bluuebunny/crossref_metadata_2025 huggingface dataset:
Association analysis of mitochondrial DNA heteroplasmic variants: methods and application
Authors: Sun Xianbang , Bulekova Katia , Yang Jian , Lai Meng , Pitsillides Achilleas N. , Liu Xue , Zhang Yuankai , Guo Xiuqing , Yong Qian , Raffield Laura M. , Rotter Jerome I. , Rich Stephen S. , Abecasis Goncalo , Carson April P. , Vasan Ramachandran S. , Bis Joshua C. , Psaty Bruce M. , Boerwinkle Eric , Fitzpatrick Annette L. , Satizabal Claudia L. , Arking Dan E. , Ding Jun , Levy Daniel ,   TOPMed mtDNA working group, Liu Chunyu
Published: January 2024

We rigorously assessed a comprehensive association testing framework for heteroplasmy, employing both simulated and real-world data. This framework employed a variant allele fraction (VAF) threshold and harnessed multiple gene-based tests for robust identification and association testing of heteroplasmy. Our simulation studies demonstrated that gene-based tests maintained an appropriate type I error rate at α=0.001. Notably, when 5% or more heteroplasmic variants within a target region were linked to an outcome, burden-extension tests (including the adaptive burden test, variable threshold burden test, and z-score weighting burden test) outperformed the sequence kernel association test (SKAT) and the original burden test. Applying this framework, we conducted association analyses on whole-blood derived heteroplasmy in 17,507 individuals of African and European ancestries (31% of African Ancestry, mean age of 62, with 58% women) with whole genome sequencing data. We performed both cohort- and ancestry-specific association analyses, followed by meta-analysis on bothpooled samples and within each ancestry group. Our results suggest that mtDNA-Enco ded genes/regions are likely to exhibit varying rates in somatic aging, with the notably strong associations observed between heteroplasmy in theRNR1andRNR2genes (p<0.001) and advance aging by the Original Burden test. In contrast, SKAT identified significant associations (p<0.001) between diabetes and the aggregated effects of heteroplasmy in several protein-coding genes. Further research is warranted to validate these findings. In summary, our proposed statistical framework represents a valuable tool for facilitating association testing of heteroplasmy with disease traits in large human populations.
Systematic proteomics in Autosomal dominant Alzheimer’s disease reveals decades-early changes of CSF proteins in neuronal death, and immune pathways
Authors: Shen Yuanyuan , Ali Muhammad , Timsina Jigyasha , Wang Ciyang , Do Anh , Western Daniel , Liu Menghan , Gorijala Priyanka , Budde John , Liu Haiyan , Gordon Brian , McDade Eric , Morris John C. , Llibre-Guerra Jorge J. , Bateman Randall J. , Joseph-Mathurin Nelly , Perrin Richard J. , Maschi Dario , Wyss-Coray Tony , Pastor Pau , Goate Alison , Renton Alan E. , Surace Ezequiel I. , Johnson Erik C. B. , Levey Allan I. , Alvarez Ignacio , Levin Johannes , Ringman John M. , Allegri Ricardo Francisco , Seyfried Nicholas , Day Gregg S. , Wu Qisi , Fernández M. Victoria ,   Dominantly Inherited Alzheimer Network, Ibanez Laura , Sung Yun Ju , Cruchaga Carlos
Published: January 2024

Background

To date, there is no high throughput proteomic study in the context of Autosomal Dominant Alzheimer’s disease (ADAD). Here, we aimed to characterize early CSF proteome changes in ADAD and leverage them as potential biomarkers for disease monitoring and therapeutic strategies.

Methods

We utilized Somascan® 7K assay to quantify protein levels in the CSF from 291 mutation carriers (MCs) and 185 non-carriers (NCs). We employed a multi-layer regression model to identify proteins with different pseudo-trajectories between MCs and NCs. We replicated the results using publicly available ADAD datasets as well as proteomic data from sporadic Alzheimer’s disease (sAD). To biologically contextualize the results, we performed network and pathway enrichment analyses. Machine learning was applied to create and validate predictive models.

Findings

We identified 125 proteins with significantly different pseudo-trajectories between MCs and NCs. Twelve proteins showed changes even before the traditional AD biomarkers (Aβ42, tau, ptau). These 125 proteins belong to three different modules that are associated with age at onset: 1) early stage module associated with stress response, glutamate metabolism, and mitochondria damage; 2) the middle stage module, enriched in neuronal death and apoptosis; and 3) the presymptomatic stage module was characterized by changes in microglia, and cell-to-cell communication processes, indicating an attempt of rebuilding and establishing new connections to maintain functionality. Machine learning identified a subset of nine proteins that can differentiate MCs from NCs better than traditional AD biomarkers (AUC>0.89).

Interpretation

Our findings comprehensively described early proteomic changes associated with ADAD and captured specific biological processes that happen in the early phases of the disease, fifteen to five years before clinical onset. We identified a small subset of proteins with the potentials to become therapy-monitoring biomarkers of ADAD MCs.

Funding

Proteomic data generation was supported by NIH: RF1AG044546
Predictors of Developing Renal Dysfunction Following Diagnosis of Transthyretin Cardiac Amyloidosis
Authors: McDonald Malcolm L , Manla Yosef , Sonnino Alice , Alonso Mileydis , Neicheril Radhika K , Sanchez Alejandro , Lafave Gabrielle , De Armas Yelenis Seijo , Camargo Antonio Lewis , Uppal Dipan , Handa Armaan , Wolinsky David , Thakkar Rivera Nina , Velez Mauricio , Baran David , Estep Jerry D. , Snipelisky David
Published: January 2024

Background

In patients with transthyretin cardiac amyloidosis (ATTR-CA), renal dysfunction is a poor prognostic indicator. Limited data are available on variables that portend worsening renal function (wRF) among ATTR-CA patients.

Objectives

This study assesses which characteristics place patients at higher risk for the development of wRF (defined as a drop of ≥ 10% in GFR) within the first year following diagnosis of ATTR-CA.

Methods

We included patients with ATTR-CA (n=134) evaluated between 2/2016 and 12/2022 and followed for up to one-year at our amyloid clinic. Patients were stratified into two groups: a group with maintained renal function (mRF) and a group with wRF and compared using appropriate testing. Significant variables in the univariate analysis were included in the multivariable logistic regression model to determine characteristics associated with wRF.

Results

Within a follow-up period of 326±118 days, the median GFR% change measured -6% [-18%, +8]. About 41.8% (n=56) had wRF, while the remainder had mRF. In addition, in patients with no prior history of CKD, 25.5% developed de-novo CKD. On multivariable logistic regression, only NYHA class ≥III (OR: 3.9, 95% CI [1.6-9.3]), history of IHD (OR:0.3, 95% CI [0.1-0.7]), and receiving SGLT-2i (OR: 0.1, 95% CI [0.02-0.5]) were significant predictors of wRF.

Conclusion

Our study demonstrated that the development of new or worsening renal dysfunction is common following the diagnosis of ATTR-CA. Additionally, we identified worse NYHA class and no prior history of IHD as significant predictors associated with developing wRF, while receiving SGLT2i therapy appeared to be protective in this population.
NSE5 subunit interacts with distant regions of the SMC arms in thePhyscomitrium patensSMC5/6 complex
Authors: Vaculíková Jitka , Holá Marcela , Králová Barbora , Lelkes Edit , Štefanovie Barbora , Vágnerová Radka , Angelis Karel J. , Paleček Jan J.
Published: January 2024

Structural Maintenance of Chromosome (SMC) complexes play roles in cohesion, condensation, replication, transcription, and DNA repair. Their cores are composed of SMC proteins with a unique structure consisting of an ATPase head, long arm, and hinge. SMC complexes form long rod-like structures, which can change to ring-like and elbow-bent conformations upon binding ATP, DNA and other regulatory factors. These SMC dynamic conformational changes are involved in their loading, translocation, and DNA loop extrusion. Here, we examined the binding and role of the PpNSE5 regulatory factor ofPhyscomitrium patensPpSMC5/6 complex. We found that the PpNSE5 C-terminal half (aa230-505) is required for binding to its PpNSE6 partner, while the N-terminal half (aa1-230) binds PpSMC subunits. Specifically, the first 71 amino acids of PpNSE5 were required for binding to PpSMC6. Interestingly, the PpNSE5 binding required the PpSMC6 head-proximal joint region and PpSMC5 hinge-proximal arm, suggesting a long distance between binding sites on PpSMC5 and PpSMC6 arms. Given the long distance between these PpSMC sites and the size of PpNSE5, we hypothesize that PpNSE5 either links two antiparallel SMC5/6 complexes or binds one SMC5/6 in elbow-bent conformation.

In addition, we generated theP. patensmutant lines (Ppnse5KO1andPpnse5KO2) with CRISPR/Cas9-integrated stop codons in PpNSE5. ThePpnse5KO1mutant line with an N-terminally truncated version of PpNSE5 (starting from an alternative aaMet72) exhibited DNA repair defects while keeping a normal number of rDNA repeats. As the first 71 amino acids of PpNSE5 are required for PpSMC6 binding, our results suggest the specific role of PpNSE5-PpSMC6 interaction in DNA repair. Altogether, our study suggests that PpNSE5 binding to distant regions of the PpSMC5 and PpSMC6 arms serves a specific role in loading at DNA lesions.
Targeted intracellular delivery of molecular cargo to hypoxic human breast cancer stem cells
Authors: Makela Ashley V , Tundo Anthony , Liu Huiping , Schneider Doug , Hermiston Terry , Khodakivskyi Pavlo , Goun Elena , Contag Christopher H
Published: January 2024

Cancer stem cells (CSCs) drive tumorigenesis, are responsible for metastasis, and resist conventional therapies thus posing significant treatment challenges. CSCs reside in hypoxic tumor regions and therefore, effective therapies must target CSCs within this specific microenvironment. CSCs are characterized by limited distinguishable features, however, surface displayed phosphatidylserine (PS) appears to be characteristic of stem cells and offers a potential target. GlaS, a truncated coagulation protein that is internalized after binding PS, was investigated for intracellular delivery of molecular payloads to CSCs. Intracellular delivery via GlaS was enhanced in patient-derived CD44+ mammary CSCs under hypoxic conditions relative to physoxia or hyperoxia.In vivo, GlaS successfully targeted hypoxic tumor regions, and functional delivery of molecular cargo was confirmed using luciferin conjugated to GlaS via a disulfide linkage (GlaS-SS-luc), which releases luciferin upon intracellular glutathione reduction. Bioluminescence imaging demonstrated effective GlaS-mediated delivery of luciferin, a model drug, to CSCs in culture andin vivo. These findings offer the promise of directed delivery of therapeutic agents to intracellular targets in CSCs.
Training interoceptive awareness with real-time haptic vs. visual heartbeat feedback
Authors: Dobrushina Olga , Tamim Yossi , Wald Iddo Yehoshua , Maimon Amber , Amedi Amir
Published: January 2024

The perception of signals from within the body, known as interoception, is increasingly recognized as a prerequisite for physical and mental health. The study is dedicated to the development of effective technological approaches for enhancing interoceptive awareness. We provide evidence of the effectiveness and practical feasibility of a novel real-time haptic heartbeat supplementation technology combining principles of biofeedback and sensory enhancement. In a randomized controlled study, we applied the developed naturalistic haptic feedback on a group of 30 adults, while another group of 30 adults received more traditional real-time visual heartbeat feedback. A single session of haptic, but not visual heartbeat feedback resulted in increased interoceptive accuracy and confidence, as measured by the heart rate discrimination task, and in a shift of attention towards the body. Participants rated the developed technology as more helpful and pleasant than the visual feedback, thus indicating high user satisfaction. The study highlights the importance of matching sensory characteristics of the feedback to the natural bodily prototype. Our work suggests that real-time haptic feedback might be a superior approach to strengthen mind-body interaction in interventions for physical and mental health.

Highlights

We developed a naturalistic real-time haptic feedback system for enhancing cardiac interoception.

The intervention resulted in higher interoceptive accuracy and confidence, and in a shift of attention towards the body.

Haptic feedback outperformed traditional visual feedback in efficacy and user satisfaction.

Results of the study indicate the importance of feedback sensory characteristics in mind-body technologies.
Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis inC. elegans
Authors: Kiontke Karin , Herrera R. Antonio , Mason D. Adam , Woronik Alyssa , Vernooy Stephanie , Patel Yash , Fitch David H. A.
Published: January 2024

Caenorhabditis elegansmales undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs.dmd-3(-)males and hermaphrodites. The transcription profile ofdmd-3(-)tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the UPR (unfolded protein response) pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.
Sexually dimorphic effects of Amylin 1 receptor activation in trigeminovascular neurons
Authors: Labastida-Ramírez Alejandro , Rubio-Beltran Eloisa , Holland Philip R. , Hoffmann Jan
Published: January 2024

Background

Migraine is more prevalent in women, and although the mechanisms involved in this disparity remain poorly understood, an interaction between the trigeminovascular system and cycling estrogen levels in biologically-predisposed women has been suggested. We investigated the role of amylin 1 (AMY1) receptor activation in the modulation of the trigeminal nociceptive system in female rats across the estrous cycle in cycle stages with falling and rising estrogen levels and compared these to the responses in males.

Methods

We recorded neuronal activityin vivowithin the trigeminocervical complex (TCC) and examined the effects of targeting AMY1receptors on ongoing spontaneous and dural stimulus-evoked firing rates of trigeminovascular neurons. The selective AMY1receptor agonist pramlintide and AMY1receptor antagonist AC 187 were used. Estrous cycle stages were identified via cytology from vaginal smears.

Results

Administration of pramlintide increased the spontaneous activity and dural stimulus-evoked neuronal responses in the TCC, only during falling estrogen phases of the female estrous cycle. Moreover, the administrationper seof AC 187 decreased spontaneous evoked firing rates of central trigeminovascular neurons in females and males, whereas pretreatment with AC 187 prevented pramlintide-induced increases in spontaneous activity and dural stimulus-evoked responses in females with falling estrogen levels.

Conclusion

AMY1receptors modulate the trigeminal nociceptive system. The facilitating effect is most pronounced in female rats during falling estrogen phases of the estrous cycle. Our data also supports selective AMY1receptor antagonists as potentially effective targets for the treatment of migraine.
Seed coating with phages for sustainable plant biocontrol of plant pathogens and influence of the seed coat mucilage
Authors: Erdrich Sebastian H. , Schurr Ulrich , Frunzke Julia , Arsova Borjana
Published: January 2024

Pathogens resistant to classical control strategies are on the rise and cause significant damage in crop yield production with seeds as one major transmission route. Bacteriophages are specialized viruses of bacteria and their interaction with seeds holds great potential as targeted and sustainable solution to this problem. In this study, we isolated and characterized two novel phages, Athelas and Alfirin, infectingPseudomonas syringaeandAgrobacterium tumefaciens, respectively, and included the recently published phage Pfeifenkraut infectingXanthomonas translucens. The three phages were tested for their interaction with the seed coat mucilage. Phage binding onArabidopsisseeds, which exude the mucilage as a polysaccharide-polymer-matrix, was assessed by comparison to seeds with removed mucilage. Two of the three phages were dependant on mucilage for seed binding, and podophage Athelas showed the highest dependency. Further podoviruses of theAutographiviridaeobtained from the systematicE. coli(BASEL) phage collection were tested and showed a similar dependency on the mucilage for seed adhesion. Comparative analysis using a set ofArabidopsisseed coat mutants revealed the diffusible cellulose fraction as important component for phage binding. Long-term activity tests revealed a high stability of phages on seed surfaces and phage coating effectively increased the survival rate of plant seedling in the presence of the pathogen. Utilization of non-virulent host strains was further successfully applied to boost the presence of infectious phage particles on seed surfaces. Altogether, our study highlights the high potential of phage-based applications as sustainable biocontrol strategy on the seed level.
PyLossless: A non-destructive EEG processing pipeline
Authors: Huberty Scott , Desjardins James , Collins Tyler , Elsabbagh Mayada , O’Reilly Christian
Published: January 2024

EEG recordings are typically long and contain large amounts of data, making manual cleaning a time-consuming and error-prone task. Automated pre-processing pipelines can facilitate the efficient and objective extraction of artifacts, enabling standardized and reproducible analyses. However, automated pre-processing pipelines typically remove data considered artifact, and return a subset of irreversibly transformed signals. This approach obfuscates pre-processing decisions, and often makes it impossible to recover the original data or modify the pre-processing steps. Further, it complicates collaboration between research teams working on a common dataset, because different analyses may require specific pre-processing routines. Given the large amount of resources that are devoted to collecting EEG, tools that can help efficiently and transparently pre-process data are greatly needed. PyLossless addresses this need by creating a non-destructive, automated pre-processing pipeline that maintains the continuous EEG structure. It offers a user-friendly API, it is well documented, tested through continuous integration, easily deployable, and integrates with the popular MNE-Python environment. The pipeline further provides a browser-based quality control review (QCR) dashboard that allows researchers to visualize and edit the automated artifact annotations on sensors, time-periods, and independent components. The end product of PyLossless is a lossless annotated data state that can be shared and used with analysis-specific artifact rejection policies, allowing for an optimal balance between flexibility and standardization.
Seasonal dynamics and drivers of microbial communities in a temperate dimictic lake: insights from metabarcoding and machine learning
Authors: Michał Karlicki , Anna Bednarska , Paweł Hałakuc , Kacper Maciszewski , Anna Karnkowska
Published: January 2024

Microbial communities, consisting of prokaryotes and protists, play a central role in ecological processes in aquatic environments. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and to track spatio-temporal dynamics in both marine and freshwater environments. While previous research has primarily focused on marine ecosystems, it is important to study microbial communities in freshwater environments, which are characterised by high diversity and susceptibility to rapid environmental change. In temperate lakes, despite extensive research on temporal changes in physico-chemical factors and microscopic studies of plankton, there is a notable research gap regarding their eukaryotic microbial communities. Our study fills this gap by investigating the diversity and seasonal changes of prokaryotic and eukaryotic communities in Lake Roś (Poland), a representative temperate lake characterised by two mixing episodes in spring and autumn and pronounced stratification in summer. Our metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. To decipher the drivers of the seasonal communities, we used machine learning and statistical methods and identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the community composition in Lake Roś are temperature, oxygen and silicon concentration. Understanding these community structures and the underlying factors is crucial in the context of climate change, which might affect mixing patterns and lead to prolonged stratification. Given the pronounced seasonal shifts observed in these communities, we can anticipate that climate change will profoundly impact the functioning of temperate dimictic lakes.
Altered firing output of VIP interneurons and early dysfunctions in CA1 hippocampal circuits in the 3xTg mouse model of Alzheimer’s disease
Authors: Michaud Felix , Francavilla Ruggiero , Topolnik Dimitry , Iloun Parisa , Tamboli Suhel , Calon Frederic , Topolnik Lisa
Published: January 2024

Alzheimer’s disease (AD) leads to progressive memory decline, and alterations in hippocampal function are among the earliest pathological features observed in human and animal studies. GABAergic interneurons (INs) within the hippocampus coordinate network activity, among which type 3 interneuron-specific (I-S3) cells expressing vasoactive intestinal polypeptide and calretinin play a crucial role. These cells provide primarily disinhibition to principal excitatory cells (PCs) in the hippocampal CA1 region, regulating incoming inputs and memory formation. However, it remains unclear whether AD pathology induces changes in the activity of I-S3 cells, impacting the hippocampal network motifs. Here, using young adult 3xTg-AD mice, we found that while the density and morphology of I-S3 cells remain unaffected, there were significant changes in their firing output. Specifically, I-S3 cells displayed elongated action potentials and decreased firing rates, which was associated with a reduced inhibition of CA1 INs and their higher recruitment during spatial decision-making and object exploration tasks. Furthermore, the activation of CA1 PCs was also impacted, signifying early disruptions in CA1 network functionality. These findings suggest that altered firing patterns of I-S3 cells might initiate early-stage dysfunction in hippocampal CA1 circuits, potentially influencing the progression of AD pathology.

Significance

This study examines VIP interneurons in the CA1 hippocampus affected by Alzheimer’s disease (AD) pathology. While these cells maintain their structural integrity, they exhibit altered firing patterns in young adult 3xTg-AD mice. These changes might correlate with enhanced CA1 inhibition and impact the activation of principal cells. These findings shed light on early dysfunction in hippocampal circuits as a potential mechanism of AD pathology and offer insights into prospective therapeutic targets.
Different outcomes of endurance and resistance exercise in skeletal muscles of Oculopharyngeal muscular dystrophy
Authors: Boulinguiez Alexis , Dhiab Jamila , Crisol Barbara , Muraine Laura , Gaut Ludovic , Rouxel Corentin , Flaire Justine , Mouigni Hadidja-Rose , Lemaitre Mégane , Giroux Benoit , Audoux Lucie , SaintPierre Benjamin , Ferry Arnaud , Mouly Vincent , Butler-Browne Gillian , Negroni Elisa , Malerba Alberto , Trollet Capucine
Published: January 2024

Background

Exercise is widely considered to have beneficial impact on skeletal muscle aging. In addition, there are also several studies demonstrating a positive effect of exercise on muscular dystrophies. Oculopharyngeal muscular dystrophy (OPMD) is a late-onset autosomal dominant inherited neuromuscular disorder caused by mutations in thePAPBN1gene. These mutations consist in short (1-8) and meiotically stable GCN trinucleotide repeat expansions in its coding region responsible for the formation of PAPBN1 intranuclear aggregates. This study aims to characterize the effects of two types of chronic exercise, resistance and endurance, on the OPMD skeletal muscle phenotype using a relevant murine model of OPMD.

Methods

In this study, we tested two protocols of exercise. In the first, based on endurance exercise, FvB (wild-type) and A17 (OPMD) mice underwent a 6-week-long motorized treadmill protocol consisting in 3 sessions per week of running 20cm/s for 20 minutes. In the second protocol, based on resistance exercise generated by chronic mechanical overload (OVL), surgical removal of gastrocnemius and soleus muscles was performed, inducing hypertrophy of the plantaris muscle. In both types of exercise, muscles of A17 and FvB mice were compared to those of respective sedentary mice. For all the groups, force measurement, muscle histology and molecular analyses were conducted.

Results

Following the endurance exercise protocol, we did not observe any major changes in the muscle physiological parameters, but an increase in the number of PABPN1 intranuclear aggregates and enhanced collagen deposition in the exercised A17 OPMD mice. In the resistance overload protocol, we also observed an increased collagen deposition in the A17 OPMD mice which was associated with larger muscle mass and fiber cross sectional area and increased absolute maximal force as well as a reduction in PABPN1 aggregate number.

Conclusions

Running exercise and mechanical overload led to very different outcome in skeletal muscles of A17 mice. Both types of exercise enhanced collagen deposition but while the running protocol increased aggregates, the OVL reduced them. More importantly OVL reversed muscle atrophy and maximal force in the A17 mice. Our study performed in a relevant model gives an indication of the effect of different types of exercise on OPMD muscle which should be further evaluated in humans for future recommendations as a part of the lifestyle of individuals with OPMD.
Single residues in the complexin N-terminus exhibit distinct phenotypes in synaptic vesicle fusion
Authors: Toulme Estelle , Murach Jacqueline , Bärfuss Simon , Kroll Jana , Malsam Jörg , Trimbuch Thorsten , Herman Melissa A. , Söllner Thomas H. , Rosenmund Christian
Published: January 2024

The release of neurotransmitters at central synapses is dependent on a cascade of protein interactions, specific to the presynaptic compartment. Amongst those dedicated molecules the cytosolic complexins play an incompletely defined role as synaptic transmission regulators. Complexins are multidomain SNARE complex binding proteins which confer both inhibitory and stimulatory functions. Using systematic mutagenesis and combining reconstitutedin vitromembrane fusion assays with electrophysiology in neurons, we deciphered the function of the N-terminus of complexin II (Cpx). The N-terminus (amino acid 1 - 27) starts with a region enriched in hydrophobic amino acids (1-12), which can lead to lipid binding. In contrast to mutants which maintain the hydrophobic character and the stimulatory function of Cpx, non-conservative exchanges largely perturbed spontaneous and evoked exocytosis. Mutants in the downstream region (amino acid 11-18) show differential effects. Cpx-A12W increased spontaneous release without affecting evoked release whereas replacing D15 with amino acids of different shapes or hydrophobic properties (but not charge) not only increased spontaneous release, but also impaired evoked release and surprisingly reduced the size of the readily releasable pool, a novel Cpx function, unanticipated from previous studies. Thus, the exact amino acid composition of the Cpx N-terminus fine tunes the degree of spontaneous and evoked neurotransmitter release.

Significance Statement

We describe in this work the importance of the N-terminal domain of the small regulatory cytosolic protein complexin in spontaneous and evoked glutamatergic neurotransmitter release at hippocampal mouse neurons. We show using a combination of biochemical, imaging and electrophysiological techniques that the binding of the proximal region of complexin (amino acids 1-10) to lipids is crucial for spontaneous synaptic vesicular release. Furthermore, we identify a single amino acid at position D15 which is structurally important since it not only is involved in spontaneous release but, when mutated, also decreases drastically the readily releasable pool, a function that was never attributed to complexin.
Wnt target gene Ascl4 is dispensable for skin appendage development
Authors: Papagno Verdiana , Sulic Ana-Marija , Satta Jyoti P. , Hoshiar Aida Kaffash , Kumar Vinod , Jernvall Jukka , Mikkola Marja L.
Published: January 2024

The development of skin appendages, including hair follicles, teeth and mammary glands is initiated through the formation of the placode – a local thickening of the epithelium. The Wnt/β-catenin signaling cascade is an evolutionary conserved pathway with an essential role in placode morphogenesis, but its downstream targets and their exact functions remain ill defined. In this study, we identifyAchaete-scute complex-like 4(Ascl4) as a novel target of the Wnt/β-catenin pathway and demonstrate its expression pattern in the signaling centers of developing hair follicles and teeth. Ascl transcription factors belong to the superfamily of basic helix-loop-helix transcriptional regulators involved in cell fate determination in many tissues. However, their specific role in the developing skin remains largely unknown. We report thatAscl4null mice have no overt phenotype. Absence of Ascl4 did not impair hair follicle morphogenesis or hair shaft formation suggesting that it is non-essential for hair follicle development. No tooth or mammary gland abnormalities were detected either. We suggest that other transcription factors may functionally compensate for the absence of Ascl4, but further research is warranted to assess this possibility.
Identification, structure and function of the methyltransferase involved in the biosynthesis of the dithiolopyrrolone antibiotic xenorhabdin
Authors: Su Li , Huber Eva M. , Westphalen Margaretha , Gellner Jonas , Bode Edna , Köbel Tania , Grün Peter , Alanjary Mohammad M. , Glatter Timo , Schindler Daniel , Groll Michael , Bode Helge B.
Published: January 2024

Xenorhabdins (XRDs) are produced byXenorhabdusspecies and are members of the dithiopyrrolone (DTP) class of natural products that have potent antibacterial, antifungal and anticancer activity. The amide moiety of their DTP core can be methylated or not to fine-tune the bioactivity properties. However, the enzyme responsible for the amideN-methylation remained elusive. Here, we identified and characterized the amide methyltransferase XrdM that is encoded nearly 600 kb away from the XRD gene cluster using proteomic analysis, methyltransferase candidate screening, gene deletion, and allied approaches. In addition, crystallographic analysis and site-directed mutagenesis proved that XrdM is completely distinct from the recently reported DTP methyltransferase DtpM, and that both have been tailored in a species-specific manner for DTP biosynthesis in Gram-negative/positive organisms. Our study expands the limited knowledge of post-NRPS amide methylation in DTP biosynthesis and reveals the evolution of two structurally completely different enzymes for the same reaction in different organisms.
Urban greenspace aerobiomes are shaped by soil conditions and land cover type
Authors: Brame Joel E. , Liddicoat Craig , Abbott Catherine A. , Cando-Dumancela Christian , Robinson Jake M. , Breed Martin F.
Published: January 2024

Growing evidence suggests that exposure to microbial biodiversity is important for human immunoregulation and health. Urban greenspaces harbour airborne bacterial communities (aerobiomes) with the potential to transfer beneficial bacteria to humans. However, limited studies have examined the ecological influences of soil, vegetation, and rainfall on aerobiomes in urban greenspaces. Here, we utilised 16S rRNA amplicon sequence data to analyse the effects of land cover, soil abiotic characteristics, surrounding vegetation diversity, and rainfall on aerobiome diversity and composition from 33 urban greenspace sites in Adelaide, South Australia. We sampled air and soil from two urban greenspace land cover types: highly-managed sports fields (n= 11) and minimally-managed nature parks (n= 22). Sports field aerobiomes had a distinct aerobiome community composition and higher alpha diversity than nature parks. Aerobiome alpha diversity was shaped more by soil abiotic characteristics, particularly soil pH and iron levels, than woody plant species diversity. Rainfall prior to sampling also had strong effects on the aerobiome community composition and associated with decreased alpha diversity. These findings point toward soil iron and pH management as pathways to increase aerobiome bacterial diversity. Our study shows that, with additional research, there is potential for greenspace managers and urban planners to target specific soil abiotic characteristics in urban greenspaces to improve microbiome-mediated urban health.
Dysregulated expanded endocannabinoid system as therapeutic targets of amyotrophic lateral sclerosis
Authors: Ito Daisuke , Iida Madoka , Iguchi Yohei , Hashizume Atsushi , Yamada Shinichiro , Kishimoto Yoshiyuki , Komori Shota , Shimamura Teppei , Takemoto Yuto , Nakatochi Masahiro , Akashi Tomohiro , Hinohara Kunihiko , Lee-Okada Hyeon-Cheol , Niwa Junichi , Sobue Gen , Tanaka Shinji , Takashina Ken , Yokomizo Takehiko , Katsuno Masahisa
Published: January 2024

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the selective loss of upper and lower motor neurons. ALS patients often manifest systemic metabolic abnormalities such as glucose intolerance. Herein, to elucidate the systemic metabolic changes related to ALS progression, we performed metabolomics analysis on the serum of ALS patients and identified several metabolites associated with the disease progression, including metabolites involved in the expanded endocannabinoid system (ECS). In particular, the levels of N-acyl taurines (NAT) were correlated with the longitudinal change in the revised ALS functional rating scale (ALSFRS-R) rating. In vitro experiments with ALS cell models and in vivo studies with SOD1G93Atransgenic mice revealed that PF-04457845, a fatty amide acid hydrolase (FAAH) inhibitor, up-regulated the expanded ECS, particularly the levels of NATs and N-acyl ethanolamine and ameliorates motor neuron degeneration through the regulation of microglial polarization, synapse plasticity, and neuronal development. Our study indicates that dysregulation of the expanded ECS is associated with ALS progression and a target for novel disease-modifying therapies.
Differential tissue deformability underlies shape divergence of the embryonic brain and spinal cord under fluid pressure
Authors: McLaren Susannah B.P. , Xue Shi-Lei , Ding Siyuan , Winkel Alex , Baldwin Oscar , Dwarakacherla Shreya , Franze Kristian , Hannezo Edouard , Xiong Fengzhu
Published: January 2024

An expanded brain enables the complex behaviours of vertebrates that promote their adaptation in diverse ecological niches1–3. Initial morphological differences between the brain and spinal cord emerge as the antero-posteriorly patterned neural plate folds to form the neural tube4–7during embryonic development. Following neural tube closure, a dramatic expansion of the brain diverges its shape from the spinal cord8, setting their distinct morphologies for further development9,10. How the brain and the spinal cord expand differentially remains unclear. Here, using the chicken embryo as a model, we show that the hindbrain expands through dorsal tissue thinning under a positive hydrostatic pressure from the neural tube lumen11,12while the dorsal spinal cord shape resists the same pressure. Using magnetic droplets and atomic force microscopy, we reveal that the dorsal tissue in the hindbrain is more fluid than in the spinal cord. The dorsal hindbrain harbours more migratory neural crest cells13and exhibits reduced apical actin and a disorganised laminin matrix compared to the dorsal spinal cord. Blocking the activity of neural crest-associated matrix metalloproteinases inhibited dorsal tissue thinning, leading to abnormal brain morphology. Transplanting early dorsal hindbrain cells to the spinal cord was sufficient to create a region with expanded brain-like morphology including a thinned-out roof. Our findings open new questions in vertebrate head evolution and neural tube defects, and suggest a general role of mechanical pre-pattern in creating shape differences in epithelial tubes.
The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells
Authors: Sugiyama Kota , Yoshioka Kazuma , Hayakawa Nao , Marutani Miyu , Masuda Ryo , Abadi Selma Alamanda , Ichisakino Maki , Seki Yoshiyuki
Published: January 2024

After fertilization, maternally deposited mRNA is cleared, andde novomRNA is transcribed from the zygotic genome through zygotic genome activation (ZGA), which is called maternal- to-zygotic transition (MZT) occurring in the mouse at 2-cell (2C) stage. 2C-like cells (2CLCs) marked by MERVL expression and transcriptionally similar to 2C embryos spontaneously emerge from mouse embryonic stem cells (mESCs). Although the emergence of 2CLCs completely depends on DUX function, a recent knockout study clearly showed that DUX is dispensable for mouse embryos, suggesting that DUX-independent molecular pathways are not recapitulated in 2CLCs. We present here that the disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates DUX-dependent and -independent molecular pathway associated with the development of early mouse embryos mediated by the upregulation of Preferentially expressed antigen of melanoma family-like 7 (PRAMEL7). Furthermore, the abnormality of the gene expression profile caused byDuxKO is partially rescued by the overexpression of PRAMEL7 in mESCs. Our study provides new insights into the DUX-independent molecular pathway for developing early mouse embryos.
Integrity assay for messenger RNA in mouse and human brain samples and synaptosomal preparations
Authors: Bujanauskiene Daina , Merkevicius Kajus , Kuliesiute Ugne , Denkovskij Jaroslav , Kutanovas Simonas , Luksys Gediminas , Rocka Saulius , Bernotiene Eiva , Neniskyte Urtė
Published: January 2024

Traditionally, RNA integrity evaluation is based on ribosomal RNAs (rRNAs). Nevertheless, gene expression studies are usually focused on protein coding messenger RNAs (mRNAs). As rRNA and mRNA have significant structural and functional differences, the assumption that rRNA integrity properly represents mRNA integrity may not be accurate. Moreover, contrary to whole tissue RNA samples, subcellular preparations such as synaptosomes contain almost no rRNA, thus prohibiting the use of traditional rRNA-based methods to assess sample RNA integrity. Here we present a RT-qPCR based assay, which estimates mRNA integrity by comparing the abundance of 3’ and 5’ mRNA fragments in a long constitutively expressed mouse or humanPGK1mRNA. The assay was tested and validated using plasmids with cloned 3’- and 5’-ends of thePGK1cDNA reflecting different ratios of 3’ and 5’ cDNA amplicons in partially degraded RNA samples. The accuracy of integrity score calculation was ensured by integrating a mathematical correction of qPCR results to account for the variable amplification efficiency of different primer pairs. The 5’:3’ assay was used to quantify RNA degradation in heat-degraded mouse and human brain tissue RNA as well as in clinical human brain RNA samples. Importantly, the expression of housekeeping genes correlated better with 5’:3’ integrity value than with the RIN. Finally, we were even able to use 5′:3′ assay to assess mRNA integrity in mouse synaptosomal preparations that lack rRNAs. We concluded that the 5’:3’ assay can be used as a reliable and sensitive method to evaluate mRNA integrity in mouse and human brain tissue and subcellular preparations.
Competitive fungal commensalism mitigates candidiasis pathology
Authors: Kralova Jarmila Sekeresova , Donic Catalina , Dassa Bareket , Livyatan Ilana , Jansen Paul Mathias , Ben-Dor Shifra , Fidel Lena , Trzebanski Sébastien , Narunsky-Haziza Lian , Asraf Omer , Brenner Ori , Dafni Hagit , Jona Ghil , Boura-Halfon Sigalit , Stettner Noa , Segal Eran , Brunke Sascha , Pilpel Yitzhak , Straussman Ravid , Zeevi David , Bacher Petra , Hube Bernhard , Shlezinger Neta , Jung Steffen
Published: January 2024

The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here we report the identification of a new fungal commensal,Kazachstania heterogenicavar.weizmannii,isolated from murine intestines.K. weizmanniiexposure preventedCandida albicanscolonization and significantly reduced the commensalC. albicansburden in colonized animals. Following immunosuppression ofC. albicanscolonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealedK. weizmanniipresence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management ofC. albicans-mediated diseases.
A genuinely hybrid, multiscale 3D cancer invasion and metastasis modelling framework
Authors: Katsaounis Dimitrios , Harbour Nicholas , Williams Thomas , Chaplain Mark , Sfakianakis Nikolaos
Published: January 2024

We introduce in this paper substantial enhancements to a previously proposed hybrid multiscale cancer invasion modelling framework to better reflect the biological reality and dynamics of cancer. These model updates contribute to a more accurate representation of cancer dynamics, they provide deeper insights and enhance our predictive capabilities.

Key updates include the integration of porous medium-like diffusion for the evolution of Epithelial-like Cancer Cells and other essential cellular constituents of the system, more realistic modelling of Epithelial-Mesenchymal Transition and Mesenchymal-Epithelial Transition models with the inclusion of Transforming Growth Factor beta within the tumour microenvironment, and the introduction of Compound Poisson Process in the Stochastic Differential Equations that describe the migration behaviour of the Mesenchymal-like Cancer Cells. Another innovative feature of the model is its extension into a multi-organ metastatic framework. This framework connects various organs through a circulatory network, enabling the study of how cancer cells spread to secondary sites.
Recurrent Evolutionary Innovations in Rodent and PrimateSchlafenGenes
Authors: Mordier Joris , Fraisse Marine , Cohen-Tannoudji Michel , Molaro Antoine
Published: January 2024

SCHLAFEN proteins are a large family of RNase-related enzymes carrying essential immune and developmental functions. Despite these important roles,Schlafengenes display varying degrees of evolutionary conservation in mammals. While this appears to influence their molecular activities, a detailed understanding of these evolutionary innovations is still lacking. Here, we used in depth phylogenomic approaches to characterize the evolutionary trajectories and selective forces shaping mammalianSchlafengenes. We traced lineage-specificSchlafenamplifications and found that recent duplicates evolved under distinct selective forces, supporting repeated sub-functionalization cycles. Codon-level natural selection analyses in primates and rodents, identified recurrent positive selection over Schlafen protein domains engaged in viral interactions. Combining crystal structures with machine learning predictions, we discovered a novel class of rapidly evolving residues enriched at the contact interface of SCHLAFEN protein dimers. Our results suggest that inter Schlafen compatibilities are under strong selective pressures and are likely to impact their molecular functions. We posit that cycles of genetic conflicts with pathogens and between paralogs drove Schlafens’ recurrent evolutionary innovations in mammals.
C. elegansepicuticlins define specific compartments in the apical extracellular matrix and function in wound repair
Authors: Pooranachithra Murugesan , Jyo Erin M. , Ernst Andreas M. , Chisholm Andrew D.
Published: January 2024

The apical extracellular matrix (aECM) of external epithelia often contains lipid-rich outer layers that contribute to permeability barrier function. The external aECM of nematode is known as the cuticle and contains an external lipid-rich layer, the epicuticle. Epicuticlins are a family of tandem repeat proteins originally identified as components of the insoluble fraction of the cuticular aECM and thought to localize in or near epicuticle. However, there has been littlein vivoanalysis of epicuticlins. Here, we report the localization analysis of the threeC. elegansepicuticlins (EPIC proteins) using fluorescent protein knock-ins to visualize endogenously expressed proteins, and further examine theirin vivofunction using genetic null mutants. By TIRF microscopy, we find that EPIC-1 and EPIC-2 localize to the surface of the cuticle in larval and adult stages in close proximity to the outer lipid layer. EPIC-1 and EPIC-2 also localize to interfacial cuticles and adult-specific cuticle struts. EPIC-3 expression is restricted to the stress-induced dauer stage, where it localizes to interfacial aECM in the buccal cavity. Strikingly, skin wounding in the adult inducesepic-3expression, and EPIC-3::mNG localizes to wound scars. Null mutants lacking one, two, or all three EPIC proteins display reduced survival after skin wounding yet are viable with low penetrance defects in epidermal morphogenesis. Our results suggest EPIC proteins define specific aECM compartments and have roles in wound repair.

Highlights

C. elegansepicuticlin (EPIC) proteins localize to specific regions in cortical and interfacial cuticle

Epicuticlins colocalize with BLI collagens in struts in adult cuticle

EPIC-3 is normally expressed in dauer stage and upregulated by skin wounding

Mutants lacking all three epicuticlins are viable and show reduced survival after skin wounding