bluuebunny/crossref_metadata_2025_split huggingface dataset:
TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics
Authors: Basharat Abdul Rehman , Xiong Xingzhao , Xu Tian , Zang Yong , Sun Liangliang , Liu Xiaowen 
Published: April 2024

AbstractTop-down mass spectrometry is widely used for proteoform identification, characterization, and quantification owing to its ability to analyze intact proteoforms. In the last decade, top-down proteomics has been dominated by top-down data-dependent acquisition mass spectrometry (TD-DDA-MS), and top-down data-independent acquisition mass spectrometry (TD-DIA-MS) has not been well studied. While TD-DIA-MS produces complex multiplexed tandem mass spectrometry (MS/MS) spectra, which are challenging to confidently identify, it selects more precursor ions for MS/MS analysis and has the potential to increase proteoform identifications compared with TD-DDA-MS. Here we present TopDIA, the first software tool for proteoform identification by TD-DIA-MS. It generates demultiplexed pseudo MS/MS spectra from TD-DIA-MS data and then searches the pseudo MS/MS spectra against a protein sequence database for proteoform identification. We compared the performance of TD-DDA-MS and TD-DIA-MS usingEscherichia coliK-12 MG1655 cells and demonstrated that TD-DIA-MS with TopDIA increased proteoform and protein identifications compared with TD-DDA-MS.
Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration
Authors: Rademacher Katerina , Doric Zak , Haddad Dominik , Mamaligas Aphroditi , Liao Szu-Chi , Creed Rose B. , Kano Kohei , Chatterton Zac , Fu Yuhong , Garcia Joseph H. , Vance Victoria , Sei Yoshitaka , Kreitzer Anatol , Halliday Glenda M , Nelson Alexandra B. , Margolis Elyssa B. , Nakamura Ken 
Published: April 2024

AbstractParkinson’s disease (PD) is characterized by the death of substantia nigra (SNc) dopamine (DA) neurons, but the pathophysiological mechanisms that precede and drive their death remain unknown. The activity of DA neurons is likely altered in PD, but we understand little about if or how chronic changes in activity may contribute to degeneration. To address this question, we developed a chemogenetic (DREADD) mouse model to chronically increase DA neuron activity, and confirmed this increase usingex vivoelectrophysiology. Chronic hyperactivation of DA neurons resulted in prolonged increases in locomotor activity during the light cycle and decreases during the dark cycle, consistent with chronic changes in DA release and circadian disturbances. We also observed early, preferential degeneration of SNc projections, recapitulating the PD hallmarks of selective vulnerability of SNc axons and the comparative resilience of ventral tegmental area axons. This was followed by eventual loss of midbrain DA neurons. Continuous DREADD activation resulted in a sustained increase in baseline calcium levels, supporting an important role for increased calcium in the neurodegeneration process. Finally, spatial transcriptomics from DREADD mice examining midbrain DA neurons and striatal targets, and cross-validation with human patient samples, provided insights into potential mechanisms of hyperactivity-induced toxicity and PD. Our results thus reveal the preferential vulnerability of SNc DA neurons to increased neural activity, and support a potential role for increased neural activity in driving degeneration in PD.
Simulation-based dosimetry of transcranial and intranasal photobiomodulation of the human brain: the roles of wavelength, power density and skin colour
Authors: Van Lankveld Hannah , Mai Anh Q. , Lim Lew , Hosseinkhah Nazanin , Cassano Paolo , Jean Chen J. 
Published: April 2024

AbstractPhotobiomodulation (PBM) is a novel technique that is actively studied for neuromodulation. However, despite the many in vivo studies, the stimulation protocols for PBM vary amongst studies, and the current understanding of neuromodulation via PBM is limited in terms of the extent of light penetration into the brain and its dosage dependence. Moreover, as near-infrared light can be absorbed by melanin in the skin, skin tone is a highly relevant but under-studied variable of interest. In this study, to address these gaps, we use Monte Carlo simulations (with MCX) of a single laser source for transcranial (tPBM) and intranasal (iPBM, nostril position) irradiated on a healthy human brain model. We investigate wavelengths of 670, 810 and 1064 nm in combination with light (“Caucasian”), medium (“Asian”) and dark (“African”) skin tones. Our simulations show that a maximum of 15% of the incidental energy for tPBM and 1% for iPBM reaches the cortex from the light source at the skin level. The rostral dorsal prefrontal cortex in tPBM and the ventromedial prefrontal cortex for iPBM accumulates the highest highest light energy, respectively for both wavelengths. Specifically, the 810 nm wavelength for tPBM and 1064 nm wavelength for iPBM produced the highest energy accumulation. Optical power density was found to be linearly correlated with energy. Moreover, we show that “Caucasian” skin allows the accumulation of higher light energy than other two skin colours. This study is the first to account for skin colour as a PBM dosing consideration, and provides evidence for hypothesis generation in in vivo studies of PBM.
Structure-function coupling and decoupling during movie-watching and resting-state: Novel insights bridging EEG and structural imaging
Authors: Subramani Venkatesh , Lioi Giulia , Jerbi Karim , Farrugia Nicolas 
Published: April 2024

AbstractThe intricate structural and functional architecture of the brain enables a wide range of cognitive processes ranging from perception and action to higher-order abstract thinking. Despite important progress, the relationship between the brain’s structural and functional properties is not yet fully established. In particular, the way the brain’s anatomy shapes its electrophysiological dynamics remains elusive. The electroencephalography (EEG) activity recorded during naturalistic tasks is thought to exhibit patterns of coupling with the underlying brain structure that vary as a function of behavior. Yet these patterns have not yet been sufficiently quantified. We address this gap by jointly examining individual Diffusion-Weighted Imaging (DWI) scans and continuous EEG recorded during video-watching and resting state, using a Graph Signal Processing (GSP) framework. By decomposing the structural graph into Eigenmodes and expressing the EEG activity as an extension of anatomy, GSP provides a way to quantify the structure-function coupling. We elucidate how the structure shapes function during naturalistic tasks such as movie-watching and how this association is modulated by tasks. We quantify the coupling relationship in a region-, time-, frequency-resolved manner. First of all, our findings indicate that the EEG activity in the sensorimotor cortex is strongly coupled with brain structure, while the activity in higher-order systems is less constrained by anatomy, i.e., shows more flexibility. In addition, we found that watching videos was associated with stronger structure-function coupling in the sensorimotor cortex, as compared to resting-state data. Second, time-resolved analysis revealed that the unimodal systems undergo minimal temporal fluctuation in structure-function association, and the transmodal system displays highest temporal fluctuations, with the exception of PCC seeing low fluctuations. Lastly, our frequency-resolved analysis revealed a consistent topography across different EEG rhythms, suggesting a similar relationship with the anatomical structure across frequency bands. Together, this unprecedented characterization of the link between structure and function using continuous EEG during naturalistic behavior underscores the role of anatomy in shaping ongoing cognitive processes. Taken together, by combining the temporal and spectral resolution of EEG and the methodological advantages of GSP, our work sheds new light onto the anatomo-functional organization of the brain.
Virus-like particle (VLP)-based vaccine targeting tau phosphorylated at Ser396/Ser404 (PHF1) site outperforms phosphorylated S199/S202 (AT8) site in reducing tau pathology and restoring cognitive deficits in the rTg4510 mouse model of tauopathy
Authors: Hulse Jonathan , Maphis Nicole , Peabody Julianne , Chackerian Bryce , Bhaskar Kiran 
Published: April 2024

AbstractTauopathies, including Alzheimer’s disease (AD) and Frontotemporal Dementia (FTD), are histopathologically defined by the aggregation of hyperphosphorylated pathological tau (pTau) as neurofibrillary tangles in the brain. Site-specific phosphorylation of tau occurs early in the disease process and correlates with progressive cognitive decline, thus serving as targetable pathological epitopes for immunotherapeutic development. Previously, we developed a vaccine (Qβ-pT181) displaying phosphorylated Thr181 tau peptides on the surface of a Qβ bacteriophage virus-like particle (VLP) that induced robust antibody responses, cleared pathological tau, and rescued memory deficits in a transgenic mouse model of tauopathy. Here we report the characterization and comparison of two additional Qβ VLP-based vaccines targeting the dual phosphorylation sites Ser199/Ser202 (Qβ-AT8) and Ser396/Ser404 (Qβ-PHF1). Both Qβ-AT8 and Qβ-PHF1 vaccines elicited high-titer antibody responses against their pTau epitopes. However, only Qβ-PHF1 rescued cognitive deficits, reduced soluble and insoluble pathological tau, and reactive microgliosis in a 4-month rTg4510 model of FTD. Both sera from Qβ-AT8 and Qβ-PHF1 vaccinated mice were specifically reactive to tau pathology in human AD post-mortem brain sections. These studies further support the use of VLP-based immunotherapies to target pTau in AD and related tauopathies and provide potential insight into the clinical efficacy of various pTau epitopes in the development of immunotherapeutics.
Peroxidasin is associated with a mesenchymal-like transcriptional phenotype and promotes invasion in metastatic melanoma
Authors: Smith-Díaz Carlos C , Kumar Abhishek , Das Andrew , Pace Paul , Chitcholtan Kenny , Magon Nicholas J , Hossain Sultana Hossain Mehbuba , Eccles Michael R , Winterbourn Christine C , Paumann-Page Martina 
Published: April 2024

AbstractCutaneous melanoma is a highly invasive, heterogeneous and treatment resistant cancer. It’s ability to dynamically shift between transcriptional states or phenotypes results in an adaptive cell plasticity that may drive cancer cell invasion or the development of therapy resistance. The expression of peroxidasin (PXDN), an extracellular matrix peroxidase, has been proposed to be associated with the invasive metastatic melanoma phenotype. We have confirmed this association by analysing the transcriptomes of 70 metastatic melanoma cell lines with variable levels of PXDN expression. This analysis highlighted a strong association between high PXDN expression and the undifferentiated invasive melanoma phenotype. To assess the functional role of PXDN in melanoma invasion, we performed a knockout of PXDN in a highly invasive cell line (NZM40). PXDN knockout decreased the invasive potential by ∼50% and decreased the expression of epithelial-mesenchymal transition and invasive marker genes as determined by RNAseq and substantiated by proteomics analysis. Bioinformatics analysis of differentially expressed genes following PXDN knockout highlighted decreases in genes linked to extracellular matrix formation, organisation and degradation as well as signalling pathways such as the WNT pathway. This study provides compelling evidence that PXDN plays a functional role in melanoma invasion by promoting an invasive, mesenchymal-like transcriptional phenotype.Research HighlightsPXDN expression is strongly associated with the invasive melanoma phenotype. Knockout of PXDN decreased invasion and expression of EMT marker genes concomitant with vast transcriptional changes relevant to many aspects of melanoma biology.
Fmo5 plays a sex-specific role in goblet cell maturation and mucus barrier formation
Authors: Schaller Megan L. , Sykes Madeline M. , Mecano Joy , Solanki Sumeet , Huang Wesley , Rebernick Ryan J. , Beydoun Safa , Wang Emily , Bugarin-Lapuz Amara , Shah Yatrik M. , Leiser Scott F. 
Published: April 2024

ABSTRACTBackground and AimsThe intestine plays a key role in metabolism, nutrient and water absorption, and provides both physical and immunological defense against dietary and luminal antigens. The protective mucosal lining in the intestine is a critical component of intestinal barrier that when compromised, can lead to increased permeability, a defining characteristic of inflammatory bowel disease (IBD), among other intestinal diseases. Here, we define a new role for the flavin-containing monooxygenase (FMO) family of enzymes in maintaining a healthy intestinal epithelium.MethodsUsingCaenorhabditis eleganswe measure intestinal barrier function, actin expression, and intestinal damage response. In mice, we utilize an intestine-specific, tamoxifen- inducible knockout model of the mammalian homolog ofCefmo-2, Fmo5, and assess histology, mucus barrier thickness, and goblet cell physiology. We also treat mice with the ER chaperone Tauroursodeoxycholic acid (TUDCA).ResultsIn nematodes, we findCefmo-2is necessary and sufficient for intestinal barrier function, intestinal actin expression, and is induced by intestinal damage. In mice, we find striking changes to the intestine within two weeks following Fmo5 disruption. Alterations include sex-dependent changes in colon epithelial histology, goblet cell localization, and mucus barrier formation. These changes are significantly more severe in female mice, mirroring differences observed in IBD patients. Furthermore, we find increased protein folding stress in Fmo5 knockout animals and successfully rescue the severe female phenotype with addition of a chemical ER chaperone.ConclusionsTogether, our results identify a highly conserved and novel role for Fmo5 in the mammalian intestine and support a key role for Fmo5 in maintenance of ER/protein homeostasis and proper mucus barrier formation.
Translational control of microglial inflammatory and neurodegenerative responses
Authors: Bermudez Sara , Choi Jung-Hyun , Vogel Jacob W. , Kim Sung-Hoon , Mahmood Niaz , Zhu Vivian Yuchan , Cozachenco Danielle , Yaqubi Moein , Zhou Linqiao , Stratton Jo Ann , Hansson Oskar , Healy Luke , Aguilar-Valles Argel , Sonenberg Nahum 
Published: April 2024

AbstractIn Alzheimer’s Disease (AD), activation of the mechanistic target of rapamycin (mTOR) pathway is essential for microglia neuroprotective roles, but it is unclear which mTOR effectors promote these neuroprotective functions. The mTOR complex 1 (mTORC1) inactivates the translation suppressors eukaryotic translation Initiation Factor 4E (eIF4E)-Binding Proteins (4E-BP) to promote mRNA translation. We show that 4E-BP1 inactivation is impaired in microglia under AD-relevant conditions. Depleting 4E-BPs in microglia increases mitochondrial metabolism, suppresses the pro-inflammatory profile, and mitigates amyloid-induced apoptosis. Furthermore, in the cerebrospinal fluid of patients with amyloid pathology, there was a positive association between microglia activation and neurodegeneration, which increases along 4E-BP1 levels. Thus, we propose the engagement mTORC1-4E-BP1 axis as a neuroprotective mechanism and a therapeutic target or biomarker for microglia modulation in AD.
Overfeeding does not increase energy expenditure or energy excretion in mice
Authors: Ranea-Robles Pablo , Lund Camilla , Lund Jens , Kleinert Maximilian , Clemmensen Christoffer 
Published: April 2024

AbstractTo curb the obesity epidemic, it is imperative that we improve our understanding of the mechanisms controlling fat mass and body weight regulation. While great progress has been made in mapping the biological feedback forces opposing weight loss, the mechanisms countering weight gain remain less well defined. Here, we integrate a mouse model of intragastric overfeeding with a comprehensive evaluation of the regulatory aspects of energy balance, encompassing food intake, energy expenditure, and fecal energy excretion. To evaluate the role of adipose tissue thermogenesis in the homeostatic protection against overfeeding-induced weight gain, we exposed uncoupling protein 1 (UCP1) knockout (KO) mice to overfeeding. Our results confirm that 7 days of 150% overfeeding induces ∼11% weight gain and triggers a potent and prolonged reduction in voluntary food intake that drives body weight back to baseline following overfeeding. Overfeeding has no effects on energy expenditure, consistent with the observation that mice lacking UCP1 are not compromised in their ability to defend against overfeeding-induced weight gain. These data emphasize that whole-body energy expenditure and adipose thermogenesis are not key contributors to protection against overfeeding in mice. Lastly, we show that fecal energy excretion decreases in response to overfeeding, primarily driven by a reduction in fecal output rather than in fecal caloric content. In conclusion, these results challenge the prevailing notion that adaptive thermogenesis contributes to the defense against weight gain induced by overfeeding. Instead, the protection against enforced weight gain in mice is primarily linked to a profound reduction in food intake.
PIEZO1 and PIEZO2 Blade domains are differentially required for channel localization and function
Authors: Sarrió-Ferrández Sergio , Selva Espe , Taberner Francisco J 
Published: April 2024

AbstractPIEZO1 and PIEZO2 are critical force-gated ion channels, detecting and transducing mechanical forces into ionic currents in many eukaryotic cell types, serving essential physiological roles. CryoEM and structure-function studies have revealed that three PIEZO monomers assemble as a 3-blade propeller, highlighting essential structural aspects for channel function. One of the most prominent features in PIEZO architecture is the Blade, a large membrane embedded domain that comprises 36 transmembrane fragments organized in 9 THU (Transmembrane Helix Units). Despite its suggested role in force transduction, the contribution of the Blade domain in channel physiology remains unclear. By systematically generating different truncated versions of PIEZO1 and PIEZO2, lacking parts of the Blade, we show the intact PIEZO1 Blade is essential for proper localization and function. Conversely, our results indicate the PIEZO2 Distal Blade segments (THU1-3) are dispensable for normal mechanical sensitivity. However, it plays a central role in channel stability and localization, containing a region that mediates the intracellular retention of a chimeric membrane protein. Our study indicates that, in addition to their biophysical properties, PIEZO1 and PIEZO2 also differ in the regulation of their localization, adding a new layer of control on PIEZO2 activity.
Neurological Research in 47 Asian Countries
Authors: Hassan Waseem , Zafar Mehreen 
Published: April 2024

AbstractNeurology research in the Asian region has seen significant growth and development over the past decade, yet comprehensive analyses of its progress remain scarce. This study aims to address this gap by providing a detailed examination of neurology research in 47 Asian countries from 2013 to 2022. Data was extracted from the Scopus database, encompassing scholarly output, citations, and citation impact metrics. Findings reveal a total of 128,306 research documents published with 1,725,678 total citations, demonstrating a commendable level of research activity. However, disparities exist among countries, with China, Japan, and Australia emerging as leading contributors in terms of both quantity and citation impact. Despite this, a substantial number of countries and universities have published fewer than 100 papers, indicating room for improvement and the need for targeted capacity-building efforts.
Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure
Authors: Rua Antonio J. , Alexandrescu Andrei T. 
Published: April 2024

AbstractDomain Z7 of nuclear transcription factor ZNF711 has the consensus last metal-ligand H23 found in odd-numbered zinc-fingers of this protein replaced by a phenylalanine. Ever since the discovery of ZNF711 it has been thought that Z7 is probably non-functional because of the H23F substitution. The presence of H26 three positions downstream prompted us to examine if this histidine could substitute as the last metal ligand. The Z7 domain adopts a stable tertiary structure upon metal binding. The NMR structure of Zn2+-bound Z7 shows the classical ββα-fold of CCHH zinc fingers. Mutagenesis and pH titration experiments indicate that H26 is not involved in metal binding and that Z7 has a tridentate metal-binding site comprised of only residues C3, C6, and H19. By contrast, an F23H mutation that introduces a histidine in the consensus position forms a tetradentate ligand. The structure of the WT Z7 is stable causing restricted ring-flipping of phenyalanines 10 and 23. Dynamics are increased with either the H26A or F23H substitutions and aromatic ring rotation is no longer hindered in the two mutants. The mutations have only small effects on theKdvalues for Zn2+and Co2+and retain the high thermal stability of the WT domain above 80 °C. Like two previously reported designed zinc fingers with the last ligand replaced by water, the WT Z7 domain is catalytically active, hydrolyzing 4-nitophenyl acetate. We discuss the implications of naturally occurring tridentate zinc fingers for cancer mutations and drug targeting of notoriously undruggable transcription factors. Our findings that Z7 can fold with only a subset of three metal ligands suggests the recent view that most everything about protein structure can be predicted through homology modeling might be premature for at least the resilient and versatile zinc-finger motif.
Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening
Authors: Gentili Matteo , Carlson Rebecca J. , Liu Bingxu , Hellier Quentin , Andrews Jocelyn , Qin Yue , Blainey Paul C. , Hacohen Nir 
Published: April 2024

AbstractSTING is an innate immune sensor that traffics across many cellular compartments to carry out its function of detecting cyclic di-nucleotides and triggering defense processes. Mutations in factors that regulate this process are often linked to STING-dependent human inflammatory disorders. To systematically identify factors involved in STING trafficking, we performed a genome-wide optical pooled screen and examined the impact of genetic perturbations on intracellular STING localization. Based on subcellular imaging of STING protein and trafficking markers in 45 million cells perturbed with sgRNAs, we defined 464 clusters of gene perturbations with similar cellular phenotypes. A higher-dimensional focused optical pooled screen on 262 perturbed genes which assayed 11 imaging channels identified 73 finer phenotypic clusters. In a cluster containing USE1, a protein that mediates Golgi to ER transport, we found a gene of unknown function, C19orf25. Consistent with the known role of USE1, loss of C19orf25 enhanced STING signaling. Other clusters contained subunits of the HOPS, GARP and RIC1-RGP1 complexes. We show that HOPS deficiency delayed STING degradation and consequently increased signaling. Similarly, GARP/RIC1-RGP1 loss increased STING signaling by delaying STING exit from the Golgi. Our findings demonstrate that genome-wide genotype-phenotype maps based on high-content cell imaging outperform other screening approaches, and provide a community resource for mining for factors that impact STING trafficking as well as other cellular processes observable in our dataset.