bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide methylation profiling of cell-free DNA in maternal plasma using Methylated DNA Sequencing (MeD-seq)
Authors: van Vliet Marjolein M. , Boers Ruben G. , Boers Joachim B. , Schäffers Olivier J.M. , van der Meeren Lotte E. , Steegers-Theunissen Régine P.M. , Gribnau Joost , Schoenmakers Sam 
Published: August 2024

AbstractBackgroundPlacental-originated cell-free DNA (cfDNA) provides unique opportunities to study (epi)genetic placental programming remotely, but studies investigating the cfDNA methylome are scarce and usually technologically challenging. Methylated DNA sequencing (MeD-seq) is well-compatible with low cfDNA concentrations and has a high genome-wide coverage. We therefore aim to investigate the feasibility of genome-wide methylation profiling of first trimester maternal cfDNA using MeD-seq, by identifying placental-specific methylation marks in cfDNA.MethodsWe collected cfDNA from non-pregnant controls (female n=6, male n=12) and pregnant women (n=10), first trimester placentas (n=10), and paired preconceptional and first trimester buffy coats (total n=20). Differentially methylated regions (DMRs) were identified between pregnant and non-pregnant women. We investigated placental-specific markers in maternal cfDNA, includingRASSF1promoter and Y-chromosomal methylation, and studied overlap with placental and buffy coat DNA methylation.ResultsWe identified 436 DMRs between cfDNA from pregnant and non-pregnant women which were validated using male cfDNA.RASSF1promoter methylation was higher in maternal cfDNA (fold change 2.87, unpaired t-test p<0.0001). Differential methylation of Y-chromosomal sequences could determine fetal sex. DMRs in maternal cfDNA showed large overlap with DNA methylation of these regions in placentas and buffy coats, indicating a placental and immune-cell contribution to the pregnancy-specific cfDNA methylation signature. Sixteen DMRs in maternal cfDNA were specifically found only in placentas. These novel potential placental-specific DMRs were more prominent thanRASSF1.ConclusionsMeD-seq can detect (novel) genome-wide placental DNA methylation marks and determine fetal sex in maternal cfDNA. This study supports future research into maternal cfDNA methylation using MeD-seq.Graphical abstractStudies investigating the maternal cell-free DNA (cfDNA) methylome are scarce and generally technologically challenging. We identified 436 autosomal differentially methylated regions (DMRs) between cfDNA from pregnant and non-pregnant women, using the innovative methylated DNA sequencing (MeD-seq) technique. Y-chromosomal methylation could determine fetal sex, we show hypermethylation of the placental-markerRASSF1, and identify 16 novel placental-specific markers in maternal cfDNA including DMRs related toTMEM240, DHRS3, andPCMTD2. This pilot study supports future research into the maternal cfDNA methylome using MeD-seq.
An affordable solution for investigating zebra finch intracranial electroencephalography (iEEG) signals
Authors: Abolghasemi Mohammad-Mahdi , Shirsavar Shahriar Rezghi , Bahramani Amirreza , Yekani Milad 
Published: August 2024

AbstractThe zebra finch is a well-studied animal model for investigating the neural mechanisms of vocal learning, and electrophysiology is the primary technique for understanding their song system. Most of the studies on zebra finches have focused on intracerebral recordings. However, these methods are only affordable for limited laboratories. Recently, different open-source hardware for acquiring electroencephalography (EEG) signals has been developed. It’s unclear whether these solutions suit zebra finch studies as they have not been evaluated. Electrocorticography signals can provide a preliminary guide for more in-depth inquiries and also aid in understanding the global behavior of the bird’s brain, as opposed to the more common localized approach. We present a detailed protocol for acquiring intracranial electroencephalography (iEEG) data from zebra finches using the OpenBCI Cyton board, an open-source device. We implemented stainless steel electrodes on the brain’s surface and recorded the brain signals from two recording sites above two auditory-responsive nuclei. To validate our method, we ran two different experiments. In the first experiment, we recorded neural activity under various concentrations of isoflurane and extracted the suppression duration to measure anesthesia depth. In the second experiment, we head-fixed the birds and, under light anesthesia, presented them with various auditory stimuli to evaluate event-related potentials (ERP) and generate spectrograms. The results showed a significant increase in suppression duration with deeper anesthesia, and the ERP and spectrogram responses to auditory stimuli differed accordingly. These findings indicate that using our methodology, one can successfully collect iEEG signals from zebra finches. These findings pave the way for future studies to use iEEG to investigate bird cognition in a more affordable way.
Evaluation of a Deep Learning Based Approach to Computational Label Free Cell Viability Quantification
Authors: Reno Allison , Tang Jianan , Sudbeck Madeline , Fe Custodio Precious , Baldus Brandi , McLaughlin Elizabeth , Peng Fei , Xiao Hai 
Published: August 2024

AbstractOne of the most common techniques found in a cell biology or tissue engineering lab is the cytotoxicity assay. This can be performed using a variety of different dyes and stains and various protocols to result in a clear indication of dead and live cells within a culture to quantify the viability of a culture and monitor for sudden drops or increases in viability by a drug, material, viral vector, etc introduced into the culture. This assay helps cell biologists determine the health of their culture and what toxicity added substances may add to the culture and whether they are appropriate and safe to use with human cells. However, many of the dyes and stains used for this process are eventually toxic to cells, rendering the cells useless after testing and preventing real time monitoring of the same culture over a period of hours or days. Computation biology is moving cell biology towards novel and innovative techniques such as in silico labeling and dye free labeling using deep learning algorithms. In this work, we investigate whether it is feasible to train a Resnet CNN model to detect morphological changes in human cells that indicate cell death in order to classify cells as live or dead without utilizing a stain or dye. This work also aims to train one CNN model to count all cells regardless of viability status to get a total cell count, and then one CNN model that specifically identifies and counts all of the dead cells for an accurate dead and live cell total by utilizing both pieces of data to determine a general viability percentage for the culture. Additionally, this work explores the use of various image enhancements to understand if this process helps or impedes the deep learning models in their detection of total cells and dead cells.
Bisphenol A Disrupts Mitochondrial Functionality Leading to Senescence and Apoptosis in Human Amniotic Mesenchymal Stromal Cells
Authors: Ficai Sara , Papait Andrea , Magatti Marta , Masserdotti Alice , Gasik Michael , Silini Antonietta Rosa , Parolini Ornella 
Published: August 2024

AbstractIn today’s context, microplastics pollution has become an increasingly pressing issue not only for the environmental fallout but also for the assumed negative effects on human health. It is now well-established that microplastics (>1 mm in size) can enter the human body through ingestion, inhalation, dermal contact and also maternal-fetal transmission. Alarming was the recent findings of microplastics within the human term placenta. Among the degradation by-products of microplastics, Bisphenol A (BPA) has emerged as a hazardous chemical, with potential toxicity at multisystemic level, particularly on the earliest stages of human development. Based on these findings, our study focuses on assessing the impact of BPA on properties and functions of mesenchymal stromal cells isolated from the amniotic membrane (hAMSC) of the human term placenta. The amniotic membrane surrounds the fetus, playing a fundamental protective role toward toxic chemicals and pollutants that the mother may encounter. Our research revealed how exposure to increasing concentrations of BPA compromise mitochondrial functionality in hAMSC, resulting in enhanced production of reactive oxygen species at mitochondrial level (mtROS). This, in turn, leads to the stabilization of p53, which triggers an increased expression of p21 and p27 encoding genes and an imbalance in the genetic expression of Bax and Bcl-2. Additionally, we observed upregulated expression of cytokines and chemokines associated with the senescence-associated secretory phenotype (SASP). The increased oxidative stress, which plays a central role in BPA-mediated toxicity, can trigger the activation of the senescence pathways, or culminate in cell death, due to the overwhelming stress conditions. Therefore, our results provide novel insights into the mechanism of action of BPA and elucidates its impact on the functionality of hAMSC. This underscores the pressing need to reconsider the use of BPA as a plastic additive, mitigating the potential adverse effects on babies.
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon
Authors: Hartley Gabrielle A. , Okhovat Mariam , Hoyt Savannah J. , Fuller Emily , Pauloski Nicole , Alexandre Nicolas , Alexandrov Ivan , Drennan Ryan , Dubocanin Danilo , Gilbert David M. , Mao Yizi , McCann Christine , Neph Shane , Ryabov Fedor , Sasaki Takayo , Storer Jessica M. , Svendsen Derek , Troy William , Wells Jackson , Core Leighton , Stergachis Andrew , Carbone Lucia , O’Neill Rachel J. 
Published: August 2024

SummaryGreat apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon,Hoolock leuconedys(HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a “perfect storm” of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.
Integrative transcriptomics and electrophysiological profiling of hiPSC-derived neurons identifies novel druggable pathways in Koolen-de Vries Syndrome
Authors: Verboven A.H.A. , Puvogel S. , Kolsters N. , Latour B. , Linda K. , Lewerissa E.I. , Mijdam R. , Dyke E. , Duineveld D. , Zoodsma M. , Claassen W.J.J. , Oudakker A. , Schoenmaker C. , Koolen D.A. , de Vries B.B.A. , ’t Hoen P.A.C. , Kasri N. Nadif 
Published: August 2024

AbstractKoolen-de Vries Syndrome (KdVS) is a neurodevelopmental disorder (NDD) with no treatment options due to a lack of understanding of its underlying pathophysiology. To investigate neuronal activity in KdVS, human induced pluripotent stem cell (hiPSC)-derived neurons from KdVS and control subjects were cultured on microelectrode arrays (MEAs). Our study identified reduced network burst rates, indicating disorganized network activity in KdVS neurons. To bridge molecular and functional aspects of the syndrome, we developed an experimental framework, MEA-seq, that integrates network activity measurements with high-throughput transcriptome profiling. This approach identified a negative correlation between the expression of the NDD-associated geneCLCN4and the network burst rate. Consequently, knockdown ofCLCN4in KdVS neurons restored the activity to control level, confirming a causal relationship between increasedCLCN4expression and reduced network burst rate. Additionally, we identified a positive correlation between mitochondrial gene expression and the network burst rate, and identified impaired mitochondrial function in KdVS hiPSC-derived neurons. The transcriptomic signature of KdVS neurons was then used for computational screening against drug perturbation signatures of the LINCS Consortium database, predicting other drug targets and compounds capable of reversing the expression of affected genes in KdVS neurons. We selected 10 compounds for experimental validation, identifying the antioxidant phloretin and the Rho-kinase inhibitor fasudil as potential candidates for restoring the network activity dysfunction in KdVS. We conclude that the integrative molecular and electrophysiological of hiPSC-derived neurons with MEA-seq has excellent potential for identifying novel drugs and druggable pathways for KdVS and other NDDs.
Palatability of Insecticides and Protein in Sugar Solutions to Argentine Ants
Authors: Wagner Thomas , Vorjans Moana , Garsi Elias , Werneke Cosmina , Czaczkes Tomer J. 
Published: August 2024

AbstractInvasive ant species likeLinepithema humilecause significant ecological and economic harm, making effective control strategies essential. Insecticide baits are currently the most effective approach for controlling ants. Therefore, quantifying how palatable or unpalatable baits, bait additives, or toxicants are, is critical for developing effective control methods. It has recently been demonstrated that in the comparative evaluation of foods, animals that are aware of both a test food and a comparator food exhibit greatly increased sensitivity when detecting the unpalatability of liquid baits. Here, we deploy a newly developed comparative evaluation methodology to examine the palatability toL. humileworkers of three toxicants used in invasive ant control: Fipronil, spinosad, and imidacloprid, as well as egg white protein.Ants showed no significant preference between pure sucrose and sucrose-toxicant solutions, indicating that they either cannot detect the toxicants or that they do not find them distasteful. Survival tests confirmed that the toxicant concentrations used were lethal, with a survival rate of 50% or below after 72 hours. However, ants found egg protein additive unpalatable, significantly preferring pure sucrose to a sucrose-egg protein mix.These findings confirm that three major toxicants are suitable for use in baits, and that reported abandonment or avoidance of toxic baits is not due to the unpalatability of these toxicants. However, the addition of egg protein to sucrose baits, even at ratios which optimise colony growth, is likely counterproductive. Future research should investigate the relative preference of invasive ants for various bait matrixes over naturally available food, ensuring more effective pest management strategies.
Patients with peripheral artery disease demonstrate altered expression of soluble and membrane-bound immune checkpoints by peripheral blood immune cells
Authors: Reitsema R.D. , Kurt S. , Rangel I. , Hjelmqvist H. , Dreifaldt M. , Sirsjö A. , Kumawat A.K. 
Published: August 2024

AbstractCardiovascular events seem to occur more frequently after treatment with immune checkpoint inhibitors. This suggests a possible role of immune checkpoints in accelerating atherosclerosis formation. We therefore aimed to assess the expression of soluble and membrane-bound immune checkpoints in patients with peripheral artery disease (PAD).We assessed the levels of 14 soluble immune checkpoints in fasting blood plasma of PAD patients (intermittent claudication, n= 37) and healthy controls (HCs, n=39) by Multiplex protein assay. We measured the levels of T-cell immunoglobulin and mucin domain 3 (TIM-3), programmed cell death 1 ligand 1 and 2 (PD-L1/2), B-and T-lymphocyte attenuator (BTLA), programmed cell death 1 (PD-1), glucocorticoid-induced TNRF-related protein (GITR), herpesvirus entry mediator (HVEM), cytotoxic T-lymphocyte associated protein 4 (CTLA-4), indoleamine 2,3-dioxygenase (IDO), CD28, CD27, CD80, CD137 and lymphocyte-activation gene 3 (LAG-3). The surface expression of CD28, PD-L2, PD-1, GITR, LAG-3, TIM-3 and BTLA on peripheral blood immune cells was determined by flow cytometry. Cytokine production capacity was measured by flow cytometry in TIM-3+ T cells to determine immune exhaustion.Soluble levels of PD-L2 were decreased in PAD patients, but only in females, whereas soluble levels of TIM-3 showed a trend towards increased concentration in female PAD patients. All monocyte subsets had increased frequencies of PD-L2+ cells in PAD patients. CD4+ T cells had increased frequencies of TIM-3+ cells, which showed little overlap with other immune exhaustion markers. TIM-3+ CD4+ T cells appeared to have a low capacity to produce pro-inflammatory cytokines, but a higher capacity to produce IL-10 compared to TIM-3-CD4+ T cells.We found that PAD patients show differences in expression of both membrane-bound and soluble immune checkpoints. Some of these differences might be caused by prolonged immune activation, although immune exhaustion markers did not always overlap.
Genomically recodedEscherichia coliwith optimized functional phenotypes
Authors: Hemez Colin , Mohler Kyle , Radford Felix , Moen Jack , Rinehart Jesse , Isaacs Farren J. 
Published: August 2024

AbstractGenomically recoded organisms hold promise for many biotechnological applications, but they may exhibit substantial fitness defects relative to their non-recoded counterparts. We used targeted metabolic screens, genetic analysis, and proteomics to identify the origins of fitness impairment in a model recoded organism,Escherichia coliC321.ΔA. We found that defects in isoleucine biosynthesis and release factor activity, caused by mutations extant in all K-12 lineage strains, elicited profound fitness impairments in C321.ΔA, suggesting that genome recoding exacerbates suboptimal traits present in precursor strains. By correcting these and other C321.ΔA-specific mutations, we engineered C321.ΔA strains with doubling time reductions of 17% and 42% in rich and minimal medium, respectively, compared to ancestral C321. Strains with improved growth kinetics also demonstrated enhanced ribosomal non-standard amino acid incorporation capabilities. Proteomic analysis indicated that C321.ΔA lacks the ability to regulate essential amino acid and nucleotide biosynthesis pathways, and that targeted mutation reversion restored regulatory capabilities. Our work outlines a strategy for the rapid and precise phenotypic optimization of genomically recoded organisms and other engineered microbes.
Otoacoustic emissions but not behavioral measurements predict cochlear-nerve frequency tuning in an avian vocal-communication specialist
Authors: Karosas Diana M. , Gonzales Leslie , Wang Yingxuan , Bergevin Christopher , Carney Laurel H. , Henry Kenneth S. 
Published: August 2024

AbstractFrequency analysis by the cochlea forms a key foundation for all subsequent auditory processing. Stimulus-frequency otoacoustic emissions (SFOAEs) are a potentially powerful alternative to traditional behavioral experiments for estimating cochlear tuning without invasive testing, as is necessary in humans. Which methods accurately predict cochlear tuning remains controversial due to only a single animal study comparing SFOAE-based, behavioral, and cochlear frequency tuning in the same species. The budgerigar (Melopsittacus undulatus) is a parakeet species with human-like behavioral sensitivity to many sounds and the capacity to mimic speech. Intriguingly, previous studies of critical bands, psychophysical tuning curves, and critical ratios in budgerigars show that behavioral tuning sharpness increases dramatically with increasing frequency from 1-3.5 kHz, doubling once per octave with peak tuning sharpness from 3.5-4 kHz. The pattern contrasts with slower monotonic growth of behavioral tuning sharpness with increasing frequency in other animals, including most avian species, suggesting a possible auditory specialization in budgerigars. We measured SFOAE-based and cochlear-afferent tuning in budgerigars, for comparison to previously reported behavioral results. SFOAE-based and cochlear-afferent tuning sharpness both increased monotonically and relatively slowly for higher frequencies, in contrast to the behavioral pattern. SFOAE-based tuning in budgerigars accurately predicted cochlear frequency tuning, and both measures aligned with typical patterns of cochlear tuning in other species. Divergent behavioral tuning in budgerigars is unlikely attributable to the periphery and could reflect specializations for central processing of masked signals. Our findings highlight the value of SFOAEs for estimating cochlear tuning and caution against direct inference of cochlear tuning from behavioral critical bands, psychophysical tuning curves, and critical ratios.
Amputation Triggers Long-Range Epidermal Permeability Changes in Evolutionarily Distant Regenerative Organisms
Authors: Dooling Kelly E. , Kim Ryan T. , Kim Elane M. , Chen Erica , Abouelela Adnan , Tajer Benjamin J. , Lopez Noah J. , Paoli Julia C. , Powell Connor J. , Luong Anna G. , Wu S.Y. Celeste , Thornton Kara N. , Singer Hani D. , Savage Aaron M. , Bateman Joel , DiTommaso Tia , Payzin-Dogru Duygu , Whited Jessica L. 
Published: August 2024

ABSTRACTPrevious studies have reported that amputation invokes body-wide responses in regenerative organisms, but most have not examined the implications of these changes beyond the region of tissue regrowth. Specifically, long-range epidermal responses to amputation are largely uncharacterized, with research on amputation-induced epidermal responses in regenerative organisms traditionally being restricted to the wound site. Here, we investigate the effect of amputation on long-range epidermal permeability in two evolutionarily distant, regenerative organisms: axolotls and planarians. We find that amputation triggers a long-range increase in epidermal permeability in axolotls, accompanied by a long-range epidermal downregulation in MAPK signaling. Additionally, we provide functional evidence that pharmacologically inhibiting MAPK signaling in regenerating planarians increases long-range epidermal permeability. These findings advance our knowledge of body-wide changes due to amputation in regenerative organisms and warrant further study on whether epidermal permeability dysregulation in the context of amputation may lead to pathology in both regenerative and non-regenerative organisms.GRAPHICAL ABSTRACT