bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escaping antibody responses to bacteriolytic enzymes Pal and Cpl-1 by epitope scanning and engineering
Authors: Harhala Marek , Gembara Katarzyna , Rybicka Izabela , Kaźmierczak Zuzanna , Miernikiewicz Paulina , Majewska Joanna , Budziar Wiktoria , Nasulewicz-Goldeman Anna , Nelson Daniel C. , Owczarek Barbara , Dąbrowska Krystyna 
Published: October 2022

AbstractBacteriolytic enzymes are promising antibacterial agents, but they can cause a typical immune responsein vivo. In this study, we used a targeted modification of two antibacterial endolysins, Pal and Cpl-1. We identified the key immunogenic amino-acids, and designed and tested new, bacteriolytic variants with altered immunogenicity. One new variant of Pal (257-259 MKS → TFG) demonstrated decreased immunogenicity while a similar mutant (257-259 MKS → TFK) demonstrated increased immunogenicity. A third variant (280-282 DKP → GGA) demonstrated significantly increased antibacterial activity and it was not cross-neutralized by antibodies induced by the wild-type enzyme. We propose this variant as a new engineered endolysin with increased antibacterial activity that is capable of escaping cross-neutralization by antibodies induced by wild-type Pal. We show that efficient antibacterial enzymes that avoid cross-neutralization by IgG can be developed by epitope scanning,in silicomodelling, and substitutions of identified key amino acids with a high rate of success. Importantly, this universal approach can be applied to many proteins beyond endolysins and has the potential for design of numerous biological drugs.
Intestinal myofibroblasts regulate intestinal epithelial cell plasticity via YAP/TAZ
Authors: Pastuła Agnieszka , Janssen Klaus-Peter , Steiger Katja , Slotta-Huspenina Julia , Friedman Richard A. , Hauck Stefanie M. , Ruiz-Fernandez Mauricio J. A. , Fottner Maximilian , Borgmann Martin , Ehmer Ursula , Schmid Roland M. , Wang Timothy C. , Quante Michael 
Published: October 2022

ABSTRACTIntestinal stromal cells play a key role as the crypt niche cells during epithelial homeostasis and tumor initiation. However, the underlying cellular and molecular mechanisms remain unclear. We developed various types of three-dimensional (3D) tissue culture models to culture small intestinal myofibroblasts (SI MFs) together with enteroids. SI MFs significantly enhanced self-renewal, lumen formation and survival of enteroids, that was mediated via a paracrine mechanism in a Wnt-independent manner. Such co-cultured enteroids resembled SI organoids derived from Apc+/1638N tumors. Microarray analysis showed upregulation of genes associated with YAP signaling in enteroids co-cultured with SI MFs, which was confirmed by protein quantification by mass spectrometry and could be correlated with findings from human colorectal tumor specimens. Mass spectrometric analysis of conditioned media and inhibitor studies pointed to a role for TGF-β in the SI MF-SI epithelium cross-talk. Altogether, utilizing different 3D stroma-epithelium co-culture models, we demonstrate here that SI MFs have the potential to induce a tumor-like phenotype in the intestinal crypts via a paracrine mechanism, that involves YAP and TGF-β, but not canonical Wnt signaling.
2D-QSAR and Molecular Docking based virtual screening of the herbal molecules against Alzheimer’s Disorder: An approach to predict CNS activity
Authors: Thakur Aman , Parashar Arun , Sharma Vivek , Kumar Ajay , Mehta Vineet 
Published: October 2022

AbstractAcetylcholinesterase (AChE) is one of the key enzyme targets that have been used clinically for the management of Alzheimer’s Disorder (AD). Numerous reports in the literature predict and demonstratein-vitro, andin-silicoanticholinergic activity of synthetic and herbal molecules, however, the majority of them failed to reproduce the results in preclinical or clinical settings. To address these issues, we developed a 2D-QSAR model that could not only efficiently predict the AChE inhibitory activity of herbal molecules but also predicted their potential to cross BBB to exert their beneficial effects during AD. Applying this model, virtual screening of the herbal molecules was performed and amentoflavone, asiaticoside, astaxanthin, bahouside, biapigenin, glycyrrhizin, hyperforin, hypericin, and tocopherol were predicted as the most promising herbal molecules for inhibiting AChE. Results were validated through molecular docking studies against human AChE (PDB ID: 4EY7). To determine whether or not these molecules can cross BBB to inhibit AChE within the CNS for being beneficial for the management of AD, we determined a CNS PPO score, which was found in the range of 1 to 3.76. Overall, the best results were observed for amentoflavone and our results demonstrated a PIC50value of 7.377 nM, molecular docking score of −11.5 kcal/mol, and CNS MPO score of 3.76. In conclusion, we successfully developed a reliable and efficient 2D-QSAR model and predicted amentoflavone to be the most promising molecule that could inhibit human AChE enzyme within the CNS and could prove beneficial for the management of AD.
Genealogical inference and more flexible sequence clustering using iterative PopPUNK
Authors: Zhao Bin , Lees John A. , Wu Hongjin , Yang Chao , Falush Daniel 
Published: October 2022

AbstractBacterial genome data are accumulating at an unprecedented speed due the routine use of sequencing in clinical diagnoses, public health surveillance and population genetics studies. Genealogical reconstruction is fundamental to many of these uses, however, inferring genealogy from large-scale genome datasets quickly, accurately, and flexibly is still a challenge. Here, we extend an alignment- and annotation-free method, PopPUNK, to increase its flexibility and interpretability across datasets. Our method, iterative-PopPUNK, rapidly produces multiple consistent cluster assignments across a range of sequence identities. By constructing a partially resolved genealogical tree with respect to these clusters, users can select a resolution most appropriate for their needs. We demonstrated the accuracy of clusters at all levels of similarity and genealogical inference of iterative-PopPUNK based on simulated data and obtained phylogenetically-concordant results in real datasets from seven bacterial species. Using two example sets ofEscherichia/Shigellagenomes andVibrio parahaemolyticusgenomes we show that iterative-PopPUNK can achieve cluster resolutions ranging from phylogroup down to sequence typing (ST). The iterative-PopPUNK algorithm is implemented in the ‘PopPUNK_iterate’ program, available as part of PopPUNK package.
Identifying Regulation with Adversarial Surrogates
Authors: Teichner Ron , Shomar Aseel , Barak O. , Brenner N. , Marom S. , Meir R. , Eytan D. 
Published: October 2022

AbstractHomeostasis, the ability to maintain a relatively constant internal environment in the face of perturbations, is a hallmark of biological systems. It is believed that this constancy is achieved through multiple internal regulation and control processes. Given observations of a system, or even a detailed model of one, it is both valuable and extremely challenging to extract the control objectives of the homeostatic mechanisms. In this work, we develop a robust data-driven method to identify these objectives, namely to understand: “what does the system care about?”. We propose an algorithm, Identifying Regulation with Adversarial Surrogates (IRAS), that receives an array of temporal measurements of the system, and outputs a candidate for the control objective, expressed as a combination of observed variables. IRAS is an iterative algorithm consisting of two competing players. The first player, realized by an artificial deep neural network, aims to minimize a measure of invariance we refer to as the coefficient of regulation. The second player aims to render the task of the first player more difficult by forcing it to extract information about the temporal structure of the data, which is absent from similar ‘surrogate’ data. We test the algorithm on two synthetic and one natural data set, demonstrating excellent empirical results. Interestingly, our approach can also be used to extract conserved quantities, e.g., energy and momentum, in purely physical systems, as we demonstrate empirically.
GABA decrease is associated with degraded neural specificity in the visual cortex of glaucoma patients
Authors: Bang Ji Won , Parra Carlos , Yu Kevin , Wollstein Gadi , Schuman Joel S. , Chan Kevin C. 
Published: October 2022

AbstractGlaucoma is an age-related neurodegenerative disease of the visual system, affecting both the eye and the brain. Yet its underlying metabolic mechanisms and neurobehavioral relevance remain largely unclear. Here, using proton magnetic resonance spectroscopy and functional magnetic resonance imaging, we investigated the GABAergic and glutamatergic systems in the visual cortex of glaucoma patients, as well as neural specificity, which is shaped by GABA and glutamate signals and underlies efficient sensory and cognitive functions. Our study showed that among the older adults, both GABA and glutamate levels decrease with increasing glaucoma severity regardless of age. Further, the reduction of GABA but not glutamate predicted the neural specificity. This association was independent of the impairments on the retina structure and age. Our results suggest that glaucoma-specific decline of GABA undermines neural specificity in the visual cortex and that targeting GABA could improve the neural specificity in glaucoma.
A cell size threshold triggers commitment to stomatal fate inArabidopsis
Authors: Gong Yan , Dale Renee , Fung Hannah F. , Amador Gabriel O. , Smit Margot E. , Bergmann Dominique C. 
Published: October 2022

AbstractHow flexible developmental programs integrate information from internal and external factors to modulate stem cell behavior is a fundamental question in developmental biology. Cells of theArabidopsisstomatal lineage modify the balance of stem cell proliferation and differentiation to adjust the size and cell type composition of mature leaves. Here, we report that meristemoids, one type of stomatal lineage stem cell, trigger the transition from asymmetric self-renewing divisions to commitment and terminal differentiation by crossing a critical cell size threshold. Through computational simulation, we demonstrate that this cell size-mediated transition allows robust, yet flexible termination of stem cell proliferation and we observe adjustments in the number of divisions before the differentiation threshold under several genetic manipulations. We experimentally evaluate several mechanisms for cell size sensing, and our data suggest that cell size is sensed via a chromatin ruler acting in the nucleus.
ASCL1 interacts with the mSWI/SNF at distal regulatory elements to regulate neural differentiation
Authors: Păun Oana , Tan Yu Xuan , Patel Harshil , Strohbuecker Stephanie , Ghanate Avinash , Cobolli-Gigli Clementina , Sopena Miriam Llorian , Gerontogianni Lina , Goldstone Robert , Ang Siew-Lan , Guillemot François , Dias Cristina 
Published: October 2022

AbstractPioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression. The role of neurogenic pioneer factor ASCL1 in shaping chromatin landscape in human neurogenesis remains unclear. Here we show that ASCL1 acts as a pioneer transcription factor in a transient population of progenitors. Using anin vitroASCL1 knockout model we show it drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a non-pioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. We find ASCL1 directly interacts with mammalian BAF SWI/SNF chromatin remodeling complexes, essential for neurogenesis and involved in multiple neurodevelopmental disorders. ASCL1 acts as a non-pioneer chromatin remodeler to regulate gene expression at a subset of loci, requiring mBAF SWI/SNF’s ATPase activity for cis-regulation of gene expression. Our findings demonstrate that ASCL1 is a key chromatin remodeler in human neurogenesis, uncovering an alternative mechanism of remodeling function dependent on partner ATPase activity.
Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion
Authors: Chatterton Zac , Lamichhane Praves , Rastegar Diba Ahmadi , Fitzpatrick Lauren , Lebhar Hélène , Marquis Christopher , Halliday Glenda , Kwok John B 
Published: October 2022

AbstractDNA methylation is a critical molecular mark involved in cellular differentiation and cell-specific processes. Single-cell whole genome DNA methylation profiling methods hold great potential to resolve the DNA methylation profiles of individual cell-types. Here we present a method that couples single-cell combinatorial indexing (sci) with enzymatic conversion (sciEM) of unmethylated cytosines. The method facilitates single-base resolution DNA methylation profiling of single-cells that is highly correlated with single-cell bisulfite-based workflows (r2>0.99) whilst improving sequencing alignment rates, reducing adapter contamination and over-estimation of DNA methylation levels (CpG and non-CpG). As proof-of-concept we perform sciEM analysis of the temporal lobe, motor cortex, hippocampus and cerebellum of the human brain to resolve single-cell DNA methylation of all major cell-types.
Differences in activity and stability drive transposable element variation in tropical and temperate maize
Authors: Ou Shujun , Collins Tyler , Qiu Yinjie , Seetharam Arun S. , Menard Claire C. , Manchanda Nancy , Gent Jonathan I. , Schatz Michael C. , Anderson Sarah N. , Hufford Matthew B. , Hirsch Candice N. 
Published: October 2022

AbstractMuch of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, tode novoannotate TEs in a pan-genome context. We then generated a unified TE annotation for a maize pan-genome derived from 26 reference-quality genomes, which revealed an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms revealed that 64.7% of the variability was contributed by LTR families that were young, less methylated, and more expressed in tropical maize, while 18.5% was driven by LTR families with removal or loss in temperate maize. This study demonstrates the use of a comprehensive pan-TE annotation to reveal the driving role of TEs in within-species genomic variation via their ongoing amplification and purging.
Geographically Weighted Linear Combination Test for Gene Set Analysis of a Continuous Spatial Phenotype as applied to Intratumor Heterogeneity
Authors: Amini Payam , Hajihosseini Morteza , Pyne Saumyadipta , Dinu Irina 
Published: October 2022

AbstractBackgroundThe impact of gene-sets on phenotype is not necessarily uniform across different locations of a cancer tissue. This study introduces a computational platform, GWLCT, for combining gene set analysis with spatial data modeling to provide a new statistical test for association of phenotypes and molecular pathways in spatial single-cell RNA-seq data collected from an input tumor sample.MethodsAt each location, the most significant linear combination is found using a geographically weighted shrunken covariance matrix and kernel function. Whether a fixed or adaptive bandwidth is determined based on a cross validation procedure. Our proposed method is compared to the global version of linear combination test (LCT), bulk and random-forest based gene-set enrichment analyses using data created by the Visium Spatial Gene Expression technique on an invasive breast cancer tissue sample, as well as 144 different simulation scenarios.ResultsIn an illustrative example, the new geographically weighted linear combination test, GWLCT, identifies the cancer hallmark gene-sets that are significantly associated at each location with the five spatially continuous phenotypic contexts in the tumors defined by different well-known markers of cancer-associated fibroblasts. Scan statistics revealed clustering in the number of significant gene-sets. A spatial heatmap of combined significance over all selected gene-sets is also produced. Extensive simulation studies demonstrate that our proposed approach outperforms other methods in the considered scenarios, especially when the spatial association increases.ConclusionsOur proposed approach considers the spatial covariance of gene expression to detect the most significant gene-sets affecting a continuous phenotype. It reveals spatially detailed information in tissue space and can thus play a key role in understanding contextual heterogeneity of cancer cells.
Insulin-like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth
Authors: Lewis Victor M. , Le Bleu Heather K. , Henner Astra L. , Markovic Hannah , Robbins Amy E. , Stewart Scott , Stankunas Kryn 
Published: October 2022

ABSTRACTZebrafish robustly regenerate fins, including their characteristic bony ray skeleton. Amputation activates intra-ray fibroblasts and dedifferentiates osteoblasts that migrate under a wound epidermis to establish an organized blastema. Coordinated proliferation and re-differentiation across lineages then sustains progressive outgrowth. We generate a single cell transcriptome dataset to characterize regenerative outgrowth and explore coordinated cell behaviors. We computationally identify sub-classes of fibroblast-lineage cells and describe novel markers of intra- and inter-ray fibroblasts and growth-promoting distal blastema cells. A pseudotemporal trajectory and in vivo photoconvertible lineage tracing indicate distal blastemal mesenchyme generates both re-differentiated intra- and inter-ray fibroblasts. Gene expression profiles across this trajectory suggest elevated protein translation in the blastemal mesenchyme state. O-propargyl-puromycin incorporation and small molecule inhibition identify insulin growth factor receptor (IGFR) / mechanistic target of rapamycin kinase (mTOR)-dependent elevated bulk translation in blastemal mesenchyme and differentiating osteoblasts. We test candidate cooperating differentiation factors identified from the osteoblast trajectory, finding IGFR/mTOR signaling expedites glucocorticoid-promoted osteoblast differentiationin vitro. Concordantly, mTOR inhibition slows but does not prevent fin regenerative outgrowthin vivo. IGFR/mTOR may elevate translation in both fibroblast- and osteoblast-lineage cells during the outgrowth phase as a tempo-coordinating rheostat.
Controlling Neocortical Epileptic Seizures using Forced Temporal Spike-Time Stimulation: AnIn SilicoComputational Study
Authors: Schmalz Joseph , Quinarez Rachel V. , Kothare Mayuresh V. , Kumar Gautam 
Published: October 2022

AbstractEpileptic seizure is typically characterized by highly synchronized episodes of neural activity. Existing stimulation therapies focus purely on suppressing the pathologically synchronized neuronal firing patterns during the ictal (seizure) period. While these strategies are effective in suppressing seizures when they occur, they fail to prevent the re-emergence of seizures once the stimulation is turned off. Previously, we developed a novel neurostimulation motif, which we refer to as “Forced Temporal Spike-Time Stimulation” (FTSTS) [1] that has shown remarkable promise in long-lasting desynchronization of excessively synchronized neuronal firing patterns by harnessing synaptic plasticity. In this paper, we build upon this prior work [1] by optimizing the parameters of the FTSTS protocol in order to efficiently desynchronize the pathologically synchronous neuronal firing patterns that occur during epileptic seizures using a recently published computational model of neocortical-onset seizures [2]. We show that the FTSTS protocol applied during the ictal period can modify the excitatory-to-inhibitory synaptic weight in order to effectively desynchronize the pathological neuronal firing patterns even after the ictal period. Our investigation opens the door to a possible new neurostimulation therapy for epilepsy.
PRAMEL7/CUL2 axis regulates NuRD stability to establish ground-state pluripotency in embryonic stem cells
Authors: Rupasinghe Meneka , Bersaglieri Cristiana , Leslie Pedrioli Deena M , Pedrioli Patrick G. A. , Hottiger Michael O. , Cinelli Paolo , Santoro Raffaella 
Published: October 2022

SummaryPluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, they only partially resemble the gene expression signature of developmental ground-state. Induced PRAMEL7 expression, a protein highly expressed in the ICM but lowly expressed in ESCs, reprograms developmentally advanced ESC+serum into ground-state pluripotency by causing DNA hypomethylation and gene expression signature close to developmental ground-state. However, how PRAMEL7 reprograms gene expression remains elusive. Here we show that PRAMEL7 associates with Cullin2 (CUL2) and this interaction is required to establish ground-state gene expression. PRAMEL7 recruits CUL2 to chromatin and targets for proteasomal degradation regulators of repressive chromatin, including NuRD complex. PRAMEL7 antagonizes NuRD-mediated repression of genes implicated in pluripotency by decreasing NuRD stability and promoter association in a CUL2-dependent manner. Our data link proteasome degradation pathways to ground-state gene expression, offering insights to generatein vitromodels to reproduce thein vivoground-state pluripotency.
PTH regulates osteogenesis and suppresses adipogenesis through Zfp 467 in a feed-forward, cyclic AMP-dependent manner
Authors: Liu Hanghang , Wada Akane , Le Isabella , Le Phuong T , Lee Andrew WF , Zhou Jun , Gori Francesca , Baron Roland , Rosen Clifford J. 
Published: October 2022

AbstractConditional deletion of the PTH1R in mesenchymal progenitors reduces osteoblast differentiation, enhances marrow adipogenesis and increases zinc finger protein 467 (Zfp467) expression. In contrast, genetic loss ofZfp467increasedPth1rexpression and shifts mesenchymal progenitor cell fate towards osteogenesis and higher bone mass. In this study we hypothesized that PTH1R and ZFP467 could constitute a feedback loop that facilitates PTH-induced osteogenesis and that conditional deletion ofZfp467in osteogenic precursors would lead to high bone mass. We report thatPrrxCre Zfp467but notAdipoCre Zfp467mice exhibit an identical phenotype to theZfp467-/-mice with high bone mass and greater osteogenic differentiation We also found that PTH suppressedZfp467expression primarily via the cyclic AMP/PKA pathway. Not surprisingly, PKA activation inhibited the expression ofZfp467and gene silencing ofPth1rcaused an increase inZfp467mRNA transcription. Dual fluorescence reporter assays and confocal immunofluorescence demonstrated that genetic deletion ofZfp467resulted in higher nuclear translocation of p50 that binds to the P2 promoter of thePth1rand increased its transcription. As expected,Zfp467-/-cells had enhanced production of cyclic AMP and increased glycolysis in response to exogenous PTH. Additionally, the osteogenic response to PTH was also enhanced inZfp467-/-calvarial osteoblasts, and the pro-osteogenic effect ofZfp467deletion was blocked by gene silencing ofPth1ror a PKA inhibitor. In conclusion, our findings suggest that loss or PTH1R-mediated repression ofZfp467results in a pathway that increasesPth1rtranscription via p50 and thus cellular responsiveness to PTH, ultimately leading to enhanced bone formation.