bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of basic helix-loop-helix transcription factors that activate betulinic acid biosynthesis by RNA-sequencing of hydroponically culturedLotus japonicus
Authors: Suzuki Hayato , Takahashi Hirokazu , Fukushima Ery Odette , Nakazono Mikio , Muranaka Toshiya , Seki Hikaru 
Published: November 2022

AbstractAlthough triterpenes are ubiquitous in plant kingdom, their biosynthetic regulatory mechanisms are limitedly understood. Here, we found that hydroponic culture dramatically activated betulinic acid (BA) biosynthesis in the model FabaceaeLotus japonicus, and investigated its transcriptional regulation. Fabaceae plants develop secondary aerenchyma (SA) on the surface of hypocotyls and roots during flooding for root air diffusion. Hydroponic culture induced SA inL. japonicusand simultaneously increased the accumulation of BA and the transcript levels of its biosynthetic genes. RNA-sequencing of soil-grown and hydroponically cultured plant tissues, including SA collected by laser microdissection, revealed that several transcription factor genes were co-upregulated with BA biosynthetic genes. Overexpression ofLjbHLH32andLjbHLH50inL. japonicustransgenic hairy roots upregulated the expression of BA biosynthesis genes, resulting in enhanced BA accumulation. However, transient luciferase reporter assays inArabidopsismesophyll cell protoplasts showed that LjbHLH32 transactivated promoters of biosynthetic genes in the soyasaponin pathway but not the BA pathway, like its homolog GubHLH3, a soyasaponin biosynthesis regulator inGlycyrrhiza uralensis. This suggested the evolutionary origin and complex regulatory mechanisms of BA biosynthesis in Fabaceae. This study sheds light on the unrevealed biosynthetic regulatory mechanisms of triterpenes in Fabaceae plants.HighlightHydroponic culture enhanced betulinic acid synthesis inLotus japonicus. RNA-sequencing and functional characterization experiments suggest that LjbHLH32 and LjbHLH50 are the transcription factors activating betulinic acid biosynthesis.
Haplotype-resolvedde novogenome assemblies of four coniferous tree species
Authors: Shirasawa Kenta , Mishima Kentaro , Hirakawa Hideki , Hirao Tomonori , Tsubomura Miyoko , Nagano Soichiro , Iki Taiichi , Isobe Sachiko , Takahashi Makoto 
Published: November 2022

AbstractConiferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we optimized the DNA library preparation protocols and employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species,Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, andCunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb inC. obtusato 16.0 Mb inL. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.
Gut Microbiome Prediction: From Current Human Evidence to Future Possibilities
Authors: Pramanick Rinku , Gazara Rajesh Kumar , Ahmad Rafi 
Published: November 2022

AbstractThe gut microbiome is an indispensable component of the human body. Alteration in the gut microbiota composition leads to various diseases such as obesity, Type 2 Diabetes, Inflammatory Bowel Syndrome, and depression. Microbiome-based precision tests offer a futuristic strategy for wellness and longevity. However, this approach is limited by the lack of definition of a healthy microbiome in different populations and accurate disease prediction.In this study, we aimed to capture the healthy gut microbiome for different populations using the xNARA Gut Profile Test kit and in-house built proprietary algorithm and reference databases. We found that gut microbiome of different populations from India, UAE, and Singapore varied significantly, indicating a distinct geographic gut microbiome signature and Gut Health Index. The gut microbial diversity as measured by the Shannon index revealed UAE had significantly greater alpha diversity than India and Singapore.Prevotella copri(19.27%),Faecalibacterium prausnitzii(4.08%) andLevilactobacillus brevis(4.0%) were the predominant species in the Indian gut.Faecalibacterium prausnitzii(8.54%),Blautia obeum(8.10%), andPhocaeicola vulgatus(4.6%) were primarily present in Singapore participants whereasPrevotella copri(14.92%),Blautia obeum(6.09%) andRoseburia intestinalis(5.81%) were present in UAE participants. Beta diversity indicated the gut microbiota of Indian-origin participants in Singapore and UAE clustered with the indigenous inhabitants of Singapore and UAE. This highlights that geographic location has a profound effect on shaping the gut microbiome architecture than ethnicity. Regional diet and lifestyle could be crucial factors responsible for shaping the gut microbiome. The prediction accuracy of the xNARA Gut algorithm ranged from 66.66-100% when matched with the blood reports. Participants agreed with the xNARA disease risk outcomes for metabolic conditions (60%-100%), gastrofitness (62.5%-100%), mental health (50%-100%), skin conditions (50%-100%) and physical fitness (50%-100%). These observations imply the promising role of gut-based personalized diet and probiotic recommendations for lifestyle and wellness management.
STopover captures spatial colocalization and interaction in the tumor microenvironment using topological analysis in spatial transcriptomics data
Authors: Bae Sungwoo , Lee Hyekyoung , Na Kwon Joong , Lee Dong Soo , Choi Hongyoon , Kim Young Tae 
Published: November 2022

AbstractUnraveling the spatial configuration of the tumor microenvironment (TME) is key to understanding tumor-immune interactions to translate them into immuno-oncology. With the advent of spatially resolved transcriptomics (SRT), the TME could be dissected for whole cell types across numerous RNAs. We suggest a novel approach, STopover, which performs topological analysis to compute the colocalization patterns between cell types and map the location of cell□cell interactions. While gradually lowering the threshold for the feature, the connected components (CCs) were extracted based on the spatial distance between the unit tissue region and the persistence of the CCs. Local and global Jaccard indices were calculated between the CCs of a feature pair to measure the extent of spatial overlap. The STopover was applied to various lung cancer data obtained from SRT platforms, both barcode and image-based SRT, and could explain the infiltration patterns of immune and stromal cells in the TME. Moreover, the method predicted the top cell□cell communication based on the ligand□receptor database and highlighted the main region of the interaction. STopover is a tool to decipher spatial interaction in the tissue and shed light on the pathophysiology underlying the microenvironment.
Contemporary human H3N2 influenza A viruses require a low threshold of suitable glycan receptors for efficient infection
Authors: Spruit Cindy M. , Sweet Igor R. , Bestebroer Theo , Lexmond Pascal , Qiu Boning , Damen Mirjam J.A. , Fouchier Ron A. M. , Snijder Joost , Herfst Sander , Boons Geert-Jan , de Vries Robert P. 
Published: November 2022

AbstractRecent human H3N2 influenza A viruses (IAV) have evolved to employ elongated glycans terminating in α2,6-linked sialic acid as their receptors. These glycans are displayed in low abundancies by cells commonly employed to propagate these viruses (MDCK and hCK), resulting in low or no viral propagation. Here, we examined whether the overexpression of the glycosyltransferases B3GNT2 and B4GALT1, which are responsible for the elongation of poly-N-acetyllactosamines (LacNAc), would result in improved A/H3N2 propagation. Stable overexpression of B3GNT2 and B4GALT1 in MDCK and hCK cells was achieved by lentiviral integration and subsequent antibiotic selection and confirmed by qPCR and protein mass spectrometry experiments. Flow cytometry and glycan mass spectrometry experiments using the B3GNT2 and/or B4GALT1 knock-in cells demonstrated increased binding of viral hemagglutinins and the presence of a larger number of LacNAc repeating units, especially on hCK-B3GNT2 cells. An increase in the number of glycan receptors did, however, not result in a greater infection efficiency of recent human H3N2 viruses. Based on these results, we propose that H3N2 IAVs require a low number of suitable glycan receptors to infect cells and that an increase in the glycan receptor display above this threshold does not result in improved infection efficiency.
Estimates for the astrocyte endfoot sheath permeability of the extra-cellular pathway
Authors: Koch Timo , Vinje Vegard , Mardal Kent-André 
Published: November 2022

AbstractBackgroundAstrocyte endfoot processes are believed to cover all micro-vessels in the brain cortex and may play a significant role in fluid and substance transport into and out of the brain parenchyma. Detailed fluid mechanical models of diffusive and advective transport in the brain are promising tools to investigate theories of transport.MethodsWe derive theoretical estimates of astrocyte endfoot sheath permeability for advective and diffusive transport and its variation in microvascular networks from mouse brain cortex. The networks are based on recently published experimental data and generated endfoot patterns are based on Voronoi tessellations of the perivascular surface. We estimate corrections for projection errors in previously published data.ResultsWe provide structural-functional relationships between vessel radius and resistance that can be directly used in flow and transport simulations. We estimate endfoot sheath filtration coefficients in the rangeLp= 0.2 × 10−10m Pa−1s−1to 2.7 × 10−10m Pa−1s−1, diffusion membrane coefficients in the rangeCM= 0.5 × 103m−1to 6 × 103m−1, and gap area fractions in the range 0.2 % to 0.6 %.ConclusionsThe astrocyte endfoot sheath surrounding microvessels forms a secondary barrier to extra-cellular transport, separating the extra-cellular space of the parenchyma and the perivascular space outside the endothelial layer. The filtration and membrane diffusion coefficients of the endfoot sheath are estimated to be an order of magnitude lower than the extra-cellular matrix while being two orders of magnitude higher than the vessel wall.
Modelling dementia inDrosophilauncovers shared and specific targets of TDP-43 proteinopathy across ALS and FTD relevant circuits
Authors: Godfrey R Keating , Bjork Reed T , Alsop Eric , Chauhan Brijesh S , Ruvalcaba Hillary C , Antone Jerry , Michael Allison F , Williams Christi , Hala’ufia Grace , Blythe Alexander D , Hall Megan , Keuren-Jensen Kendall Van , Zarnescu Daniela C 
Published: November 2022

ABSTRACTAmyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD) comprise a spectrum of neurodegenerative diseases linked to TDP-43 proteinopathy, which at the cellular level, is characterized by loss of nuclear TDP-43 and accumulation of cytoplasmic TDP-43 puncta that ultimately cause RNA processing defects including dysregulation of splicing, mRNA transport and translation. Complementing our previous models of ALS, here we report a novel model of FTD based on overexpression of TDP-43 in theDrosophilamushroom body (MB) circuit. This model recapitulates several aspects of FTD pathology including age-dependent neuronal loss, and nuclear depletion and cytoplasmic accumulation of TDP-43, accompanied by behavioral deficits in working memory and sleep that occur before axonal degeneration ensues. RNA immunoprecipitations identify several candidate mRNA targets of TDP-43 in MBs, some of which are unique to the MB circuit while others are shared with motor neurons. Among the latter is the glypican Dally-like-protein (Dlp), a modulator of Wg/Wnt signaling. Using genetic interactions we show that overexpression of Dlp in MBs mitigates TDP-43 dependent working memory deficits. These results highlight the utility of modelling TDP-43 proteinopathy inDrosophilaand provide a novel platform for studying the molecular mechanisms underlying FTD, and potentially uncovering shared and circuit specific vulnerabilities in ALS/FTD.
Independent control over cell patterning and adhesion on hydrogel substrates for tissue interface mechanobiology
Authors: Prahl Louis S. , Porter Catherine M. , Liu Jiageng , Viola John M. , Hughes Alex J. 
Published: November 2022

AbstractReplicating organizational principles that establish fine-scale tissue structure is critical to our capacity for building functional replacement tissues. Tissue boundaries such as epithelial-mesenchymal interfaces are engines for morphogenesisin vivo. However, despite a wealth of micropatterning approaches available to control tissue size, shape, and mechanical environmentin vitro, fine-scale spatial control of cell composition within tissue constructs remains an engineering challenge. To address this, we augment DNA “velcro” technology for selective patterning of ssDNA-labeled cells with long-term culture on mechanically defined polyacrylamide hydrogels. We co-functionalize photoactive benzophenone-containing polyacrylamide gels (BP-PA gels) with spatially precise ssDNA features that confer temporary cell adhesion and with extracellular matrix (ECM) proteins that confer long-term adhesion. We find that co-functionalization does not compromise ssDNA patterning fidelity or cell capture, nor hydrogel mechanical properties or mechanosensitive fibroblast spreading, enabling mechanobiology studies of precise cell interfaces. We then co-pattern colonies of fibroblasts and epithelial cells to study interface formation and extracellular signal-related kinase (ERK) activity at cellular contacts. Combining DNA velcro and ECM functionalization approaches provides independent control of initial cell placement, adhesion, and mechanical environment, constituting a new tool for studying biological interfaces and for programming multicellular interactions in engineered tissues.
Proteasomal activity is differentially regulated in source and sink tissues of Arabidopsis
Authors: Wang Haojie , Dongen Joost T. van , schippers Jos HM 
Published: November 2022

AbstractProtein homeostasis controlled by the 26S proteasome plays a pivotal role in the adaption of plants to environmental stress, contributing to survival and longevity. During ageing in animals, proteasome activity declines resulting in senescence, however, in plants this is so far largely unexplored. Herein, we found that 26S proteasome capacity deteriorates with leaf age, while 20S proteasome activity increases. Interestingly, expression of proteasomal genes increases during leaf senescence, both at the steady-state mRNA level and poly-ribosome associated mRNA level. However, the increase in transcript level does not correlate with protein abundance and proteasome activity in senescing leaves. Furthermore, chemical inhibition of the proteasome results in accelerated leaf senescence. Interestingly, deterioration of proteasome activity in senescent leaves could be restored by cytokinin application. In Arabidopsis, feed-back regulation between proteasome activity and gene expression exists, and we propose that this is the cause for the high amount of proteasomal subunit mRNA during leaf senescence. In sink tissues like mature siliques and seeds, an increased 26S proteasome activity is observed. This increased activity is mainly due to enhanced proteasome assembly. This work provides new insights into the regulation of proteasome activity which deepens our understanding on source-sink relations and their impact on plant yield.
Cell response to extracellular matrix energy dissipation outweighs rigidity sensing
Authors: Huerta-López Carla , Clemente-Manteca Alejandro , Velázquez-Carreras Diana , Espinosa Francisco M. , Sanchez Juan G. , Sáez Pablo , Martínez-del-Pozo Álvaro , García-García María , Martín-Colomo Sara , Rodríguez-Blanco Andrea , Esteban-González Ricardo , Martín-Zamora Francisco M. , Gutierrez-Rus Luis I. , García Ricardo , Roca-Cusachs Pere , Elosegui-Artola Alberto , del Pozo Miguel A. , Herrero-Galán Elías , Plaza Gustavo R. , Alegre-Cebollada Jorge 
Published: November 2022

AbstractThe mechanical properties of the extracellular matrix (ECM) determine cell differentiation, proliferation and migration through mechanoresponsive proteins including YAP. However, how different mechanical signals cooperate, synergize or compete to steer cell behavior remains poorly understood. Here, we have examined competition between the two major ECM mechanical cues, i.e. rigidity, which activates cell mechanosensing, and viscous energy dissipation, which reduces stiffness blunting cell mechanotransduction. To trigger competition, we have engineered protein hydrogels allowing concomitant modulation of stiffness and viscosity by mechanisms characteristic of native ECM. Culturing cells on these hydrogels, we have found that substrate energy dissipation attenuates YAP mechanosensing prevailing over stiffness cues. Hampered YAP activation on more dissipative substrates correlates with faster actin flow and smaller focal adhesions. Mechanistically, inhibition of actomyosin contractility reverses the outcome of the competition between rigidity and energy dissipation. Our results highlight the dominating contribution of substrate viscosity to the biology of the cell.
The Centralspindlin proteins Pavarotti and Tumbleweed work with WASH to regulate Nuclear Envelope budding
Authors: Davidson Kerri A. , Nakamura Mitsutoshi , Verboon Jeffrey M. , Parkhurst Susan M. 
Published: November 2022

ABSTRACTNuclear envelope (NE) budding is a nuclear pore independent nuclear export pathway, analogous to the egress of herpesviruses, and required for protein quality control, synapse development and mitochondrial integrity. The physical formation of NE buds is dependent on the Wiskott-Aldrich Syndrome protein Wash, its regulatory complex (SHRC), and Arp2/3, and requires Wash’s actin nucleation activity. However, the machinery governing cargo recruitment and organization within the NE bud remains unknown. Here, we identify Pavarotti (Pav) and Tumbleweed (Tum) as new molecular components of NE budding. Pav and Tum interact directly with Wash and define a second nuclear Wash-containing complex required for NE budding. Interestingly, we find that the actin bundling activities of Wash and Pav are required, suggesting a structural role in the physical and/or organizational aspects of NE buds. Thus, Pav and Tum are providing exciting new entry points into the physical machineries of this alternative nuclear export pathway for large cargos during cell differentiation and development.
Three-dimensional molecular architecture of mouse organogenesis
Authors: Qu Fangfang , Li Wenjia , Xu Jian , Zhang Ruifang , Ke Jincan , Ren Xiaodie , Meng Xiaogao , Qin Lexin , Zhang Jingna , Lu Fangru , Zhou Xin , Luo Xi , Zhang Zhen , Wu Guangming , Pei Duanqing , Chen Jiekai , Cui Guizhong , Suo Shengbao , Peng Guangdun 
Published: November 2022

AbstractMammalian embryos have sophisticated cell organizations that are orchestrated by molecular regulation at cellular and tissue level. It has recently been appreciated that the cells that make up the animal body themselves harbor significant heterogeneity in the context of both cellular and particularly spatial dimension. However, current spatial transcriptomics profiling of embryonic tissues either lack three-dimensional representation or are restricted to limited depth and organs. Here, we reported a holistic spatial transcriptome atlas of all major organs at embryonic day 13.5 of mouse embryo and delineated a 3D rendering of the molecular regulation of embryonic patterning. By integrating with corresponding single-cell transcriptome data, the spatial organogenesis atlas provides rich molecular annotation of the dynamic organ nature, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ-engineering and stem-cell based regenerative medicine.
Binary or non-binary fission? Reproductive mode of a predatory bacterium depends on prey size
Authors: Pląskowska Karolina , Makowski Łukasz , Strzałka Agnieszka , Zakrzewska-Czerwińska Jolanta 
Published: November 2022

AbstractMost eukaryotic and bacterial cells divide by binary fission, where one mother cell produces two progeny cells, or, rarely, by non-binary fission. All bacteria studied to date use only one of these two reproduction modes. Here, we demonstrate for the first time that the predatory bacteriumBdellovibrio bacteriovorusreproduces through both binary and non-binary fission. Switching between the two modes correlates with the prey size. In relatively small host cells,B. bacteriovorusundergoes binary fission; the FtsZ ring assembles in the midcell and the mother cell splits into two daughter cells. In larger host cells,B. bacteriovorusswitches to non-binary fission and creates multiple FtsZ rings to produce three or more daughter cells. Completion of bacterial cell cycle critically depends on precise spatiotemporal coordination of chromosome replication and segregation with other cell-cycle events, including cell division. Our studies reveal thatB. bacteriovorusalways initiates chromosome replication at the invasive pole of the cell, but the spatiotemporal choreography of subsequent steps depends on the fission mode and/or the number of progeny cells. In non-binary dividing filaments producing five or more progeny cells, the last round(s) of replication may also be initiated at the noninvasive pole. Finally, we show that binary-dividingB. bacteriovorusneeds to extensively rebuild the flagellated pole of the mother cell to turn it into the invasive pole of a daughter cell. Altogether, we find thatB. bacteriovorusreproduces through bimodal fission and that extracellular factors, such as the host size, can shape replication choreography, providing new insights about bacterial life cycles.