bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survivin prevents the Polycomb Repressor Complex 2 from methylating Histone 3 lysine 27
Authors: Jensen Maja , García-Bonete María-José , Anindya Atsarina Larasati , Andersson Karin , Erlandsson Malin C. , Oparina Nina , Brath Ulrika , Chandrasekaran Venkataragavan , Maria Bokarewa I. , Katona Gergely 
Published: April 2022

AbstractSurvivin is a small protein that belongs to the inhibitor of apoptosis protein family and participates in cell division and apoptosis. It was actively studied in human cancers, inflammatory diseases and in autoimmune diseases. Here, we reveal that survivin takes part in epigenetic gene silencing by interaction with the polycomb repressive complex 2 (PRC2). PRC2 silences gene expression through tri-methylation of lysine 27 on histone 3 (H3K27). We detected differential expression of PRC2 core subunits in CD4+T cells with different survivin expression. ChIP-seq experiments indicated that survivin binds chromatin that overlap with the regions occupied by PRC2. ChIP-seq of H3K27 in CD4+T cells indicate that inhibition of survivin leads to a substantial increase in H3K27 tri-methylation by PRC2 in contrast to other histone modifications, which lends support to that survivin prevents PRC2 from functioning. Survivin binds peptides derived from PRC2 subunits EZH2, EED, SUZ12 and JARID2 in a peptide microarray that cover intersubunit interfaces, catalytic residues, and present binding sites for substrates, DNA, and regulatory proteins. Amino acid composition of the peptides has substantial predictive power for survivin interaction in the peptide microarray as determined by multilayer perceptron classification analysis. NMR experiments with 15N labelled survivin indicate that peptide colocalization does not entirely depend on binding mediated by short range interactions. These results indicate that survivin interacts with PRC2, preventing the methylation of H3K27 and specific gene silencing. This has transcriptional consequences and specific gene silencing.
Mutation rates and adaptive variation among the clinically dominant clusters ofMycobacterium abscessus
Authors: Commins Nicoletta , Sullivan Mark R. , McGowen Kerry , Koch Evan , Rubin Eric J. , Farhat Maha 
Published: April 2022

AbstractMycobacterium abscessus(Mab) is a multi-drug resistant pathogen increasingly responsible for severe pulmonary infections. Analysis of whole genome sequences (WGS) ofMabdemonstrates dense genetic clustering of clinical isolates collected from disparate geographic locations. This has been interpreted as supporting patient-to-patient transmission, but epidemiological studies have contradicted this interpretation. Here we present evidence for a slowing of theMabmolecular clock rate coincident with the emergence of phylogenetic clusters. We find that clustered isolates are enriched in mutations affecting DNA repair machinery and have lower spontaneous mutation ratesin vitro. We propose thatMabadaptation to the host environment through variation in DNA repair genes affects the organism’s mutation rate and that this manifests as phylogenetic clustering. These results inform our understanding of niche switching for facultative pathogens and challenge the model of transmission as the major mode of dissemination of clinically dominantMabclusters.
Digital whole-community phenotyping to assess morphological and physiological features of plant communities in the field
Authors: Zieschank Verena , Junker Robert R. 
Published: April 2022

SummaryTraits link observable patterns in plants to ecosystem functions and processes and help to derive general rules and predictions about responses to environmental gradients, global change and perturbations. Ecological field studies often use manual low-throughput methods to assess plant phenotypes and integrate species-specific traits to community-wide indices. In contrast, greenhouse or lab-based studies, mostly in agriculture, employ high-throughput phenotyping for plant individuals to track their growth or fertilizer and water demand. We customized an automated plant phenotyping system (PlantEye F500, Phenospex, Heerlen, The Netherlands) for its mobile application in the field for digital whole-community phenotyping (DWCP). By scanning whole plant communities, we gather, within seconds and non-invasively, multispectral and physiological information while simultaneously capturing the 3-dimensional structure of the vegetation. We demonstrated the potential of DWCP by tracking plant community responses to experimental land-use treatments over two years. DWCP captured short- and long-term changes in morphological and physiological plant community properties in response to mowing and fertilizer treatments and thus reliably informed about changes in land-use. In contrast, manually measured community-weighted mean traits and species composition remained largely unaffected and were not informative about these treatments. Thus, DWCP proved to be an efficient method to measure morphological and physiological characteristics of plant communities, complements other methods in trait-based ecology, provides indicators of ecosystem states, and may help to forecast tipping points in plant communities often associated with irreversible changes in ecosystems.
Interplay between R2R3 MYB-type activators and repressors regulates proanthocyanidin biosynthesis in banana (Musa acuminata)
Authors: Rajput Ruchika , Naik Jogindra , Stracke Ralf , Pandey Ashutosh 
Published: April 2022

SummaryProanthocyanidins are oligomeric flavonoid pigments that promote plant disease resistance and benefit human health. However, the transcriptional regulatory network that fine-tunes proanthocyanidin biosynthesis in banana (Musa acuminata) fruit remains poorly understood.We characterized two proanthocyanidin-specific R2R3 MYB activators (MaMYBPA1-MaMYBPA2) and four repressors (MaMYBPR1–MaMYBPR4) to elucidate the mechanisms underlying the transcriptional regulation of proanthocyanidin biosynthesis in banana.Heterologous expression ofMaMYBPA1andMaMYBPA2partially complemented theArabidopsis thalianaproanthocyanidin-deficienttransparent testa2mutant. MaMYBPA1 and MaMYBPA2 interacted physically with MaMYCs and bound the promoters of the genes encoding anthocyanin synthase, leucoanthocyanidin reductase, and anthocyanidin reductasein vitroand form functional MBW complexes with MaTTG1 inA. thalianaprotoplasts to transactivated these promotersin vivo.Overexpression ofMaMYBPAs alone or withMaMYCin banana fruits induced proanthocyanidin accumulation and the transcription of proanthocyanidin biosynthesis– related genes. MaMYBPR repressors are also shown to interact with MaMYCs, forming repressing MBW complexes, and diminished proanthocyanidin accumulation. Interestingly the overexpression of MaMYBPA induces the expression of MaMYBPR, indicating an agile regulation of proanthocyanidin biosynthesis via the formation of competitive MBW complex. Taken together, our results reveal regulatory modules of R2R3 MYB- that fine-tune proanthocyanidin biosynthesis and offer possible targets for genetic manipulation in banana.
Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues
Authors: Yu Peng , Zhou Siting , Gao Yan , Liang Yu , Guo Wenbin , Wang Dan Ohtan , Ding Shuaiwen , Lin Shuibin , Wang Jinkai , Cun Yixian 
Published: April 2022

AbstractAlthough the function of tRNA in translational process is well established, it remains controversial whether tRNA abundance is tightly associated withtranslational efficiency(TE) in mammals. For example, how critically the expression of tRNAs contributes to the establishment oftissue-specificproteomes in mammals has not been well addressed. Here, we measured bothtRNA expressionusing DM-tRNA-seq and ribosome-associated mRNAs in the brain, heart, and testis of RiboTag mice. Remarkable variation in the expression of tRNA isodecoders was observed among the different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the tissue-variations of anticodon expression, an unexpected smaller variation ofanticodon usage bias, and an unexpected larger variation of tRNA isotype expression. Regardless whether or not they share the same anticodons, isotypes encoding the same amino acids are co-expressed across different tissues. Based on the tRNA expression and TE computed from RiboTag-seq, we find that the tRNA adaptation index (tAI) values and TE are significantly correlated in the same tissues but not among tissues; tRNAs and theamino acid compositionsof translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be related to post-transcriptional mechanisms, such as aminoacylation, modification, and tRNA-derived small RNAs (tsRNAs). This study provides a resource for tRNA and translation studies to gain novel insights into the dynamics of tRNAs and their role in translational regulation.
Proteomics identifies substrates and a novel component in hSnd2-dependent ER protein targeting
Authors: Tirincsi Andrea , O’Keefe Sarah , Nguyen Duy , Sicking Mark , Dudek Johanna , Förster Friedrich , Jung Martin , Hadzibeganovic Drazena , Helms Volkhard , High Stephen , Zimmermann Richard , Lang Sven 
Published: April 2022

SUMMARYProtein import into the endoplasmic reticulum (ER) is essential for about 30% of the human proteome. It involves targeting of precursor proteins to the ER and insertion into or translocation across the ER membrane. Furthermore, it relies on signals in the precursor polypeptides and components, which read the signals and facilitate their targeting to a protein-conducting channel in the ER membrane, the Sec61 complex. Compared to the SRP- and TRC-dependent pathways, little is known about the SRP-independent/SND pathway. Our aim was to identify additional components and characterize the client spectrum of the human SND pathway. The established strategy of combining depletion of the central hSnd2-component from HeLa cells with proteomic- and differential protein abundance-analysis was used. The SRP and TRC targeting pathways were analyzed in comparison. TMEM109 was characterized as hSnd3. Unlike SRP but similar to TRC, the SND clients are predominantly membrane proteins with N-terminal, central, or C-terminal targeting signals.
Stardust: improving spatial transcriptomics data analysis through space aware modularity optimization based clustering
Authors: Avesani Simone , Viesi Eva , Alessandrì Luca , Motterle Giovanni , Bonnici Vincenzo , Beccuti Marco , Calogero Raffaele , Giugno Rosalba 
Published: April 2022

AbstractBackgroundSpatial transcriptomics (ST) combines stained tissue images with spatially resolved high-throughput RNA sequencing. The spatial transcriptomic analysis includes challenging tasks like clustering, where a partition among data points (spots) is defined by means of a similarity measure. Improving clustering results is a key factor as clustering affects subsequent downstream analysis. State-of-the-art approaches group data by taking into account transcriptional similarity and some by exploiting spatial information as well. However, it is not yet clear how much the spatial information combined with transcriptomics improves the clustering result.ResultsWe propose a new clustering method, Stardust, that easily exploits the combination of space and transcriptomic information in the clustering procedure through a manual or fully automatic tuning of algorithm parameters. Moreover, a parameter-free version of the method is also provided where the spatial contribution depends dynamically on the expression distances distribution in the space. We evaluated the proposed methods results by analysing ST datasets available on the 10x Genomics website and comparing clustering performances with state-of-the-art approaches by measuring the spots stability in the clusters and their biological coherence. Stability is defined by the tendency of each point to remain clustered with the same neighbours when perturbations are applied.ConclusionsStardust is an easy-to-use methodology allowing to define how much spatial information should influence clustering on different tissues and achieving more stable results than state-of-the-art approaches.
Correlative light and electron microscopy reveals fork-shaped structures at actin entry sites of focal adhesions
Authors: Legerstee Karin , Sueters Jason , Kremers Gert-Jan , Hoogenboom Jacob P. , Houtsmuller Adriaan B 
Published: April 2022

AbstractFocal adhesions (FAs) are the main cellular structures to link the intracellular cytoskeleton to the extracellular matrix. FAs mediate cell adhesion, are important for cell migration and are involved in many (patho)-physiological processes. Here we examined FAs and their associated actin fibres using correlative fluorescence and scanning electron microscopy (SEM). We used fluorescence images of cells expressing paxillin-GFP to define the boundaries of FA complexes in SEM images, without using SEM contrast enhancing stains. We observed that SEM contrast was increased around the actin fibre entry site in 98% of FAs, indicating increases in protein density and possibly also phosphorylation levels in this area. In nearly three quarters of the FAs, these nanostructures had a fork shape, with the actin forming the stem and the high contrast FA areas the fork. In conclusion, the combination of fluorescent and electron microscopy allowed accurate localisation of a highly abundant, novel fork structure at the FA-actin interface.
Improved sequence mapping using a complete reference genome and lift-over
Authors: Chen Nae-Chyun , Paulin Luis F , Sedlazeck Fritz J , Koren Sergey , Phillippy Adam M , Langmead Ben 
Published: April 2022

AbstractComplete, telomere-to-telomere genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a new method called levioSAM2 that accounts for reference changes and performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of multiple references, we demonstrate that aligning reads to a high-quality reference (e.g. T2T-CHM13) and lifting to an older reference (e.g. GRCh38) actually improves the accuracy of the resulting variant calls on the old reference. By leveraging the quality improvements of T2T-CHM13, levioSAM2 reduces small-variant calling errors by 11.4-39.5% compared to GRC-based mapping using real Illumina datasets. LevioSAM2 also improves long-read-based structural variant calling and reduces errors from 3.8-11.8% for a PacBio HiFi dataset. Performance is especially improved for a set of complex medically-relevant genes, where the GRC references are lower quality. The software is available at https://github.com/milkschen/leviosam2 under the MIT license.
Targeting Apollo-NADP+to image NADPH generation in pancreatic beta-cell organelles
Authors: Chang Huntley H. , Bennett Alexander M. , Cameron William D. , Floro Eric , Au Aaron , McFaul Christopher M. , Yip Christopher M. , Rocheleau Jonathan V. 
Published: April 2022

ABSTRACTNADPH/NADP+redox state supports numerous reactions related to cell growth and survival; yet the full impact is difficult to appreciate due to organelle compartmentalization of NADPH and NADP+. To study glucose-stimulated NADPH production in pancreatic beta-cell organelles, we targeted the Apollo-NADP+sensor by first selecting the most pH stable version of the single colour sensor. We subsequently targeted mTurquoise2-Apollo-NADP+to various organelles and confirmed activity in the cytoplasm, mitochondrial matrix, nucleus, and peroxisome. Finally, we measured the glucose- and glutamine-stimulated NADPH responses by single and dual colour imaging of the targeted sensors. Overall, we developed multiple organelle-targeted Apollo-NADP+sensors to reveal the prominent role of beta-cell mitochondria in determining NADPH production in the cytoplasm, nucleus, and peroxisome.
Two enhancer binding proteins activate σ54-dependent transcription of a quorum regulatory RNA in a bacterial symbiont
Authors: Surrett Ericka D. , Guckes Kirsten R. , Cousins Shyan , Ruskoski Terry B. , Cecere Andrew G. , Ludvik Denise A. , Okafor C. Denise , Mandel Mark J. , Miyashiro Tim I. 
Published: April 2022

AbstractTo colonize a host, bacteria depend on an ensemble of signaling systems to convert information about the various environments encountered within the host into specific cellular activities. How these signaling systems coordinate transitions between cellular states in vivo remains poorly understood. To address this knowledge gap, we investigated how the bacterial symbiont Vibrio fischeri initially colonizes the light organ of the Hawaiian bobtail squid Euprymna scolopes. Previous work has shown that the small RNA Qrr1, which is a regulatory component of the quorum-sensing system in V. fischeri, promotes host colonization. Here, we report that transcriptional activation of Qrr1 is repressed by the regulator BinK, which inhibits cellular aggregation by V. fischeri prior to light organ entry. We show that Qrr1 expression depends on the alternative sigma factor σ54 and the transcription factors LuxO and SypG, which function together as an OR logic gate, thereby ensuring Qrr1 is expressed during colonization. Finally, we provide evidence that this regulatory mechanism is widespread throughout the Vibrionaceae family. Together, our work reveals how coordination between the signaling pathways underlying aggregation and quorum sensing promotes host colonization, which provides insight into how integration among signaling systems facilitates complex processes in bacteria.
Induction of Sis1 promotes fitness but not feedback in the heat shock response
Authors: Garde Rania , Singh Abhyudai , Ali Asif , Pincus David 
Published: April 2022

ABSTRACTPreviously, we combined modeling and experiments to demonstrate that the heat shock response (HSR) functions as a negative feedback loop in which undefined chaperone clients activate the HSR by sequestering Hsp70, and subsequent induction of Hsp70 deactivates the response (Zheng et al., 2016; Krakowiak et al., 2018). Here, we formally define newly synthesized proteins (NSPs) as a major class of HSR activators and determine the role of Sis1, a co-chaperone of Hsp70, in HSR regulation. We develop and experimentally validate a new mathematical model that incorporates NSPs and Sis1. Unexpectedly, genetic decoupling and pulse-labeling experiments reveal that Sis1 induction promotes fitness during prolonged stress rather than providing negative feedback to the HSR. These results support an overall model in which NSPs signal the HSR by sequestering Sis1 and Hsp70, while induction of Hsp70 – but not Sis1 – attenuates the response.
EGFR inhibition led ROCK activation enhances desmosome assembly and cohesion in cardiomyocytes
Authors: Shoykhet Maria , Dervishi Orsela , Menauer Philipp , Hiermaier Matthias , Osterloh Colin , Ludwig Ralf J. , Waschke Jens , Yeruva Sunil 
Published: April 2022

AbstractArrhythmogenic cardiomyopathy (AC) is a familial heart disease partly caused by impaired desmosome turnover. Thus, stabilization of desmosome integrity may provide potential new treatment options. Desmosomes, apart from cellular cohesion, provide the structural framework of a signaling hub. Here, we investigated the role of the epidermal growth factor receptor (EGFR) in cardiomyocyte cohesion. We inhibited EGFR under physiological and pathophysiological conditions using the murine plakoglobin knockout AC model, in which EGFR was upregulated. EGFR inhibition enhanced cardiomyocyte cohesion. Immunoprecipitation showed an interaction of EGFR and desmoglein 2 (DSG2). Immunostaining and AFM revealed enhanced DSG2 localization and binding at cell borders upon EGFR inhibition. Enhanced area composita length and desmosome assembly were observed upon EGFR inhibition, confirmed by enhanced DSG2 and desmoplakin (DP) recruitment to cell borders. Erlotinib, an EGFR inhibitor, activated ROCK. Erlotinib mediated desmosome assembly and cardiomyocyte cohesion were abolished upon ROCK inhibition. Thus, inhibiting EGFR, thereby stabilizing desmosome integrity, might provide new treatment options for AC.SummaryShoykhet et al. show that EGFR inhibition led ROCK activation enhances cardiomyocyte cohesion via enhanced desmosomal assembly which is evidenced by enhanced DP/DSG2 localization at cell borders. It is the first step towards a novel therapeutic approach for arrhythmogenic cardiomyopathy.
Dapagliflozin improves endothelial integrity and hemodynamics in endotoxin treated mice through an apolipoprotein M dependent pathway
Authors: Ripoll Carla Valenzuela , Guo Zhen , Kumari Tripti , Miyata Kana N. , Ozcan Mualla , Diab Ahmed , Girardi Amanda , He Li , Kovacs Attila , Weinheimer Carla , Nigro Jess , Oscarsson Jan , Esterline Russell , Schilling Joel , Kosiborod Mikhail , Christoffersen Christina , Cho Jaehyung , Javaheri Ali 
Published: April 2022

AbstractRationaleSodium-glucose co-transporter inhibitors (SGLT2i) are under active clinical investigation in patients with acute inflammatory conditions, based on their clinical cardio-and nephroprotective effects, and a pre-clinical study that demonstrated SGLT2i improve renal outcomes and survival in a lipopolysaccharide (LPS) model. However, a unified mechanism that explains how SGLT2i could prevent hemodynamic consequences of inflammatory conditions has not been described. Apolipoprotein M (ApoM) is inversely associated with mortality in inflammatory conditions and improves cardiac function in endotoxin-treated mice via sphingosine-1-phosphate (S1P) signaling.ObjectiveTest the hypothesis that pre-treatment with SGLT2i dapagliflozin (Dapa) improves hemodynamics in endotoxin-treated mice via the ApoM/S1P pathway.Methods and ResultsMice with diet-induced obesity were gavaged with vehicle or Dapa for 4 days prior to LPS (10 mg/kg, IP). We found that mice receiving Dapa restored circulating ApoM levels, likely by increasing expression of the multi-ligand protein receptor megalin in the proximal tubules. Dapa attenuated LPS-induced reductions in cardiac dysfunction including reductions in ejection fraction, cardiac index, and coronary sinus area as well as vascular permeability as ascertained by intravital microscopy. Using both ApoM transgenic and knockout mice and S1P receptor inhibitors, we show that the ApoM/S1P pathway is important for the beneficial effects of Dapa in the LPS model.ConclusionsIn the setting of acute inflammation, our data suggest that SGLT2i maintains levels of megalin, leading to preservation of ApoM, which in turn promotes endothelial barrier integrity and improves hemodynamics. Our studies suggest a novel mechanism by which SGLT2i can preserve intravascular volume in the acute inflammatory setting.