bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of Race, Ethnicity, and Socioeconomic Status on the Severity of Menopause Symptoms: A Study of 68,864 Women
Authors: Kochersberger Alison , Coakley Aeowynn , Millheiser Leah , Morris Jerrine R. , Manneh Claire , Jackson Alicia , Garrison Jennifer L. , Hariton Eduardo
Published: December 2023

Objective

To evaluate how race, ethnicity, and socioeconomic status (SES) affect the severity of menopause symptoms in a large, diverse sample of women.

Methods

For this cross-sectional study conducted between March 24, 2019, and January 13, 2023, a total of 68,864 women were enrolled from the Evernow online telehealth platform. Participants underwent a clinical intake survey, which encompassed demographic information, detailed medical questionnaires, and a modified Menopause Rating Scale (MRS). The modified scale was adapted for ease of use online and is available in the supplementary material along with the full intake. Symptom severity was evaluated using a multivariate binomial generalized linear model, accounting for factors such as race, ethnicity, age, BMI, smoking status, bilateral oophorectomy status, and SES. Odds ratios and confidence intervals were calculated based on the linear regression coefficients.

Results

Of the participants, 67,867 (98.6%) were included in the analysis after excluding outliers and those with unknown oophorectomy status. The majority of respondents identified as White (77.4%), followed by Hispanic (9.0%), Black (6.7%), two or more races/ethnicities (4.4%), Asian (1.2%), Indigenous/First Nations (0.8%), Middle Eastern (0.3%), and South Asian (0.2%). Notably, individuals identifying as Black, Hispanic, Indigenous/First Nations, Middle Eastern, or with two or more races/ethnicities reported higher levels of symptom severity compared to their White counterparts. Conversely, Asian and South Asian participants reported lower symptom severity. Even after incorporating SES into the linear model, racial and ethnic groups with lower SES (Black, Hispanic, Indigenous, and multiple ethnicities) exhibited slight shifts in odds ratios, while maintaining high statistical significance.

Conclusions

Our study suggests that the relationship between race and ethnicity and the severity of menopause symptoms is not solely explained by differences in SES but is itself an independent factor. Understanding and addressing social, cultural, and economic factors is crucial to reduce disparities in menopausal symptoms.
Identification of new proviral and antiviral factors through the study of the Dicer-2 interactomein vivoduring viral infection inDrosophila melanogaster
Authors: Rousseau Claire , Lauret Émilie , Kuhn Lauriane , Chicher Johana , Hammann Philippe , Meignin Carine
Published: December 2023

RNA interference, which has a major role in the control of viral infection in insects, is initialized by the sensing of double stranded RNA (dsRNA) by the RNAse III enzyme Dicer-2. Although manyin vitrostudies have helped understand how Dicer-2 is able to discriminate between different dsRNA substrate termini, much less is known about how this translates to thein vivorecognition of viral dsRNA. Indeed, although Dicer-2 associates with several dsRNA-binding proteins (dsRBPs) that can modify its specificity for a substrate, it remains unknown how Dicer-2 is able to recognize the protected termini of viral dsRNAs. In order to study how the ribonucleoprotein network of Dicer-2 impacts antiviral immunity, we used an IP-MS approach to identifyin vivointeractants of different versions of GFP::Dicer-2 in transgenic lines. We provide a global overview of the partners of Dicer-2in vivo, and reveal how this interactome is modulated by different factors such as the viral infection and/or different point mutations inactivating the helicase or RNase III domains of GFP::Dicer-2. Our analysis uncovers several previously unknown Dicer-2 interactants associated with RNA granules (i.e. Me31B, Rump, eIF4E1 & Syp). Functional characterization of the candidates reveals pro- and antiviral factors in the context of the infection by the picorna-like DCV virus. In particular, the protein Rasputin has been identified as a novel antiviral candidate. The resources provided by this work can be used to gain a better understanding of the molecular complexes assembled around Dicer-2 in the context of antiviral RNAi and beyond.
Switching perspective: Comparing ground-level and bird’s-eye views for bumblebees navigating dense environments
Authors: Sonntag Annkathrin , Sauzet Odile , Lihoreau Mathieu , Egelhaaf Martin , Bertrand Olivier
Published: December 2023

Animals navigating in three dimensions encounter different perspectives of their world, often transitioning from bird’s eye views at higher altitudes to ground views closer to the ground. How they integrate this information to pinpoint a goal location is virtually unknown. Here we tested the ability of bumblebees to use both types of views when homing in a dense environment in the vicinity of their inconspicuous nest entrance. Our combined modelling and experimental approach examined various views for localising a goal in dense settings. Whereas, bird’s-eye views performed best in simulations of current nest-centered snapshot homing models, behavioural experiments revealed that bumblebees predominantly relied on ground views when pinpointing nest entrances in dense environments. These findings reveal the limitations of snapshot-homing models and suggest that bumblebees use a combination of navigational tools to successfully find their way home in dense environments. This is not only relevant for understanding bee navigation, but also for other animals and humans navigating in 3D as well as the development of technologies inspired by natural systems, such as autonomous flying robots.
Phase diagrams of bone remodeling using a 3D stochastic cellular automaton
Authors: Heller Anna-Dorothea , Valleriani Angelo , Cipitria Amaia
Published: December 2023

We propose a 3D stochastic cellular automaton model, governed by evolutionary game theory, to simulate bone remodeling dynamics. The model includes four voxel states:Formation, Quiescence, Resorption, andEnvironment. We simulate theResorptionandFormationprocesses on separate time scales to explore the parameter space and derive a phase diagram that illustrates the sensitivity of these processes to parameter changes. Combining these results, we simulate a full bone remodeling cycle. Furthermore, we show the importance of modeling small neighborhoods for studying local bone microenvironment controls. This model can guide experimental design and, in combination with other models, it could assist to further explore external impacts on bone remodeling. Consequently, this model contributes to an improved understanding of complex dynamics in bone remodeling dynamics and exploring alterations due to disease or drug treatment.

Author summary

Functional well-balanced bone remodeling is crucial for a healthy skeleton. Understanding the various causes for the disruption of this complex process requires models that combine behavior on micro- and macro-level. We propose a 3D stochastic cellular automaton model, where each voxel can take one of four different states representing phases of bone remodeling:Formation, Quiescence, ResorptionandEnvironment. With a qualitative analysis, we show how and when small changes in key interaction parameters can make the difference between healthy and pathological bone remodeling. We also highlight the importance of spatial modeling and the size of the neighborhood for investigating local mechanisms. Our proposed model opens the window to explore the complex interplay of factors essential for healthy bone remodeling and potential alterations due to disease or drug treatment. In the long term this could help with the development of new treatment options for bone diseases.
Western diet feeding since adolescence impairs functional hyperemia probed by functional ultrasound imaging at adulthood and middle age: rescue by a balanced ω-3:ω-6 polyunsaturated fatty acids ratio in the diet
Authors: Soleimanzad Haleh , Morisset Clémentine , Montaner Mireia , Pain Frédéric , Magnan Christophe , Tanter Mickaël , Gurden Hirac
Published: December 2023

Obesity is a devastating worldwide metabolic disease, with the highest prevalence in children and adolescence. Obesity impacts neuronal function but the fate of functional hyperemia, a vital mechanism making possible cerebral blood supply to active brain areas, is unknown in organisms fed a high caloric Western Diet (WD) since adolescence. We mapped changes in cerebral blood volume (CBV) in the somatosensory cortex in response to whiskers stimulation in adolescent, adult and middle-aged mice fed a WD since adolescence. To this aim, we used non-invasive and high-resolution functional ultrasound imaging (fUS). Functional hyperemia is compromised as early as 3 weeks of WD and remains impaired thereafter. Starting WD in adult mice does not trigger the profound impairment in sensory-evoked CBV observed in young mice, suggesting a cerebrovascular vulnerability to WD during adolescence. A balanced ω-6:ω-3 polyunsaturated fatty acids ratio in WD achieved by docosahexaenoic acid supplementation is efficient to restore glucose homeostasis and functional hyperemia in adults.
TheZea maysPeptideAtlas – a new maize community resource
Authors: van Wijk Klaas J. , Leppert Tami , Sun Zhi , Guzchenko Isabell , Debley Erica , Sauermann Georgia , Routray Pratyush , Mendoza Luis , Sun Qi , Deutsch Eric W.
Published: December 2023

We developed the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize were collected from ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds, including the inbred lines B73 and W22, many hybrids and their respective parents. Samples were collected from field trials, controlled environmental conditions, a range of (a)biotic conditions and different tissues, cell types and subcellular fractions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of the proteins (one isoform per protein coding gene) in the most recent B73 nuclear genome annotation (v5). Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other searched B73 genome annotations will aid to improve maize genome annotation. We also illustrate high confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical and biological metadata. This new PeptideAtlas is integrated with community resources including MaizeGDB athttps://www.maizegdb.org/and a peptide track in JBrowse.
Chloroplast Methyltransferase Homolog RMT2 is Involved in Photosystem I Biogenesis
Authors: Kim Rick G. , Huang Weichao , Findinier Justin , Bunbury Freddy , Redekop Petra , Shrestha Ruben , Grismer TaraBryn S , Vilarrasa-Blasi Josep , Jinkerson Robert E. , Fakhimi Neda , Fauser Friedrich , Jonikas Martin C. , Onishi Masayuki , Xu Shou-Ling , Grossman Arthur R.
Published: December 2023

Oxygen (O2), a dominant element in the atmosphere and essential for most life on Earth, is produced by the photosynthetic oxidation of water. However, metabolic activity can cause accumulation of reactive O2species (ROS) and severe cell damage. To identify and characterize mechanisms enabling cells to cope with ROS, we performed a high-throughput O2sensitivity screen on a genome-wide insertional mutant library of the unicellular algaChlamydomonas reinhardtii. This screen led to identification of a gene encoding a protein designated Rubisco methyltransferase 2 (RMT2). Although homologous to methyltransferases, RMT2 has not been experimentally demonstrated to have methyltransferase activity. Furthermore, thermt2mutant was not compromised for Rubisco (first enzyme of Calvin-Benson Cycle) levels but did exhibit a marked decrease in accumulation/activity of photosystem I (PSI), which causes light sensitivity, with much less of an impact on other photosynthetic complexes. This mutant also shows increased accumulation of Ycf3 and Ycf4, proteins critical for PSI assembly. Rescue of the mutant phenotype with a wild-type (WT) copy of RMT2 fused to the mNeonGreen fluorophore indicates that the protein localizes to the chloroplast and appears to be enriched in/around the pyrenoid, an intrachloroplast compartment present in many algae that is packed with Rubisco and potentially hypoxic. These results indicate that RMT2 serves an important role in PSI biogenesis which, although still speculative, may be enriched around or within the pyrenoid.

Significance Statement

A high-throughput genetic screen was used to identify O2sensitive mutants ofChlamydomonas reinhardtii(Chlamydomonas throughout) that experience elevated oxidative stress in the light relative to WT cells. Identification of genes altered in these mutants offers opportunities to discover activities thata) protect photosynthetic cells from oxidative damage,b) participate in rapid assembly of photosynthetic complexes, which would limit accessibility of intermediates to O2, and/orc) facilitate repair of damaged cellular complexes. A mutant from this screen disrupted forRMT2, originally described as encoding a Rubisco methyltransferase, was defective for PSI biogenesis. Additionally, RMT2 appears to be enriched in/around the pyrenoid, a chloroplast localized compartment harboring much of the Chlamydomonas Rubisco, raising the possibility that this compartment plays a role in PSI biogenesis.
Usingfanyito reduce language barriers, promote information absorption, and communication
Authors: Wang Difei , Chen Guannan , Luo Xiao , Zhan Li , Xu Shuangbin , Wang Qianwen , Li Junrui , Wang Rui , Wen Shaodi , Yu Guangchuang
Published: December 2023

Understanding the latest research advancements and sharing one’s own achievements is extremely important for young researchers. However, language barriers restrict the absorption of knowledge and career development. To address these issues, we have developed the fanyi package, which utilizes AI-driven online translation services to accurately translate between multiple languages. This helps researchers rapidly capture information, promotes the preservation of a multilingual environment, and ultimately fosters innovation in the academic community. Interpreting genes of interest (such as mutant genes) contributes to proposing molecular mechanisms, but accessing such information typically requires tedious manual retrieval. The fanyi package also provides tools for retrieving gene information from NCBI, enhancing the accessibility of gene information. Being able to quickly and efficiently obtain these pieces of information, coupled with translation capabilities, can help researchers better understand the information. The fanyi package is freely available viahttps://github.com/YuLab-SMU/fanyi. The translation functions are not limited to biomedicine research, they can be applied to any other domain as well.
Characterizing uncertainty in predictions of genomic sequence-to-activity models
Authors: Bajwa Ayesha , Rastogi Ruchir , Kathail Pooja , Shuai Richard W. , Ioannidis Nilah M.
Published: December 2023

Genomic sequence-to-activity models are increasingly utilized to understand gene regulatory syntax and probe the functional consequences of regulatory variation. Current models make accurate predictions of relative activity levels across the human reference genome, but their performance is more limited for predicting the effects of genetic variants, such as explaining gene expression variation across individuals. To better understand the causes of these shortcomings, we examine the uncertainty in predictions of genomic sequence-to-activity models using an ensemble of Basenji2 model replicates. We characterize prediction consistency on four types of sequences: reference genome sequences, reference genome sequences perturbed with TF motifs, eQTLs, and personal genome sequences. We observe that models tend to make high-confidence predictions on reference sequences, even when incorrect, and low-confidence predictions on sequences with variants. For eQTLs and personal genome sequences, we find that model replicates make inconsistent predictions in >50% of cases. Our findings suggest strategies to improve performance of these models.
FlowAtlas.jl: an interactive tool bridging FlowJo with computational tools in Julia
Authors: Coppard Valerie , Szep Grisha , Georgieva Zoya , Howlett Sarah K. , Jarvis Lorna B. , Rainbow Daniel B. , Suchanek Ondrej , Needham Edward J. , Mousa Hani S. , Menon David K. , Feyertag Felix , Mahbubani Krishna T. , Saeb-Parsy Kourosh , Jones Joanne L.
Published: December 2023

As the dimensionality, throughput, and complexity of cytometry data increases, so does the demand for user-friendly, interactive analysis tools that leverage high-performance machine learning frameworks. Here we introduce FlowAtlas.jl: an interactive web application that bridges the user-friendly environment of FlowJo and computational tools in Julia developed by the scientific machine learning community. We demonstrate the capabilities of FlowAtlas using a novel human multi-tissue, multi-donor immune cell dataset, highlighting key immunological findings.
Transcriptional and Cellular Response of hiPSC-derived Microglia-Neural Progenitor Co-Cultures Exposed to IL-6
Authors: Couch Amalie C. M. , Brown Amelia M. , Raimundo Catarina , Solomon Shiden , Taylor Morgan , Sichlinger Laura , Matuleviciute Rugile , Srivastava Deepak P. , Vernon Anthony C.
Published: December 2023

Elevated interleukin (IL-)6 levels during prenatal development have been linked to increased risk for neurodevelopmental disorders (NDD) in the offspring, but the mechanism remains unclear. Human-induced pluripotent stem cell (hiPSC) models offer a valuable tool to study the effects of IL-6 on features relevant for human neurodevelopmentin vitro. We previously reported that hiPSC-derived microglia-like cells (MGLs) respond to IL-6, but neural progenitor cells (NPCs) in monoculture do not. Therefore, we investigated whether co-culturing hiPSC-derived MGLs with NPCs would trigger a cellular response to IL-6 stimulation via secreted factors from the MGLs. Using N=4 donor lines without psychiatric diagnosis, we first confirmed that NPCs can respond to IL-6 through trans-signalling when recombinant IL-6Ra is present, and that this response is dose-dependent. MGLs secreted soluble IL-6R, but at lower levels than foundin vivoand below that needed to activate trans-signalling in NPCs. Whilst transcriptomic and secretome analysis confirmed that MGLs undergo substantial transcriptomic changes after IL-6 exposure and subsequently secrete a cytokine milieu, NPCs in co-culture with MGLs exhibited a minimal transcriptional response. Furthermore, there were no significant cell fate-acquisition changes when differentiated into post-mitotic cultures, nor alterations in synaptic densities in mature neurons. These findings highlight the need to investigate if trans-IL-6 signalling to NPCs is a relevant disease mechanism linking prenatal IL-6 exposure to increased risk for psychiatric disorders. Moreover, our findings underscore the importance of establishing more complexin vitrohuman models with diverse cell types, which may show cell-specific responses to microglia-released cytokines to fully understand how IL-6 exposure may influence human neurodevelopment.
Development of a non-invasive novel individual marmoset holder for evaluation by awake functional magnetic resonance brain imaging
Authors: Seki Fumiko , Yurimoto Terumi , Kamioka Michiko , Inoue Takashi , Komaki Yuji , Iriki Atsushi , Sasaki Erika , Yamazaki Yumiko
Published: December 2023

Background

Although functional MRI (fMRI) in awake marmosets (Callithrix jacchus) is fascinating for functional brain mapping and evaluation of brain disease models, it is difficult to launch awake fMRI on scanners with less than 15 cm of bore size. A universal marmoset holder for the small-bore size MRI was designed, and evaluated whether this holder could conduct auditory stimulation fMRI in the awake state.

New Method

The marmoset holder was designed with an outer diameter of 71.9 mm. A holder was designed to allow adjustment according to the individual head shape, enabling to use the holder universally. An awake fMRI study of auditory response was conducted to evaluate the practicality of the new holder. Whole-brain activation was investigated when marmosets heard the marmoset social communication “phee call,” an artificial tone sound, music (bossa nova), and reversed of those.

Results

The prefrontal cortex was significantly activated in response to phee calls, whereas only the auditory cortex was activated in response to pure tones. In response to bossa nova, the marmoset’s visual and auditory cortices were activated. In contrast, the auditory response was decreased when marmosets heard phee calls and bossa nova music played backward. Their stimulus-specific responses indicated they perceived and differentiated sound characteristics in the fMRI environment.

Comparison with Existing Methods

A holder does not require surgical intervention or custom-made helmet to minimize head movement in small space.

Conclusion

Our newly developed holder made it possible to perform longitudinal fMRI experiments on multiple marmosets in a less invasive manner.

Highlight

We designed a universal marmoset holder for the optimization of small-bore size MRI. We aimed to evaluate whether the data acquired by fMRI with this holder indicated that awake marmosets were likely to recognize sounds during fMRI and whether the brain activity shown as fMRI signals reflected the characteristics of each sound.

After the acclimatization of the marmosets to the holder, an awake fMRI study was conducted to evaluate the practicality of the new holder and successfully acquired the auditory responses to the set of sound stimuli.

Our newly developed holder does not require surgical intervention to minimize head movement, which allows for less invasive fMRI experiments and makes it easier to conduct longitudinal fMRI for multiple marmosets.
Trophic microRNA: Precursor and mature microRNA ingestion downregulates the target transcripts and hampers larval development inPlutella xylostella
Authors: Bardapurkar Rutwik , Pandit Sagar
Published: December 2023

MicroRNAs (miRNAs) are post-transcriptional gene regulators. In the miRNA pathway’s cytoplasmic part, the miRNA is processed from a hairpin-structured precursor (pre-miRNA) to a double-stranded (ds) mature RNA and ultimately to a single-stranded mature miRNA. In insects, ingesting these two ds forms can regulate the target gene expression; this inspired the trophic miRNA’s use as a functional genomics and pest management tool. However, systematic studies enabling comparisons of pre- and mature forms, dosages, administration times, and instar-wise effects on target transcripts and phenotypes, which can help develop a miRNA administration method, are unavailable due to the different focuses of the previous investigations. We investigated the impact of trophically deliveredPx-let-7 miRNA on the Brassicaceae pest,Plutella xylostella, to compare the efficacies of its pre- and ds-mature forms. Continuous feeding on the miRNA-supplemented diet suppressed expressions ofFTZ-F1andE74, the target ecdysone pathway genes. Both the pre-let-7 and mature let-7 miRNA forms similarly downregulated the target transcripts in all four larval instars. Pre-let-7 and let-7 ingestions decreasedP. xylostella’s larval mass and instar duration and increased mortality in all instars, exhibiting adverse effects on larval growth and development. Pre-miRNA processingDicer-1was upregulated upon pre-let-7 ingestion, indicating the miRNA uptake by the midgut cells. The scrambled sequence controls did not affect the target transcripts, suggesting the sequence-specific targeting by the mature miRNA and hairpin cassette’s non-involvement in the target downregulation. This work provides a framework for miRNA and target gene function analyses and potentiates the trophic miRNA’s utility in pest management.
KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants
Authors: Oliveira Ludmila , Neumann Pavel , Mata-Sucre Yennifer , Kuo Yi-Tzu , Marques André , Schubert Veit , Macas Jiří
Published: December 2023

Centromere is the chromosomal site of kinetochore assembly and microtubule attachment for chromosome segregation. Given its importance, markers that allow specific labeling of centromeric chromatin throughout the cell cycle and across all chromosome types are sought for facilitating various centromere studies. Antibodies against the N-terminal region of CENH3 are commonly used for this purpose, since CENH3 is the near-universal marker of functional centromeres. However, because the N-terminal region of CENH3 is highly variable among plant species, antibodies directed against this region usually function only in a small group of closely related species. As a more versatile alternative, we present here antibodies targeted to the conserved domains of two outer kinetochore proteins, KNL1 and NDC80. Sequence comparison of these domains across more than 350 plant species revealed a high degree of conservation, particularly within a six amino acid motif, FFGPVS in KNL1, suggesting that both antibodies would function in a wide range of plant species. This assumption was confirmed by immunolabeling experiments in angiosperm (monocot and dicot) and gymnosperm species, including those with mono-, holo-, and meta-polycentric chromosomes. In addition to centromere labeling on condensed chromosomes during cell division, both antibodies detected the corresponding regions in the interphase nuclei of most species tested. These results demonstrated that KNL1 and NDC80 are better suited for immunolabeling centromeres than CENH3, because antibodies against these proteins offer incomparably greater versatility across different plant species which is particularly convenient for studying the organization and function of the centromere in non-model species.
Metabolism of ʟ -arabinose converges with virulence regulation to promote enteric pathogen fitness
Authors: Cottam Curtis , White Rhys T , Beck Lauren C , Stewart Christopher J , Beatson Scott A , Lowe Elisabeth C , Grinter Rhys , Connolly James PR
Published: December 2023

Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified a novel transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagicEscherichia coli(EHEC), required for full competitive fitness in the mouse gut and highly expressed during human infection. Accordingly, we discovered that ʟ-arabinose induces expression of the EHEC type 3 secretion system, enhancing its ability to attach to host cells, and that the underlying mechanism is dependent on products of its catabolism rather than the sensing of ʟ-arabinose as a signal. Finally, using the murine pathogenCitrobacter rodentium,we show that ʟ-arabinose metabolism provides a fitness benefit during enteric infection via virulence factor regulation, as opposed to supporting pathogen growth. This study describes an intrinsic mechanism of integrating central sugar metabolism with virulence regulation and highlights the unexpected impact that nutrient utilisation can have in enteric pathogens.
Campycins are novel broad spectrum antibacterials killingCampylobacter jejuniby targeting the essential major outer membrane protein (MOMP)
Authors: Zampara Athina , Gencay Yilmaz Emre , Brøndsted Lone , Sørensen Martine Camilla Holst
Published: December 2023

Pyocins are high molecular weight bacteriocins produced byPseudomonas aeruginosathat can be retargeted to new bacterial species by exchanging the pyocin tail fibers with bacteriophage receptor binding proteins (RBPs). Here, we develop retargeted pyocins called campycins as new antibacterials to specifically and effectively kill the major foodborne pathogenCampylobacter jejuni.We used two diverse RBPs (H-fibers) encoded by CJIE1 prophages found in the genomes ofC. jejunistrains CAMSA2147 and RM1221 to construct Campycin 1 and Campycin 2, respectively. Together Campycin 1 and 2 could target allC. jejunistrains tested due to complementary antibacterial spectrums. In addition, both campycins led to more than 3 log reductions inC. jejunicounts under microaerobic conditions at 42°C, whereas the killing efficiency was less efficient under anaerobic conditions at 5°C. We furthermore discovered that both H-fibers used to construct the campycins bind to the essential major outer membrane protein (MOMP) present in allC. jejuni,in a strain specific manner. Protein sequence alignment and structural modelling suggest that the highly variable extracellular loops of MOMP form the binding sites of the diverse H-fibers. Furtherin silicoanalyses of 5000 MOMP sequences suggest that the protein fall into three major clades predicted to be targeted by either Campycin 1 or Campycin 2. Thus, campycins are promising antibacterials againstC. jejuniexpected to broadly target numerous strains of this human pathogen found in nature and agriculture.

IMPORTANCE

Campylobacter jejuniis the leading cause of bacterial foodborne gastroenteritis and responsible for more than 800 million cases globally each year posing a continuous risk to human health and a huge economic and societal burden. Here, we developed re-targeted R2 pyocins (campycins) as novel antibacterials againstC. jejuniby using the receptor binding proteins of CJIE1 prophages observed in manyC. jejunigenomes. Notably, campycins broadly target the highly variable yet essential major outer membrane protein (MOMP), and result in more than 3-log reductions inC. jejunicounts under conditions promoting bacterial growth. We therefore propose that campycins have the potential to lowerC. jejunicolonization levels in the chicken gut, the main reservoir and cause of human disease, representing a novel efficient antibacterial solution specifically developed to target this widespread foodborne pathogen.
Sequential Transitions of Male Sexual Behaviors Driven by Dual Acetylcholine-Dopamine Dynamics
Authors: Miyasaka Ai , Kanda Takeshi , Nonaka Naoki , Terakoshi Yuka , Cherasse Yoan , Ishikawa Yukiko , Li Yulong , Takizawa Hotaka , Seita Jun , Yanagisawa Masashi , Sakurai Takeshi , Sakurai Katsuyasu , Liu Qinghua
Published: December 2023

The neural mechanisms regulating sequential transitions of male sexual behaviors, such as mounting, intromission, and ejaculation, in the brain remain unclear. Here, we report that dopamine (DA) and acetylcholine (ACh) dynamics in the ventral shell of the nucleus accumbens (vsNAc) closely aligns with serial transitions of sexual behaviors in male mice. During intromission, the vsNAc exhibits dual ACh-DA rhythms generated by reciprocal regulation between ACh and DA signaling via nicotinic acetylcholine (nAChR) and dopamine D2 (D2R) receptors. Knockdown of choline acetyl transferase (ChAT) or D2R in the vsNAc diminished the likelihood of intromission and ejaculation. Optogenetic manipulations reveal that DA signaling sustains male sexual behaviors by suppressing activities of D2RvsNAcneurons. Moreover, ACh signaling promotes the initiation of mounting and intromission, but also induces the intromission-to-ejaculation transition by triggering a slowdown of DA rhythm. Therefore, dual ACh-DA dynamics harmonize in the vsNAc to drive sequential transitions of male mating behaviors.
Substantial decline of phasic dopamine signaling in senescent male rats does not impact dopamine-dependent Pavlovian conditioning
Authors: Sandberg Stefan G. , Sanford Christina A. , Phillips Paul E. M.
Published: December 2023

Normal aging is associated with cognitive decline which impacts financial decision making. One of the underlying features of decision making is probability estimation, in which nucleus accumbens dopamine signaling has been implicated. Here we used fast-scan cyclic voltammetry to probe for age differences in dopamine signaling, and pharmacological manipulation to test for age differences in the dopamine dependence of Pavlovian conditioning. We found differences in phasic dopamine signaling to reward delivery, and unconditioned and conditioned stimuli, but no difference in conditioned approach between adult and senescent groups. In addition, we found that dopamine receptor antagonism with flupenthixol (225 μg/kg, i.p.) partially inhibited conditioned approach in the adult group, whereas it completely blocked conditioned approach in the senescent group. Further increase in concentration to 300 μg/kg, i.p. resulted in complete inhibition of conditioned approach behavior in both age groups. Therefore, while phasic dopamine signaling in the nucleus accumbens of senescent animals is greatly diminished in concentration, these animals maintain dopamine dependent Pavlovian conditioning.
Early Jurassic origin of avian endothermy and thermophysiological diversity in Dinosauria
Authors: Chiarenza Alfio Alessandro , Cantalapiedra Juan L. , Jones Lewis A. , Gamboa Sara , Galván Sofía , Farnsworth Alexander J. , Valdes Paul J. , Sotelo Graciela , Varela Sara
Published: December 2023

A fundamental question in dinosaur evolution is how they adapted to substantial long-term shifts in Earth System during the Mesozoic and when they developed environmentally independent, avian-style acclimatization due to the evolution of an endothermic physiology. Combining fossil occurrences with macroevolutionary and paleoclimatic models, we unveil distinct evolutionary pathways in the main dinosaur lineages: ornithischians and theropods diversified across broader climatic landscapes, trending toward cooler niches. An Early Jurassic shift to colder climates in Theropoda suggests an early adoption of endothermic thermophysiology. Conversely, sauropodomorphs exhibited prolonged climatic conservatism associated with higher thermal conditions. Paleo-biome mapping emphasizes temperature, rather than plant productivity, as the primary driver of this pattern, suggesting poikilothermic physiology with a stronger dependence on higher temperatures in sauropods since the Early Jurassic.

One-Sentence Summary

Dinosaur climatic evolution reveals early endothermy emergence in theropods, ornithischians but heterotherm sauropodomorphs.
WNT Signalling Promotes NF-κB Activation and Drug Resistance in KRAS-Mutant Colorectal Cancer
Authors: Cong Bojie , Stamou Evangelia , Pennel Kathryn , Mckenzie Molly , Matly Amna , Gopinath Sindhura , Edwards Joanne , Cagan Ross
Published: December 2023

Approximately 40% of colorectal cancer (CRC) cases are characterized by KRAS mutations, rendering them insensitive to most CRC therapies. While the reasons for this resistance remain incompletely understood, one key aspect is genetic complexity: in CRC, oncogenic KRAS is most commonly paired with mutations that alter WNT and P53 activities (“RAP”). Here, we demonstrate that elevated WNT activity upregulates canonical (NF-κB) signalling in bothDrosophilaand human RAS mutant tumours. This upregulation required Toll-1 and Toll-9 and resulted in reduced efficacy of RAS pathway targeted drugs such as the MEK inhibitor trametinib. Inhibiting WNT activity pharmacologically significantly suppressed trametinib resistance in RAP tumours and more genetically complex RAP-containing ‘patient avatar’ models. WNT/MEK drug inhibitor combinations were further improved by targetingbrm,shg,ago,rhoGAPp190andupf1, highlighting these genes as candidate biomarkers for patients sensitive to this duel approach. These findings shed light on how genetic complexity impacts drug resistance and proposes a therapeutic strategy to reverse this resistance.
Colon Cancer Cells Evade Drug Action by Enhancing Drug Metabolism
Authors: Cong Bojie , Thakur Teena , Uribe Alejandro Huerta , Stamou Evangelia , Gopinath Sindhura , Maddocks Oliver , Cagan Ross
Published: December 2023

Colorectal cancer (CRC) is the second most deadly cancer worldwide. One key reason is the failure of therapies that target RAS proteins, which represent approximately 40% of CRC cases. Despite the recent discovery of multiple alternative signalling pathways that contribute to resistance, durable therapies remain an unmet need. Here, we use liquid chromatography/ mass spectrometry (LC/MS) analyses onDrosophilaCRC tumour models to identify multiple metabolites in the glucuronidation pathway—a toxin clearance pathway—as upregulated in trametinib-resistantRAS/APC/P53(“RAP”) tumours compared to trametinib-sensitiveRASG12Vtumours. Elevating glucuronidation was sufficient to direct trametinib resistance inRASG12Vanimals while, conversely, inhibiting different steps along the glucuronidation pathway strongly reversedRAPresistance to trametinib. For example, blocking an initial HDAC1-mediated deacetylation step with the FDA-approved drug vorinostat strongly suppressed trametinib resistance inDrosophila RAPtumours. We provide functional evidence that pairing oncogenic RAS with hyperactive WNT activity strongly elevates PI3K/AKT/GLUT signalling, which in turn directs elevated glucose and subsequent glucuronidation. Finally, we show that this mechanism of trametinib resistance is conserved in anKRAS/APC/TP53mouse CRC tumour organoid model. Our observations demonstrate a key mechanism by which oncogenic RAS/WNT activity promotes increased drug clearance in CRC. The majority of targeted therapies are glucuronidated, and our results provide a specific path towards abrogating this resistance in clinical trials.s
Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants
Authors: Ke Zunlong , Peacock Thomas P. , Brown Jonathan C. , Sheppard Carol M. , Croll Tristan I. , Kotecha Abhay , Goldhill Daniel H. , Barclay Wendy S. , Briggs John A.G.
Published: December 2023

The evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins that are the major target for the adaptive immune response. Single-particle cryo-EM analysis of soluble S from SARS-CoV-2 variants has revealed this structural adaptation at high-resolution. The analysis of S trimers in situ on intact virions has the potential to provide more functionally relevant insights into S structure and virion morphology. Here, we characterized B.1, Alpha, Beta, Gamma, Delta, Kappa, and Mu variants by cryo-electron microscopy and tomography, assessing S cleavage, virion morphology, S incorporation, “in-situ” high-resolution S structures and the range of S conformational states. We found no evidence for adaptive changes in virion morphology, but describe multiple different positions in the S protein where amino acid changes alter local protein structure. Considered together, our data is consistent with a model where amino acid changes at multiple positions from the top to the base of the spike cause structural changes that can modulate the conformational dynamics of S.
Efficacy of Drpitor1a, a Dynamin-Related Protein 1 inhibitor, in Pulmonary Arterial Hypertension
Authors: Wu Danchen , Jansen-van Vuuren Ross D. , Dasgupta Asish , Al-Qazazi Ruaa , Chen Kuang-Hueih , Martin Ashley , Mewburn Jeffrey D. , Alizadeh Elahe , Lima Patricia D.A. , Jones Oliver , Colpman Pierce , Breault Nolan M. , Emon Isaac M. , Jedlovčnik Luka , Zhao Yuan Yuan , Wells Michael , Sutendra Gopinath , Archer Stephen L.
Published: December 2023

Rationale

Dynamin-related protein 1 (Drp1), a large GTPase, mediates mitochondrial fission. Increased Drp1-mediated fission permits accelerated mitosis, contributing to hyperproliferation of pulmonary artery smooth muscle cells (PASMC), which characterizes pulmonary arterial hypertension (PAH). We developed a Drp1 inhibitor, Drpitor1a, and tested its ability to regress PAH.

Objectives

Assess Drpitor1a’s efficacy and toxicity in: a)normal and PAH human PASMC (hPASMC); b)normal rats versus rats with established monocrotaline (MCT)-induced PAH.

Methods

Drpitor1a’s effects on recombinant and endogenous Drp1-GTPase activity, mitochondrial fission, and cell proliferation were studied in hPASMCs (normal=3; PAH=5). Drpitor1a’s pharmacokinetics and tissue concentrations were measured (n=3 rats/sex). In a pilot study (n=3-4/sex/dose), Drpitor1a (1mg/kg/48-hours, intravenous) reduced adverse PA remodeling only in females. Consequently, we compared Drpitor1a to vehicle in normal (n=6 versus 8) and MCT-PAH (n=9 and 11) females, respectively. Drpitor1a treatment began 17-days post-MCT with echocardiography and cardiac catheterization performed 28-29 days post-MCT.

Results

Drpitor1a inhibited recombinant and endogenous Drp1 GTPase activity, which was increased in PAH hPASMC. Drpitor1a inhibited mitochondrial fission and proliferation and induced apoptosis, in PAH hPASMC but not normal hPASMC. Drpitor1a tissue levels were higher in female versus male RVs. In MCT-PAH females, Drpitor1a regressed PA obstruction, lowered pulmonary vascular resistance, and improved RV function, without hematologic, renal, or hepatic toxicity.

Conclusions

Drpitor1a inhibits Drp1 GTPase, reduces mitochondrial fission, and inhibits cell proliferation in PAH hPASMC. Drpitor1a caused no toxicity in MCT-PAH and had no significant effect on normal rats or hPASMCs. Drpitor1a is a potential PAH therapeutic which displays an interesting therapeutic sexual dimorphism.
A Novel Pathway Implicated in Regulating Cognitive disfunction in aDrosophilaAlzheimer’s Disease Model through Acer Inhibition and CG2233 Modulation
Authors: Ghalayini Judy , Lee Shin-Hann , Gluscencova Oxana , Iliadi Konstantin G. , Boulianne Gabrielle L.
Published: December 2023

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, accounting for most dementia cases worldwide. Current therapies for AD have limited effectiveness in slowing disease progression or delivering a cure. As such, there is an immediate need for ongoing research and innovative strategies to tackle this multifaceted disease. Recently, several studies have implicated the renin-angiotensin system (RAS), known to regulate blood pressure, as a possible therapeutic target for AD. RAS-inhibiting drugs, including angiotensin-converting enzyme inhibitors (ACE-Is), have been shown to reduce the incidence and progression of AD. However, the literature describing their beneficial effects is inconsistent, with contradictory findings reporting no effects. How these drugs may function in AD remains poorly understood. Our previous work inDrosophilamodels expressing AD-related transgenes investigated the benefits of captopril, an ACE-I, and found it effectively rescued AD-related phenotypes including cognitive performance independent of Aβ42 changes. Importantly, our study implicated Acer, a homolog of mammalian ACE, as a key player. In our current study, we demonstrate that the beneficial outcomes of Acer inhibition depend on preventing its catalytic activity and downstream target processing. We identify CG2233 as a prospective target and reveal its functional interaction with Acer. Furthermore, we show CG2233 is implicated in AD-related pathways in Aβ42 expressing flies. Together, these findings provide a new avenue to study the role of ACE in AD.

Significance Statement

AD is a devastating neurodegenerative disorder with limited therapeutic success. Emerging research highlights the potential of inhibiting the renin-angiotensin system (RAS) in AD. Epidemiological findings and experimental studies have shown promising outcomes with RAS-targeting drugs including angiotensin-converting enzyme inhibitors (ACE-Is). Our previous work inDrosophilaAD models revealed the efficacy of captopril, an ACE-I, in improving AD-related phenotypes. Moreover, we identified Acer as a key player in these mechanisms. Our current study further elucidates the role of Acer, identifies CG2233 as a potential target, and uncovers their functional interaction, shedding light on pathways relevant to AD phenotypes. This research underscores the significance of investigating ACE and ACE-I mechanisms in AD, offering potential innovative means for AD therapy.
Environmental DNA reveals fine scale spatial and temporal variation of prey species for marine mammals in a Scottish marine protected area
Authors: Boyse Elizabeth , Robinson Kevin P. , Beger Maria , Carr Ian M. , Taylor Morag , Valsecchi Elena , Goodman Simon J.
Published: December 2023

Marine mammal foraging grounds are popular focal points for marine protected area (MPA) implementation, but may be temporally dynamic, requiring continuous monitoring to infer prey availability and abundance. Marine mammal distributions are assumed to be driven by their prey in foraging areas, but limited understanding of prey distributions often prevents us from exploring how shifting prey availability impacts both seasonal and long-term marine mammal distributions. Environmental DNA (eDNA) metabarcoding could enhance understanding of marine mammal habitat use in relation to their prey through simultaneous monitoring of both. However, eDNA applications focused on marine mammals or predator-prey dynamics have been limited to date. In this study, we assess spatiotemporal changes in the availability and abundance of minke whale (Balaenoptera acutorostrata) prey species in a newly established MPA, employing eDNA metabarcoding. We recovered 105 molecular operational taxonomic units (OTUs) from marine vertebrates using two primer sets targeting 12S and 16S genes, along with 112 OTUs from a broader eukaryotic primer set targeting 18S rRNA. Overall, key forage fish prey species, sandeels and clupeids, were the most abundant teleost fishes detected, although their availability varied temporally and with distance from shore. We also found clear spatial partitioning between coastal bottlenose dolphins and the more pelagic minke whales and harbour porpoises, paralleling availability of their main prey species. Other species of conservation interest were also detected including the critically endangered European eel (Anguilla anguilla), blue fin tuna (Thunnus thynnus), and the invasive pink salmon (Oncorhynchus gorbuscha). This study demonstrates the application of eDNA to detect spatiotemporal trends in the occurrence and abundance of cetacean predators and their prey, furthering our understanding of fine-scale habitat use within MPAs. Future, long-term monitoring of predator-prey dynamics with eDNA could improve our ability to predict climate-induced shifts in foraging grounds and enhance rapid responses with appropriate management actions.