bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection
Authors: Currie Jordan , Ng Dominic C. M. , Pandi Boomathi , Black Alexander , Manda Vyshnavi , Pavelka Jay , Lam Maggie P. Y. , Lau Edward 
Published: June 2024

AbstractThe synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass spectrometry to measure protein turnover rates, but the optimal analytical approaches to derive turnover rates from the isotopomer patterns of deuterium labeled peptides continue to be a subject of research. Here we describe a method, which comprises a reverse lookup of numerically approximated peptide isotope envelopes, coupled to the selection of optimal isotopomer pairs based on peptide sequence, to calculate the molar fraction of new peptide synthesis in heavy water labeling mass spectrometry experiments. We validated this approach using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes. We then re-analyzed 17 proteome-wide turnover experiments from four mouse organs, and showed that the method increases the coverage of well-fitted peptides in protein turnover experiments by 25–82%. The method is implemented in the Riana software tool for protein turnover analysis, and may avail ongoing efforts to study the synthesis and degradation kinetics of proteins in animals on a proteome-wide scale.What’s newWe describe a reverse lookup method to calculate the molar fraction of new synthesis from numerically approximated peptide isotopomer profiles in heavy water labeling mass spectrometry experiments. Using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes at various proportions, we show that this method provides a straightforward way to calculate the proportion of new proteins in a protein pool from arbitrarily chosen isotopomer ratios. We next analyzed which of the isotopomer pairs within the peptide isotope envelope yielded isotopomer time courses that fit most closely to kinetic models, and found that the identity of the isotopomer pair depends partially on the number of deuterium accessible labeling sites of the peptide. We next derived a strategy to automatically select the isotopomer pairs to calculate turnover rates based on peptide sequence, and showed that this increases the coverage of existing proteome-wide turnover experiments in multiple data sets of the mouse heart, liver, kidney, and skeletal muscle by up to 25–82%.
The node of Ranvier influences thein vivoaxonal transport of mitochondria and signalling endosomes
Authors: Tosolini Andrew P. , Abatecola Federico , Negro Samuele , Sleigh James N. , Schiavo Giampietro 
Published: June 2024

AbstractEfficient long-range axonal transport is essential for maintaining neuronal function, and perturbations in this process underlie severe neurological diseases. We have previously demonstrated that signalling endosomes are transportedin vivoat comparable speeds across motor neurons (MNs) innervating different hindlimb muscles, as well as between forelimb and hindlimb peripheral nerves. In contrast, axonal transport is faster in MNs compared to sensory neurons innervating the same muscle. Found periodically across the myelin sheath, Nodes of Ranvier (NoR) are short uncovered axonal domains that facilitate action potential propagation. Currently, it remains unresolved how the distinct molecular structures of the NoR impact axonal transport dynamics. Here, using intravital time-lapse microscopy of sciatic nerves in live, anaesthetised mice, we assessed diverse organelle dynamics at the NoR. We first observed that axonal morphologies were similar between fast and slow MNs, and found that signalling endosomes and mitochondria accumulate on the distal side of the NoR in both motor neuron subtypes. Assessment of axonal transport of signalling endosomes and mitochondria revealed a decrease in velocity and increase in pausing as the organelles transit through the NoR, followed by an increase in speed in the adjacent intranodal region. Collectively, this study has established axonal transport dynamics of two independent organelles at the NoRin vivo, and has relevance for several pathologies affecting peripheral nerves and the NoR, such as peripheral neuropathy, motor neuron diseases, and/or multiple sclerosis.
The AID2 system offers a potent tool for rapid, reversible, or sustained degradation of essential proteins in live mice
Authors: Sladky Valentina C , Strong Margaret A , Tapias-Gomez Daniel , Jewett Cayla E , Drown Chelsea G , Scott Phillip M , Holland Andrew J 
Published: June 2024

AbstractStudying essential genes required for dynamic processes in live mice is challenging as genetic perturbations are irreversible and limited by slow protein depletion kinetics. The first-generation auxin-inducible-degron (AID) system is a powerful tool for analyzing inducible protein loss in cultured cells. However, auxin administration is toxic to mice, preventing its long-term use in animals. Here, we use an optimized second-generation AID system to achieve the conditional and reversible loss of the essential centrosomal protein CEP192 in live mice. We show that the auxin derivative 5-Ph-IAA is well tolerated over two weeks and drives near-complete CEP192-mAID degradation in less than one hourin vivo. Prolonged CEP192 loss led to cell division failure and cell death in proliferative tissues. Thus, the second-generation AID system is well suited for rapid and/or sustained protein depletion in live mice, offering a valuable new tool for interrogating protein functionin vivo.
Diet predicts performance trade-offs along Atlantic salmon ontology
Authors: Aykanat Tutku , Jacobsen Jan Arge , Hindar Kjetil 
Published: June 2024

AbstractUnderstanding the mechanistic basis of life history divergence is fundamental for predictive ecology. Variation in resource use impacts life history divergence and provides a framework for studying life history trade-offs. Contrary to the theory, empirical evidence does not support that resource allocation alone mediates life history divergence in the wild, which subsequently suggests a pivotal role for resource acquisition, but this has not been empirically demonstrated in free-living populations. Here, we sampled wild Atlantic salmon (Salmo salar) from different age groups during their marine feeding stage and hypothesized that prey taxa (consumption of crustaceansversusfish) has an age-dependent effect on the condition factor. We found salmon in their first year at sea had a higher condition factor when foraging on larger numbers of crustaceans and a lower condition factor when foraging on larger numbers of fish, andvice versain older sea age groups, a result that supported our hypothesis. Provided that condition factor is a predictor of age-at-maturity, our results show that resource acquisition may be an important process shaping life history variation in Atlantic salmon via modulating age-dependent performance trade-offs. Our results also emphasize the importance of bottom-up trophic cascades for maturation age and help to better predict the maturation dynamics of wild populations in the marine environment.
Trigeminal ganglion and tooth innervation modifications following genetic and pharmacological Nogo-A inhibition
Authors: Pirenne Laurence , Balic Anamaria , Santis Ilaria De , Bevilacqua Alessandro , Lai Chai Foong , Pagella Pierfrancesco , Schwab Martin E. , Mitsiadis Thimios A. 
Published: June 2024

AbstractNogo-A is a major regulator of neural development and regeneration, but its role in tooth innervation remains largely unknown. Neurons from trigeminal ganglia support teeth homeostasis and regeneration, and disorders of their function could have significant pathophysiological consequences. In this study, we show that Nogo-A is expressed in the trigeminal ganglia and in the neurons innervating the teeth, and that its deletion affects both the number and patterning of neurons in teeth. In organotypic cultures, Nogo-A blocking antibodies affect the trigeminal ganglia-derived neuronal outgrowths and allow premature innervation of tooth germs. RNA sequencing analysis revealed that Nogo-A deletion induces alterations linked to functions at synapses and interference with neurotrophin signalling during the differentiation and maturation of trigeminal neurons. Taken together, these results reveal for the first time the importance of Nogo-A as a major regulator of tooth innervation and point to its potential as a clinical therapeutic target.
Discovery and mechanistic characterization of a probiotic-origin 3β-OH-Δ5-6-cholesterol-5β-reductase directly converting cholesterol to coprostanol
Authors: Netter Urmila , Bisht Vishakha , Gaurav Amit , Sharma Rekha , Ghosh Avik , Bisht Vinod Singh , Ambatipudi Kiran , Sharma Hanuman Prasad , Mohanty Sujata , Loat Shubham , Sarkar Mihir , Tahlan Kapil , Navani Naveen K 
Published: June 2024

AbstractOn the one hand, cholesterol is a foundational molecule for various structural and biochemical pathways, while elevated cholesterol levels are associated with cardiovascular diseases. Some selected strains of Lactobacilli are also known for modulating cholesterol levels. However, the molecular mechanism of cholesterol transformation by lactobacilli has remained challenging to reveal. This study reports the discovery and role of a microbial 3β-OH-Δ5-6-cholesterol-5β-reductase fromLimosilactobacillus fermentumNKN51, which directly converts cholesterol to coprostanol, thereby resolving the enigma. Protein engineering of the reductase enzyme identified the cholesterol and NADP+interacting amino acids, detailing the catalytic mechanism of 5βChR. Phylogenetic studies emphasize the abundance of 5βChRs in gut commensal lactobacilli, which shares a common ancestor with plant 5β reductases. Meta-analysis results of healthy participant microbiomes underline the significance of 5βChR homologs, while a cohort study reveals an association between higher 5βChR abundance and diabetes. The discovery of the 5βChR enzyme and its molecular mechanism in cholesterol metabolism pave the way for a better understanding of the gut-associated microbiome and the design of practical applications to ameliorate dyslipidemia.
OSBA: An open neonatal neuroimaging atlas and template for spina bifida aperta
Authors: Speckert Anna , Ji Hui , Payette Kelly , Grehten Patrice , Kottke Raimund , Ackermann Samuel , Padden Beth , Mazzone Luca , Moehrlen Ueli ,   SPINA BIFIDA STUDY GROUP ZURICH, Jakab Andras 
Published: June 2024

AbstractWe present the Open Spina Bifida Aperta (OSBA) atlas, an open atlas and set of neuroimaging templates for spina bifida aperta (SBA). Traditional brain atlases may not adequately capture anatomical variations present in pediatric or disease-specific cohorts. The OSBA atlas fills in this gap by representing the computationally averaged anatomy of the neonatal brain with SBA after fetal surgical repair. The OSBA atlas was constructed using structural T2-weighted and diffusion tensor MRI of 28 newborns with SBA who underwent prenatal surgical correction. The corrected gestational age at MRI was 38.1 ± 1.1 weeks (mean ± SD). The OSBA atlas consists of T2-weighted and fractional anisotropy templates, along with 9 tissue prior maps and region of interest (ROI) delineations. The OSBA atlas offers a standardized reference space for spatial normalization and anatomical ROI definition. Our image segmentation and cortical ribbon definition is based on a human-in-the-loop approach including manual segmentation. The precise alignment of the ROIs was achieved by a combination of manual image alignment and automated, non-linear image registration. By providing a dedicated neonatal atlas for SBA, we enable more accurate spatial standardization and support advanced analyses such as diffusion tractography and connectomic studies in newborns affected by this condition.
A history-dependent integrase recorder of plant gene expression with single cell resolution
Authors: Maranas Cassandra J. , George Wesley , Scallon Sarah K. , VanGilder Sydney , Nemhauser Jennifer L. , Guiziou Sarah 
Published: June 2024

AbstractDuring development, most cells experience a progressive restriction of fate that ultimately results in a fully differentiated mature state. Understanding more about the gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, we present a four-state integrase-based recorder of gene expression history and demonstrate its use in tracking gene expression events in Arabidopsis thaliana in two developmental contexts: lateral root initiation and stomatal differentiation. The recorder uses two serine integrases to mediate sequential DNA recombination events, resulting in step-wise, history-dependent switching between expression of fluorescent reporters. By using promoters that express at different times along each of the two differentiation pathways to drive integrase expression, we successfully tied fluorescent status to an ordered progression of gene expression along the developmental trajectory. In one snapshot of a mature tissue, our recorder was able to reveal past gene expression with single cell resolution. In this way, we were able to capture heterogeneity in stomatal development, confirming the existence of two alternate paths of differentiation.
LCN2 promotes focal adhesion formation and invasion by stimulating Src activation
Authors: Choudhary Bhagya Shree , Chaudhary Nazia , Vijan Aditi , Mandal Dibita , Pilankar Leena , Gawand Shubham , Khan Bushra K. , Shivashankar Anusha , Doloi Rinki , Joshi Neha , Das Manjula , Dalal Sorab N. 
Published: June 2024

AbstractPrevious work has demonstrated that Lipocalin2 (LCN2) expression promotes invasion and migration in multiple tumor types. The mechanisms by which LCN2 promotes invasion and migration remain unclear. Previous work from our laboratory demonstrated that LCN2 promotes actin filament formation by inhibiting actin glutathionylation. In this report, we demonstrate that in addition to inhibiting actin glutathionylation, LCN2 stimulates invasion by promoting the formation of focal adhesions, which is independent of the ability of LCN2 to bind iron. LCN2 promotes focal adhesion formation by promoting the activation of c-Src by stimulating the expression of the transcription factor ETS1. ETS1 activates the expression of the protein phosphatase, PTP1B, resulting in the auto-activation of c-Src and increased paxillin phosphorylation leading to focal adhesion formation. These results demonstrate that LCN2 has iron-dependent and independent functions in promoting invasion and highlight the multiple mechanisms by which LCN2 promotes invasion and suggest that c-Src inhibitors could be used to treat invasive colorectal cancer.SUMMARYExpression of LCN2 is elevated in invasive colorectal cancer. We demonstrate that LCN2 promotes invasion by stimulating the formation of focal adhesions by promoting Src activation.
Conformational dynamics of electrostatically charged Intrinsically Disordered Proteins
Authors: Schwarz Simon , Sarkar Subhartha , Sakhapov Damir , Enderlein Jörg , Sturm Anja , Wardetzky Max 
Published: June 2024

AbstractWe experimentally and computationally study the dynamics of homogeneously electrically charged intrinsically disordered proteins (IDPs) in ionic solutions (aqueous solutions containing salt). Computationally, this is achieved by extending a recently introduced discrete elastic rod (DER) model to include electrostatic interactions. The respective model includes only three free parameters: bending stiffness, bond length, and hydrodynamic radius. These parameters were obtained by fitting the measured conformational dynamics of uncharged polypeptides as reported in a previous publication [8]. We compare our computational results with photo-electron transfer fluorescence correlation spectroscopy (PET-FCS) measurements of the conformational dynamics of the highly charged (-44 e−) intrinsically disordered protein Prothymosin α. We here report on an agreement between the loop-closing rates obtained from our computational model and the respective experimental measurements, with rate values significantly slower than those observed for uncharged IDPs.
Arid1bhaploinsufficiency in pyramidal neurons causes cellular and circuit changes in neocortex but is not sufficient to produce behavioral or seizure phenotypes
Authors: Marshall Alec H. , Hanson Meretta A. , Boyle Danielle J. , Nagarajan Devipriyanka , Bibi Noor , Fitzgerald Julie , Gaitten Emilee , Kokiko-Cochran Olga N. , Gu Bin , Wester Jason C. 
Published: June 2024

ABSTRACTArid1bis a high confidence risk gene for autism spectrum disorder that encodes a subunit of a chromatin remodeling complex expressed in neuronal progenitors. Haploinsufficiency causes a broad range of social, behavioral, and intellectual disability phenotypes, including Coffin-Siris syndrome. Recent work using transgenic mouse models suggests pathology is due to deficits in proliferation, survival, and synaptic development of cortical neurons. However, there is conflicting evidence regarding the relative roles of excitatory projection neurons and inhibitory interneurons in generating abnormal cognitive and behavioral phenotypes. Here, we conditionally knocked out either one or both copies ofArid1bfrom excitatory projection neuron progenitors and systematically investigated the effects on intrinsic membrane properties, synaptic physiology, social behavior, and seizure susceptibility. We found that disruptingArid1bexpression in excitatory neurons alters their membrane properties, including hyperpolarizing action potential threshold; however, these changes depend on neuronal subtype. Using paired whole-cell recordings, we found increased synaptic connectivity rate between projection neurons. Furthermore, we found reduced strength of excitatory synapses to parvalbumin (PV)-expression inhibitory interneurons. These data suggest an increase in the ratio of excitation to inhibition. However, the strength of inhibitory synapses from PV interneurons to excitatory neurons was enhanced, which may rebalance this ratio. Indeed,Arid1bhaploinsufficiency in projection neurons was insufficient to cause social deficits and seizure phenotypes observed in a preclinical germline haploinsufficient mouse model. Our data suggest that while excitatory projection neurons likely contribute to autistic phenotypes, pathology in these cells is not the primary cause.
The protamines of the noble false widow spiderSteatoda nobilisprovide an example of liquid-liquid phase separation chromatin transitions during spermiogenesis
Authors: Leyden Melissa R. , Michalik Peter , Baruffaldi Luciana , Mahmood Susheen , Kalani Ladan , Hunt Donald F. , Eirin-Lopez Jose Maria , Andrade Maydianne C.B. , Shabanowitz Jeffrey , Ausió Juan 
Published: June 2024

ABSTRACTWhile there is extensive information about sperm nuclear basic proteins (SNBP) in vertebrates, there is very little information about Arthropoda by comparison. This paper aims to contribute to filling this gap by analyzing these proteins in the sperm of the noble false widow spiderSteatoda nobilis(Order Araneae, Family Theridiidae). To this end, we have developed a protein extraction method that allows the extraction of cysteine-containing protamines suitable for the preparation and analysis of SNBPs from samples where the amount of starting tissue material is limited. We carried out top-down mass spectrometry sequencing and molecular phylogenetic analyses to characterize the protamines ofS. nobilisand other spiders. We also used electron microscopy to analyze the chromatin organization of the sperm, and we found it to exhibit liquid-liquid phase spinodal decomposition during the late stages of spermiogenesis. These studies further our knowledge of the distribution of SNBPs within the animal kingdom and provide additional support for a proposed evolutionary origin of many protamines from a histone H1 (H5) replication-independent precursor.
Unraveling the Role of G-Quadruplexes in Alternative Polyadenylation (APA): A Focus on Neogenin 1
Authors: Lejault Pauline , Bolduc François , Turcotte Marc-Antoine , Perreault Jean Pierre 
Published: June 2024

AbstractPolyadenylation is a crucial step in mRNA maturation. In half of the cases, alternative polyadenylation sites are used instead of canonical ones, affecting the length of the transcript’s 3’UTR. The mechanisms controlling the selection of these alternative polyadenylation sites are still unknown. Using a unique sequencing method (PolyAclick-seq) to identify different polyadenylated isoforms, we selected events modulated by RHPS4, a ligand known to stabilize G-quadruplex (G4). Throughin silicoselection,in vitroassays, and G4 mutagenesis construction, the pivotal role of rG4 structures in determining polyadenylation sites was uncovered, particularly for the gene encoding Neogenin-1 (NEO1). This research highlights the importance of focusing on G4 RNA mediated APA regulation in the 3’UTR, as a method to alter isoform choice and impact protein synthesis opening up new avenues for RNA-based therapies.
TSC2loss in neural progenitor cells suppresses translation of ASD/NDD-associated transcripts in an mTORC1- and MNK1/2-reversible fashion
Authors: Martin Pauline , Szkop Krzysztof J. , Robert Francis , Bhattacharyya Srirupa , Beauchamp Roberta L. , Brenner Jacob , Redmond Nicholas E. , Huang Sidong , Erdin Serkan , Larsson Ola , Ramesh Vijaya 
Published: June 2024

SUMMARYTuberous sclerosis complex (TSC) is an inherited neurodevelopmental disorder (NDD) with frequent manifestations of epilepsy and autism spectrum disorder (ASD). TSC is caused by inactivating mutations inTSC1orTSC2tumor suppressor genes, with encoded proteins hamartin (TSC1) and tuberin (TSC2) forming a functional complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. This has led to treatment with allosteric mTORC1 inhibitor rapamycin analogs (“rapalogs”) for TSC tumors; however, rapalogs are ineffective for treating neurodevelopmental manifestations. mTORC1 signaling controls protein synthesis by regulating formation of the eIF4F complex, with further modulation by MNK1/2 kinases via phosphorylation of the eIF4F subunit eIF4E. While both these pathways modulate translation, comparing their impact on transcriptome-wide mRNA translation, as well as effects of inhibiting these pathways in TSC has not been explored. Here, employing CRISPR-modified, isogenic TSC2 patient-derived neural progenitor cells (NPCs), we have examined transcriptome-wide changes in mRNA translation uponTSC2loss. Our results reveal dysregulated translation inTSC2-Null NPCs, which significantly overlaps with the translatome fromTSC1-Null NPCs. Interestingly, numerous non-monogenic ASD-, NDD-and epilepsy-associated genes identified in patients harboring putative loss-of-function mutations, were translationally suppressed inTSC2-Null NPCs. Importantly, translation of these ASD- and NDD-associated genes was reversed upon inhibition of either mTORC1 or MNK1/2 signaling using RMC-6272 or eFT-508, respectively. This study establishes the importance of mTORC1-eIF4F- and MNK-eIF4E-sensitive mRNA translation in TSC, ASD and other neurodevelopmental disorders laying the groundwork for evaluating drugs in clinical development that target these pathways as a treatment strategy for these disorders.