bluuebunny/crossref_metadata_2025_split huggingface dataset:
pyTFM: A tool for Traction Force and Monolayer Stress Microscopy
Authors: Bauer Andreas , Prechová Magdalena , Gregor Martin , Fabry Ben 
Published: September 2020

AbstractCellular force generation and force transduction are of fundamental importance for numerous biological processes and can be studied with the methods of Traction Force Microscopy (TFM) and Monolayer Stress Microscopy. Traction Force Microscopy and Monolayer Stress Microscopy solve the inverse problem of reconstructing cell-matrix tractions and inter- and intra-cellular stresses from the measured cell force-induced deformations of an adhesive substrate with known elasticity. Although several laboratories have developed software for Traction Force Microscopy and Monolayer Stress Microscopy computations, there is currently no software package available that allows non-expert users to perform a full evaluation of such experiments. Here we present pyTFM, a tool to perform Traction Force Microscopy and Monolayer Stress Microscopy on single cells, cell patches and cell layers grown in a 2-dimensional environment. pyTFM was optimized for ease-of-use; it is open-source and well documented (hosted athttps://pytfm.readthedocs.io/) including usage examples and explanations of the theoretical background. pyTFM can be used as a standalone Python package or as an add-on to the image annotation toolClickPoints. In combination with theClickPointsenvironment, pyTFM allows the user to set all necessary analysis parameters, select regions of interest, examine the input data and intermediary results, and calculate a wide range of parameters describing forces, stresses, and their distribution. The Monolayer Stress Microscopy implementation in pyTFM allows for the analysis of small cell patches and single cells; we analyze the accuracy and performance of Traction Force Microscopy and Monolayer Stress Microscopy algorithms using synthetic and experimental data from epithelial cell patches.
Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling
Authors: Aboukilila Mohamed Y. , Sami Josephine D. , Wang Jingtian , England Whitney , Spitale Robert C. , Cleary Michael D. 
Published: September 2020

AbstractObtaining neuron transcriptomes is challenging; their complex morphology and interconnected microenvironments make it difficult to isolate neurons without potentially altering gene expression. Multidendritic sensory neurons (md neurons) ofDrosophilalarvae are commonly used to study peripheral nervous system biology, particularly dendrite arborization. We sought to test if EC-tagging, a biosynthetic RNA tagging and purification method that avoids the caveats of physical isolation, would enable discovery of novel regulators of md neuron dendrite arborization. RNAs were biosynthetically tagged by expressing CD:UPRT (a nucleobase-converting fusion enzyme) in md neurons and feeding 5-ethynylcytosine (EC) to larvae. Tagged RNAs were subsequently purified and used for RNA-sequencing. Reference RNA was prepared in a similar manner using 5-ethynyluridine (EUd) to tag RNA in all cells and negative control RNA-seq was performed on “mock tagged” samples to identify non-specifically purified transcripts. Differential expression analysis identified md neuron enriched and depleted transcripts. Three candidate genes encoding RNA-binding proteins (RBPs) were tested for a role in md neuron dendrite arborization. Loss-of-function for the m6A-binding factor Ythdc1 did not cause any dendrite arborization defects while RNAi of the other two candidates, the poly(A) polymerase Hiiragi and the translation regulator Hephaestus, caused significant defects in dendrite arborization. This work provides an expanded view of transcription in md neurons and a technical framework for combining EC-tagging with RNA-seq to profile transcription in cells that may not be amenable to physical isolation.
FRUITFULL-like genes regulate flowering time and inflorescence architecture in tomato
Authors: Jiang Xiaobing , Lubini Greice , Hernandes-Lopes José , Rijnsburger Kim , Veltkamp Vera , de Maagd Ruud A. , Angenent Gerco C. , Bemer Marian 
Published: September 2020

ABSTRACTThe timing of flowering and inflorescence architecture are critical for the reproductive success of tomato, but the gene regulatory networks underlying these traits have not been fully explored. Here we show that the tomatoFRUITFULL-like (FUL-like) genesFUL2andMADS-BOX PROTEIN 20 (MBP20)induce flowering and repress inflorescence branching by promoting floral meristem determinacy.FUL1fulfils a less prominent role and appears to depend on FUL2 and MBP20 for its upregulation in the inflorescence- and floral meristems.MBP10, the fourth tomatoFUL-like gene, has probably lost its function. The tomato FUL-like proteins cannot homodimerize inin vitroassays, but heterodimerize with various other MADS-domain proteins, potentially forming distinct complexes in the transition meristem and floral meristem. Transcriptome analysis of the primary shoot meristems revealed various interesting downstream targets, including four repressors of cytokinin signalling that are upregulated during the vegetative-to-reproductive transition inful1 ful2 mbp10 mbp20mutants. FUL2 and MBP20 can also bindin vitroto the upstream regions of these genes, thereby probably directly stimulating cell division in the meristem upon the transition to flowering. The control of inflorescence branching does not occur via the CKXs, but appears regulated by repression of transcription factors such asTM3, APETALA 2b(AP2b) andAP2a.
Multiple pathways of LRRK2-G2019S / Rab10 interaction in dopaminergic neurons
Authors: Fellgett Alison , Middleton C. Adam , Munns Jack , Ugbode Chris , Jaciuch David , Wilson Laurence , Chawla Sangeeta , Elliott Christopher J. H. 
Published: September 2020

AbstractBackgroundInherited mutations in the LRRK2 protein are the most common known cause of Parkinson’s, but the mechanisms by which increased kinase activity of mutant LRRK2 leads to pathological events remain to be determined.In vitroassays (heterologous cell culture, phospho-protein mass spectrometry) suggest that several Rab proteins might be directly phosphorylated byLRRK2-G2019S. Which Rabs interact with LRRK2 in dopaminergic neurons to facilitate normal and pathological physiological responses remains to be determined. Anin vivoscreen of Rab expression in dopaminergic neurons in young adult Drosophila demonstrated a strong genetic interaction between LRRK2-G2019Sand Rab10. We now ask if Rab10 is required for LRRK2-induced physiological responses in DA neurons.MethodsLRRK2-G2019Swas expressed in Drosophila dopaminergic neurons and the effects of Rab10 depletion on Proboscis Extension, vision, circadian activity pattern and courtship memory determined in aged flies.ResultsRab10 loss-of-function rescued bradykinesia of the Proboscis Extension Response (PER) and visual defects of aged flies expressing LRRK2-G2019S in DA neurons. Rab10 knock-down however, did not rescue the marked sleep phenotype which results from dopaminergic expression ofLRRK2-G2019S. Courtship memory is not affected by LRRK2 expression, but is markedly improved by Rab10 depletion. Anatomically, both LRRK2-G2019S and Rab10 are seen in the cytoplasm and at the synaptic endings of dopaminergic neurons.ConclusionsWe conclude that, in Drosophila dopaminergic neurons, Rab10 is involved differentially in LRRK2-induced behavioral deficits. Therefore, variations in Rab expression may contribute to susceptibility of different dopaminergic nuclei to neurodegeneration seen in people with Parkinson’s.Graphical AbstractRab10 depletion ameliorates the proboscis extension bradykinesia and loss of synaptic signalling in the retina induced byLRRK2-G2019Sexpression (magenta arrows / orange crosses). Rab10 manipulation does not affect the ‘sleep’ phenotype fromLRRK2-G2019S(magenta arrow). Reduction of Rab10 facilitates conditioned courtship memory, but LRRK2 has no effect (yellow arrow). All manipulations of Rab10 andG2019Sin dopaminergic neurons, shown in the outline of the brain (filled cells have high levels of Rab10). We conclude that Rab10 and LRRK2 interact in some, but not all dopaminergic neurons. This may underlie differences in the susceptibility of different human striatal dopaminergic cells to Parkinson’s and explain why different symptoms initiate particular ages.
Metabolomic Profiling and Mechanotransduction of Single Chondrocytes Encapsulated in Alginate Microgels
Authors: Fredrikson Jacob P. , Brahmachary Priyanka , Erdoğan Ebru , Archambault Zach , June Ronald K. , Chang Connie B. 
Published: September 2020

AbstractHuman articular cartilage is comprised of two main components, the extracellular matrix (ECM) and the pericellular matrix (PCM). The PCM helps to protect chondrocytes in the cartilage from mechanical loads, but in patients with osteoarthritis, the PCM is weakened resulting in increased chondrocyte stress. As chondrocytes are responsible for cartilage synthesis and maintenance, it is important to understand how mechanical loads affect cellular responses of chondrocytes. Many studies have examined the chondrocyte response toin vitromechanical loading by embedding in stiff agarose. However, these experiments are mostly performed in the absence of PCM which may obscure important responses to mechanotransduction. Here, we demonstrate that drop-based microfluidics allows culture of single chondrocytes in alginate microgels for cell-directed PCM synthesis that closely mimics thein vivomicroenvironment. Chondrocytes form PCM over 10 days in these single cell microenvironments. Single cell microgels and monolayer controls were encapsulated in high stiffness agarose to mimic the cartilage PCM. After physiological dynamic compression in a custom-built bioreactor, microgels exhibited distinct metabolomic profiles from both uncompressed and monolayer controls. These results demonstrate the potential of single cell encapsulation in alginate microgels to advance cartilage tissue engineering and basic chondrocyte mechanobiology.
Phenolic acid-degradingParaburkholderiaprime decomposition in forest soil
Authors: Wilhelm Roland C. , DeRito Christopher M. , Shapleigh James P. , Madsen Eugene L. , Buckley Daniel H. 
Published: September 2020

AbstractPlant-derived phenolic acids are metabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria would enhance SOC mineralization in forest soils when primed with13C-labeledp-hydroxybenzoic acid (PHB). We further investigated whether PHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. The activity ofParaburkholderiaandCaballeroniadominated PHB degradation in all soils regardless of tree species or soil type. We isolated the principal PHB-degrading phylotype (Paraburkholderia madsenianaRP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, aryl-alcohol oxidase and DyP-type peroxidase, and confirmed its ability to degrade phenolics. The addition of PHB to soil led to significant enrichment (23-fold) of the RP11Tphylotype (RP11ASV), as well as enrichment of other phylotypes ofParaburkholderiaandCaballeronia. Metabolism of PHB primed significant loss of SOC (3 to 13 µmols C g-1dry wt soil over 7 days). In contrast, glucose addition reduced SOC mineralization (−3 to -8 µmols C g-1dry wt soil over 7 days). RP11ASVabundance and the expression of PHB monooxygenase (pobA) correlated with PHB respiration and were inversely proportional to SOC content in the field. We propose that plant-derived phenolics stimulate the activity of phenolic acid-degrading bacteria thereby causing soil priming and SOC loss. We show thatBurkholderiaceaedominate soil priming in diverse forest soils and this observation counters the prevailing view that priming phenomena are a generalized non-specific response of community metabolism.
Genetic structure of Photosystem II functionality in rice unraveled by GWAS analysis
Authors: Vilas Juan Manuel , Burgos Estanislao , Puig Maria Lucrecia , Colazo Jose , Livore Alberto , Ruiz Oscar Adolfo , Carrari Fernando , Rodriguez Andrés Alberto , Maiale Santiago Javier 
Published: September 2020

AbstractRice production is a particularly important crop for the half-world population. Therefore, knowledge about which genes are implicated in the functionality of the Photosystem II, that are still poorly explored could collaborate in the assisted selection of rice improving. In the present study, we applied Genome wide Association Studies of PSII chlorophyll fluorescence under two contrasting environmental conditions in 283 rice accessions highly diverse. A total of 110 significant association SNP-phenotype were observed, and 69 quantitative trait loci identified with a total of 157 genes, of which 38 were highly significant, mapped spread out through rice genome. These underlying regions are enriched in genes related to biotic and abiotic stresses, transcription factors, Calvin cycle, senescence, and grain characters. The correlations analyses PSII chlorophyll fluorescence parameters and some panicle characteristics found here suggest the possibility of developing molecular markers to assist the breeding programs that improve photosynthesis and yield in rice.HighlightThe genetic structure of the Photosystem II functionality in rice was studied by using genome-wide association through chlorophyll fluorescence.
A rapidly evolving actin mediates fertility and developmental tradeoffs inDrosophila
Authors: Schroeder Courtney M. , Tomlin Sarah A. , Valenzuela John R. , Malik Harmit S. 
Published: September 2020

AbstractMost actin-related proteins (Arps) are highly conserved in eukaryotes, where they carry out well-defined cellular functions.Drosophilaand mammals also encode divergent non-canonical Arps in their male-germline whose roles remain unknown. Here, we show that Arp53D, a rapidly-evolvingDrosophilaArp, localizes to fusomes and actin cones, two male germline-specific actin structures critical for sperm maturation, via its non-canonical N-terminal tail. Although we expected thatArp53Dloss would reduce male fertility, we instead find thatArp53D-KO males are more fertile, both in isolation and in competition with wildtype males. Upon investigating why evolution would retain a gene that negatively impacts male fertility, we unexpectedly found thatArp53D-KOfemales are less fertile. Moreover, KO embryos exhibit reduced viability, which worsens under heat stress. We conclude that ‘testis-specific’Arp53Dis detrimental to male fertility, but is required for female fertility and early development, leading to its long-term retention and recurrent adaptation inDrosophila.
Allele frequency differentiation at height-associated SNPs among continental human populations
Authors: Chen Minhui , Chiang Charleston W. K. 
Published: September 2020

AbstractPolygenic adaptation is thought to be an important mechanism of phenotypic evolution in humans, although recent evidence of confounding due to residual stratification in consortium GWAS made studies of polygenic adaptation more difficult to interpret. Using FSTas a measure of allele frequency differentiation, a previous study has shown that the mean FSTamong African, East Asian, and European populations is significantly higher at height-associated SNPs than that found at matched non-associated SNPs, suggesting that polygenic adaptation is one of the reasons for differences in human height among these continental populations. However, we showed here even though the height-associated SNPs were identified using only European ancestry individuals, the estimated effect sizes are significantly associated with structures across continental populations, potentially explaining the elevated level of differentiation previously reported. To alleviate concerns of biased ascertainment of SNPs, we re-examined the distribution of FSTat height-associated alleles ascertained from two biobank level GWAS (UK Biobank, UKB, and Biobank Japan, BBJ). We showed that when compared to non-associated SNPs, height-associated SNPs remain significantly differentiated among African, East Asian, and European populations from both 1000 Genomes (p= 0.0012 andp= 0.0265 when height SNPs were ascertained from UKB and BBJ, respectively), and Human Genome Diversity Panels (p= 0.0225 for UKB andp= 0.0032 for BBJ analyses). In contrast to FST-based analyses, we found no significant difference or consistent ranked order among continental populations in polygenic height scores constructed from SNPs ascertained from UKB and BBJ. In summary, our results suggest that, consistent with previous reports, height-associated SNPs are significantly differentiated in frequencies among continental populations after removing concerns of confounding by uncorrected stratification. Polygenic score-based analysis in this context appears to be susceptible to the choice of SNPs and, as we compared to FST-based statistics in simulations, would lose power in detecting polygenic adaptation if there are independent converging selections in more than one population.
Trim39 regulates neuronal apoptosis by acting as a SUMO-targeted E3 ubiquitin-ligase for the transcription factor NFATc3
Authors: Shrivastava Meenakshi Basu , Mojsa Barbara , Mora Stéphan , Robbins Ian , Bossis Guillaume , Lassot Iréna , Desagher Solange 
Published: September 2020

AbstractNFATc3 is the predominant member of the NFAT family of transcription factor in neurons, where it plays a pro-apoptotic role. Mechanisms controlling NFAT protein stability are poorly understood. Here we identify Trim39 as an E3 ubiquitin-ligase of NFATc3. Indeed, Trim39 ubiquitinates NFATc3in vitroand in cells, whereas silencing of endogenous Trim39 decreases NFATc3 ubiquitination. We also show that Trim17 inhibits Trim39-mediated ubiquitination of NFATc3 by reducing both the E3 ubiquitin-ligase activity of Trim39 and the NFATc3/Trim39 interaction. Moreover, mutation of SUMOylation sites in NFATc3 or SUMO-interacting motif in Trim39 reduces the NFATc3/Trim39 interaction and Trim39-induced ubiquitination of NFATc3. As a consequence, silencing of Trim39 increases the protein level and transcriptional activity of NFATc3, resulting in enhanced neuronal apoptosis. Likewise, a SUMOylation-deficient mutant of NFATc3 exhibits increased stability and pro-apoptotic activity. Taken together, these data indicate that Trim39 modulates neuronal apoptosis by acting as a SUMO-targeted E3 ubiquitin-ligase for NFATc3.
A two-step model of autophagy: autophagosome formation, degradation and net turnover
Authors: Plaza-Zabala Ainhoa , Sierra-Torre Virginia , Sierra Amanda 
Published: September 2020

AbstractAutophagy is a complex process that encompasses the enclosure of cytoplasmic debris or dysfunctional organelles in membranous vesicles, the autophagosomes, for their elimination in the lysosomes. A gold-standard method to assess its induction is the analysis of the autophagic flux using as a surrogate the expression of the microtubule-associated light chain protein 3 conjugated to phosphatidylethanolamine (LC3-II) by Western blot, in the presence of lysosomal inhibitors. Therefore, the current definition of autophagy flux actually puts the focus on the degradation stage of autophagy. In contrast, the most important autophagy controlling genes that have been identified in the last few years in fact target early stages of autophagosome formation. From a biological standpoint is therefore conceivable that autophagosome formation and degradation are independently regulated and we argue that both stages need to be systematically analyzed. Here, we propose a simple two-step model to understand changes in autophagosome formation and degradation using data from conventional LC3-II Western blot, and test it using two models of autophagy modulation in cultured microglia, the brain macrophages: rapamycin and the ULK1/2 inhibitor, MRT68921. Our model provides a comprehensive understanding of the autophagy process and will help to unravel the effect of genetic, pharmacological, and environmental manipulations on both the formation and degradation of autophagosomes.
Structural variant evolution after telomere crisis
Authors: Dewhurst S.M , Yao X , Rosiene Joel , Tian Huasong , Behr Julie , Bosco Nazario , Takai Kaori K. , de Lange T , Imielinski M 
Published: September 2020

AbstractTelomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of previous experimental telomere crisis studies. We examine the spectrum of SVs instigated by natural telomere crisis. Spontaneous post-crisis clones from prior studies had both complex and simple SVs without BFB cycles or chromothripsis. In contrast, BFB cycles and chromothripsis occurred in clones that escaped from telomere crisis after CRISPR-controlled telomerase activation in MRC5 fibroblasts. This system revealed convergent evolutionary lineages altering one allele of 12p, where a short telomere likely predisposed to fusion. Remarkably, the 12p chromothripsis and BFB events were stabilized by independent fusions to 21. Telomere crisis can therefore generate a wide spectrum of SVs, and lack of BFB patterns and chromothripsis does not indicate absence of past crisis.
Globalisation and regional income growth disparity in India and the People’s Republic of China (PRC)
Authors: Mallick Jagannath , Fukumi Atsushi 
Published: September 2020

PurposeThis study aims to explain the role of globalisation on the regional income growth disparities in the states of India and provinces in the People’s Republic of China (PRC).Design/methodology/approachThe authors use two approaches to analyse regional growth disparities: growth accounting and the panel spatial Durbin model.FindingsThe growth accounting shows that contributions of growth of capital intensity (GKI) and total factor productivity growth (TFPG) distinguish the high-income (HI) regions from medium-income (MI) and lower-income (LI) regions in India. In the PRC, the contributions of GKI and TFPG in MI regions are slightly higher than HI regions, but significantly higher than the LI regions. The empirical results find that foreign direct investment (FDI), domestic investment, human capital, and interaction of FDI and human capital explain income growth states/provinces in India and the PRC. A region’s income growth and FDI inflows spread the benefit to neighbourhoods in both countries.Originality/valueThe paper contributes by performing a comparative analysis of Indian states and the PRC’s provinces by capturing the neighbourhood effects of economic growth, FDI, investment and human capital and also the interaction effects of FDI with human capital and domestic investment. A comparison of the decomposition of income growth to the growth of factor inputs and efficiency in Indian states and the PRC’s provinces also adds to the existing literature.