bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression
Authors: Sokolowski Dustin J. , Ahn Jedid , Erdman Lauren , Hou Huayun , Ellis Kai , Wang Liangxi , Goldenberg Anna , Wilson Michael D. 
Published: August 2022

ABSTRACTDifferential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review.HighlightsBy curating metadata from uniformly processed human RNA-seq studies, we created a database of 3162 differential expression analyses.These analyses include TCGA, GTEx, and 142 unique studies in SRA, involving 985 distinct experimental conditions.The Differential Expression Enrichment Tool (DEET) allows users to systematically compare their gene lists to this database.
Evolution of m6A related genes in insects and function of METTL3 in embryonic development of silkworm
Authors: Liu Shuai-Qi , Jia Shun-Ze , Li Ying-Hui , Hu Kai-Wen , Tao Jian-Guo , Lu Yi-Cheng , Xu Yu-Song , Wang Hua-Bing 
Published: August 2022

AbstractN6-methyladenosine (m6A), the most prevalent modification in eukaryotic RNAs, plays a key role in biological processes. However, the evolutionary relationships and function of m6A related genes in insects are still largely unknown. Here, we analyzed the phylogenetics of m6A related genes among 207 insects and find that m6A related genes are evolutionarily conserved in insects. We apply the lepidopteran model insect Bombyx. mori as a study system. Subcellular localization experiments in BmN cells confirmed that YTHDF3 localizes in the cytoplasm, METTL3, METTL14 and YTHDC localize in the nucleus, while FL2D localizes in both nucleus and cytoplasm. We also detected expression pattern of m6A related genes during the embryonic development of B. mori and found that m6A related genes expression pattern is temporally specific. To elucidate the function of METTL3 during embryonic stage, RNA sequencing was performed to measure differential expressions of mRNA from silkworm eggs after METTL3 knockdown, and METTL3-overexpressing BmN cells. The global transcriptional pattern showed that METTL3 knockdown affected multiple cellular processes, including oxidoreductase activity, transcription regulator activity, cation binding and fundamental many metabolism processes, such as carbon metabolism, purine metabolism, biosynthesis of amino acids, and the citrate cycle, were affected. In addition, METTL3 knockdown significantly affected Wnt and Toll/Imd pathways in embryonic stage. The results suggest that METTL3 plays an important role during the embryonic development of B. mori. This study deepens our understanding of the function of m6A related genes in insects.
Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography
Authors: Yano Naomine , Kondo Tatsuya , Kusaka Katsuhiro , Yamada Taro , Arakawa Takatoshi , Sakamoto Tatsuji , Fushinobu Shinya 
Published: August 2022

AbstractGum arabic (GA) is widely used as an emulsion stabilizer and edible coating, and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidic chains of GA and modify their properties are valuable tools for structural analysis and industrial application. Cryogenic X-ray crystal structure of GA-specific L-rhamnose-α-1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1), belonging to the polysaccharide lyase (PL) family 42, has been previously reported. To determine the specific reaction mechanism based on its hydrogen-containing enzyme structure, we performed joint X-ray/neutron crystallography of FoRham1. Large crystals were grown in the presence of L-rhamnose (a reaction product), and neutron and X-ray diffraction datasets were collected at room temperature up to 1.80 and 1.25 Å resolutions, respectively. The active site contained L-rhamnose and acetate, the latter being a partial analog of glucuronate. Incomplete H/D exchange between Arg166 and acetate suggested that a strong salt-bridge interaction was maintained. Doubly deuteronated His105 and deuteronated Tyr150 supported this interaction. The unusually hydrogen-rich environment functions as a charge neutralizer for glucuronate and stabilizes the oxyanion intermediate. The NE2 atom of His85 was deprotonated and formed a hydrogen bond with the deuterated O1 hydroxy of L-rhamnose, indicating the function of His85 as the base/acid catalyst for bond cleavage via β-elimination. Asp83 functions as a pivot between the two catalytic histidine residues by bridging them, and this His–His–Asp structural motif is conserved in the three PL families.Significance StatementAlthough hydrogen transfer plays an important role in enzymatic reactions, hydrogen atoms are generally invisible in macromolecular X-ray crystallography. In the reaction of polysaccharide lyases, substrate activation by negative charge stabilization of uronic acid and base/acid-catalyzed β-elimination reaction have been postulated. Here, we report the neutron crystallography of polysaccharide lyase. Joint X-ray/neutron crystallography of L-rhamnose-α-1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1) complexed with L-rhamnose was performed, and the hydrogen and deuterium atoms were visualized at a high resolution. FoRham1 catalyzes the specific cleavage of the cap structure of gum arabic, which is useful for various applications in the food, cosmetic, and pharmaceutical industries. A detailed catalytic mechanism for FoRham1 was proposed based on the key structural features of its active site.
Wild grass isolates of Magnaporthe (Syn. Pyricularia) spp. from Germany can cause blast disease on cereal crops
Authors: Barragan A. Cristina , Latorre Sergio M. , Mock Paul G. , Harant Adeline , Win Joe , Malmgren Angus , Burbano Hernán A. , Kamoun Sophien , Langner Thorsten 
Published: August 2022

AbstractPathogens that cause destructive crop diseases often infect wild host plants. However, surveys of major plant pathogens tend to be skewed towards cultivated crops and often neglect the wild hosts. Here, we report an emerging disease threat generated by the blast fungus Magnaporthe (Syn. Pyricularia) spp. in central Europe. We found that this notoriously devastating plant pathogen infects the wild grasses foxtail millet (Setaria spp.) and crabgrass (Digitaria spp.) in south-western Germany, a region previously deemed unfavorable for blast disease. Using phenotypic characterization and genomic analyses, we determined that the observed disease symptoms are associated with the Setaria spp.-infecting lineage of M. oryzae and its sister species Magnaporthe grisea. We showed that M. oryzae isolates can infect barley and wheat, thus highlighting the risk of pathogen spread to crops. In addition, M. oryzae isolates which co-occur in natural populations display compatible mating types and variable candidate effector gene content, which may enhance the pathogen’s adaptive potential. Our findings stress the risk of blast fungus infections expanding into European cereal crops through migration and host jumps. This underlines the importance for pathogen surveillance not only on cultivated crops, but also on wild host plants.Author SummaryWild plant species are often overlooked during pathogen virulence surveys. However, many of the diseases we observe in crops are a consequence of host jumps from wild to cultivated plant species. This is reminiscent of zoonotic diseases, where host jumps from wild animals to humans result in new disease outbreaks. Here, we report that the notoriously devastating blast fungus Magnaporthe (Syn. Pyricularia) spp. occurs on wild grasses in south-western Germany. This region, which is at the center of the European cereal belt, has so far been viewed as having unfavorable climatic conditions for the blast disease. The newly identified blast fungus isolates have the capacity to infect wheat and barley cultivars, highlighting the risk of the disease spreading to staple cereal crops. In addition, there is potential for sexual recombination in local populations, which may increase the evolutionary potential of the fungus and might facilitate host jumps to cereal crops. Our findings emphasize the urgent need for surveillance of plant diseases on both wild hosts and crops.
Characterization of primary structure of the major silk gene,h-fibroin, across caddisfly suborders (Trichoptera)
Authors: Heckenhauer Jacqueline , Stewart Russell J. , Ríos-Touma Blanca , Powell Ashlyn , Dorji Tshering , Frandsen Paul B. , Pauls Steffen U. 
Published: August 2022

AbstractBackgroundLarvae of Trichoptera produce silk to build various underwater structures allowing them to exploit a wide range of aquatic environments. Theheavy chain fibroin(h-fibroin) gene encodes the primary protein component of their silk. Studies on this long (>20 kbp) and highly repetitive gene have been limited by difficulties in its sequence assembly. Recently, high-quality long-read sequencing techniques have been successfully applied to obtain the full-lengthh-fibroinsequence.ResultsWe used three new and five previously published genomes to identify eight full-length h-fibroin gene and protein sequences of h-fibroin across the order Trichoptera covering various endpoints of the diversity of ecological silk use in caddisflies. We analyze these together with four existing high-quality h-fibroin sequences. Across the order, we observed conserved patterns in h-fibroin (high similarity of amino(n)-/carboxyl(c)-termini, presence of characteristic repeating structural modules). However, the sequence, number, and arrangement of these repeating modules varied across clades with increasing structural complexity of h-fibroin in fixed retreat and tube-case builders compared to cocoon-builders. We also found a higher percentage of proline in fixed-retreat makers.ConclusionThis study provides characterizations of the primary structure of h-fibroin from a diverse set of caddisflies. The interplay of conserved termini and basic motif structure with high variation in repeating modules as well as the variation in the percentage of proline might be linked to differences in mechanical properties (i.e., tensile strength, toughness) related to the different silk usage. This sets a starting point for future studies to screen and correlate amino acid motifs and other sequence features with quantifiable silk properties.
Reconstitution of ribosome self-replication outside a living cell
Authors: Kosaka Yuishin , Miyawaki Yumi , Mori Megumi , Aburaya Shunsuke , Fukuyama Mao , Ueda Mitsuyoshi , Aoki Wataru 
Published: August 2022

SummaryRibosome biogenesis, a recursive process of pre-existing ribosomes self-replicating nascent ones, is pivotal in the self-replication of life. In Escherichia coli, three ribosomal RNAs (rRNAs) are transcribed, and 54 ribosomal proteins (r-proteins) are synthesized by pre-existing ribosomes as structural components1, 2. They are cotranscriptionally assembled in a cooperative hierarchy under the support of ∼100 accessory factors1–3. The reconstitution of ribosome biogenesis outside a living cell is an essential goal to understand the self-replication of life. However, this goal could not have been achieved so far due to its complexity. Here, we report the successful in vitro reconstitution of the entire ribosome biogenesis process. We hypothesized that mimicking in vivo ribosome biogenesis1–6 could result in in vitro ribosome biogenesis. Specifically, we found that coactivating the transcription of an rRNA operon, as well as the transcription and translation of 54 r-protein genes encoding r-proteins, and the coordinated ribosomal assembly in a cytoplasm-mimicking reaction solution, resulted in highly efficient in vitro reconstitution of ribosome biogenesis. Our achievement represents a critical step toward revealing fundamental principles underlying the self-replication of life and creating self-replicating artificial cells7. We also succeeded in engineering rRNA and r-proteins by only adding mutant ribosomal genes in the reaction, enabling high-throughput and unconstrained creation of artificial ribosomes with altered or enhanced functionality8–12.
DNA damage leads to microtubule stabilisation through an increase in Golgi-derived microtubules
Authors: Venkataravi Aishwarya , Lahiri Mayurika 
Published: August 2022

AbstractThe site of nucleation strongly determines microtubule organisation and dynamics. The centrosome is a primary site for microtubule nucleation and organisation in most animal cells. In recent years, the Golgi apparatus has emerged as a site of microtubule nucleation and stabilisation. The microtubules originating from Golgi are essential for maintaining Golgi integrity post-Golgi trafficking, establishing cell polarity and enabling cell motility. Although the mechanism of nucleation and functional relevance of the Golgi-nucleated microtubule is well established, its regulation needs to be better studied. In this study, we report that DNA damage leads to aberrant Golgi structure and function accompanied by reorganisation of the microtubule network. Characterisation of microtubule dynamics post DNA damage showed the presence of a stable pool of microtubules resistant to depolymerisation by nocodazole and enriched in acetylated tubulin. Investigation of the functional association between Golgi dispersal and microtubule stability revealed that the Golgi elements were distributed along the acetylated microtubules. Microtubule regrowth assays showed an increase in Golgi-derived microtubule post DNA damage. Interestingly, reversal of Golgi dispersal reduces microtubule stabilisation. Altered intracellular trafficking resulting in mislocalisation of cell-cell junction proteins was observed post DNA damage. We propose that the increase in stable microtubules deregulates intracellular trafficking, resulting in cell polarity changes. This study would thus be the first to demonstrate the link between Golgi dispersal and microtubule reorganisation orchestrating changes in cell polarity.
Correlated stabilizing selection shapes the topology of gene regulatory networks
Authors: Petit Apolline J. R. , Guez Jeremy , Rouzic Arnaud Le 
Published: August 2022

AbstractThe evolution of gene expression is constrained by the topology of gene regulatory networks, as co-expressed genes are likely to have their expressions affected together by mutations. Conversely, co-expression can also be an advantage when genes are under joint selection. Here, we assessed theoretically whether correlated selection (selection for a combination of traits) was able to affect the pattern of correlated gene expressions and the underlying gene regulatory networks. We ran individual-based simulations, applying a stabilizing correlated fitness function to three genetic architectures: a quantitative genetics (multilinear) model featuring epistasis and pleiotropy, a quantitative genetics model where each genes has an independent mutational structure, and a gene regulatory model, mimicking the mechanisms of gene expression regulation. Simulations showed that correlated mutational effects evolved in the three genetic architectures as a response to correlated selection, but the response in gene networks was specific. The intensity of gene co-expression was mostly explained by the regulatory distance between genes (largest correlations being associated to genes directly interacting with each other), and the sign of co-expression was associated with the nature of the regulation (transcription activation or inhibition). These results concur to the idea that gene network topologies could partly reflects past correlated selection patterns on gene expression.
Harnessing Immunotherapy to Enhance the Systemic Anti-Tumor Effects of Thermosensitive Liposomes
Authors: Regenold Maximilian , Wang Xuehan , Kaneko Kan , Bannigan Pauric , Allen Christine 
Published: August 2022

AbstractChemotherapy plays an important role in debulking tumors in advance of surgery and/or radiotherapy, tackling residual disease, and treating metastatic disease. In recent years many promising advanced drug delivery strategies have emerged that offer more targeted delivery approaches to chemotherapy treatment. For example, thermosensitive liposome mediated drug delivery in combination with localized mild hyperthermia can increase local drug concentrations resulting in a reduction in systemic toxicity and an improvement in local disease control. However, the majority of solid tumor associated deaths are due to metastatic spread. A therapeutic approach focused on a localized target area harbors the risk of overlooking and undertreating potential metastatic spread. Previous studies reported systemic, albeit limited, anti-tumor effects following treatment with thermosensitive liposomal chemotherapy and localized mild hyperthermia. This work explores the systemic treatment capabilities of a thermosensitive liposome formulation of the vinca alkaloid vinorelbine in combination with mild hyperthermia in an immunocompetent murine model of rhabdomyosarcoma. This treatment approach was found to be highly effective at heated, primary tumor sites. However, it demonstrated limited anti-tumor effects in secondary, distant tumors. As a result, the addition of immune checkpoint inhibition therapy was pursued to further enhance the systemic anti-tumor effect of this treatment approach. Once combined with immune checkpoint inhibition therapy, a significant improvement in systemic treatment capability was achieved. We believe this is one of the first studies to demonstrate that a triple combination of thermosensitive liposomes, localized mild hyperthermia, and immune checkpoint inhibition therapy can enhance the systemic treatment capabilities of thermosensitive liposomes.Graphical abstract
Spatially coordinated cell cycle activity and motility govern mammary ductal growth and tip bifurcation
Authors: Myllymäki SM , Kaczynska B , Lan Q , Mikkola ML 
Published: August 2022

AbstractBranching morphogenesis is the common evolutionary solution of multiple organs to combine maximal epithelial function with compact organ size. It involves successive rounds of branch elongation and branch point generation to generate a branched epithelial network. Branch points form most commonly at the tips of branches as they split into two. However, it is unclear how epithelial cells in tips drive both elongation and branching. In this study, we used ex vivo live imaging to identify these fundamental cellular mechanisms in the embryonic mammary gland. Our 4D analyses show that tips of branches are driven forward by directional cell migration, while elongation of the subtending duct is supported by cell proliferation that feeds a retrograde flow of lagging cells into the duct, established upon differential cell motility. Tip bifurcation involved localized repression of both cell cycle and cell motility at the branch point. Cells in the nascent daughter tips remained proliferative, but changed the direction of their movement to elongate new branches. Our study also reports the fundamental importance of the contractile actin cytoskeleton in regulating branch point generation in the mammary epithelium.
Dexamethasone Enhances CAR T Cell Persistence and Function by Upregulating Interleukin 7 Receptor
Authors: Munoz Ashlie , Urak Ryan , Taus Ellie , Hsieh Claire , Jin Katherine , Lin Shu-Hong , Awuah Dennis , Vyas Vibhuti , Priceman Saul J. , Clark Mary C. , Forman Stephen J. , Wang Xiuli 
Published: August 2022

AbstractDexamethasone (dex) is a glucocorticoid that is a mainstay for treatment of inflammatory pathologies, including immunotherapy-associated toxicities. Dex suppresses the endogenous immune response and is also believed to suppress the function of chimeric antigen receptor (CAR) T cells. However, recent reports observed higher CAR T cell numbers in patients treated with dex, highlighting the rationale for interrogating the specific effects of dex on CAR T cells. Here, we found that dex did not inhibit CAR T cell expansion or function. A single dose of dex during the manufacturing process upregulated the pro-persistence interleukin 7 receptor α (IL7Rα) on CAR T cells and induced expression of genes involved in activation, migration, and persistence. The ex vivo upregulation of IL7Rα induced by dex significantly enhanced CAR T cell persistence and anti-tumor efficacy in vivo when combined with exogenous IL-7. Moreover, the combination of dex and IL-7 resulted in increased persistence of CAR T cells and led to complete remission of mice. Overall, our studies in both in vitro and in vivo treatment support a positive role of dex on CAR T cell potency and provide insight into the application of glucocorticoids in cellular anti-cancer therapy.
Tissue recoil in the early Drosophila embryo is a passive not active process
Authors: Goldner Amanda Nicole , Fessehaye Salena M. , Mapes Kelly Ann , Osterfield Miriam , Doubrovinski Konstantin 
Published: August 2022

AbstractUnderstanding tissue morphogenesis is impossible without knowing the mechanical properties of the tissue being shaped. Although techniques for measuring tissue material properties are continually being developed, methods for determining how individual proteins contribute to mechanical properties are very limited. Here, we developed two complementary techniques for the acute inactivation of sqh (the Drosophila myosin regulatory light chain), one based on the recently introduced AID2 system, and the other based on a novel method for conditional protein aggregation. Combining these techniques with rheological measurements, we show that passive material properties of the cellularization-stage Drosophila embryo are essentially unaffected by myosin activity. The significance of this study is two-fold. We introduce a system for the nearly instantaneous inactivation of proteins in a variety of systems. Additionally, we demonstrate a method to distinguish between active and passive contributions to effective tissue elasticity.SummaryTechniques to examine the contribution of specific proteins to tissue mechanical properties are extremely limited. Here, Goldner et al. develop two complementary techniques for rapid protein depletion combined with mechanical measurements, and show that myosin activity is dispensable for tissue elasticity.