bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly activeBurkholderiapolyketoacyl-CoA thiolase for production of triacetic acid lactone
Authors: Wang Zilong , Cheong Seokjung , Pereira Jose Henrique , Kim Jinho , DeGiovanni Andy , Guo Yifan , Lan Guangxu , Barcelos Carolina Araujo , Haushalter Robert , Lee Taek Soon , Adams Paul D. , Keasling Jay D. 
Published: December 2022

AbstractTriacetic acid lactone (TAL) is a platform chemical biosynthesized primarily through decarboxylative Claisen condensation by type III polyketide synthase 2-pyrone synthase (2-PS). However, this reaction suffers from intrinsic energy inefficiency and feedback inhibition by and competition for malonyl-CoA. TAL production through non-decarboxylative Claisen condensation by polyketoacyl-CoA thiolase alleviates many of these disadvantages. We discovered five more thiolases with TAL production activity by exploring homologs of a previously reported polyketoacyl-CoA thiolase, BktB, fromCupriavidus necator. Among them, the BktB homolog fromBurkholderiasp. RF2-non_BP3 has ∼ 30 times higherin vitroandin vivoTAL production activity and led to ∼10 times higher TAL titer than 2-PS when expressed inEscherichia coli, achieving a titer of 2.8 g/L in fed-batch fermentations. This discovery of a novel polyketoacyl-CoA thiolase with superior TAL production activity paves the way for realization of total biomanufacturing of TAL.
What are we learning with Yoga: a text mining approach to literature
Authors: Raittz Rosangela Ieger , De Pierri Camilla R. , Perico Camila P. , Machado Diogo J. , Marchaukoski Jeroniza N. , Raittz Roberto T. 
Published: December 2022

AbstractTechniques used in yoga existed long before science as we know it. However, with Yoga westernization, the proliferation of scientific studies addressing the subject is exponential. Even though the literature presents thousands of related articles, many studies are considered flimsy — the diversity of methods, areas of interest, and focus cause it to become a complex environment without general guidelines for the researcher. This status may represent one of the impediments to the field’s evolution. This study aims to elaborate a global structure of the literature on Yoga to open the door for multidisciplinary collaboration and bring new light to some relevant aspects. Due to its complexity, we understand that techniques to model complex domains are necessary. Contemporary methods of Artificial Intelligence have promoted advances in Bioinformatics, including text mining to scientific literature. Through the vector representation of texts, we got semantic abilities and could organize data in a way that allowed us to acquire a global vision of this literature. Additionally, we made the platforms available to Yoga researchers to enable them to evaluate our findings and make their forays into the literature. Besides better understanding why we study Yoga, we discovered that the literature offers insights into the relationships in broader aspects.
Dissecting the cell of origin of aberrant SALL4 expression in myelodysplastic syndrome
Authors: Tatetsu Hiro , Watanabe Miho , Liu Jun , Tokunaga Kenji , Iwanaga Eisaku , Komohara Yoshihiro , Thrash Emily , Masao Matsuoka , Tenen Daniel G. , Chai Li 
Published: December 2022

AbstractMyelodysplastic syndrome (MDS) is a group of heterogeneous diseases characterized by cytologic dysplasia and cytopenias resulting from ineffective hematopoiesis. Oncofetal protein SALL4 is a known oncogene in MDS and its baseline expression level serves as a prognostic biomarker for MDS at the time of diagnosis. In addition, a recent study showed that SALL4 upregulation following hypomethylating agent treatment in MDS patients correlates with poor outcomes. Despite its important mechanistic and diagnostic significance, the cellular identity of bone marrow cells with aberrant SALL4 expression in MDS patients remains unknown.In this study, we analyzed MDS bone marrow cells on single cell level by mass cytometry (CyTOF) and found that SALL4 was mainly aberrantly expressed in the hematopoietic stem and progenitor cells (HSPC) as well as myeloid lineages. Within the HSPC population from MDS patients, SALL4 and p53 were co-expressed, with the highest co-expressing clones harboring pathogenic TP53 mutations. Overall, our study characterizes for the first time the aberrant SALL4 expression in primary MDS patient samples at a single-cell level. Further studies on the SALL4/p53 network for in-depth mechanistic investigation are needed in the future.Key PointsSALL4 expression in various MDS BM cells confirmed by mass cytometry (CyTOF). SALL4 and p53 double positive cells were predominantly found in the hematopoietic stem and progenitor cell (HSPC) population and associated with pathogenic TP53 mutation status.
iPSC-Derived PSEN2 (N141I) Astrocytes and Microglia Exhibit a Primed Inflammatory Phenotype
Authors: Sullivan Michael A. , Lane Samuel D. , Ball Sarah R. , Sunde Margaret , Neely G. Gregory. , Moreno Cesar , Werry Eryn L. , Kassiou Michael 
Published: December 2022

AbstractBackgroundWidescale evidence points to the involvement of glia and immune pathways in the progression of Alzheimer’s disease (AD). AD-associated iPSC-derived glial cells show a diverse range of AD-related phenotypic states encompassing cytokine/chemokine release, phagocytosis and morphological profiles, but to date studies are limited to cells derived from PSEN1, APOE and APP mutations or sporadic patients. The aim of the current study was to successfully differentiate iPSC-derived microglia and astrocytes from patients harbouring an AD-causative PSEN2 (N141I) mutation and characterise the inflammatory and morphological profile of these cells.MethodsiPSCs from three healthy control individuals and three familial AD patients harbouring a heterozygous PSEN2 (N141I) mutation were used to derive astrocytes and microglia-like cells and cell identity and morphology were characterised through immunofluorescent microscopy. Cellular characterisation involved the stimulation of these cells by LPS and Aβ42and analysis of cytokine/chemokine release was conducted through ELISAs and multi-cytokine arrays. The phagocytic capacity of these cells was then indexed by the uptake of fluorescently labelled fibrillar Aβ42.ResultsAD-derived astrocytes and microglia-like cells exhibited an atrophied and less complex morphological appearance than healthy controls. AD-derived astrocytes showed increased basal expression of GFAP, S100β and increased secretion and phagocytosis of Aβ42while AD-derived microglia-like cells showed decreased IL-8 secretion compared to healthy controls. Upon immunological challenge AD-derived astrocytes and microglia-like cells show exaggerated secretion of the pro-inflammatory IL-6, CXCL1, ICAM-1 and IL-8 from astrocytes and IL-18 and MIF from microglia.ConclusionOur study showed, for the first time, the differentiation and characterisation of iPSC-derived astrocytes and microglia-like cells harbouring a PSEN2 (N141I) mutation. PSEN2 (N141I)-mutant astrocytes and microglia-like cells presented with a ‘primed’ phenotype characterised by reduced morphological complexity, exaggerated pro-inflammatory cytokine secretion and altered Aβ42production and phagocytosis.
Frame Editors for Precise, Template-Free Frameshifting
Authors: Nakade Shota , Nakamae Kazuki , Tang Tzu-Chieh , Yu Dou , Sakuma Tetsushi , Yamamoto Takashi , Lu Timothy K. 
Published: December 2022

AbstractEfficiency and accuracy are paramount in genome editing. While CRISPR-Cas nucleases are efficient at editing target genes, their accuracy is limited because following DNA cleavage by Cas proteins, error-prone repair mechanisms introduce random mutations. Improving the accuracy of CRISPR-Cas by reducing random repairs using DNA- or RNA-based templates can compromise efficiency. To simultaneously improve both editing efficiency and accuracy, we created a frameshifting genome-editing technology by fusing Cas9 with DNA polymerases. These Frame Editors (FEs) introduce precise and controlled frameshifts into target loci via specific DNA repairs near Cas9-induced cleavage loci. We demonstrate two types of FEs: the insertion-inducing frame editor (iFE) and the deletion-inducing frame editor (dFE). For iFE, DNA polymerase beta (POLB) is fused with Cas9, which increases the frequency of 1-bp insertions. For dFE, T4 DNA polymerase (T4pol) is fused with Cas9, which increases the frequency of 1-bp deletions. Both types of FEs reduce the number of random mutations at target loci compared with Cas9. We show that off-target editing can be reduced by substituting Cas9 with high-fidelity variants, such as HiFi Cas9 or LZ3 Cas9. Thus, FEs can introduce frameshifts into target loci with much improved mutation profiles compared with Cas9 alone and without the requirement for template sequences, offering a new strategy for repairing pathogenic frameshifts.
Generation of adult hippocampal neural stem cells occurs in the early postnatal dentate gyrus and depends on cyclin D2
Authors: Pastor-Alonso Oier , Zahra Anum Syeda , Kaske Bente , García-Moreno Fernando , Tetzlaff Felix , Bockelmann Enno , Grunwald Vanessa , Martin-Suarez Soraya , Riecken Kristoffer , Witte Otto Wilhelm , Encinas Juan Manuel , Urbach Anja 
Published: December 2022

SUMMARYIn the hippocampus, lifelong neurogenesis is maintained by a pool of multipotent adult neural stem cells (aNSCs) residing in the subgranular zone of the dentate gyrus (DG). Yet, the mechanisms guiding the transition of NSCs from developmental to adult remain unclear. By using nestin-reporter mice deficient for D2, a cyclin expressed mainly postnatally, we show that the aNSC pool is established through D2-dependent proliferation during the first two weeks of life. The absence of D2 allows the normal development of the DG until birth but prevents the postnatal formation of radial glia-like aNSCs. Additionally, retroviral fate mapping demonstrates that aNSCs are born on-site from precursors located in the DG shortly after birth. Altogether, our data suggest that aNSCs are a population distinct from developmental NSCs and thus imply that adult hippocampal neurogenesis is not a mere continuation of development.
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR
Authors: Obana Nozomu , Takada Hiraku , Crowe-McAuliffe Caillan , Iwamoto Mizuki , Egorov Artyom A. , Wu Kelvin J.Y. , Murina Victoriia , Paternoga Helge , Tresco Ben I.C. , Nomura Nobuhiko , Myers Andrew G. , Atkinson Gemma C. , Wilson Daniel N. , Hauryliuk Vasili 
Published: December 2022

ABSTRACTGenome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 fromStreptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacteriumNeobacillus vireti) and Clostridia (CplR fromClostridium perfringens,Clostridium sporogenesandClostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate thatC. difficileCplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to theC. difficile630 clinical isolate. Finally, assisted by our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction ofcplRexpression upon an antibiotic challenge.
Isolation and genome characterization of Lloviu virus from Italian Schreibers’ bent-winged bats
Authors: Tóth Gábor E. , Hume Adam J. , Suder Ellen L. , Zeghbib Safia , Ábrahám Ágota , Lanszki Zsófia , Varga Zsaklin , Tauber Zsófia , Földes Fanni , Zana Brigitta , Scaravelli Dino , Scicluna Maria Teresa , Pereswiet-Soltan Andrea , Görföl Tamás , Terregino Calogero , De Benedictis Paola , Garcıa-Dorival Isabel , Alonso Covadonga , Jakab Ferenc , Mühlberger Elke , Leopardi Stefania , Kemenesi Gábor 
Published: December 2022

AbstractLloviu cuevavirus (LLOV) was the first identified member ofFiloviridaefamily outside theEbolaandMarburgvirusgenera. A massive die-off of Schreibers’ bent-winged bats (Miniopterus schreibersii) in the Iberian Peninsula in 2002 led to its discovery.Studies with recombinant and wild-type LLOV isolates confirmed the susceptibility of human-derived cell lines and primary human macrophages to LLOV infectionin vitro. Based on these data, LLOV is now considered as a potential zoonotic virus with unknown pathogenicity to humans and bats.We examined bat samples from Italy for the presence of LLOV in an area outside of the currently known distribution range of the virus. We detected one positive sample from 2020, sequenced the complete coding sequence of the viral genome and established an infectious isolate of the virus. In addition, we performed the first comprehensive evolutionary analysis of the virus, using the Spanish, Hungarian and the Italian sequences.The most important achievement of this article is the establishment of an additional infectious LLOV isolate from a bat sample using the SuBK12-08 cells, demonstrating that this cell line is highly susceptible to LLOV infection. These results further confirms the role of these bats as the host of this virus, possibly throughout their entire geographic range. This is an important result to further understand the role of bats as the natural hosts for zoonotic filoviruses.
Predicting distributed working memory activity in a large-scale mouse brain: the importance of the cell type-specific connectome
Authors: Ding Xingyu , Froudist-Walsh Sean , Jaramillo Jorge , Jiang Junjie , Wang Xiao-Jing 
Published: December 2022

AbstractRecent advances in connectome and neurophysiology make it possible to probe whole-brain mechanisms of cognition and behavior. We developed a large-scale model of the mouse multiregional brain for a cardinal cognitive function called working memory, the brain’s ability to internally hold and process information without sensory input. The model is built on mesoscopic connectome data for inter-areal cortical connections and endowed with a macroscopic gradient of measured parvalbumin-expressing interneuron density. We found that working memory coding is distributed yet exhibits modularity; the spatial pattern of mnemonic representation is determined by long-range cell type-specific targeting and density of cell classes. Cell type-specific graph measures predict the activity patterns and a core subnetwork for memory maintenance. The model shows numerous self-sustained internal states (each engaging a distinct subset of areas). This work provides a framework to interpret large-scale recordings of brain activity during cognition, while highlighting the need for cell type-specific connectomics.
Multi-omics analysis identifies RFX7 targets involved in tumor suppression and neuronal processes
Authors: Schwab Katjana , Coronel Luis , Riege Konstantin , Sacramento Erika K. , Rahnis Norman , Häckes David , Cirri Emilio , Groth Marco , Hoffmann Steve , Fischer Martin 
Published: December 2022

AbstractRecurrently mutated in lymphoid neoplasms, the transcription factor RFX7 is emerging as a tumor suppressor. Previous reports suggested that RFX7 may also have a role in neurological and metabolic disorders. We recently reported that RFX7 responds to p53 signaling and cellular stress. Furthermore, we found RFX7 target genes to be dysregulated in numerous cancer types also beyond the hematological system. However, our understanding of RFX7’s target gene network and its role in health and disease remains limited. Here, we generated RFX7 knock-out cells and employed a multi-omics approach integrating transcriptome, cistrome, and proteome data to obtain a more comprehensive picture of RFX7 targets. We identify novel target genes linked to RFX’s tumor suppressor function and underscoring its potential role in neurological disorders. Importantly, our data reveal RFX7 as a mechanistic link that enables the activation of these genes in response to p53 signaling.
De novo linear phosphorylation site motifs for BCR-ABL kinase revealed by phospho-proteomics in yeast
Authors: Smolnig Martin , Fasching Sandra , Stelzl Ulrich 
Published: December 2022

AbstractBCR-ABL is the oncogenic fusion product of tyrosine kinase ABL1 and a highly frequent driver of acute lymphocytic leukemia (ALL) and chronic myeloid leukemia (CML). The kinase activity of BCR-ABL is strongly elevated, however changes of substrate specificity in comparison to wild-type ABL1 kinase are less well characterized. Here, we heterologously expressed full-length BCR-ABL kinases in yeast. We exploited the proteome of living yeast asin vivophospho-tyrosine substrate for assaying human kinases specificity. Phospho-proteomic analysis of ABL1 and BCR-ABL isoforms p190 and p210 yielded a high-confidence dataset of 1127 phospho-tyrosine sites on 821 yeast proteins. We used this data set to generate linear phosphorylation site motifs for ABL1 and the oncogenic ABL1 fusion proteins. The oncogenic kinases yielded a substantially different linear motif when compared to ABL1. Kinase set enrichment analysis with human pY-sites that have high linear motif scores well recalled BCR-ABL driven cancer cell lines from human phospho-proteome data sets.HighlightsFull-length BCR-ABL kinase expression in yeast1,127 pY-sites on 821 yeast proteins originating from ABL1 and BCR-ABL kinase activityDistinct linear kinase motif forABL1 and BCR-ABL p190 and p210 isoformsValidation of the kinase motifs through KSEA of human cancer cell line phospho-proteome dataSignificanceThe fusion protein BCR-ABL is a predominant oncogene in leukemia observed at very high frequency in chronic myeloid leukemia (BCR-ABL p210) and B-cell acute lymphoid (BCR-ABL p190) leukemia. In both cases the malignant transformation is reliant on elevated tyrosine kinase activity, however ABL1 kinase activation as such is not sufficient. At least in part, leukemias may therefore be driven by a specificity switch of the fusion kinase in comparison to the wild-type ABL1.We investigated BCR-ABL kinase substrates in yeast through phospho-proteomics and established linear kinase phosphorylation-motifs for the full length BCR-ABL isoforms p210 and p190. These novel motifs differ substantially from the corresponding specificity determinants of wild-type ABL1 kinase, providing direct experimental evidence for altered phosphorylation-specificity of the oncogenic kinase fusion proteins.
Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy
Authors: Last Mart G. F. , Tuijtel Maarten W. , Voortman Lenard M. , Sharp Thomas H. 
Published: December 2022

AbstractCryogenic transmission electron microscopy (cryo-TEM) and super-resolution fluorescence microscopy (FM) are two popular and ever improving methods for high-resolution imaging of biological samples. In recent years, the combination of these two techniques into one correlated workflow has gained attention as a promising route towards contextualizing and enriching cryo-TEM imagery. A problem that is often encountered in the combination of these methods is that of light-induced damage to the sample during fluorescence imaging that renders the sample structure unsuitable for TEM imaging. In this paper, we describe how absorption of light by TEM sample support grids leads to sample damage, and we systematically explore the importance of parameters of grid design. We explain how, by changing the grid geometry and materials, one can increase the maximum illumination power density in fluorescence microscopy by up to an order of magnitude, and demonstrate the significant improvements in super-resolution image quality that are enabled by the selection of support grids that are optimally suited for correlated microscopy.
Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging
Authors: Vandiver Amy R. , Hoang Austin N. , Herbst Allen , Lee Cathy C. , Aiken Judd M. , McKenzie Debbie , Timp Winston , Wanagat Jonathan 
Published: December 2022

AbstractBackgroundMitochondrial DNA (mtDNA) deletion mutations cause many human diseases and are linked to age-induced mitochondrial dysfunction. Mapping the mutation spectrum and quantifying mtDNA deletion mutation frequency is challenging with next generation sequencing methods. We hypothesized that long-read sequencing of human mtDNA across the lifespan would detect a broader spectrum of mtDNA rearrangements and provide a more accurate measurement of their frequency.ResultsWe employed nanopore Cas9-targed sequencing (nCATS) to map and quantitate mtDNA deletion mutations and develop analyses that are fit-for-purpose. We analyzed total DNA from vastus lateralis muscle in 15 males ranging from 20 to 81 years of age and substantia nigra from three 20-year-old and three 79-year-old men. We found that mtDNA deletion mutations detected by nCATS increased exponentially with age and mapped to a wider region of the mitochondrial genome than previously reported. Using simulated data, we observed that large deletions are often reported as chimeric alignments. To address this, we developed two algorithms for deletion identification which yield consistent deletion mapping and identify both previously reported and novel mtDNA deletion breakpoints. The identified mtDNA deletion frequency measured by nCATS correlates strongly with chronological age and predicts the deletion frequency as measured by digital PCR approaches. In substantia nigra, we observed a similar frequency of age-related mtDNA deletions to those observed in muscle samples, but noted a distinct spectrum of deletion breakpoints.ConclusionsNCATS-mtDNA sequencing allows identification of mtDNA deletions on a single molecule level, characterizing the strong relationship between mtDNA deletion frequency and chronological aging.