bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale genomic rearrangements boost SCRaMbLE inSaccharomyces cerevisiae
Authors: Li Tianyi , Zhao Shijun , Cheng Li , Hou Sha , Luo Zhouqing , Xu Jinsheng , Yu Wenfei , Jiang Shuangying , Monti Marco , Schindler Daniel , Zhang Weimin , Hou Chunhui , Ma Yingxin , Cai Yizhi , Boeke Jef D. , Dai Junbiao 
Published: May 2023

SummaryGenomic rearrangements contribute to gene copy number alterations, disruption of protein-coding sequences and/or perturbation of cis-regulatory networks. SCRaMbLE, a Cre/loxP-based system implanted in synthetic yeast chromosomes, can effectively introduce genomic rearrangements, and is thus a potential tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we constructed a yeast strain, SparLox83, containing 83 loxPsym sites distributed across all 16 chromosomes, with at least two sites per chromosome. Inducing Cre recombinase expression in SparLox83 produced versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, SCRaMbLE of the hetero-diploid strains derived from crossing SparLox83 with strains possessing synthetic chromosome III (synIII) from the Sc2.0 project led to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to a strain with only synIII. Analysis of these evolved strains demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and can consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool to study the consequence of genomic rearrangements and help accelerate strain engineering in Saccharomyces cerevisiae.
PENet: A phenotype encoding network for automatic extraction and representation of morphological discriminative features
Authors: Zhao Zhengyu , Lu Yuanyuan , Tong Yijie , Chen Xin , Bai Ming 
Published: May 2023

AbstractDiscriminative traits are important in biodiversity and macroevolution, but extracting and representing these features from huge natural history collections using traditional methods can be challenging and time-consuming. To fully utilize the collections and their associated metadata, it is urgent now to increase the efficiency of automatic feature extraction and sample retrieval. We developed a Phenotype Encoding Network (PENet), a deep learning-based model that combines hashing methods to automatically extract and encode discriminative features into hash codes. We tested the performance of PENet on six datasets, including a newly constructed beetle dataset with six subfamilies and 6566 images, which covers more than 60% of the genera in the family Scarabaeidae. PENet showed excellent performance in feature extraction and image retrieval. Two visualization methods, t-SNE, and Grad-CAM, were used to evaluate the representation ability of the hash codes. Further, by using the hash codes generated from PENet, a phenetic distance tree was constructed based on the beetle dataset. The result indicated the hash codes could reveal the phenetic distances and relationships among categories to a certain extent. PENet provides an automatic way to extract and represent morphological discriminative features with higher efficiency, and the generated hash codes serve as a low-dimensional carrier of discriminative features and phenotypic distance information, allowing for broader applications in systematics and ecology.
Massive invasion of organellar DNA drives nuclear genome evolution inToxoplasma
Authors: Namasivayam Sivaranjani , Sun Cheng , Bah Assiatu B , Oberstaller Jenna , Pierre-Louis Edwin , Etheridge Ronald Drew , Feschotte Cedric , Pritham Ellen J. , Kissinger Jessica C. 
Published: May 2023

AbstractToxoplasma gondiiis a zoonotic protist pathogen that infects up to 1/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extantT. gondiiME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but notku80mutant,Toxoplasmaparasites. Comparisons withNeospora caninum, a species that diverged fromToxoplasma∼28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.Significance StatementThis study reveals how DNA located in cellular compartments called organelles can be transferred to the nucleus of the cell and inserted into the nuclear genome of apicomplexan parasiteToxoplasma. Insertions alter the DNA sequence and may lead to significant changes in how genes function. Unexpectedly, we found that the human protist pathogen,Toxoplasma gondiiand closely-related species have the largest observed organellar genome fragment content (>11,000 insertion comprising over 1 Mb of DNA) inserted into their nuclear genome sequence despite their compact 65 Mb nuclear genome. Insertions are occurring at a rate that makes them a significant mutational force that deserves further investigation when examining causes of adaptation and virulence of these parasites.
Sexual dimorphism in melanocyte stem cell behavior reveals combinational therapeutic strategies for cutaneous repigmentation
Authors: An Luye , Kim Dahihm , Donahue Leanne , Mejooli Menansili Abraham , Eom Chi-Yong , Nishimura Nozomi , White Andrew C 
Published: May 2023

AbstractVitiligo is an autoimmune skin disease caused by cutaneous melanocyte loss. Although phototherapy and T cell suppression therapy have been widely used to induce epidermal re-pigmentation, full pigmentation recovery is rarely achieved due to our poor understanding of the cellular and molecular mechanisms governing this process. Here, we identify unique melanocyte stem cell (McSC) epidermal migration rates between male and female mice, which is due to sexually dimorphic cutaneous inflammatory responses generated by ultra-violet B exposure. Using genetically engineered mouse models, and unbiased bulk and single-cell mRNA sequencing approaches, we determine that manipulating the inflammatory response through cyclooxygenase and its downstream prostaglandin product regulates McSC proliferation and epidermal migration in response to UVB exposure. Furthermore, we demonstrate that a combinational therapy that manipulates both macrophages and T cells (or innate and adaptive immunity) significantly promotes epidermal melanocyte re-population. With these findings, we propose a novel therapeutic strategy for repigmentation in patients with depigmentation conditions such as vitiligo.
N4-acetylcytidine (ac4C) promotes mRNA localization to stress granules
Authors: Kudrin Pavel , Singh Ankita , Meierhofer David , Kuśnierczyk Anna , Vang Ørom Ulf Andersson 
Published: May 2023

SummaryStress granules are an integral part of the stress response that are formed from non-translating mRNAs aggregated with proteins. While much is known about stress granules, the factors that drive their mRNA localization are incompletely described. Modification of mRNA can alter the properties of the nucleobases and affect processes as translation, splicing and localization of individual transcript. Here, we show that the RNA modification N4-acetylcytidine (ac4C) on mRNA associates with transcripts enriched in stress granules and that stress granule localized transcripts with ac4C are particularly translationally regulated. In addition, we show that ac4C on mRNA can mediate co-localization of the protein NOP58 to stress granules. Our results show that acetylation of mRNA regulates localization of both stress-sensitive transcripts and RNA-binding proteins to stress granules and adds to our understanding of the molecular mechanisms responsible for stress granule formation.
Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
Authors: Mishra Rishi Kumar , Sharma Prafful , Khaja Faisal Tarique , Uday Adwaith B. , Hussain Tanweer 
Published: May 2023

AbstractRibosomes from plants have unique plant-specific features that may aid in rapid gene expression and regulation in response to changing environmental conditions due to their sessile nature. Here, we present high-resolution cryo-electron microscopy structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). We compare wheat ribosome with closely related ribosomes from a dicot plant and other eukaryotes from yeast to humans. While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in peptide exit tunnel, Zinc-finger motif in eL34 is absent and uL4 is extended making an exclusive interaction network. We note striking differences in eL15-Helix 11 (25S) interaction network, eL6-Expansion segment 7 assembly and certain rRNA chemical modifications between monocot and dicot ribosomes. Among eukaryotic ribosomes, we observe that rRNA modification (Gm75) in 5.8S rRNA is highly conserved and a base flipping (G1506) in peptide exit tunnel, and these features are likely involved in sensing nascent peptide. Finally, we discuss importance of universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs
Authors: Hochstoeger Tobias , Papasaikas Panagiotis , Piskadlo Ewa , Chao Jeffrey A. 
Published: May 2023

AbstractA central mechanism of mTOR complex 1 (mTORC1) signaling is the coordinated translation of ribosomal protein and translation factor mRNAs mediated by the 5′-terminal oligopyrimidine motif (5′TOP). Recently, La-related protein 1 (LARP1) has been proposed to be the specific regulator of 5′TOP mRNA translation downstream of mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested to have a general role in repression. Here, we employ single-molecule translation site imaging of 5′TOP and canonical mRNAs to study the translational dynamics of single mRNAs in living cells. Our data reveals that 4EBP1/2 has a dominant role in translation repression of both 5′TOP and canonical mRNAs during pharmacological inhibition of mTOR. In contrast, we find that LARP1 selectively protects 5′TOP mRNAs from degradation in a transcriptome-wide analysis of mRNA half-lives. Our results clarify the roles of 4EBP1/2 and LARP1 in regulating 5′TOP mRNAs and provides a framework to further study how these factors control cell growth during development and disease.
Vimentin filaments integrate low complexity domains in a highly complex helical structure
Authors: Eibauer Matthias , Weber Miriam S. , Kronenberg-Tenga Rafael , Beales Charlie T. , Boujemaa-Paterski Rajaa , Turgay Yagmur , Sivagurunathan Suganya , Kraxner Julia , Köster Sarah , Goldman Robert D. , Medalia Ohad 
Published: May 2023

AbstractIntermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion beam milling, cryo-electron microscopy and tomography, to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, densely-packed and highly-ordered helical symmetric structure of 40 α-helices in cross-section, organized into 5 protofibrils. Surprisingly, the intrinsically disordered head domains form an amyloid-like fiber in the center of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking strength and stretchability.
Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1
Authors: Kupke Janina , Klimmt Julien , Mudlaff Franziska , Schwab Maximilian , Lutsik Pavlo , Plass Christoph , Sticht Carsten , Oliveira Ana M.M. 
Published: May 2023

AbstractEpigenetic factors are well established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role for DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA-sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
Changes of Cd content in chloroplasts are mirrored by the activity of photosystem I, but not by photosystem II
Authors: Lysenko Eugene A. , Kusnetsov Victor V. 
Published: May 2023

AbstractCd is one of the most toxic heavy metals and widespread pollutant. We searched for a direct Cd action on the photosynthetic electron transport chain using induced chlorophyll fluorescence and P700light absorption. Young barley and maize plants were treated with Cd in toxic (80 μM) and nearly lethal (250 μM) concentrations. The maximal and relative photochemical activities of PSI, its major limitation at the donor side, and partially acceptor-side limitation of PSII changed in agreement with Cd accumulation in the corresponding chloroplasts. Probably, acceptor-side limitation of PSII increased with a direct Cd action under 80 μM that was overcome with an indirect Cd action under 250 μM. These alterations can be explained by Cd/Cu substitution in plastocyanin. The photochemical and non-photochemical quenching by PSII varied diversely that cannot be explained unambiguously by any mechanism. The limitations of PSI (Y(ND), Y(NA)) and PSII (qC) were compared for the first time. They were ranged as follows: Y(NA) < qC < Y(ND). Short segments of qC and Y(ND) dynamics varied proportionally to each other. This implies the existence of an unknown mechanism adjusting limitations at the acceptor side of PSII (qC) and at the donor side of PSI (Y(ND)).HighlightsPSI activity changed in agreement with the changes of Cd content in chloroplastsThe data on PSII activity cannot be clearly explained by Cd actionPSII acceptor-side limitation qC was governed by opposed direct and indirect Cd actionsPSI and qC changes can be explained by Cd/Cu substitution in plastocyaninLimitations qC of PSII and Y(ND) of PSI changed proportionally for a short time
Identifying cellular markers of focal cortical dysplasia type II with cell-type deconvolution and single-cell signatures
Authors: Galvão Isabella C. , Kandratavicius Ludmyla , Messias Lauana A. , Athié Maria C. P. , Assis-Mendonça Guilherme R. , Alvim Marina K. M. , Ghizoni Enrico , Tedeschi Helder , Yasuda Clarissa L. , Cendes Fernando , Vieira André S. , Rogerio Fabio , Lopes-Cendes Iscia , Veiga Diogo F. T. 
Published: May 2023

AbstractFocal cortical dysplasia (FCD) is a brain malformation that causes medically refractory epilepsy. FCD is classified into three categories based on structural and cellular abnormalities, with FCD type II being the most common and characterized by disrupted organization of the cortex and abnormal neuronal development. In this study, we employed cell-type deconvolution and single-cell signatures to analyze bulk RNA-seq from multiple transcriptomic studies, aiming to characterize the cellular composition of brain lesions in patients with FCD IIa and IIb subtypes. Our deconvolution analyses revealed specific cellular changes in FCD IIb, including neuronal loss and an increase in reactive astrocytes (astrogliosis) when compared to FCD IIa. Astrogliosis in FCD IIb was further supported by a gene signature analysis and histologically confirmed by glia fibrilla acidic protein (GAP) immunostaining. Overall, our findings demonstrate that FCD II subtypes exhibit differential neuronal and glial compositions, with astrogliosis emerging as a hallmark of FCD IIb. These observations, validated in independent patient cohorts and confirmed using immunohistochemistry, offer novel insights into the involvement of glial cells in FCD type II pathophysiology and may contribute to the development of targeted therapies for this condition.
Stem cells tightly regulate dead cell clearance to maintain tissue fitness
Authors: Stewart Katherine S , Gonzales Kevin AU , Yuan Shaopeng , Tierney Matthew T , Bonny Alain R , Yang Yihao , Infarinato Nicole R , Cowley Christopher J , Levorse John M , Pasolli Hilda Amalia , Ghosh Sourav , Rothlin Carla V , Fuchs Elaine 
Published: May 2023

Summary ParagraphMacrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial number of these dying cells are cleared by ‘non-professional phagocytes’, local epithelial cells that are critical to organismal fitness. How non-professional phagocytes sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying their multifunctionality. Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires both local lipids produced by apoptotic corpses to activate RXRα, and tissue-specific retinoids for RARγ activation. This dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an effective mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche.
Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system inClostridioides difficile
Authors: Muzyukina Polina , Shkaruta Anton , Guzman Noemi M. , Andreani Jessica , Borges Adair L. , Bondy-Denomy Joseph , Maikova Anna , Semenova Ekaterina , Severinov Konstantin , Soutourina Olga 
Published: May 2023

AbstractCRISPR-Cas systems provide their prokaryotic hosts with adaptive immunity against mobile genetic elements. Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit host defense. The identification of Acr proteins is challenging due to their small size and high sequence diversity, and only a limited number has been characterized to date. In this study, we report the discovery of a novel Acr protein, AcrIB2, encoded by the φCD38-2Clostridioides difficilephage that efficiently inhibits interference by the type I-B CRISPR-Cas system of the host and likely acts as a DNA mimic. MostC. difficilestrains contain twocasoperons, one encoding a full set of interference and adaptation proteins and another encoding interference proteins only. Unexpectedly, we show that only the partial operon is required for interference and is subject to inhibition by AcrIB2.
The medial prefrontal cortex during flexible decisions: Evidence for its role in distinct working memory processes
Authors: Kidder Kevan , Gillis Ryan , Miles Jesse , Mizumori Sheri 
Published: May 2023

AbstractDuring decisions that involve working memory, task-related information must be encoded, maintained across delays, and retrieved. Few studies have attempted to causally disambiguate how different brain structures contribute to each of these components of working memory. In the present study, we used transient optogenetic disruptions of rat medial prefrontal cortex (mPFC) during a serial spatial reversal learning (SSRL) task to test its role in these specific working memory processes. By analyzing numerous performance metrics, we found: 1) mPFC disruption impaired performance during only the choice epoch of initial discrimination learning of the SSRL task, 2) mPFC disruption impaired performance in dissociable ways across all task epochs (delay, choice, return) during flexible decision-making, 3) mPFC disruption resulted in a reduction of the typical vicarious-trial-and-error (VTE) rate modulation that was related to changes in task demands. Taken together, these findings suggest that the mPFC plays an outsized role in working memory retrieval, becomes involved in encoding and maintenance when recent memories conflict with task demands, and enables animals to flexibly utilize working memory to update behavior as environments change.
Distinctive cellular and junctional dynamics independently regulate the rotation and elongation of the internal organ
Authors: Inaki Mikiko , Higashi Takamasa , Okuda Satoru , Matsuno Kenji 
Published: May 2023

AbstractComplex structures of organs are formed at high reproducibility, and deformations of epithelia play major roles in these processes. To acquire the intricate morphology, an epithelium simultaneously suffers multiple structural changes. For example, to form the left-right asymmetric structure ofDrosophilaembryonic hindgut, its epithelial tube concurrently rotates and elongates, which are driven by cell sliding and convergent extension, respectively. However, how an epithelium simultaneously accomplishes multiple structural changes remains unclear. To address this issue, we here studied the relevancy between these two mechanisms in the hindgut morphogenesis. Our live imaging analysis revealed thatMyosin1DandE-cadherin, orPar-3are required only for cell sliding or convergent extension, respectively, while Myosin II is essential for both. Mathematical models showed that these cellular dynamics share a single mechanical system in the same time window. Such specificity and universality of the machineries controlling epithelial dynamics might be a general strategy adopted in complex tissue morphogenesis.