bluuebunny/crossref_metadata_2025 huggingface dataset:
Addressing the challenges of estimating the target population in calculation of routine infant immunization coverage in Kenya
Authors: Karanja-Chege Christine , Agweyu Ambrose , Were Fred , van Hensbroek Michael Boele , Ogallo William
Published: February 2025

Target population estimation for immunization coverage calculations through extrapolation of annual births from census data is often inaccurate. This study aimed to evaluate the accuracy of the traditional census extrapolation method in comparison with three alternative approaches: the Cohort-Component Population Projections Method (CCPPM), using the Expanded Program on Immunisation (EPI) numerator as a denominator, and estimates derived from first antenatal care clinic (ANC1) visits.

We obtained target population estimates from 1999 - 2023 using all 4 methods with data for ANC1 available only for 2020-2023. We assessed the accuracy of the estimates for 2003 to 2018 by computing the Mean Absolute Error (MAE), Mean Absolute Percentage Error (MAPE) and the Pearson Correlation Coefficient (r), excluding outliers. A sub-analysis for the period 2020-2023 included ANC1 data.

The CCPPM method had the largest population estimates while the census-based method had pronounced discontinuities at the census years. The CCPPM method compared to the DTP1 doses was associated with the greatest error magnitude (MAE = 212917.19 and MAPE = 18.18) while the DTP1 doses and census-based methods showed the smallest error (MAE = 44317.16 and MAPE = 3.77). Sub-analysis of target populations for the period 2020-2023 showed similar upward trends except for the census-based method which exhibited a relatively flat and significantly divergent trajectory. Comparison between the ANC1 and DTP1 doses showed the strongest linear correlation (r = 1.00).

The results reveal significant inaccuracies in the current target population estimation methods which may have serious implications on immunisation coverage assessments. Immunisation programs should utilise diverse sources of data and triangulate results to approximate the true population. Additionally, there is an urgent need to come up with innovative approaches to estimating the target populations for immunisation.
Progression of biological markers in spinocerebellar ataxia type 3: analysis of longitudinal data from the ESMI cohort
Authors: Berger Moritz , Garcia-Moreno Hector , Ferreira Monica , Hubener-Schmid Jeannette , Schaprian Tamara , Wegner Philipp , Elter Tim , Teichmann Kennet , Santana Magda M , Grobe-Einsler Marcus , Onder Demet , Koyak Berkan , Bernsen Sarah , Pereira de Almeida Luís , Silva Patrick , Ribeiro Joana Afonso , Cunha Inês , Gonzalez-Robles Cristina , Khan Shamsher , Heslegrave Amanda , Zetterberg Henrik , Lima Manuela , Raposo Mafalda , Ferreira Ana F. , Vasconcelos João , van de Warrenburg Bart P. , van Gaalen Judith , van Prooije Teije H. , de Vries Jeroen , Schols Ludger , Riess Olaf , Synofzik Matthis , Timmann Dagmar , Thieme Andreas , Erdlenbruch Friedrich , Infante Jon , Pelayo Ana Lara , Manrique Leire , Reetz Kathrin , Dogan Imis , Oz Gulin , Joers James M. , Bushara Khalaf , Onyike Chiadikaobi , Povazan Michal , Jacobi Heike , Schmahmann Jeremy D , Ratai Eva-Maria , Schmid Matthias , Giunti Paola , Klockgether Thomas , Faber Jennifer
Published: February 2025

Background

Spinocerebellar ataxia type 3 (SCA3) is an autosomal dominantly inherited adult-onset disease. We aimed to describe longitudinal changes in clinical and biological findings and to identify predictors for clinical progression.

Methods

We used data from participants enrolled in the ESMI cohort collected between Nov 09, 2016 and July 18, 2023. The data freeze included data from 14 sites in five European countries and the United States. We assessed ataxia with the Scale for the Assessment and Rating of Ataxia (SARA). We measured disease-specific mutant ataxin-3 protein (ATXN3) and neurofilament light chain (NfL) in plasma and performed MRIs. Data were analysed by regression modelling on a timescale defined by onset. The onset of abnormality of a marker was defined as the time at which its value, as determined by modelling, exceeded the mean ±2 SD of healthy controls. To study responsiveness of markers, we determined the sensitivity to change ratios (SCSs).

Results

Data from 291 SCA3 mutation carriers before and after clinical onset and 121 healthy controls were included. NfL levels became abnormal more than 20 years (-21.5 years [95% CI n.d. –9.5]) before onset. The earliest MRI abnormality was volume loss of medulla oblongata (-4.7 years [95% CI n.d. – 3.3]). The responsiveness of markers depended on the disease stage. Across all stages, pons volume had the highest responsiveness with an SCS of 1.35 [95% CI 1.11 – 1.78] exceeding that of SARA (0.99 [95% CI 0.88 – 1.11]). Lower age (p=0.0459) and lower medulla oblongata volume (p<0.0001) were predictors of SARA progression.

Conclusion

Our study provides quantitative information on the progression of biological markers in SCA3 mutation carriers before and after onset of ataxia, and allowed the identification of predictors for clinical progression. Our data could prove useful for the design of future clinical trials.
Clinical relevance of zebrafish for gene variants testing. Proof-of-principle withSMN1/SMA
Authors: Stringer Brett W. , Zhang Yougang , Taghipour-Sheshdeh Afsaneh , Goh Shuxiang , Kölbel Heike , Farrar Michelle A , Wirth Brunhilde , Giacomotto Jean
Published: February 2025

Spinal muscular atrophy (SMA) results fromSMN1gene loss-of-function (LOF), with disease severity directly linked to the level of remaining SMN protein. Nusinersen, risdiplam and onasemnogene abeparvovec are revolutionary treatments but should ideally be implemented before clinical symptoms appear. Because of this, prenatal and newborn screenings are increasingly used to identify commonSMN1mutations and patients requiring therapy. However, for novel mutations, clinicians lack robust analytic tools to predict pathogenicity before irreversible damage occurs.

To address this gap, we deployed a zebrafish model presentingsmn1-LOF, exhibiting progressive motor defects and death by only six days of age. We evaluated twoSMN1-variants (VUS) identified in newborn patients awaiting definite diagnosis and treatment recommendations.

We demonstrated that while known pathogenic variants did not change the disease course, wild-typeSMN1and both patient variants rescued SMA hallmarks in zebrafish, demonstrating the relevance of this approach for VUS-testing within a crucial timeframe for patients. Both VUS turned out to be non-pathogenic, and therapeutic costs of >US$2 million per child were avoided.

Beyond SMA, this study provides robust proof-of-principle that the zebrafish represents a powerful translational tool for VUS-analysis, and that such approaches should be considered in clinical settings for supporting diagnosis and treatment decisions.
Sources of non-uniform coverage in short-read RNA-Seq data
Authors: Brooks Thomas G , Lahens Nicholas F , Mrčela Antonijo , Yang Jianing , Purohit Souparna , Naik Amruta , Ricciotti Emanuela , Sengupta Shaon , Choi Peter , Grant Gregory R
Published: February 2025

Many normal functions and pathologies trace back to RNA splicing. As such, RNA splicing is currently the focus of a vast array of studies. To quantify the transcriptome, short read RNA-Seq remains the standard assay. The primary technical artifact of RNA-Seq library prep, which severely interferes with analysis, is extreme non-uniformity in coverage across transcripts. This non-uniformity is present in both bulk and single-cell RNA-Seq and is observed even when the sample contains only full-length transcripts. This issue dramatically affects the accuracy of isoform-level quantification of multi-isoform genes. Understanding the sources of this non-uniformity is critical to developing improved protocols and analysis methods. Here we explore eight potential sources of non-uniformity. We demonstrate that the non-uniformity cannot be explained one factor alone. We performed targeted experiments to investigate the effect of fragment length, ramp rate and ribosomal depletion and we assessed existing data sets with varying sample quality, PCR cycle count, reverse transcriptases, and technical or biological replicates. We argue that, in spite of widespread belief, interference of reverse transcription by secondary structure is unlikely to be the major contributing factor here.
Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids
Authors: Robles Nemo V. , Moran Ben M. , Rodríguez-Barrera María José , Jofre Gaston I. , Gunn Theresa , Iverson Erik N.K. , Beskid Sofia , Baczenas JJ , Sedghifar Alisa , Andolfatto Peter , Powell Daniel L. , Brandvain Yaniv , Havird Justin C. , Rosenthal Gil G , Schumer Molly
Published: February 2025

How barriers to gene flow arise between closely related species is one of the oldest questions in evolutionary biology. Classic models in evolutionary biology predict that negative epistatic interactions between variants in the genomes of diverged lineages, known as hybrid incompatibilities, will reduce viability or fertility in hybrids. The genetic architecture of these interactions and the evolutionary paths through which they arise have profound implications for the efficacy of hybrid incompatibilities as barriers to gene flow between species. While these questions have been studied using theoretical approaches for several decades, only recently has it become possible to map larger numbers of hybrid incompatibilities empirically. Here, we use admixture mapping in natural hybrid populations of swordtail fish (Xiphophorus) to identify genetic incompatibilities involving interactions between the mitochondrial and nuclear genomes. We find that at least nine regions of the genome are involved in mitonuclear incompatibilities that vary in their genetic architecture, the strength of selection they experience, and the degree to which they limit gene flow in natural hybrid populations. Our results build a deeper understanding of the complex architecture of selection against incompatibilities in naturally hybridizing species and highlight an important role of mitonuclear interactions in the evolution of reproductive barriers between closely related species.
Müllerian mimicry in Neotropical butterflies: One mimicry ring to bring them all, and in the jungle bind them
Authors: Pérochon Eddie , Rosser Neil , Kozak Krzysztof , McMillan W. Owen , Huertas Blanca , Mallet James , Ready Jonathan , Willmott Keith , Elias Marianne , Doré Maël
Published: February 2025

Understanding the mechanisms underlying species distributions and coexistence is essential to predict and prevent the impacts of global change, particularly in biodiversity hotspots. However, the effects of biotic interactions may be challenging to investigate at large spatial scales. Leveraging well-characterized Müllerian mimetic systems in Neotropical butterflies, we investigated spatial patterns of mutualistic mimetic interactions within and between two tribes of aposematic Nymphalid butterflies: the Heliconiini (Heliconiinae) and the Ithomiini (Danainae). Despite 85 My of independent evolutionary histories, many species share similar warning wing patterns across the Neotropics.

In this study we show that both tribes form similar biodiversity hotspots with a high prevalence of rare species and mimetic patterns in the tropical Andes. However, we reveal a higher relative richness of heliconiine butterflies than ithomiines in the Amazon basin contrasting with the Andean concentration of ithomiine diversity. Despite this difference in broadscale diversity patterns, we also document large-scale spatial associations among phenotypically similar species within and between tribes, thereby providing new empirical evidence for Fritz Müller’s historical model of mutualistic mimicry at a continental scale. Furthermore, comparative phylogenetic analyses suggest that co-mimetic species within and between tribes have converged towards similar climatic niches as a response to selection favoring co-occurrence.

Our findings illustrate the strength of mutualistic interactions in shaping biodiversity patterns at continental scale and in supporting niche convergence even across millions of years of evolution. Critically, it also emphasizes the pervasive vulnerability of mimetic communities, bound by positive interactions, to disassembly induced by climate change.

Significance statement

Müllerian mimicry is a remarkable example of convergent evolution driven by natural selection where coexisting prey species converge in their warning signal advertising their defenses to predators. Heliconiine and ithomiine butterflies found throughout Neotropical rainforests were instrumental in Fritz Müller’s historical model, which provided the mechanism for such resemblance. Leveraging decades of fieldwork and museum collections, we show that species with similar color patterns present strikingly similar spatial distributions, regardless of how closely related they are. Such co-occurrence appears reinforced by the evolution of similar climatic requirements among look-alike species. Our findings emphasize the key role of mutualistic interactions in shaping large-scale patterns of biodiversity and supporting convergence in the climatic niches of species spanning across phylogenetically distant clades.
Modelling the willingness to pay for honey: the role of sensory characteristics and EEG neurometrics
Authors: Zaripova Julia , Semenova Daria , Provorova Anna , Kulikova Sofya
Published: February 2025

It is currently unclear which honey attributes are most important for consumers and, more importantly, from an economic perspective, for which of them consumers are willing to pay for. The aim of this study was to examine the role of sensory attributes in consumers’ willingness to pay for honey. The study was performed in two steps. First, we ran a behavioural experiment in which 25 participants were asked to blindly taste and evaluate 21 sensory attributes of 7 different flower honey samples. Based on the obtained data, we conducted a factor analysis and aggregated all sensory attributes into 6 factors, which were used in the second part of the study during a neuromarketing experiment. The neuromarketing experiment involved another 25 respondents who also blindly tasted honey, evaluated its 6 sensory characteristics (corresponding to the 6 above-mentioned factors), as well as their willingness to pay, the perceived quality and taste of the samples. While the respondents were evaluating honey samples, their brain activity was recorded using an electroencephalograph (EEG). Based on the obtained data, the willingness to pay was modeled using a linear regression, which has demonstrated that consumers’ willingness to pay for honey is significantly influenced by the taste of honey, the perceived quality indicated by various sensory characteristics, the male gender, and the brain activity in the frontal areas.
Digging into the general dynamic model: Island ontogeny predicts shifting micro-evolutionary processes in a Mascarene flowering plant radiation
Authors: Mashburn Brock , Linan Alexander G. , Le Péchon Timothée , Sevathian Jean Claude , Olsen Kenneth M. , Edwards Christine E.
Published: February 2025

Abstract

Island studies have been integral in the development of process-oriented biodiversity models such as the general dynamic model (GDM) of oceanic island biogeography. While empirical tests of the GDM primarily come from phylogeographic studies, tests incorporating comprehensive population-level sampling of island radiations are rare. In this study, we elucidate the evolutionary processes driving the diversification ofHibiscussectionLilibiscusin the Mascarene archipelago using population-level sampling and 2bRAD sequencing. Our goals were to: 1) assess species relationships and resolve taxonomic issues; 2) test patterns of intra- and interspecific genetic differentiation under a model of shifting speciation processes as islands age; and 3) utilize demographic modeling to infer the relative divergence times of populations in the archipelago. We found the Mascarene radiation of sect.Lilibiscusto be monophyletic and confirmed the presence of six morphologically distinct species. Species richness and phylogenetic relationships supported the expectations of the GDM. Namely, we found that morphologically similar populations of the same species on the intermediate-aged island, Mauritius, diverged earlier and showed greater divergence than morphologically disparate species on the youngest Mascarene island, Réunion. These patterns are consistent with the hypothesis that ecological selection may be affecting speciation on the youngest island, drift may be the most important force on the middle-aged island. Although not tested here, given that the oldest island is in a late stage of subsidence, extinction may be the most important evolution force occurring on the oldest island, consistent with the expectation that evolutionary processes occurring across each of these islands may be influenced by ontogenetic stage. We also found evidence that some species in the group may be naturally rare, suggesting that the rarity of species may not only be from recent habitat loss. Our study is the first to use population-level data to test complex predictions of the GDM and demonstrate that the most important evolutionary processes shift depending on island ontogeny.
Genome-scale transcriptome augmentation duringArabidopsis thalianaphotomorphogenesis
Authors: Schivre Geoffrey , Wolff Léa , Mirasole Filippo Maria , Armanet Elodie , Davidson Mhairi L. H. , Vidal Adrien , Cuménal Delphine , Dumont Marie , Bourge Mickael , Baroux Célia , Bourbousse Clara , Barneche Fredy
Published: February 2025

Plant photomorphogenesis is a light-induced developmental switch that combines massive reprogramming of gene expression and a general enhancement in RNA Polymerase II activity. Yet, transcriptome analyses have failed to demonstrate a clear tendency toward gene upregulation. To solve this conundrum, we optimized a spike-in RNA-seq experimental and analysis pipeline and reconciled transcriptome dynamics with epigenomic and cytogenetic observations. We found that light induces a two-fold expansion of the transcriptome duringArabidopsis thalianacotyledon photomorphogenesis, with 94% of the 9,128 differentially expressed genes being upregulated within the first six hours. Transcriptome augmentation was further detected at a similar strength in spike-free RNA-seq datasets from independent laboratories renormalized using stable genes that mimic the spike-in information. On this new basis, reinterpretation of light-mediated gene regulatory pathways revealed a quasi-exclusive positive effect of HY5 and other key light-induced transcription factors at target genes. This new standpoint unveiled the unilateral impact of light on the transcriptome of Arabidopsis cotyledons at the genome scale and opens new avenues for investigating global genome regulation during plant developmental and environmental responses.
Metabolic reprogramming in the spinal cord drives the transition to pain chronicity
Authors: Tagne Alex Mabou , Fotio Yannick , Lee Hye-Lim , Jung Kwang-Mook , Katz Jean , Ahmed Faizy , Le Johnny , Bazinet Richard , Jang Cholsoon , Piomelli Daniele
Published: February 2025

Acute injuries can progress into painful states that endure long after healing. The mechanism underlying this transition remains unclear, but metabolic adaptations to the bioenergy demands imposed by injury are plausible contributors. Here we show that peripheral injury activates AKT/mTORC1 in afferent segments of the mouse spinal cord, redirecting local core metabolism toward biomass production while simultaneously suppressing autophagy-mediated biomass reclamation. This metabolic shift supports neuroplasticity, but creates a resource bottleneck that depletes critical spinal cord nutrients. Preventing this depletion with a modified diet normalizes biomass generation and autophagy and halts the transition to chronic pain. This effect, observed across multiple pain models, requires activation of the nutrient sensors, sirtuin-1 and AMPK, as well as restoration of autophagy. The findings identify metabolic reprogramming as a key driver of the progression to pain chronicity and point to nutritional and pharmacological interventions that could prevent this progression after surgery or other physical traumas.
No Evidence of Anti-influenza Nucleoprotein Antibodies in Retail Milk from Across Canada (April – July 2024)
Authors: Wallace Hannah L. , Wight Jordan , Rzeszutek Gabriela J. , Jafri Mustafa S. , Baz Mariana , Dowding Barbara , Flamand Louis , Hobman Tom , Jean François , Joy Jeffrey B. , Lang Andrew S. , MacParland Sonya , McCormick Craig , Noyce Ryan , Russell Rodney S. , Sagan Selena M. , Snyman Jumari , Bogoch Isaac I. , Rasmussen Angela L. , Rimoin Anne W. , Kindrachuk Jason
Published: February 2025

Following reports of HPAI H5N1 infections of dairy cattle in the United States (US) in March 2024, we established a Pan-Canadian Milk network to monitor retail milk in Canada. Milk samples from across Canada that had previously tested negative for influenza A virus (IAV) RNA were tested for the presence of anti-IAV nucleoprotein (NP) antibodies, as an indicator of past infection of dairy cattle. None of the 109 milk samples tested had evidence of anti-IAV NP antibodies. This is consistent with previous findings from our academic group as well as others including federal testing initiatives that have not found any IAV RNA in milk. Although not surprising given that no cases of H5N1 in cattle have been reported in Canada to date, this work further supports that the extensive outbreak in dairy cattle in the US has not extended northward into Canada, and the integrity of the Canadian milk supply remains intact.
Characterisation ofDMPKand MBNL1 expression in cell models of Myotonic Dystrophy: A platform for drug screening
Authors: López-Martínez Andrea , Martín-González Sergio , Torres-Conde Noemi , Alcalá-Manso Nahia , Al-Ani Abdullah , López de Munain Adolfo , Bigot Anne , Mamchaoui Kamel , Nogales-Gadea Gisela , Arechavala-Gomeza Virginia
Published: February 2025

Myotonic dystrophy type I (DM1) is caused by CTG repeat expansions in theDMPKgene leading to mRNA toxicity and sequestration of the splicing regulator MBNL1, affecting many tissues. We have developed anin vitroscreening platform based on ddPCR and in-cell western to quantify these mRNAs and proteins and characterised more than 20 cell models to define DM1 biomarkers that could be useful for drug screening. DMPK protein levels were reduced in DM1-immortalised myoblasts and myotubes, but not in fibroblasts, while MBNL1 protein was consistently lower in all DM1 myogenic cultures, whether primary or immortalised. Myogenic differentiation of cultures led to an increase inDMPKmRNA expression, which was translated into increased MBNL1 sequestration in foci. We further corroborated the platform’s ability to assess therapeutic outcomes, evaluating the effect of a DMPK gapmer ASO and one siRNA: while the gapmer increased MBNL1 protein levels, the siRNA had no significant effect on MBNL1 release. Our platform and the in-depth characterisation of some of the most used models would be of use to the DM1 research community.

Significance statement

Myotonic dystrophy type I (DM1) is a multisystemic disease with a complex pathogenesis and multiple outcome measures for drug assessmentin vitro. In the last years, the increasing number of new potential therapies targeting DM1 in clinical trials has increased the need for robust and rapid evaluation of preclinical candidates, as well as in-depth knowledge of the cell models used. Here, we present a new cell-based platform that enables robust quantification of DMPK and MBNL1 in cell culture for cell model characterisation and drug screening. Indeed, we highlight the differences observed in DMPK and MBNL1 protein quantification in primary fibroblasts and myotubes, immortalised fibroblasts, myoblasts and myotubes. We then, we performed a proof-of-concept drug evaluation of potential therapeutic strategies targeting DMPK, showing the most suitable for targeting theDMPKexpanded transcript.
Proteasome Inhibition Enhances Lysosome-mediated Targeted Protein Degradation
Authors: Elshazly Ahmed M. , Hosseini Nayyerehalsadat , Shen Shanwei , Neely Victoria , Harada Hisashi , Grant Steven , Radhakrishnan Senthil K.
Published: February 2025

Proteasome inhibitor drugs are currently used in the clinic to treat multiple myeloma and mantle cell lymphoma. These inhibitors cause accumulation of undegraded proteins, thus inducing proteotoxic stress and consequent cell death. However, cancer cells counteract this effect by activating an adaptive response through the transcription factor Nuclear factor erythroid 2-related factor 1 (NRF1, also known as NFE2L1). NRF1 induces transcriptional upregulation of proteasome and autophagy/lysosomal genes, thereby reducing proteotoxic stress and diminishing the effectiveness of proteasome inhibition. While suppressing this protective autophagy response is one potential strategy, here we investigated whether this heightened autophagy could instead be leveraged therapeutically. To this end, we designed an autophagy-targeting chimera (AUTAC) compound to selectively degrade the anti-apoptotic protein Mcl1 via the lysosome. Our results show that this lysosome-mediated targeted degradation is significantly amplified in the presence of proteasome inhibition, in a NRF1-dependent manner. The combination of the proteasome inhibitor carfilzomib and Mcl1 AUTAC synergistically promoted cell death in both wild-type and proteasome inhibitor-resistant multiple myeloma and lung cancer cells. Thus, our work offers a novel strategy for enhancing proteasome inhibitor efficacy by exploiting the adaptive autophagy response. More broadly, our study establishes a framework for amplifying lysosome-mediated targeted protein degradation, with potential applications in cancer therapeutics and beyond.
Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): Multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis
Authors: Tanca Alessandro , Schallert Kay , Grenga Lucia , Peters Samantha L. , Abbondio Marcello , De Diego Laura , Deledda Maria Antonietta , Haange Sven-Bastiaan , Miotello Guylaine , Sáenz Johan S. , Wolf Maximilian , Bastida Felipe , Devos Simon , Hernandez-Raquet Guillermina , Seifert Jana , Wilmes Paul , Van Den Bossche Tim , Kunath Benoit J. , Heyer Robert , Jehmlich Nico , Benndorf Dirk , Hettich Robert L. , Armengaud Jean , Uzzau Sergio
Published: February 2025

Background

Fecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. Fecal metaproteomics provides valuable insights by tracking changes in the relative abundance of microbial taxa and their protein functions. To ensure reliable results, it is crucial to minimize alterations in the metaproteome occurring from sample collection to protein extraction. Therefore, employing effective stabilization methods is essential to preserve the integrity of the fecal metaproteome from sample collection to laboratory analysis, particularly over long distances or when rapid freezing options are not readily available. In line with these needs, the second edition of the Critical Assessment of MetaProteome Investigation (CAMPI-2) was specifically focused on improving sample stabilization prior to metaproteomic analysis.

Results

This collaborative multicenter study assessed the ability of five different stabilization methods, based on two commercial devices and three specific reagents (acetone, lithium dodecyl sulfate, and an RNAlater-like buffer), respectively, to stabilize the fecal metaproteome during room-temperature storage (14 days) and shipment to mass spectrometry facilities. The five methods were tested simultaneously by eight different laboratories across Europe, using aliquots from the same fecal sample. After protein extraction and digestion, duplicate aliquots of the resulting peptides were analyzed independently by two mass spectrometry facilities at distinct international locations. Analysis of the mass spectrometric data using two different search engines revealed that the fecal metaproteome profile differed considerably depending on the stabilization method used in terms of richness, alpha and beta diversity, reproducibility, and quantitative distribution of main taxa and functions. Although each method showed unique strengths and weaknesses, a commercial swab-based device stood out for its remarkable reproducibility and ranked highest for most of the metrics measured.

Conclusions

CAMPI-2 allowed a robust evaluation of five different methods for preserving fecal metaproteome samples. The present investigation provides useful data for the design of metaproteomics and multi-omics studies where fecal sampling cannot be immediately followed by long-term storage at −80°C. Further optimization of the tested protocols is necessary to improve stabilization efficiency and control bias in the taxonomic and functional profile of the gut microbiome.
Promoter-Driven Modulation of Flagellin Expression and Motility inEscherichia coli
Authors: Bayana Karima Bharati , Wang Xinyue
Published: February 2025

Synthetic biology offers powerful tools to engineer biological systems for diverse applications. However, key challenges persists before achieving real-world applications like environmental bioremediation or therapeutic microrobots for targeted drug delivery. This study aimed to precisely control bacterial movement by modulating gene expression using engineered promoters in Escherichia coli. We focused on Escherichia coli, a model organism, and manipulated its motility by engineering the expression of flagellin, a crucial protein for bacterial movement. To achieve this, specific genetic promoters were employed to regulate the production of flagellin, thereby dictating the movement capabilities of these bacteria. The promoters enabled targeted adjustments to flagellin expression, which in turn allowed for the enhancement or suppression of bacterial locomotion. Interestingly, the relationship between promoter design parameters and gene expression levels was non-linear, highlighting complex underlying dynamics. Optimal bacterial motility occurred at 30°C, illustrating the influence of environmental factors. Our findings demonstrate the ability to effectively regulate complex microbial phenotypes like motility using genetic engineering strategies. The results not only extend our understanding of bacterial gene regulation but also highlight the transformative potential of synthetic biology in creating functional and adaptable microbial phenotypes for diverse biotechnological applications.

Abstract Figure
Adaptive strategies of Caribbean sponge holobionts beyond the mesophotic zone
Authors: Paix Benoît , Thivet Alexane , Domingos Celso , Erol Özlem , van der Windt Niels , Choi Young H. , de Voogd Nicole J.
Published: February 2025

Marine sponges and their microbiomes function together as holobionts, playing essential roles in ecosystem dynamics and exhibiting remarkable adaptability across depth gradients. This study utilized a multi-omics approach, integrating microbiome and metabolome analyses, to investigate adaptive strategies in sponge holobionts inhabiting the mesophotic (80-125 m), upper-rariphotic (125-200 m), and lower-rariphotic (200-305 m) zones of Curaçao. We hypothesized that depth-related environmental factors drive distinct adaptive strategies, similar to patterns observed in fish and coral assemblages.

Results revealed major differences in holometabolomes and microbial communities between Demospongiae and Hexactinellida sponges, reflecting class-specific adaptive strategies. Notably, phospholipid homeoviscous adaptation to temperature and pressure emerged as a key mechanism in phosphorus metabolism. Adaptations in nitrogen metabolism were linked to diverse ammonia oxidizing archaea (AOA) symbionts, and dissolved organic matter cycling. Hexactinellid microbiomes exhibited intra-specific heterogeneity; however, species-specific associations with AOA symbionts such asCenarchaeumandNitrosopumiluswere observed. Additionally, the lower-rariphotic hexactinellid holometabolomes highlighted the significance of the nested ecosystem concept through the identification of secondary metabolites produced by their associated fauna (aphrocallistins by zoanthids, and xanthurenic acid by shrimp).

This study highlights the ecological significance of sponge holobionts in mesophotic and rariphotic ecosystems, revealing diverse adaptations to unique physicochemical conditions and biotic interactions.
TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and -independent mitophagy
Authors: Levi-D’Ancona Elena , Walker Emily M. , Zhu Jie , Deng Yamei , Sidarala Vaibhav , Stendahl Ava M. , Reck Emma C. , Henry-Kanarek Belle A. , Lietzke Anne C. , Pasmooij Mabelle B. , Hubers Dre L. , Basrur Venkatesha , Ghosh Sankar , Stiles Linsey , Nesvizhskii Alexey I. , Shirihai Orian S. , Soleimanpour Scott A.
Published: February 2025

Activation of innate immune signaling occurs during the progression of immunometabolic diseases, including type 2 diabetes (T2D), yet the impact of innate immune signaling on glucose homeostasis is controversial. Here, we report that the E3 ubiquitin ligase TRAF6 integrates innate immune signals following diet-induced obesity to promote glucose homeostasis through the induction of mitophagy. Whereas TRAF6 was dispensable for glucose homeostasis and pancreatic β-cell function under basal conditions, TRAF6 was pivotal for insulin secretion, mitochondrial respiration, and increases in mitophagy following metabolic stress in both mouse and human islets. Indeed, TRAF6 was critical for the recruitment and function of machinery within both the ubiquitin-mediated (Parkin-dependent) and receptor-mediated (Parkin-independent) mitophagy pathways upon metabolic stress. Intriguingly, the effect of TRAF6 deficiency on glucose homeostasis and mitophagy was fully reversed by concomitant Parkin deficiency. Thus, our results implicate a role for TRAF6 in the cross-regulation of both ubiquitin- and receptor- mediated mitophagy through the restriction of Parkin. Together, we illustrate that β-cells engage innate immune signaling to adaptively respond to a diabetogenic environment.
Polyamine biosynthesis dysregulation in Alzheimer’s disease and Down syndrome cellular models
Authors: Sola Andres , Sandberg Alex , Pham Caitlin , Revier Alexandra , Hebinck Mia , Penney Alexandra , Caviedes Pablo , Kumar Sunil , Granholm Ann-Charlotte , Linseman Daniel A. , Paredes Daniel A.
Published: February 2025

BACKGROUND

Individuals with Down Syndrome (DS) frequently develop early onset Alzheimer’s disease (AD) with pathological hallmarks closely resembling AD due to several triplicated genes on chromosome 21. Polyamines are small, organic molecules that play a pivotal role for growth and differentiation, and a dysregulation of polyamine pathways is implicated in AD pathology. However, their role in DS-associated AD is unclear.

METHODS

We analyzed polyamines and their metabolite levels in mouse hippocampal cells and human DS-AD and AD hippocampal tissue and assessed the effects of the ODC inhibitor difluoromethylornithine (DFMO) on Aβ42 aggregation and protein expression in DS fibroblasts.

RESULTS

Amyloid-β42 increased polyamine levels via ornithine decarboxylase (ODC) activation in a dose-dependent manner. DFMO reduced Aβ42 aggregation, decreased amyloid precursor protein (APP) levels, and normalized proteins linked to AD pathology in DS fibroblasts. Polyamine levels were elevated in DS-AD hippocampal tissue, with colocalization of ODC and Aβ42 aggregates.

CONCLUSION

These findings suggest that polyamine biosynthesis may exacerbate Aβ42 toxicity and APP expression, contributing to AD progression in DS. The ability of DFMO to reduce Aβ42 aggregation and restore protein homeostasis presents the polyamine pathway as a therapeutic target for DS-AD management.
Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene
Authors: Kothe Jennifer A.F. , Sauerwein Till , Dietz Theresa , Scheuer Robina , Elhossary Muhammad , Barth-Weber Susanne , Wähling Jan , Förstner Konrad U. , Evguenieva-Hackenberg Elena
Published: February 2025

The Gram-negative, soil-dwelling plant symbiontSinorhizobium melilotishares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analyzed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. Instead, upregulated genes were mostly first in operons and often small, while downregulated genes were downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the begin of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene.
Mapping the GDF15 Arm of the Integrated Stress Response in Human Cells and Tissues
Authors: Smith Janell LM , Tanner Kamaryn , Devine Jack , Monzel Anna S , Cohen Alan A , Picard Martin
Published: February 2025

Mitochondrial stress activates the integrated stress response (ISR) and triggers cell-cell communication through secretion of the metabokine growth differentiation factor 15 (GDF15). However, the gene network underlying the ISR remains poorly defined, particularly across metabolically diverse cellular states and tissues. Using RNAseq data from fibroblasts subjected to metabolic perturbations, we develop anISRGDF15indexquantifying the GDF15 arm of the ISR activation in human cells. Validation ofISRGDF15indexacross 44 postmortem human tissues illustrates how this index can be applied to investigate tissue-specific and age-related ISR activation.
Regulation of early-stage tomato fruit growth by the splicing factor RS2Z36
Authors: Vraggalas Stavros , Rosenkranz Remus RE , Keller Mario , Pérez-Pérez Yolanda , Bachiri Samia , Zehl Kerstin J , Bold Jessica , Simm Stefan , Ghatak Arindam , Weckwerth Wolfram , Afjehi-Sadat Leila , Chaturvedi Palak , Testillano Pilar S , Müller-McNicoll Michaela , Zarnack Kathi , Fragkostefanakis Sotirios
Published: February 2025

Fruit size and shape are determined by cell division and expansion. In tomato, the model plant for fleshy fruit development, both processes are associated with changes in gene expression, including transcription and RNA processing. While several transcription factors have been identified as regulators of genes involved in fruit development, the contribution of splicing regulators remains unknown. Profiling of RNA splicing-related genes revealed stage-preferential expression of several factors, including RS2Z36, a serine/arginine-rich splicing factor highly expressed during the early stages of fruit development. Mutations in RS2Z36 lead to smaller ellipsoid fruits than the wild type, with histological analysis showing elongated pericarp cells in the ovaries along the longitudinal axis. RNA-seq analysis uncovered numerous alternatively spliced genes involved in different biological processes. Complementary proteome analysis identified proteins with altered abundance and peptides corresponding to novel RNA splice isoforms, underscoring the role of RS2Z36 in shaping both transcriptome and proteome diversity. Immunofluorescence screening of cell wall proteins further demonstrated an increased abundance of LM6-recognized arabinan epitopes of rhamnogalacturonan-I pectins and arabinogalactan protein (AGP) epitopes inrs2z36.1pericarp cells compared to the wild type. These findings highlight RS2Z36 as a critical regulator of alternative splicing, impacting fruit development through diverse transcriptome and proteome changes.
Discovery of a distinct BAM complex in the Bacteroidetes
Authors: Silale Augustinas , Madej Mariusz , Mikruta Katarzyna , Frey Andrew M. , Hart Adam J. , Baslé Arnaud , Scavenius Carsten , Enghild Jan J. , Trost Matthias , Hirt Robert P. , van den Berg Bert
Published: February 2025

The BAM (β-barrel assembly machinery) complex is an evolutionarily conserved, multiprotein machine that catalyses the folding and membrane insertion of newly synthesised β-barrel outer membrane (OM) proteins in Gram-negative bacteria. Based on Proteobacteria, bacterial BAM is also structurally conserved, with an essential BamAD core and up to three auxiliary periplasmic lipoproteins of poorly defined function. Here we show, using structural biology, quantitative proteomics and functional assays, that the BAM complex is radically different within the Bacteroidetes, a large and important phylum widely distributed within the environment and animal microbiomes. Cryogenic electron microscopy (cryo-EM) structures of BAM complexes from the human gut symbiontBacteroides thetaiotaomicronand the human oral pathogenPorphyromonas gingivalisshow similar, seven-component complexes of ∼325 kDa in size with most of the mass in the extracellular space. In addition to canonical BamA and BamD, the complexes contain an integral OM protein named BamF that is essential and intimately associated with BamA, as well as four surface-exposed lipoproteins (SLPs) named BamG-J. Together, BamF-J form a large, extracellular dome that likely serves as an assembly cage for the β-barrel-SLP complexes that are a hallmark of the Bacteroidetes. Our data suggest that BAM functionality in Bacteroidetes is substantially expanded from that in Proteobacteria and underscores the importance of studying other phyla for a more complete understanding of fundamental biological processes.
Progesterone regulation of cervix ripening in preterm and term birth
Authors: Yellon Steven M. , Ward Daylan , Thompson Ashley , Vazquez Brigitte M. , Daniel Baldwin D. , Oldford Elaine J. , Kirby Michael A.
Published: February 2025

The cervix functions both as gatekeeper barrier to maintain pregnancy and virtually vanish for birth at term in mammals. The period of remodeling well-before term is characterized by an inflammatory process associated with reduced cell nuclei density and cross-linked collagen, as well as increased density of resident macrophages in cervix stroma. Contemporarily, progesterone (P4) is at or near peak concentrations in maternal circulation. The functional or actual loss of response to P4 is thought to drive the process that enhances uterine contractile activity for labor and parturition at term. The objective of the present study was to determine if actual or functional loss of P4 regulated cytomorphological characteristics associated with prepartum cervix ripening at term and with preterm birth. On day 16 of pregnancy. Ovaries were removed to eliminate the main source of P4 production and a silastic capsule implanted (with vehicle or P4, Ovx or Ovx+P4, respectively).

Controls received a vehicle-filled capsule, while a P4 capsule was implanted into an addition group of Intact mice to ensure sustained concentrations throughout pregnancy (Intact+P4). Pups were born in controls at term (days 19-20 postbreeding), but deliveries were preterm in Ovx mice within 24h (day 17). In the Ovx+P4 group, births were delayed to term and post-term in most Intact+P4 mice with adverse pregnancy outcomes commonplace. Characteristics of cell nuclei and degradation of cross-linked collagen were advanced with preterm birth in Ovx mice compared to controls that gave birth by at term. Treatment of Ovx mice with P4 blocked preterm birth, but parturition was complicated by dystocia. In addition, P4 given to ovary-intact mice sustained peak pregnancy concentrations, but had minimal effects on cytoarchitecture of the prepartum cervix stroma except term birth was forestalled with dystocia and fetal morbidity. Density of resident macrophages in the cervix stroma in term Ovx+P4 mice was reduced along with area of macrophage stain versus postpartum controls. Thus, analyses of cervix cellular cytoarchitecture provided useful biomarkers of local inflammation to assessment the ripening process for preterm and term parturition. Collectively, findings suggest a functional loss of prepartum cervix responses to progesterone are part of a final common mechanism for parturition across mammals.

Loss of response to progesterone withdrawal is associated with cervix ripening while some cytoarchitectural characteristics of remodeling are regulated to block preterm birth and dystocia at term
VIP interneurons control hippocampal place cell remapping through transient disinhibition in novel environments.
Authors: Neubrandt Mate , Lenkey Nora , Vervaeke Koen
Published: February 2025

Hippocampal place cells dynamically reorganize their activity, or 'remap', to encode novel spatial environments, a process tightly regulated by inhibitory networks. Here, we identify vasoactive intestinal peptide (VIP)-expressing interneurons as key regulators of this plasticity. Using all-optical methods in mice navigating virtual reality, we show that novel environments trigger a transient increase in VIP interneuron activity, which facilitates rapid place field formation and stable spatial map construction. Bidirectional optogenetic manipulation -suppressing or upregulating VIP interneuron activity- modulates the speed of spatial map formation and alters signatures of behavioral timescale plasticity (BTSP), a mechanism critical for place field induction. Both insufficient and excessive VIP interneuron activity impair reward-seeking behavior specifically in novel environments, revealing that a precise balance of VIP activity is essential for spatial learning. Our findings demonstrate that VIP interneurons gate a temporal window for place cell plasticity, mediating the impact of environmental novelty on hippocampal remapping and spatial memory.