bluuebunny/crossref_metadata_2025 huggingface dataset:
How to measure response diversity
Authors: Ross Samuel R.P-J. , Petchey Owen L. , Sasaki Takehiro , Armitage David W.
Published: April 2022

The insurance effect of biodiversity—that diversity stabilises aggregate ecosystem properties—is mechanistically underlain by inter- and intraspecific trait variation in organismal responses to the environment. This variation, termedresponse diversity, is therefore a potentially critical determinant of ecological stability. However, response diversity has yet to be widely quantified, possibly due to difficulties in its measurement. Even when it has been measured, approaches have varied.

Here, we review methods for measuring response diversity and from them distil a methodological framework for quantifying response diversity from experimental and/or observational data, which can be practically applied in lab and field settings across a range of taxa.

Previous empirical studies on response diversity most commonly invoke response traits as proxies aimed at capturing species’ ecological responses to the environment. Our approach, which is based on environment-dependent ecological responses to any biotic or abiotic environmental variable, is conceptually simple and robust to any form of environmental response, including nonlinear responses. Given its derivation from empirical data on species’ ecological responses, this approach should more directly reflect response diversity than the trait-based approach dominant in the literature.

By capturing even subtle inter- or intraspecific variation in environmental responses, and environment-dependencies in response diversity, we hope this framework will motivate tests of the diversity-stability relationship from a new perspective, and provide an approach for mapping, monitoring, and conserving this critical dimension of biodiversity.
P681 mutations within the polybasic motif of spike dictate fusogenicity and syncytia formation of SARS CoV-2 variants
Authors: Kuzmina Alona , Atari Nofar , Ottolenghi Aner , Korovin Dina , lass Ido Cohen , Rosental Benyamin , Rosenberg Elli , Mandelboim Michal , Taube Ran
Published: April 2022

The rapid spread and dominance of the Omicron SARS-CoV-2 over its Delta variant has posed severe global challenges. While extensive research on the role of the Receptor Binding Domain on viral infectivity and vaccine sensitivity has been documented, the role of the spike681PRRAR/SV687polybasic motif is less clear. Here we monitored infectivity and vaccine sensitivity of Omicron SARS-CoV-2 pseudovirus against sera samples that were drawn four months post administration of the third dose of BNT162b2 mRNA vaccine. Our findings show that relative to Wuhan-Hu and Delta SARS-CoV-2, Omicron displayed enhanced infectivity and a sharp decline in its sensitivity to vaccine-induced neutralizing antibodies. Furthermore, while the spike proteins form Wuhan-Hu (P681), Omicron (H681) and BA.2 (H681) pseudoviruses modestly promoted cell fusion and syncytia formation, Delta spike (P681R) displayed enhanced fusogenic activity and syncytia formation capability. Live-viruses plaque formation assays confirmed these findings and demonstrated that relatively to the Wuhan-Hu and Omicron SARS-CoV-2, Delta formed more plaques that were smaller in size. Introducing a single P681R point mutation within the Wuhan-Hu spike, or H681R within Omicron spike, restored fusion potential to similar levels observed for Delta spike. Conversely, a R681P point mutation within Delta spike efficiency abolished fusion potential. We conclude that over time, the efficiency of the third dose of the Pfizer vaccine against SARS CoV-2 is waned, and cannot neutralize Omicron. We further verify that the P681 position of the viral spike dictates fusogenicity and syncytia formation.
Multi-level analysis of adipose tissue reveals the relevance of perivascular subpopulations and an increased endothelial permeability in early-stage lipedema
Authors: Strohmeier Karin , Hofmann Martina , Jacak Jaroslaw , Narzt Marie-Sophie , Wahlmueller Marlene , Mairhofer Mario , Schaedl Barbara , Holnthoner Wolfgang , Barsch Martin , Sandhofer Matthias , Wolbank Susanne , Priglinger Eleni
Published: April 2022

Lipedema is a chronic, progressive disease of adipose tissue with unknown etiology. Based on the relevance of the stromal vascular fraction (SVF) cell population in lipedema, we performed a thorough characterization of subcutaneous adipose tissue, SVF isolated thereof and the sorted populations of endothelial cells (EC), pericytes and cultured adipose-derived stromal/stem cells (ASC) of early-stage lipedema patients. We employed histological and gene expression analysis and investigated the endothelial barrier by immunofluorescence and analysis of endothelial permeability in vitro. Although there were no significant differences in histological stainings, we found altered gene expression of factors relevant for local estrogen metabolism (aromatase), preadipocyte commitment (ZNF423) and immune cell infiltration (CD11c) in lipedema on tissue level as well as in distinct cellular subpopulations. Machine learning analysis of immunofluorescence images of CD31 and ZO-1 revealed a morphological difference in the cellular junctions of EC cultures derived from healthy and lipedema individuals. Furthermore, the secretome of lipedema-derived SVF cells was sufficient to significantly increase leakiness of healthy human primary EC, which was also reflected by decreased mRNA expression of VE-cadherin. Here we showed for the first time, that the secretome of SVF cells creates an environment that triggers endothelial barrier dysfunction in early-stage lipedema. Moreover, since alterations in gene expression were detected on the cellular and/or tissue level, the choice of sample material is of high importance in elucidating this complex disease.
Preclinical interstitial lung disease in relatives of familial pulmonary fibrosis patients
Authors: Lucas Sionne EM , Raspin Kelsie , Mackintosh John , Glaspole Ian , Reynolds Paul N , Chia Collin , Grainge Christopher , Kendall Peter , Troy Lauren , Schwartz David A , Wood-Baker Richard , Walsh Simon LF , Moodley Yuben , Robertson James , Macansh Sacha , Walters Eugene H , Chambers Daniel , Corte Tamera J , Dickinson Joanne L
Published: April 2022

Family history is amongst the strongest risk factors for interstitial lung disease (ILD), with emerging evidence for a shared genetic aetiology across ILD subtypes. Recruited families comprised at least two first-degree relatives who had been previously diagnosed with an ILD. All living cases and available unaffected first-degree relatives underwent a clinical examination for evidence of ILD. Preclinical ILD was diagnosed in 47.7% of first-degree relatives who had previously self-reported as unaffected. This study highlights the strong genetic predisposition in family members of ILD cases, and supports the call for routine screening of individuals with a family history of ILD.
Urban greenspace and anxiety symptoms during the COVID-19 pandemic: A 20-month follow up of 19,848 participants in England
Authors: Bu Feifei , Mak Hei Wan , Steptoe Andrew , Wheeler Benedict W , Fancourt Daisy
Published: April 2022

This study examined the association between greenspace and the growth trajectories of anxiety symptoms during the COVID-19 pandemic. Using data from 19,848 urban residents in England who were followed for 20 months between March 2020 and October 2021, we found that living in an area with higher greenspace coverage was associated with fewer anxiety symptoms over time independent of population density, area deprivation levels, socio-demographics, and health profiles. There was limited evidence that greenspace was related to the change of anxiety symptoms over time. No association with anxiety trajectories was found when using greenspace proximity.
Removal of Clinically Relevant SARS-CoV-2 Variants by An Affinity Resin Containing Galanthus nivalis Agglutinin
Authors: Gooldy Melanie , Roux Christelle M. , LaRosa Steven P. , Spaulding Nicole , Fisher Charles J.
Published: April 2022

The Coronavirus-19 (COVID-19) pandemic due to the SARS-CoV-2 virus has now exceeded two years in duration. The pandemic has been characterized by the development of a succession of variants containing mutations in the spike protein affecting infectiousness, virulence and efficacy of vaccines and monoclonal antibodies. Resistance to vaccination and limitations in the current treatments available require the ongoing development of therapies especially for those with severe disease. The plant lectin Galanthus nivalis binds to mannose structures in the viral envelope. We hypothesized that viral binding should be unaffected by spike protein mutations. Known concentrations of seven clinically relevant SARS-CoV-2 variants were spiked in medium and passed three times over columns containing 1 gm of GNA affinity resin. Percent decrease in viral titer was compared with a control sample. Viral capture efficiency was found to range from 53 to 89% for all variants. Extrapolation indicated that an adult Aethlon Hemopurifier® would have more than sufficient binding capacity for viral loads observed in adult patients with severe COVID-19 infection.
Coordination between ECM and cell-cell adhesion regulates the development of islet aggregation, architecture, and functional maturation
Authors: Tixi Wilma , Maldonado Maricela , Chang Ya-Ting , Chiu Amy , Yeung Wilson , Parveen Nazia , Nelson Michael , Hart Ryan , Wang Shihao , Hsu Wu Jih , Fueger Patrick , Kopp Janel L. , Huising Mark O. , Dhawan Sangeeta , Shih Hung-Ping
Published: April 2022

Pancreatic islets are 3-dimensional cell aggregates consisting of unique cellular composition, cell-to-cell contacts, and interactions with blood vessels. Cell aggregation is essential for islet endocrine function; however, it remains unclear how developing islets establish aggregation. By combining genetic animal models, imaging tools, and gene expression profiling, we demonstrate that islet aggregation is regulated by extracellular matrix signaling and cell-cell adhesion. Islet endocrine cell-specific inactivation of extracellular matrix receptor Integrin β1 disrupted blood vessel interactions but promoted cell-cell adhesion and the formation of larger islets. In contrast, ablation of cell-cell adhesion molecule α-Catenin promoted blood vessel interactions yet compromised islet clustering. Simultaneous removal of Integrin β1 and α-Catenin disrupts islet aggregation and the endocrine cell maturation process, demonstrating that establishment of islet aggregates is essential for functional maturation. Our study provides new insights into understanding the fundamental self-organizing mechanism for islet aggregation, architecture, and functional maturation.

HIGHLIGHTS

Islet vascularization and aggregation are regulated via ECM-Itgb1 signaling

ECM-Itgb1 signaling negatively controls islet aggregation via regulation of cell-cell adhesion during development

Cell-cell adhesion negatively regulates the interaction of endocrine cell-vasculature in islets

Differential cell adhesion regulates the establishment of islet architecture

Endocrine functional maturation depends on islet aggregation regulated by the coordination of ECM-Itgb1 signaling and cell-cell adhesion
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

Survivin 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

Mycobacterium 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

Traits 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

Proanthocyanidins 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

Although 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

Protein 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

Background

Spatial 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.

Results

We 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.

Conclusions

Stardust 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

Focal 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

Complete, 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

NADPH/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

To 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

Previously, 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

Arrhythmogenic 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.

Shoykhet 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

Rationale

Sodium-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.

Objective

Test the hypothesis that pre-treatment with SGLT2i dapagliflozin (Dapa) improves hemodynamics in endotoxin-treated mice via the ApoM/S1P pathway.

Methods and Results

Mice 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.

Conclusions

In 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.
Diverse states and stimuli tune olfactory receptor expression levels to modulate food-seeking behavior
Authors: McLachlan Ian G. , Kramer Talya S. , Dua Malvika , DiLoreto Elizabeth M. , Dag Ugur , Srinivasan Jagan , Flavell Steven W.
Published: April 2022

Animals must weigh competing needs and states to generate adaptive behavioral responses to the environment. Sensorimotor circuits are thus tasked with integrating diverse external and internal cues relevant to these needs to generate context-appropriate behaviors. However, the mechanisms that underlie this integration are largely unknown. Here, we show that a wide range of states and stimuli converge upon a single C. elegans olfactory neuron to modulate food-seeking behavior. Using an unbiased ribotagging approach, we find that the expression of olfactory receptor genes in the AWA olfactory neuron is influenced by a wide array of states and stimuli, including feeding state, physiological stress, and recent sensory cues. We identify odorants that activate these state-dependent olfactory receptors and show that altered expression of these receptors influences food-seeking and foraging. Further, we dissect the molecular and neural circuit pathways through which these diverse cues are integrated by AWA. This reveals a modular organization in which state-related signals arising from different cell types in the body converge on AWA and independently control chemoreceptor expression. The synthesis of these signals by AWA allows animals to generate sensorimotor responses that reflect the animal’s overall state. Our findings suggest a general model in which state-dependent transcriptional changes at the sensory periphery modulate animals’ sensorimotor responses to meet their ongoing needs and states.
Characterization of the cluster MabR prophages of Mycobacterium abscessus and Mycobacterium chelonae
Authors: Cote Jacob , Welch Colin , Kimble Madeline , Archambault Dakota , Ross John Curtis , Orellana Hector , Amero Katelyn , Bourett Claire , Daigle Andre , Hutchison Keith W. , Molloy Sally D.
Published: April 2022

Mycobacterium abscessus is an emerging pathogen of concern in cystic fibrosis and immunocompromised patients and is considered one of the most drug-resistant mycobacteria. The majority of clinical M. abscessus isolates carry one or more prophages that are hypothesized to contribute to virulence and bacterial fitness. The prophage McProf was identified in the genome of the Bergey strain of M. chelonae, and is distinct from previously described prophages of M. abscessus. The McProf genome increases intrinsic antibiotic resistance of M. chelonae and drives expression of the intrinsic antibiotic resistance gene, whiB7, when superinfected by a second phage. The prevalence of McProf-like genomes was determined in sequenced mycobacterial genomes. Related prophage genomes were identified in the genomes of 25 clinical isolates of M. abscessus and assigned to the novel cluster, MabR. The MabR genomes share less than 10% gene content with previously described prophages; however, share features typical of prophages, including polymorphic toxin immunity (PT-Imm) systems.
Diversity and abundance of archaeal amoA genes in the permanent and temporary oxygen minimum zones of Indian Ocean
Authors: Chinnamani Prasannakumar , Elamaran Anandjothi
Published: April 2022

Oxygen minimum zones are results of oxygen consumption exceeding the oxygen availability in stratified water columns of the marine environment. We compared the ammonia monooxygenase subunit A (amoA) gene abundance and the diversity of ammonia-oxidising archaea (AOA) in the Arabian Sea (AS) with those of the Bay of Bengal (BoB). Three primer pairs targeting amoA genes of water column A (WCA), water column B (WCB) and total AOA (amoAt) captured different densities of gene copy numbers in both marginal seas. Water column A (WCA) ecotypes were more abundant in the AS than in the BoB. Core-OMZ depths of the BoB contained 10 times lower amoA copy numbers than those of the AS. Along with sampling depth, concentration of ammonia shapes the WCA/WCB ecotypes in AS/BoB. Among the total AOA populations, WCB ecotypes were more abundant. The amoA gene sequences were either of Nitrosopumilales or Ca. Nitrosotaleales members and belonged to NP-γ, NP-δ, NS-β, NS-γ and NS-ε sub-clades. Pairwise distance and nucleotide diversity index analysis reveals that BoB nurtures two times more diverse amoA sequences than the AS. The core OMZ region of the BoB contains a two-fold higher diversity of amoA gene sequences compared to the AS, whereas the AS contains 13 times more abundant amoA copies than the BoB.
AnkG-Neurofascin complex structure reveals binding mechanisms required for integrity of the AIS
Authors: He Liping , Jiang Wenli , Li Jianchao , Wang Chao
Published: April 2022

The axon initial segment (AIS) has characteristically clustering of voltage-gated sodium channels (Nav), cell adhesion molecule Neurofascin (Nfasc), and neuronal scaffold protein Ankyrin-G (AnkG) in neurons, which facilitate generation of action potential and maintenance of axonal polarity. However, the mechanisms underlying AIS assembly and maintenance remain poorly understood. Here we report the high-resolution crystal structure of the AnkG in complex with a fragment from Nfasc cytoplasmic tail that shows, in conjunction with binding affinity assays, the molecular basis of AnkG-Nfasc binding. We confirm AnkG interacts with the FIGQY motif in Nfasc, and identify another region required for their high affinity binding. Structural analysis revealed that ANK repeats form four hydrophobic or hydrophilic layers in the AnkG inner groove that coordinate interactions with Nfasc. Moreover, disruption of the AnkG-Nfasc complex abolishes Nfasc enrichment at the AIS in hippocampal neurons. Finally, structural and biochemical analysis indicated that L1 syndrome-associated mutations in L1CAM compromise binding with ankyrins. These results define the mechanisms underlying AnkG-Nfasc complex formation and show that AnkG-dependent clustering of Nfasc is required for AIS integrity.
Parkinson mutations in DNAJC6 cause lipid defects and neurodegeneration that are rescued by Synj1
Authors: Jacquemyn Julie , Kuenen Sabine , Swerts Jef , Pavie Benjamin , Vijayan Vinoy , Kilic Ayse , Chabot Dries , Wang Yu-Chun , Schoovaerts Nils , Verstreken Patrik
Published: April 2022

Recent evidence links dysfunctional lipid metabolism to the pathogenesis of Parkinson’s disease, but the mechanisms are not resolved. Here, we created a new Drosophila knock-in model of DNAJC6/Auxilin and find that the pathogenic mutation causes synaptic dysfunction, neurological defects and neurodegeneration, as well as specific lipid metabolism alterations. In these mutants membrane lipids containing long-chain polyunsaturated fatty acids, including phosphatidylinositol lipid species that are key for synaptic vesicle recycling and organelle function are reduced. Overexpression of another protein mutated in Parkinson’s disease, Synaptojanin-1, known to bind and synthesize specific phosphoinositides, strongly rescues the DNAJC6/Auxilin neuronal defects and neurodegeneration. Our work reveals a functional relation between two proteins mutated in Parkinson’s disease and implicates deregulated phosphoinositide metabolism in the maintenance of neuronal integrity and neuronal survival in Parkinsonism.
Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release
Authors: Hsieh Yu-Ting , Tsai Tsung-Lin , Tu Chia-Chun , Huang Shen-Yan , Heng Jian-Wen , Tsai Pei-Yuan , Chao Tai-Ling , Tsai Ya-Min , Chang Pei-Ching , Lee Chien-Kuo , Yu Guann-Yi , Chang Sui-Yuan , Dzhagalov Ivan L. , Hsu Chia-Lin
Published: April 2022

An increasing body of evidence emphasizes the role of metabolic reprogramming in immune cells to fight off infections. However, little is known about the regulation of metabolite transporters that facilitate and support metabolic demands. In this study, we found that equilibrative nucleoside transporter 3 (ENT3) expression is part of the innate immune response, and is rapidly upregulated upon bacterial and viral infection. The transcription of ENT3 is directly under the regulation of IFN-induced signaling, positioning this metabolite transporter as an Interferon-stimulated gene (ISG). Moreover, we unveil that several viruses, including SARS-CoV2, require ENT3 to facilitate their entry into the cytoplasm. The removal or suppression of ENT3 expression is sufficient to significantly decrease viral replication in vitro and in vivo.
Cortical magnification eliminates differences in contrast sensitivity across but not around the visual field
Authors: Jigo Michael , Tavdy Daniel , Himmelberg Marc M. , Carrasco Marisa
Published: April 2022

Human visual performance changes dramatically both across (eccentricity) and around (polar angle) the visual field. Performance is better at the fovea, decreases with eccentricity, and is better along the horizontal than vertical meridian and along the lower than the upper vertical meridian. However, all neurophysiological and virtually all behavioral studies of cortical magnification have investigated eccentricity effects without considering polar angle. Most performance differences due to eccentricity are eliminated when stimulus size is cortically magnified (M-scaled) to equate the size of its cortical representation in primary visual cortex (V1). But does cortical magnification underlie performance differencesaroundthe visual field? Here, to assess contrast sensitivity, human adult observers performed an orientation discrimination task with constant stimulus size at different locations as well as when stimulus size was M-scaled according to stimulus eccentricity and polar angle location. We found that although M-scaling stimulus size eliminates differences across eccentricity, it does not eliminate differences around the polar angle. This finding indicates that limits in contrast sensitivity across eccentricity and around the visual field are mediated by different anatomical and computational constraints.
Inhibiting succinate release worsens cardiac reperfusion injury by enhancing mitochondrial reactive oxygen species generation
Authors: Milliken Alexander S. , Nadtochiy Sergiy M. , Brookes Paul S.
Published: April 2022

The metabolite succinate accumulates during cardiac ischemia. Within 5 min. of reperfusion, succinate returns to baseline levels via both its release from cells and oxidation by mitochondrial complex II (Cx-II). The latter drives reactive oxygen species (ROS) generation and subsequent opening of the mitochondrial permeability transition (PT) pore, leading to cell death. Targeting succinate dynamics (accumulation/oxidation/release) may be therapeutically beneficial in cardiac ischemia-reperfusion (IR) injury. It has been proposed that blocking monocarboxylate transporter 1 (MCT-1) may be beneficial in IR, by preventing succinate release and subsequent engagement of downstream inflammatory signaling pathways. In contrast, herein we hypothesized that blocking MCT-1 would retain succinate in cells, exacerbating ROS generation and IR injury. Using the mitochondrial ROS probe mitoSOX, and a custom-built murine heart perfusion rig built into a spectrofluorometer, we measured ROS generation in-situ during the first moments of reperfusion, and found that acute MCT-1 inhibition enhanced mitochondrial ROS generation at reperfusion, and worsened IR injury (recovery of function and infarct size). Both these effects were abrogated by tandem inhibition of Cx-II, suggesting that succinate retention worsens IR due to driving more mitochondrial ROS generation. Furthermore, using the PT pore inhibitor cyclosporin A, along with monitoring of PT pore opening via the mitochondrial membrane potential indicator TMRE, we herein provide evidence that ROS generation during early reperfusion is upstream of the PT pore, not downstream as proposed by others. In addition, pore opening was exacerbated by MCT-1 inhibition. Together, these findings highlight the importance of succinate dynamics and mitochondrial ROS generation, as key determinants of PT pore opening and IR injury outcomes.
MYXOBACTERIA FROM VIETNAM: ISOLATION, PHYLOGENETIC ANALYSIS AND BIOPROSPECTION
Authors: Nguyen Yen Thi Ngoc , Duong Chung Dinh , Nguyen Hong Thi Kim , Nguyen Cham Phuong , Vo Nhan Thi , Dinh Linh Thi Lan , Nguyen Ngoc Le Bao , Nguyen Thai Minh , Nguyen Nga Dinh , Nguyen Anh Tu
Published: April 2022

Forty-three myxobacterial strains were isolated and identified from 20 soil samples collected in Vietnam. The information on morphological characteristics and 16S ribosomal gene sequencing showed that these strains were designated to seven genera belonging to Angiococcus, Archangium, Chondromyces, Corallococcus, Cystobacter, Melittangium, and Myxococcus, in suborder Cystobacterineae and Sorangiineae. The phylogenetic tree was constructed to clarify the genetic relationship between myxobacterial isolates. Myxobacteria were cultured, and crude extracts were obtained after 10-day fermentation in P-medium in the presence of the Amberlite XAD 16N adsorbent resin. Elution was carried out with acetone and methanol to obtain the crude extracts. Evaluation of antioxidant activity used the DPPH and ABTS assay, the minimum inhibitory concentration values were determined by the microdilution method. The total extract from CT21 had the highest total antioxidant activity (IC50 = 52.34 ± 1.47 µg/mL, 30.28 ± 0.74 µg/mL for DPPH and ABTS assays, respectively). The other potential strain was TG131 and GL41 that IC50 values were 40.28 ± 1.13 and 57.24 ± 1.52 µg/mL, respectively (by the DPPH method), and 48.35 ± 0.58 and 42.76 ± 0.50 µg/mL, respectively (by the ABTS method). Interestingly, 100% isolated myxobacterial strains show inhibitory activity against at least one of the tested microorganisms. The potential antimicrobial strain was GL41, which inhibited all tested microorganisms, and the MIC values were 1 µg/mL against MRSA, MSSA, S. faecalis, C. albicans, and A. niger. The highest active strains were members of Myxococcus sp. genus.