bluuebunny/crossref_metadata_2025_split huggingface dataset:
MICU1 occludes the mitochondrial calcium uniporter in divalent-free conditions
Authors: Rodríguez-Prados Macarena , Berezhnaya Elena , Castromonte Maria Teresa , Menezes-Filho Sergio L. , Paillard Melanie , Hajnóczky György 
Published: May 2023

Mitochondrial Ca
2+
uptake is mediated by the mitochondrial uniporter complex (mtCU) that includes a tetramer of the pore-forming subunit, MCU, a scaffold protein, EMRE, and the EF-hand regulatory subunit, MICU1 either homodimerized or heterodimerized with MICU2/3. MICU1 has been proposed to regulate Ca
2+
uptake via the mtCU by physically occluding the pore and preventing Ca
2+
flux at resting cytoplasmic [Ca
2+
] (free calcium concentration) and to increase Ca
2+
flux at high [Ca
2+
] due to cooperative activation of MICUs EF-hands. However, mtCU and MICU1 functioning when its EF-hands are unoccupied by Ca
2+
is poorly studied due to technical limitations. To overcome this barrier, we have studied the mtCU in divalent-free conditions by assessing the Ru265-sensitive Na
+
influx using fluorescence-based measurement of mitochondrial matrix [Na
+
] (free sodium concentration) rise and the ensuing depolarization and swelling. We show an increase in all these measures of Na
+
uptake in MICU1KO cells as compared to wild-type (WT) and rescued MICU1KO HEK cells. However, mitochondria in WT cells and MICU1 stable-rescued cells still allowed some Ru265-sensitive Na
+
influx that was prevented by MICU1 in excess upon acute overexpression. Thus, MICU1 restricts the cation flux across the mtCU in the absence of Ca
2+
, but even in cells with high endogenous MICU1 expression such as HEK, some mtCU seem to lack MICU1-dependent gating. We also show rearrangement of the mtCU and altered number of functional channels in MICU1KO and different rescues, and loss of MICU1 during mitoplast preparation, that together might have obscured the pore-blocking function of MICU1 in divalent-free conditions in previous studies.
Epigenetic silencing of selected hypothalamic neuropeptides in narcolepsy with cataplexy
Authors: Seifinejad Ali , Ramosaj Mergim , Shan Ling , Li Sha , Possovre Marie-Laure , Pfister Corinne , Fronczek Rolf , Garrett-Sinha Lee A. , Frieser David , Honda Makoto , Arribat Yoan , Grepper Dogan , Amati Francesca , Picot Marie , Agnoletto Andrea , Iseli Christian , Chartrel Nicolas , Liblau Roland , Lammers Gert J. , Vassalli Anne , Tafti Mehdi 
Published: May 2023

Narcolepsy with cataplexy is a sleep disorder caused by deficiency in the hypothalamic neuropeptide hypocretin/orexin (HCRT), unanimously believed to result from autoimmune destruction of hypocretin-producing neurons. HCRT deficiency can also occur in secondary forms of narcolepsy and be only temporary, suggesting it can occur without irreversible neuronal loss. The recent discovery that narcolepsy patients also show loss of hypothalamic (corticotropin-releasing hormone) CRH-producing neurons suggests that other mechanisms than cell-specific autoimmune attack, are involved. Here, we identify the HCRT cell-colocalized neuropeptide QRFP as the best marker of HCRT neurons. We show that if HCRT neurons are ablated in mice, in addition to
Hcrt,
Qrfp
transcript is also lost in the lateral hypothalamus, while in mice where only the
Hcrt
gene is inactivated
Qrfp
is unchanged. Similarly, postmortem hypothalamic tissues of narcolepsy patients show preserved
QRFP
expression, suggesting the neurons are present but fail to actively produce HCRT. We show that the promoter of the
HCRT
gene of patients exhibits hypermethylation at a methylation-sensitive and evolutionary-conserved PAX5:ETS1 transcription factor-binding site, suggesting the gene is subject to transcriptional silencing. We show also that in addition to HCRT,
CRH
and Dynorphin (
PDYN
) gene promoters, exhibit hypermethylation in the hypothalamus of patients. Altogether, we propose that
HCRT
,
PDYN
, and
CRH
are epigenetically silenced by a hypothalamic assault (inflammation) in narcolepsy patients, without concurrent cell death. Since methylation is reversible, our findings open the prospect of reversing or curing narcolepsy.
High sensitivity top–down proteomics captures single muscle cell heterogeneity in large proteoforms
Authors: Melby Jake A. , Brown Kyle A. , Gregorich Zachery R. , Roberts David S. , Chapman Emily A. , Ehlers Lauren E. , Gao Zhan , Larson Eli J. , Jin Yutong , Lopez Justin R. , Hartung Jared , Zhu Yanlong , McIlwain Sean J. , Wang Daojing , Guo Wei , Diffee Gary M. , Ge Ying 
Published: May 2023

Single-cell proteomics has emerged as a powerful method to characterize cellular phenotypic heterogeneity and the cell-specific functional networks underlying biological processes. However, significant challenges remain in single-cell proteomics for the analysis of proteoforms arising from genetic mutations, alternative splicing, and post-translational modifications. Herein, we have developed a highly sensitive functionally integrated top–down proteomics method for the comprehensive analysis of proteoforms from single cells. We applied this method to single muscle fibers (SMFs) to resolve their heterogeneous functional and proteomic properties at the single-cell level. Notably, we have detected single-cell heterogeneity in large proteoforms (>200 kDa) from the SMFs. Using SMFs obtained from three functionally distinct muscles, we found fiber-to-fiber heterogeneity among the sarcomeric proteoforms which can be related to the functional heterogeneity. Importantly, we detected multiple isoforms of myosin heavy chain (~223 kDa), a motor protein that drives muscle contraction, with high reproducibility to enable the classification of individual fiber types. This study reveals single muscle cell heterogeneity in large proteoforms and establishes a direct relationship between sarcomeric proteoforms and muscle fiber types, highlighting the potential of top–down proteomics for uncovering the molecular underpinnings of cell-to-cell variation in complex systems.
Direct tests of cytochrome
c
and
c
1
functions in the electron transport chain of malaria parasites
Authors: Espino-Sanchez Tanya J. , Wienkers Henry , Marvin Rebecca G. , Nalder Shai-anne , García-Guerrero Aldo E. , VanNatta Peter E. , Jami-Alahmadi Yasaman , Mixon Blackwell Amanda , Whitby Frank G. , Wohlschlegel James A. , Kieber-Emmons Matthew T. , Hill Christopher P. , A. Sigala Paul 
Published: May 2023

The mitochondrial electron transport chain (ETC) of
Plasmodium
malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt
c
homologs (
c
and
c
-2) with unusually sparse sequence identity and uncertain fitness contributions.
P. falciparum
cyt
c
-2 is the most divergent eukaryotic cyt
c
homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt
c
homologs and the related cyt
c
1
for inducible knockdown. Translational repression of cyt
c
and cyt
c
1
was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt
c
-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt
c
for ETC function. Biochemical and structural studies revealed that both cyt
c
and
c
-2 are hemylated by holocytochrome
c
synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt
c
-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent
Plasmodium
cytochrome
c
with molecular adaptations that defy a conserved role in eukaryotic evolution.
Intestinal bile acids provide a surmountable barrier against
C. difficile
TcdB-induced disease pathogenesis
Authors: Icho Simoun , Ward Jennifer S. , Tam John , Kociolek Larry K. , Theriot Casey M. , Melnyk Roman A. 
Published: May 2023

Intestinal bile acids play an essential role in the
Clostridioides difficile
lifecycle having been shown in vitro to modulate various aspects of pathogenesis, including spore germination, vegetative growth, and more recently the action of the primary virulence determinant, TcdB. Here, we investigated whether physiological levels of the total pool of intestinal bile acids in mice and humans protect against TcdB action. Small molecules extracted from the lumenal contents of the small intestine, cecum, colon, and feces were found to inhibit TcdB in accordance with the differential amounts of total bile acids in each compartment. Extracts from antibiotic-treated and germ-free mice, despite harboring dramatically altered bile acid profiles, unexpectedly also prevented TcdB-induced cell rounding to similar extents. We show that protection, however, is surmountable and can be overcome at higher doses of TcdB—typical to those seen during severe
C. difficile
infection—suggesting that the protective properties of intestinal bile acids are operant primarily under low to moderate toxin levels. Taken together, these findings demonstrate a role for intestinal bile acids in attenuating virulence, provide insights into asymptomatic carriage of toxigenic
C. difficile
, and inform strategies to manipulate bile acid levels for therapeutic benefit.
AAFL: automatic association feature learning for gene signature identification of cancer subtypes in single-cell RNA-seq data
Authors: Huang Meng , Long Changzhou , Ma Jiangtao 
Published: May 2023

Abstract
Single-cell RNA-sequencing (scRNA-seq) technologies have enabled the study of human cancers in individual cells, which explores the cellular heterogeneity and the genotypic status of tumors. Gene signature identification plays an important role in the precise classification of cancer subtypes. However, most existing gene selection methods only select the same informative genes for each subtype. In this study, we propose a novel gene selection method, automatic association feature learning (AAFL), which automatically identifies different gene signatures for different cell subpopulations (cancer subtypes) at the same time. The proposed AAFL method combines the residual network with the low-rank network, which selects genes that are most associated with the corresponding cell subpopulations. Moreover, the differential expression genes are acquired before gene selection to filter the redundant genes. We apply the proposed feature learning method to the real cancer scRNA-seq data sets (melanoma) to identify cancer subtypes and detect gene signatures of identified cancer subtypes. The experimental results demonstrate that the proposed method can automatically identify different gene signatures for identified cancer subtypes. Gene ontology enrichment analysis shows that the identified gene signatures of different subtypes reveal the key biological processes and pathways. These gene signatures are expected to bring important implications for understanding cellular heterogeneity and the complex ecosystem of tumors.
SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data
Authors: Qiu Yushan , Yan Chang , Zhao Pu , Zou Quan 
Published: May 2023

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) technology attracts extensive attention in the biomedical field. It can be used to measure gene expression and analyze the transcriptome at the single-cell level, enabling the identification of cell types based on unsupervised clustering. Data imputation and dimension reduction are conducted before clustering because scRNA-seq has a high ‘dropout’ rate, noise and linear inseparability. However, independence of dimension reduction, imputation and clustering cannot fully characterize the pattern of the scRNA-seq data, resulting in poor clustering performance. Herein, we propose a novel and accurate algorithm, SSNMDI, that utilizes a joint learning approach to simultaneously perform imputation, dimensionality reduction and cell clustering in a non-negative matrix factorization (NMF) framework. In addition, we integrate the cell annotation as prior information, then transform the joint learning into a semi-supervised NMF model. Through experiments on 14 datasets, we demonstrate that SSNMDI has a faster convergence speed, better dimensionality reduction performance and a more accurate cell clustering performance than previous methods, providing an accurate and robust strategy for analyzing scRNA-seq data. Biological analysis are also conducted to validate the biological significance of our method, including pseudotime analysis, gene ontology and survival analysis. We believe that we are among the first to introduce imputation, partial label information, dimension reduction and clustering to the single-cell field.

Availability and implementation
The source code for SSNMDI is available at https://github.com/yushanqiu/SSNMDI.
Navigating Available Treatment Options for Carbapenem-ResistantAcinetobacter baumannii-calcoaceticusComplex Infections
Authors: Shields Ryan K , Paterson David L , Tamma Pranita D 
Published: May 2023

AbstractCarbapenem-resistant Acinetobacter baumannii-calcoaceticus complex (CRAB) is one of the top-priority pathogens for new antibiotic development. Unlike other antibiotic-resistant threats, none of the available therapies have been shown to consistently reduce mortality or improve patient outcomes in clinical trials. Antibiotic combination therapy is routinely used in clinical practice; however, the preferred combination has not been defined. This narrative review focuses on evidence-based solutions for the treatment of invasive CRAB infections. We dissect the promise and perils of traditional agents used in combination, such as colistin, sulbactam, and the tetracyclines, and offer clinical pearls based on our interpretation of the available data. Next, we investigate the merits of newly developed β-lactam agents like cefiderocol and sulbactam-durlobactam, which have demonstrated contrasting results in recent randomized clinical trials. The review concludes with the authors’ perspective on the evolving treatment landscape for CRAB infections, which is complicated by limited clinical data, imperfect treatment options, and a need for future clinical trials. We propose that effective treatment for CRAB infections requires a personalized approach that incorporates host factors, the site of infection, pharmacokinetic-pharmacodynamic principles, local molecular epidemiology of CRAB isolates, and careful interpretation of antibiotic susceptibility testing results. In most clinical scenarios, a dose-optimized, sulbactam-based regimen is recommended with the addition of at least one other in vitro active agent. Should sulbactam-durlobactam receive regulatory approval, recommendations will need to be re-evaluated with the most recent evidence.
Durlobactam, a Broad-Spectrum Serine β-lactamase Inhibitor, Restores Sulbactam Activity AgainstAcinetobacterSpecies
Authors: Papp-Wallace Krisztina M , McLeod Sarah M , Miller Alita A 
Published: May 2023

AbstractSulbactam-durlobactam is a pathogen-targeted β-lactam/β-lactamase inhibitor combination in late-stage development for the treatment of Acinetobacter infections, including those caused by multidrug-resistant strains. Durlobactam is a member of the diazabicyclooctane class of β-lactamase inhibitors with broad-spectrum serine β-lactamase activity. Sulbactam is a first-generation, narrow-spectrum β-lactamase inhibitor that also has intrinsic antibacterial activity against Acinetobacter spp. due to its ability to inhibit penicillin-binding proteins 1 and 3. The clinical utility of sulbactam for the treatment of contemporary Acinetobacter infections has been eroded over the last decades due to its susceptibility to cleavage by numerous β-lactamases present in this species. However, when combined with durlobactam, the activity of sulbactam is restored against this problematic pathogen. The following summary describes what is known about the molecular drivers of activity and resistance as well as results from surveillance and in vivo efficacy studies for this novel combination.
Big tau aggregation disrupts microtubule tyrosination and causes myocardial diastolic dysfunction: from discovery to therapy
Authors: Luciani Marco , Montalbano Mauro , Troncone Luca , Bacchin Camilla , Uchida Keita , Daniele Gianlorenzo , Jacobs Wolf Bethany , Butler Helen M , Kiel Justin , Berto Stefano , Gensemer Cortney , Moore Kelsey , Morningstar Jordan , Diteepeng Thamonwan , Albayram Onder , Abisambra José F , Norris Russell A , Di Salvo Thomas G , Prosser Benjamin , Kayed Rakez , del Monte Federica 
Published: May 2023

Abstract

Background
Amyloid plaques and neurofibrillary tangles, the molecular lesions that characterize Alzheimer’s disease (AD) and other forms of dementia, are emerging as determinants of proteinopathies ‘beyond the brain’. This study aims to establish tau’s putative pathophysiological mechanistic roles and potential future therapeutic targeting of tau in heart failure (HF).

Methods and results
A mouse model of tauopathy and human myocardial and brain tissue from patients with HF, AD, and controls was employed in this study. Tau protein expression was examined together with its distribution, and in vitro tau-related pathophysiological mechanisms were identified using a variety of biochemical, imaging, and functional approaches. A novel tau-targeting immunotherapy was tested to explore tau-targeted therapeutic potential in HF. Tau is expressed in normal and diseased human hearts, in contradistinction to the current oft-cited observation that tau is expressed specifically in the brain. Notably, the main cardiac isoform is high-molecular-weight (HMW) tau (also known as big tau), and hyperphosphorylated tau segregates in aggregates in HF and AD hearts. As previously described for amyloid-beta, the tauopathy phenotype in human myocardium is of diastolic dysfunction. Perturbation in the tubulin code, specifically a loss of tyrosinated microtubules, emerged as a potential mechanism of myocardial tauopathy. Monoclonal anti-tau antibody therapy improved myocardial function and clearance of toxic aggregates in mice, supporting tau as a potential target for novel HF immunotherapy.

Conclusion
The study presents new mechanistic evidence and potential treatment for the brain–heart tauopathy axis in myocardial and brain degenerative diseases and ageing.
Personalized pulmonary vein antrum isolation guided by left atrial wall thickness for persistent atrial fibrillation
Authors: Falasconi Giulio , Penela Diego , Soto-Iglesias David , Francia Pietro , Teres Cheryl , Saglietto Andrea , Jauregui Beatriz , Viveros Daniel , Bellido Aldo , Alderete Jose , Meca-Santamaria Julia , Franco Paula , Gaspardone Carlo , San Antonio Rodolfo , Huguet Marina , Cámara Óscar , Ortiz-Pérez José-Tomás , Martí-Almor Julio , Berruezo Antonio 
Published: May 2023

Abstract

Aims
Pulmonary vein (PV) antrum isolation proved to be effective for treating persistent atrial fibrillation (PeAF). We sought to investigate the results of a personalized approach aimed at adapting the ablation index (AI) to the local left atrial wall thickness (LAWT) in a cohort of consecutive patients with PeAF.

Methods and results
Consecutive patients referred for PeAF first ablation were prospectively enrolled. The LAWT three-dimensional maps were obtained from pre-procedure multidetector computed tomography and integrated into the navigation system. Ablation index was titrated according to the local LAWT, and the ablation line was personalized to avoid the thickest regions while encircling the PV antrum. A total of 121 patients (69.4% male, age 64.5 ± 9.5 years) were included. Procedure time was 57 min (IQR 50–67), fluoroscopy time was 43 s (IQR 20–71), and radiofrequency (RF) time was 16.5 min (IQR 14.3–18.4). The median AI tailored to the local LAWT was 387 (IQR 360–410) for the anterior wall and 335 (IQR 300–375) for the posterior wall. First-pass PV antrum isolation was obtained in 103 (85%) of the right PVs and 103 (85%) of the left PVs. Median LAWT values were higher for PVs without first-pass isolation as compared to the whole cohort (P = 0.02 for left PVs and P = 0.03 for right PVs). Recurrence-free survival was 79% at 12 month follow-up.

Conclusion
In this prospective study, LAWT-guided PV antrum isolation for PeAF was effective and efficient, requiring low procedure, fluoroscopy, and RF time. A randomized trial comparing the LAWT-guided ablation with the standard of practice is in progress (ClinicalTrials.gov, NCT05396534).
RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes
Authors: Henry Camille , Kaur Gurleen , Cherry Megan E , Henrikus Sarah S , Bonde Nina J , Sharma Nischal , Beyer Hope A , Wood Elizabeth A , Chitteni-Pattu Sindhu , van Oijen Antoine M , Robinson Andrew , Cox Michael M 
Published: May 2023

Abstract
The bacterial RecF, RecO, and RecR proteins are an epistasis group involved in loading RecA protein into post-replication gaps. However, the targeting mechanism that brings these proteins to appropriate gaps is unclear. Here, we propose that targeting may involve a direct interaction between RecF and DnaN. In vivo, RecF is commonly found at the replication fork. Over-expression of RecF, but not RecO or a RecF ATPase mutant, is extremely toxic to cells. We provide evidence that the molecular basis of the toxicity lies in replisome destabilization. RecF over-expression leads to loss of genomic replisomes, increased recombination associated with post-replication gaps, increased plasmid loss, and SOS induction. Using three different methods, we document direct interactions of RecF with the DnaN β-clamp and DnaG primase that may underlie the replisome effects. In a single-molecule rolling-circle replication system in vitro, physiological levels of RecF protein trigger post-replication gap formation. We suggest that the RecF interactions, particularly with DnaN, reflect a functional link between post-replication gap creation and gap processing by RecA. RecF’s varied interactions may begin to explain how the RecFOR system is targeted to rare lesion-containing post-replication gaps, avoiding the potentially deleterious RecA loading onto thousands of other gaps created during replication.
Therapeutic disruption of RAD52–ssDNA complexation via novel drug-like inhibitors
Authors: Bhat Divya S , Malacaria Eva , Biagi Ludovica Di , Razzaghi Mortezaali , Honda Masayoshi , Hobbs Kathryn F , Hengel Sarah R , Pichierri Pietro , Spies M Ashley , Spies Maria 
Published: May 2023

Abstract
RAD52 protein is a coveted target for anticancer drug discovery. Similar to poly-ADP-ribose polymerase (PARP) inhibitors, pharmacological inhibition of RAD52 is synthetically lethal with defects in genome caretakers BRCA1 and BRCA2 (∼25% of breast and ovarian cancers). Emerging structure activity relationships for RAD52 are complex, making it challenging to transform previously identified disruptors of the RAD52–ssDNA interaction into drug-like leads using traditional medicinal chemistry approaches. Using pharmacophoric informatics on the RAD52 complexation by epigallocatechin (EGC), and the Enamine in silico REAL database, we identified six distinct chemical scaffolds that occupy the same physical space on RAD52 as EGC. All six were RAD52 inhibitors (IC50 ∼23–1200 μM) with two of the compounds (Z56 and Z99) selectively killing BRCA-mutant cells and inhibiting cellular activities of RAD52 at micromolar inhibitor concentrations. While Z56 had no effect on the ssDNA-binding protein RPA and was toxic to BRCA-mutant cells only, Z99 inhibited both proteins and displayed toxicity towards BRCA-complemented cells. Optimization of the Z99 scaffold resulted in a set of more powerful and selective inhibitors (IC50 ∼1.3–8 μM), which were only toxic to BRCA-mutant cells. RAD52 complexation by Z56, Z99 and its more specific derivatives provide a roadmap for next generation of cancer therapeutics.