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1. Endosidin 5 disruption of the Golgi apparatus and extracellular matrix secretion in the unicellular charophyte Penium margaritaceum

   https://doi.org/10.1093/aob/mcad054  

   LoRicco, Josephine G. ; Kozel, Li ; Bagdan, Kaylee ; Epstein, Ruby ; Domozych, David S. ( April 2023 , Annals of Botany)

   Endosidins are a group of low-molecular-weight compounds, first identified by ‘chemical biology’ screening assays, that have been used to target specific components of the endomembrane system. In this study, we employed multiple microscopy-based screening techniques to elucidate the effects of endosidin 5 (ES5) on the Golgi apparatus and the secretion of extracellular matrix (ECM) components in Penium margaritaceum. These effects were compared with those caused by treatments with brefeldin A and concanamycin A. Penium margaritaceum’s extensive Golgi apparatus and endomembrane system make it an outstanding model organism for screening changes to the endomembrane system. Here we detail changes to the Golgi apparatus and secretion of ECM material caused by ES5.

   Changes to extracellular polymeric substance (EPS) secretion and cell wall expansion were screened using fluorescence microscopy. Confocal laser scanning microscopy and transmission electron microscopy were used to assess changes to the Golgi apparatus, the cell wall and the vesicular network. Electron tomography was also performed to detail the changes to the Golgi apparatus.

   While other endosidins were able to impact EPS secretion and cell wall expansion, only ES5 completely inhibited EPS secretion and cell wall expansion over 24 h. Short treatments of ES5 resulted in displacementmore »of the Golgi bodies from their typical linear alignment. The number of cisternae decreased per Golgi stack and trans face cisternae in-curled to form distinct elongate circular profiles. Longer treatment resulted in a transformation of the Golgi body to an irregular aggregate of cisternae. These alterations could be reversed by removal of ES5 and returning cells to culture.

   ES5 alters secretion of ECM material in Penium by affecting the Golgi apparatus and does so in a markedly different way from other endomembrane inhibitors such as brefeldin A and concanamycin A.

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2. Substrate topographies modulate the secretory activity of human bone marrow mesenchymal stem cells

   https://doi.org/10.1186/s13287-023-03450-0  

   Rosado-Galindo, Heizel ; Domenech, Maribella ( August 2023 , Stem Cell Research & Therapy)

   Mesenchymal stem cells (MSCs) secrete a diversity of factors with broad therapeutic potential, yet current culture methods limit potency outcomes. In this study, we used topographical cues on polystyrene films to investigate their impact on the secretory profile and potency of bone marrow-derived MSCs (hBM-MSCs). hBM-MSCs from four donors were cultured on topographic substrates depicting defined roughness, curvature, grooves and various levels of wettability.

   The topographical PS-based array was developed using razor printing, polishing and plasma treatment methods. hBM-MSCs from four donors were purchased from RoosterBio and used in co-culture with peripheral blood mononuclear cells (PBMCs) from Cell Applications Inc. in an immunopotency assay to measure immunosuppressive capacity. Cells were cultured on low serum (2%) for 24–48 h prior to analysis. Image-based analysis was used for cell quantification and morphology assessment. Metabolic activity of BM-hMSCs was measured as the mitochondrial oxygen consumption rate using an extracellular flux analyzer. Conditioned media samples of BM-hMSCs were used to quantify secreted factors, and the data were analyzed using R statistics. Enriched bioprocesses were identify using the Gene Ontology toolenrichGOfrom theclusterprofiler.One-way and two-way ANOVAs were carried out to identify significant changes between the conditions. Results were deemed statistically significant for combinedP < 0.05 for at leastmore »three independent experiments.

   Cell viability was not significantly affected in the topographical substrates, and cell elongation was enhanced at least twofold in microgrooves and surfaces with a low contact angle. Increased cell elongation correlated with a metabolic shift from oxidative phosphorylation to a glycolytic state which is indicative of a high-energy state. Differential protein expression and gene ontology analyses identified bioprocesses enriched across donors associated with immune modulation and tissue regeneration. The growth of peripheral blood mononuclear cells (PBMCs) was suppressed in hBM-MSCs co-cultures, confirming enhanced immunosuppressive potency. YAP/TAZ levels were found to be reduced on these topographies confirming a mechanosensing effect on cells and suggesting a potential role in the immunomodulatory function of hMSCs.

   This work demonstrates the potential of topographical cues as a culture strategy to improve the secretory capacity and enrich for an immunomodulatory phenotype in hBM-MSCs.

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3. Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation

   https://doi.org/10.1186/s12870-022-04026-5  

   Hanlon, Meredith T. ; Vejchasarn, Phanchita ; Fonta, Jenna E. ; Schneider, Hannah M. ; McCouch, Susan R. ; Brown, Kathleen M. ( January 2023 , BMC Plant Biology)

   Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus,indica,temperate japonica, andtropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets.

   We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variationmore »in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice andArabidopsis.

   Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.

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4. Telomere length analysis from minimally‐invasively collected samples: Methods development and meta‐analysis of the validity of different sampling techniques: American Journal of Human Biology

   https://doi.org/10.1002/ajhb.23410  

   Rej, Peter H. ; Bondy, Madison H. ; Lin, Jue ; Prather, Aric A. ; Kohrt, Brandon A. ; Worthman, Carol M. ; Eisenberg, Dan T. A. ( March 2020 , American Journal of Human Biology)

   Telomeres are the protective caps of chromosomes. They shorten with cell replication, age, and possibly environmental stimuli (eg, infection and stress). Short telomere length (TL) predicts subsequent worse health. Although venous whole blood (VWB) is most commonly used for TL measurement, other, more minimally invasive, sampling techniques are becoming increasingly common due to their field‐friendliness, allowing for feasible measurement in low‐resource contexts. We conducted statistical validation work for measuring TL in dried blood spots (DBS) and incorporated our results into a meta‐analysis evaluating minimally invasive sampling techniques to measure TL.

   We isolated DNA extracts from DBS using a modified extraction protocol and tested how they endured different shipping conditions and long‐term cryostorage. We then included our in‐house DBS TL validation statistics (correlation values with VWB TL and age) in a series of meta‐analyses of results from 24 other studies that published similar associations for values between TL measured in DBS, saliva, and buccal cells.

   Our modified DBS extraction technique produced DNA yields that were roughly twice as large as previously recorded. Partially extracted DBS DNA was stable for 7 days at room temperature, and still provided reliable TL measurements, as determined by external validation statistics. In our meta‐analysis, DBS TLmore »had the highest external validity, followed by saliva, and then buccal cells—possibly reflecting similarities/differences in cellular composition vs VWB.

   DBS DNA is the best proxy for VWB from the three minimally‐invasively specimen types evaluated and can be used to expand TL research to diverse settings and populations.

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5. The International Tree‐Ring Data Bank ( ITRDB ) revisited: Data availability and global ecological representativity

   https://doi.org/10.1111/jbi.13488  

   Zhao, Shoudong ; Pederson, Neil ; D'Orangeville, Loïc ; HilleRisLambers, Janneke ; Boose, Emery ; Penone, Caterina ; Bauer, Bruce ; Jiang, Yuan ; Manzanedo, Rubén D. ( December 2018 , Journal of Biogeography)

   The International Tree‐Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: (a) quantify its biases, (b) assess how well it represents global forests, (c) develop tools to identify priority areas to improve its representativity, and d) make available the corrected database.

   Worldwide.

   Contributed datasets between 1974 and 2017.

   Trees.

   We identified and corrected formatting issues in all individual datasets of theITRDB. We then calculated the representativity of theITRDBwith respect to species, spatial coverage, climatic regions, elevations, need for data update, climatic limitations on growth, vascular plant diversity, and associated animal diversity. We combined these metrics into a global Priority Sampling Index (PSI) to highlight ways to improveITRDBrepresentativity.

   Our refined dataset provides access to a network of >52 million growth data points worldwide. We found, however, that the database is dominated by trees from forests with low diversity, in semi‐arid climates, coniferous species, and in western North America. Conifers represented 81% of theITRDBand even in well‐sampled areas, broadleaves were poorly represented. OurPSIstressed the need to increase the database diversity in termsmore »of broadleaf species and identified poorly represented regions that require scientific attention. Great gains will be made by increasing research and data sharing in African, Asian, and South American forests.

   The extensive data and coverage of theITRDBshow great promise to address macroecological questions. To achieve this, however, we have to overcome the significant gaps in the representativity of theITRDB. A strategic and organized group effort is required, and we hope the tools and data provided here can guide the efforts to improve this invaluable database.

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