and selective molecules from large libraires of diverse macrocycles. However, there are currently limited examples of macrocycles that can be used to disrupt protein-protein interactions and even fewer examples that function by formation of a covalent bond to a target protein. In this work, we describe a directed counter-selection method that enables identification of covalent macrocyclic ligands targeting a protein-protein interaction using a phage display screening platform. This method utilizes binary and ternary screenings of a chemically modified phage display library, employing the stable and weakly reactive aryl fluorosulfate electrophile. We demonstrate the utility of this approach using the SARS-CoV-2 Spike-ACE2 protein-protein interaction and identify multiple covalent macrocyclic inhibitors that disrupt this interaction. The resulting compounds displayed antiviral activity against live virus that was irreversible after washout due to the covalent binding mechanism. These results highlight the potential of this screening platform for developing covalent macrocyclic drugs that disrupt protein-protein interactions with long lasting effects.
Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating
Authors: Fujiwara Takayoshi , Hosaka Toshiaki , Hasegawa-Takano Masumi , Nishimura Yosuke , Tominaga Kento , Mori Kaho , Nishino Satoshi , Takahashi Yuno , Uchikubo-Kamo Tomomi , Hanada Kazuharu , Maoka Takashi , Takaichi Shinichi , Inoue Keiichi , Shirouzu Mikako , Yoshizawa Susumu
Published: November 2024

Microbial rhodopsins, photoreceptor proteins widely distributed in marine microorganisms, receive large amount of light energy that sustains marine ecosystems. Although rhodopsins generally harbor retinal as their only chromophore, a recent study reported that carotenoid antennae transfer light energy to the retinal in proteorhodopsins, proton pump rhodopsins abundant in marine environments. Here, using marine bacterial isolates, we detected energy transfer from a carotenoid (myxol) to retinal not only in proteorhodopsin but also in the chloride ion-pumping rhodopsin. Carotenoid binding improved the light utilization efficiency of the proteorhodopsin by accelerating the photocycle, together with facilitating light-harvesting. The carotenoid-binding ability is conserved in rhodopsins of the phylumBacteroidota, which are widely transcribed in the photic zone. These findings suggest that the distribution of carotenoid-binding rhodopsins is more taxon-specific than previously thought, thus underscoring the importance of carotenoid-binding rhodopsins that provide an extended light utilization strategy in the environmental adaptation of marine bacteria.
Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance inCandida albicans
Authors: Obermeier Mariella , Esparza Mora Margy Alejandra , Heese Olivia , Cohen Nir , Varma Sreejith Jayasree , Tober-Lau Pinkus , Hartl Johannes , Kurth Florian , Berman Judith , Ralser Markus
Published: November 2024

Background

Fungal infections are an increasing concern, particularly among immunocompromised patients and those with comorbidities who require multiple medications. However, the effects of drugs targeting human pathways on fungal cells, and whether they influence antifungal drug responses, are poorly understood.

Methods

We systematically analyzed clinical guidelines to shortlist non-antifungal drugs commonly used in conditions that increase the likelihood of fungal infections. Focusing on the most prevalent fungal pathogen, we then tested how these drugs affected the antifungal response ofCandida albicansto two commonly used antifungals, fluconazole and anidulafungin. Drug interactions identified were further assessed using checkerboard and disk diffusion assays. Finally, antifungal treatment efficacy of fluconazole in combination with negatively interacting drugs was evaluated in anin vivo Galleria mellonellamodel of disseminatedC. albicansinfection.

Findings

Out of 119 drugs frequently co-administered with antifungals in 40 conditions associated with a high risk of fungal infections, 34 compounds affected the antifungal drug response inC. albicans, with most drugs reducing or antagonising antifungal efficacy, several through increasing resistance or tolerance. Notably, fluconazole combinations with carvedilol and loperamide promoted antifungal resistance in both fungal cultures and inGalleria mellonella.

Interpretation

Our findings suggest that medications frequently taken by patients at risk of fungal infections regularly act on the fungal pathogens and can affect the effectiveness of antifungals. We propose that human drugs acting on fungal pathogens may be an underestimated factor contributing to the evolution of antifungal tolerance and resistance.
A recurrent vision transformer shows signatures of primate visual attention
Authors: Morgan Jonathan , Albanna Badr , Herman James P.
Published: November 2024

We present a Recurrent Vision Transformer (Recurrent ViT) that integrates a capacity-limited spatial memory module with self-attention to emulate primate-like visual attention. Trained via reinforcement learning on a spatially cued orientation-change detection task, our model exhibits hallmark behavioral signatures of primate attention—including improved detection accuracy and faster reaction times for cued stimuli that scale with cue validity. Analysis of its self-attention maps reveals rich temporal dynamics: spatial biases induced by cues are maintained during blank intervals and reactivated prior to anticipated stimulus changes, mirroring the top–down modulation observed in primate studies. Moreover, targeted manipulations of internal attention weights yield performance changes analogous to those produced by microstimulation in attentional control regions such as the frontal eye fields and superior colliculus. These findings demonstrate that embedding recurrent, memory-driven mechanisms within transformer architectures may provide a computational framework for linking artificial and biological attention
Sex differences in central amygdala glutamate responses to calcitonin gene-related peptide
Authors: Lorsung Rebecca , Cramer Nathan , Alipio Jason Bondoc , Ji Yadong , Han Sung , Masri Radi , Keller Asaf
Published: November 2024

Women are disproportionately affected by chronic pain compared to men. While societal and environmental factors contribute to this disparity, sex-based biological differences in the processing of pain are also believed to play significant roles. The central lateral nucleus of the amygdala (CeLC) is a key region for the emotional-affective dimension of pain, and a prime target for exploring sex differences in pain processing since a recent study demonstrated sex differences in CGRP actions in this region. Inputs to CeLC from the parabrachial nucleus (PB) play a causal role in aversive processing, and release both glutamate and calcitonin gene-related peptide (CGRP). CGRP is thought to play a crucial role in chronic pain by potentiating glutamatergic signaling in CeLC.

However, it is not known if this CGRP-mediated synaptic plasticity occurs similarly in males and females. Here, we tested the hypothesis that female CeLC neurons experience greater potentiation of glutamatergic signaling than males followingendogenousCGRP exposure. Using trains of optical stimuli to evoke transient CGRP release from PB terminals in CeLC, we find that subsequent glutamatergic responses are preferentially potentiated in CeLC neurons from female mice. This potentiation was CGRP-dependent and involved a postsynaptic mechanism. This sex difference in CGRP sensitivity may explain sex differences in affective pain processing.

Significance statement

The central lateral nucleus of the amygdala (CeLC) receives a dense projection from parabrachial nucleus (PB) neurons that corelease calcitonin gene-related peptide (CGRP) and glutamate following aversive stimuli. This PBCGRP→CeLC projection plays a causal role in chronic pain. We show that endogenous CGRP release potentiates glutamate signaling in female, but not male, CeLC neurons. In the context of previous work in male CeLC, this suggests that that females are more sensitive to even transient CGRP release events. Understanding how this sex difference in CGRP sensitivity arises could enhance strategies for treating chronic pain in both women and men.