bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capturing the blue-light activated state of the Phot-LOV1 domain fromChlamydomonas reinhardtiiusing time-resolved serial synchrotron crystallography
Authors: Gotthard Guillaume , Mous Sandra , Weinert Tobias , Antonelli Maia Raiza Nara , James Daniel , Dworkowski Florian , Gashi Dardan , Furrer Antonia , Ozerov Dmitry , Panepucci Ezequiel , Wang Meitian , Schertler Gebhard F. X. , Heberle Joachim , Standfuss Joerg , Nogly Przemyslaw 
Published: November 2023

AbstractLight-Oxygen-Voltage (LOV) domains are small photosensory flavoprotein modules that allow converting external stimuli (sunlight) into intracellular signals responsible for various cell behavior (e.g.,phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that results in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the observation of the activation cascade of the LOV domain in real-time, which has been elusive.In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 fromChlamydomonas reinhardtii(CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to the actual data collection process, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the obtained crystals preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations ofCrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.
Oleoylethanolamide effects on stress-induced alcohol consumption: a lipid at crossroads between stress, reward and neuroinflammation
Authors: González-Portilla Macarena , Montagud-Romero Sandra , Mellado Susana , Rodríguez de Fonseca Fernando , Pascual María , Rodríguez-Arias Marta 
Published: November 2023

AbstractThe endocannabinoid system is involved in multiple drug-related behavior as well as in the stress response. The transient increase in endogenous cannabinoids as well as endocannabinoid-like molecules contributes to healthy adaptation to stress exposure. In this study, we tested the effect of systemic OEA treatment (10mg/kg) before or after social defeat (SD) on alcohol self-administration (SA). Mice were divided into non-stressed (EXP) and stressed mice (SD) and randomly assigned to a treatment condition (CTRL, OEA or 10OEA). Mice in the EXP/SD-OEA group received four doses before each SD encounter while mice in the EXP/SD-10OEA mice received 10 daily doses after stress exposure. Three weeks after SD, mice were trained to alcohol 20% (vol/vol) SA. Upon extinction, a cue-induced reinstatement test was performed. Our results showed that only multiple-dose chronic OEA treatment (SD-10OEA group) was effective in preventing the stress-induced increase in alcohol consumption observed in defeated mice. We did not observe any effects of OEA on relapse-like behavior. Altogether, these data suggest that exogenously increasing OEA levels counteracts the adverse effects of stress on alcohol drinking.
Circadian coupling of mitochondria in a deep-diving mammal
Authors: Ciccone Chiara , Kante Fayiri , Folkow Lars P. , Hazlerigg David G. , West Alexander C. , Wood Shona H. 
Published: November 2023

ABSTRACTRegulation of mitochondrial oxidative phosphorylation is essential to match energy supply to changing cellular energy demands, and to cope with periods of hypoxia. Recent work implicates the circadian molecular clock in control of mitochondrial function and hypoxia sensing. Since diving mammals experience intermittent episodes of severe hypoxia, with diel patterning in dive depth and duration, it is interesting to consider circadian - mitochondrial interaction in this group. Here we demonstrate that the hooded seal (Cystophora cristata), a deep diving Arctic pinniped, shows strong daily patterning of diving behaviour in the wild. Cultures of hooded seal skin fibroblasts exhibit robust circadian oscillation of the core clock genesper2andarntl. In liver tissue collected from captive hooded seals, expression ofarntlwas some 4-fold higher in the middle of night than in the middle of the day. To explore the clock-mitochondria relationship, we measured the mitochondrial oxygen consumption in synchronized hooded seal skin fibroblasts and found a circadian variation in mitochondrial activity, with higher coupling efficiency of complex I coinciding with the trough ofarntlexpression. These results open the way for further studies of circadian - hypoxia interactions in pinnipeds during diving.SUMMARY STATEMENTA functional clockwork and circadian variation in mitochondrial complex I efficiency is demonstrated in skin fibroblasts from the deep diving hooded seal.
Antiproliferative Activity of Cephalotaxus Esters: Overcoming Chemoresistance in Cancer Therapy
Authors: Yong-Gonzalez Vladimir , Radu Constantine , Calder Paul A. , Shum David , Gin David Y. , Frattini Mark G. , Djaballah Hakim 
Published: November 2023

AbstractOmacetaxine, a semisynthetic form of Homoharringtonine (HHT), was approved for the treatment of chronic myeloid leukemia (CML). Previously, we published the synthesis of this natural alkaloid and three of its derivatives: deoxyharringtonine (DHT), deoxyhomoharringtonine (DHHT), and bis(demethyl)-deoxyharringtonine (BDHT); and reported on its refractory activity against the HL-60/RV+ cells over-expressing P-glycoprotein 1 (MDR1). In this study, we explored the extent of this resistance by first expanding the panel of established cell lines and second, using a panel of 21 leukemia patient derived primary cells. Here, we report a consistent resistance to HTT in K562 derived cells and in MES-SA/MX2 derived cells resistant to mitoxanthrone; all of them over-express MDR1, while we found U87MG-ABCG2 and H69AR cells to be very sensitive to HTT. In contrast, DHT, DHHT, and BDHT seemingly overcome this resistance due to the changes made to the acyl chain of HTT rendering the derivatives less susceptible to efflux. Surprisingly, the leukemia primary cells were very sensitive to HHT and its derivatives with low nanomolar potencies, followed by a new class of CDC7 kinase inhibitors, the anthracycline class of topoisomerase inhibitors, the DNA intercalator actinomycin-D, and the vinca alkaloid class of microtubule inhibitors. The mechanism of cell death induced by HTT and DHHT was found to be mediated via Caspase 3 cleavage leading to apoptosis. Taken together, our results confirm that HHT is a substrate for MDR1. It opens the door to a new opportunity to clinically evaluate HHT and its derivatives for the treatment of AML and other cancers.
Advance Glycation End-products accelerate amyloid deposits in adipocyte’s lipid droplets
Authors: Izgilov Roza , Kislev Nadav , Omari Eman , Benayahu Dafna 
Published: November 2023

AbstractAdipose tissue dysfunction is central to insulin resistance, and the emergence of type 2 diabetes (T2D) is associated with elevated levels of carbonyl metabolites from glucose metabolism. In this study, using methylglyoxal (MGO) and glycolaldehyde (GAD) carbonyl metabolites, induced protein glycation leading to misfolding and β-sheet formation and generation of advanced glycation end products (AGEs). The formed AGEs compromise adipocytes activity.Microscopic and spectroscopic assays were used to examine the impact of MGO and GAD on lipid droplet - associated proteins. The results provide information about how glycation leads to the appearance of amyloidogenic proteins formation that hinders metabolism and autophagy in adipocytes. We measured the beneficial effects of metformin, an anti-diabetic drug, on misfolded protein as assessed by thioflavin (ThT) spectroscopy and improved autophagy. In vitro findings were complemented by in vivo analysis of white adipose tissue (WAT), where lipid droplet-associated β-amyloid deposits were predominantly linked to adipose triglyceride lipase (ATGL), a lipid droplet protein. Bioinformatics, imaging, and biochemical methods affirm ATGL’s role in β-sheet secondary structure creation. Our results highlighted the pronounced presence of amyloidogenic proteins in adipocytes treated with carbonyl compounds, potentially reshaping our understanding of adipocyte pathology in the context of T2D. This in-depth exploration offers novel perspectives on related pathophysiology and underscores the potential of adipocytes as pivotal therapeutic targets, bridging T2D, amyloidosis, protein glycation, and adipocyte malfunction.Significance StatementThe generation of advanced glycation end products (AGEs) has a strong connection to diabetes severity . Adipose tissue is known to play a key role in the metabolic impairment and obesity associated with diabetes. We used the carbonyl compounds methylglyoxal (MGO) and glycolaldehyde (GAD) to create AGEs in adipocytes. The results of this study indicate that glycation not only affects cell metabolism and impairs adipocyte lipolysis, but also alters autophagy and increases protein amyloid deposits related to the membrane of lipid droplets. We identify the ATGL as a protein prone to β sheet alteration. consequently, ATGL emerges as a pivotal actor in lipid droplet metabolism and a prospective therapeutic target for T2D complications.
Potential climate change effects on the distribution of urban and sylvatic dengue and yellow fever vectors
Authors: Aliaga-Samanez Alisa , Romero David , Murray Kris , Segura Marina , Real Raimundo , Olivero Jesús 
Published: November 2023

AbstractClimate change may increase the risk of dengue and yellow fever transmission by urban and sylvatic mosquito vectors. Previous research primarily focused onAedes aegyptiandAedes albopictus. However, these diseases involve a complex transmission cycle in which sylvatic vectors are also involved. Our aim was to analyse which mosquito species could contribute to the increased risk of transmission of these diseases due to climate change, and to identify where the risk increase could most likely occur. Using a biogeographical approach, we mapped areas where mosquito favourability could increase, decrease or remain stable in the near (2041-2060) and distant (2061-2080) future.Models predict dengue vectors expanding in West and Central Africa and in South-East Asia, reaching Borneo. Yellow fever vectors could spread in West and Central Africa and in the Amazon. In Europe, the models suggest a re-establishment ofAe. aegypti, whileAe. albopictuswill continue to find new favourable areas. The results underline the need to focus more on vectorsAe. vittatus,Ae. luteocephalusandAe. africanusin West and Central sub-Saharan Africa, especially Cameroon, Central Africa Republic, and northern Democratic Republic of Congo; and suggest the need for a protocol to prevent dengue and yellow fever that include surveillance of neglected sylvatic vectors.
Enzalutamide Induces Cytotoxicity in Desmoplastic Small Round Cell Tumor Independent of the Androgen Receptor
Authors: Magrath Justin W. , Goldberg Ilon N. , Truong Danh D. , Hartono Alifiani B. , Sampath Shruthi Sanjitha , Jackson Chandler E. , Ghosh Anushka , Cardin Derrick L. , Zhang Haitao , Ludwig Joseph A. , Lee Sean B. 
Published: November 2023

AbstractDesmoplastic Small Round Cell Tumor (DSRCT) is a rare, pediatric cancer caused by the EWSR1::WT1 fusion protein. DSRCT predominantly occurs in males, which comprise 80-90% of the patient population. While the reason for this male predominance remains unknown, one hypothesis is that the androgen receptor (AR) plays a critical role in DSRCT and elevated testosterone levels in males help drive tumor growth. Here, we demonstrate that AR is highly expressed in DSRCT relative to other fusion-driven sarcomas and that the AR antagonists enzalutamide and flutamide reduce DSRCT growth. However, despite these findings, which suggest an important role for AR in DSRCT, we show that DSRCT cell lines form xenografts in female mice at the same rate as male mice and AR depletion does not significantly alter DSRCT growthin vitro. Further, we find that AR antagonists reduce DSRCT growth in cells depleted of AR, establishing an AR-independent mechanism of action. These findings suggest that AR dependence is not the reason for male predominance in DSRCT and that AR-targeted therapies may provide therapeutic benefit primarily through an AR-independent mechanism that requires further elucidation.
PROLONG: Penalized Regression for Outcome guided Longitudinal Omics analysis with Network and Group constraints
Authors: Broll Steve , Basu Sumanta , Lee Myung Hee , Wells Martin T. 
Published: November 2023

AbstractMotivationThere is a growing interest in longitudinal omics data, but there are gaps in existing methodology in the high-dimensional setting. This paper focuses on selecting metabolites that co-vary with Tuberculosis mycobacterial load. The proposed method is applied to general continuous longitudinal outcomes with continuous longitudinal omics predictors. Simple longitudinal models examining a single omic predictor at a time do not leverage the correlation across predictors, thus losing power. We propose a penalized regression approach on the first differences of the data that extends the lasso + Laplacian method (Li and Li 2008) to a longitudinal group lasso + Laplacian approach. Our method, PROLONG, leverages the first differences of the data to address the piecewise linear structure and the observed time dependence. The Laplacian network constraint incorporates the dependence structure of the predictors, and the group lasso constraint induces sparsity while grouping metabolites across their first differenced observations.ResultsWith an automated selection of model hyper-parameters, PROLONG correctly selects target metabolites with high specificity and sensitivity across simulation scenarios and sizes. PROLONG selects a set of metabolites from the real data that includes interesting targets identified during EDA.AvailabilityR package ‘prolong’ is in development.ConclusionsPROLONG is a powerful method for selecting interesting features in high dimensional longitudinal omics data that co-vary with some continuous clinical outcome.Contactsb2643@cornell.edu
Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinoma
Authors: Caeiro Lucas D. , Nakata Yuichiro , Borges Rodrigo L. , Garcia-Martinez Liliana , Bañuelos Carolina P. , Stransky Stephanie , Chan Ho Lam , Brabson John , Domínguez Diana , Zhang Yusheng , Lewis Peter W. , Aznar-Benitah Salvador , Cimmino Luisa , Bilbao Daniel , Sidoli Simone , Verdun Ramiro E. , Morey Lluis 
Published: November 2023

AbstractApproximately 20% of head and neck squamous cell carcinomas (HNSCC) exhibit reduced methylation on lysine 36 of histone H3 (H3K36me) due to mutations in histone methylase NSD1 or a lysine-to-methionine mutation in histone H3 (H3K36M). Whether such alterations of H3K36me can be exploited for therapeutic interventions is still unknown. Here, we show that HNSCC models expressing H3K36M can be divided into two groups: those that display aberrant accumulation of H3K27me3 and those that maintain steady levels of H3K27me3. The first group shows decreased proliferation, genome instability, and increased sensitivity to genotoxic agents, such as PARP1/2 inhibitors. In contrast, the H3K36M HNSCC models with steady H3K27me3 levels do not exhibit these characteristics unless H3K27me3 levels are elevated, either by DNA hypomethylating agents or by inhibiting the H3K27me3 demethylases KDM6A/B. Mechanistically, we found that H3K36M reduces H3K36me by directly impeding the activities of the histone methyltransferase NSD3 and the histone demethylase LSD2. Notably, we found that aberrant H3K27me3 levels induced by H3K36M expression is not a bona fide epigenetic mark in HNSCC since it requires continuous expression of H3K36M to be inherited. Moreover, increased sensitivity of H3K36M HNSCC models to PARP1/2 inhibitors solely depends on the increased H3K27me3 levels. Indeed, aberrantly high H3K27me3 levels decrease BRCA1 and FANCD2-dependent DNA repair, resulting in higher sensitivity to DNA breaks and replication stress. Finally, in support of our in vitro findings, a PARP1/2 inhibitor alone reduce tumor burden in a H3K36M HNSCC xenograft model with elevated H3K27me3, whereas in a H3K36M HNSCC xenograft model with consistent H3K27me3 levels, a combination of PARP1/2 inhibitors and agents that upregulate H3K27me3 proves to be successful. In conclusion, our findings underscore a delicate balance between H3K36 and H3K27 methylation, essential for maintaining genome stability. This equilibrium presents promising therapeutic opportunities for patients with H3K36me-deficient tumors.
Hidden rAAV Breakpoints Detected Using Single-Molecule, Modified Base Sequencing
Authors: Hanscom Terrence , Soares Luis M M , Zheng Alice , Bourgeois Nathanael , Gall Katherine , St Martin Thia , Wright Jason , Selby Donald E 
Published: November 2023

AbstractThe AAV genome is a single stranded DNA molecule packaged in an icosahedral protein capsid. Vector genomes of plus and minus polarities are packaged and complementary genomic strands hybridize when lysedin vitro. Standard sequencing library methods cause loss of information from individual genomes when mismatches and gaps are repaired. To retain original molecular information, modified bases are used during the repair step which allows pre-existing DNA to be distinguished from DNA added during library preparation. Modified bases introduced during repair are identified using the Sequel II system and used to detect HIDdEN DNA breakpoints (HIDEN-Seq). The most frequent breakpoints in an AAV vector subject to high strand breakage during packaging were linked to adjacent secondary structure, prompting changes in nearby sequences to reduce breakage. This use of modified bases for localizing DNA breaks enables better vector design, resulting in higher quality gene therapy vectors. The same approach can be used in other systems where knowledge of pre-existing sequence and structure is important.
Loss of function ofAtrxleads to activation of alternative lengthening of telomeres in a primary mouse model of sarcoma
Authors: Pierpoint Matthew , Floyd Warren , Wisdom Amy J. , Luo Lixia , Ma Yan , Waitkus Matthew S. , Kirsch David G. 
Published: November 2023

AbstractThe development of a telomere maintenance mechanism is essential for immortalization in human cancer. While most cancers elongate their telomeres by expression of telomerase, 10-15% of human cancers use a pathway known as alternative lengthening of telomeres (ALT). In this work, we developed a genetically engineered primary mouse model of sarcoma in CAST/EiJ mice which displays multiple molecular features of ALT activation after CRISPR/Cas9 introduction of oncogenicKrasG12Dand loss of function mutations ofTrp53andAtrx.In this model, we demonstrate that the loss ofAtrxcontributes to the development of ALT in an autochthonous tumor, and this process occurs independently of telomerase function by variation of mTR alleles. Furthermore, we find that telomere shortening from the loss of telomerase leads to higher chromosomal instability while loss ofAtrxand activation of ALT lead to an increase in telomeric instability, telomere sister chromatid exchange, c-circle production, and formation of ALT-associated promyelocytic leukemia bodies (APBs). The development of this primary mouse model of ALT could enable future investigations into therapeutic vulnerabilities of ALT activation and its mechanism of action.
Neural markers of reduced arousal and consciousness in Mild Cognitive Impairment
Authors: Estarellas Mar , Huntley Jonathan , Bor Daniel 
Published: November 2023

ABSTRACTObjectivesPeople with Alzheimer’s Disease (AD) experience changes in their level and content of consciousness, but there is little research on biomarkers of consciousness in pre-clinical AD and MCI. This study investigated whether levels of consciousness are decreased in people with MCI.MethodsA multi-site MEG dataset, BIOFIND, comprising 83 people with MCI and 83 age matched controls, was analysed. Arousal (and drowsiness) was assessed by computing the theta-alpha ratio (TAR). The Lempel-Ziv algorithm (LZ) was used to quantify the information content of brain activity, with higher LZ values indicating greater complexity and potentially a higher level of consciousness.ResultsLZ was lower in the MCI group vs controls, indicating a reduced level of consciousness in MCI. TAR was higher in the MCI group vs controls, indicating a reduced level of arousal (i.e. increased drowsiness) in MCI. LZ was also found to be correlated with MMSE scores, suggesting a direct link between cognitive impairment and level of consciousness in people with MCI.ConclusionsA decline in consciousness and arousal can be seen in MCI. As cognitive impairment worsens, measured by MMSE scores, levels of consciousness and arousal decrease. These findings highlight how monitoring consciousness using biomarkers could help understand and manage impairments found at the preclinical stages of AD. Further research is needed to explore markers of consciousness between people who progress from MCI to dementia and those who do not, and in people with moderate and severe AD, to promote person-centred care.
TBXT dose sensitivity and the decoupling of nascent mesoderm specification from EMT progression in 2D human gastruloids
Authors: Bulger Emily A. , Muncie-Vasic Ivana , Libby Ashley R.G. , McDevitt Todd C. , Bruneau Benoit G. 
Published: November 2023

ABSTRACTIn the nascent mesoderm, levels of Brachyury (TBXT) expression must be precisely regulated to ensure cells exit the primitive streak and pattern the anterior-posterior axis, but how this varying dosage informs morphogenesis is not well understood. In this study, we define the transcriptional consequences of TBXT dose reduction during early human gastrulation using human induced pluripotent stem cell (hiPSC)-based models of gastrulation and mesoderm differentiation. Multiomic single-nucleus RNA and single-nucleus ATAC sequencing of 2D gastruloids comprised of WT, TBXT heterozygous (TBXT-Het), or TBXT null (TBXT-KO) hiPSCs reveal that varying TBXT dosage does not compromise a cell’s ability to differentiate into nascent mesoderm, but that the loss of TBXT significantly delays the temporal progression of the epithelial to mesenchymal transition (EMT). This delay is dependent on TBXT dose, as cells heterozygous for TBXT proceed with EMT at an intermediate pace relative to WT or TBXT-KO. By differentiating iPSCs of the allelic series into nascent mesoderm in a monolayer format, we further illustrate that TBXT dose directly impacts the persistence of junctional proteins and cell-cell adhesions. These results demonstrate that EMT progression can be decoupled from the acquisition of mesodermal identity in the early gastrula and shed light on the mechanisms underlying human embryogenesis.